-- dump date 20140619_231455 -- class Genbank::CDS -- table cds -- table main -- field 1 id -- field 2 GI -- field 3 GeneID -- field 4 chrom_position -- field 5 chromosome -- field 6 codon_start -- field 7 contig -- field 8 description -- field 9 end_pos -- field 10 gene -- field 11 gene_id -- field 12 name -- field 13 organism -- field 14 product -- field 15 protein_id -- field 16 start_pos -- field 17 strand -- field 18 taxid -- field 19 type -- header -- id GI GeneID chrom_position chromosome codon_start contig description end_pos gene gene_id name organism product protein_id start_pos strand taxid type YP_913814.1 119382758 4579419 170..616 1 NC_008686.1 PFAM: conserved hypothetical protein 701; KEGG: sil:SPO3893 hypothetical protein; hypothetical protein 616 4579419 Pden_0001 Paracoccus denitrificans PD1222 hypothetical protein YP_913814.1 170 D 318586 CDS YP_913815.1 119382759 4579420 709..2013 1 NC_008686.1 An RNA-DNA helicase that actively releases nascent mRNAs from paused transcription complexes; transcription termination factor Rho 2013 rho 4579420 rho Paracoccus denitrificans PD1222 transcription termination factor Rho YP_913815.1 709 D 318586 CDS YP_913816.1 119382760 4579421 2030..3289 1 NC_008686.1 TIGRFAM: tRNA modification GTPase TrmE; small GTP-binding protein; PFAM: GTP-binding protein, HSR1-related; KEGG: rde:RD1_0433 tRNA modification GTPase TrmE; tRNA modification GTPase TrmE 3289 4579421 Pden_0003 Paracoccus denitrificans PD1222 tRNA modification GTPase TrmE YP_913816.1 2030 D 318586 CDS YP_913817.1 119382761 4578545 3298..5157 1 NC_008686.1 GidA; glucose-inhibited cell division protein A; involved in the 5-carboxymethylaminomethyl modification (mnm(5)s(2)U) of the wobble uridine base in some tRNAs; tRNA uridine 5-carboxymethylaminomethyl modification protein GidA 5157 4578545 Pden_0004 Paracoccus denitrificans PD1222 tRNA uridine 5-carboxymethylaminomethyl modification protein GidA YP_913817.1 3298 D 318586 CDS YP_913818.1 119382762 4578546 5157..5738 1 NC_008686.1 TIGRFAM: methyltransferase GidB; PFAM: glucose inhibited division protein; KEGG: rde:RD1_0431 methyltransferase GidB; methyltransferase GidB 5738 4578546 Pden_0005 Paracoccus denitrificans PD1222 methyltransferase GidB YP_913818.1 5157 D 318586 CDS YP_913819.1 119382763 4578547 5731..6507 1 NC_008686.1 PFAM: Cobyrinic acid a,c-diamide synthase; KEGG: sit:TM1040_2867 cobyrinic acid a,c-diamide synthase; cobyrinic acid a,c-diamide synthase 6507 4578547 Pden_0006 Paracoccus denitrificans PD1222 cobyrinic acid a,c-diamide synthase YP_913819.1 5731 D 318586 CDS YP_913820.1 119382764 4578548 6517..7395 1 NC_008686.1 TIGRFAM: parB-like partition proteins; PFAM: ParB domain protein nuclease; KEGG: rsp:RSP_1225 ParB-like partition protein; parB-like partition proteins 7395 4578548 Pden_0007 Paracoccus denitrificans PD1222 parB-like partition proteins YP_913820.1 6517 D 318586 CDS YP_913821.1 119382765 4578549 complement(7526..8065) 1 NC_008686.1 PFAM: GrpE protein; KEGG: rsp:RSP_1219 chaperone protein GrpE (heat shock protein); heat shock protein GrpE 8065 4578549 Pden_0008 Paracoccus denitrificans PD1222 heat shock protein GrpE YP_913821.1 7526 R 318586 CDS YP_913822.1 119382766 4578550 complement(8073..9128) 1 NC_008686.1 Negative regulator of class I heat shock genes (grpE-dnaK-dnaJ and groELS operons). Prevents heat-shock induction of these operons; heat-inducible transcription repressor 9128 hrcA 4578550 hrcA Paracoccus denitrificans PD1222 heat-inducible transcription repressor YP_913822.1 8073 R 318586 CDS YP_913823.1 119382767 4578551 9211..9936 1 NC_008686.1 RNase PH; tRNA nucleotidyltransferase; forms hexamers in Bacillus subtilis; phosphoroltic 3'-5' exoribonuclease; involved in maturation of tRNA precursors and removes terminal nucleotides near CCA acceptor arms of mature tRNAs; ribonuclease PH 9936 rph 4578551 rph Paracoccus denitrificans PD1222 ribonuclease PH YP_913823.1 9211 D 318586 CDS YP_913824.1 119382768 4578552 9924..10529 1 NC_008686.1 HAM1-like protein; Rec-dependent growth; RgdB; yggV; it is suspected that this protein functions to remove misincorporated bases such as xanthine or hypoxanthine; deoxyribonucleotide triphosphate pyrophosphatase 10529 4578552 Pden_0011 Paracoccus denitrificans PD1222 deoxyribonucleotide triphosphate pyrophosphatase YP_913824.1 9924 D 318586 CDS YP_913825.1 119382769 4578553 10522..10896 1 NC_008686.1 PFAM: Endoribonuclease L-PSP; KEGG: rsp:RSP_1223 translation initiation inhibitor, YjgF family / endoribonuclease L-PSP; endoribonuclease L-PSP 10896 4578553 Pden_0012 Paracoccus denitrificans PD1222 endoribonuclease L-PSP YP_913825.1 10522 D 318586 CDS YP_913826.1 119382770 4578554 10905..12089 1 NC_008686.1 catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III; coproporphyrinogen III oxidase 12089 4578554 Pden_0013 Paracoccus denitrificans PD1222 coproporphyrinogen III oxidase YP_913826.1 10905 D 318586 CDS YP_913827.1 119382771 4578555 12091..12444 1 NC_008686.1 PFAM: protein of unknown function DUF454; KEGG: atc:AGR_C_4462 hypothetical protein; hypothetical protein 12444 4578555 Pden_0014 Paracoccus denitrificans PD1222 hypothetical protein YP_913827.1 12091 D 318586 CDS YP_913828.1 119382772 4578556 12535..13119 1 NC_008686.1 catalyzes the reaction of formaldehyde with glutathione to form S-hydroxymethylglutathione; glutathione-dependent formaldehyde-activating protein 13119 4578556 Pden_0015 Paracoccus denitrificans PD1222 glutathione-dependent formaldehyde-activating protein YP_913828.1 12535 D 318586 CDS YP_913829.1 119382773 4578557 13223..14350 1 NC_008686.1 PFAM: Alcohol dehydrogenase, zinc-binding domain protein; Alcohol dehydrogenase GroES domain protein; KEGG: rsp:RSP_2576 alcohol dehydrogenase class III; alcohol dehydrogenase 14350 4578557 Pden_0016 Paracoccus denitrificans PD1222 alcohol dehydrogenase YP_913829.1 13223 D 318586 CDS YP_913830.1 119382774 4578558 14426..15061 1 NC_008686.1 PFAM: peptidase S14, ClpP; KEGG: hne:HNE_0542 ATP-dependent Clp protease, proteolytic subunit ClpP; endopeptidase Clp 15061 4578558 Pden_0017 Paracoccus denitrificans PD1222 endopeptidase Clp YP_913830.1 14426 D 318586 CDS YP_913831.1 119382775 4578559 15058..15579 1 NC_008686.1 PFAM: GCN5-related N-acetyltransferase; KEGG: sus:Acid_2411 GCN5-related N-acetyltransferase; N-acetyltransferase 15579 4578559 Pden_0018 Paracoccus denitrificans PD1222 N-acetyltransferase YP_913831.1 15058 D 318586 CDS YP_913832.1 119382776 4578560 15576..16415 1 NC_008686.1 PFAM: esterase; KEGG: sil:SPO3829 S-formylglutathione hydrolase; carboxylesterase 16415 4578560 Pden_0019 Paracoccus denitrificans PD1222 carboxylesterase YP_913832.1 15576 D 318586 CDS YP_913833.1 119382777 4578561 16615..18417 1 NC_008686.1 PFAM: Pyrrolo-quinoline quinone; KEGG: rsp:RSP_2578 pqq dehydrogenase protein; Pyrrolo-quinoline quinone 18417 4578561 Pden_0020 Paracoccus denitrificans PD1222 Pyrrolo-quinoline quinone YP_913833.1 16615 D 318586 CDS YP_913834.1 119382778 4578562 18519..19199 1 NC_008686.1 KEGG: sme:SMb20174 cytochrome c protein; hypothetical protein 19199 4578562 Pden_0021 Paracoccus denitrificans PD1222 hypothetical protein YP_913834.1 18519 D 318586 CDS YP_913835.1 119382779 4578563 19196..20008 1 NC_008686.1 SMART: extracellular solute-binding protein, family 3; KEGG: rsp:RSP_2580 methanol oxidation protein; extracellular solute-binding protein 20008 4578563 Pden_0022 Paracoccus denitrificans PD1222 extracellular solute-binding protein YP_913835.1 19196 D 318586 CDS YP_913836.1 119382780 4578877 20005..20535 1 NC_008686.1 KEGG: rsp:RSP_2581 rhodanese; rhodanese 20535 4578877 Pden_0023 Paracoccus denitrificans PD1222 rhodanese YP_913836.1 20005 D 318586 CDS YP_913837.1 119382781 4578878 complement(20567..21118) 1 NC_008686.1 KEGG: rde:RD1_0896 hypothetical protein; hypothetical protein 21118 4578878 Pden_0024 Paracoccus denitrificans PD1222 hypothetical protein YP_913837.1 20567 R 318586 CDS YP_913838.1 119382782 4578879 complement(21122..21679) 1 NC_008686.1 KEGG: rsp:RSP_2574 hypothetical protein; hypothetical protein 21679 4578879 Pden_0025 Paracoccus denitrificans PD1222 hypothetical protein YP_913838.1 21122 R 318586 CDS YP_913839.1 119382783 4578880 21795..22982 1 NC_008686.1 KEGG: rsp:RSP_2582 hypothetical protein; hypothetical protein 22982 4578880 Pden_0026 Paracoccus denitrificans PD1222 hypothetical protein YP_913839.1 21795 D 318586 CDS YP_913840.1 119382784 4578881 22991..23962 1 NC_008686.1 TIGRFAM: 40-residue YVTN family beta-propeller repeat protein; KEGG: rsp:RSP_2583 hypothetical protein; hypothetical protein 23962 4578881 Pden_0027 Paracoccus denitrificans PD1222 hypothetical protein YP_913840.1 22991 D 318586 CDS YP_913841.1 119382785 4578882 23986..24555 1 NC_008686.1 KEGG: rsp:RSP_2584 hypothetical protein; hypothetical protein 24555 4578882 Pden_0028 Paracoccus denitrificans PD1222 hypothetical protein YP_913841.1 23986 D 318586 CDS YP_913842.1 119382786 4578883 24593..25312 1 NC_008686.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rsp:RSP_2586 ABC multidrug efflux transporter, ATPase subunit; ABC transporter 25312 4578883 Pden_0029 Paracoccus denitrificans PD1222 ABC transporter YP_913842.1 24593 D 318586 CDS YP_913843.1 119382787 4578884 25309..26127 1 NC_008686.1 PFAM: ABC-2 type transporter; KEGG: rsp:RSP_2587 ABC multidrug efflux transporter, inner membrane subunit; ABC transporter 26127 4578884 Pden_0030 Paracoccus denitrificans PD1222 ABC transporter YP_913843.1 25309 D 318586 CDS YP_913844.1 119382788 4578885 26124..26714 1 NC_008686.1 KEGG: rsp:RSP_2588 hypothetical protein; hypothetical protein 26714 4578885 Pden_0031 Paracoccus denitrificans PD1222 hypothetical protein YP_913844.1 26124 D 318586 CDS YP_913845.1 119382789 4578886 26711..27313 1 NC_008686.1 TIGRFAM: molybdopterin-guanine dinucleotide biosynthesis protein A; PFAM: 4-diphosphocytidyl-2C-methyl-D-erythritol synthase; KEGG: sit:TM1040_3754 molybdopterin-guanine dinucleotide biosynthesis protein A; molybdopterin-guanine dinucleotide biosynthesis protein MobA 27313 4578886 Pden_0032 Paracoccus denitrificans PD1222 molybdopterin-guanine dinucleotide biosynthesis protein MobA YP_913845.1 26711 D 318586 CDS YP_913846.1 119382790 4578887 complement(27310..28041) 1 NC_008686.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: sit:TM1040_3658 binding-protein-dependent transport systems inner membrane component; binding-protein-dependent transport system inner membrane protein 28041 4578887 Pden_0033 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_913846.1 27310 R 318586 CDS YP_913847.1 119382791 4578888 complement(28038..28796) 1 NC_008686.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sil:SPO0052 ABC transporter, ATP-binding protein; ABC transporter 28796 4578888 Pden_0034 Paracoccus denitrificans PD1222 ABC transporter YP_913847.1 28038 R 318586 CDS YP_913848.1 119382792 4578889 complement(28793..29467) 1 NC_008686.1 PFAM: TENA/THI-4 domain protein; KEGG: rde:RD1_3613 transcriptional regulator; TenA family transcription regulator 29467 4578889 Pden_0035 Paracoccus denitrificans PD1222 TenA family transcription regulator YP_913848.1 28793 R 318586 CDS YP_913849.1 119382793 4578890 complement(29464..30435) 1 NC_008686.1 KEGG: sit:TM1040_3655 NlpA lipoprotein; NlpA lipoprotein 30435 4578890 Pden_0036 Paracoccus denitrificans PD1222 NlpA lipoprotein YP_913849.1 29464 R 318586 CDS YP_913850.1 119382794 4578891 complement(30432..31394) 1 NC_008686.1 PFAM: UBA/THIF-type NAD/FAD binding protein; MoeZ/MoeB domain protein; KEGG: sit:TM1040_3654 UBA/ThiF-type NAD/FAD binding fold; UBA/THIF-type NAD/FAD binding protein 31394 4578891 Pden_0037 Paracoccus denitrificans PD1222 UBA/THIF-type NAD/FAD binding protein YP_913850.1 30432 R 318586 CDS YP_913851.1 119382795 4578892 complement(31391..31987) 1 NC_008686.1 Condenses 4-methyl-5-(beta-hydroxyethyl)-thiazole monophosphate and 4-amino-5-hydroxymethyl pyrimidine pyrophosphate to form thiamine monophosphate; thiamine-phosphate pyrophosphorylase 31987 thiE 4578892 thiE Paracoccus denitrificans PD1222 thiamine-phosphate pyrophosphorylase YP_913851.1 31391 R 318586 CDS YP_913852.1 119382796 4578893 complement(31984..32748) 1 NC_008686.1 functions in thiamine (vitamin B1) biosynthesis; in Bacillus subtilis this enzyme catalyzes the formation of thiazole from dehydroxyglycine and 1-deoxy-D-xylulose-5-phosphate and ThiS-thiocarboxylate; thiazole synthase 32748 thiG 4578893 thiG Paracoccus denitrificans PD1222 thiazole synthase YP_913852.1 31984 R 318586 CDS YP_913853.1 119382797 4578894 complement(32750..32947) 1 NC_008686.1 TIGRFAM: thiamine biosynthesis protein ThiS; PFAM: thiamineS protein; KEGG: bmb:BruAb1_0211 thiamine biosynthesis ThiS; thiamine biosynthesis protein ThiS 32947 4578894 Pden_0040 Paracoccus denitrificans PD1222 thiamine biosynthesis protein ThiS YP_913853.1 32750 R 318586 CDS YP_913854.1 119382798 4578895 complement(32931..33908) 1 NC_008686.1 PFAM: FAD dependent oxidoreductase; KEGG: rde:RD1_0747 thiamine biosynthesis oxidoreductase ThiO; FAD dependent oxidoreductase 33908 4578895 Pden_0041 Paracoccus denitrificans PD1222 FAD dependent oxidoreductase YP_913854.1 32931 R 318586 CDS YP_913855.1 119382799 4578896 complement(33905..34759) 1 NC_008686.1 KEGG: sil:SPO0045 phosphomethylpyrimidine kinase; TIGRFAM: phosphomethylpyrimidine kinase; PFAM: Phosphomethylpyrimidine kinase type-1; phosphomethylpyrimidine kinase 34759 4578896 Pden_0042 Paracoccus denitrificans PD1222 phosphomethylpyrimidine kinase YP_913855.1 33905 R 318586 CDS YP_913856.1 119382800 4579074 35028..35630 1 NC_008686.1 TIGRFAM: HAD-superfamily hydrolase, subfamily IA, variant 3; HAD-superfamily hydrolase, subfamily IA, variant 1; PFAM: Haloacid dehalogenase domain protein hydrolase; KEGG: rpa:RPA4047 haloacid dehalogenase-like hydrolase; HAD family hydrolase 35630 4579074 Pden_0043 Paracoccus denitrificans PD1222 HAD family hydrolase YP_913856.1 35028 D 318586 CDS YP_913857.1 119382801 4579075 35726..36292 1 NC_008686.1 KEGG: sit:TM1040_3505 conserved hypothetical protein; hypothetical protein 36292 4579075 Pden_0044 Paracoccus denitrificans PD1222 hypothetical protein YP_913857.1 35726 D 318586 CDS YP_913858.1 119382802 4579076 complement(36357..36791) 1 NC_008686.1 KEGG: bja:bll6386 3-dehydroquinate dehydratase; TIGRFAM: 3-dehydroquinate dehydratase, type II; PFAM: dehydroquinase, class II; 3-dehydroquinate dehydratase 36791 4579076 Pden_0045 Paracoccus denitrificans PD1222 3-dehydroquinate dehydratase YP_913858.1 36357 R 318586 CDS YP_913859.1 119382803 4579077 complement(36818..37519) 1 NC_008686.1 PFAM: response regulator receiver; transcriptional regulator domain protein; KEGG: rsp:RSP_2281 two-component trancriptional regulator, winged helix family; two component transcriptional regulator 37519 4579077 Pden_0046 Paracoccus denitrificans PD1222 two component transcriptional regulator YP_913859.1 36818 R 318586 CDS YP_913860.1 119382804 4579078 complement(37512..39392) 1 NC_008686.1 PFAM: response regulator receiver; ATP-binding region, ATPase domain protein domain protein; histidine kinase A domain protein domain protein; PAS fold-4 domain protein; KEGG: rsp:RSP_2280 PAS sensor hybrid histidine kinase; PAS/PAC sensor hybrid histidine kinase 39392 4579078 Pden_0047 Paracoccus denitrificans PD1222 PAS/PAC sensor hybrid histidine kinase YP_913860.1 37512 R 318586 CDS YP_913861.1 119382805 4579079 39505..41481 1 NC_008686.1 PFAM: AMP-dependent synthetase and ligase; KEGG: rsp:RSP_2279 long chain acyl-CoA synthetase; AMP-dependent synthetase/ligase 41481 4579079 Pden_0048 Paracoccus denitrificans PD1222 AMP-dependent synthetase/ligase YP_913861.1 39505 D 318586 CDS YP_913862.1 119382806 4579080 41478..42287 1 NC_008686.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sit:TM1040_0114 ABC transporter related; ABC transporter 42287 4579080 Pden_0049 Paracoccus denitrificans PD1222 ABC transporter YP_913862.1 41478 D 318586 CDS YP_913863.1 119382807 4579081 42298..43278 1 NC_008686.1 PFAM: inner-membrane translocator; KEGG: rsp:RSP_2277 ABC branched amino acid transporter family, inner membrane subunit; inner-membrane translocator 43278 4579081 Pden_0050 Paracoccus denitrificans PD1222 inner-membrane translocator YP_913863.1 42298 D 318586 CDS YP_913864.1 119382808 4579082 43354..44460 1 NC_008686.1 PFAM: inner-membrane translocator; KEGG: rsp:RSP_2276 ABC branched amino acid transporter family, inner membrane subunit; inner-membrane translocator 44460 4579082 Pden_0051 Paracoccus denitrificans PD1222 inner-membrane translocator YP_913864.1 43354 D 318586 CDS YP_913865.1 119382809 4579083 44505..45785 1 NC_008686.1 KEGG: rsp:RSP_2275 ABC branched amino acid transporter family, periplasmic substrate-binding subunit; Fis family transcriptional regulator 45785 4579083 Pden_0052 Paracoccus denitrificans PD1222 Fis family transcriptional regulator YP_913865.1 44505 D 318586 CDS YP_913866.1 119382810 4579084 45839..46663 1 NC_008686.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rsp:RSP_2274 ABC branched amino acid transporter family, ATPase subunit; ABC transporter 46663 4579084 Pden_0053 Paracoccus denitrificans PD1222 ABC transporter YP_913866.1 45839 D 318586 CDS YP_913867.1 119382811 4579085 46682..47899 1 NC_008686.1 KEGG: sil:SPO3289 phenylacetate-CoA ligase; phenylacetate-CoA ligase 47899 4579085 Pden_0054 Paracoccus denitrificans PD1222 phenylacetate-CoA ligase YP_913867.1 46682 D 318586 CDS YP_913868.1 119382812 4579086 complement(48379..48504) 1 NC_008686.1 PFAM: ribosomal protein L36; KEGG: hne:HNE_3350 ribosomal protein L36; 50S ribosomal protein L36 48504 4579086 Pden_0055 Paracoccus denitrificans PD1222 50S ribosomal protein L36 YP_913868.1 48379 R 318586 CDS YP_913869.1 119382813 4579087 48847..49710 1 NC_008686.1 PFAM: N-formylglutamate amidohydrolase; KEGG: rde:RD1_0718 N-formylglutamate amidohydrolase; N-formylglutamate amidohydrolase 49710 4579087 Pden_0056 Paracoccus denitrificans PD1222 N-formylglutamate amidohydrolase YP_913869.1 48847 D 318586 CDS YP_913870.1 119382814 4579088 49729..50616 1 NC_008686.1 PFAM: band 7 protein; KEGG: rsp:RSP_1401 band 7 protein; hypothetical protein 50616 4579088 Pden_0057 Paracoccus denitrificans PD1222 hypothetical protein YP_913870.1 49729 D 318586 CDS YP_913871.1 119382815 4579089 50750..51301 1 NC_008686.1 PFAM: NUDIX hydrolase; KEGG: sil:SPO3279 NUDIX domain protein; NUDIX hydrolase 51301 4579089 Pden_0058 Paracoccus denitrificans PD1222 NUDIX hydrolase YP_913871.1 50750 D 318586 CDS YP_913872.1 119382816 4579090 51353..51982 1 NC_008686.1 PFAM: Glutathione S-transferase, N-terminal domain; KEGG: bpe:BP1270 glutathione S-transferase; glutathione S-transferase domain-containing protein 51982 4579090 Pden_0059 Paracoccus denitrificans PD1222 glutathione S-transferase domain-containing protein YP_913872.1 51353 D 318586 CDS YP_913873.1 119382817 4579091 complement(51983..52687) 1 NC_008686.1 type 1 subfamily; involved in last step of pyrimidine biosynthesis; converts orotidine 5'-phosphate to UMP and carbon dioxide; OMP decarboxylase; OMPDCase; OMPdecase; orotidine 5'-phosphate decarboxylase 52687 4579091 Pden_0060 Paracoccus denitrificans PD1222 orotidine 5'-phosphate decarboxylase YP_913873.1 51983 R 318586 CDS YP_913874.1 119382818 4579092 52790..53563 1 NC_008686.1 KEGG: mmr:Mmar10_0746 hypothetical protein; hypothetical protein 53563 4579092 Pden_0061 Paracoccus denitrificans PD1222 hypothetical protein YP_913874.1 52790 D 318586 CDS YP_913875.1 119382819 4580939 53670..56297 1 NC_008686.1 PFAM: AAA ATPase, central domain protein; Clp N terminal domain protein; ATPase associated with various cellular activities, AAA_5; ATPase AAA-2 domain protein; SMART: AAA ATPase; KEGG: sit:TM1040_0130 ATPase AAA-2; ATPase 56297 4580939 Pden_0062 Paracoccus denitrificans PD1222 ATPase YP_913875.1 53670 D 318586 CDS YP_913876.1 119382820 4580940 56428..57324 1 NC_008686.1 in Escherichia coli this periplasmic enzyme was found to encode the periplasmic catalytic subunit of an oxidoreductase; sulfite oxidase activity not demonstrated; requires inner membrane anchor protein YedZ; sulfite oxidase subunit YedY 57324 4580940 Pden_0063 Paracoccus denitrificans PD1222 sulfite oxidase subunit YedY YP_913876.1 56428 D 318586 CDS YP_913877.1 119382821 4580941 57324..57950 1 NC_008686.1 PFAM: Ferric reductase domain protein transmembrane component, N-terminal domain; KEGG: sit:TM1040_0134 ferric reductase-like transmembrane component-like; ferric reductase 57950 4580941 Pden_0064 Paracoccus denitrificans PD1222 ferric reductase YP_913877.1 57324 D 318586 CDS YP_913878.1 119382822 4580942 57925..58224 1 NC_008686.1 hypothetical protein 58224 4580942 Pden_0065 Paracoccus denitrificans PD1222 hypothetical protein YP_913878.1 57925 D 318586 CDS YP_913879.1 119382823 4580943 complement(64006..64503) 1 NC_008686.1 KEGG: bhe:BH15450 hypothetical protein; hypothetical protein 64503 4580943 Pden_0066 Paracoccus denitrificans PD1222 hypothetical protein YP_913879.1 64006 R 318586 CDS YP_913880.1 119382824 4580944 64712..65059 1 NC_008686.1 PFAM: IS66 Orf2 family protein; KEGG: sme:SMa1613 hypothetical protein; IS66 Orf2 family protein 65059 4580944 Pden_0067 Paracoccus denitrificans PD1222 IS66 Orf2 family protein YP_913880.1 64712 D 318586 CDS YP_913881.1 119382825 4580945 65122..66750 1 NC_008686.1 PFAM: transposase IS66; KEGG: sme:SMa2171 hypothetical protein; transposase IS66 66750 4580945 Pden_0068 Paracoccus denitrificans PD1222 transposase IS66 YP_913881.1 65122 D 318586 CDS YP_913882.1 119382826 4580946 66750..67046 1 NC_008686.1 KEGG: sme:SMa1608 hypothetical protein; hypothetical protein 67046 4580946 Pden_0069 Paracoccus denitrificans PD1222 hypothetical protein YP_913882.1 66750 D 318586 CDS YP_913883.1 119382827 4580947 complement(67024..67266) 1 NC_008686.1 KEGG: nma:NMA2178 hypothetical protein; hypothetical protein 67266 4580947 Pden_0070 Paracoccus denitrificans PD1222 hypothetical protein YP_913883.1 67024 R 318586 CDS YP_913884.1 119382828 4580948 67303..67578 1 NC_008686.1 hypothetical protein 67578 4580948 Pden_0071 Paracoccus denitrificans PD1222 hypothetical protein YP_913884.1 67303 D 318586 CDS YP_913885.1 119382829 4580949 67679..69196 1 NC_008686.1 PFAM: CHAD domain containing protein; KEGG: neu:NE1494 hypothetical protein; CHAD domain-containing protein 69196 4580949 Pden_0072 Paracoccus denitrificans PD1222 CHAD domain-containing protein YP_913885.1 67679 D 318586 CDS YP_913886.1 119382830 4580950 69196..69945 1 NC_008686.1 PFAM: Cobyrinic acid a,c-diamide synthase; KEGG: neu:NE1495 ParA family ATPase; cobyrinic acid a,c-diamide synthase 69945 4580950 Pden_0073 Paracoccus denitrificans PD1222 cobyrinic acid a,c-diamide synthase YP_913886.1 69196 D 318586 CDS YP_913887.1 119382831 4580951 69942..70397 1 NC_008686.1 PFAM: adenylate cyclase; KEGG: neu:NE1496 hypothetical protein; adenylate cyclase 70397 4580951 Pden_0074 Paracoccus denitrificans PD1222 adenylate cyclase YP_913887.1 69942 D 318586 CDS YP_913888.1 119382832 4580952 complement(70419..70706) 1 NC_008686.1 KEGG: jan:Jann_1003 hypothetical protein; hypothetical protein 70706 4580952 Pden_0075 Paracoccus denitrificans PD1222 hypothetical protein YP_913888.1 70419 R 318586 CDS YP_913889.1 119382833 4580953 complement(70813..71199) 1 NC_008686.1 hypothetical protein 71199 4580953 Pden_0076 Paracoccus denitrificans PD1222 hypothetical protein YP_913889.1 70813 R 318586 CDS YP_913890.1 119382834 4580954 71248..71667 1 NC_008686.1 KEGG: gox:GOX2729 transposase; transposase 71667 4580954 Pden_0077 Paracoccus denitrificans PD1222 transposase YP_913890.1 71248 D 318586 CDS YP_913891.1 119382835 4580955 71795..72022 1 NC_008686.1 KEGG: gox:GOX2722 truncated transposase; transposase 72022 4580955 Pden_0078 Paracoccus denitrificans PD1222 transposase YP_913891.1 71795 D 318586 CDS YP_913892.1 119382836 4580956 72151..72867 1 NC_008686.1 PFAM: response regulator receiver; transcriptional regulator domain protein; KEGG: nar:Saro_0441 two component transcriptional regulator, winged helix family; two component transcriptional regulator 72867 4580956 Pden_0079 Paracoccus denitrificans PD1222 two component transcriptional regulator YP_913892.1 72151 D 318586 CDS YP_913893.1 119382837 4580957 72869..75208 1 NC_008686.1 TIGRFAM: PAS sensor protein; PFAM: response regulator receiver; ATP-binding region, ATPase domain protein domain protein; histidine kinase A domain protein domain protein; KEGG: ccr:CC0026 sensory box histidine kinase/response regulator; PAS/PAC sensor hybrid histidine kinase 75208 4580957 Pden_0080 Paracoccus denitrificans PD1222 PAS/PAC sensor hybrid histidine kinase YP_913893.1 72869 D 318586 CDS YP_913894.1 119382838 4580958 75555..77324 1 NC_008686.1 PFAM: regulatory protein, LuxR; KEGG: sil:SPO1388 transcriptional regulator, LuxR family/hydrolase, alpha/beta fold family; LuxR family transcriptional regulator 77324 4580958 Pden_0081 Paracoccus denitrificans PD1222 LuxR family transcriptional regulator YP_913894.1 75555 D 318586 CDS YP_913895.1 119382839 4578604 77426..77737 1 NC_008686.1 hypothetical protein 77737 4578604 Pden_0082 Paracoccus denitrificans PD1222 hypothetical protein YP_913895.1 77426 D 318586 CDS YP_913896.1 119382840 4578605 complement(77791..78135) 1 NC_008686.1 hypothetical protein 78135 4578605 Pden_0083 Paracoccus denitrificans PD1222 hypothetical protein YP_913896.1 77791 R 318586 CDS YP_913897.1 119382841 4578606 78314..78568 1 NC_008686.1 KEGG: rso:RSc2496 hypothetical signal peptide protein; hypothetical protein 78568 4578606 Pden_0084 Paracoccus denitrificans PD1222 hypothetical protein YP_913897.1 78314 D 318586 CDS YP_913898.1 119382842 4578607 79049..79255 1 NC_008686.1 hypothetical protein 79255 4578607 Pden_0085 Paracoccus denitrificans PD1222 hypothetical protein YP_913898.1 79049 D 318586 CDS YP_913899.1 119382843 4578608 79239..79514 1 NC_008686.1 hypothetical protein 79514 4578608 Pden_0086 Paracoccus denitrificans PD1222 hypothetical protein YP_913899.1 79239 D 318586 CDS YP_913900.1 119382844 4578609 79557..80267 1 NC_008686.1 PFAM: acylneuraminate cytidylyltransferase; KEGG: aeh:Mlg_2324 acylneuraminate cytidylyltransferase; acylneuraminate cytidylyltransferase 80267 4578609 Pden_0087 Paracoccus denitrificans PD1222 acylneuraminate cytidylyltransferase YP_913900.1 79557 D 318586 CDS YP_913901.1 119382845 4578610 80264..81310 1 NC_008686.1 KEGG: ccr:CC2854 flagellin modification protein FlmD; flagellin modification protein FlmD 81310 4578610 Pden_0088 Paracoccus denitrificans PD1222 flagellin modification protein FlmD YP_913901.1 80264 D 318586 CDS YP_913902.1 119382846 4578611 81485..82816 1 NC_008686.1 KEGG: dvu:DVU1387 hypothetical protein; hypothetical protein 82816 4578611 Pden_0089 Paracoccus denitrificans PD1222 hypothetical protein YP_913902.1 81485 D 318586 CDS YP_913903.1 119382847 4578612 82819..83619 1 NC_008686.1 KEGG: eca:ECA3144 hypothetical protein; hypothetical protein 83619 4578612 Pden_0090 Paracoccus denitrificans PD1222 hypothetical protein YP_913903.1 82819 D 318586 CDS YP_913904.1 119382848 4578613 complement(83710..84885) 1 NC_008686.1 hypothetical protein 84885 4578613 Pden_0091 Paracoccus denitrificans PD1222 hypothetical protein YP_913904.1 83710 R 318586 CDS YP_913905.1 119382849 4578614 complement(85055..86716) 1 NC_008686.1 hypothetical protein 86716 4578614 Pden_0092 Paracoccus denitrificans PD1222 hypothetical protein YP_913905.1 85055 R 318586 CDS YP_913906.1 119382850 4578615 complement(86854..87855) 1 NC_008686.1 PFAM: NAD-dependent epimerase/dehydratase; short-chain dehydrogenase/reductase SDR; 3-beta hydroxysteroid dehydrogenase/isomerase; polysaccharide biosynthesis protein CapD; dTDP-4-dehydrorhamnose reductase; Male sterility C-terminal domain; KEGG: son:SO3271 polysaccharide biosynthesis protein; polysaccharide biosynthesis protein CapD 87855 4578615 Pden_0093 Paracoccus denitrificans PD1222 polysaccharide biosynthesis protein CapD YP_913906.1 86854 R 318586 CDS YP_913907.1 119382851 4578616 complement(88201..88311) 1 NC_008686.1 KEGG: nha:Nham_3939 transposase IS116/IS110/IS902; transposase IS116/IS110/IS902 88311 4578616 Pden_0094 Paracoccus denitrificans PD1222 transposase IS116/IS110/IS902 YP_913907.1 88201 R 318586 CDS YP_913908.1 119382852 4578617 complement(88450..89019) 1 NC_008686.1 PFAM: Resolvase, N-terminal domain; Resolvase helix-turn-helix domain protein; KEGG: bpm:BURPS1710b_2170 DNA invertase; resolvase domain-containing protein 89019 4578617 Pden_0095 Paracoccus denitrificans PD1222 resolvase domain-containing protein YP_913908.1 88450 R 318586 CDS YP_913909.1 119382853 4578618 89344..89625 1 NC_008686.1 KEGG: bmb:BruAb1_1581 hypothetical protein; hypothetical protein 89625 4578618 Pden_0096 Paracoccus denitrificans PD1222 hypothetical protein YP_913909.1 89344 D 318586 CDS YP_913910.1 119382854 4578619 complement(89793..90434) 1 NC_008686.1 hypothetical protein 90434 4578619 Pden_0097 Paracoccus denitrificans PD1222 hypothetical protein YP_913910.1 89793 R 318586 CDS YP_913911.1 119382855 4578620 complement(90443..90688) 1 NC_008686.1 PFAM: Conjugal transfer TraD family protein; KEGG: rpc:RPC_4518 conjugal transfer TraD; conjugal transfer TraD family protein 90688 4578620 Pden_0098 Paracoccus denitrificans PD1222 conjugal transfer TraD family protein YP_913911.1 90443 R 318586 CDS YP_913912.1 119382856 4578621 complement(90690..91028) 1 NC_008686.1 KEGG: rpe:RPE_3258 hypothetical protein; hypothetical protein 91028 4578621 Pden_0099 Paracoccus denitrificans PD1222 hypothetical protein YP_913912.1 90690 R 318586 CDS YP_913913.1 119382857 4578622 91189..94185 1 NC_008686.1 MobA/MobL family protein; conjugal transfer relaxase TraA 94185 4578622 Pden_0100 Paracoccus denitrificans PD1222 conjugal transfer relaxase TraA YP_913913.1 91189 D 318586 CDS YP_913914.1 119382858 4580879 complement(94406..94681) 1 NC_008686.1 hypothetical protein 94681 4580879 Pden_0101 Paracoccus denitrificans PD1222 hypothetical protein YP_913914.1 94406 R 318586 CDS YP_913915.1 119382859 4580880 94879..95094 1 NC_008686.1 PFAM: Prophage CP4-57 regulatory; KEGG: rpe:RPE_3260 phage transcriptional regulator, AlpA; phage transcriptional regulator AlpA 95094 4580880 Pden_0102 Paracoccus denitrificans PD1222 phage transcriptional regulator AlpA YP_913915.1 94879 D 318586 CDS YP_913916.1 119382860 4580881 95326..95817 1 NC_008686.1 KEGG: rru:Rru_A1415 protein of unknown function DUF132; hypothetical protein 95817 4580881 Pden_0103 Paracoccus denitrificans PD1222 hypothetical protein YP_913916.1 95326 D 318586 CDS YP_913917.1 119382861 4580882 95814..96074 1 NC_008686.1 KEGG: sus:Acid_1920 conserved hypothetical protein; hypothetical protein 96074 4580882 Pden_0104 Paracoccus denitrificans PD1222 hypothetical protein YP_913917.1 95814 D 318586 CDS YP_913918.1 119382862 4580883 96094..97743 1 NC_008686.1 PFAM: Resolvase, N-terminal domain; Recombinase; KEGG: nwi:Nwi_2841 resolvase; recombinase 97743 4580883 Pden_0105 Paracoccus denitrificans PD1222 recombinase YP_913918.1 96094 D 318586 CDS YP_913919.1 119382863 4580884 complement(97636..99429) 1 NC_008686.1 PFAM: Resolvase, N-terminal domain; Recombinase; KEGG: nha:Nham_3864 recombinase; recombinase 99429 4580884 Pden_0106 Paracoccus denitrificans PD1222 recombinase YP_913919.1 97636 R 318586 CDS YP_913920.1 119382864 4580885 99430..99915 1 NC_008686.1 hypothetical protein 99915 4580885 Pden_0107 Paracoccus denitrificans PD1222 hypothetical protein YP_913920.1 99430 D 318586 CDS YP_913921.1 119382865 4580886 complement(100054..101091) 1 NC_008686.1 PFAM: aldo/keto reductase; KEGG: rsp:RSP_3201 oxidoreductase; aldo/keto reductase 101091 4580886 Pden_0108 Paracoccus denitrificans PD1222 aldo/keto reductase YP_913921.1 100054 R 318586 CDS YP_913922.1 119382866 4580887 101268..102167 1 NC_008686.1 PFAM: helix-turn-helix- domain containing protein, AraC type; AraC-type transcriptional regulator domain protein; KEGG: rsp:RSP_3202 transcriptional regulator, AraC family; AraC family transcriptional regulator 102167 4580887 Pden_0109 Paracoccus denitrificans PD1222 AraC family transcriptional regulator YP_913922.1 101268 D 318586 CDS YP_913923.1 119382867 4580888 complement(102305..102685) 1 NC_008686.1 hypothetical protein 102685 4580888 Pden_0110 Paracoccus denitrificans PD1222 hypothetical protein YP_913923.1 102305 R 318586 CDS YP_913924.1 119382868 4580889 complement(102697..103602) 1 NC_008686.1 hypothetical protein 103602 4580889 Pden_0111 Paracoccus denitrificans PD1222 hypothetical protein YP_913924.1 102697 R 318586 CDS YP_913925.1 119382869 4580890 complement(103599..105035) 1 NC_008686.1 KEGG: mmc:Mmcs_3174 hypothetical protein; hypothetical protein 105035 4580890 Pden_0112 Paracoccus denitrificans PD1222 hypothetical protein YP_913925.1 103599 R 318586 CDS YP_913926.1 119382870 4580891 complement(105698..106597) 1 NC_008686.1 SMART: TIR protein; KEGG: bmb:BruAb1_0274 hypothetical protein; TIR protein 106597 4580891 Pden_0113 Paracoccus denitrificans PD1222 TIR protein YP_913926.1 105698 R 318586 CDS YP_913927.1 119382871 4580892 complement(106933..107211) 1 NC_008686.1 PFAM: SH3, type 3 domain protein; KEGG: rsp:RSP_6161 hypothetical protein; SH3 type 3 domain-containing protein 107211 4580892 Pden_0114 Paracoccus denitrificans PD1222 SH3 type 3 domain-containing protein YP_913927.1 106933 R 318586 CDS YP_913928.1 119382872 4580893 complement(107337..108014) 1 NC_008686.1 TIGRFAM: yecA family protein; PFAM: SEC-C motif domain protein; KEGG: rpe:RPE_2282 YecA family protein; hypothetical protein 108014 4580893 Pden_0115 Paracoccus denitrificans PD1222 hypothetical protein YP_913928.1 107337 R 318586 CDS YP_913929.1 119382873 4580894 complement(108141..108776) 1 NC_008686.1 PFAM: transferase hexapeptide repeat containing protein; KEGG: atc:AGR_L_286 chloramphenicol acetyltransferase; hexapaptide repeat-containing transferase 108776 4580894 Pden_0116 Paracoccus denitrificans PD1222 hexapaptide repeat-containing transferase YP_913929.1 108141 R 318586 CDS YP_913930.1 119382874 4580895 109037..109393 1 NC_008686.1 hypothetical protein 109393 4580895 Pden_0117 Paracoccus denitrificans PD1222 hypothetical protein YP_913930.1 109037 D 318586 CDS YP_913931.1 119382875 4580896 109402..109755 1 NC_008686.1 KEGG: bcl:ABC1987 hypothetical protein; hypothetical protein 109755 4580896 Pden_0118 Paracoccus denitrificans PD1222 hypothetical protein YP_913931.1 109402 D 318586 CDS YP_913932.1 119382876 4580897 109994..110410 1 NC_008686.1 KEGG: mes:Meso_3831 hypothetical protein; hypothetical protein 110410 4580897 Pden_0119 Paracoccus denitrificans PD1222 hypothetical protein YP_913932.1 109994 D 318586 CDS YP_913933.1 119382877 4580898 110943..111620 1 NC_008686.1 PFAM: DNA methylase N-4/N-6 domain protein; KEGG: nha:Nham_0569 DNA methylase N-4/N-6; DNA methylase N-4/N-6 domain-containing protein 111620 4580898 Pden_0120 Paracoccus denitrificans PD1222 DNA methylase N-4/N-6 domain-containing protein YP_913933.1 110943 D 318586 CDS YP_913934.1 119382878 4579500 111692..111982 1 NC_008686.1 hypothetical protein 111982 4579500 Pden_0121 Paracoccus denitrificans PD1222 hypothetical protein YP_913934.1 111692 D 318586 CDS YP_913935.1 119382879 4579501 112280..112741 1 NC_008686.1 PFAM: GCN5-related N-acetyltransferase; KEGG: atc:AGR_L_1711 acetyltransferase; hypothetical protein 112741 4579501 Pden_0122 Paracoccus denitrificans PD1222 hypothetical protein YP_913935.1 112280 D 318586 CDS YP_913936.1 119382880 4579502 113488..113898 1 NC_008686.1 TIGRFAM: single-strand binding protein; PFAM: single-strand binding protein/Primosomal replication protein n; KEGG: nha:Nham_4669 single-strand binding protein; single-strand binding protein 113898 4579502 Pden_0123 Paracoccus denitrificans PD1222 single-strand binding protein YP_913936.1 113488 D 318586 CDS YP_913937.1 119382881 4579503 113876..114208 1 NC_008686.1 hypothetical protein 114208 4579503 Pden_0124 Paracoccus denitrificans PD1222 hypothetical protein YP_913937.1 113876 D 318586 CDS YP_913938.1 119382882 4579504 114444..114647 1 NC_008686.1 hypothetical protein 114647 4579504 Pden_0125 Paracoccus denitrificans PD1222 hypothetical protein YP_913938.1 114444 D 318586 CDS YP_913939.1 119382883 4579505 115048..115260 1 NC_008686.1 hypothetical protein 115260 4579505 Pden_0126 Paracoccus denitrificans PD1222 hypothetical protein YP_913939.1 115048 D 318586 CDS YP_913940.1 119382884 4579506 complement(115281..115730) 1 NC_008686.1 KEGG: mes:Meso_3838 hypothetical protein; hypothetical protein 115730 4579506 Pden_0127 Paracoccus denitrificans PD1222 hypothetical protein YP_913940.1 115281 R 318586 CDS YP_913941.1 119382885 4579507 complement(115825..116091) 1 NC_008686.1 hypothetical protein 116091 4579507 Pden_0128 Paracoccus denitrificans PD1222 hypothetical protein YP_913941.1 115825 R 318586 CDS YP_913942.1 119382886 4579508 complement(116238..116501) 1 NC_008686.1 KEGG: nwi:Nwi_0844 hypothetical protein; hypothetical protein 116501 4579508 Pden_0129 Paracoccus denitrificans PD1222 hypothetical protein YP_913942.1 116238 R 318586 CDS YP_913943.1 119382887 4579509 complement(116687..116923) 1 NC_008686.1 PFAM: helix-turn-helix domain protein; KEGG: mlo:msr6108 transcriptional regulator; XRE family transcriptional regulator 116923 4579509 Pden_0130 Paracoccus denitrificans PD1222 XRE family transcriptional regulator YP_913943.1 116687 R 318586 CDS YP_913944.1 119382888 4579510 117115..117384 1 NC_008686.1 KEGG: nwi:Nwi_0845 hypothetical protein; hypothetical protein 117384 4579510 Pden_0131 Paracoccus denitrificans PD1222 hypothetical protein YP_913944.1 117115 D 318586 CDS YP_913945.1 119382889 4579511 117381..118250 1 NC_008686.1 KEGG: nwi:Nwi_0846 possible replication protein A; replication protein A 118250 4579511 Pden_0132 Paracoccus denitrificans PD1222 replication protein A YP_913945.1 117381 D 318586 CDS YP_913946.1 119382890 4579512 118506..119006 1 NC_008686.1 KEGG: mes:Meso_2334 hypothetical protein; hypothetical protein 119006 4579512 Pden_0133 Paracoccus denitrificans PD1222 hypothetical protein YP_913946.1 118506 D 318586 CDS YP_913947.1 119382891 4579513 119003..120622 1 NC_008686.1 PFAM: C-5 cytosine-specific DNA methylase; transposase IS116/IS110/IS902 family protein; KEGG: mlo:mll5964 transposase; transposase IS116/IS110/IS902 family protein 120622 4579513 Pden_0134 Paracoccus denitrificans PD1222 transposase IS116/IS110/IS902 family protein YP_913947.1 119003 D 318586 CDS YP_913948.1 119382892 4579514 121111..121665 1 NC_008686.1 hypothetical protein 121665 4579514 Pden_0135 Paracoccus denitrificans PD1222 hypothetical protein YP_913948.1 121111 D 318586 CDS YP_913949.1 119382893 4579515 121919..122851 1 NC_008686.1 PFAM: protein of unknown function DUF736; KEGG: mes:Meso_3845 conjugal transfer protein precursor; hypothetical protein 122851 4579515 Pden_0136 Paracoccus denitrificans PD1222 hypothetical protein YP_913949.1 121919 D 318586 CDS YP_913950.1 119382894 4579516 122855..123550 1 NC_008686.1 PFAM: Lytic transglycosylase, catalytic; KEGG: mes:Meso_0517 lytic transglycosylase, catalytic; lytic transglycosylase, catalytic 123550 4579516 Pden_0137 Paracoccus denitrificans PD1222 lytic transglycosylase, catalytic YP_913950.1 122855 D 318586 CDS YP_913951.1 119382895 4579517 123600..124181 1 NC_008686.1 hypothetical protein 124181 4579517 Pden_0138 Paracoccus denitrificans PD1222 hypothetical protein YP_913951.1 123600 D 318586 CDS YP_913952.1 119382896 4579518 124423..126159 1 NC_008686.1 KEGG: bja:bll0044 hypothetical protein; hypothetical protein 126159 4579518 Pden_0139 Paracoccus denitrificans PD1222 hypothetical protein YP_913952.1 124423 D 318586 CDS YP_913953.1 119382897 4580164 126242..126493 1 NC_008686.1 TIGRFAM: prevent-host-death family protein; PFAM: protein of unknown function DUF172; KEGG: rru:Rru_A0090 prevent-host-death protein; prevent-host-death family protein 126493 4580164 Pden_0140 Paracoccus denitrificans PD1222 prevent-host-death family protein YP_913953.1 126242 D 318586 CDS YP_913954.1 119382898 4580165 126578..126934 1 NC_008686.1 KEGG: rru:Rru_A0091 PilT protein-like; twitching motility protein PilT 126934 4580165 Pden_0141 Paracoccus denitrificans PD1222 twitching motility protein PilT YP_913954.1 126578 D 318586 CDS YP_913955.1 119382899 4580166 127107..129131 1 NC_008686.1 type IV secretion VirD4 coupling protein family; conjugal transfer protein TraG 129131 4580166 Pden_0142 Paracoccus denitrificans PD1222 conjugal transfer protein TraG YP_913955.1 127107 D 318586 CDS YP_913956.1 119382900 4580167 129135..129545 1 NC_008686.1 KEGG: bja:bll0042 hypothetical protein; hypothetical protein 129545 4580167 Pden_0143 Paracoccus denitrificans PD1222 hypothetical protein YP_913956.1 129135 D 318586 CDS YP_913957.1 119382901 4580168 complement(129586..129894) 1 NC_008686.1 PFAM: plasmid stabilization system; KEGG: sme:SMb20627 hypothetical protein; plasmid stabilization system protein 129894 4580168 Pden_0144 Paracoccus denitrificans PD1222 plasmid stabilization system protein YP_913957.1 129586 R 318586 CDS YP_913958.1 119382902 4580169 complement(129891..130160) 1 NC_008686.1 PFAM: CopG domain protein DNA-binding domain protein; KEGG: sme:SMb20628 hypothetical protein; CopG family transcriptional regulator 130160 4580169 Pden_0145 Paracoccus denitrificans PD1222 CopG family transcriptional regulator YP_913958.1 129891 R 318586 CDS YP_913959.1 119382903 4580170 complement(130357..130599) 1 NC_008686.1 KEGG: mes:Meso_0499 hypothetical protein; hypothetical protein 130599 4580170 Pden_0146 Paracoccus denitrificans PD1222 hypothetical protein YP_913959.1 130357 R 318586 CDS YP_913960.1 119382904 4580171 complement(130604..131779) 1 NC_008686.1 PFAM: conjugation TrbI family protein; KEGG: mes:Meso_0500 conjugation TrbI-like protein; conjugation TrbI family protein 131779 4580171 Pden_0147 Paracoccus denitrificans PD1222 conjugation TrbI family protein YP_913960.1 130604 R 318586 CDS YP_913961.1 119382905 4580172 complement(131779..132783) 1 NC_008686.1 PFAM: Conjugal transfer protein TrbG/VirB9/CagX; KEGG: mes:Meso_0501 conjugal transfer protein TrbG/VirB9/CagX; conjugal transfer protein TrbG/VirB9/CagX 132783 4580172 Pden_0148 Paracoccus denitrificans PD1222 conjugal transfer protein TrbG/VirB9/CagX YP_913961.1 131779 R 318586 CDS YP_913962.1 119382906 4580173 complement(132780..133469) 1 NC_008686.1 PFAM: Conjugal transfer protein; KEGG: mes:Meso_0502 conjugal transfer protein; conjugal transfer protein TrbF 133469 4580173 Pden_0149 Paracoccus denitrificans PD1222 conjugal transfer protein TrbF YP_913962.1 132780 R 318586 CDS YP_913963.1 119382907 4580174 complement(133466..134785) 1 NC_008686.1 type IV secretion VirB6 family; conjugal transfer protein TrbL 134785 4580174 Pden_0150 Paracoccus denitrificans PD1222 conjugal transfer protein TrbL YP_913963.1 133466 R 318586 CDS YP_913964.1 119382908 4580175 complement(134793..135080) 1 NC_008686.1 KEGG: mes:Meso_2319 hypothetical protein; hypothetical protein 135080 4580175 Pden_0151 Paracoccus denitrificans PD1222 hypothetical protein YP_913964.1 134793 R 318586 CDS YP_913965.1 119382909 4580176 complement(135101..135901) 1 NC_008686.1 KEGG: mes:Meso_3855 conjugal transfer protein TrbJ; conjugal transfer protein TrbJ 135901 4580176 Pden_0152 Paracoccus denitrificans PD1222 conjugal transfer protein TrbJ YP_913965.1 135101 R 318586 CDS YP_913966.1 119382910 4580177 complement(135898..138516) 1 NC_008686.1 type IV secretion system VirB4 family; conjugal transfer ATPase TrbE 138516 4580177 Pden_0153 Paracoccus denitrificans PD1222 conjugal transfer ATPase TrbE YP_913966.1 135898 R 318586 CDS YP_913967.1 119382911 4580178 complement(138528..138809) 1 NC_008686.1 KEGG: mes:Meso_0507 conjugal transfer protein TrbB; conjugal transfer protein TrbB 138809 4580178 Pden_0154 Paracoccus denitrificans PD1222 conjugal transfer protein TrbB YP_913967.1 138528 R 318586 CDS YP_913968.1 119382912 4580179 complement(138809..139138) 1 NC_008686.1 PFAM: Conjugal transfer protein TrbC; KEGG: mes:Meso_2323 conjugal transfer protein TrbC; conjugal transfer protein TrbC 139138 4580179 Pden_0155 Paracoccus denitrificans PD1222 conjugal transfer protein TrbC YP_913968.1 138809 R 318586 CDS YP_913969.1 119382913 4580180 complement(139135..140139) 1 NC_008686.1 PFAM: type II secretion system protein E; KEGG: mes:Meso_2324 type II secretion system protein E; type II secretion system protein E 140139 4580180 Pden_0156 Paracoccus denitrificans PD1222 type II secretion system protein E YP_913969.1 139135 R 318586 CDS YP_913970.1 119382914 4580181 complement(140328..141215) 1 NC_008686.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: nwi:Nwi_0252 transcriptional regulatory protein, LysR family; LysR family transcriptional regulator 141215 4580181 Pden_0157 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_913970.1 140328 R 318586 CDS YP_913971.1 119382915 4580182 complement(141246..141467) 1 NC_008686.1 KEGG: mlo:mlr6069 transposase; hypothetical protein 141467 4580182 Pden_0158 Paracoccus denitrificans PD1222 hypothetical protein YP_913971.1 141246 R 318586 CDS YP_913972.1 119382916 4580183 complement(141627..141974) 1 NC_008686.1 hypothetical protein 141974 4580183 Pden_0159 Paracoccus denitrificans PD1222 hypothetical protein YP_913972.1 141627 R 318586 CDS YP_913973.1 119382917 4579714 complement(142033..145134) 1 NC_008686.1 PFAM: acriflavin resistance protein; KEGG: atc:AGR_L_494 RND pump protein; acriflavin resistance protein 145134 4579714 Pden_0160 Paracoccus denitrificans PD1222 acriflavin resistance protein YP_913973.1 142033 R 318586 CDS YP_913974.1 119382918 4579715 complement(145138..146280) 1 NC_008686.1 TIGRFAM: efflux transporter, RND family, MFP subunit; PFAM: secretion protein HlyD family protein; KEGG: atc:AGR_L_492 nodulation protein NolF; RND family efflux transporter MFP subunit 146280 4579715 Pden_0161 Paracoccus denitrificans PD1222 RND family efflux transporter MFP subunit YP_913974.1 145138 R 318586 CDS YP_913975.1 119382919 4579716 complement(146505..147182) 1 NC_008686.1 PFAM: MltA-interacting MipA family protein; KEGG: ccr:CC0351 outer membrane protein; MltA-interacting MipA family protein 147182 4579716 Pden_0162 Paracoccus denitrificans PD1222 MltA-interacting MipA family protein YP_913975.1 146505 R 318586 CDS YP_913976.1 119382920 4579717 147265..147627 1 NC_008686.1 hypothetical protein 147627 4579717 Pden_0163 Paracoccus denitrificans PD1222 hypothetical protein YP_913976.1 147265 D 318586 CDS YP_913977.1 119382921 4579718 147614..148240 1 NC_008686.1 PFAM: regulatory protein, TetR; KEGG: sco:SCO1193 TetR-family transcriptional regulator; TetR family transcriptional regulator 148240 4579718 Pden_0164 Paracoccus denitrificans PD1222 TetR family transcriptional regulator YP_913977.1 147614 D 318586 CDS YP_913978.1 119382922 4579719 complement(148664..149005) 1 NC_008686.1 SMART: regulatory protein, ArsR; KEGG: nwi:Nwi_3123 transcriptional regulatory protein, ArsR family; regulatory protein ArsR 149005 4579719 Pden_0166 Paracoccus denitrificans PD1222 regulatory protein ArsR YP_913978.1 148664 R 318586 CDS YP_913979.1 119382923 4579720 149251..150348 1 NC_008686.1 PFAM: Cupin 2, conserved barrel domain protein; KEGG: mes:Meso_3565 cupin 2, conserved barrel; cupin 150348 4579720 Pden_0167 Paracoccus denitrificans PD1222 cupin YP_913979.1 149251 D 318586 CDS YP_913980.1 119382924 4579721 150370..151140 1 NC_008686.1 KEGG: mes:Meso_3566 hypothetical protein; hypothetical protein 151140 4579721 Pden_0168 Paracoccus denitrificans PD1222 hypothetical protein YP_913980.1 150370 D 318586 CDS YP_913981.1 119382925 4579722 complement(151137..151964) 1 NC_008686.1 PFAM: regulatory proteins, IclR; KEGG: dar:Daro_0384 regulatory proteins, IclR; regulatory proteins, IclR 151964 4579722 Pden_0169 Paracoccus denitrificans PD1222 regulatory proteins, IclR YP_913981.1 151137 R 318586 CDS YP_913982.1 119382926 4579723 complement(151979..152380) 1 NC_008686.1 PFAM: thioesterase superfamily protein; KEGG: gka:GK1990 4-hydroxybenzoyl-CoA thioesterase; thioesterase 152380 4579723 Pden_0170 Paracoccus denitrificans PD1222 thioesterase YP_913982.1 151979 R 318586 CDS YP_913983.1 119382927 4579724 152463..153608 1 NC_008686.1 PFAM: monooxygenase, FAD-binding; KEGG: bja:blr0106 probable monooxygenase; FAD-binding monooxygenase 153608 4579724 Pden_0171 Paracoccus denitrificans PD1222 FAD-binding monooxygenase YP_913983.1 152463 D 318586 CDS YP_913984.1 119382928 4579725 153619..155283 1 NC_008686.1 TIGRFAM: benzoate-CoA ligase family; PFAM: AMP-dependent synthetase and ligase; KEGG: bja:blr0107 probable coenzyme A ligase; benzoate-CoA ligase family 155283 4579725 Pden_0172 Paracoccus denitrificans PD1222 benzoate-CoA ligase family YP_913984.1 153619 D 318586 CDS YP_913985.1 119382929 4579726 155383..156093 1 NC_008686.1 PFAM: fumarylacetoacetate (FAA) hydrolase; KEGG: rme:Rmet_4907 fumarylacetoacetate (FAA) hydrolase; fumarylacetoacetate (FAA) hydrolase 156093 4579726 Pden_0173 Paracoccus denitrificans PD1222 fumarylacetoacetate (FAA) hydrolase YP_913985.1 155383 D 318586 CDS YP_913986.1 119382930 4579727 156090..156743 1 NC_008686.1 TIGRFAM: maleylacetoacetate isomerase; PFAM: Glutathione S-transferase, N-terminal domain; KEGG: mlo:mlr1135 maleylacetoacetate isomerase; maleylacetoacetate isomerase 156743 4579727 Pden_0174 Paracoccus denitrificans PD1222 maleylacetoacetate isomerase YP_913986.1 156090 D 318586 CDS YP_913987.1 119382931 4579728 156769..157950 1 NC_008686.1 KEGG: bja:blr1052 ABC transporter binding protein; ABC transporter binding protein 157950 4579728 Pden_0175 Paracoccus denitrificans PD1222 ABC transporter binding protein YP_913987.1 156769 D 318586 CDS YP_913988.1 119382932 4579729 157992..158912 1 NC_008686.1 PFAM: inner-membrane translocator; KEGG: bja:blr1064 ABC transporter permease protein; inner-membrane translocator 158912 4579729 Pden_0176 Paracoccus denitrificans PD1222 inner-membrane translocator YP_913988.1 157992 D 318586 CDS YP_913989.1 119382933 4579730 158917..159918 1 NC_008686.1 PFAM: inner-membrane translocator; KEGG: bja:blr1065 ABC transporter permease protein; inner-membrane translocator 159918 4579730 Pden_0177 Paracoccus denitrificans PD1222 inner-membrane translocator YP_913989.1 158917 D 318586 CDS YP_913990.1 119382934 4579731 159915..160664 1 NC_008686.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: bja:blr1066 ABC transporter ATP-binding protein; ABC transporter 160664 4579731 Pden_0178 Paracoccus denitrificans PD1222 ABC transporter YP_913990.1 159915 D 318586 CDS YP_913991.1 119382935 4579732 160664..161365 1 NC_008686.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: bja:blr1067 ABC transporter ATP-binding protein; ABC transporter 161365 4579732 Pden_0179 Paracoccus denitrificans PD1222 ABC transporter YP_913991.1 160664 D 318586 CDS YP_913992.1 119382936 4578818 161423..162874 1 NC_008686.1 PFAM: aldehyde dehydrogenase; KEGG: mlo:mll7197 dehydrogenase; aldehyde dehydrogenase 162874 4578818 Pden_0180 Paracoccus denitrificans PD1222 aldehyde dehydrogenase YP_913992.1 161423 D 318586 CDS YP_913993.1 119382937 4578819 162937..164652 1 NC_008686.1 PFAM: glucose-methanol-choline oxidoreductase; GMC oxidoreductase; KEGG: xcv:XCV2149 choline dehydrogenase; glucose-methanol-choline oxidoreductase 164652 4578819 Pden_0181 Paracoccus denitrificans PD1222 glucose-methanol-choline oxidoreductase YP_913993.1 162937 D 318586 CDS YP_913994.1 119382938 4578820 164730..165875 1 NC_008686.1 KEGG: rme:Rmet_3785 beta-lactamase-like protein; beta-lactamase-like protein 165875 4578820 Pden_0182 Paracoccus denitrificans PD1222 beta-lactamase-like protein YP_913994.1 164730 D 318586 CDS YP_913995.1 119382939 4578821 complement(165932..167233) 1 NC_008686.1 catalyzes the oxidative deamination of D-amino acids; D-amino acid dehydrogenase small subunit 167233 4578821 Pden_0183 Paracoccus denitrificans PD1222 D-amino acid dehydrogenase small subunit YP_913995.1 165932 R 318586 CDS YP_913996.1 119382940 4578822 complement(167506..168204) 1 NC_008686.1 KEGG: oih:OB0952 hypothetical protein; hypothetical protein 168204 4578822 Pden_0184 Paracoccus denitrificans PD1222 hypothetical protein YP_913996.1 167506 R 318586 CDS YP_913997.1 119382941 4578823 complement(168231..168968) 1 NC_008686.1 KEGG: oih:OB0951 hypothetical protein; hypothetical protein 168968 4578823 Pden_0185 Paracoccus denitrificans PD1222 hypothetical protein YP_913997.1 168231 R 318586 CDS YP_913998.1 119382942 4578824 complement(169001..170164) 1 NC_008686.1 KEGG: bja:blr5691 amidohydrolase; TIGRFAM: amidohydrolase; PFAM: peptidase M20; peptidase dimerisation domain protein; amidohydrolase 170164 4578824 Pden_0186 Paracoccus denitrificans PD1222 amidohydrolase YP_913998.1 169001 R 318586 CDS YP_913999.1 119382943 4578825 170313..170816 1 NC_008686.1 PFAM: regulatory protein, MarR; KEGG: sil:SPO1261 transcriptional regulator, MarR family; MarR family transcriptional regulator 170816 4578825 Pden_0187 Paracoccus denitrificans PD1222 MarR family transcriptional regulator YP_913999.1 170313 D 318586 CDS YP_914000.1 119382944 4578826 complement(170847..171662) 1 NC_008686.1 PFAM: regulatory proteins, IclR; KEGG: bps:BPSS2127 IclR transcriptional regulator protein; regulatory proteins, IclR 171662 4578826 Pden_0188 Paracoccus denitrificans PD1222 regulatory proteins, IclR YP_914000.1 170847 R 318586 CDS YP_914001.1 119382945 4578827 complement(171675..173552) 1 NC_008686.1 PFAM: TRAP C4-dicarboxylate transport system permease DctM subunit; KEGG: rpe:RPE_1982 TRAP C4-dicarboxylate transport system permease DctM subunit; TRAP dicarboxylate transporter subunit DctM 173552 4578827 Pden_0189 Paracoccus denitrificans PD1222 TRAP dicarboxylate transporter subunit DctM YP_914001.1 171675 R 318586 CDS YP_914002.1 119382946 4578828 complement(173552..174082) 1 NC_008686.1 PFAM: Tripartite ATP-independent periplasmic transporter, DctQ component; KEGG: mlo:mll5171 hypothetical protein; tripartite ATP-independent periplasmic transporter DctQ 174082 4578828 Pden_0190 Paracoccus denitrificans PD1222 tripartite ATP-independent periplasmic transporter DctQ YP_914002.1 173552 R 318586 CDS YP_914003.1 119382947 4578829 complement(174180..174593) 1 NC_008686.1 PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase; KEGG: cme:CMP184C hypothetical protein, conserved Pfam: Glyoxalase; glyoxalase/bleomycin resistance protein/dioxygenase 174593 4578829 Pden_0191 Paracoccus denitrificans PD1222 glyoxalase/bleomycin resistance protein/dioxygenase YP_914003.1 174180 R 318586 CDS YP_914004.1 119382948 4578830 complement(174620..175390) 1 NC_008686.1 PFAM: short-chain dehydrogenase/reductase SDR; KR; KEGG: tma:TM1724 3-oxoacyl-(acyl carrier protein) reductase; short-chain dehydrogenase/reductase SDR 175390 4578830 Pden_0192 Paracoccus denitrificans PD1222 short-chain dehydrogenase/reductase SDR YP_914004.1 174620 R 318586 CDS YP_914005.1 119382949 4578831 complement(175536..176624) 1 NC_008686.1 PFAM: TRAP dicarboxylate transporter- DctP subunit; KEGG: mlo:mlr5166 periplasmic mannitol-binding protein; SmoM; TRAP dicarboxylate transporter- DctP subunit 176624 4578831 Pden_0193 Paracoccus denitrificans PD1222 TRAP dicarboxylate transporter- DctP subunit YP_914005.1 175536 R 318586 CDS YP_914006.1 119382950 4578832 176899..177723 1 NC_008686.1 KEGG: bxe:Bxe_C0656 hypothetical protein; hypothetical protein 177723 4578832 Pden_0194 Paracoccus denitrificans PD1222 hypothetical protein YP_914006.1 176899 D 318586 CDS YP_914007.1 119382951 4578833 177720..178925 1 NC_008686.1 PFAM: L-carnitine dehydratase/bile acid-inducible protein F; KEGG: rpa:RPA4557 hypothetical protein; L-carnitine dehydratase/bile acid-inducible protein F 178925 4578833 Pden_0195 Paracoccus denitrificans PD1222 L-carnitine dehydratase/bile acid-inducible protein F YP_914007.1 177720 D 318586 CDS YP_914008.1 119382952 4578834 178909..179730 1 NC_008686.1 PFAM: short-chain dehydrogenase/reductase SDR; KEGG: psp:PSPPH_1258 3-oxoacyl-(acyl-carrier-protein) reductase; short-chain dehydrogenase/reductase SDR 179730 4578834 Pden_0196 Paracoccus denitrificans PD1222 short-chain dehydrogenase/reductase SDR YP_914008.1 178909 D 318586 CDS YP_914009.1 119382953 4578835 179751..181280 1 NC_008686.1 converts 3-hydroxyadipyl-CoA to beta-ketoadipyl-CoA in phenylacetate degradation; 3-hydroxyacyl-CoA dehydrogenase 181280 4578835 Pden_0197 Paracoccus denitrificans PD1222 3-hydroxyacyl-CoA dehydrogenase YP_914009.1 179751 D 318586 CDS YP_914010.1 119382954 4578836 complement(181335..182495) 1 NC_008686.1 PFAM: acyl-CoA dehydrogenase domain protein; Acyl-CoA dehydrogenase, type 2, C-terminal domain; KEGG: mag:amb2599 acyl-CoA dehydrogenase; butyryl-CoA dehydrogenase 182495 4578836 Pden_0198 Paracoccus denitrificans PD1222 butyryl-CoA dehydrogenase YP_914010.1 181335 R 318586 CDS YP_914011.1 119382955 4579016 complement(183912..185984) 1 NC_008686.1 PFAM: Enoyl-CoA hydratase/isomerase; 3-hydroxyacyl-CoA dehydrogenase domain protein; 3-hydroxyacyl-CoA dehydrogenase, NAD-binding; KEGG: jan:Jann_0676 3-hydroxyacyl-CoA dehydrogenase, NAD-binding; 3-hydroxyacyl-CoA dehydrogenase 185984 4579016 Pden_0201 Paracoccus denitrificans PD1222 3-hydroxyacyl-CoA dehydrogenase YP_914011.1 183912 R 318586 CDS YP_914012.1 119382956 4579017 186326..186856 1 NC_008686.1 PFAM: flavin reductase domain protein, FMN-binding; KEGG: bte:BTH_II2298 flavin reductase domain protein; flavin reductase domain-containing protein 186856 4579017 Pden_0202 Paracoccus denitrificans PD1222 flavin reductase domain-containing protein YP_914012.1 186326 D 318586 CDS YP_914013.1 119382957 4579018 186916..188004 1 NC_008686.1 PFAM: luciferase family protein; KEGG: jan:Jann_2939 luciferase-like; luciferase family protein 188004 4579018 Pden_0203 Paracoccus denitrificans PD1222 luciferase family protein YP_914013.1 186916 D 318586 CDS YP_914014.1 119382958 4579019 188036..188707 1 NC_008686.1 PFAM: 3,4-dihydroxy-2-butanone 4-phosphate synthase; KEGG: mta:Moth_0917 3,4-dihydroxy-2-butanone 4-phosphate synthase; 3,4-dihydroxy-2-butanone 4-phosphate synthase 188707 4579019 Pden_0204 Paracoccus denitrificans PD1222 3,4-dihydroxy-2-butanone 4-phosphate synthase YP_914014.1 188036 D 318586 CDS YP_914015.1 119382959 4579020 complement(188774..189028) 1 NC_008686.1 hypothetical protein 189028 4579020 Pden_0205 Paracoccus denitrificans PD1222 hypothetical protein YP_914015.1 188774 R 318586 CDS YP_914016.1 119382960 4579021 complement(189154..189945) 1 NC_008686.1 PFAM: short-chain dehydrogenase/reductase SDR; KR; KEGG: pau:PA14_10280 short-chain dehydrogenase; short-chain dehydrogenase/reductase SDR 189945 4579021 Pden_0206 Paracoccus denitrificans PD1222 short-chain dehydrogenase/reductase SDR YP_914016.1 189154 R 318586 CDS YP_914017.1 119382961 4579022 complement(190129..191124) 1 NC_008686.1 PFAM: alpha/beta hydrolase fold; KEGG: rso:RS05450 hydrolase signal peptide protein; alpha/beta hydrolase 191124 4579022 Pden_0207 Paracoccus denitrificans PD1222 alpha/beta hydrolase YP_914017.1 190129 R 318586 CDS YP_914018.1 119382962 4579023 complement(191172..191351) 1 NC_008686.1 PFAM: 4-oxalocrotonate tautomerase; KEGG: rso:RS05436 hypothetical protein; 4-oxalocrotonate tautomerase 191351 4579023 Pden_0208 Paracoccus denitrificans PD1222 4-oxalocrotonate tautomerase YP_914018.1 191172 R 318586 CDS YP_914019.1 119382963 4579024 191454..192362 1 NC_008686.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: psb:Psyr_2945 regulatory protein, LysR:LysR, substrate-binding; LysR family transcriptional regulator 192362 4579024 Pden_0209 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_914019.1 191454 D 318586 CDS YP_914020.1 119382964 4579025 complement(192405..193013) 1 NC_008686.1 KEGG: rso:RS05437 hypothetical protein; hypothetical protein 193013 4579025 Pden_0210 Paracoccus denitrificans PD1222 hypothetical protein YP_914020.1 192405 R 318586 CDS YP_914021.1 119382965 4579026 complement(193178..193600) 1 NC_008686.1 PFAM: regulatory protein, MerR; KEGG: rsp:RSP_1790 probable transcriptional regulator; MerR family transcriptional regulator 193600 4579026 Pden_0211 Paracoccus denitrificans PD1222 MerR family transcriptional regulator YP_914021.1 193178 R 318586 CDS YP_914022.1 119382966 4579027 193651..195927 1 NC_008686.1 TIGRFAM: ATPase, P-type (transporting), HAD superfamily, subfamily IC; cadmium-translocating P-type ATPase; heavy metal translocating P-type ATPase; PFAM: Haloacid dehalogenase domain protein hydrolase; Heavy metal transport/detoxification protein; E1-E2 ATPase-associated domain protein; KEGG: rsp:RSP_1791 heavy metal-(Cd/Co/Hg/Pb/Zn)-translocating P-type ATPase; heavy metal translocating P-type ATPase 195927 4579027 Pden_0212 Paracoccus denitrificans PD1222 heavy metal translocating P-type ATPase YP_914022.1 193651 D 318586 CDS YP_914023.1 119382967 4579028 195927..196523 1 NC_008686.1 KEGG: tfu:Tfu_1571 hypothetical protein; S-isoprenylcysteine methyltransferase-like protein 196523 4579028 Pden_0213 Paracoccus denitrificans PD1222 S-isoprenylcysteine methyltransferase-like protein YP_914023.1 195927 D 318586 CDS YP_914024.1 119382968 4579029 complement(196604..197680) 1 NC_008686.1 TIGRFAM: arsenical-resistance protein; PFAM: Bile acid:sodium symporter; KEGG: sal:Sala_2405 arsenical-resistance protein; arsenical-resistance protein 197680 4579029 Pden_0214 Paracoccus denitrificans PD1222 arsenical-resistance protein YP_914024.1 196604 R 318586 CDS YP_914025.1 119382969 4579030 complement(197709..198137) 1 NC_008686.1 TIGRFAM: arsenate reductase; PFAM: arsenate reductase and related; KEGG: rpa:RPA3554 arsenate reductase; arsenate reductase 198137 4579030 Pden_0215 Paracoccus denitrificans PD1222 arsenate reductase YP_914025.1 197709 R 318586 CDS YP_914026.1 119382970 4579031 complement(198147..198683) 1 NC_008686.1 PFAM: low molecular weight phosphotyrosine protein phosphatase; KEGG: nwi:Nwi_3124 low molecular weight phosphotyrosine protein phosphatase; protein tyrosine phosphatase 198683 4579031 Pden_0216 Paracoccus denitrificans PD1222 protein tyrosine phosphatase YP_914026.1 198147 R 318586 CDS YP_914027.1 119382971 4579032 complement(198676..199038) 1 NC_008686.1 SMART: regulatory protein, ArsR; KEGG: nwi:Nwi_3123 transcriptional regulatory protein, ArsR family; regulatory protein ArsR 199038 4579032 Pden_0217 Paracoccus denitrificans PD1222 regulatory protein ArsR YP_914027.1 198676 R 318586 CDS YP_914028.1 119382972 4579033 199089..199535 1 NC_008686.1 PFAM: regulatory protein, LysR; KEGG: gvi:glr3360 LysR family transcriptional regulatory protein; LysR family transcriptional regulator 199535 4579033 Pden_0218 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_914028.1 199089 D 318586 CDS YP_914029.1 119382973 4579034 199766..200146 1 NC_008686.1 KEGG: ttj:TTHB244 phenol hydroxylase component B; hypothetical protein 200146 4579034 Pden_0219 Paracoccus denitrificans PD1222 hypothetical protein YP_914029.1 199766 D 318586 CDS YP_914030.1 119382974 4580800 200561..201643 1 NC_008686.1 PFAM: luciferase family protein; KEGG: jan:Jann_2939 luciferase-like; luciferase family protein 201643 4580800 Pden_0220 Paracoccus denitrificans PD1222 luciferase family protein YP_914030.1 200561 D 318586 CDS YP_914031.1 119382975 4580801 201702..202565 1 NC_008686.1 KEGG: bxe:Bxe_C0656 hypothetical protein; hypothetical protein 202565 4580801 Pden_0221 Paracoccus denitrificans PD1222 hypothetical protein YP_914031.1 201702 D 318586 CDS YP_914032.1 119382976 4580802 202555..203775 1 NC_008686.1 PFAM: L-carnitine dehydratase/bile acid-inducible protein F; KEGG: pol:Bpro_5571 L-carnitine dehydratase/bile acid-inducible protein F; L-carnitine dehydratase/bile acid-inducible protein F 203775 4580802 Pden_0222 Paracoccus denitrificans PD1222 L-carnitine dehydratase/bile acid-inducible protein F YP_914032.1 202555 D 318586 CDS YP_914033.1 119382977 4580803 203895..205325 1 NC_008686.1 PFAM: aldehyde dehydrogenase; KEGG: bmb:BruAb2_0802 aldehyde dehydrogenase family protein; succinate-semialdehyde dehydrogenase (NAD(P)(+)) 205325 4580803 Pden_0223 Paracoccus denitrificans PD1222 succinate-semialdehyde dehydrogenase (NAD(P)(+)) YP_914033.1 203895 D 318586 CDS YP_914034.1 119382978 4580804 complement(205387..207240) 1 NC_008686.1 PFAM: sigma-54 factor, interaction domain-containing protein; helix-turn-helix, Fis-type; SMART: AAA ATPase; KEGG: aeh:Mlg_2736 GAF modulated sigma54 specific transcriptional regulator, fis family; Fis family transcriptional regulator 207240 4580804 Pden_0224 Paracoccus denitrificans PD1222 Fis family transcriptional regulator YP_914034.1 205387 R 318586 CDS YP_914035.1 119382979 4580805 complement(207290..207832) 1 NC_008686.1 PFAM: flavin reductase domain protein, FMN-binding; KEGG: rsp:RSP_3957 flavoprotein oxidoreductase; flavin reductase domain-containing protein 207832 4580805 Pden_0225 Paracoccus denitrificans PD1222 flavin reductase domain-containing protein YP_914035.1 207290 R 318586 CDS YP_914036.1 119382980 4580806 complement(208050..208970) 1 NC_008686.1 PFAM: luciferase family protein; KEGG: ppu:PP_3171 hypothetical protein; luciferase family protein 208970 4580806 Pden_0226 Paracoccus denitrificans PD1222 luciferase family protein YP_914036.1 208050 R 318586 CDS YP_914037.1 119382981 4580807 complement(209038..209307) 1 NC_008686.1 hypothetical protein 209307 4580807 Pden_0227 Paracoccus denitrificans PD1222 hypothetical protein YP_914037.1 209038 R 318586 CDS YP_914038.1 119382982 4580808 complement(209307..209846) 1 NC_008686.1 PFAM: Xylose isomerase domain protein TIM barrel; KEGG: sus:Acid_5864 xylose isomerase domain protein TIM barrel; xylose isomerase domain-containing protein 209846 4580808 Pden_0228 Paracoccus denitrificans PD1222 xylose isomerase domain-containing protein YP_914038.1 209307 R 318586 CDS YP_914039.1 119382983 4580809 complement(209861..210658) 1 NC_008686.1 PFAM: Xylose isomerase domain protein TIM barrel; KEGG: sus:Acid_5864 xylose isomerase domain protein TIM barrel; xylose isomerase domain-containing protein 210658 4580809 Pden_0229 Paracoccus denitrificans PD1222 xylose isomerase domain-containing protein YP_914039.1 209861 R 318586 CDS YP_914040.1 119382984 4580810 complement(210655..211734) 1 NC_008686.1 PFAM: luciferase family protein; KEGG: psb:Psyr_1559 luciferase; luciferase family protein 211734 4580810 Pden_0230 Paracoccus denitrificans PD1222 luciferase family protein YP_914040.1 210655 R 318586 CDS YP_914041.1 119382985 4580811 211824..212726 1 NC_008686.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: bcn:Bcen_1980 transcriptional regulator, LysR family; LysR family transcriptional regulator 212726 4580811 Pden_0231 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_914041.1 211824 D 318586 CDS YP_914042.1 119382986 4580812 complement(212737..213429) 1 NC_008686.1 PFAM: regulatory protein, TetR; KEGG: pae:PA3678 probable transcriptional regulator; TetR family transcriptional regulator 213429 4580812 Pden_0232 Paracoccus denitrificans PD1222 TetR family transcriptional regulator YP_914042.1 212737 R 318586 CDS YP_914043.1 119382987 4580813 213456..215417 1 NC_008686.1 KEGG: gme:Gmet_2060 fusaric acid resistance protein conserved region; hypothetical protein 215417 4580813 Pden_0233 Paracoccus denitrificans PD1222 hypothetical protein YP_914043.1 213456 D 318586 CDS YP_914044.1 119382988 4580814 215564..215908 1 NC_008686.1 KEGG: xcb:XC_0382 b-ketoadipate enol-lactone hydrolase; hypothetical protein 215908 4580814 Pden_0234 Paracoccus denitrificans PD1222 hypothetical protein YP_914044.1 215564 D 318586 CDS YP_914045.1 119382989 4580815 complement(215905..216918) 1 NC_008686.1 KEGG: rfr:Rfer_0981 oligopeptide/dipeptide ABC transporter, ATP-binding protein-like; TIGRFAM: oligopeptide/dipeptide ABC transporter, ATPase subunit; PFAM: ABC transporter related; Oligopeptide/dipeptide ABC transporter, C-terminal domain protein; SMART: AAA ATPase; oligopeptide/dipeptide ABC transporter ATPase 216918 4580815 Pden_0235 Paracoccus denitrificans PD1222 oligopeptide/dipeptide ABC transporter ATPase YP_914045.1 215905 R 318586 CDS YP_914046.1 119382990 4580816 complement(216915..217913) 1 NC_008686.1 KEGG: rme:Rmet_5091 oligopeptide/dipeptide ABC transporter, ATP-binding protein-like protein; TIGRFAM: oligopeptide/dipeptide ABC transporter, ATPase subunit; PFAM: ABC transporter related; Oligopeptide/dipeptide ABC transporter, C-terminal domain protein; SMART: AAA ATPase; oligopeptide/dipeptide ABC transporter ATPase 217913 4580816 Pden_0236 Paracoccus denitrificans PD1222 oligopeptide/dipeptide ABC transporter ATPase YP_914046.1 216915 R 318586 CDS YP_914047.1 119382991 4580817 complement(217913..218785) 1 NC_008686.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: psp:PSPPH_2784 dipeptide transport system permease protein DppC AGR_L_321; binding-protein-dependent transport system inner membrane protein 218785 4580817 Pden_0237 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_914047.1 217913 R 318586 CDS YP_914048.1 119382992 4580818 complement(218785..219720) 1 NC_008686.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: ppu:PP_4455 opine ABC transporter, periplasmic binding protein; binding-protein-dependent transport system inner membrane protein 219720 4580818 Pden_0238 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_914048.1 218785 R 318586 CDS YP_914049.1 119382993 4580819 complement(219738..221327) 1 NC_008686.1 PFAM: extracellular solute-binding protein, family 5; KEGG: pol:Bpro_4344 extracellular solute-binding protein, family 5; extracellular solute-binding protein 221327 4580819 Pden_0239 Paracoccus denitrificans PD1222 extracellular solute-binding protein YP_914049.1 219738 R 318586 CDS YP_914050.1 119382994 4579733 complement(221408..222094) 1 NC_008686.1 PFAM: regulatory protein GntR, HTH; GntR domain protein; KEGG: mes:Meso_4461 transcriptional regulator, GntR family; GntR family transcriptional regulator 222094 4579733 Pden_0240 Paracoccus denitrificans PD1222 GntR family transcriptional regulator YP_914050.1 221408 R 318586 CDS YP_914051.1 119382995 4579734 222145..223182 1 NC_008686.1 PFAM: Malate/L-lactate dehydrogenase; KEGG: mes:Meso_4453 malate/L-lactate dehydrogenase; (R)-2-hydroxyacid dehydrogenase 223182 4579734 Pden_0241 Paracoccus denitrificans PD1222 (R)-2-hydroxyacid dehydrogenase YP_914051.1 222145 D 318586 CDS YP_914052.1 119382996 4579735 223208..224464 1 NC_008686.1 PFAM: iron-containing alcohol dehydrogenase; KEGG: rpc:RPC_0105 alcohol dehydrogenase; iron-containing alcohol dehydrogenase 224464 4579735 Pden_0242 Paracoccus denitrificans PD1222 iron-containing alcohol dehydrogenase YP_914052.1 223208 D 318586 CDS YP_914053.1 119382997 4579736 224461..225939 1 NC_008686.1 PFAM: aldehyde dehydrogenase; KEGG: mes:Meso_4451 aldehyde dehydrogenase; succinate-semialdehyde dehydrogenase (NAD(P)(+)) 225939 4579736 Pden_0243 Paracoccus denitrificans PD1222 succinate-semialdehyde dehydrogenase (NAD(P)(+)) YP_914053.1 224461 D 318586 CDS YP_914054.1 119382998 4579737 225977..227128 1 NC_008686.1 PFAM: Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein; Mandelate racemase/muconate lactonizing enzyme, C-terminal domain protein; KEGG: pat:Patl_0897 mandelate racemase/muconate lactonizing enzyme-like; mandelate racemase 227128 4579737 Pden_0244 Paracoccus denitrificans PD1222 mandelate racemase YP_914054.1 225977 D 318586 CDS YP_914055.1 119382999 4579738 227187..228044 1 NC_008686.1 PFAM: fumarylacetoacetate (FAA) hydrolase; KEGG: reu:Reut_A0050 5-carboxymethyl-2-hydroxymuconate delta-isomerase; 5-carboxymethyl-2-hydroxymuconate delta-isomerase 228044 4579738 Pden_0245 Paracoccus denitrificans PD1222 5-carboxymethyl-2-hydroxymuconate delta-isomerase YP_914055.1 227187 D 318586 CDS YP_914056.1 119383000 4579739 228259..229149 1 NC_008686.1 PFAM: Xylose isomerase domain protein TIM barrel; KEGG: msu:MS0202 hypothetical protein; xylose isomerase domain-containing protein 229149 4579739 Pden_0246 Paracoccus denitrificans PD1222 xylose isomerase domain-containing protein YP_914056.1 228259 D 318586 CDS YP_914057.1 119383001 4579740 229193..230239 1 NC_008686.1 PFAM: periplasmic binding protein/LacI transcriptional regulator; KEGG: msu:MS0201 RbsB protein; periplasmic binding protein/LacI transcriptional regulator 230239 4579740 Pden_0247 Paracoccus denitrificans PD1222 periplasmic binding protein/LacI transcriptional regulator YP_914057.1 229193 D 318586 CDS YP_914058.1 119383002 4579741 230457..231896 1 NC_008686.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: msu:MS0200 MglA protein; ABC transporter 231896 4579741 Pden_0248 Paracoccus denitrificans PD1222 ABC transporter YP_914058.1 230457 D 318586 CDS YP_914059.1 119383003 4579742 231893..232855 1 NC_008686.1 PFAM: inner-membrane translocator; KEGG: msu:MS0199 ribose/xylose/arabinose/galactoside ABC-type transport systems, permease components; inner-membrane translocator 232855 4579742 Pden_0249 Paracoccus denitrificans PD1222 inner-membrane translocator YP_914059.1 231893 D 318586 CDS YP_914060.1 119383004 4579743 232852..233715 1 NC_008686.1 involved in rpiB and als operon repression; DNA-binding transcriptional repressor RpiR 233715 4579743 Pden_0250 Paracoccus denitrificans PD1222 DNA-binding transcriptional repressor RpiR YP_914060.1 232852 D 318586 CDS YP_914061.1 119383005 4579744 233732..234574 1 NC_008686.1 PFAM: PfkB domain protein; KEGG: msu:MS0197 RbsK protein; ribokinase-like domain-containing protein 234574 4579744 Pden_0251 Paracoccus denitrificans PD1222 ribokinase-like domain-containing protein YP_914061.1 233732 D 318586 CDS YP_914062.1 119383006 4579745 complement(234598..234849) 1 NC_008686.1 KEGG: gox:GOX2677 transposase (class I); transposase (class I) 234849 4579745 Pden_0252 Paracoccus denitrificans PD1222 transposase (class I) YP_914062.1 234598 R 318586 CDS YP_914063.1 119383007 4579746 complement(234955..235479) 1 NC_008686.1 hypothetical protein 235479 4579746 Pden_0253 Paracoccus denitrificans PD1222 hypothetical protein YP_914063.1 234955 R 318586 CDS YP_914064.1 119383008 4579747 235511..235789 1 NC_008686.1 hypothetical protein 235789 4579747 Pden_0254 Paracoccus denitrificans PD1222 hypothetical protein YP_914064.1 235511 D 318586 CDS YP_914065.1 119383009 4579748 236307..236864 1 NC_008686.1 hypothetical protein 236864 4579748 Pden_0255 Paracoccus denitrificans PD1222 hypothetical protein YP_914065.1 236307 D 318586 CDS YP_914066.1 119383010 4579749 236988..237242 1 NC_008686.1 hypothetical protein 237242 4579749 Pden_0256 Paracoccus denitrificans PD1222 hypothetical protein YP_914066.1 236988 D 318586 CDS YP_914067.1 119383011 4579750 complement(237429..237779) 1 NC_008686.1 KEGG: nfa:nfa39970 hypothetical protein; hypothetical protein 237779 4579750 Pden_0257 Paracoccus denitrificans PD1222 hypothetical protein YP_914067.1 237429 R 318586 CDS YP_914068.1 119383012 4579751 complement(237776..238126) 1 NC_008686.1 hypothetical protein 238126 4579751 Pden_0258 Paracoccus denitrificans PD1222 hypothetical protein YP_914068.1 237776 R 318586 CDS YP_914069.1 119383013 4578897 238183..238512 1 NC_008686.1 hypothetical protein 238512 4578897 Pden_0259 Paracoccus denitrificans PD1222 hypothetical protein YP_914069.1 238183 D 318586 CDS YP_914070.1 119383014 4578898 complement(238789..239064) 1 NC_008686.1 hypothetical protein 239064 4578898 Pden_0260 Paracoccus denitrificans PD1222 hypothetical protein YP_914070.1 238789 R 318586 CDS YP_914071.1 119383015 4578899 complement(239190..239984) 1 NC_008686.1 PFAM: D12 class N6 adenine-specific DNA methyltransferase; KEGG: ypm:YP_1932 methyltransferase; D12 class N6 adenine-specific DNA methyltransferase 239984 4578899 Pden_0261 Paracoccus denitrificans PD1222 D12 class N6 adenine-specific DNA methyltransferase YP_914071.1 239190 R 318586 CDS YP_914072.1 119383016 4578900 complement(239981..240562) 1 NC_008686.1 KEGG: mes:Meso_0232 hypothetical protein; hypothetical protein 240562 4578900 Pden_0262 Paracoccus denitrificans PD1222 hypothetical protein YP_914072.1 239981 R 318586 CDS YP_914073.1 119383017 4578901 complement(240559..242226) 1 NC_008686.1 TIGRFAM: DNA-cytosine methyltransferase; PFAM: C-5 cytosine-specific DNA methylase; KEGG: bte:BTH_II1364 DNA methyltransferase; DNA-cytosine methyltransferase 242226 4578901 Pden_0263 Paracoccus denitrificans PD1222 DNA-cytosine methyltransferase YP_914073.1 240559 R 318586 CDS YP_914074.1 119383018 4578902 242420..242716 1 NC_008686.1 KEGG: sme:SMc00822 hypothetical protein; hypothetical protein 242716 4578902 Pden_0264 Paracoccus denitrificans PD1222 hypothetical protein YP_914074.1 242420 D 318586 CDS YP_914075.1 119383019 4578903 242716..243093 1 NC_008686.1 KEGG: sit:TM1040_0815 transcriptional regulator, XRE family; XRE family transcriptional regulator 243093 4578903 Pden_0265 Paracoccus denitrificans PD1222 XRE family transcriptional regulator YP_914075.1 242716 D 318586 CDS YP_914076.1 119383020 4578904 243083..243817 1 NC_008686.1 hypothetical protein 243817 4578904 Pden_0266 Paracoccus denitrificans PD1222 hypothetical protein YP_914076.1 243083 D 318586 CDS YP_914077.1 119383021 4578905 complement(243957..244910) 1 NC_008686.1 PFAM: Peptidoglycan-binding domain 1 protein; KEGG: eli:ELI_07940 bacteriophage-acquired protein; peptidoglycan binding domain-containing protein 244910 4578905 Pden_0267 Paracoccus denitrificans PD1222 peptidoglycan binding domain-containing protein YP_914077.1 243957 R 318586 CDS YP_914078.1 119383022 4578906 complement(244980..245237) 1 NC_008686.1 hypothetical protein 245237 4578906 Pden_0268 Paracoccus denitrificans PD1222 hypothetical protein YP_914078.1 244980 R 318586 CDS YP_914079.1 119383023 4578907 complement(245264..245617) 1 NC_008686.1 KEGG: sil:SPO2726 hypothetical protein; hypothetical protein 245617 4578907 Pden_0269 Paracoccus denitrificans PD1222 hypothetical protein YP_914079.1 245264 R 318586 CDS YP_914080.1 119383024 4578908 complement(245625..249644) 1 NC_008686.1 KEGG: nwi:Nwi_0792 gene transfer agent (GTA) like protein; gene transfer agent (GTA) like protein 249644 4578908 Pden_0270 Paracoccus denitrificans PD1222 gene transfer agent (GTA) like protein YP_914080.1 245625 R 318586 CDS YP_914081.1 119383025 4578909 complement(249649..250086) 1 NC_008686.1 TIGRFAM: phage cell wall peptidase, NlpC/P60 family; PFAM: NLP/P60 protein; KEGG: sil:SPO2729 hypothetical protein; NlpC/P60 family phage cell wall peptidase 250086 4578909 Pden_0271 Paracoccus denitrificans PD1222 NlpC/P60 family phage cell wall peptidase YP_914081.1 249649 R 318586 CDS YP_914082.1 119383026 4578910 complement(250083..250967) 1 NC_008686.1 KEGG: rpb:RPB_3460 phage conserved hypothetical protein BR0599; phage protein 250967 4578910 Pden_0272 Paracoccus denitrificans PD1222 phage protein YP_914082.1 250083 R 318586 CDS YP_914083.1 119383027 4578911 complement(250964..251590) 1 NC_008686.1 KEGG: mmr:Mmar10_0930 hypothetical protein; hypothetical protein 251590 4578911 Pden_0273 Paracoccus denitrificans PD1222 hypothetical protein YP_914083.1 250964 R 318586 CDS YP_914084.1 119383028 4578912 complement(251590..252849) 1 NC_008686.1 KEGG: dvu:DVU1490 tail tape measure protein; hypothetical protein 252849 4578912 Pden_0274 Paracoccus denitrificans PD1222 hypothetical protein YP_914084.1 251590 R 318586 CDS YP_914085.1 119383029 4578913 complement(252834..253898) 1 NC_008686.1 hypothetical protein 253898 4578913 Pden_0275 Paracoccus denitrificans PD1222 hypothetical protein YP_914085.1 252834 R 318586 CDS YP_914086.1 119383030 4578914 254344..254865 1 NC_008686.1 KEGG: bmb:BruAb2_0879 hypothetical sugar-binding protein; sugar-binding protein 254865 4578914 Pden_0276 Paracoccus denitrificans PD1222 sugar-binding protein YP_914086.1 254344 D 318586 CDS YP_914087.1 119383031 4578915 complement(254938..255678) 1 NC_008686.1 PFAM: ChaC family protein; KEGG: mlo:mll2256 cation transport protein; ChaC family protein 255678 4578915 Pden_0277 Paracoccus denitrificans PD1222 ChaC family protein YP_914087.1 254938 R 318586 CDS YP_914088.1 119383032 4578916 256203..257528 1 NC_008686.1 PFAM: General substrate transporter; major facilitator superfamily MFS_1; KEGG: rxy:Rxyl_2255 general substrate transporter; major facilitator superfamily transporter 257528 4578916 Pden_0278 Paracoccus denitrificans PD1222 major facilitator superfamily transporter YP_914088.1 256203 D 318586 CDS YP_914089.1 119383033 4580184 257705..259090 1 NC_008686.1 PFAM: regulatory protein GntR, HTH; aminotransferase, class I and II; KEGG: ret:RHE_PF00188 transcriptional regulator protein, GntR family; GntR family transcriptional regulator 259090 4580184 Pden_0279 Paracoccus denitrificans PD1222 GntR family transcriptional regulator YP_914089.1 257705 D 318586 CDS YP_914090.1 119383034 4580185 259188..259973 1 NC_008686.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sme:SMb20427 amino acid ABC transporter ATP-binding protein; ABC transporter 259973 4580185 Pden_0280 Paracoccus denitrificans PD1222 ABC transporter YP_914090.1 259188 D 318586 CDS YP_914091.1 119383035 4580186 259973..260818 1 NC_008686.1 PFAM: extracellular solute-binding protein, family 3; KEGG: mlo:mlr7133 amino acid ABC transporter protein, solute-binding component; extracellular solute-binding protein 260818 4580186 Pden_0281 Paracoccus denitrificans PD1222 extracellular solute-binding protein YP_914091.1 259973 D 318586 CDS YP_914092.1 119383036 4580187 260877..261533 1 NC_008686.1 TIGRFAM: polar amino acid ABC transporter, inner membrane subunit; amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine; PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: sme:SMb20429 amino acid ABC transporter permease protein; amino acid ABC transporter permease 261533 4580187 Pden_0282 Paracoccus denitrificans PD1222 amino acid ABC transporter permease YP_914092.1 260877 D 318586 CDS YP_914093.1 119383037 4580188 261535..262194 1 NC_008686.1 TIGRFAM: polar amino acid ABC transporter, inner membrane subunit; amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine; PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: sme:SMb20430 amino acid ABC transporter permease protein; amino acid ABC transporter permease 262194 4580188 Pden_0283 Paracoccus denitrificans PD1222 amino acid ABC transporter permease YP_914093.1 261535 D 318586 CDS YP_914094.1 119383038 4580189 262191..262934 1 NC_008686.1 PFAM: Asp/Glu racemase; KEGG: sme:SMb20431 hypothetical arylmalonate decarboxylase protein; Asp/Glu racemase 262934 4580189 Pden_0284 Paracoccus denitrificans PD1222 Asp/Glu racemase YP_914094.1 262191 D 318586 CDS YP_914095.1 119383039 4580190 262931..263887 1 NC_008686.1 catalyzes the formation of 2-oxobutanoate from L-threonine; involved in ectoine utilization; threonine dehydratase 263887 eutB 4580190 eutB Paracoccus denitrificans PD1222 threonine dehydratase YP_914095.1 262931 D 318586 CDS YP_914096.1 119383040 4580191 263884..264861 1 NC_008686.1 cyclodeaminase; ectoine utilization protein EutC 264861 4580191 Pden_0286 Paracoccus denitrificans PD1222 ectoine utilization protein EutC YP_914096.1 263884 D 318586 CDS YP_914097.1 119383041 4580192 264873..266054 1 NC_008686.1 PFAM: peptidase M24; KEGG: sme:SMb20434 hydrolasepeptidase protein; peptidase M24 266054 4580192 Pden_0287 Paracoccus denitrificans PD1222 peptidase M24 YP_914097.1 264873 D 318586 CDS YP_914098.1 119383042 4580193 266068..267069 1 NC_008686.1 PFAM: Succinylglutamate desuccinylase/aspartoacylase; KEGG: sme:SMb20435 hypothetical protein; succinylglutamate desuccinylase/aspartoacylase 267069 4580193 Pden_0288 Paracoccus denitrificans PD1222 succinylglutamate desuccinylase/aspartoacylase YP_914098.1 266068 D 318586 CDS YP_914099.1 119383043 4580194 267066..268517 1 NC_008686.1 PFAM: aldehyde dehydrogenase; KEGG: sil:SPO1137 succinate-semialdehyde dehydrogenase; succinate-semialdehyde dehydrogenase (NAD(P)(+)) 268517 4580194 Pden_0289 Paracoccus denitrificans PD1222 succinate-semialdehyde dehydrogenase (NAD(P)(+)) YP_914099.1 267066 D 318586 CDS YP_914100.1 119383044 4580195 268517..269887 1 NC_008686.1 PFAM: aminotransferase class-III; KEGG: sit:TM1040_2691 aminotransferase class-III; hypothetical protein 269887 4580195 Pden_0290 Paracoccus denitrificans PD1222 hypothetical protein YP_914100.1 268517 D 318586 CDS YP_914101.1 119383045 4580196 269891..271033 1 NC_008686.1 PFAM: Alcohol dehydrogenase, zinc-binding domain protein; Alcohol dehydrogenase GroES domain protein; KEGG: csa:Csal_2340 alcohol dehydrogenase, zinc-binding; alcohol dehydrogenase 271033 4580196 Pden_0291 Paracoccus denitrificans PD1222 alcohol dehydrogenase YP_914101.1 269891 D 318586 CDS YP_914102.1 119383046 4580197 complement(271049..272245) 1 NC_008686.1 PFAM: protein of unknown function DUF1006; KEGG: jan:Jann_2912 protein of unknown function DUF1006; hypothetical protein 272245 4580197 Pden_0292 Paracoccus denitrificans PD1222 hypothetical protein YP_914102.1 271049 R 318586 CDS YP_914103.1 119383047 4580198 complement(272403..272990) 1 NC_008686.1 hypothetical protein 272990 4580198 Pden_0293 Paracoccus denitrificans PD1222 hypothetical protein YP_914103.1 272403 R 318586 CDS YP_914104.1 119383048 4580199 complement(273336..275105) 1 NC_008686.1 PFAM: Hemolysin-type calcium-binding region; KEGG: sil:SPO1617 type I secretion target repeat protein; hemolysin-type calcium-binding protein 275105 4580199 Pden_0294 Paracoccus denitrificans PD1222 hemolysin-type calcium-binding protein YP_914104.1 273336 R 318586 CDS YP_914105.1 119383049 4580200 275682..276158 1 NC_008686.1 KEGG: rsp:RSP_3055 transcriptional regulator, MarR family; MarR family transcriptional regulator 276158 4580200 Pden_0295 Paracoccus denitrificans PD1222 MarR family transcriptional regulator YP_914105.1 275682 D 318586 CDS YP_914106.1 119383050 4580201 complement(276190..278148) 1 NC_008686.1 PFAM: TonB-dependent receptor; TonB-dependent receptor, plug; KEGG: rsp:RSP_3056 TonB dependent-iron siderophore receptor; TonB-dependent receptor 278148 4580201 Pden_0296 Paracoccus denitrificans PD1222 TonB-dependent receptor YP_914106.1 276190 R 318586 CDS YP_914107.1 119383051 4580202 complement(278251..279009) 1 NC_008686.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: atc:AGR_C_4492 ferrichrome ABC transporter (ATP-binding protein); ABC transporter 279009 4580202 Pden_0297 Paracoccus denitrificans PD1222 ABC transporter YP_914107.1 278251 R 318586 CDS YP_914108.1 119383052 4579694 complement(279006..279965) 1 NC_008686.1 PFAM: transport system permease protein; KEGG: atc:AGR_C_4491 ferrichrome ABC transporter (permease) homolog; transport system permease 279965 4579694 Pden_0298 Paracoccus denitrificans PD1222 transport system permease YP_914108.1 279006 R 318586 CDS YP_914109.1 119383053 4579695 complement(279955..280911) 1 NC_008686.1 PFAM: transport system permease protein; KEGG: atc:AGR_C_4489 ferrichrome ABC transporter (permease); transport system permease 280911 4579695 Pden_0299 Paracoccus denitrificans PD1222 transport system permease YP_914109.1 279955 R 318586 CDS YP_914110.1 119383054 4579696 complement(280913..281818) 1 NC_008686.1 PFAM: periplasmic binding protein; KEGG: atc:AGR_C_4488 unknown conserved protein; periplasmic binding protein 281818 4579696 Pden_0300 Paracoccus denitrificans PD1222 periplasmic binding protein YP_914110.1 280913 R 318586 CDS YP_914111.1 119383055 4579697 282034..283434 1 NC_008686.1 PFAM: Cys/Met metabolism pyridoxal-phosphate-dependent enzymes; L-seryl-tRNA selenium transferase; KEGG: pen:PSEEN0568 selenocysteine synthase (with SelD); L-seryl-tRNA(Sec) selenium transferase 283434 4579697 Pden_0301 Paracoccus denitrificans PD1222 L-seryl-tRNA(Sec) selenium transferase YP_914111.1 282034 D 318586 CDS YP_914112.1 119383056 4579698 complement(283449..284342) 1 NC_008686.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: sme:SMa1782 LysR-family transcriptional regulator; LysR family transcriptional regulator 284342 4579698 Pden_0302 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_914112.1 283449 R 318586 CDS YP_914113.1 119383057 4579699 284436..284876 1 NC_008686.1 PFAM: transmembrane pair domain protein; KEGG: sme:SMa1780 hypothetical protein; transmembrane pair domain-containing protein 284876 4579699 Pden_0303 Paracoccus denitrificans PD1222 transmembrane pair domain-containing protein YP_914113.1 284436 D 318586 CDS YP_914114.1 119383058 4579700 complement(284873..285757) 1 NC_008686.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: mlo:mll4929 transcriptional regulator; LysR family transcriptional regulator 285757 4579700 Pden_0304 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_914114.1 284873 R 318586 CDS YP_914115.1 119383059 4579701 285838..286125 1 NC_008686.1 hypothetical protein 286125 4579701 Pden_0305 Paracoccus denitrificans PD1222 hypothetical protein YP_914115.1 285838 D 318586 CDS YP_914116.1 119383060 4579702 complement(286535..288052) 1 NC_008686.1 PFAM: protein of unknown function DUF112, transmembrane; KEGG: sme:SMb20726 conserved hypothetical membrane protein; hypothetical protein 288052 4579702 Pden_0306 Paracoccus denitrificans PD1222 hypothetical protein YP_914116.1 286535 R 318586 CDS YP_914117.1 119383061 4579703 complement(288056..288550) 1 NC_008686.1 KEGG: atc:AGR_C_4484 tricarboxylic transport membrane protein; tricarboxylic transport membrane protein 288550 4579703 Pden_0307 Paracoccus denitrificans PD1222 tricarboxylic transport membrane protein YP_914117.1 288056 R 318586 CDS YP_914118.1 119383062 4579704 complement(288547..289488) 1 NC_008686.1 PFAM: Uncharacterized protein UPF0065; KEGG: sme:SMb20724 tricarboxylic transport membrane protein; hypothetical protein 289488 4579704 Pden_0308 Paracoccus denitrificans PD1222 hypothetical protein YP_914118.1 288547 R 318586 CDS YP_914119.1 119383063 4579705 complement(289661..290758) 1 NC_008686.1 KEGG: atc:AGR_C_4480 periplasmic iron-binding protein; periplasmic iron-binding protein 290758 4579705 Pden_0309 Paracoccus denitrificans PD1222 periplasmic iron-binding protein YP_914119.1 289661 R 318586 CDS YP_914120.1 119383064 4579706 290820..291491 1 NC_008686.1 PFAM: response regulator receiver; transcriptional regulator domain protein; KEGG: sme:SMb20722 two-component response regulator protein; two component transcriptional regulator 291491 4579706 Pden_0310 Paracoccus denitrificans PD1222 two component transcriptional regulator YP_914120.1 290820 D 318586 CDS YP_914121.1 119383065 4579707 291488..292918 1 NC_008686.1 PFAM: ATP-binding region, ATPase domain protein domain protein; histidine kinase, HAMP region domain protein; histidine kinase A domain protein domain protein; Two-component sensor kinase N-terminal domain protein; KEGG: ret:RHE_CH03588 probable two-component sensor histidine kinase protein; integral membrane sensor signal transduction histidine kinase 292918 4579707 Pden_0311 Paracoccus denitrificans PD1222 integral membrane sensor signal transduction histidine kinase YP_914121.1 291488 D 318586 CDS YP_914122.1 119383066 4579708 293052..294146 1 NC_008686.1 PFAM: protein of unknown function DUF475; KEGG: rsp:RSP_0459 hypothetical protein; hypothetical protein 294146 4579708 Pden_0312 Paracoccus denitrificans PD1222 hypothetical protein YP_914122.1 293052 D 318586 CDS YP_914123.1 119383067 4579709 294237..295178 1 NC_008686.1 KEGG: sil:SPO0845 hypothetical protein; hypothetical protein 295178 4579709 Pden_0313 Paracoccus denitrificans PD1222 hypothetical protein YP_914123.1 294237 D 318586 CDS YP_914124.1 119383068 4579710 295262..295834 1 NC_008686.1 PFAM: AmiS/UreI transporter; KEGG: bpa:BPP1188 transporter protein; AmiS/UreI transporter 295834 4579710 Pden_0314 Paracoccus denitrificans PD1222 AmiS/UreI transporter YP_914124.1 295262 D 318586 CDS YP_914125.1 119383069 4579711 complement(295835..297919) 1 NC_008686.1 PFAM: oxidoreductase domain protein; dihydrodipicolinate reductase; NAD-dependent epimerase/dehydratase; 3-beta hydroxysteroid dehydrogenase/isomerase; homoserine dehydrogenase, NAD-binding; dTDP-4-dehydrorhamnose reductase; NmrA family protein; Male sterility C-terminal domain; KEGG: sil:SPO0852 oxidoreductase, Gfo/Idh/MocA family; oxidoreductase domain-containing protein 297919 4579711 Pden_0315 Paracoccus denitrificans PD1222 oxidoreductase domain-containing protein YP_914125.1 295835 R 318586 CDS YP_914126.1 119383070 4579712 complement(297929..298891) 1 NC_008686.1 PFAM: glycosyl transferase, family 2; KEGG: sil:SPO0853 glycosyl transferase, group 2 family protein; glycosyl transferase family protein 298891 4579712 Pden_0316 Paracoccus denitrificans PD1222 glycosyl transferase family protein YP_914126.1 297929 R 318586 CDS YP_914127.1 119383071 4579713 complement(298982..300166) 1 NC_008686.1 PFAM: CBS domain containing protein; HPP family protein+B94; KEGG: rsp:RSP_0830 CBS-domain-containing membrane protein; hypothetical protein 300166 4579713 Pden_0317 Paracoccus denitrificans PD1222 hypothetical protein YP_914127.1 298982 R 318586 CDS YP_914128.1 119383072 4578799 complement(300271..300927) 1 NC_008686.1 PFAM: regulatory protein GntR, HTH; GntR domain protein; KEGG: psb:Psyr_0495 regulatory protein, GntR:bacterial regulatory protein, GntR; GntR family transcriptional regulator 300927 4578799 Pden_0318 Paracoccus denitrificans PD1222 GntR family transcriptional regulator YP_914128.1 300271 R 318586 CDS YP_914129.1 119383073 4578800 301221..302456 1 NC_008686.1 KEGG: atc:AGR_L_1874 hypothetical protein; hypothetical protein 302456 4578800 Pden_0319 Paracoccus denitrificans PD1222 hypothetical protein YP_914129.1 301221 D 318586 CDS YP_914130.1 119383074 4578801 302525..303298 1 NC_008686.1 PFAM: LamB/YcsF family protein; KEGG: pst:PSPTO_5378 LamB/YcsF family protein; LamB/YcsF family protein 303298 4578801 Pden_0320 Paracoccus denitrificans PD1222 LamB/YcsF family protein YP_914130.1 302525 D 318586 CDS YP_914131.1 119383075 4578802 303295..304086 1 NC_008686.1 PFAM: protein of unknown function DUF1445; KEGG: atc:AGR_L_1868 hypothetical protein; hypothetical protein 304086 4578802 Pden_0321 Paracoccus denitrificans PD1222 hypothetical protein YP_914131.1 303295 D 318586 CDS YP_914132.1 119383076 4578803 304074..305642 1 NC_008686.1 PFAM: Allophanate hydrolase subunit 2; Allophanate hydrolase subunit 1; KEGG: atc:AGR_L_1866 hypothetical protein; allophanate hydrolase subunit 2 305642 4578803 Pden_0322 Paracoccus denitrificans PD1222 allophanate hydrolase subunit 2 YP_914132.1 304074 D 318586 CDS YP_914133.1 119383077 4578804 305639..307405 1 NC_008686.1 PFAM: biotin/lipoyl attachment domain-containing protein; phosphoribosylglycinamide synthetase; ATP-dependent carboxylate-amine ligase domain protein, ATP-grasp; Carbamoyl-phosphate synthase L chain, ATP-binding; Carbamoyl-phosphate synthetase large chain domain protein; biotin carboxylase domain protein; KEGG: atc:AGR_L_1864 biotin carboxylase protein A2; carbamoyl-phosphate synthase subunit L 307405 4578804 Pden_0323 Paracoccus denitrificans PD1222 carbamoyl-phosphate synthase subunit L YP_914133.1 305639 D 318586 CDS YP_914134.1 119383078 4578805 307485..308516 1 NC_008686.1 PFAM: ammonia monooxygenase; KEGG: jan:Jann_2088 ammonia monooxygenase; ammonia monooxygenase 308516 4578805 Pden_0324 Paracoccus denitrificans PD1222 ammonia monooxygenase YP_914134.1 307485 D 318586 CDS YP_914135.1 119383079 4578806 308566..309129 1 NC_008686.1 PFAM: protein of unknown function DUF886; KEGG: mlo:mlr8324 hypothetical protein; hypothetical protein 309129 4578806 Pden_0325 Paracoccus denitrificans PD1222 hypothetical protein YP_914135.1 308566 D 318586 CDS YP_914136.1 119383080 4578807 complement(309179..310213) 1 NC_008686.1 PFAM: luciferase family protein; KEGG: mlo:mll2315 alkanal monooxygenase (bacterial liciferase alpha chain) like protein; luciferase family protein 310213 4578807 Pden_0326 Paracoccus denitrificans PD1222 luciferase family protein YP_914136.1 309179 R 318586 CDS YP_914137.1 119383081 4578808 complement(310210..311184) 1 NC_008686.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: pau:PA14_48770 transcriptional regulator; LysR family transcriptional regulator 311184 4578808 Pden_0327 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_914137.1 310210 R 318586 CDS YP_914138.1 119383082 4578809 311304..312248 1 NC_008686.1 PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase; KEGG: sme:SMc01961 hypothetical protein; glyoxalase/bleomycin resistance protein/dioxygenase 312248 4578809 Pden_0328 Paracoccus denitrificans PD1222 glyoxalase/bleomycin resistance protein/dioxygenase YP_914138.1 311304 D 318586 CDS YP_914139.1 119383083 4578810 312401..312802 1 NC_008686.1 KEGG: bja:blr6753 hypothetical protein; hypothetical protein 312802 4578810 Pden_0329 Paracoccus denitrificans PD1222 hypothetical protein YP_914139.1 312401 D 318586 CDS YP_914140.1 119383084 4578811 complement(312834..313427) 1 NC_008686.1 PFAM: NADPH-dependent FMN reductase; KEGG: mlo:mll2599 probable reductase; NADPH-dependent FMN reductase 313427 4578811 Pden_0330 Paracoccus denitrificans PD1222 NADPH-dependent FMN reductase YP_914140.1 312834 R 318586 CDS YP_914141.1 119383085 4578812 complement(313684..315213) 1 NC_008686.1 PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase; KEGG: sme:SMc01956 hypothetical protein; glyoxalase/bleomycin resistance protein/dioxygenase 315213 4578812 Pden_0331 Paracoccus denitrificans PD1222 glyoxalase/bleomycin resistance protein/dioxygenase YP_914141.1 313684 R 318586 CDS YP_914142.1 119383086 4578813 complement(315226..315843) 1 NC_008686.1 PFAM: Glutathione S-transferase, N-terminal domain; Glutathione S-transferase, C-terminal domain; KEGG: bpa:BPP2935 glutathione S-transferase; glutathione S-transferase domain-containing protein 315843 4578813 Pden_0332 Paracoccus denitrificans PD1222 glutathione S-transferase domain-containing protein YP_914142.1 315226 R 318586 CDS YP_914143.1 119383087 4578814 complement(315957..316754) 1 NC_008686.1 catalyzes the formation of indole and glyceraldehyde 3-phosphate from indoleglycerol phosphate in tryptophan biosynthesis; tryptophan synthase subunit alpha 316754 trpA 4578814 trpA Paracoccus denitrificans PD1222 tryptophan synthase subunit alpha YP_914143.1 315957 R 318586 CDS YP_914144.1 119383088 4578815 316884..317981 1 NC_008686.1 translation-associated GTPase; the crystal structure of the Haemophilus influenzae YchF protein showed similarity to the yeast structure (PDB: 1NI3); fluorescence spectroscopy revealed nucleic acid binding; the yeast protein YBR025c interacts with the translation elongation factor eEF1; GTP-dependent nucleic acid-binding protein EngD 317981 4578815 Pden_0334 Paracoccus denitrificans PD1222 GTP-dependent nucleic acid-binding protein EngD YP_914144.1 316884 D 318586 CDS YP_914145.1 119383089 4578816 complement(318371..319441) 1 NC_008686.1 PFAM: phage integrase family protein; KEGG: gox:GOX2318 prophage integrase; phage integrase family protein 319441 4578816 Pden_0335 Paracoccus denitrificans PD1222 phage integrase family protein YP_914145.1 318371 R 318586 CDS YP_914146.1 119383090 4578817 complement(319640..319954) 1 NC_008686.1 hypothetical protein 319954 4578817 Pden_0336 Paracoccus denitrificans PD1222 hypothetical protein YP_914146.1 319640 R 318586 CDS YP_914147.1 119383091 4579035 complement(319992..320720) 1 NC_008686.1 KEGG: rsp:RSP_3624 hypothetical protein; hypothetical protein 320720 4579035 Pden_0337 Paracoccus denitrificans PD1222 hypothetical protein YP_914147.1 319992 R 318586 CDS YP_914148.1 119383092 4579036 complement(320717..321160) 1 NC_008686.1 hypothetical protein 321160 4579036 Pden_0338 Paracoccus denitrificans PD1222 hypothetical protein YP_914148.1 320717 R 318586 CDS YP_914149.1 119383093 4579037 complement(321356..322261) 1 NC_008686.1 KEGG: pst:PSPTO_3428 hypothetical protein; hypothetical protein 322261 4579037 Pden_0339 Paracoccus denitrificans PD1222 hypothetical protein YP_914149.1 321356 R 318586 CDS YP_914150.1 119383094 4579038 complement(322258..322677) 1 NC_008686.1 hypothetical protein 322677 4579038 Pden_0340 Paracoccus denitrificans PD1222 hypothetical protein YP_914150.1 322258 R 318586 CDS YP_914151.1 119383095 4579039 complement(322674..325319) 1 NC_008686.1 PFAM: DNA methylase N-4/N-6 domain protein; KEGG: mes:Meso_1199 helicase-like; DNA methylase N-4/N-6 domain-containing protein 325319 4579039 Pden_0341 Paracoccus denitrificans PD1222 DNA methylase N-4/N-6 domain-containing protein YP_914151.1 322674 R 318586 CDS YP_914152.1 119383096 4579040 complement(325323..326441) 1 NC_008686.1 KEGG: jan:Jann_0002 DNA polymerase III, beta subunit; TIGRFAM: DNA polymerase III, beta subunit; PFAM: DNA polymerase III, beta chain; DNA polymerase III subunit beta 326441 4579040 Pden_0342 Paracoccus denitrificans PD1222 DNA polymerase III subunit beta YP_914152.1 325323 R 318586 CDS YP_914153.1 119383097 4579041 complement(326577..326789) 1 NC_008686.1 hypothetical protein 326789 4579041 Pden_0343 Paracoccus denitrificans PD1222 hypothetical protein YP_914153.1 326577 R 318586 CDS YP_914154.1 119383098 4579042 327011..327613 1 NC_008686.1 hypothetical protein 327613 4579042 Pden_0344 Paracoccus denitrificans PD1222 hypothetical protein YP_914154.1 327011 D 318586 CDS YP_914155.1 119383099 4579043 328067..328573 1 NC_008686.1 hypothetical protein 328573 4579043 Pden_0345 Paracoccus denitrificans PD1222 hypothetical protein YP_914155.1 328067 D 318586 CDS YP_914156.1 119383100 4579044 328573..329100 1 NC_008686.1 hypothetical protein 329100 4579044 Pden_0346 Paracoccus denitrificans PD1222 hypothetical protein YP_914156.1 328573 D 318586 CDS YP_914157.1 119383101 4579045 complement(329084..329443) 1 NC_008686.1 hypothetical protein 329443 4579045 Pden_0347 Paracoccus denitrificans PD1222 hypothetical protein YP_914157.1 329084 R 318586 CDS YP_914158.1 119383102 4579046 329665..329997 1 NC_008686.1 hypothetical protein 329997 4579046 Pden_0348 Paracoccus denitrificans PD1222 hypothetical protein YP_914158.1 329665 D 318586 CDS YP_914159.1 119383103 4579047 329990..330304 1 NC_008686.1 hypothetical protein 330304 4579047 Pden_0349 Paracoccus denitrificans PD1222 hypothetical protein YP_914159.1 329990 D 318586 CDS YP_914160.1 119383104 4579048 330301..330513 1 NC_008686.1 hypothetical protein 330513 4579048 Pden_0350 Paracoccus denitrificans PD1222 hypothetical protein YP_914160.1 330301 D 318586 CDS YP_914161.1 119383105 4579049 complement(330675..331004) 1 NC_008686.1 hypothetical protein 331004 4579049 Pden_0351 Paracoccus denitrificans PD1222 hypothetical protein YP_914161.1 330675 R 318586 CDS YP_914162.1 119383106 4579050 331125..332267 1 NC_008686.1 KEGG: sit:TM1040_1631 hypothetical protein; hypothetical protein 332267 4579050 Pden_0352 Paracoccus denitrificans PD1222 hypothetical protein YP_914162.1 331125 D 318586 CDS YP_914163.1 119383107 4579051 332260..334101 1 NC_008686.1 TIGRFAM: phage/plasmid primase, P4 family; PFAM: Poxvirus D5 protein; KEGG: bld:BLi03629 hypothetical protein; P4 family phage/plasmid primase 334101 4579051 Pden_0353 Paracoccus denitrificans PD1222 P4 family phage/plasmid primase YP_914163.1 332260 D 318586 CDS YP_914164.1 119383108 4579052 complement(334153..334449) 1 NC_008686.1 hypothetical protein 334449 4579052 Pden_0354 Paracoccus denitrificans PD1222 hypothetical protein YP_914164.1 334153 R 318586 CDS YP_914165.1 119383109 4579053 334560..335318 1 NC_008686.1 KEGG: rsp:RSP_3778 hypothetical protein; hypothetical protein 335318 4579053 Pden_0355 Paracoccus denitrificans PD1222 hypothetical protein YP_914165.1 334560 D 318586 CDS YP_914166.1 119383110 4579054 335488..335838 1 NC_008686.1 PFAM: HNH endonuclease; SMART: HNH nuclease; KEGG: rsp:RSP_2072 phage-related holin protein; HNH endonuclease 335838 4579054 Pden_0356 Paracoccus denitrificans PD1222 HNH endonuclease YP_914166.1 335488 D 318586 CDS YP_914167.1 119383111 4580514 335888..336148 1 NC_008686.1 hypothetical protein 336148 4580514 Pden_0357 Paracoccus denitrificans PD1222 hypothetical protein YP_914167.1 335888 D 318586 CDS YP_914168.1 119383112 4580515 336322..336825 1 NC_008686.1 PFAM: Resolvase helix-turn-helix domain protein; KEGG: sit:TM1040_1626 hypothetical protein; resolvase domain-containing protein 336825 4580515 Pden_0358 Paracoccus denitrificans PD1222 resolvase domain-containing protein YP_914168.1 336322 D 318586 CDS YP_914169.1 119383113 4580516 336815..338536 1 NC_008686.1 PFAM: phage Terminase; KEGG: rsp:RSP_2070 phage-related terminase; phage terminase 338536 4580516 Pden_0359 Paracoccus denitrificans PD1222 phage terminase YP_914169.1 336815 D 318586 CDS YP_914170.1 119383114 4580517 338536..339873 1 NC_008686.1 TIGRFAM: phage portal protein, HK97 family; PFAM: phage portal protein; KEGG: rsp:RSP_2069 phage portal protein, HK97 family; HK97 family phage portal protein 339873 4580517 Pden_0360 Paracoccus denitrificans PD1222 HK97 family phage portal protein YP_914170.1 338536 D 318586 CDS YP_914171.1 119383115 4580518 339860..340702 1 NC_008686.1 PFAM: peptidase S14, ClpP; KEGG: rsp:RSP_2068 ClpP-like protease; peptidase S14, ClpP 340702 4580518 Pden_0361 Paracoccus denitrificans PD1222 peptidase S14, ClpP YP_914171.1 339860 D 318586 CDS YP_914172.1 119383116 4580519 340714..342063 1 NC_008686.1 TIGRFAM: phage major capsid protein, HK97 family; KEGG: rsp:RSP_2067 prophage LambdaSo, major capsid protein, HK97 family; HK97 family phage major capsid protein 342063 4580519 Pden_0362 Paracoccus denitrificans PD1222 HK97 family phage major capsid protein YP_914172.1 340714 D 318586 CDS YP_914173.1 119383117 4580520 342121..342429 1 NC_008686.1 hypothetical protein 342429 4580520 Pden_0363 Paracoccus denitrificans PD1222 hypothetical protein YP_914173.1 342121 D 318586 CDS YP_914174.1 119383118 4580521 342471..342965 1 NC_008686.1 hypothetical protein 342965 4580521 Pden_0364 Paracoccus denitrificans PD1222 hypothetical protein YP_914174.1 342471 D 318586 CDS YP_914175.1 119383119 4580522 342934..343482 1 NC_008686.1 KEGG: sit:TM1040_1619 phage conserved hypothetical protein, phiE125 gp8; hypothetical protein 343482 4580522 Pden_0365 Paracoccus denitrificans PD1222 hypothetical protein YP_914175.1 342934 D 318586 CDS YP_914176.1 119383120 4580523 343476..343835 1 NC_008686.1 TIGRFAM: phage head-tail adaptor; phage head-tail adaptor 343835 4580523 Pden_0366 Paracoccus denitrificans PD1222 phage head-tail adaptor YP_914176.1 343476 D 318586 CDS YP_914177.1 119383121 4580524 343922..344218 1 NC_008686.1 hypothetical protein 344218 4580524 Pden_0367 Paracoccus denitrificans PD1222 hypothetical protein YP_914177.1 343922 D 318586 CDS YP_914178.1 119383122 4580525 complement(344215..344742) 1 NC_008686.1 hypothetical protein 344742 4580525 Pden_0368 Paracoccus denitrificans PD1222 hypothetical protein YP_914178.1 344215 R 318586 CDS YP_914179.1 119383123 4580526 344752..345042 1 NC_008686.1 hypothetical protein 345042 4580526 Pden_0369 Paracoccus denitrificans PD1222 hypothetical protein YP_914179.1 344752 D 318586 CDS YP_914180.1 119383124 4580527 345234..345695 1 NC_008686.1 hypothetical protein 345695 4580527 Pden_0370 Paracoccus denitrificans PD1222 hypothetical protein YP_914180.1 345234 D 318586 CDS YP_914181.1 119383125 4580528 345695..346084 1 NC_008686.1 hypothetical protein 346084 4580528 Pden_0371 Paracoccus denitrificans PD1222 hypothetical protein YP_914181.1 345695 D 318586 CDS YP_914182.1 119383126 4580529 346245..349151 1 NC_008686.1 KEGG: rsp:RSP_3791 hypothetical protein; hypothetical protein 349151 4580529 Pden_0372 Paracoccus denitrificans PD1222 hypothetical protein YP_914182.1 346245 D 318586 CDS YP_914183.1 119383127 4580530 349151..349831 1 NC_008686.1 hypothetical protein 349831 4580530 Pden_0373 Paracoccus denitrificans PD1222 hypothetical protein YP_914183.1 349151 D 318586 CDS YP_914184.1 119383128 4580531 349828..350394 1 NC_008686.1 hypothetical protein 350394 4580531 Pden_0374 Paracoccus denitrificans PD1222 hypothetical protein YP_914184.1 349828 D 318586 CDS YP_914185.1 119383129 4580532 350379..350750 1 NC_008686.1 KEGG: mes:Meso_1234 hypothetical protein; hypothetical protein 350750 4580532 Pden_0375 Paracoccus denitrificans PD1222 hypothetical protein YP_914185.1 350379 D 318586 CDS YP_914186.1 119383130 4579558 350750..352792 1 NC_008686.1 KEGG: nar:Saro_2739 hypothetical protein; hypothetical protein 352792 4579558 Pden_0376 Paracoccus denitrificans PD1222 hypothetical protein YP_914186.1 350750 D 318586 CDS YP_914187.1 119383131 4579559 352856..354613 1 NC_008686.1 hypothetical protein 354613 4579559 Pden_0377 Paracoccus denitrificans PD1222 hypothetical protein YP_914187.1 352856 D 318586 CDS YP_914188.1 119383132 4579560 354623..355363 1 NC_008686.1 hypothetical protein 355363 4579560 Pden_0378 Paracoccus denitrificans PD1222 hypothetical protein YP_914188.1 354623 D 318586 CDS YP_914189.1 119383133 4579561 355399..355695 1 NC_008686.1 hypothetical protein 355695 4579561 Pden_0379 Paracoccus denitrificans PD1222 hypothetical protein YP_914189.1 355399 D 318586 CDS YP_914190.1 119383134 4579562 complement(355711..355959) 1 NC_008686.1 hypothetical protein 355959 4579562 Pden_0380 Paracoccus denitrificans PD1222 hypothetical protein YP_914190.1 355711 R 318586 CDS YP_914191.1 119383135 4579563 356004..356636 1 NC_008686.1 KEGG: syw:SYNW0477 hypothetical protein; hypothetical protein 356636 4579563 Pden_0381 Paracoccus denitrificans PD1222 hypothetical protein YP_914191.1 356004 D 318586 CDS YP_914192.1 119383136 4579564 356648..357043 1 NC_008686.1 KEGG: rsp:RSP_6192 hypothetical protein; hypothetical protein 357043 4579564 Pden_0382 Paracoccus denitrificans PD1222 hypothetical protein YP_914192.1 356648 D 318586 CDS YP_914193.1 119383137 4579565 complement(357161..357364) 1 NC_008686.1 hypothetical protein 357364 4579565 Pden_0383 Paracoccus denitrificans PD1222 hypothetical protein YP_914193.1 357161 R 318586 CDS YP_914194.1 119383138 4579566 complement(357761..357928) 1 NC_008686.1 hypothetical protein 357928 4579566 Pden_0384 Paracoccus denitrificans PD1222 hypothetical protein YP_914194.1 357761 R 318586 CDS YP_914195.1 119383139 4579567 complement(358047..359285) 1 NC_008686.1 PFAM: Resolvase, N-terminal domain; Recombinase; KEGG: nwi:Nwi_1951 resolvase; recombinase 359285 4579567 Pden_0385 Paracoccus denitrificans PD1222 recombinase YP_914195.1 358047 R 318586 CDS YP_914196.1 119383140 4579568 359492..360115 1 NC_008686.1 PFAM: protein of unknown function DUF159; KEGG: sit:TM1040_1580 protein of unknown function DUF159; hypothetical protein 360115 4579568 Pden_0386 Paracoccus denitrificans PD1222 hypothetical protein YP_914196.1 359492 D 318586 CDS YP_914197.1 119383141 4579569 360185..360424 1 NC_008686.1 hypothetical protein 360424 4579569 Pden_0387 Paracoccus denitrificans PD1222 hypothetical protein YP_914197.1 360185 D 318586 CDS YP_914198.1 119383142 4579570 360445..360705 1 NC_008686.1 hypothetical protein 360705 4579570 Pden_0388 Paracoccus denitrificans PD1222 hypothetical protein YP_914198.1 360445 D 318586 CDS YP_914199.1 119383143 4579571 361152..361484 1 NC_008686.1 hypothetical protein 361484 4579571 Pden_0389 Paracoccus denitrificans PD1222 hypothetical protein YP_914199.1 361152 D 318586 CDS YP_914200.1 119383144 4579572 361651..362016 1 NC_008686.1 PFAM: protein of unknown function DUF983; KEGG: ccr:CC1021 hypothetical protein; hypothetical protein 362016 4579572 Pden_0390 Paracoccus denitrificans PD1222 hypothetical protein YP_914200.1 361651 D 318586 CDS YP_914201.1 119383145 4579573 complement(362346..362717) 1 NC_008686.1 hypothetical protein 362717 4579573 Pden_0391 Paracoccus denitrificans PD1222 hypothetical protein YP_914201.1 362346 R 318586 CDS YP_914202.1 119383146 4579574 362922..363236 1 NC_008686.1 KEGG: jan:Jann_0243 hypothetical protein; hypothetical protein 363236 4579574 Pden_0392 Paracoccus denitrificans PD1222 hypothetical protein YP_914202.1 362922 D 318586 CDS YP_914203.1 119383147 4579575 363233..363715 1 NC_008686.1 KEGG: bms:BR0799 hypothetical protein; hypothetical protein 363715 4579575 Pden_0393 Paracoccus denitrificans PD1222 hypothetical protein YP_914203.1 363233 D 318586 CDS YP_914204.1 119383148 4579576 364225..364824 1 NC_008686.1 KEGG: rde:RD1_A0063 succinoglycan biosynthesis protein ExoI; hypothetical protein 364824 4579576 Pden_0394 Paracoccus denitrificans PD1222 hypothetical protein YP_914204.1 364225 D 318586 CDS YP_914205.1 119383149 4579577 365115..365942 1 NC_008686.1 PFAM: diaminopimelate epimerase; KEGG: sil:SPO0278 diaminopimelate epimerase; diaminopimelate epimerase 365942 4579577 Pden_0395 Paracoccus denitrificans PD1222 diaminopimelate epimerase YP_914205.1 365115 D 318586 CDS YP_914206.1 119383150 4578683 365939..367201 1 NC_008686.1 KEGG: rsp:RSP_0935 MiaB-like radical SAM protein; TIGRFAM: RNA modification enzyme, MiaB family; MiaB-like tRNA modifying enzyme; PFAM: Radical SAM domain protein; Protein of unknown function UPF0004-like; SMART: Elongator protein 3/MiaB/NifB; MiaB-like tRNA modifying enzyme 367201 4578683 Pden_0396 Paracoccus denitrificans PD1222 MiaB-like tRNA modifying enzyme YP_914206.1 365939 D 318586 CDS YP_914207.1 119383151 4578684 367359..368318 1 NC_008686.1 PFAM: histone deacetylase superfamily; KEGG: rsp:RSP_1137 histone deacetylase family protein; histone deacetylase superfamily protein 368318 4578684 Pden_0397 Paracoccus denitrificans PD1222 histone deacetylase superfamily protein YP_914207.1 367359 D 318586 CDS YP_914208.1 119383152 4578685 368315..368557 1 NC_008686.1 TIGRFAM: exodeoxyribonuclease VII, small subunit; PFAM: Exonuclease VII, small subunit; KEGG: jan:Jann_0090 exodeoxyribonuclease VII, small subunit; exodeoxyribonuclease VII small subunit 368557 4578685 Pden_0398 Paracoccus denitrificans PD1222 exodeoxyribonuclease VII small subunit YP_914208.1 368315 D 318586 CDS YP_914209.1 119383153 4578686 368557..369420 1 NC_008686.1 PFAM: Polyprenyl synthetase; KEGG: rsp:RSP_1135 geranylgeranyl pyrophosphate synthetase; polyprenyl synthetase 369420 4578686 Pden_0399 Paracoccus denitrificans PD1222 polyprenyl synthetase YP_914209.1 368557 D 318586 CDS YP_914210.1 119383154 4578687 369446..371368 1 NC_008686.1 catalyzes the formation of 1-deoxy-D-xylulose 5-phosphate from pyruvate and D-glyceraldehyde 3-phosphate; 1-deoxy-D-xylulose-5-phosphate synthase 371368 4578687 Pden_0400 Paracoccus denitrificans PD1222 1-deoxy-D-xylulose-5-phosphate synthase YP_914210.1 369446 D 318586 CDS YP_914211.1 119383155 4578688 371378..371998 1 NC_008686.1 PFAM: SH3, type 3 domain protein; KEGG: sil:SPO0041 hypothetical protein; SH3 type 3 domain-containing protein 371998 4578688 Pden_0401 Paracoccus denitrificans PD1222 SH3 type 3 domain-containing protein YP_914211.1 371378 D 318586 CDS YP_914212.1 119383156 4578689 complement(371995..372858) 1 NC_008686.1 PFAM: NAD-dependent epimerase/dehydratase; dTDP-4-dehydrorhamnose reductase; KEGG: jan:Jann_0273 NAD-dependent epimerase/dehydratase; NAD-dependent epimerase/dehydratase 372858 4578689 Pden_0402 Paracoccus denitrificans PD1222 NAD-dependent epimerase/dehydratase YP_914212.1 371995 R 318586 CDS YP_914213.1 119383157 4578690 complement(372855..373841) 1 NC_008686.1 PFAM: luciferase family protein; KEGG: sil:SPO2518 bacterial luciferase family protein; luciferase family protein 373841 4578690 Pden_0403 Paracoccus denitrificans PD1222 luciferase family protein YP_914213.1 372855 R 318586 CDS YP_914214.1 119383158 4578691 373937..375421 1 NC_008686.1 Catalyzes the hydrolysis of AMP to form adenine and ribose 5-phosphate using water as the nucleophile; AMP nucleosidase 375421 4578691 Pden_0404 Paracoccus denitrificans PD1222 AMP nucleosidase YP_914214.1 373937 D 318586 CDS YP_914215.1 119383159 4578692 375573..375872 1 NC_008686.1 PFAM: histone family protein DNA-binding protein; KEGG: rsp:RSP_1388 DNA-binding protein HU, form N; histone family protein DNA-binding protein 375872 4578692 Pden_0405 Paracoccus denitrificans PD1222 histone family protein DNA-binding protein YP_914215.1 375573 D 318586 CDS YP_914216.1 119383160 4578693 376017..376937 1 NC_008686.1 PFAM: protein of unknown function DUF6, transmembrane; KEGG: rsp:RSP_1390 transporter, DMT superfamily; hypothetical protein 376937 4578693 Pden_0406 Paracoccus denitrificans PD1222 hypothetical protein YP_914216.1 376017 D 318586 CDS YP_914217.1 119383161 4578694 complement(376892..377485) 1 NC_008686.1 KEGG: hne:HNE_1223 glutathione S-transferase; glutathione S-transferase 377485 4578694 Pden_0407 Paracoccus denitrificans PD1222 glutathione S-transferase YP_914217.1 376892 R 318586 CDS YP_914218.1 119383162 4578695 377546..378247 1 NC_008686.1 PFAM: Helix-turn-helix, type 11 domain protein; KEGG: hne:HNE_1222 hypothetical protein; helix-turn-helix, type 11 domain-containing protein 378247 4578695 Pden_0408 Paracoccus denitrificans PD1222 helix-turn-helix, type 11 domain-containing protein YP_914218.1 377546 D 318586 CDS YP_914219.1 119383163 4578696 complement(378225..379646) 1 NC_008686.1 PFAM: aminotransferase, class V; KEGG: ret:RHE_PE00221 hypothetical protein; class V aminotransferase 379646 4578696 Pden_0409 Paracoccus denitrificans PD1222 class V aminotransferase YP_914219.1 378225 R 318586 CDS YP_914220.1 119383164 4578697 379720..380193 1 NC_008686.1 PFAM: regulatory protein, AsnC/Lrp family; KEGG: ret:RHE_PE00222 probable transcriptional regulator protein, AsnC family; AsnC family transcriptional regulator 380193 4578697 Pden_0410 Paracoccus denitrificans PD1222 AsnC family transcriptional regulator YP_914220.1 379720 D 318586 CDS YP_914221.1 119383165 4578698 380224..381213 1 NC_008686.1 KEGG: ret:RHE_CH01163 exonuclease protein involved in mRNA processing; exonuclease protein involved in mRNA processing 381213 4578698 Pden_0411 Paracoccus denitrificans PD1222 exonuclease protein involved in mRNA processing YP_914221.1 380224 D 318586 CDS YP_914222.1 119383166 4578699 381210..382754 1 NC_008686.1 PFAM: ATP dependent DNA ligase domain protein; ATP dependent DNA ligase; KEGG: ccr:CC3610 DNA ligase, ATP-dependent; ATP dependent DNA ligase 382754 4578699 Pden_0412 Paracoccus denitrificans PD1222 ATP dependent DNA ligase YP_914222.1 381210 D 318586 CDS YP_914223.1 119383167 4578700 382751..385186 1 NC_008686.1 PFAM: helicase domain protein; DEAD/DEAH box helicase domain protein; DEAD/H associated domain protein; SMART: DEAD-like helicases-like; KEGG: rsp:RSP_0658 probable ATP-dependent helicase; DEAD/DEAH box helicase 385186 4578700 Pden_0413 Paracoccus denitrificans PD1222 DEAD/DEAH box helicase YP_914223.1 382751 D 318586 CDS YP_914224.1 119383168 4578701 385183..385839 1 NC_008686.1 KEGG: rsp:RSP_0659 metallo-phosphoesterase; metallo-phosphoesterase 385839 4578701 Pden_0414 Paracoccus denitrificans PD1222 metallo-phosphoesterase YP_914224.1 385183 D 318586 CDS YP_914225.1 119383169 4579461 complement(385901..386668) 1 NC_008686.1 KEGG: mlo:mll1390 outer membrane protein; outer membrane protein 386668 4579461 Pden_0415 Paracoccus denitrificans PD1222 outer membrane protein YP_914225.1 385901 R 318586 CDS YP_914226.1 119383170 4579462 complement(386880..389318) 1 NC_008686.1 negatively supercoils closed circular double-stranded DNA; DNA gyrase subunit B 389318 gyrB 4579462 gyrB Paracoccus denitrificans PD1222 DNA gyrase subunit B YP_914226.1 386880 R 318586 CDS YP_914227.1 119383171 4579463 complement(389505..389840) 1 NC_008686.1 PFAM: protein of unknown function DUF1491; KEGG: rsp:RSP_1677 hypothetical protein; hypothetical protein 389840 4579463 Pden_0417 Paracoccus denitrificans PD1222 hypothetical protein YP_914227.1 389505 R 318586 CDS YP_914228.1 119383172 4579464 complement(389833..390744) 1 NC_008686.1 Era; Escherichia coli Ras-like protein; Bex; Bacillus Era-complementing segment; essential protein in Escherichia coli that is involved in many cellular processes; GTPase; binds the cell membrane through apparent C-terminal domain; mutants are arrested during the cell cycle; Streptococcus pneumoniae Era binds to RNA and Escherichia coli Era binds 16S rRNA and 30S ribosome; GTP-binding protein Era 390744 era 4579464 era Paracoccus denitrificans PD1222 GTP-binding protein Era YP_914228.1 389833 R 318586 CDS YP_914229.1 119383173 4579465 complement(390741..391466) 1 NC_008686.1 PFAM: ribonuclease III; double-stranded RNA binding domain protein; KEGG: rsp:RSP_1675 ribonuclease III; ribonuclease III 391466 4579465 Pden_0419 Paracoccus denitrificans PD1222 ribonuclease III YP_914229.1 390741 R 318586 CDS YP_914230.1 119383174 4579466 complement(391475..392266) 1 NC_008686.1 KEGG: rsp:RSP_1674 type 1 signal peptidase; TIGRFAM: signal peptidase I; PFAM: peptidase S24, S26A and S26B; signal peptidase I 392266 4579466 Pden_0420 Paracoccus denitrificans PD1222 signal peptidase I YP_914230.1 391475 R 318586 CDS YP_914231.1 119383175 4579467 complement(392326..392745) 1 NC_008686.1 Catalyzes the formation of holo-ACP, which mediates the essential transfer of acyl fatty acid intermediates during the biosynthesis of fatty acids and lipids; 4'-phosphopantetheinyl transferase 392745 acpS 4579467 acpS Paracoccus denitrificans PD1222 4'-phosphopantetheinyl transferase YP_914231.1 392326 R 318586 CDS YP_914232.1 119383176 4579468 complement(392794..393528) 1 NC_008686.1 involved in the de novo synthesis of pyridoxine (Vitamin B6); pyridoxine 5'-phosphate synthase 393528 4579468 Pden_0422 Paracoccus denitrificans PD1222 pyridoxine 5'-phosphate synthase YP_914232.1 392794 R 318586 CDS YP_914233.1 119383177 4579469 complement(393559..394380) 1 NC_008686.1 KEGG: rsp:RSP_1779 4-diphosphocytidyl-2C-methyl-D-erythritol kinase; TIGRFAM: 4-diphosphocytidyl-2C-methyl-D-erythritol kinase; PFAM: GHMP kinase; GHMP kinase, C terminal domain protein; 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase 394380 4579469 Pden_0423 Paracoccus denitrificans PD1222 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase YP_914233.1 393559 R 318586 CDS YP_914234.1 119383178 4579470 complement(394384..396312) 1 NC_008686.1 PFAM: TPR repeat-containing protein; Tetratricopeptide TPR_2 repeat protein; SMART: Tetratricopeptide domain protein; KEGG: rde:RD1_3403 TPR domain protein; hypothetical protein 396312 4579470 Pden_0424 Paracoccus denitrificans PD1222 hypothetical protein YP_914234.1 394384 R 318586 CDS YP_914235.1 119383179 4579471 complement(396309..397955) 1 NC_008686.1 PFAM: fumarate reductase/succinate dehydrogenase flavoprotein domain protein; FAD dependent oxidoreductase; electron transfer flavoprotein-ubiquinone oxidoreductase; KEGG: sil:SPO0316 electrotransfer ubiquinone oxidoreductase family protein; electron-transferring-flavoprotein dehydrogenase 397955 4579471 Pden_0425 Paracoccus denitrificans PD1222 electron-transferring-flavoprotein dehydrogenase YP_914235.1 396309 R 318586 CDS YP_914236.1 119383180 4579472 398232..398702 1 NC_008686.1 necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites; arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by cleavage factors such as GreA or GreB allows the resumption of elongation from the new 3'terminus; transcription elongation factor GreA 398702 greA 4579472 greA Paracoccus denitrificans PD1222 transcription elongation factor GreA YP_914236.1 398232 D 318586 CDS YP_914237.1 119383181 4579473 398720..399667 1 NC_008686.1 KEGG: sil:SPO0311 hypothetical protein; hypothetical protein 399667 4579473 Pden_0427 Paracoccus denitrificans PD1222 hypothetical protein YP_914237.1 398720 D 318586 CDS YP_914238.1 119383182 4579474 complement(399664..400251) 1 NC_008686.1 PFAM: GCN5-related N-acetyltransferase; KEGG: rsp:RSP_0736 MobC protein; N-acetyltransferase 400251 4579474 Pden_0428 Paracoccus denitrificans PD1222 N-acetyltransferase YP_914238.1 399664 R 318586 CDS YP_914239.1 119383183 4579475 400357..401133 1 NC_008686.1 PFAM: AzlC family protein; KEGG: rsp:RSP_0739 branched chain amino acid efflux pump, large (AzlC) subunit; AzlC family protein 401133 4579475 Pden_0429 Paracoccus denitrificans PD1222 AzlC family protein YP_914239.1 400357 D 318586 CDS YP_914240.1 119383184 4579476 401130..401462 1 NC_008686.1 PFAM: branched-chain amino acid transport; KEGG: rde:RD1_3412 hypothetical protein; branched-chain amino acid transport 401462 4579476 Pden_0430 Paracoccus denitrificans PD1222 branched-chain amino acid transport YP_914240.1 401130 D 318586 CDS YP_914241.1 119383185 4579477 complement(401447..402094) 1 NC_008686.1 KEGG: rsp:RSP_6127 hypothetical protein; hypothetical protein 402094 4579477 Pden_0431 Paracoccus denitrificans PD1222 hypothetical protein YP_914241.1 401447 R 318586 CDS YP_914242.1 119383186 4579478 complement(402118..402318) 1 NC_008686.1 PFAM: aa3 type cytochrome c oxidase subunit IV; KEGG: rsp:RSP_6128 Aa3-type cytochrome c oxidase subunit IV; aa3 type cytochrome c oxidase subunit IV 402318 4579478 Pden_0432 Paracoccus denitrificans PD1222 aa3 type cytochrome c oxidase subunit IV YP_914242.1 402118 R 318586 CDS YP_914243.1 119383187 4579479 complement(402332..403354) 1 NC_008686.1 PFAM: beta-lactamase domain protein; KEGG: rsp:RSP_0741 metallo-beta-lactamase family protein; beta-lactamase domain-containing protein 403354 4579479 Pden_0433 Paracoccus denitrificans PD1222 beta-lactamase domain-containing protein YP_914243.1 402332 R 318586 CDS YP_914244.1 119383188 4579480 complement(403351..405042) 1 NC_008686.1 PFAM: acyl-CoA dehydrogenase domain protein; Acyl-CoA dehydrogenase, type 2, C-terminal domain; KEGG: rsp:RSP_0742 probable acyl-CoA dehydrogenase; acyl-CoA dehydrogenase 405042 4579480 Pden_0434 Paracoccus denitrificans PD1222 acyl-CoA dehydrogenase YP_914244.1 403351 R 318586 CDS YP_914245.1 119383189 4578838 405159..406109 1 NC_008686.1 TIGRFAM: Sua5/YciO/YrdC/YwlC family protein; PFAM: SUA5 domain protein; SUA5/yciO/yrdC, N-terminal domain; KEGG: rsp:RSP_0743 translation factor; Sua5/YciO/YrdC/YwlC family protein 406109 4578838 Pden_0435 Paracoccus denitrificans PD1222 Sua5/YciO/YrdC/YwlC family protein YP_914245.1 405159 D 318586 CDS YP_914246.1 119383190 4578839 complement(406113..406685) 1 NC_008686.1 PFAM: protein of unknown function DUF179; KEGG: sil:SPO0296 transcriptional regulator; hypothetical protein 406685 4578839 Pden_0436 Paracoccus denitrificans PD1222 hypothetical protein YP_914246.1 406113 R 318586 CDS YP_914247.1 119383191 4578840 406794..407576 1 NC_008686.1 KEGG: rde:RD1_3420 hypothetical protein; hypothetical protein 407576 4578840 Pden_0437 Paracoccus denitrificans PD1222 hypothetical protein YP_914247.1 406794 D 318586 CDS YP_914248.1 119383192 4578841 complement(407573..408388) 1 NC_008686.1 TIGRFAM: phage SPO1 DNA polymerase-related protein; PFAM: Uracil-DNA glycosylase superfamily; KEGG: rsp:RSP_1001 DNA polymerase bacteriophage-type; phage SPO1 DNA polymerase-related protein 408388 4578841 Pden_0438 Paracoccus denitrificans PD1222 phage SPO1 DNA polymerase-related protein YP_914248.1 407573 R 318586 CDS YP_914249.1 119383193 4578842 complement(408494..408895) 1 NC_008686.1 hypothetical protein 408895 4578842 Pden_0439 Paracoccus denitrificans PD1222 hypothetical protein YP_914249.1 408494 R 318586 CDS YP_914250.1 119383194 4578843 409050..410171 1 NC_008686.1 catalyzes the oxidation of 3-isopropylmalate to 3-carboxy-4-methyl-2-oxopentanoate in leucine biosynthesis; 3-isopropylmalate dehydrogenase 410171 4578843 Pden_0440 Paracoccus denitrificans PD1222 3-isopropylmalate dehydrogenase YP_914250.1 409050 D 318586 CDS YP_914251.1 119383195 4578844 410232..411185 1 NC_008686.1 PFAM: protein of unknown function DUF6, transmembrane; KEGG: rsp:RSP_0858 transporter, RhaT family, DMT superfamily; hypothetical protein 411185 4578844 Pden_0441 Paracoccus denitrificans PD1222 hypothetical protein YP_914251.1 410232 D 318586 CDS YP_914252.1 119383196 4578845 411827..412228 1 NC_008686.1 hypothetical protein 412228 4578845 Pden_0442 Paracoccus denitrificans PD1222 hypothetical protein YP_914252.1 411827 D 318586 CDS YP_914253.1 119383197 4578846 412240..412752 1 NC_008686.1 PFAM: protein of unknown function DUF955; KEGG: gbe:GbCGDNIH1_1521 hypothetical protein; hypothetical protein 412752 4578846 Pden_0443 Paracoccus denitrificans PD1222 hypothetical protein YP_914253.1 412240 D 318586 CDS YP_914254.1 119383198 4578847 412764..413840 1 NC_008686.1 KEGG: gbe:GbCGDNIH1_1520 hypothetical protein; hypothetical protein 413840 4578847 Pden_0444 Paracoccus denitrificans PD1222 hypothetical protein YP_914254.1 412764 D 318586 CDS YP_914255.1 119383199 4578848 414070..414585 1 NC_008686.1 KEGG: sil:SPOA0122 ISSpo9, transposase; hypothetical protein 414585 4578848 Pden_0445 Paracoccus denitrificans PD1222 hypothetical protein YP_914255.1 414070 D 318586 CDS YP_914256.1 119383200 4578849 415141..416178 1 NC_008686.1 PFAM: zinc finger, CHC2-family protein; KEGG: bpa:BPP0490 DNA primase; CHC2-family zinc finger protein 416178 4578849 Pden_0446 Paracoccus denitrificans PD1222 CHC2-family zinc finger protein YP_914256.1 415141 D 318586 CDS YP_914257.1 119383201 4578850 416175..419363 1 NC_008686.1 KEGG: bpa:BPP0491 hypothetical protein; hypothetical protein 419363 4578850 Pden_0447 Paracoccus denitrificans PD1222 hypothetical protein YP_914257.1 416175 D 318586 CDS YP_914258.1 119383202 4578851 419360..420268 1 NC_008686.1 KEGG: bpa:BPP0493 hypothetical protein; hypothetical protein 420268 4578851 Pden_0448 Paracoccus denitrificans PD1222 hypothetical protein YP_914258.1 419360 D 318586 CDS YP_914259.1 119383203 4578852 420268..421179 1 NC_008686.1 PFAM: Exonuclease, RNase T and DNA polymerase III; SMART: Exonuclease; KEGG: ret:RHE_PE00402 probable polymerase epsilon subunit protein; exonuclease 421179 4578852 Pden_0449 Paracoccus denitrificans PD1222 exonuclease YP_914259.1 420268 D 318586 CDS YP_914260.1 119383204 4578853 complement(421270..421986) 1 NC_008686.1 KEGG: bmb:BruAb2_0399 hypothetical protein; hypothetical protein 421986 4578853 Pden_0450 Paracoccus denitrificans PD1222 hypothetical protein YP_914260.1 421270 R 318586 CDS YP_914261.1 119383205 4578854 complement(421964..422515) 1 NC_008686.1 KEGG: bmb:BruAb2_0400 hypothetical protein; hypothetical protein 422515 4578854 Pden_0451 Paracoccus denitrificans PD1222 hypothetical protein YP_914261.1 421964 R 318586 CDS YP_914262.1 119383206 4578855 complement(423504..423761) 1 NC_008686.1 hypothetical protein 423761 4578855 Pden_0453 Paracoccus denitrificans PD1222 hypothetical protein YP_914262.1 423504 R 318586 CDS YP_914263.1 119383207 4578856 complement(423758..424588) 1 NC_008686.1 hypothetical protein 424588 4578856 Pden_0454 Paracoccus denitrificans PD1222 hypothetical protein YP_914263.1 423758 R 318586 CDS YP_914264.1 119383208 4580027 424675..424929 1 NC_008686.1 PFAM: helix-turn-helix domain protein; KEGG: rde:RD1_0810 DNA-binding protein; helix-turn-helix domain-containing protein 424929 4580027 Pden_0455 Paracoccus denitrificans PD1222 helix-turn-helix domain-containing protein YP_914264.1 424675 D 318586 CDS YP_914265.1 119383209 4580028 complement(425445..425816) 1 NC_008686.1 hypothetical protein 425816 4580028 Pden_0456 Paracoccus denitrificans PD1222 hypothetical protein YP_914265.1 425445 R 318586 CDS YP_914266.1 119383210 4580029 425929..426456 1 NC_008686.1 KEGG: rpb:RPB_2539 hypothetical protein; hypothetical protein 426456 4580029 Pden_0457 Paracoccus denitrificans PD1222 hypothetical protein YP_914266.1 425929 D 318586 CDS YP_914267.1 119383211 4580030 426466..428598 1 NC_008686.1 PFAM: Integrase, catalytic region; KEGG: bmb:BruAb1_0746 transposase, hypothetical; integrase catalytic subunit 428598 4580030 Pden_0458 Paracoccus denitrificans PD1222 integrase catalytic subunit YP_914267.1 426466 D 318586 CDS YP_914268.1 119383212 4580031 428588..429586 1 NC_008686.1 KEGG: rde:RD1_0796 transposition protein; transposition protein 429586 4580031 Pden_0459 Paracoccus denitrificans PD1222 transposition protein YP_914268.1 428588 D 318586 CDS YP_914269.1 119383213 4580032 429588..431069 1 NC_008686.1 KEGG: nha:Nham_2090 hypothetical protein; hypothetical protein 431069 4580032 Pden_0460 Paracoccus denitrificans PD1222 hypothetical protein YP_914269.1 429588 D 318586 CDS YP_914270.1 119383214 4580033 431234..432751 1 NC_008686.1 PFAM: Integrase, catalytic region; KEGG: sme:SMc03282 transposase number 1 for insertion sequence ISRM27; integrase catalytic subunit 432751 4580033 Pden_0461 Paracoccus denitrificans PD1222 integrase catalytic subunit YP_914270.1 431234 D 318586 CDS YP_914271.1 119383215 4580034 432748..433326 1 NC_008686.1 PFAM: IstB domain protein ATP-binding protein; KEGG: sme:SMc03281 transposase; IstB ATP binding domain-containing protein 433326 4580034 Pden_0462 Paracoccus denitrificans PD1222 IstB ATP binding domain-containing protein YP_914271.1 432748 D 318586 CDS YP_914272.1 119383216 4580035 433296..434282 1 NC_008686.1 PFAM: Recombinase; KEGG: rsp:RSP_3812 recombinase; recombinase 434282 4580035 Pden_0463 Paracoccus denitrificans PD1222 recombinase YP_914272.1 433296 D 318586 CDS YP_914273.1 119383217 4580036 434326..435324 1 NC_008686.1 PFAM: transposase, IS111A/IS1328/IS1533; transposase IS116/IS110/IS902 family protein; KEGG: nha:Nham_3955 transposase IS116/IS110/IS902; transposase IS116/IS110/IS902 family protein 435324 4580036 Pden_0464 Paracoccus denitrificans PD1222 transposase IS116/IS110/IS902 family protein YP_914273.1 434326 D 318586 CDS YP_914274.1 119383218 4580037 436286..437371 1 NC_008686.1 PFAM: ABC transporter related; Transport-associated OB domain protein; SMART: AAA ATPase; KEGG: psb:Psyr_4615 spermidine/putrescine ABC transporter ATP-binding subunit; ABC transporter 437371 4580037 Pden_0466 Paracoccus denitrificans PD1222 ABC transporter YP_914274.1 436286 D 318586 CDS YP_914275.1 119383219 4580038 437384..438448 1 NC_008686.1 KEGG: bmb:BruAb2_0855 hypothetical spermidine/putrescine ABC transporter, periplasmic spermidine/putrescine-binding protein; spermidine/putrescine-binding protein 438448 4580038 Pden_0467 Paracoccus denitrificans PD1222 spermidine/putrescine-binding protein YP_914275.1 437384 D 318586 CDS YP_914276.1 119383220 4580039 438445..439695 1 NC_008686.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: ppu:PP_0413 polyamine ABC transporter, permease protein; binding-protein-dependent transport system inner membrane protein 439695 4580039 Pden_0468 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_914276.1 438445 D 318586 CDS YP_914277.1 119383221 4580040 439692..440477 1 NC_008686.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: pst:PSPTO_0565 polyamine ABC transporter, permease protein; binding-protein-dependent transport system inner membrane protein 440477 4580040 Pden_0469 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_914277.1 439692 D 318586 CDS YP_914278.1 119383222 4580041 440577..441365 1 NC_008686.1 PFAM: regulatory protein GntR, HTH; GntR domain protein; KEGG: pau:PA14_72890 transcriptional regulator; GntR family transcriptional regulator 441365 4580041 Pden_0470 Paracoccus denitrificans PD1222 GntR family transcriptional regulator YP_914278.1 440577 D 318586 CDS YP_914279.1 119383223 4580042 441610..442539 1 NC_008686.1 PFAM: protein of unknown function DUF849; KEGG: bur:Bcep18194_C7701 protein of unknown function DUF849; hypothetical protein 442539 4580042 Pden_0471 Paracoccus denitrificans PD1222 hypothetical protein YP_914279.1 441610 D 318586 CDS YP_914280.1 119383224 4580043 442556..444619 1 NC_008686.1 PFAM: Hydantoinase/oxoprolinase; Hydantoinaseoxoprolinase domain protein; KEGG: reu:Reut_C6223 5-oxoprolinase (ATP-hydrolyzing); 5-oxoprolinase 444619 4580043 Pden_0472 Paracoccus denitrificans PD1222 5-oxoprolinase YP_914280.1 442556 D 318586 CDS YP_914281.1 119383225 4580044 444631..446397 1 NC_008686.1 PFAM: Hydantoinase B/oxoprolinase; KEGG: reu:Reut_C6222 hydantoinase B/oxoprolinase; hydantoinase B/oxoprolinase 446397 4580044 Pden_0473 Paracoccus denitrificans PD1222 hydantoinase B/oxoprolinase YP_914281.1 444631 D 318586 CDS YP_914282.1 119383226 4580045 446394..447158 1 NC_008686.1 catalyzes the first of the two reduction steps in the elongation cycle of fatty acid synthesis; 3-ketoacyl-ACP reductase 447158 fabG 4580045 fabG Paracoccus denitrificans PD1222 3-ketoacyl-ACP reductase YP_914282.1 446394 D 318586 CDS YP_914283.1 119383227 4580046 447146..447538 1 NC_008686.1 hypothetical protein 447538 4580046 Pden_0475 Paracoccus denitrificans PD1222 hypothetical protein YP_914283.1 447146 D 318586 CDS YP_914284.1 119383228 4579093 447538..447990 1 NC_008686.1 PFAM: thioesterase superfamily protein; KEGG: bja:blr1345 hypothetical protein; thioesterase 447990 4579093 Pden_0476 Paracoccus denitrificans PD1222 thioesterase YP_914284.1 447538 D 318586 CDS YP_914285.1 119383229 4579094 448044..448658 1 NC_008686.1 PFAM: helix-turn-helix domain protein; Cupin 2, conserved barrel domain protein; KEGG: bur:Bcep18194_B1227 transcriptional regulator, XRE family with cupin sensor domain; XRE family transcriptional regulator 448658 4579094 Pden_0477 Paracoccus denitrificans PD1222 XRE family transcriptional regulator YP_914285.1 448044 D 318586 CDS YP_914286.1 119383230 4579095 448844..450010 1 NC_008686.1 PFAM: protein of unknown function DUF1100, hydrolase family protein; KEGG: ppu:PP_3195 hypothetical protein; hypothetical protein 450010 4579095 Pden_0478 Paracoccus denitrificans PD1222 hypothetical protein YP_914286.1 448844 D 318586 CDS YP_914287.1 119383231 4579096 450007..450780 1 NC_008686.1 PFAM: short-chain dehydrogenase/reductase SDR; KEGG: reu:Reut_C6224 short-chain dehydrogenase/reductase SDR; short-chain dehydrogenase/reductase SDR 450780 4579096 Pden_0479 Paracoccus denitrificans PD1222 short-chain dehydrogenase/reductase SDR YP_914287.1 450007 D 318586 CDS YP_914288.1 119383232 4579097 450916..452154 1 NC_008686.1 PFAM: major facilitator superfamily MFS_1; KEGG: rha:RHA1_ro04907 transporter, MFS superfamily; major facilitator superfamily transporter 452154 4579097 Pden_0480 Paracoccus denitrificans PD1222 major facilitator superfamily transporter YP_914288.1 450916 D 318586 CDS YP_914289.1 119383233 4579098 complement(452349..452849) 1 NC_008686.1 KEGG: gbe:GbCGDNIH1_1799 transposase; hypothetical protein 452849 4579098 Pden_0481 Paracoccus denitrificans PD1222 hypothetical protein YP_914289.1 452349 R 318586 CDS YP_914290.1 119383234 4579099 453006..453269 1 NC_008686.1 PFAM: SpoVT/AbrB domain protein; KEGG: sme:SMc03949 nitrogen regulatory protein; SpoVT/AbrB domain-containing protein 453269 4579099 Pden_0482 Paracoccus denitrificans PD1222 SpoVT/AbrB domain-containing protein YP_914290.1 453006 D 318586 CDS YP_914291.1 119383235 4579100 453266..453667 1 NC_008686.1 PFAM: PilT protein domain protein; SMART: Nucleotide binding protein, PINc; KEGG: sme:SMa0981 probable NtrR2 transcription regulator; twitching motility protein PilT 453667 4579100 Pden_0483 Paracoccus denitrificans PD1222 twitching motility protein PilT YP_914291.1 453266 D 318586 CDS YP_914292.1 119383236 4579101 454495..454833 1 NC_008686.1 KEGG: eba:ebB86 RelE-like cytotoxic translational repressor of toxin-antitoxin stability system; RelE-like cytotoxic translational repressor of toxin-antitoxin stability system 454833 4579101 Pden_0484 Paracoccus denitrificans PD1222 RelE-like cytotoxic translational repressor of toxin-antitoxin stability system YP_914292.1 454495 D 318586 CDS YP_914293.1 119383237 4579102 454815..455108 1 NC_008686.1 KEGG: noc:Noc_2738 transcriptional regulator, XRE family; XRE family transcriptional regulator 455108 4579102 Pden_0485 Paracoccus denitrificans PD1222 XRE family transcriptional regulator YP_914293.1 454815 D 318586 CDS YP_914294.1 119383238 4579103 455218..455601 1 NC_008686.1 KEGG: sme:SMc01416 hypothetical protein; hypothetical protein 455601 4579103 Pden_0486 Paracoccus denitrificans PD1222 hypothetical protein YP_914294.1 455218 D 318586 CDS YP_914295.1 119383239 4579104 complement(455768..456088) 1 NC_008686.1 hypothetical protein 456088 4579104 Pden_0487 Paracoccus denitrificans PD1222 hypothetical protein YP_914295.1 455768 R 318586 CDS YP_914296.1 119383240 4579105 complement(456189..460739) 1 NC_008686.1 PFAM: glutamine amidotransferase, class-II; glutamate synthase, alpha subunit domain protein; ferredoxin-dependent glutamate synthase; glutamate synthase; KEGG: rsp:RSP_1146 glutamine-pyruvate aminotransferase; glutamate synthase 460739 4579105 Pden_0488 Paracoccus denitrificans PD1222 glutamate synthase YP_914296.1 456189 R 318586 CDS YP_914297.1 119383241 4579106 complement(460736..461500) 1 NC_008686.1 KEGG: rsp:RSP_1148 hypothetical protein; hypothetical protein 461500 4579106 Pden_0489 Paracoccus denitrificans PD1222 hypothetical protein YP_914297.1 460736 R 318586 CDS YP_914298.1 119383242 4579107 complement(461513..463006) 1 NC_008686.1 function undetermined; similar to glutamate synthase beta subunit and related oxidoreductases which transfer electrons from NADPH to an acceptor protein or protein domain; oxidoreductase 463006 4579107 Pden_0490 Paracoccus denitrificans PD1222 oxidoreductase YP_914298.1 461513 R 318586 CDS YP_914299.1 119383243 4579108 complement(463157..463960) 1 NC_008686.1 BacA; phosphatase activity in Escherichia coli not kinase; involved in bacitracin resistance as bacitracin supposedly sequesters undecaprenyl disphosphate which reduces the pool of lipid carrier available to the cell; undecaprenyl pyrophosphate phosphatase 463960 4579108 Pden_0491 Paracoccus denitrificans PD1222 undecaprenyl pyrophosphate phosphatase YP_914299.1 463157 R 318586 CDS YP_914300.1 119383244 4579109 complement(463960..464952) 1 NC_008686.1 PFAM: NAD-dependent epimerase/dehydratase; short-chain dehydrogenase/reductase SDR; 3-beta hydroxysteroid dehydrogenase/isomerase; dTDP-4-dehydrorhamnose reductase; NmrA family protein; Male sterility C-terminal domain; KEGG: sit:TM1040_2820 3-beta hydroxysteroid dehydrogenase/isomerase; NAD-dependent epimerase/dehydratase 464952 4579109 Pden_0492 Paracoccus denitrificans PD1222 NAD-dependent epimerase/dehydratase YP_914300.1 463960 R 318586 CDS YP_914301.1 119383245 4579110 complement(464983..466581) 1 NC_008686.1 PFAM: glucose-methanol-choline oxidoreductase; GMC oxidoreductase; KEGG: ter:Tery_1077 glucose-methanol-choline oxidoreductase; glucose-methanol-choline oxidoreductase 466581 4579110 Pden_0493 Paracoccus denitrificans PD1222 glucose-methanol-choline oxidoreductase YP_914301.1 464983 R 318586 CDS YP_914302.1 119383246 4579111 467184..467624 1 NC_008686.1 PFAM: NUDIX hydrolase; KEGG: rsp:RSP_1208 NUDIX hydrolase; NUDIX hydrolase 467624 4579111 Pden_0494 Paracoccus denitrificans PD1222 NUDIX hydrolase YP_914302.1 467184 D 318586 CDS YP_914303.1 119383247 4581037 complement(467633..468904) 1 NC_008686.1 PFAM: response regulator receiver; Stage II sporulation E family protein; SMART: protein phosphatase 2C domain protein; KEGG: rde:RD1_0413 response regulator; response regulator receiver protein 468904 4581037 Pden_0495 Paracoccus denitrificans PD1222 response regulator receiver protein YP_914303.1 467633 R 318586 CDS YP_914304.1 119383248 4581038 469024..469374 1 NC_008686.1 PFAM: Hpt domain protein; KEGG: sit:TM1040_2886 Hpt protein; Hpt protein 469374 4581038 Pden_0496 Paracoccus denitrificans PD1222 Hpt protein YP_914304.1 469024 D 318586 CDS YP_914305.1 119383249 4581039 complement(469382..470620) 1 NC_008686.1 catalyzes the formation of 2-oxobutanoate from L-threonine; biosynthetic; threonine dehydratase 470620 4581039 Pden_0497 Paracoccus denitrificans PD1222 threonine dehydratase YP_914305.1 469382 R 318586 CDS YP_914306.1 119383250 4581040 complement(470699..471541) 1 NC_008686.1 hypothetical protein 471541 4581040 Pden_0498 Paracoccus denitrificans PD1222 hypothetical protein YP_914306.1 470699 R 318586 CDS YP_914307.1 119383251 4581041 471591..472817 1 NC_008686.1 catalyzes the formation of 2-N(omega)-(L-arginino)succinate from L-citrulline and L-aspartate in arginine biosynthesis, AMP-forming; argininosuccinate synthase 472817 4581041 Pden_0499 Paracoccus denitrificans PD1222 argininosuccinate synthase YP_914307.1 471591 D 318586 CDS YP_914308.1 119383252 4581042 472955..473434 1 NC_008686.1 PFAM: 3-demethylubiquinone-9 3-methyltransferase; KEGG: nwi:Nwi_0688 3-demethylubiquinone-9 3-methyltransferase; 3-demethylubiquinone-9 3-methyltransferase 473434 4581042 Pden_0500 Paracoccus denitrificans PD1222 3-demethylubiquinone-9 3-methyltransferase YP_914308.1 472955 D 318586 CDS YP_914309.1 119383253 4581043 473477..474028 1 NC_008686.1 TIGRFAM: molybdenum cofactor synthesis domain; PFAM: molybdopterin binding domain; KEGG: bmb:BruAb2_0726 MogA, molybdenum cofactor biosynthesis protein; molybdenum cofactor synthesis domain-containing protein 474028 4581043 Pden_0501 Paracoccus denitrificans PD1222 molybdenum cofactor synthesis domain-containing protein YP_914309.1 473477 D 318586 CDS YP_914310.1 119383254 4581044 complement(474003..474617) 1 NC_008686.1 KEGG: rsp:RSP_0986 hypothetical protein; hypothetical protein 474617 4581044 Pden_0502 Paracoccus denitrificans PD1222 hypothetical protein YP_914310.1 474003 R 318586 CDS YP_914311.1 119383255 4581045 complement(474658..475452) 1 NC_008686.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sme:SMc02169 ATP-binding ABC transporter protein; ABC transporter 475452 4581045 Pden_0503 Paracoccus denitrificans PD1222 ABC transporter YP_914311.1 474658 R 318586 CDS YP_914312.1 119383256 4581046 complement(475449..476522) 1 NC_008686.1 PFAM: inner-membrane translocator; KEGG: rsp:RSP_0989 ABC sugar transporter, inner membrane subunit; inner-membrane translocator 476522 4581046 Pden_0504 Paracoccus denitrificans PD1222 inner-membrane translocator YP_914312.1 475449 R 318586 CDS YP_914313.1 119383257 4581047 complement(476615..477634) 1 NC_008686.1 PFAM: periplasmic binding protein/LacI transcriptional regulator; KEGG: rsp:RSP_0990 ABC sugar transporter, periplasmic sugar binding subunit; periplasmic binding protein/LacI transcriptional regulator 477634 4581047 Pden_0505 Paracoccus denitrificans PD1222 periplasmic binding protein/LacI transcriptional regulator YP_914313.1 476615 R 318586 CDS YP_914314.1 119383258 4581048 477754..478944 1 NC_008686.1 PFAM: ROK family protein; regulatory protein, MarR; KEGG: rsp:RSP_0991 transcriptional regulator, ROK family; ROK family protein 478944 4581048 Pden_0506 Paracoccus denitrificans PD1222 ROK family protein YP_914314.1 477754 D 318586 CDS YP_914315.1 119383259 4581049 478963..479877 1 NC_008686.1 PFAM: heat shock protein DnaJ domain protein; chaperone DnaJ domain protein; KEGG: sme:SMa0116 DnaJ/CbpA-type protein; molecular chaperone DnaJ 479877 4581049 Pden_0507 Paracoccus denitrificans PD1222 molecular chaperone DnaJ YP_914315.1 478963 D 318586 CDS YP_914316.1 119383260 4581050 479874..480221 1 NC_008686.1 KEGG: rru:Rru_A2016 hypothetical protein; hypothetical protein 480221 4581050 Pden_0508 Paracoccus denitrificans PD1222 hypothetical protein YP_914316.1 479874 D 318586 CDS YP_914317.1 119383261 4581051 complement(480218..480385) 1 NC_008686.1 PFAM: protein of unknown function DUF1289; KEGG: jan:Jann_2180 protein of unknown function DUF1289; hypothetical protein 480385 4581051 Pden_0509 Paracoccus denitrificans PD1222 hypothetical protein YP_914317.1 480218 R 318586 CDS YP_914318.1 119383262 4581052 complement(480382..480858) 1 NC_008686.1 similar to RuvC resolvase with substantial differences; NMR structural information suggests this protein is monomeric; unknown cellular function; Holliday junction resolvase-like protein 480858 4581052 Pden_0510 Paracoccus denitrificans PD1222 Holliday junction resolvase-like protein YP_914318.1 480382 R 318586 CDS YP_914319.1 119383263 4581053 complement(480855..482102) 1 NC_008686.1 KEGG: rsp:RSP_2685 cytochrome c-type biogenesis protein, CycH; cytochrome c-type biogenesis protein, CycH 482102 4581053 Pden_0511 Paracoccus denitrificans PD1222 cytochrome c-type biogenesis protein, CycH YP_914319.1 480855 R 318586 CDS YP_914320.1 119383264 4581054 482305..483576 1 NC_008686.1 TIGRFAM: sarcosine oxidase, beta subunit family; PFAM: FAD dependent oxidoreductase; KEGG: rsp:RSP_2686 sarcosine oxidase beta subunit; sarcosine oxidase subunit beta 483576 4581054 Pden_0512 Paracoccus denitrificans PD1222 sarcosine oxidase subunit beta YP_914320.1 482305 D 318586 CDS YP_914321.1 119383265 4581055 483734..483985 1 NC_008686.1 KEGG: rsp:RSP_1403 conserved hypoothetical protein; hypothetical protein 483985 4581055 Pden_0513 Paracoccus denitrificans PD1222 hypothetical protein YP_914321.1 483734 D 318586 CDS YP_914322.1 119383266 4581056 484296..484676 1 NC_008686.1 PFAM: Sarcosine oxidase, delta subunit, heterotetrameric; KEGG: rsp:RSP_2688 sarcosine oxidase delta subunit protein; sarcosine oxidase, delta subunit, heterotetrameric 484676 4581056 Pden_0514 Paracoccus denitrificans PD1222 sarcosine oxidase, delta subunit, heterotetrameric YP_914322.1 484296 D 318586 CDS YP_914323.1 119383267 4578702 484673..487606 1 NC_008686.1 TIGRFAM: sarcosine oxidase, alpha subunit family; PFAM: FAD dependent oxidoreductase; glycine cleavage T protein (aminomethyl transferase); Glycine cleavage T-protein, C-terminal barrel; KEGG: rsp:RSP_2689 sarcosine oxidase, alpha subunit; sarcosine oxidase subunit alpha 487606 4578702 Pden_0515 Paracoccus denitrificans PD1222 sarcosine oxidase subunit alpha YP_914323.1 484673 D 318586 CDS YP_914324.1 119383268 4578703 487599..488117 1 NC_008686.1 PFAM: Sarcosine oxidase, gamma subunit; KEGG: rsp:RSP_2690 sarcosine oxidase gamma subunit; sarcosine oxidase, gamma subunit 488117 4578703 Pden_0516 Paracoccus denitrificans PD1222 sarcosine oxidase, gamma subunit YP_914324.1 487599 D 318586 CDS YP_914325.1 119383269 4578704 488190..488645 1 NC_008686.1 KEGG: rde:RD1_1770 hypothetical protein; hypothetical protein 488645 4578704 Pden_0517 Paracoccus denitrificans PD1222 hypothetical protein YP_914325.1 488190 D 318586 CDS YP_914326.1 119383270 4578705 488754..489353 1 NC_008686.1 PFAM: manganese and iron superoxide dismutase; KEGG: rsp:RSP_2693 superoxide dismutase, Fe-Mn family; superoxide dismutase 489353 4578705 Pden_0518 Paracoccus denitrificans PD1222 superoxide dismutase YP_914326.1 488754 D 318586 CDS YP_914327.1 119383271 4578706 489405..489929 1 NC_008686.1 PFAM: protein of unknown function DUF461; KEGG: rde:RD1_1682 hypothetical protein; hypothetical protein 489929 4578706 Pden_0519 Paracoccus denitrificans PD1222 hypothetical protein YP_914327.1 489405 D 318586 CDS YP_914328.1 119383272 4578707 complement(489926..490564) 1 NC_008686.1 PFAM: lipolytic enzyme, G-D-S-L family; KEGG: rsp:RSP_3601 lipolytic enzyme, G-D-S-L family; GDSL family lipase 490564 4578707 Pden_0520 Paracoccus denitrificans PD1222 GDSL family lipase YP_914328.1 489926 R 318586 CDS YP_914329.1 119383273 4578708 complement(490561..492984) 1 NC_008686.1 TIGRFAM: ATPase, P-type (transporting), HAD superfamily, subfamily IC; copper-translocating P-type ATPase; heavy metal translocating P-type ATPase; PFAM: Haloacid dehalogenase domain protein hydrolase; Heavy metal transport/detoxification protein; E1-E2 ATPase-associated domain protein; KEGG: sil:SPO0794 copper-translocating P-type ATPase; heavy metal translocating P-type ATPase 492984 4578708 Pden_0521 Paracoccus denitrificans PD1222 heavy metal translocating P-type ATPase YP_914329.1 490561 R 318586 CDS YP_914330.1 119383274 4578709 493412..493990 1 NC_008686.1 PFAM: ErfK/YbiS/YcfS/YnhG family protein; KEGG: mes:Meso_4112 ErfK/YbiS/YcfS/YnhG; ErfK/YbiS/YcfS/YnhG family protein 493990 4578709 Pden_0522 Paracoccus denitrificans PD1222 ErfK/YbiS/YcfS/YnhG family protein YP_914330.1 493412 D 318586 CDS YP_914331.1 119383275 4578710 493991..495088 1 NC_008686.1 catalyzes the selenophosphate-dependent transfer of selenium from selenophosphate for conversion of 2-thiouridine to 2-selenouridine at the wobble position in tRNA; tRNA 2-selenouridine synthase 495088 4578710 Pden_0523 Paracoccus denitrificans PD1222 tRNA 2-selenouridine synthase YP_914331.1 493991 D 318586 CDS YP_914332.1 119383276 4578711 complement(495107..495910) 1 NC_008686.1 catalyzes the formation of a purine and ribose phosphate from a purine nucleoside; in E. coli this enzyme functions in xanthosine degradation; purine nucleoside phosphorylase 495910 4578711 Pden_0524 Paracoccus denitrificans PD1222 purine nucleoside phosphorylase YP_914332.1 495107 R 318586 CDS YP_914333.1 119383277 4578712 complement(495894..496859) 1 NC_008686.1 PFAM: inner-membrane translocator; KEGG: rsp:RSP_2208 ABC sugar transporter, inner membrane subunit; inner-membrane translocator 496859 4578712 Pden_0525 Paracoccus denitrificans PD1222 inner-membrane translocator YP_914333.1 495894 R 318586 CDS YP_914334.1 119383278 4578713 complement(496859..498037) 1 NC_008686.1 PFAM: inner-membrane translocator; KEGG: rsp:RSP_2209 ABC sugar transporter, inner membrane subunit; inner-membrane translocator 498037 4578713 Pden_0526 Paracoccus denitrificans PD1222 inner-membrane translocator YP_914334.1 496859 R 318586 CDS YP_914335.1 119383279 4578714 complement(498015..499640) 1 NC_008686.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sil:SPO0378 sugar ABC transporter, ATP-binding protein; ABC transporter 499640 4578714 Pden_0527 Paracoccus denitrificans PD1222 ABC transporter YP_914335.1 498015 R 318586 CDS YP_914336.1 119383280 4578715 complement(499640..500626) 1 NC_008686.1 PFAM: basic membrane lipoprotein; KEGG: rsp:RSP_2211 ABC transporter, periplasmic substrate-binding protein; basic membrane lipoprotein 500626 4578715 Pden_0528 Paracoccus denitrificans PD1222 basic membrane lipoprotein YP_914336.1 499640 R 318586 CDS YP_914337.1 119383281 4578716 complement(500718..501119) 1 NC_008686.1 TIGRFAM: ribosomal-protein-alanine acetyltransferase; PFAM: GCN5-related N-acetyltransferase; KEGG: rsp:RSP_2212 acetyltransferase; ribosomal-protein-alanine acetyltransferase 501119 4578716 Pden_0529 Paracoccus denitrificans PD1222 ribosomal-protein-alanine acetyltransferase YP_914337.1 500718 R 318586 CDS YP_914338.1 119383282 4578717 complement(501116..501709) 1 NC_008686.1 PFAM: peptidase M22, glycoprotease; KEGG: rsp:RSP_2213 hypothetical protein; peptidase M22, glycoprotease 501709 4578717 Pden_0530 Paracoccus denitrificans PD1222 peptidase M22, glycoprotease YP_914338.1 501116 R 318586 CDS YP_914339.1 119383283 4578718 complement(501702..502256) 1 NC_008686.1 PFAM: nitrogen-fixing NifU domain protein; KEGG: sit:TM1040_3091 nitrogen-fixing NifU-like; NifU domain-containing protein 502256 4578718 Pden_0531 Paracoccus denitrificans PD1222 NifU domain-containing protein YP_914339.1 501702 R 318586 CDS YP_914340.1 119383284 4578719 complement(502470..502925) 1 NC_008686.1 PFAM: UspA domain protein; KEGG: sit:TM1040_3730 UspA; UspA domain-containing protein 502925 4578719 Pden_0532 Paracoccus denitrificans PD1222 UspA domain-containing protein YP_914340.1 502470 R 318586 CDS YP_914341.1 119383285 4578720 503082..503831 1 NC_008686.1 PFAM: sugar transferase; KEGG: rsp:RSP_1189 sugar transferase; sugar transferase 503831 4578720 Pden_0533 Paracoccus denitrificans PD1222 sugar transferase YP_914341.1 503082 D 318586 CDS YP_914342.1 119383286 4579772 complement(504029..504814) 1 NC_008686.1 mediates pseudouridylation (positions 38, 39, 40) at the tRNA anticodon region which contributes to the structural stability; tRNA pseudouridine synthase A 504814 truA 4579772 truA Paracoccus denitrificans PD1222 tRNA pseudouridine synthase A YP_914342.1 504029 R 318586 CDS YP_914343.1 119383287 4579773 complement(504818..505792) 1 NC_008686.1 KEGG: sil:SPO2985 hypothetical protein; hypothetical protein 505792 4579773 Pden_0535 Paracoccus denitrificans PD1222 hypothetical protein YP_914343.1 504818 R 318586 CDS YP_914344.1 119383288 4579774 506263..507711 1 NC_008686.1 PFAM: cation transporter; KEGG: rsp:RSP_1854 potassium uptake transporter, transmembrane component, TrkH; cation transporter 507711 4579774 Pden_0536 Paracoccus denitrificans PD1222 cation transporter YP_914344.1 506263 D 318586 CDS YP_914345.1 119383289 4579775 complement(507708..508946) 1 NC_008686.1 PFAM: Peptidoglycan-binding domain 1 protein; KEGG: rsp:RSP_1855 hypothetical protein; peptidoglycan binding domain-containing protein 508946 4579775 Pden_0537 Paracoccus denitrificans PD1222 peptidoglycan binding domain-containing protein YP_914345.1 507708 R 318586 CDS YP_914346.1 119383290 4579776 509237..510187 1 NC_008686.1 glycine--tRNA ligase alpha chain; GlyRS; class II aminoacyl tRNA synthetase; tetramer of alpha(2)beta(2); catalyzes a two-step reaction; first charging a glycine molecule by linking its carboxyl group to the alpha-phosphate of ATP; second by transfer of the aminoacyl-adenylate to its tRNA; glycyl-tRNA synthetase subunit alpha 510187 glyQ 4579776 glyQ Paracoccus denitrificans PD1222 glycyl-tRNA synthetase subunit alpha YP_914346.1 509237 D 318586 CDS YP_914347.1 119383291 4579777 510184..510666 1 NC_008686.1 KEGG: sit:TM1040_2311 conserved hypothetical protein; signal transduction histidine kinase regulating citrate/malate metabolism 510666 4579777 Pden_0539 Paracoccus denitrificans PD1222 signal transduction histidine kinase regulating citrate/malate metabolism YP_914347.1 510184 D 318586 CDS YP_914348.1 119383292 4579778 510666..512723 1 NC_008686.1 KEGG: rsp:RSP_1858 glycyl-tRNA synthetase beta subunit; glycine--tRNA ligase 512723 4579778 Pden_0540 Paracoccus denitrificans PD1222 glycine--tRNA ligase YP_914348.1 510666 D 318586 CDS YP_914349.1 119383293 4579779 512830..515391 1 NC_008686.1 catalyzes the formation of phosphoenolpyruvate from pyruvate; pyruvate phosphate dikinase 515391 4579779 Pden_0541 Paracoccus denitrificans PD1222 pyruvate phosphate dikinase YP_914349.1 512830 D 318586 CDS YP_914350.1 119383294 4579780 515619..516158 1 NC_008686.1 PFAM: cell wall hydrolase, SleB; KEGG: rsp:RSP_1860 hypothetical protein; cell wall hydrolase SleB 516158 4579780 Pden_0542 Paracoccus denitrificans PD1222 cell wall hydrolase SleB YP_914350.1 515619 D 318586 CDS YP_914351.1 119383295 4579781 516201..517019 1 NC_008686.1 PFAM: dihydroneopterin aldolase; KEGG: rsp:RSP_1861 probable dihydroneopterin aldolase; dihydroneopterin aldolase 517019 4579781 Pden_0543 Paracoccus denitrificans PD1222 dihydroneopterin aldolase YP_914351.1 516201 D 318586 CDS YP_914352.1 119383296 4579782 517064..518035 1 NC_008686.1 KEGG: rsp:RSP_1862 dihydropteroate synthase, DhpS; TIGRFAM: dihydropteroate synthase; PFAM: dihydropteroate synthase, DHPS; dihydropteroate synthase 518035 4579782 Pden_0544 Paracoccus denitrificans PD1222 dihydropteroate synthase YP_914352.1 517064 D 318586 CDS YP_914353.1 119383297 4579783 518046..519389 1 NC_008686.1 catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate; phosphoglucosamine mutase 519389 glmM 4579783 glmM Paracoccus denitrificans PD1222 phosphoglucosamine mutase YP_914353.1 518046 D 318586 CDS YP_914354.1 119383298 4579784 complement(519472..520593) 1 NC_008686.1 PFAM: monooxygenase, FAD-binding; KEGG: rsp:RSP_2656 salicylate hydroxylase (salicylate 1-monooxygenase); FAD-binding monooxygenase 520593 4579784 Pden_0546 Paracoccus denitrificans PD1222 FAD-binding monooxygenase YP_914354.1 519472 R 318586 CDS YP_914355.1 119383299 4579785 complement(520635..521057) 1 NC_008686.1 TIGRFAM: RNA polymerase-binding protein DksA; PFAM: zinc finger, DksA/TraR C4-type; KEGG: rsp:RSP_2654 DnaK suppressor protein, DksA family; TraR/DksA family transcriptional regulator 521057 4579785 Pden_0547 Paracoccus denitrificans PD1222 TraR/DksA family transcriptional regulator YP_914355.1 520635 R 318586 CDS YP_914356.1 119383300 4579786 521219..522058 1 NC_008686.1 PFAM: AAA ATPase, central domain protein; ATPase associated with various cellular activities, AAA_5; SMART: AAA ATPase; KEGG: rsp:RSP_2653 ATPase, AAA family; ATPase 522058 4579786 Pden_0548 Paracoccus denitrificans PD1222 ATPase YP_914356.1 521219 D 318586 CDS YP_914357.1 119383301 4579787 522070..522510 1 NC_008686.1 PFAM: GCN5-related N-acetyltransferase; KEGG: rde:RD1_2794 acetyltransferase; N-acetyltransferase 522510 4579787 Pden_0549 Paracoccus denitrificans PD1222 N-acetyltransferase YP_914357.1 522070 D 318586 CDS YP_914358.1 119383302 4579788 complement(522559..523053) 1 NC_008686.1 PFAM: Lytic transglycosylase, catalytic; KEGG: sil:SPO2284 transglycosylase SLT domain protein; lytic transglycosylase, catalytic 523053 4579788 Pden_0550 Paracoccus denitrificans PD1222 lytic transglycosylase, catalytic YP_914358.1 522559 R 318586 CDS YP_914359.1 119383303 4579789 complement(523200..524594) 1 NC_008686.1 TIGRFAM: dihydrolipoamide dehydrogenase; PFAM: FAD-dependent pyridine nucleotide-disulphide oxidoreductase; fumarate reductase/succinate dehydrogenase flavoprotein domain protein; pyridine nucleotide-disulphide oxidoreductase dimerisation region; HI0933 family protein; FAD dependent oxidoreductase; KEGG: sil:SPO0340 2-oxoglutarate dehydrogenase, E3 component, dihydrolipoamide dehydrogenase; dihydrolipoamide dehydrogenase 524594 4579789 Pden_0551 Paracoccus denitrificans PD1222 dihydrolipoamide dehydrogenase YP_914359.1 523200 R 318586 CDS YP_914360.1 119383304 4579790 complement(524645..525037) 1 NC_008686.1 KEGG: jan:Jann_0835 inner membrane protein; inner membrane protein 525037 4579790 Pden_0552 Paracoccus denitrificans PD1222 inner membrane protein YP_914360.1 524645 R 318586 CDS YP_914361.1 119383305 4579791 complement(525037..525294) 1 NC_008686.1 hypothetical protein 525294 4579791 Pden_0553 Paracoccus denitrificans PD1222 hypothetical protein YP_914361.1 525037 R 318586 CDS YP_914362.1 119383306 4579675 complement(525437..526969) 1 NC_008686.1 component of 2-oxoglutarate dehydrogenase complex; catalyzes the transfer of acetyl from acetyldihydrolipoamide to coenzyme A to form acetyl CoA as part of the conversion of 2-oxoglutarate to succinyl-CoA; dihydrolipoamide acetyltransferase 526969 4579675 Pden_0554 Paracoccus denitrificans PD1222 dihydrolipoamide acetyltransferase YP_914362.1 525437 R 318586 CDS YP_914363.1 119383307 4579676 complement(526971..529937) 1 NC_008686.1 SucA; E1 component of the oxoglutarate dehydrogenase complex which catalyzes the formation of succinyl-CoA from 2-oxoglutarate; SucA catalyzes the reaction of 2-oxoglutarate with dihydrolipoamide succinyltransferase-lipoate to form dihydrolipoamide succinyltransferase-succinyldihydrolipoate and carbon dioxide; 2-oxoglutarate dehydrogenase E1 529937 sucA 4579676 sucA Paracoccus denitrificans PD1222 2-oxoglutarate dehydrogenase E1 YP_914363.1 526971 R 318586 CDS YP_914364.1 119383308 4579677 complement(529934..530182) 1 NC_008686.1 hypothetical protein 530182 4579677 Pden_0556 Paracoccus denitrificans PD1222 hypothetical protein YP_914364.1 529934 R 318586 CDS YP_914365.1 119383309 4579678 530201..530545 1 NC_008686.1 hypothetical protein 530545 4579678 Pden_0557 Paracoccus denitrificans PD1222 hypothetical protein YP_914365.1 530201 D 318586 CDS YP_914366.1 119383310 4579679 complement(530589..531473) 1 NC_008686.1 TIGRFAM: succinyl-CoA synthetase, alpha subunit; PFAM: CoA-binding domain protein; ATP-citrate lyase/succinyl-CoA ligase; KEGG: rsp:RSP_0966 succinyl-CoA synthetase, alpha subunit; succinyl-CoA synthetase subunit alpha 531473 4579679 Pden_0558 Paracoccus denitrificans PD1222 succinyl-CoA synthetase subunit alpha YP_914366.1 530589 R 318586 CDS YP_914367.1 119383311 4579680 complement(531478..532671) 1 NC_008686.1 catalyzes the interconversion of succinyl-CoA and succinate; succinyl-CoA synthetase subunit beta 532671 sucC 4579680 sucC Paracoccus denitrificans PD1222 succinyl-CoA synthetase subunit beta YP_914367.1 531478 R 318586 CDS YP_914368.1 119383312 4579681 532894..536133 1 NC_008686.1 PFAM: Hemolysin-type calcium-binding region; KEGG: pol:Bpro_4929 hemolysin-type calcium-binding region; hemolysin-type calcium-binding protein 536133 4579681 Pden_0560 Paracoccus denitrificans PD1222 hemolysin-type calcium-binding protein YP_914368.1 532894 D 318586 CDS YP_914369.1 119383313 4579682 complement(536193..537155) 1 NC_008686.1 Catalyzes the reversible oxidation of malate to oxaloacetate; malate dehydrogenase 537155 4579682 Pden_0561 Paracoccus denitrificans PD1222 malate dehydrogenase YP_914369.1 536193 R 318586 CDS YP_914370.1 119383314 4579683 537341..538075 1 NC_008686.1 PFAM: protein of unknown function DUF81; KEGG: rsp:RSP_0969 integral membrane protein; hypothetical protein 538075 4579683 Pden_0562 Paracoccus denitrificans PD1222 hypothetical protein YP_914370.1 537341 D 318586 CDS YP_914371.1 119383315 4579684 538156..538995 1 NC_008686.1 PFAM: HpcH/HpaI aldolase; KEGG: rsp:RSP_0970 citrate lyase beta chain; citryl-CoA lyase 538995 4579684 Pden_0563 Paracoccus denitrificans PD1222 citryl-CoA lyase YP_914371.1 538156 D 318586 CDS YP_914372.1 119383316 4579685 539041..539592 1 NC_008686.1 PFAM: NnrUfamily protein; KEGG: jan:Jann_0815 NnrU; NnrU family protein 539592 4579685 Pden_0564 Paracoccus denitrificans PD1222 NnrU family protein YP_914372.1 539041 D 318586 CDS YP_914373.1 119383317 4579686 539594..539800 1 NC_008686.1 KEGG: sil:SPO0354 hypothetical protein; hypothetical protein 539800 4579686 Pden_0565 Paracoccus denitrificans PD1222 hypothetical protein YP_914373.1 539594 D 318586 CDS YP_914374.1 119383318 4579687 539810..540844 1 NC_008686.1 PFAM: MaoC domain protein dehydratase; KEGG: sil:SPO0355 hypothetical protein; dehydratase 540844 4579687 Pden_0566 Paracoccus denitrificans PD1222 dehydratase YP_914374.1 539810 D 318586 CDS YP_914375.1 119383319 4579688 541157..541549 1 NC_008686.1 PFAM: succinate dehydrogenase, cytochrome b subunit; KEGG: rsp:RSP_0974 succinate dehydrogenase cytochrome b-556 subunit; succinate dehydrogenase, cytochrome b subunit 541549 4579688 Pden_0567 Paracoccus denitrificans PD1222 succinate dehydrogenase, cytochrome b subunit YP_914375.1 541157 D 318586 CDS YP_914376.1 119383320 4579689 541566..541955 1 NC_008686.1 KEGG: rsp:RSP_0975 succinate dehydrogenase, hydrophobic membrane anchor protein; succinate dehydrogenase, hydrophobic membrane anchor protein 541955 4579689 Pden_0568 Paracoccus denitrificans PD1222 succinate dehydrogenase, hydrophobic membrane anchor protein YP_914376.1 541566 D 318586 CDS YP_914377.1 119383321 4579690 541965..543767 1 NC_008686.1 part of four member succinate dehydrogenase enzyme complex that forms a trimeric complex (trimer of tetramers); SdhA/B are the catalytic subcomplex and can exhibit succinate dehydrogenase activity in the absence of SdhC/D which are the membrane components and form cytochrome b556; SdhC binds ubiquinone; oxidizes succinate to fumarate while reducing ubiquinone to ubiquinol; succinate dehydrogenase flavoprotein subunit 543767 sdhA 4579690 sdhA Paracoccus denitrificans PD1222 succinate dehydrogenase flavoprotein subunit YP_914377.1 541965 D 318586 CDS YP_914378.1 119383322 4579691 543767..544123 1 NC_008686.1 KEGG: jan:Jann_0807 hypothetical protein; hypothetical protein 544123 4579691 Pden_0570 Paracoccus denitrificans PD1222 hypothetical protein YP_914378.1 543767 D 318586 CDS YP_914379.1 119383323 4579692 544123..544449 1 NC_008686.1 KEGG: rsp:RSP_0978 hypothetical protein; hypothetical protein 544449 4579692 Pden_0571 Paracoccus denitrificans PD1222 hypothetical protein YP_914379.1 544123 D 318586 CDS YP_914380.1 119383324 4579693 544520..545299 1 NC_008686.1 part of four member succinate dehydrogenase enzyme complex that forms a trimeric complex (trimer of tetramers); SdhA/B are the catalytic subcomplex and can exhibit succinate dehydrogenase activity in the absence of SdhC/D which are the membrane components and form cytochrome b556; SdhC binds ubiquinone; oxidizes succinate to fumarate while reducing ubiquinone to ubiquinol; the catalytic subunits are similar to fumarate reductase; succinate dehydrogenase iron-sulfur subunit 545299 sdhB 4579693 sdhB Paracoccus denitrificans PD1222 succinate dehydrogenase iron-sulfur subunit YP_914380.1 544520 D 318586 CDS YP_914381.1 119383325 4579617 545816..546649 1 NC_008686.1 KEGG: rde:RD1_1633 hypothetical protein; hypothetical protein 546649 4579617 Pden_0573 Paracoccus denitrificans PD1222 hypothetical protein YP_914381.1 545816 D 318586 CDS YP_914382.1 119383326 4579618 complement(546646..547338) 1 NC_008686.1 PFAM: beta-lactamase domain protein; KEGG: rsp:RSP_2268 metallo beta lactamase superfamily; beta-lactamase domain-containing protein 547338 4579618 Pden_0574 Paracoccus denitrificans PD1222 beta-lactamase domain-containing protein YP_914382.1 546646 R 318586 CDS YP_914383.1 119383327 4579619 547470..547757 1 NC_008686.1 allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases; reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA; some Mycoplasma proteins contain an N-terminal fusion to an unknown domain; aspartyl/glutamyl-tRNA amidotransferase subunit C 547757 gatC 4579619 gatC Paracoccus denitrificans PD1222 aspartyl/glutamyl-tRNA amidotransferase subunit C YP_914383.1 547470 D 318586 CDS YP_914384.1 119383328 4579620 547754..549235 1 NC_008686.1 allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases; reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA; aspartyl/glutamyl-tRNA amidotransferase subunit A 549235 gatA 4579620 gatA Paracoccus denitrificans PD1222 aspartyl/glutamyl-tRNA amidotransferase subunit A YP_914384.1 547754 D 318586 CDS YP_914385.1 119383329 4579621 549259..549783 1 NC_008686.1 KEGG: rsp:RSP_2271 hypothetical protein; hypothetical protein 549783 4579621 Pden_0577 Paracoccus denitrificans PD1222 hypothetical protein YP_914385.1 549259 D 318586 CDS YP_914386.1 119383330 4579622 549780..550406 1 NC_008686.1 PFAM: N-acetylmuramoyl-L-alanine amidase, family 2; KEGG: rsp:RSP_2272 N-acetylmuramoyl-L-alanine amidase, family 2; N-acetylmuramoyl-L-alanine amidase 550406 4579622 Pden_0578 Paracoccus denitrificans PD1222 N-acetylmuramoyl-L-alanine amidase YP_914386.1 549780 D 318586 CDS YP_914387.1 119383331 4579623 complement(550394..551167) 1 NC_008686.1 PFAM: protein of unknown function DUF519; KEGG: sil:SPO0421 hypothetical protein; hypothetical protein 551167 4579623 Pden_0579 Paracoccus denitrificans PD1222 hypothetical protein YP_914387.1 550394 R 318586 CDS YP_914388.1 119383332 4579624 complement(551716..552015) 1 NC_008686.1 PFAM: protein of unknown function DUF1127; KEGG: sit:TM1040_2023 protein of unknown function DUF1127; hypothetical protein 552015 4579624 Pden_0580 Paracoccus denitrificans PD1222 hypothetical protein YP_914388.1 551716 R 318586 CDS YP_914389.1 119383333 4579625 552277..553380 1 NC_008686.1 KEGG: rsp:RSP_2093 Mrp (multidrug resistance-associated proteins) family protein; Mrp (multidrug resistance-associated proteins) family protein 553380 4579625 Pden_0581 Paracoccus denitrificans PD1222 Mrp (multidrug resistance-associated proteins) family protein YP_914389.1 552277 D 318586 CDS YP_914390.1 119383334 4579626 554021..554530 1 NC_008686.1 MraZ; UPF0040; crystal structure shows similarity to AbrB; cell division protein MraZ 554530 4579626 Pden_0582 Paracoccus denitrificans PD1222 cell division protein MraZ YP_914390.1 554021 D 318586 CDS YP_914391.1 119383335 4579627 554532..555500 1 NC_008686.1 TIGRFAM: S-adenosyl-methyltransferase MraW; PFAM: methyltransferase; KEGG: rsp:RSP_6038 methyltransferase MraW/YabC; S-adenosyl-methyltransferase MraW 555500 mraW 4579627 mraW Paracoccus denitrificans PD1222 S-adenosyl-methyltransferase MraW YP_914391.1 554532 D 318586 CDS YP_914392.1 119383336 4579628 555500..555883 1 NC_008686.1 KEGG: sil:SPO1180 hypothetical protein; hypothetical protein 555883 4579628 Pden_0584 Paracoccus denitrificans PD1222 hypothetical protein YP_914392.1 555500 D 318586 CDS YP_914393.1 119383337 4579629 555880..557685 1 NC_008686.1 PFAM: penicillin-binding protein, transpeptidase; Penicillin-binding protein, dimerisation domain; KEGG: rsp:RSP_2098 cell division protein FtsI/penicillin-binding protein 2; peptidoglycan glycosyltransferase 557685 4579629 Pden_0585 Paracoccus denitrificans PD1222 peptidoglycan glycosyltransferase YP_914393.1 555880 D 318586 CDS YP_914394.1 119383338 4579630 557715..559184 1 NC_008686.1 involved in cell wall formation; peptidoglycan synthesis; cytoplasmic enzyme; catalyzes the addition of meso-diaminopimelic acid to the nucleotide precursor UDP-N-aceylmuramoyl-l-alanyl-d-glutamate; UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase 559184 murE 4579630 murE Paracoccus denitrificans PD1222 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase YP_914394.1 557715 D 318586 CDS YP_914395.1 119383339 4579631 559181..560566 1 NC_008686.1 TIGRFAM: UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate--D-alanyl-D-alanyl ligase; PFAM: cytoplasmic peptidoglycan synthetase domain protein; cytoplasmic peptidoglycan synthetases domain protein; Mur ligase, middle domain protein; KEGG: sil:SPO1183 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate--D-alanyl-D-alanyl ligase 560566 4579631 Pden_0587 Paracoccus denitrificans PD1222 UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate--D-alanyl-D-alanyl ligase YP_914395.1 559181 D 318586 CDS YP_914396.1 119383340 4579632 560566..561648 1 NC_008686.1 First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan; phospho-N-acetylmuramoyl-pentapeptide- transferase 561648 mraY 4579632 mraY Paracoccus denitrificans PD1222 phospho-N-acetylmuramoyl-pentapeptide- transferase YP_914396.1 560566 D 318586 CDS YP_914397.1 119383341 4579633 561731..563131 1 NC_008686.1 UDP-N-acetylmuramoylalanine--D-glutamate ligase; involved in peptidoglycan biosynthesis; cytoplasmic; catalyzes the addition of glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanine during cell wall formation; UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase 563131 murD 4579633 murD Paracoccus denitrificans PD1222 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase YP_914397.1 561731 D 318586 CDS YP_914398.1 119383342 4579634 complement(563332..564489) 1 NC_008686.1 PFAM: membrane protein involved in aromatic hydrocarbon degradation; KEGG: rsp:RSP_0007 outer membrane protein; aromatic hydrocarbon degradation membrane protein 564489 4579634 Pden_0590 Paracoccus denitrificans PD1222 aromatic hydrocarbon degradation membrane protein YP_914398.1 563332 R 318586 CDS YP_914399.1 119383343 4579635 564656..565627 1 NC_008686.1 KEGG: rsp:RSP_2869 possible tellurite resistance protein; tellurite resistance protein 565627 4579635 Pden_0591 Paracoccus denitrificans PD1222 tellurite resistance protein YP_914399.1 564656 D 318586 CDS YP_914400.1 119383344 4579636 565697..567145 1 NC_008686.1 KEGG: rsp:RSP_2868 inosine-5'-monophosphate dehydrogenase; TIGRFAM: inosine-5'-monophosphate dehydrogenase; PFAM: CBS domain containing protein; IMP dehydrogenase/GMP reductase; inosine-5'-monophosphate dehydrogenase 567145 4579636 Pden_0592 Paracoccus denitrificans PD1222 inosine-5'-monophosphate dehydrogenase YP_914400.1 565697 D 318586 CDS YP_914401.1 119383345 4579637 567470..568273 1 NC_008686.1 KEGG: rsp:RSP_1319 possible invasion protein; hypothetical protein 568273 4579637 Pden_0593 Paracoccus denitrificans PD1222 hypothetical protein YP_914401.1 567470 D 318586 CDS YP_914402.1 119383346 4579638 568349..569500 1 NC_008686.1 PFAM: Fmu (Sun) domain protein; KEGG: rsp:RSP_0455 possible NOL1/NOP2/sun family protein; Fmu (Sun) domain-containing protein 569500 4579638 Pden_0594 Paracoccus denitrificans PD1222 Fmu (Sun) domain-containing protein YP_914402.1 568349 D 318586 CDS YP_914403.1 119383347 4579639 569558..571600 1 NC_008686.1 PFAM: response regulator receiver; ATP-binding region, ATPase domain protein domain protein; histidine kinase A domain protein domain protein; PAS fold-4 domain protein; KEGG: sit:TM1040_1228 multi-sensor hybrid histidine kinase; multi-sensor hybrid histidine kinase 571600 4579639 Pden_0595 Paracoccus denitrificans PD1222 multi-sensor hybrid histidine kinase YP_914403.1 569558 D 318586 CDS YP_914404.1 119383348 4579640 complement(571624..572208) 1 NC_008686.1 KEGG: rsp:RSP_0453 hypothetical protein; hypothetical protein 572208 4579640 Pden_0596 Paracoccus denitrificans PD1222 hypothetical protein YP_914404.1 571624 R 318586 CDS YP_914405.1 119383349 4579641 572452..573522 1 NC_008686.1 catalyzes the hydrolysis of ATP in the presence of single-stranded DNA, the ATP-dependent uptake of single-stranded DNA by duplex DNA, and the ATP-dependent hybridization of homologous single-stranded DNAs; recombinase A 573522 recA 4579641 recA Paracoccus denitrificans PD1222 recombinase A YP_914405.1 572452 D 318586 CDS YP_914406.1 119383350 4579642 573749..576406 1 NC_008686.1 Catalyzes a two-step reaction, first charging an alanyl molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; alanyl-tRNA synthetase 576406 alaS 4579642 alaS Paracoccus denitrificans PD1222 alanyl-tRNA synthetase YP_914406.1 573749 D 318586 CDS YP_914407.1 119383351 4579643 576403..576693 1 NC_008686.1 PFAM: protein of unknown function DUF1330; KEGG: rsp:RSP_0450 hypothetical protein; hypothetical protein 576693 4579643 Pden_0599 Paracoccus denitrificans PD1222 hypothetical protein YP_914407.1 576403 D 318586 CDS YP_914408.1 119383352 4579644 576760..577554 1 NC_008686.1 KEGG: rsp:RSP_0449 glutamine amidotransferase; glutamine amidotransferase 577554 4579644 Pden_0600 Paracoccus denitrificans PD1222 glutamine amidotransferase YP_914408.1 576760 D 318586 CDS YP_914409.1 119383353 4579645 complement(577694..577939) 1 NC_008686.1 hypothetical protein 577939 4579645 Pden_0601 Paracoccus denitrificans PD1222 hypothetical protein YP_914409.1 577694 R 318586 CDS YP_914410.1 119383354 4579646 complement(577960..578181) 1 NC_008686.1 hypothetical protein 578181 4579646 Pden_0602 Paracoccus denitrificans PD1222 hypothetical protein YP_914410.1 577960 R 318586 CDS YP_914411.1 119383355 4579647 578569..579861 1 NC_008686.1 catalyzes the formation of N6-(1,2,-dicarboxyethyl)-AMP from L-aspartate, inosine monophosphate and GTP in AMP biosynthesis; adenylosuccinate synthetase 579861 4579647 Pden_0603 Paracoccus denitrificans PD1222 adenylosuccinate synthetase YP_914411.1 578569 D 318586 CDS YP_914412.1 119383356 4579648 579873..580085 1 NC_008686.1 KEGG: sil:SPO1317 hypothetical protein; hypothetical protein 580085 4579648 Pden_0604 Paracoccus denitrificans PD1222 hypothetical protein YP_914412.1 579873 D 318586 CDS YP_914413.1 119383357 4579649 580103..580738 1 NC_008686.1 TIGRFAM: thiamine pyrophosphokinase; PFAM: Thiamin pyrophosphokinase, catalytic region; KEGG: rde:RD1_1915 thiamine pyrophosphokinase; thiamine pyrophosphokinase 580738 4579649 Pden_0605 Paracoccus denitrificans PD1222 thiamine pyrophosphokinase YP_914413.1 580103 D 318586 CDS YP_914414.1 119383358 4579650 complement(580824..581795) 1 NC_008686.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: sil:SPO2816 peptide/nickel/opine uptake family ABC transporter, permease protein; binding-protein-dependent transport system inner membrane protein 581795 4579650 Pden_0606 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_914414.1 580824 R 318586 CDS YP_914415.1 119383359 4579651 complement(581788..582795) 1 NC_008686.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: sil:SPO2815 peptide/nickel/opine uptake family ABC transporter, permease protein; binding-protein-dependent transport system inner membrane protein 582795 4579651 Pden_0607 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_914415.1 581788 R 318586 CDS YP_914416.1 119383360 4579652 complement(582803..584503) 1 NC_008686.1 PFAM: extracellular solute-binding protein, family 5; KEGG: sil:SPO2814 peptide/opine/nickel uptake family ABC transporter, periplasmic substrate-binding protein; extracellular solute-binding protein 584503 4579652 Pden_0608 Paracoccus denitrificans PD1222 extracellular solute-binding protein YP_914416.1 582803 R 318586 CDS YP_914417.1 119383361 4579653 584724..586553 1 NC_008686.1 PFAM: ABC transporter related; Oligopeptide/dipeptide ABC transporter, C-terminal domain protein; SMART: AAA ATPase; KEGG: sil:SPO2813 peptide/nickel/opine uptake family ABC transporter, ATP-binding protein; ABC transporter 586553 4579653 Pden_0609 Paracoccus denitrificans PD1222 ABC transporter YP_914417.1 584724 D 318586 CDS YP_914418.1 119383362 4579654 586652..587821 1 NC_008686.1 KEGG: sit:TM1040_0719 peptidase M20D, amidohydrolase; TIGRFAM: amidohydrolase; PFAM: peptidase M20; peptidase dimerisation domain protein; amidohydrolase 587821 4579654 Pden_0610 Paracoccus denitrificans PD1222 amidohydrolase YP_914418.1 586652 D 318586 CDS YP_914419.1 119383363 4579655 complement(587908..589299) 1 NC_008686.1 E3 component of pyruvate complex; catalyzes the oxidation of dihydrolipoamide to lipoamide; dihydrolipoamide dehydrogenase 589299 4579655 Pden_0611 Paracoccus denitrificans PD1222 dihydrolipoamide dehydrogenase YP_914419.1 587908 R 318586 CDS YP_914420.1 119383364 4578996 complement(589345..589926) 1 NC_008686.1 PFAM: protein of unknown function DUF924; KEGG: sil:SPO2224 hypothetical protein; hypothetical protein 589926 4578996 Pden_0612 Paracoccus denitrificans PD1222 hypothetical protein YP_914420.1 589345 R 318586 CDS YP_914421.1 119383365 4578997 complement(589984..591234) 1 NC_008686.1 PFAM: major facilitator superfamily MFS_1; KEGG: rsp:RSP_2970 transporter, major facilitator superfamily (MFS); major facilitator superfamily transporter 591234 4578997 Pden_0613 Paracoccus denitrificans PD1222 major facilitator superfamily transporter YP_914421.1 589984 R 318586 CDS YP_914422.1 119383366 4578998 complement(591234..592313) 1 NC_008686.1 Synthesizes oQ from preQ1 in a single S-adenosylmethionine-requiring step; S-adenosylmethionine--tRNA ribosyltransferase-isomerase 592313 queA 4578998 queA Paracoccus denitrificans PD1222 S-adenosylmethionine--tRNA ribosyltransferase-isomerase YP_914422.1 591234 R 318586 CDS YP_914423.1 119383367 4578999 592411..592701 1 NC_008686.1 KEGG: sit:TM1040_2200 bacterioferritin-associated ferredoxin; bacterioferritin-associated ferredoxin 592701 4578999 Pden_0615 Paracoccus denitrificans PD1222 bacterioferritin-associated ferredoxin YP_914423.1 592411 D 318586 CDS YP_914424.1 119383368 4579000 592649..593134 1 NC_008686.1 TIGRFAM: bacterioferritin; PFAM: Rubrerythrin; Ferritin, Dps family protein; KEGG: rsp:RSP_3342 bacterioferritin; bacterioferritin 593134 4579000 Pden_0616 Paracoccus denitrificans PD1222 bacterioferritin YP_914424.1 592649 D 318586 CDS YP_914425.1 119383369 4579001 complement(593194..593868) 1 NC_008686.1 KEGG: rsp:RSP_2504 phosphoglycolate phosphatase; TIGRFAM: HAD-superfamily hydrolase, subfamily IA, variant 3; HAD-superfamily hydrolase, subfamily IA, variant 1; PFAM: Haloacid dehalogenase domain protein hydrolase; HAD family hydrolase 593868 4579001 Pden_0617 Paracoccus denitrificans PD1222 HAD family hydrolase YP_914425.1 593194 R 318586 CDS YP_914426.1 119383370 4579002 593973..595313 1 NC_008686.1 forms a homotrimer; catalyzes the acetylation of glucosamine-1-phosphate and uridylation of N-acetylglucosamine-1-phosphate to produce UDP-GlcNAc; function in cell wall synthesis; bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase 595313 glmU 4579002 glmU Paracoccus denitrificans PD1222 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase YP_914426.1 593973 D 318586 CDS YP_914427.1 119383371 4579003 595315..597132 1 NC_008686.1 Catalyzes the first step in hexosamine metabolism, converting fructose-6P into glucosamine-6P using glutamine as a nitrogen source; glucosamine--fructose-6-phosphate aminotransferase 597132 4579003 Pden_0619 Paracoccus denitrificans PD1222 glucosamine--fructose-6-phosphate aminotransferase YP_914427.1 595315 D 318586 CDS YP_914428.1 119383372 4579004 complement(597136..598119) 1 NC_008686.1 PFAM: peptidase S58, DmpA; KEGG: sit:TM1040_2667 peptidase S58, DmpA; peptidase S58, DmpA 598119 4579004 Pden_0620 Paracoccus denitrificans PD1222 peptidase S58, DmpA YP_914428.1 597136 R 318586 CDS YP_914429.1 119383373 4579005 598259..598843 1 NC_008686.1 KEGG: rpa:RPA4834 peptide methionine sulfoxide reductase; TIGRFAM: peptide methionine sulfoxide reductase; PFAM: Methionine sulfoxide reductase A; peptide methionine sulfoxide reductase 598843 4579005 Pden_0621 Paracoccus denitrificans PD1222 peptide methionine sulfoxide reductase YP_914429.1 598259 D 318586 CDS YP_914430.1 119383374 4579006 598844..599713 1 NC_008686.1 PFAM: methyltransferase small; ribosomal L11 methyltransferase; Methyltransferase type 11; KEGG: sit:TM1040_2376 ribosomal L11 methyltransferase; ribosomal L11 methyltransferase 599713 4579006 Pden_0622 Paracoccus denitrificans PD1222 ribosomal L11 methyltransferase YP_914430.1 598844 D 318586 CDS YP_914431.1 119383375 4579007 complement(599834..600028) 1 NC_008686.1 PFAM: protein of unknown function DUF1127; KEGG: sit:TM1040_2374 protein of unknown function DUF1127; hypothetical protein 600028 4579007 Pden_0623 Paracoccus denitrificans PD1222 hypothetical protein YP_914431.1 599834 R 318586 CDS YP_914432.1 119383376 4579008 complement(600267..600986) 1 NC_008686.1 in Escherichia coli RsmE methylates the N3 position of the U1498 base in 16S rRNA; cells lacking this function can grow, but are outcompeted by wild-type; SAM-dependent m(3)U1498 methyltransferase; 16S ribosomal RNA methyltransferase RsmE 600986 4579008 Pden_0624 Paracoccus denitrificans PD1222 16S ribosomal RNA methyltransferase RsmE YP_914432.1 600267 R 318586 CDS YP_914433.1 119383377 4579009 601003..601974 1 NC_008686.1 UbiA prenyltransferase family catalyzes the transfer of a prenyl group to various acceptors with hydrophobic ring structures in the biosynthesis of respiratory quinones, hemes, chlorophylls, vitamin E, and shikonin; 4-hydroxybenzoate polyprenyltransferase 601974 ubiA 4579009 ubiA Paracoccus denitrificans PD1222 4-hydroxybenzoate polyprenyltransferase YP_914433.1 601003 D 318586 CDS YP_914434.1 119383378 4579010 602001..604307 1 NC_008686.1 PFAM: OmpA/MotB domain protein; KEGG: rde:RD1_4081 OmpA domain protein; OmpA/MotB domain-containing protein 604307 4579010 Pden_0626 Paracoccus denitrificans PD1222 OmpA/MotB domain-containing protein YP_914434.1 602001 D 318586 CDS YP_914435.1 119383379 4579011 604338..604664 1 NC_008686.1 KEGG: rsp:RSP_1011 hypothetical protein; hypothetical protein 604664 4579011 Pden_0627 Paracoccus denitrificans PD1222 hypothetical protein YP_914435.1 604338 D 318586 CDS YP_914436.1 119383380 4579012 complement(604661..605521) 1 NC_008686.1 hypothetical protein 605521 4579012 Pden_0628 Paracoccus denitrificans PD1222 hypothetical protein YP_914436.1 604661 R 318586 CDS YP_914437.1 119383381 4579013 complement(605518..605964) 1 NC_008686.1 hypothetical protein 605964 4579013 Pden_0629 Paracoccus denitrificans PD1222 hypothetical protein YP_914437.1 605518 R 318586 CDS YP_914438.1 119383382 4579014 complement(606107..607291) 1 NC_008686.1 catalyzes the formation of L-glutamate and an aromatic oxo acid from an aromatic amino acid and 2-oxoglutarate; aromatic amino acid aminotransferase 607291 4579014 Pden_0630 Paracoccus denitrificans PD1222 aromatic amino acid aminotransferase YP_914438.1 606107 R 318586 CDS YP_914439.1 119383383 4579015 complement(607291..608151) 1 NC_008686.1 PFAM: Rhodanese domain protein; KEGG: rsp:RSP_0885 thiosulfate sulfurtransferase, rhodanese-like; 3-mercaptopyruvate sulfurtransferase 608151 4579015 Pden_0631 Paracoccus denitrificans PD1222 3-mercaptopyruvate sulfurtransferase YP_914439.1 607291 R 318586 CDS YP_914440.1 119383384 4580243 complement(608217..608687) 1 NC_008686.1 binds to ssrA RNA (tmRNA) and is required for its successful binding to ribosomes; also appears to function in the trans-translation step by promoting accommodation of tmRNA into the ribosomal A site; SmpB protects the tmRNA from RNase R degradation in Caulobacter crescentus; both the tmRNA and SmpB are regulated in cell cycle-dependent manner; functions in release of stalled ribosomes from damaged mRNAs and targeting proteins for degradation; SsrA-binding protein 608687 smpB 4580243 smpB Paracoccus denitrificans PD1222 SsrA-binding protein YP_914440.1 608217 R 318586 CDS YP_914441.1 119383385 4580244 608839..610500 1 NC_008686.1 catalyzes the formation of 2-acetolactate from pyruvate, leucine sensitive; also known as acetolactate synthase large subunit; thiamine pyrophosphate protein 610500 4580244 Pden_0633 Paracoccus denitrificans PD1222 thiamine pyrophosphate protein YP_914441.1 608839 D 318586 CDS YP_914442.1 119383386 4580245 complement(610511..611935) 1 NC_008686.1 PFAM: phosphate transporter; KEGG: rsp:RSP_2170 phosphate transporter, Pit family; phosphate transporter 611935 4580245 Pden_0634 Paracoccus denitrificans PD1222 phosphate transporter YP_914442.1 610511 R 318586 CDS YP_914443.1 119383387 4580246 complement(611932..612402) 1 NC_008686.1 PFAM: NUDIX hydrolase; KEGG: sit:TM1040_0668 NUDIX hydrolase; NUDIX hydrolase 612402 4580246 Pden_0635 Paracoccus denitrificans PD1222 NUDIX hydrolase YP_914443.1 611932 R 318586 CDS YP_914444.1 119383388 4580247 complement(612399..612830) 1 NC_008686.1 PFAM: Class I peptide chain release factor; KEGG: rsp:RSP_1366 hypothetical protein; peptidyl-tRNA hydrolase domain-containing protein 612830 4580247 Pden_0636 Paracoccus denitrificans PD1222 peptidyl-tRNA hydrolase domain-containing protein YP_914444.1 612399 R 318586 CDS YP_914445.1 119383389 4580248 complement(612897..614948) 1 NC_008686.1 TIGRFAM: penicillin-binding protein 1C; PFAM: glycosyl transferase, family 51; penicillin-binding protein, transpeptidase; Penicillin-binding domain protein; KEGG: sil:SPO0135 penicillin-binding protein 1C; penicillin-binding protein 1C 614948 4580248 Pden_0637 Paracoccus denitrificans PD1222 penicillin-binding protein 1C YP_914445.1 612897 R 318586 CDS YP_914446.1 119383390 4580249 complement(615033..616142) 1 NC_008686.1 PFAM: conserved hypothetical protein 1620; KEGG: sil:SPO3140 hypothetical protein; hypothetical protein 616142 4580249 Pden_0638 Paracoccus denitrificans PD1222 hypothetical protein YP_914446.1 615033 R 318586 CDS YP_914447.1 119383391 4580250 complement(616152..617519) 1 NC_008686.1 PFAM: protein of unknown function DUF463, YcjX family protein; KEGG: sil:SPO3142 hypothetical protein; hypothetical protein 617519 4580250 Pden_0639 Paracoccus denitrificans PD1222 hypothetical protein YP_914447.1 616152 R 318586 CDS YP_914448.1 119383392 4580251 617618..620026 1 NC_008686.1 KEGG: rsp:RSP_2013 DEAD/DEAH box helicase; TIGRFAM: ATP-dependent helicase HrpB; PFAM: helicase domain protein; helicase-associated domain protein; DEAD/DEAH box helicase domain protein; Helicase ATP-dependent, C-terminal domain protein; SMART: DEAD-like helicases-like; ATP-dependent helicase HrpB 620026 4580251 Pden_0640 Paracoccus denitrificans PD1222 ATP-dependent helicase HrpB YP_914448.1 617618 D 318586 CDS YP_914449.1 119383393 4580252 complement(620066..620614) 1 NC_008686.1 KEGG: bpe:BP1216 hypothetical protein; hypothetical protein 620614 4580252 Pden_0641 Paracoccus denitrificans PD1222 hypothetical protein YP_914449.1 620066 R 318586 CDS YP_914450.1 119383394 4580253 complement(620768..621661) 1 NC_008686.1 TIGRFAM: methionyl-tRNA formyltransferase; PFAM: formyl transferase domain protein; KEGG: rsp:RSP_0875 methionyl-tRNA formyl transferase; methionyl-tRNA formyltransferase 621661 4580253 Pden_0642 Paracoccus denitrificans PD1222 methionyl-tRNA formyltransferase YP_914450.1 620768 R 318586 CDS YP_914451.1 119383395 4580254 complement(621688..622566) 1 NC_008686.1 KEGG: mmr:Mmar10_2929 dienelactone hydrolase; dienelactone hydrolase 622566 4580254 Pden_0643 Paracoccus denitrificans PD1222 dienelactone hydrolase YP_914451.1 621688 R 318586 CDS YP_914452.1 119383396 4580255 complement(622551..624188) 1 NC_008686.1 KEGG: sit:TM1040_1832 conserved hypothetical protein; hypothetical protein 624188 4580255 Pden_0644 Paracoccus denitrificans PD1222 hypothetical protein YP_914452.1 622551 R 318586 CDS YP_914453.1 119383397 4580256 complement(624493..624993) 1 NC_008686.1 TIGRFAM: peptide deformylase; PFAM: formylmethionine deformylase; KEGG: rsp:RSP_0874 formylmethionine deformylase; peptide deformylase 624993 4580256 Pden_0645 Paracoccus denitrificans PD1222 peptide deformylase YP_914453.1 624493 R 318586 CDS YP_914454.1 119383398 4580257 complement(625277..625834) 1 NC_008686.1 PFAM: formylmethionine deformylase; KEGG: rsp:RSP_0872 formylmethionine deformylase; peptide deformylase 625834 4580257 Pden_0646 Paracoccus denitrificans PD1222 peptide deformylase YP_914454.1 625277 R 318586 CDS YP_914455.1 119383399 4580258 complement(625827..626348) 1 NC_008686.1 KEGG: rsp:RSP_0872 formylmethionine deformylase; TIGRFAM: peptide deformylase; PFAM: formylmethionine deformylase; peptide deformylase 626348 4580258 Pden_0647 Paracoccus denitrificans PD1222 peptide deformylase YP_914455.1 625827 R 318586 CDS YP_914456.1 119383400 4580259 626439..627623 1 NC_008686.1 PFAM: aminotransferase, class I and II; KEGG: rsp:RSP_0871 aminotransferase; class I and II aminotransferase 627623 4580259 Pden_0648 Paracoccus denitrificans PD1222 class I and II aminotransferase YP_914456.1 626439 D 318586 CDS YP_914457.1 119383401 4580260 627620..628249 1 NC_008686.1 PFAM: ErfK/YbiS/YcfS/YnhG family protein; KEGG: sat:SYN_02183 protein ErfK; ErfK/YbiS/YcfS/YnhG family protein 628249 4580260 Pden_0649 Paracoccus denitrificans PD1222 ErfK/YbiS/YcfS/YnhG family protein YP_914457.1 627620 D 318586 CDS YP_914458.1 119383402 4580261 628306..629682 1 NC_008686.1 TIGRFAM: MATE efflux family protein; PFAM: multi antimicrobial extrusion protein MatE; KEGG: rsp:RSP_0764 multi antimicrobial extrusion (MATE) family efflux pump NorM; MATE efflux family protein 629682 4580261 Pden_0650 Paracoccus denitrificans PD1222 MATE efflux family protein YP_914458.1 628306 D 318586 CDS YP_914459.1 119383403 4578956 629713..629949 1 NC_008686.1 PFAM: regulatory protein, AsnC/Lrp family; KEGG: rsp:RSP_0958 RAM domain protein; AsnC family transcriptional regulator 629949 4578956 Pden_0651 Paracoccus denitrificans PD1222 AsnC family transcriptional regulator YP_914459.1 629713 D 318586 CDS YP_914460.1 119383404 4578957 629991..631136 1 NC_008686.1 catalyzes the formation of histidinol phosphate and 2-oxoglutarate from glutamate and imidazole acetol-phosphate; histidinol-phosphate aminotransferase 631136 4578957 Pden_0652 Paracoccus denitrificans PD1222 histidinol-phosphate aminotransferase YP_914460.1 629991 D 318586 CDS YP_914461.1 119383405 4578958 complement(631186..631668) 1 NC_008686.1 PFAM: regulatory protein, AsnC/Lrp family; KEGG: rde:RD1_2963 glutamate uptake regulatory protein; AsnC family transcriptional regulator 631668 4578958 Pden_0653 Paracoccus denitrificans PD1222 AsnC family transcriptional regulator YP_914461.1 631186 R 318586 CDS YP_914462.1 119383406 4578959 631740..632120 1 NC_008686.1 KEGG: rsp:RSP_1943 hypothetical protein; hypothetical protein 632120 4578959 Pden_0654 Paracoccus denitrificans PD1222 hypothetical protein YP_914462.1 631740 D 318586 CDS YP_914463.1 119383407 4578960 632113..633768 1 NC_008686.1 PFAM: nitrite/sulfite reductase, hemoprotein beta-component, ferrodoxin domain protein; nitrite and sulphite reductase 4Fe-4S region; KEGG: rsp:RSP_1942 sulfite/nitrite reductase hemoprotein subunit; nitrite/sulfite reductase hemoprotein beta subunit 633768 4578960 Pden_0655 Paracoccus denitrificans PD1222 nitrite/sulfite reductase hemoprotein beta subunit YP_914463.1 632113 D 318586 CDS YP_914464.1 119383408 4578961 633761..634492 1 NC_008686.1 catalyzes the reduction of 3'-phosphoadenylyl sulfate into sulfite; phosphoadenosine phosphosulfate reductase 634492 4578961 Pden_0656 Paracoccus denitrificans PD1222 phosphoadenosine phosphosulfate reductase YP_914464.1 633761 D 318586 CDS YP_914465.1 119383409 4578962 634489..634860 1 NC_008686.1 KEGG: rsp:RSP_1940 hypothetical protein; hypothetical protein 634860 4578962 Pden_0657 Paracoccus denitrificans PD1222 hypothetical protein YP_914465.1 634489 D 318586 CDS YP_914466.1 119383410 4578963 634914..635750 1 NC_008686.1 PFAM: oxidoreductase FAD/NAD(P)-binding domain protein; Oxidoreductase FAD-binding domain protein; KEGG: rsp:RSP_1939 NADPH-ferredoxin reductase; ferredoxin-NADP reductase 635750 4578963 Pden_0658 Paracoccus denitrificans PD1222 ferredoxin-NADP reductase YP_914466.1 634914 D 318586 CDS YP_914467.1 119383411 4578964 635875..638430 1 NC_008686.1 catalyzes the ATP-dependent breakage of single-stranded DNA followed by passage and rejoining, maintains net negative superhelicity; DNA topoisomerase I 638430 4578964 Pden_0659 Paracoccus denitrificans PD1222 DNA topoisomerase I YP_914467.1 635875 D 318586 CDS YP_914468.1 119383412 4578965 638639..640381 1 NC_008686.1 KEGG: rru:Rru_A0385 gamma-glutamyltransferase; TIGRFAM: gamma-glutamyltransferase; PFAM: gamma-glutamyltranspeptidase; gamma-glutamyltransferase 640381 4578965 Pden_0660 Paracoccus denitrificans PD1222 gamma-glutamyltransferase YP_914468.1 638639 D 318586 CDS YP_914469.1 119383413 4578966 complement(640375..640722) 1 NC_008686.1 PFAM: protein of unknown function DUF488; KEGG: rfr:Rfer_4130 protein of unknown function DUF488; hypothetical protein 640722 4578966 Pden_0661 Paracoccus denitrificans PD1222 hypothetical protein YP_914469.1 640375 R 318586 CDS YP_914470.1 119383414 4578967 complement(641089..642597) 1 NC_008686.1 TIGRFAM: amino acid carrier protein; PFAM: sodium:alanine symporter; KEGG: sme:SMc04263 amino acid carrier transmembrane protein; amino acid carrier protein 642597 4578967 Pden_0662 Paracoccus denitrificans PD1222 amino acid carrier protein YP_914470.1 641089 R 318586 CDS YP_914471.1 119383415 4578968 complement(642700..644766) 1 NC_008686.1 TIGRFAM: TRAP transporter, 4TM/12TM fusion protein; PFAM: TRAP C4-dicarboxylate transport system permease DctM subunit; KEGG: bmb:BruAb1_1197 hypothetical membrane protein; TRAP transporter, 4TM/12TM fusion protein 644766 4578968 Pden_0663 Paracoccus denitrificans PD1222 TRAP transporter, 4TM/12TM fusion protein YP_914471.1 642700 R 318586 CDS YP_914472.1 119383416 4578969 complement(644849..645850) 1 NC_008686.1 TIGRFAM: TRAP transporter solute receptor, TAXI family; KEGG: bmb:BruAb1_1199 outer membrane protein, hypothetical; TRAP transporter solute receptor TAXI family protein 645850 4578969 Pden_0664 Paracoccus denitrificans PD1222 TRAP transporter solute receptor TAXI family protein YP_914472.1 644849 R 318586 CDS YP_914473.1 119383417 4578970 646155..647639 1 NC_008686.1 PFAM: phosphate transporter; KEGG: sit:TM1040_0608 phosphate transporter; phosphate transporter 647639 4578970 Pden_0665 Paracoccus denitrificans PD1222 phosphate transporter YP_914473.1 646155 D 318586 CDS YP_914474.1 119383418 4578971 647851..649314 1 NC_008686.1 TIGRFAM: amino acid carrier protein; PFAM: sodium:alanine symporter; KEGG: cjk:jk0467 Na+/alanine symporter; amino acid carrier protein 649314 4578971 Pden_0666 Paracoccus denitrificans PD1222 amino acid carrier protein YP_914474.1 647851 D 318586 CDS YP_914475.1 119383419 4578972 complement(649453..650526) 1 NC_008686.1 hypothetical protein 650526 4578972 Pden_0667 Paracoccus denitrificans PD1222 hypothetical protein YP_914475.1 649453 R 318586 CDS YP_914476.1 119383420 4578973 complement(650523..651113) 1 NC_008686.1 PFAM: regulatory protein, TetR; KEGG: sit:TM1040_1583 transcriptional regulator, TetR family; TetR family transcriptional regulator 651113 4578973 Pden_0668 Paracoccus denitrificans PD1222 TetR family transcriptional regulator YP_914476.1 650523 R 318586 CDS YP_914477.1 119383421 4578974 651205..652191 1 NC_008686.1 PFAM: 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal domain protein; 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III; KEGG: pfl:PFL_6132 3-oxoacyl-(acyl-carrier-protein) synthase III; 3-oxoacyl-ACP synthase 652191 4578974 Pden_0669 Paracoccus denitrificans PD1222 3-oxoacyl-ACP synthase YP_914477.1 651205 D 318586 CDS YP_914478.1 119383422 4578975 652191..653123 1 NC_008686.1 PFAM: NAD-dependent epimerase/dehydratase; 3-beta hydroxysteroid dehydrogenase/isomerase; polysaccharide biosynthesis protein CapD; dTDP-4-dehydrorhamnose reductase; NmrA family protein; Male sterility C-terminal domain; KEGG: pfl:PFL_6133 3-beta hydroxysteroid dehydrogenase/isomerase family protein; NAD-dependent epimerase/dehydratase 653123 4578975 Pden_0670 Paracoccus denitrificans PD1222 NAD-dependent epimerase/dehydratase YP_914478.1 652191 D 318586 CDS YP_914479.1 119383423 4578741 653111..653893 1 NC_008686.1 PFAM: beta-lactamase domain protein; KEGG: pfl:PFL_6134 metallo-beta-lactamase protein; beta-lactamase domain-containing protein 653893 4578741 Pden_0671 Paracoccus denitrificans PD1222 beta-lactamase domain-containing protein YP_914479.1 653111 D 318586 CDS YP_914480.1 119383424 4578742 653890..655170 1 NC_008686.1 TIGRFAM: adenylate-forming enzyme; KEGG: pfl:PFL_6135 PF5220; adenylate-forming enzyme 655170 4578742 Pden_0672 Paracoccus denitrificans PD1222 adenylate-forming enzyme YP_914480.1 653890 D 318586 CDS YP_914481.1 119383425 4578743 complement(655286..656311) 1 NC_008686.1 PFAM: regulatory protein, LacI; periplasmic binding protein/LacI transcriptional regulator; KEGG: sme:SMb20290 transcriptional regulator protein; regulatory protein, LacI 656311 4578743 Pden_0673 Paracoccus denitrificans PD1222 regulatory protein, LacI YP_914481.1 655286 R 318586 CDS YP_914482.1 119383426 4578744 656409..657740 1 NC_008686.1 PFAM: Benzoate membrane transport protein; Xanthine/uracil/vitamin C permease; KEGG: sme:SMb20289 permease protein; xanthine/uracil/vitamin C permease 657740 4578744 Pden_0674 Paracoccus denitrificans PD1222 xanthine/uracil/vitamin C permease YP_914482.1 656409 D 318586 CDS YP_914483.1 119383427 4578745 657740..659137 1 NC_008686.1 PFAM: amidohydrolase; Amidohydrolase 3; KEGG: sme:SMb20288 hypothetical protein; amidohydrolase 659137 4578745 Pden_0675 Paracoccus denitrificans PD1222 amidohydrolase YP_914483.1 657740 D 318586 CDS YP_914484.1 119383428 4578746 659134..659844 1 NC_008686.1 PFAM: protein of unknown function DUF81; KEGG: sme:SMb20287 hypothetical protein; hypothetical protein 659844 4578746 Pden_0676 Paracoccus denitrificans PD1222 hypothetical protein YP_914484.1 659134 D 318586 CDS YP_914485.1 119383429 4578747 complement(659972..660733) 1 NC_008686.1 KEGG: sme:SMc04361 hydantoin racemase protein; hydantoin racemase protein 660733 4578747 Pden_0677 Paracoccus denitrificans PD1222 hydantoin racemase protein YP_914485.1 659972 R 318586 CDS YP_914486.1 119383430 4578748 complement(660737..662089) 1 NC_008686.1 PFAM: permease for cytosine/purines, uracil, thiamine, allantoin; KEGG: pcr:Pcryo_0405 permease for cytosine/purines, uracil, thiamine, allantoin; cytosine/purines uracil thiamine allantoin permease 662089 4578748 Pden_0678 Paracoccus denitrificans PD1222 cytosine/purines uracil thiamine allantoin permease YP_914486.1 660737 R 318586 CDS YP_914487.1 119383431 4578749 complement(662118..662828) 1 NC_008686.1 PFAM: Asp/Glu racemase; KEGG: pcr:Pcryo_0404 Asp/Glu racemase; Asp/Glu racemase 662828 4578749 Pden_0679 Paracoccus denitrificans PD1222 Asp/Glu racemase YP_914487.1 662118 R 318586 CDS YP_914488.1 119383432 4578750 662953..663633 1 NC_008686.1 PFAM: regulatory protein GntR, HTH; GntR domain protein; KEGG: pcr:Pcryo_0403 transcriptional regulator, GntR family; GntR family transcriptional regulator 663633 4578750 Pden_0680 Paracoccus denitrificans PD1222 GntR family transcriptional regulator YP_914488.1 662953 D 318586 CDS YP_914489.1 119383433 4578751 663687..664271 1 NC_008686.1 KEGG: rsp:RSP_6118 hypothetical protein; hypothetical protein 664271 4578751 Pden_0681 Paracoccus denitrificans PD1222 hypothetical protein YP_914489.1 663687 D 318586 CDS YP_914490.1 119383434 4578752 664351..664755 1 NC_008686.1 TIGRFAM: 4-hydroxybenzoyl-CoA thioesterase; PFAM: thioesterase superfamily protein; KEGG: rsp:RSP_0673 thioesterase; 4-hydroxybenzoyl-CoA thioesterase 664755 4578752 Pden_0682 Paracoccus denitrificans PD1222 4-hydroxybenzoyl-CoA thioesterase YP_914490.1 664351 D 318586 CDS YP_914491.1 119383435 4578753 664857..665552 1 NC_008686.1 PFAM: MotA/TolQ/ExbB proton channel; KEGG: sil:SPO3112 proton transporter TolQ; MotA/TolQ/ExbB proton channel 665552 4578753 Pden_0683 Paracoccus denitrificans PD1222 MotA/TolQ/ExbB proton channel YP_914491.1 664857 D 318586 CDS YP_914492.1 119383436 4578754 665554..666018 1 NC_008686.1 PFAM: Biopolymer transport protein ExbD/TolR; KEGG: sil:SPO3111 biopolymer transport protein, ExbD/TolR family; biopolymer transport protein ExbD/TolR 666018 4578754 Pden_0684 Paracoccus denitrificans PD1222 biopolymer transport protein ExbD/TolR YP_914492.1 665554 D 318586 CDS YP_914493.1 119383437 4578755 666022..667566 1 NC_008686.1 PFAM: TolA family protein; KEGG: rsp:RSP_0670 possible TolA protein; TolA family protein 667566 4578755 Pden_0685 Paracoccus denitrificans PD1222 TolA family protein YP_914493.1 666022 D 318586 CDS YP_914494.1 119383438 4578756 667568..668953 1 NC_008686.1 forms dimers; may be involved in cell envelope integrity; interacts with outer membrane proteins and with the C-terminal domain of inner membrane protein TolA; translocation protein TolB 668953 tolB 4578756 tolB Paracoccus denitrificans PD1222 translocation protein TolB YP_914494.1 667568 D 318586 CDS YP_914495.1 119383439 4578757 668964..669485 1 NC_008686.1 TIGRFAM: OmpA domain protein; PFAM: OmpA/MotB domain protein; KEGG: jan:Jann_0976 OmpA/MotB; OmpA domain-containing protein 669485 4578757 Pden_0687 Paracoccus denitrificans PD1222 OmpA domain-containing protein YP_914495.1 668964 D 318586 CDS YP_914496.1 119383440 4578758 669482..670411 1 NC_008686.1 KEGG: rsp:RSP_0667 hypothetical protein; hypothetical protein 670411 4578758 Pden_0688 Paracoccus denitrificans PD1222 hypothetical protein YP_914496.1 669482 D 318586 CDS YP_914497.1 119383441 4578759 670401..671630 1 NC_008686.1 TIGRFAM: tRNA(Ile)-lysidine synthetase; PFAM: PP-loop domain protein; KEGG: rsp:RSP_0666 probable cell cycle protein; tRNA(Ile)-lysidine synthetase 671630 4578759 Pden_0689 Paracoccus denitrificans PD1222 tRNA(Ile)-lysidine synthetase YP_914497.1 670401 D 318586 CDS YP_914498.1 119383442 4580631 671691..673586 1 NC_008686.1 KEGG: rsp:RSP_0665 FtsH; TIGRFAM: ATP-dependent metalloprotease FtsH; PFAM: peptidase M41; AAA ATPase, central domain protein; peptidase M41, FtsH extracellular; ATPase associated with various cellular activities, AAA_5; SMART: AAA ATPase; ATP-dependent metalloprotease FtsH 673586 4580631 Pden_0690 Paracoccus denitrificans PD1222 ATP-dependent metalloprotease FtsH YP_914498.1 671691 D 318586 CDS YP_914499.1 119383443 4580632 673915..674232 1 NC_008686.1 PFAM: Chorismate mutase; KEGG: rsp:RSP_0662 chorismate mutase; chorismate mutase 674232 4580632 Pden_0691 Paracoccus denitrificans PD1222 chorismate mutase YP_914499.1 673915 D 318586 CDS YP_914500.1 119383444 4580633 complement(674269..674679) 1 NC_008686.1 TIGRFAM: uncharacterized domain 1; PFAM: thioesterase superfamily protein; KEGG: rde:RD1_2106 hypothetical protein; hypothetical protein 674679 4580633 Pden_0692 Paracoccus denitrificans PD1222 hypothetical protein YP_914500.1 674269 R 318586 CDS YP_914501.1 119383445 4580634 complement(674672..675697) 1 NC_008686.1 promotes strand exchange during homologous recombination; RuvAB complex promotes branch migration; RuvABC complex scans the DNA during branch migration and resolves Holliday junctions at consensus sequences; forms hexameric rings around opposite DNA arms; requires ATP for branch migration and orientation of RuvAB complex determines direction of migration; Holliday junction DNA helicase RuvB 675697 ruvB 4580634 ruvB Paracoccus denitrificans PD1222 Holliday junction DNA helicase RuvB YP_914501.1 674672 R 318586 CDS YP_914502.1 119383446 4580635 complement(675694..676572) 1 NC_008686.1 PFAM: peptidase M48, Ste24p; KEGG: rsp:RSP_0554 heat shock protein HtpX; peptidase M48, Ste24p 676572 4580635 Pden_0694 Paracoccus denitrificans PD1222 peptidase M48, Ste24p YP_914502.1 675694 R 318586 CDS YP_914503.1 119383447 4580636 complement(676578..677249) 1 NC_008686.1 plays an essential role in ATP-dependent branch migration of the Holliday junction; Holliday junction DNA helicase RuvA 677249 ruvA 4580636 ruvA Paracoccus denitrificans PD1222 Holliday junction DNA helicase RuvA YP_914503.1 676578 R 318586 CDS YP_914504.1 119383448 4580637 complement(677260..677754) 1 NC_008686.1 TIGRFAM: crossover junction endodeoxyribonuclease RuvC; PFAM: Crossover junction endodeoxyribonuclease RuvC; KEGG: rsp:RSP_0556 Holliday junction resolvase; crossover junction endodeoxyribonuclease RuvC 677754 4580637 Pden_0696 Paracoccus denitrificans PD1222 crossover junction endodeoxyribonuclease RuvC YP_914504.1 677260 R 318586 CDS YP_914505.1 119383449 4580638 677879..680719 1 NC_008686.1 subunit A of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; in S. meliloti it is known to be involved with K+; monovalent cation/H+ antiporter subunit A 680719 4580638 Pden_0697 Paracoccus denitrificans PD1222 monovalent cation/H+ antiporter subunit A YP_914505.1 677879 D 318586 CDS YP_914506.1 119383450 4580639 680719..681072 1 NC_008686.1 subunit C of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; monovalent cation/H+ antiporter subunit C 681072 4580639 Pden_0698 Paracoccus denitrificans PD1222 monovalent cation/H+ antiporter subunit C YP_914506.1 680719 D 318586 CDS YP_914507.1 119383451 4580640 681069..682661 1 NC_008686.1 subunit D of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; contains an oxidoreductase domain; catalyzes the transfer of electrons from NADH to ubiquinone; monovalent cation/H+ antiporter subunit D 682661 4580640 Pden_0699 Paracoccus denitrificans PD1222 monovalent cation/H+ antiporter subunit D YP_914507.1 681069 D 318586 CDS YP_914508.1 119383452 4580641 682658..683149 1 NC_008686.1 subunit E of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; in S. meliloti it is known to be involved specifically with K+ transport; monovalent cation/H+ antiporter subunit E 683149 4580641 Pden_0700 Paracoccus denitrificans PD1222 monovalent cation/H+ antiporter subunit E YP_914508.1 682658 D 318586 CDS YP_914509.1 119383453 4580642 683146..683415 1 NC_008686.1 PFAM: multiple resistance and pH regulation protein F; KEGG: jan:Jann_3719 multiple resistance and pH regulation protein F; multiple resistance and pH regulation protein F 683415 4580642 Pden_0701 Paracoccus denitrificans PD1222 multiple resistance and pH regulation protein F YP_914509.1 683146 D 318586 CDS YP_914510.1 119383454 4580643 683425..683808 1 NC_008686.1 TIGRFAM: monovalent cation/proton antiporter, MnhG/PhaG subunit; PFAM: Na+/H+ antiporter subunit; KEGG: jan:Jann_3720 Na+/H+ antiporter subunit; monovalent cation/proton antiporter subunit MnhG/PhaG 683808 4580643 Pden_0702 Paracoccus denitrificans PD1222 monovalent cation/proton antiporter subunit MnhG/PhaG YP_914510.1 683425 D 318586 CDS YP_914511.1 119383455 4580644 683815..684087 1 NC_008686.1 hypothetical protein 684087 4580644 Pden_0703 Paracoccus denitrificans PD1222 hypothetical protein YP_914511.1 683815 D 318586 CDS YP_914512.1 119383456 4580645 complement(684138..685013) 1 NC_008686.1 catalyzes the formation of dihydrodipicolinate from L-aspartate 4-semialdehyde and pyruvate in lysine and diaminopimelate biosynthesis; dihydrodipicolinate synthase 685013 4580645 Pden_0704 Paracoccus denitrificans PD1222 dihydrodipicolinate synthase YP_914512.1 684138 R 318586 CDS YP_914513.1 119383457 4580646 685120..687270 1 NC_008686.1 PFAM: Lytic transglycosylase, catalytic; KEGG: rsp:RSP_0881 soluble lytic transglycosylase; lytic transglycosylase, catalytic 687270 4580646 Pden_0705 Paracoccus denitrificans PD1222 lytic transglycosylase, catalytic YP_914513.1 685120 D 318586 CDS YP_914514.1 119383458 4580647 complement(687224..688183) 1 NC_008686.1 PFAM: protein of unknown function DUF6, transmembrane; KEGG: jan:Jann_0141 protein of unknown function DUF6, transmembrane; hypothetical protein 688183 4580647 Pden_0706 Paracoccus denitrificans PD1222 hypothetical protein YP_914514.1 687224 R 318586 CDS YP_914515.1 119383459 4580648 complement(688246..689034) 1 NC_008686.1 PFAM: inositol monophosphatase; KEGG: rsp:RSP_2169 inositol monophosphatase family protein; inositol monophosphatase 689034 4580648 Pden_0707 Paracoccus denitrificans PD1222 inositol monophosphatase YP_914515.1 688246 R 318586 CDS YP_914516.1 119383460 4580649 complement(689103..689804) 1 NC_008686.1 PFAM: regulatory protein GntR, HTH; UbiC transcription regulator-associated domain protein; KEGG: sil:SPO1369 transcriptional regulator, GntR family; UbiC transcription regulator-associated domain-containing protein 689804 4580649 Pden_0708 Paracoccus denitrificans PD1222 UbiC transcription regulator-associated domain-containing protein YP_914516.1 689103 R 318586 CDS YP_914517.1 119383461 4580650 complement(689801..691162) 1 NC_008686.1 catalyzes the deimination of N-formimino-L-glutamate to ammonia and N-formyl-L-glutamate; N-formimino-L-glutamate deiminase 691162 4580650 Pden_0709 Paracoccus denitrificans PD1222 N-formimino-L-glutamate deiminase YP_914517.1 689801 R 318586 CDS YP_914518.1 119383462 4579519 691259..692461 1 NC_008686.1 catalyzing the hydrolysis of 4-imidazolone-5-propionate to N-formimidoyl-L-glutamate, the third step in the histidine degradation pathway; imidazolonepropionase 692461 4579519 Pden_0710 Paracoccus denitrificans PD1222 imidazolonepropionase YP_914518.1 691259 D 318586 CDS YP_914519.1 119383463 4579520 692454..693995 1 NC_008686.1 catalyzes the degradation of histidine to urocanate and ammmonia; histidine ammonia-lyase 693995 4579520 Pden_0711 Paracoccus denitrificans PD1222 histidine ammonia-lyase YP_914519.1 692454 D 318586 CDS YP_914520.1 119383464 4579521 693992..694783 1 NC_008686.1 PFAM: N-formylglutamate amidohydrolase; KEGG: bme:BMEII0366 formiminoglutamase; N-formylglutamate amidohydrolase 694783 4579521 Pden_0712 Paracoccus denitrificans PD1222 N-formylglutamate amidohydrolase YP_914520.1 693992 D 318586 CDS YP_914521.1 119383465 4579522 694780..695928 1 NC_008686.1 PFAM: L-carnitine dehydratase/bile acid-inducible protein F; KEGG: rde:RD1_3680 CaiB/BaiF family protein; L-carnitine dehydratase/bile acid-inducible protein F 695928 4579522 Pden_0713 Paracoccus denitrificans PD1222 L-carnitine dehydratase/bile acid-inducible protein F YP_914521.1 694780 D 318586 CDS YP_914522.1 119383466 4579523 695925..697079 1 NC_008686.1 PFAM: acyl-CoA dehydrogenase domain protein; Acyl-CoA dehydrogenase, type 2, C-terminal domain; KEGG: rde:RD1_3681 acyl-CoA dehydrogenase; butyryl-CoA dehydrogenase 697079 4579523 Pden_0714 Paracoccus denitrificans PD1222 butyryl-CoA dehydrogenase YP_914522.1 695925 D 318586 CDS YP_914523.1 119383467 4579524 697092..698756 1 NC_008686.1 catalyzes the formation of 4-imidazolone-5-propanoate from urocanate during histidine metabolism; urocanate hydratase 698756 4579524 Pden_0715 Paracoccus denitrificans PD1222 urocanate hydratase YP_914523.1 697092 D 318586 CDS YP_914524.1 119383468 4579525 698821..699639 1 NC_008686.1 PFAM: extracellular solute-binding protein, family 3; SMART: ionotropic glutamate receptor; KEGG: rru:Rru_A1295 extracellular solute-binding protein, family 3; extracellular solute-binding protein 699639 4579525 Pden_0716 Paracoccus denitrificans PD1222 extracellular solute-binding protein YP_914524.1 698821 D 318586 CDS YP_914525.1 119383469 4579526 699697..700344 1 NC_008686.1 TIGRFAM: polar amino acid ABC transporter, inner membrane subunit; PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: rru:Rru_A1296 amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine; polar amino acid ABC transporter inner membrane subunit 700344 4579526 Pden_0717 Paracoccus denitrificans PD1222 polar amino acid ABC transporter inner membrane subunit YP_914525.1 699697 D 318586 CDS YP_914526.1 119383470 4579527 700344..701006 1 NC_008686.1 TIGRFAM: polar amino acid ABC transporter, inner membrane subunit; PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: rru:Rru_A1297 amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine; polar amino acid ABC transporter inner membrane subunit 701006 4579527 Pden_0718 Paracoccus denitrificans PD1222 polar amino acid ABC transporter inner membrane subunit YP_914526.1 700344 D 318586 CDS YP_914527.1 119383471 4579528 701011..701781 1 NC_008686.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rru:Rru_A1298 ABC transporter component; ABC transporter 701781 4579528 Pden_0719 Paracoccus denitrificans PD1222 ABC transporter YP_914527.1 701011 D 318586 CDS YP_914528.1 119383472 4579529 701997..703100 1 NC_008686.1 PFAM: NADH:flavin oxidoreductase/NADH oxidase; KEGG: mes:Meso_1173 NADH:flavin oxidoreductase/NADH oxidase; NADH:flavin oxidoreductase 703100 4579529 Pden_0720 Paracoccus denitrificans PD1222 NADH:flavin oxidoreductase YP_914528.1 701997 D 318586 CDS YP_914529.1 119383473 4579530 complement(703138..704292) 1 NC_008686.1 PFAM: Patatin; KEGG: rpa:RPA4207 patatin-like phospholipase domain; patatin 704292 4579530 Pden_0721 Paracoccus denitrificans PD1222 patatin YP_914529.1 703138 R 318586 CDS YP_914530.1 119383474 4579531 complement(704289..704567) 1 NC_008686.1 hypothetical protein 704567 4579531 Pden_0722 Paracoccus denitrificans PD1222 hypothetical protein YP_914530.1 704289 R 318586 CDS YP_914531.1 119383475 4579532 704594..705871 1 NC_008686.1 PFAM: CBS domain containing protein; protein of unknown function DUF21; transporter-associated region; KEGG: atc:AGR_L_2203 TlyC; hemolysin; hypothetical protein 705871 4579532 Pden_0723 Paracoccus denitrificans PD1222 hypothetical protein YP_914531.1 704594 D 318586 CDS YP_914532.1 119383476 4579533 705953..706936 1 NC_008686.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: mlo:mll6938 transcriptional regulator; LysR family transcriptional regulator 706936 4579533 Pden_0724 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_914532.1 705953 D 318586 CDS YP_914533.1 119383477 4579534 complement(706917..707765) 1 NC_008686.1 TIGRFAM: TonB family protein; KEGG: rpb:RPB_1657 TonB-like protein; TonB family protein 707765 4579534 Pden_0725 Paracoccus denitrificans PD1222 TonB family protein YP_914533.1 706917 R 318586 CDS YP_914534.1 119383478 4579535 complement(707762..708325) 1 NC_008686.1 PFAM: Biopolymer transport protein ExbD/TolR; KEGG: atc:AGR_C_265 biopolymer transport ExbD protein; biopolymer transport protein ExbD/TolR 708325 4579535 Pden_0726 Paracoccus denitrificans PD1222 biopolymer transport protein ExbD/TolR YP_914534.1 707762 R 318586 CDS YP_914535.1 119383479 4579536 complement(708329..709624) 1 NC_008686.1 PFAM: MotA/TolQ/ExbB proton channel; KEGG: atc:AGR_C_264 biopolymer transport ExbB protein; MotA/TolQ/ExbB proton channel 709624 4579536 Pden_0727 Paracoccus denitrificans PD1222 MotA/TolQ/ExbB proton channel YP_914535.1 708329 R 318586 CDS YP_914536.1 119383480 4579537 complement(709715..710752) 1 NC_008686.1 PFAM: Siderophore-interacting protein; FAD-binding 9, siderophore-interacting domain protein; KEGG: rsp:RSP_3678 siderophore-interacting protein; FAD-binding 9, siderophore-interacting domain-containing protein 710752 4579537 Pden_0728 Paracoccus denitrificans PD1222 FAD-binding 9, siderophore-interacting domain-containing protein YP_914536.1 709715 R 318586 CDS YP_914537.1 119383481 4579597 complement(710813..711985) 1 NC_008686.1 PFAM: aminotransferase, class V; KEGG: rsp:RSP_0245 serine-pyruvate aminotransferase/aspartate aminotransferase; class V aminotransferase 711985 4579597 Pden_0729 Paracoccus denitrificans PD1222 class V aminotransferase YP_914537.1 710813 R 318586 CDS YP_914538.1 119383482 4579598 712246..713985 1 NC_008686.1 PFAM: ABC transporter, transmembrane region; ABC transporter related; SMART: AAA ATPase; KEGG: rsp:RSP_0246 ABC lipid efflux transporter, fused ATPase and inner membrane subunits; ABC transporter 713985 4579598 Pden_0730 Paracoccus denitrificans PD1222 ABC transporter YP_914538.1 712246 D 318586 CDS YP_914539.1 119383483 4579599 713985..714701 1 NC_008686.1 PFAM: glycine cleavage T protein (aminomethyl transferase); KEGG: sit:TM1040_1985 glycine cleavage T protein (aminomethyl transferase); glycine cleavage T protein (aminomethyl transferase) 714701 4579599 Pden_0731 Paracoccus denitrificans PD1222 glycine cleavage T protein (aminomethyl transferase) YP_914539.1 713985 D 318586 CDS YP_914540.1 119383484 4579600 714698..715789 1 NC_008686.1 PFAM: UMUC domain protein DNA-repair protein; KEGG: sme:SMa2355 DNA polymerase IV; DNA-directed DNA polymerase 715789 4579600 Pden_0732 Paracoccus denitrificans PD1222 DNA-directed DNA polymerase YP_914540.1 714698 D 318586 CDS YP_914541.1 119383485 4579601 complement(715780..716727) 1 NC_008686.1 KEGG: jan:Jann_1800 hypothetical protein; hypothetical protein 716727 4579601 Pden_0733 Paracoccus denitrificans PD1222 hypothetical protein YP_914541.1 715780 R 318586 CDS YP_914542.1 119383486 4579602 716936..718111 1 NC_008686.1 EF-Tu; promotes GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis; when the tRNA anticodon matches the mRNA codon, GTP hydrolysis results; the inactive EF-Tu-GDP leaves the ribosome and release of GDP is promoted by elongation factor Ts; many prokaryotes have two copies of the gene encoding EF-Tu; elongation factor Tu 718111 4579602 Pden_0734 Paracoccus denitrificans PD1222 elongation factor Tu YP_914542.1 716936 D 318586 CDS YP_914543.1 119383487 4579603 718358..719248 1 NC_008686.1 PFAM: dienelactone hydrolase; KEGG: mmr:Mmar10_2526 carboxymethylenebutenolidase; carboxymethylenebutenolidase 719248 4579603 Pden_0735 Paracoccus denitrificans PD1222 carboxymethylenebutenolidase YP_914543.1 718358 D 318586 CDS YP_914544.1 119383488 4579604 719300..719692 1 NC_008686.1 PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase; KEGG: bja:blr0519 hypothetical protein; glyoxalase/bleomycin resistance protein/dioxygenase 719692 4579604 Pden_0736 Paracoccus denitrificans PD1222 glyoxalase/bleomycin resistance protein/dioxygenase YP_914544.1 719300 D 318586 CDS YP_914545.1 119383489 4579605 719689..720102 1 NC_008686.1 PFAM: glutathione-dependent formaldehyde-activating, GFA; KEGG: sme:SMc04046 hypothetical protein; glutathione-dependent formaldehyde-activating protein 720102 4579605 Pden_0737 Paracoccus denitrificans PD1222 glutathione-dependent formaldehyde-activating protein YP_914545.1 719689 D 318586 CDS YP_914546.1 119383490 4579606 720338..720991 1 NC_008686.1 PFAM: transferase hexapeptide repeat containing protein; KEGG: rsp:RSP_1706 acetyltransferase; hexapaptide repeat-containing transferase 720991 4579606 Pden_0738 Paracoccus denitrificans PD1222 hexapaptide repeat-containing transferase YP_914546.1 720338 D 318586 CDS YP_914547.1 119383491 4579607 721049..722890 1 NC_008686.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: bme:BMEI0471 ABC transporter ATP-binding protein; ABC transporter 722890 4579607 Pden_0739 Paracoccus denitrificans PD1222 ABC transporter YP_914547.1 721049 D 318586 CDS YP_914548.1 119383492 4579608 723027..723938 1 NC_008686.1 KEGG: jan:Jann_3368 hypothetical protein; hypothetical protein 723938 4579608 Pden_0740 Paracoccus denitrificans PD1222 hypothetical protein YP_914548.1 723027 D 318586 CDS YP_914549.1 119383493 4579609 723963..724208 1 NC_008686.1 TIGRFAM: preprotein translocase, SecE subunit; PFAM: protein secE/sec61-gamma protein; KEGG: sit:TM1040_0226 SecE subunit of protein translocation complex; Preprotein translocase subunit SecE 724208 4579609 Pden_0741 Paracoccus denitrificans PD1222 Preprotein translocase subunit SecE YP_914549.1 723963 D 318586 CDS YP_914550.1 119383494 4579610 724404..724943 1 NC_008686.1 KEGG: rsp:RSP_1704 probable transcription antitermination protein NusG; TIGRFAM: transcription termination/antitermination factor NusG; PFAM: transcription antitermination protein NusG; KOW domain protein; SMART: NGN domain protein; KOW (Kyrpides, Ouzounis, Woese) domain protein; NusG antitermination factor 724943 4579610 Pden_0742 Paracoccus denitrificans PD1222 NusG antitermination factor YP_914550.1 724404 D 318586 CDS YP_914551.1 119383495 4579611 725043..725495 1 NC_008686.1 binds directly to 23S ribosomal RNA; 50S ribosomal protein L11 725495 rplK 4579611 rplK Paracoccus denitrificans PD1222 50S ribosomal protein L11 YP_914551.1 725043 D 318586 CDS YP_914552.1 119383496 4579612 725499..726200 1 NC_008686.1 in Escherichia coli and Methanococcus, this protein autoregulates expression; the binding site in the mRNA mimics the binding site in the 23S rRNA; 50S ribosomal protein L1 726200 rplA 4579612 rplA Paracoccus denitrificans PD1222 50S ribosomal protein L1 YP_914552.1 725499 D 318586 CDS YP_914553.1 119383497 4579613 726682..727197 1 NC_008686.1 binds the two ribosomal protein L7/L12 dimers and anchors them to the large ribosomal subunit; 50S ribosomal protein L10 727197 rplJ 4579613 rplJ Paracoccus denitrificans PD1222 50S ribosomal protein L10 YP_914553.1 726682 D 318586 CDS YP_914554.1 119383498 4579614 727265..727639 1 NC_008686.1 present in two forms; L12 is normal, while L7 is aminoacylated at the N-terminal serine; the only multicopy ribosomal protein; 4:1 ratio of L7/L12 per ribosome; two L12 dimers bind L10; critically important for translation efficiency and fidelity; stimulates GTPase activity of translation factors; 50S ribosomal protein L7/L12 727639 rplL 4579614 rplL Paracoccus denitrificans PD1222 50S ribosomal protein L7/L12 YP_914554.1 727265 D 318586 CDS YP_914555.1 119383499 4579615 727881..732029 1 NC_008686.1 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates; beta subunit is part of the catalytic core which binds with a sigma factor to produce the holoenzyme; DNA-directed RNA polymerase subunit beta 732029 rpoB 4579615 rpoB Paracoccus denitrificans PD1222 DNA-directed RNA polymerase subunit beta YP_914555.1 727881 D 318586 CDS YP_914556.1 119383500 4579616 732032..732343 1 NC_008686.1 hypothetical protein 732343 4579616 Pden_0748 Paracoccus denitrificans PD1222 hypothetical protein YP_914556.1 732032 D 318586 CDS YP_914557.1 119383501 4580047 732340..736548 1 NC_008686.1 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Subunit beta' binds to sigma factor allowing it to bind to the -10 region of the promoter; DNA-directed RNA polymerase subunit beta' 736548 4580047 Pden_0749 Paracoccus denitrificans PD1222 DNA-directed RNA polymerase subunit beta' YP_914557.1 732340 D 318586 CDS YP_914558.1 119383502 4580048 736780..737055 1 NC_008686.1 hypothetical protein 737055 4580048 Pden_0750 Paracoccus denitrificans PD1222 hypothetical protein YP_914558.1 736780 D 318586 CDS YP_914559.1 119383503 4580049 737215..738156 1 NC_008686.1 PFAM: protein of unknown function DUF6, transmembrane; KEGG: rsp:RSP_1711 possible transporter, RhaT family, DMT superfamily; hypothetical protein 738156 4580049 Pden_0751 Paracoccus denitrificans PD1222 hypothetical protein YP_914559.1 737215 D 318586 CDS YP_914560.1 119383504 4580050 738156..738995 1 NC_008686.1 KEGG: jan:Jann_0574 hypothetical protein; hypothetical protein 738995 4580050 Pden_0752 Paracoccus denitrificans PD1222 hypothetical protein YP_914560.1 738156 D 318586 CDS YP_914561.1 119383505 4580051 739289..739660 1 NC_008686.1 interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone; located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side; mutations in the S12 gene confer streptomycin resistance; 30S ribosomal protein S12 739660 rpsL 4580051 rpsL Paracoccus denitrificans PD1222 30S ribosomal protein S12 YP_914561.1 739289 D 318586 CDS YP_914562.1 119383506 4580052 739673..740143 1 NC_008686.1 binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit; 30S ribosomal protein S7 740143 4580052 Pden_0754 Paracoccus denitrificans PD1222 30S ribosomal protein S7 YP_914562.1 739673 D 318586 CDS YP_914563.1 119383507 4580053 740162..742285 1 NC_008686.1 EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene; elongation factor G 742285 4580053 Pden_0755 Paracoccus denitrificans PD1222 elongation factor G YP_914563.1 740162 D 318586 CDS YP_914564.1 119383508 4580054 742372..743547 1 NC_008686.1 EF-Tu; promotes GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis; when the tRNA anticodon matches the mRNA codon, GTP hydrolysis results; the inactive EF-Tu-GDP leaves the ribosome and release of GDP is promoted by elongation factor Ts; many prokaryotes have two copies of the gene encoding EF-Tu; elongation factor Tu 743547 4580054 Pden_0756 Paracoccus denitrificans PD1222 elongation factor Tu YP_914564.1 742372 D 318586 CDS YP_914565.1 119383509 4580055 complement(743731..744531) 1 NC_008686.1 hypothetical protein 744531 4580055 Pden_0757 Paracoccus denitrificans PD1222 hypothetical protein YP_914565.1 743731 R 318586 CDS YP_914566.1 119383510 4580056 744795..745103 1 NC_008686.1 NusE; involved in assembly of the 30S subunit; in the ribosome, this protein is involved in the binding of tRNA; in Escherichia coli this protein was also found to be involved in transcription antitermination; NusB/S10 heterodimers bind boxA sequences in the leader RNA of rrn operons which is required for antitermination; binding of NusB/S10 to boxA nucleates assembly of the antitermination complex; 30S ribosomal protein S10 745103 rpsJ 4580056 rpsJ Paracoccus denitrificans PD1222 30S ribosomal protein S10 YP_914566.1 744795 D 318586 CDS YP_914567.1 119383511 4580057 745114..745851 1 NC_008686.1 binds directly near the 3' end of the 23S rRNA, where it nucleates assembly of the 50S subunit; essential for peptidyltransferase activity; mutations in this gene confer resistance to tiamulin; 50S ribosomal protein L3 745851 rplC 4580057 rplC Paracoccus denitrificans PD1222 50S ribosomal protein L3 YP_914567.1 745114 D 318586 CDS YP_914568.1 119383512 4580058 745851..746471 1 NC_008686.1 L4 is important during the early stages of 50S assembly; it initially binds near the 5' end of the 23S rRNA; 50S ribosomal protein L4 746471 rplD 4580058 rplD Paracoccus denitrificans PD1222 50S ribosomal protein L4 YP_914568.1 745851 D 318586 CDS YP_914569.1 119383513 4580059 746468..746764 1 NC_008686.1 binds third domain of 23S rRNA and protein L29; part of exit tunnel; 50S ribosomal protein L23 746764 rplW 4580059 rplW Paracoccus denitrificans PD1222 50S ribosomal protein L23 YP_914569.1 746468 D 318586 CDS YP_914570.1 119383514 4580060 746860..747699 1 NC_008686.1 one of the primary rRNA-binding proteins; required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation; 50S ribosomal protein L2 747699 rplB 4580060 rplB Paracoccus denitrificans PD1222 50S ribosomal protein L2 YP_914570.1 746860 D 318586 CDS YP_914571.1 119383515 4580061 747703..747981 1 NC_008686.1 protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA; 30S ribosomal protein S19 747981 rpsS 4580061 rpsS Paracoccus denitrificans PD1222 30S ribosomal protein S19 YP_914571.1 747703 D 318586 CDS YP_914572.1 119383516 4580062 747987..748367 1 NC_008686.1 binds specifically to 23S rRNA during the early stages of 50S assembly; makes contact with all 6 domains of the 23S rRNA in the assembled 50S subunit and ribosome; mutations in this gene result in erythromycin resistance; located near peptidyl-transferase center; 50S ribosomal protein L22 748367 rplV 4580062 rplV Paracoccus denitrificans PD1222 50S ribosomal protein L22 YP_914572.1 747987 D 318586 CDS YP_914573.1 119383517 4580063 748367..749089 1 NC_008686.1 forms a complex with S10 and S14; binds the lower part of the 30S subunit head and the mRNA in the complete ribosome to position it for translation; 30S ribosomal protein S3 749089 rpsC 4580063 rpsC Paracoccus denitrificans PD1222 30S ribosomal protein S3 YP_914573.1 748367 D 318586 CDS YP_914574.1 119383518 4580064 749102..749515 1 NC_008686.1 located in the peptidyl transferase center and may be involved in peptidyl transferase activity; similar to archaeal L10e; 50S ribosomal protein L16 749515 rplP 4580064 rplP Paracoccus denitrificans PD1222 50S ribosomal protein L16 YP_914574.1 749102 D 318586 CDS YP_914575.1 119383519 4580065 749633..749911 1 NC_008686.1 PFAM: ribosomal protein L29; KEGG: jan:Jann_0599 ribosomal protein L29; 50S ribosomal protein L29 749911 4580065 Pden_0767 Paracoccus denitrificans PD1222 50S ribosomal protein L29 YP_914575.1 749633 D 318586 CDS YP_914576.1 119383520 4579987 749924..750172 1 NC_008686.1 primary binding protein; helps mediate assembly; involved in translation fidelity; 30S ribosomal protein S17 750172 rpsQ 4579987 rpsQ Paracoccus denitrificans PD1222 30S ribosomal protein S17 YP_914576.1 749924 D 318586 CDS YP_914577.1 119383521 4579988 750236..750604 1 NC_008686.1 binds to the 23S rRNA between the centers for peptidyl transferase and GTPase; 50S ribosomal protein L14 750604 rplN 4579988 rplN Paracoccus denitrificans PD1222 50S ribosomal protein L14 YP_914577.1 750236 D 318586 CDS YP_914578.1 119383522 4579989 750604..750909 1 NC_008686.1 assembly initiator protein; binds to 5' end of 23S rRNA and nucleates assembly of the 50S; surrounds polypeptide exit tunnel; 50S ribosomal protein L24 750909 rplX 4579989 rplX Paracoccus denitrificans PD1222 50S ribosomal protein L24 YP_914578.1 750604 D 318586 CDS YP_914579.1 119383523 4579990 750909..751469 1 NC_008686.1 part of 50S and 5S/L5/L18/L25 subcomplex; contacts 5S rRNA and P site tRNA; forms a bridge to the 30S subunit in the ribosome by binding to S13; 50S ribosomal protein L5 751469 rplE 4579990 rplE Paracoccus denitrificans PD1222 50S ribosomal protein L5 YP_914579.1 750909 D 318586 CDS YP_914580.1 119383524 4579991 751488..751793 1 NC_008686.1 located in the peptidyl transferase center and involved in assembly of 30S ribosome subunit; similar to what is observed with proteins L31 and L33, some proteins in this family contain CXXC motifs that are involved in zinc binding; if two copies are present in a genome, then the duplicated copy appears to have lost the zinc-binding motif and is instead regulated by zinc; the proteins in this group do not appear to have the zinc-binding motif; 30S ribosomal protein S14 751793 rpsN 4579991 rpsN Paracoccus denitrificans PD1222 30S ribosomal protein S14 YP_914580.1 751488 D 318586 CDS YP_914581.1 119383525 4579992 751803..752201 1 NC_008686.1 binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit; 30S ribosomal protein S8 752201 rpsH 4579992 rpsH Paracoccus denitrificans PD1222 30S ribosomal protein S8 YP_914581.1 751803 D 318586 CDS YP_914582.1 119383526 4579993 752213..752746 1 NC_008686.1 ribosomal protein L6 appears to have arisen as a result of an ancient gene duplication as based on structural comparison of the Bacillus stearothermophilus protein; RNA-binding appears to be in the C-terminal domain; mutations in the L6 gene confer resistance to aminoglycoside antibiotics such as gentamicin and these occur in truncations of the C-terminal domain; it has been localized to a region between the base of the L7/L12 stalk and the central protuberance; 50S ribosomal protein L6 752746 rplF 4579993 rplF Paracoccus denitrificans PD1222 50S ribosomal protein L6 YP_914582.1 752213 D 318586 CDS YP_914583.1 119383527 4579994 752758..753117 1 NC_008686.1 binds 5S rRNA along with protein L5 and L25; 50S ribosomal protein L18 753117 rplR 4579994 rplR Paracoccus denitrificans PD1222 50S ribosomal protein L18 YP_914583.1 752758 D 318586 CDS YP_914584.1 119383528 4579995 753236..753802 1 NC_008686.1 located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body; contacts S4 and S8; with S4 and S12 plays a role in translational accuracy; mutations in this gene result in spectinomycin resistance; 30S ribosomal protein S5 753802 rpsE 4579995 rpsE Paracoccus denitrificans PD1222 30S ribosomal protein S5 YP_914584.1 753236 D 318586 CDS YP_914585.1 119383529 4579996 753815..754003 1 NC_008686.1 L30 binds domain II of the 23S rRNA and the 5S rRNA; similar to eukaryotic protein L7; 50S ribosomal protein L30 754003 rpmD 4579996 rpmD Paracoccus denitrificans PD1222 50S ribosomal protein L30 YP_914585.1 753815 D 318586 CDS YP_914586.1 119383530 4579997 754133..754855 1 NC_008686.1 KEGG: rsp:RSP_2084 hypothetical protein; hypothetical protein 754855 4579997 Pden_0778 Paracoccus denitrificans PD1222 hypothetical protein YP_914586.1 754133 D 318586 CDS YP_914587.1 119383531 4579998 755010..755495 1 NC_008686.1 late assembly protein; 50S ribosomal protein L15 755495 rplO 4579998 rplO Paracoccus denitrificans PD1222 50S ribosomal protein L15 YP_914587.1 755010 D 318586 CDS YP_914588.1 119383532 4579999 755600..756973 1 NC_008686.1 forms heterotrimeric complex in the membrane; in bacteria the complex consists of SecY which forms the channel pore and SecE and SecG; the SecG subunit is not essential; in bacteria translocation is driven via the SecA ATPase; preprotein translocase subunit SecY 756973 secY 4579999 secY Paracoccus denitrificans PD1222 preprotein translocase subunit SecY YP_914588.1 755600 D 318586 CDS YP_914589.1 119383533 4580000 757011..757667 1 NC_008686.1 essential enzyme that recycles AMP in active cells; converts ATP and AMP to two molecules of ADP; adenylate kinase 757667 adk 4580000 adk Paracoccus denitrificans PD1222 adenylate kinase YP_914589.1 757011 D 318586 CDS YP_914590.2 162139378 4580001 757831..758199 1 NC_008686.1 located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA; makes contact with the large subunit via RNA-protein interactions and via protein-protein interactions with L5; contacts P-site tRNA; 30S ribosomal protein S13 758199 rpsM 4580001 rpsM Paracoccus denitrificans PD1222 30S ribosomal protein S13 YP_914590.2 757831 D 318586 CDS YP_914591.1 119383535 4580002 758212..758601 1 NC_008686.1 located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA; forms part of the Shine-Dalgarno cleft in the 70S ribosome; interacts with S7 and S18 and IF-3; 30S ribosomal protein S11 758601 4580002 Pden_0783 Paracoccus denitrificans PD1222 30S ribosomal protein S11 YP_914591.1 758212 D 318586 CDS YP_914592.1 119383536 4580003 758721..759737 1 NC_008686.1 catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Dimerization of the alpha subunit is the first step in the sequential assembly of subunits to form the holoenzyme; DNA-directed RNA polymerase subunit alpha 759737 4580003 Pden_0784 Paracoccus denitrificans PD1222 DNA-directed RNA polymerase subunit alpha YP_914592.1 758721 D 318586 CDS YP_914593.1 119383537 4580004 759854..760276 1 NC_008686.1 is a component of the macrolide binding site in the peptidyl transferase center; 50S ribosomal protein L17 760276 rplQ 4580004 rplQ Paracoccus denitrificans PD1222 50S ribosomal protein L17 YP_914593.1 759854 D 318586 CDS YP_914594.1 119383538 4580005 760626..761237 1 NC_008686.1 PFAM: regulatory protein, LuxR; Autoinducer-binding domain protein; KEGG: jan:Jann_0619 transcriptional regulator, LuxR family; response regulator receiver protein 761237 4580005 Pden_0786 Paracoccus denitrificans PD1222 response regulator receiver protein YP_914594.1 760626 D 318586 CDS YP_914595.1 119383539 4580006 761305..761895 1 NC_008686.1 KEGG: jan:Jann_0620 N-acyl-L-homoserine lactone synthetase-like; N-acyl-L-homoserine lactone synthetase-like 761895 4580006 Pden_0787 Paracoccus denitrificans PD1222 N-acyl-L-homoserine lactone synthetase-like YP_914595.1 761305 D 318586 CDS YP_914596.1 119383540 4580612 761957..763285 1 NC_008686.1 PFAM: AAA ATPase, central domain protein; ATPase associated with various cellular activities, AAA_5; SMART: AAA ATPase; KEGG: rsp:RSP_1743 ATPase, AAA family; recombination factor protein RarA 763285 4580612 Pden_0788 Paracoccus denitrificans PD1222 recombination factor protein RarA YP_914596.1 761957 D 318586 CDS YP_914597.1 119383541 4580613 763282..763656 1 NC_008686.1 TIGRFAM: CrcB protein; PFAM: Camphor resistance CrcB protein; KEGG: rsp:RSP_1744 CrcB-like protein; CrcB protein 763656 4580613 Pden_0789 Paracoccus denitrificans PD1222 CrcB protein YP_914597.1 763282 D 318586 CDS YP_914598.1 119383542 4580614 763653..764699 1 NC_008686.1 TIGRFAM: pseudouridine synthase, RluA family; PFAM: RNA-binding S4 domain protein; pseudouridine synthase; KEGG: rsp:RSP_1745 pseudouridine synthase; RluA family pseudouridine synthase 764699 4580614 Pden_0790 Paracoccus denitrificans PD1222 RluA family pseudouridine synthase YP_914598.1 763653 D 318586 CDS YP_914599.1 119383543 4580615 764696..765358 1 NC_008686.1 TIGRFAM: HAD-superfamily hydrolase, subfamily IA, variant 3; HAD-superfamily hydrolase, subfamily IA, variant 1; PFAM: Haloacid dehalogenase domain protein hydrolase; KEGG: sil:SPO0517 HAD-superfamily hydrolase, subfamily IA, variant 1; HAD family hydrolase 765358 4580615 Pden_0791 Paracoccus denitrificans PD1222 HAD family hydrolase YP_914599.1 764696 D 318586 CDS YP_914600.1 119383544 4580616 765351..766061 1 NC_008686.1 PFAM: ATP12 ATPase; KEGG: jan:Jann_0626 ATP12 ATPase; ATP12 ATPase 766061 4580616 Pden_0792 Paracoccus denitrificans PD1222 ATP12 ATPase YP_914600.1 765351 D 318586 CDS YP_914601.1 119383545 4580617 766214..767239 1 NC_008686.1 TIGRFAM: cationic amino acid ABC transporter, periplasmic binding protein; SMART: extracellular solute-binding protein, family 3; KEGG: rsp:RSP_1747 ABC glutamate/glutamine/aspartate/asparagine transporter, periplasmic substrate-binding protein; cationic amino acid ABC transporter substrate-binding protein 767239 4580617 Pden_0793 Paracoccus denitrificans PD1222 cationic amino acid ABC transporter substrate-binding protein YP_914601.1 766214 D 318586 CDS YP_914602.1 119383546 4580618 767355..768608 1 NC_008686.1 TIGRFAM: polar amino acid ABC transporter, inner membrane subunit; PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: rsp:RSP_1748 ABC glutamate/glutamine/aspartate/asparagine transporter, inner membrane subunit BztB; polar amino acid ABC transporter inner membrane subunit 768608 4580618 Pden_0794 Paracoccus denitrificans PD1222 polar amino acid ABC transporter inner membrane subunit YP_914602.1 767355 D 318586 CDS YP_914603.1 119383547 4580619 768610..770064 1 NC_008686.1 TIGRFAM: polar amino acid ABC transporter, inner membrane subunit; PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: rsp:RSP_1749 ABC glutamate/glutamine/aspartate/asparagine transporter, inner membrane subunit BztC; polar amino acid ABC transporter inner membrane subunit 770064 4580619 Pden_0795 Paracoccus denitrificans PD1222 polar amino acid ABC transporter inner membrane subunit YP_914603.1 768610 D 318586 CDS YP_914604.1 119383548 4580620 770075..770848 1 NC_008686.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sil:SPO0522 glutamate/glutamine/aspartate/asparagine ABC transporter, ATP-binding protein; ABC transporter 770848 4580620 Pden_0796 Paracoccus denitrificans PD1222 ABC transporter YP_914604.1 770075 D 318586 CDS YP_914605.1 119383549 4580621 770948..771850 1 NC_008686.1 KEGG: rde:RD1_B0053 rhizobiocin; hypothetical protein 771850 4580621 Pden_0797 Paracoccus denitrificans PD1222 hypothetical protein YP_914605.1 770948 D 318586 CDS YP_914606.1 119383550 4580622 complement(771923..772783) 1 NC_008686.1 PFAM: aminotransferase, class IV; KEGG: rsp:RSP_1768 aminotransferase class IV , D-alanine aminotransferase; aminotransferase, class IV 772783 4580622 Pden_0798 Paracoccus denitrificans PD1222 aminotransferase, class IV YP_914606.1 771923 R 318586 CDS YP_914607.1 119383551 4580623 772881..773906 1 NC_008686.1 PFAM: HpcH/HpaI aldolase; KEGG: rde:RD1_1001 citrate lyase, beta subunit; citrate (pro-3S)-lyase 773906 4580623 Pden_0799 Paracoccus denitrificans PD1222 citrate (pro-3S)-lyase YP_914607.1 772881 D 318586 CDS YP_914608.1 119383552 4580624 complement(774324..775946) 1 NC_008686.1 PFAM: ABC transporter related; Oligopeptide/dipeptide ABC transporter, C-terminal domain protein; SMART: AAA ATPase; KEGG: sil:SPO0098 peptide/opine/nickel uptake family ABC transporter, ATP-binding protein; ABC transporter 775946 4580624 Pden_0800 Paracoccus denitrificans PD1222 ABC transporter YP_914608.1 774324 R 318586 CDS YP_914609.1 119383553 4580625 complement(775943..776755) 1 NC_008686.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: sil:SPO0099 peptide/opine/nickel uptake family ABC transporter, permease protein; binding-protein-dependent transport system inner membrane protein 776755 4580625 Pden_0801 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_914609.1 775943 R 318586 CDS YP_914610.1 119383554 4580626 complement(776752..777690) 1 NC_008686.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: sit:TM1040_3436 binding-protein-dependent transport systems inner membrane component; binding-protein-dependent transport system inner membrane protein 777690 4580626 Pden_0802 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_914610.1 776752 R 318586 CDS YP_914611.1 119383555 4580627 complement(777739..779373) 1 NC_008686.1 PFAM: protein of unknown function DUF894, DitE; major facilitator superfamily MFS_1; KEGG: bms:BRA0311 transporter; hypothetical protein 779373 4580627 Pden_0803 Paracoccus denitrificans PD1222 hypothetical protein YP_914611.1 777739 R 318586 CDS YP_914612.1 119383556 4580628 779632..780933 1 NC_008686.1 catalyzes the oxidative deamination of D-amino acids; D-amino acid dehydrogenase small subunit 780933 4580628 Pden_0804 Paracoccus denitrificans PD1222 D-amino acid dehydrogenase small subunit YP_914612.1 779632 D 318586 CDS YP_914613.1 119383557 4580629 complement(780997..781257) 1 NC_008686.1 PFAM: Transglycosylase-associated protein; KEGG: bur:Bcep18194_B2685 transglycosylase-associated protein; transglycosylase-associated protein 781257 4580629 Pden_0805 Paracoccus denitrificans PD1222 transglycosylase-associated protein YP_914613.1 780997 R 318586 CDS YP_914614.1 119383558 4580630 complement(781254..781526) 1 NC_008686.1 hypothetical protein 781526 4580630 Pden_0806 Paracoccus denitrificans PD1222 hypothetical protein YP_914614.1 781254 R 318586 CDS YP_914615.1 119383559 4580553 781572..782318 1 NC_008686.1 PFAM: ErfK/YbiS/YcfS/YnhG family protein; KEGG: rsp:RSP_1754 hypothetical protein; ErfK/YbiS/YcfS/YnhG family protein 782318 4580553 Pden_0807 Paracoccus denitrificans PD1222 ErfK/YbiS/YcfS/YnhG family protein YP_914615.1 781572 D 318586 CDS YP_914616.1 119383560 4580554 782443..782997 1 NC_008686.1 KEGG: tpa:TP0470 hypothetical protein; hypothetical protein 782997 4580554 Pden_0808 Paracoccus denitrificans PD1222 hypothetical protein YP_914616.1 782443 D 318586 CDS YP_914617.1 119383561 4580555 783068..783979 1 NC_008686.1 PFAM: Lytic transglycosylase, catalytic; KEGG: sme:SMc01230 transglycosylase transmembrane protein; lytic transglycosylase, catalytic 783979 4580555 Pden_0809 Paracoccus denitrificans PD1222 lytic transglycosylase, catalytic YP_914617.1 783068 D 318586 CDS YP_914618.1 119383562 4580556 complement(784055..785524) 1 NC_008686.1 PFAM: extracellular solute-binding protein, family 5; KEGG: jan:Jann_0782 extracellular solute-binding protein, family 5; extracellular solute-binding protein 785524 4580556 Pden_0810 Paracoccus denitrificans PD1222 extracellular solute-binding protein YP_914618.1 784055 R 318586 CDS YP_914619.1 119383563 4580557 complement(785581..786273) 1 NC_008686.1 PFAM: CDP-alcohol phosphatidyltransferase; KEGG: rsp:RSP_0565 phosphatidylcholine synthase; phosphatidylcholine synthase 786273 4580557 Pden_0811 Paracoccus denitrificans PD1222 phosphatidylcholine synthase YP_914619.1 785581 R 318586 CDS YP_914620.1 119383564 4580558 complement(786368..787243) 1 NC_008686.1 KEGG: sil:SPO3353 phosphoserine phosphatase; TIGRFAM: phosphoserine phosphatase SerB; HAD-superfamily hydrolase, subfamily IB (PSPase-like); PFAM: Haloacid dehalogenase domain protein hydrolase; phosphoserine phosphatase SerB 787243 4580558 Pden_0812 Paracoccus denitrificans PD1222 phosphoserine phosphatase SerB YP_914620.1 786368 R 318586 CDS YP_914621.1 119383565 4580559 787437..788591 1 NC_008686.1 catalyzes the formation of 3-phosphonooxypyruvate and glutamate from O-phospho-L-serine and 2-oxoglutarate; phosphoserine aminotransferase 788591 4580559 Pden_0813 Paracoccus denitrificans PD1222 phosphoserine aminotransferase YP_914621.1 787437 D 318586 CDS YP_914622.1 119383566 4580560 788704..790293 1 NC_008686.1 catalyzes the formation of 3-phosphonooxypyruvate from 3-phospho-D-glycerate in serine biosynthesis; can also reduce alpha ketoglutarate to form 2-hydroxyglutarate; D-3-phosphoglycerate dehydrogenase 790293 4580560 Pden_0814 Paracoccus denitrificans PD1222 D-3-phosphoglycerate dehydrogenase YP_914622.1 788704 D 318586 CDS YP_914623.1 119383567 4580561 790346..791074 1 NC_008686.1 PFAM: metallophosphoesterase; KEGG: rsp:RSP_1353 protein phosphatase; metallophosphoesterase 791074 4580561 Pden_0815 Paracoccus denitrificans PD1222 metallophosphoesterase YP_914623.1 790346 D 318586 CDS YP_914624.1 119383568 4580562 791211..792839 1 NC_008686.1 TIGRFAM: sodium-dependent inorganic phosphate (Pi) transporter; PFAM: Na+/Pi-cotransporter; KEGG: ret:RHE_CH03044 probable sodium-dependent phosphate transporter protein; sodium-dependent inorganic phosphate (Pi) transporter 792839 4580562 Pden_0816 Paracoccus denitrificans PD1222 sodium-dependent inorganic phosphate (Pi) transporter YP_914624.1 791211 D 318586 CDS YP_914625.1 119383569 4580563 793035..793496 1 NC_008686.1 PFAM: CreA family protein; KEGG: rsp:RSP_2505 possible CreA protein; CreA family protein 793496 4580563 Pden_0817 Paracoccus denitrificans PD1222 CreA family protein YP_914625.1 793035 D 318586 CDS YP_914626.1 119383570 4580564 793728..794060 1 NC_008686.1 TIGRFAM: hemimethylated DNA binding protein; KEGG: rsp:RSP_1498 hypothetical protein; hemimethylated DNA binding protein 794060 4580564 Pden_0818 Paracoccus denitrificans PD1222 hemimethylated DNA binding protein YP_914626.1 793728 D 318586 CDS YP_914627.1 119383571 4580565 complement(794073..794630) 1 NC_008686.1 KEGG: jan:Jann_4052 anti-sigma regulatory factor (serine/threonine protein kinase); anti-sigma regulatory factor 794630 4580565 Pden_0819 Paracoccus denitrificans PD1222 anti-sigma regulatory factor YP_914627.1 794073 R 318586 CDS YP_914628.1 119383572 4580566 complement(794627..794992) 1 NC_008686.1 TIGRFAM: anti-anti-sigma factor; PFAM: Sulfate transporter/antisigma-factor antagonist STAS; KEGG: rsp:RSP_1501 antisigma-factor antagonist (STAS) domain protein; anti-sigma-factor antagonist 794992 4580566 Pden_0820 Paracoccus denitrificans PD1222 anti-sigma-factor antagonist YP_914628.1 794627 R 318586 CDS YP_914629.1 119383573 4580567 795231..795608 1 NC_008686.1 hypothetical protein 795608 4580567 Pden_0821 Paracoccus denitrificans PD1222 hypothetical protein YP_914629.1 795231 D 318586 CDS YP_914630.1 119383574 4580568 795629..798091 1 NC_008686.1 PFAM: Hemolysin-type calcium-binding region; peptidase M10A and M12B, matrixin and adamalysin; peptidase domain protein; SMART: peptidase, metallopeptidases; KEGG: rsp:RSP_0230 neutral zinc metallopeptidase; peptidase domain-containing protein 798091 4580568 Pden_0822 Paracoccus denitrificans PD1222 peptidase domain-containing protein YP_914630.1 795629 D 318586 CDS YP_914631.1 119383575 4580569 798302..799714 1 NC_008686.1 PFAM: protein of unknown function DUF404; protein of unknown function DUF407; KEGG: rsp:RSP_2415 hypothetical protein; hypothetical protein 799714 4580569 Pden_0823 Paracoccus denitrificans PD1222 hypothetical protein YP_914631.1 798302 D 318586 CDS YP_914632.1 119383576 4580570 799729..800688 1 NC_008686.1 PFAM: protein of unknown function DUF403; KEGG: rsp:RSP_2416 hypothetical protein; hypothetical protein 800688 4580570 Pden_0824 Paracoccus denitrificans PD1222 hypothetical protein YP_914632.1 799729 D 318586 CDS YP_914633.1 119383577 4580571 800699..801505 1 NC_008686.1 PFAM: transglutaminase domain protein; transglutaminase, N-terminal domain protein; KEGG: rsp:RSP_2417 hypothetical protein; transglutaminase domain-containing protein 801505 4580571 Pden_0825 Paracoccus denitrificans PD1222 transglutaminase domain-containing protein YP_914633.1 800699 D 318586 CDS YP_914634.1 119383578 4580572 801536..802294 1 NC_008686.1 PFAM: 20S proteasome, A and B subunits; KEGG: rsp:RSP_2420 proteasome-type protease; 20S proteasome subunits A/B 802294 4580572 Pden_0826 Paracoccus denitrificans PD1222 20S proteasome subunits A/B YP_914634.1 801536 D 318586 CDS YP_914635.1 119383579 4579442 complement(802307..804943) 1 NC_008686.1 This protein performs the mismatch recognition step during the DNA repair process; DNA mismatch repair protein MutS 804943 4579442 Pden_0827 Paracoccus denitrificans PD1222 DNA mismatch repair protein MutS YP_914635.1 802307 R 318586 CDS YP_914636.1 119383580 4579443 805100..805939 1 NC_008686.1 KEGG: sit:TM1040_2771 hydratase/decarboxylase; hydratase/decarboxylase 805939 4579443 Pden_0828 Paracoccus denitrificans PD1222 hydratase/decarboxylase YP_914636.1 805100 D 318586 CDS YP_914637.1 119383581 4579444 806084..807190 1 NC_008686.1 PFAM: extracellular solute-binding protein, family 1; KEGG: rsp:RSP_0346 ABC transporter, substrate binding protein; extracellular solute-binding protein 807190 4579444 Pden_0829 Paracoccus denitrificans PD1222 extracellular solute-binding protein YP_914637.1 806084 D 318586 CDS YP_914638.1 119383582 4579445 807211..808092 1 NC_008686.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: rsp:RSP_0347 ABC transporter, inner membrane subunit; binding-protein-dependent transport system inner membrane protein 808092 4579445 Pden_0830 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_914638.1 807211 D 318586 CDS YP_914639.1 119383583 4579446 808089..808871 1 NC_008686.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: atc:AGR_C_3893 probable ABC transport system permease; binding-protein-dependent transport system inner membrane protein 808871 4579446 Pden_0831 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_914639.1 808089 D 318586 CDS YP_914640.1 119383584 4579447 808868..809902 1 NC_008686.1 PFAM: ABC transporter related; Transport-associated OB domain protein; SMART: AAA ATPase; KEGG: rsp:RSP_0349 ABC transporter, ATPase subunit; ABC transporter 809902 4579447 Pden_0832 Paracoccus denitrificans PD1222 ABC transporter YP_914640.1 808868 D 318586 CDS YP_914641.1 119383585 4579448 810408..812123 1 NC_008686.1 PFAM: Hemolysin-type calcium-binding region; KEGG: bja:bll7673 hypothetical protein; hemolysin-type calcium-binding protein 812123 4579448 Pden_0833 Paracoccus denitrificans PD1222 hemolysin-type calcium-binding protein YP_914641.1 810408 D 318586 CDS YP_914642.1 119383586 4579449 complement(812160..812933) 1 NC_008686.1 TIGRFAM: glycosyl transferase, WecB/TagA/CpsF family; PFAM: glycosyl transferase WecB/TagA/CpsF; KEGG: sil:SPO0851 glycosyl transferase, WecB/TagA/CpsF family; WecB/TagA/CpsF family glycosyl transferase 812933 4579449 Pden_0834 Paracoccus denitrificans PD1222 WecB/TagA/CpsF family glycosyl transferase YP_914642.1 812160 R 318586 CDS YP_914643.1 119383587 4579450 813051..814475 1 NC_008686.1 KEGG: sit:TM1040_2399 membrane protein; hypothetical protein 814475 4579450 Pden_0835 Paracoccus denitrificans PD1222 hypothetical protein YP_914643.1 813051 D 318586 CDS YP_914644.1 119383588 4579451 814575..820856 1 NC_008686.1 PFAM: beta-ketoacyl synthase; Thioesterase; acyl transferase domain protein; NAD-dependent epimerase/dehydratase; short-chain dehydrogenase/reductase SDR; 3-beta hydroxysteroid dehydrogenase/isomerase; phosphopantetheine-binding; KR; KEGG: sil:SPO0849 non-ribosomal peptide synthase; beta-ketoacyl synthase 820856 4579451 Pden_0836 Paracoccus denitrificans PD1222 beta-ketoacyl synthase YP_914644.1 814575 D 318586 CDS YP_914645.1 119383589 4579452 820859..821851 1 NC_008686.1 PFAM: glycosyl transferase, family 2; KEGG: sil:SPO0848 glycosyl transferase, group 2 family protein; glycosyl transferase family protein 821851 4579452 Pden_0837 Paracoccus denitrificans PD1222 glycosyl transferase family protein YP_914645.1 820859 D 318586 CDS YP_914646.1 119383590 4579453 821848..826473 1 NC_008686.1 TIGRFAM: amino acid adenylation domain; PFAM: AMP-dependent synthetase and ligase; formyl transferase domain protein; phosphopantetheine-binding; luciferase family protein; KEGG: sil:SPO0847 non-ribosomal peptide synthetase; amino acid adenylation protein 826473 4579453 Pden_0838 Paracoccus denitrificans PD1222 amino acid adenylation protein YP_914646.1 821848 D 318586 CDS YP_914647.1 119383591 4579454 826470..827093 1 NC_008686.1 PFAM: 4'-phosphopantetheinyl transferase; KEGG: sma:SAV1748 phosphopantetheinyl transferase; 4'-phosphopantetheinyl transferase 827093 4579454 Pden_0839 Paracoccus denitrificans PD1222 4'-phosphopantetheinyl transferase YP_914647.1 826470 D 318586 CDS YP_914648.1 119383592 4579455 complement(827074..828279) 1 NC_008686.1 PFAM: glycosyl transferase, group 1; KEGG: sil:SPO0842 glycosyl transferase, group 1 family protein; group 1 glycosyl transferase 828279 4579455 Pden_0840 Paracoccus denitrificans PD1222 group 1 glycosyl transferase YP_914648.1 827074 R 318586 CDS YP_914649.1 119383593 4579456 828462..828674 1 NC_008686.1 hypothetical protein 828674 4579456 Pden_0841 Paracoccus denitrificans PD1222 hypothetical protein YP_914649.1 828462 D 318586 CDS YP_914650.1 119383594 4579457 complement(828668..829366) 1 NC_008686.1 PFAM: sugar transferase; KEGG: jan:Jann_4237 undecaprenyl-phosphate galactosephosphotransferase; undecaprenyl-phosphate galactose phosphotransferase 829366 4579457 Pden_0842 Paracoccus denitrificans PD1222 undecaprenyl-phosphate galactose phosphotransferase YP_914650.1 828668 R 318586 CDS YP_914651.1 119383595 4579458 829672..830442 1 NC_008686.1 KEGG: sil:SPO0844 hypothetical protein; hypothetical protein 830442 4579458 Pden_0843 Paracoccus denitrificans PD1222 hypothetical protein YP_914651.1 829672 D 318586 CDS YP_914652.1 119383596 4579459 complement(830439..831266) 1 NC_008686.1 PFAM: glycosyl transferase, family 2; KEGG: sil:SPO0843 glycosyl transferase, group 2 family protein; glycosyl transferase family protein 831266 4579459 Pden_0844 Paracoccus denitrificans PD1222 glycosyl transferase family protein YP_914652.1 830439 R 318586 CDS YP_914653.1 119383597 4579460 831535..832272 1 NC_008686.1 KEGG: sil:SPO0839 exopolysaccharide biosynthesis domain protein; chromosome partitioning ATPase-like protein 832272 4579460 Pden_0845 Paracoccus denitrificans PD1222 chromosome partitioning ATPase-like protein YP_914653.1 831535 D 318586 CDS YP_914654.1 119383598 4578643 832333..833799 1 NC_008686.1 PFAM: lipopolysaccharide biosynthesis; KEGG: pen:PSEEN2947 exopolysaccharide transport protein; lipopolysaccharide biosynthesis protein 833799 4578643 Pden_0846 Paracoccus denitrificans PD1222 lipopolysaccharide biosynthesis protein YP_914654.1 832333 D 318586 CDS YP_914655.1 119383599 4578644 833799..835172 1 NC_008686.1 PFAM: polysaccharide biosynthesis protein; KEGG: sil:SPO0841 polysaccharide biosynthesis protein; polysaccharide biosynthesis protein 835172 4578644 Pden_0847 Paracoccus denitrificans PD1222 polysaccharide biosynthesis protein YP_914655.1 833799 D 318586 CDS YP_914656.1 119383600 4578645 835257..837539 1 NC_008686.1 NADP-dependent; catalyzes the oxidative decarboxylation of malate to form pyruvate; decarboxylates oxaloacetate; malic enzyme 837539 4578645 Pden_0848 Paracoccus denitrificans PD1222 malic enzyme YP_914656.1 835257 D 318586 CDS YP_914657.1 119383601 4578646 complement(837600..838199) 1 NC_008686.1 KEGG: rsp:RSP_2718 possible outer membrane protein; outer membrane protein 838199 4578646 Pden_0849 Paracoccus denitrificans PD1222 outer membrane protein YP_914657.1 837600 R 318586 CDS YP_914658.1 119383602 4578647 complement(838421..839389) 1 NC_008686.1 PFAM: Rhodanese domain protein; KEGG: sil:SPO0091 rhodanese-like domain protein; rhodanese domain-containing protein 839389 4578647 Pden_0850 Paracoccus denitrificans PD1222 rhodanese domain-containing protein YP_914658.1 838421 R 318586 CDS YP_914659.1 119383603 4578648 839444..840040 1 NC_008686.1 PFAM: isochorismatase hydrolase; KEGG: rde:RD1_0585 pyrazinamidase/nicotinamidase; nicotinamidase 840040 4578648 Pden_0851 Paracoccus denitrificans PD1222 nicotinamidase YP_914659.1 839444 D 318586 CDS YP_914660.1 119383604 4578649 840040..841347 1 NC_008686.1 catalyzes the formation of nictonate and 5-phospho-alpha-D-ribose 1-diphosphate from nicotinate D-ribonucleotide and diphosphate; nicotinate phosphoribosyltransferase 841347 4578649 Pden_0852 Paracoccus denitrificans PD1222 nicotinate phosphoribosyltransferase YP_914660.1 840040 D 318586 CDS YP_914661.1 119383605 4578650 complement(841517..843187) 1 NC_008686.1 NH(3)-dependent; catalyzes the formation of nicotinamide adenine dinucleotide (NAD) from nicotinic acid adenine dinucleotide (NAAD) using either ammonia or glutamine as the amide donor and ATP; ammonia-utilizing enzymes include the ones from Bacillus and Escherichia coli while glutamine-utilizing enzymes include the Mycobacterial one; forms homodimers; NAD synthetase 843187 nadE 4578650 nadE Paracoccus denitrificans PD1222 NAD synthetase YP_914661.1 841517 R 318586 CDS YP_914662.1 119383606 4578651 843319..844785 1 NC_008686.1 PFAM: MORN repeat-containing protein; KEGG: rsp:RSP_2332 hypothetical protein; MORN repeat-containing protein 844785 4578651 Pden_0854 Paracoccus denitrificans PD1222 MORN repeat-containing protein YP_914662.1 843319 D 318586 CDS YP_914663.1 119383607 4578652 complement(844892..845389) 1 NC_008686.1 catalyzes the conversion of guanine, xanthine and, to a lesser extent, hypoxanthine to GMP, XMP and IMP, respectively; xanthine-guanine phosphoribosyltransferase 845389 4578652 Pden_0855 Paracoccus denitrificans PD1222 xanthine-guanine phosphoribosyltransferase YP_914663.1 844892 R 318586 CDS YP_914664.1 119383608 4578653 complement(845399..846001) 1 NC_008686.1 PFAM: Lysine exporter protein (LYSE/YGGA); KEGG: rde:RD1_3200 threonine efflux protein; lysine exporter protein LysE/YggA 846001 4578653 Pden_0856 Paracoccus denitrificans PD1222 lysine exporter protein LysE/YggA YP_914664.1 845399 R 318586 CDS YP_914665.1 119383609 4578654 complement(846011..846838) 1 NC_008686.1 Catalyzes a key regulatory step in fatty acid biosynthesis; enoyl-ACP reductase 846838 4578654 Pden_0857 Paracoccus denitrificans PD1222 enoyl-ACP reductase YP_914665.1 846011 R 318586 CDS YP_914666.1 119383610 4578655 846922..847584 1 NC_008686.1 PFAM: pyridoxamine 5'-phosphate oxidase-related, FMN-binding; KEGG: sil:SPO2141 pyridoxamine 5''-phosphate oxidase; pyridoxamine-phosphate oxidase 847584 4578655 Pden_0858 Paracoccus denitrificans PD1222 pyridoxamine-phosphate oxidase YP_914666.1 846922 D 318586 CDS YP_914667.1 119383611 4578656 847715..848308 1 NC_008686.1 PFAM: Cold-shock protein, DNA-binding; SMART: Cold shock protein; KEGG: rsp:RSP_2346 cold-shock DNA-binding domain protein; cold-shock DNA-binding domain-containing protein 848308 4578656 Pden_0859 Paracoccus denitrificans PD1222 cold-shock DNA-binding domain-containing protein YP_914667.1 847715 D 318586 CDS YP_914668.1 119383612 4578657 848305..848799 1 NC_008686.1 PFAM: protein of unknown function DUF192; KEGG: sil:SPO2139 hypothetical protein; hypothetical protein 848799 4578657 Pden_0860 Paracoccus denitrificans PD1222 hypothetical protein YP_914668.1 848305 D 318586 CDS YP_914669.1 119383613 4578658 849700..850956 1 NC_008686.1 KEGG: rsp:RSP_1849 aspartate kinase; TIGRFAM: aspartate kinase; PFAM: aspartate/glutamate/uridylate kinase; amino acid-binding ACT domain protein; aspartate kinase 850956 4578658 Pden_0862 Paracoccus denitrificans PD1222 aspartate kinase YP_914669.1 849700 D 318586 CDS YP_914670.1 119383614 4578659 850988..853231 1 NC_008686.1 TIGRFAM: phosphoenolpyruvate-protein phosphotransferase; PFAM: PEP-utilizing enzyme; GAF domain protein; PEP-utilising enzyme, mobile region; PEP-utilising enzyme domain protein; KEGG: jan:Jann_3205 PTSINtr with GAF domain, PtsP; phosphoenolpyruvate-protein phosphotransferase PtsP 853231 4578659 Pden_0863 Paracoccus denitrificans PD1222 phosphoenolpyruvate-protein phosphotransferase PtsP YP_914670.1 850988 D 318586 CDS YP_914671.1 119383615 4578660 complement(853260..854033) 1 NC_008686.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rpd:RPD_2478 ABC transporter related; ABC transporter 854033 4578660 Pden_0864 Paracoccus denitrificans PD1222 ABC transporter YP_914671.1 853260 R 318586 CDS YP_914672.1 119383616 4578661 complement(854021..854989) 1 NC_008686.1 PFAM: transport system permease protein; ABC-3 protein; KEGG: rpd:RPD_2479 transport system permease protein; transport system permease 854989 4578661 Pden_0865 Paracoccus denitrificans PD1222 transport system permease YP_914672.1 854021 R 318586 CDS YP_914673.1 119383617 4578662 complement(855006..856037) 1 NC_008686.1 PFAM: periplasmic binding protein; KEGG: rpa:RPA0151 possible iron ABC transporter periplasmic binding protein; periplasmic binding protein 856037 4578662 Pden_0866 Paracoccus denitrificans PD1222 periplasmic binding protein YP_914673.1 855006 R 318586 CDS YP_914674.1 119383618 4579263 complement(856034..856495) 1 NC_008686.1 PFAM: protein of unknown function UPF0066; KEGG: bja:bll5136 VirR; hypothetical protein 856495 4579263 Pden_0867 Paracoccus denitrificans PD1222 hypothetical protein YP_914674.1 856034 R 318586 CDS YP_914675.1 119383619 4579264 complement(856488..856622) 1 NC_008686.1 hypothetical protein 856622 4579264 Pden_0868 Paracoccus denitrificans PD1222 hypothetical protein YP_914675.1 856488 R 318586 CDS YP_914676.1 119383620 4579265 complement(856647..857168) 1 NC_008686.1 KEGG: sit:TM1040_2053 conserved hypothetical protein; hypothetical protein 857168 4579265 Pden_0869 Paracoccus denitrificans PD1222 hypothetical protein YP_914676.1 856647 R 318586 CDS YP_914677.1 119383621 4579266 857422..857712 1 NC_008686.1 hypothetical protein 857712 4579266 Pden_0870 Paracoccus denitrificans PD1222 hypothetical protein YP_914677.1 857422 D 318586 CDS YP_914678.1 119383622 4579267 complement(857878..859314) 1 NC_008686.1 PFAM: ATP-binding region, ATPase domain protein domain protein; histidine kinase, HAMP region domain protein; histidine kinase A domain protein domain protein; KEGG: rsp:RSP_1056 periplasmic sensor signal transduction histidine kinase; integral membrane sensor signal transduction histidine kinase 859314 4579267 Pden_0871 Paracoccus denitrificans PD1222 integral membrane sensor signal transduction histidine kinase YP_914678.1 857878 R 318586 CDS YP_914679.1 119383623 4579268 859553..859690 1 NC_008686.1 in Escherichia coli transcription of this gene is enhanced by polyamines; 50S ribosomal protein L34 859690 rpmH 4579268 rpmH Paracoccus denitrificans PD1222 50S ribosomal protein L34 YP_914679.1 859553 D 318586 CDS YP_914680.1 119383624 4579269 859720..860169 1 NC_008686.1 TIGRFAM: ribonuclease P protein component; PFAM: ribonuclease P protein; KEGG: rsp:RSP_1060 ribonuclease P protein component; ribonuclease P protein component 860169 4579269 Pden_0873 Paracoccus denitrificans PD1222 ribonuclease P protein component YP_914680.1 859720 D 318586 CDS YP_914681.1 119383625 4579270 860166..860408 1 NC_008686.1 PFAM: protein of unknown function DUF37; KEGG: rsp:RSP_1061 hypothetical protein; hypothetical protein 860408 4579270 Pden_0874 Paracoccus denitrificans PD1222 hypothetical protein YP_914681.1 860166 D 318586 CDS YP_914682.1 119383626 4579271 860460..861353 1 NC_008686.1 TtcA; YdaO; catalyzes the thiolation of cytosine 32 in specific tRNAs; C32 tRNA thiolase 861353 4579271 Pden_0875 Paracoccus denitrificans PD1222 C32 tRNA thiolase YP_914682.1 860460 D 318586 CDS YP_914683.1 119383627 4579272 861414..862685 1 NC_008686.1 PFAM: EAL domain protein; KEGG: rde:RD1_1456 EAL domain protein; diguanylate phosphodiesterase 862685 4579272 Pden_0876 Paracoccus denitrificans PD1222 diguanylate phosphodiesterase YP_914683.1 861414 D 318586 CDS YP_914684.1 119383628 4579273 862908..864815 1 NC_008686.1 functions to insert inner membrane proteins into the IM in Escherichia coli; interacts with transmembrane segments; functions in both Sec-dependent and -independent membrane insertion; similar to Oxa1p in mitochondria; inner membrane protein translocase component YidC 864815 4579273 Pden_0877 Paracoccus denitrificans PD1222 inner membrane protein translocase component YidC YP_914684.1 862908 D 318586 CDS YP_914685.1 119383629 4579274 864812..865570 1 NC_008686.1 PFAM: MOSC domain containing protein; KEGG: rsp:RSP_1065 hypothetical protein; MOSC domain-containing protein 865570 4579274 Pden_0878 Paracoccus denitrificans PD1222 MOSC domain-containing protein YP_914685.1 864812 D 318586 CDS YP_914686.1 119383630 4579275 865567..866217 1 NC_008686.1 binds guanine nucleotides; in Escherichia coli depletion results in defective cell division and filamentation; in Bacillus subtilis this gene is essential; ribosome biogenesis GTP-binding protein YsxC 866217 engB 4579275 engB Paracoccus denitrificans PD1222 ribosome biogenesis GTP-binding protein YsxC YP_914686.1 865567 D 318586 CDS YP_914687.1 119383631 4579276 866295..867209 1 NC_008686.1 catalyzes the phosphorylation of N-acetyl-L-glutamate to form N-acetyl-L-glutamate 5-phosphate; acetylglutamate kinase 867209 4579276 Pden_0880 Paracoccus denitrificans PD1222 acetylglutamate kinase YP_914687.1 866295 D 318586 CDS YP_914688.1 119383632 4579277 867318..867836 1 NC_008686.1 PFAM: Phosphoglycerate mutase; KEGG: rsp:RSP_1070 hypothetical protein; phosphohistidine phosphatase, SixA 867836 4579277 Pden_0881 Paracoccus denitrificans PD1222 phosphohistidine phosphatase, SixA YP_914688.1 867318 D 318586 CDS YP_914689.1 119383633 4579278 complement(867833..868792) 1 NC_008686.1 PFAM: PfkB domain protein; KEGG: rsp:RSP_2334 carbohydrate kinase, PfkB; ribokinase-like domain-containing protein 868792 4579278 Pden_0882 Paracoccus denitrificans PD1222 ribokinase-like domain-containing protein YP_914689.1 867833 R 318586 CDS YP_914690.1 119383634 4579279 complement(868792..869199) 1 NC_008686.1 PFAM: protein of unknown function DUF1025; KEGG: jan:Jann_3637 protein of unknown function DUF1025; hypothetical protein 869199 4579279 Pden_0883 Paracoccus denitrificans PD1222 hypothetical protein YP_914690.1 868792 R 318586 CDS YP_914691.1 119383635 4579280 869278..870603 1 NC_008686.1 Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation; glutamyl-tRNA synthetase 870603 gltX 4579280 gltX Paracoccus denitrificans PD1222 glutamyl-tRNA synthetase YP_914691.1 869278 D 318586 CDS YP_914692.1 119383636 4579281 complement(870566..870937) 1 NC_008686.1 hypothetical protein 870937 4579281 Pden_0885 Paracoccus denitrificans PD1222 hypothetical protein YP_914692.1 870566 R 318586 CDS YP_914693.1 119383637 4578564 871051..871317 1 NC_008686.1 hypothetical protein 871317 4578564 Pden_0886 Paracoccus denitrificans PD1222 hypothetical protein YP_914693.1 871051 D 318586 CDS YP_914694.1 119383638 4578565 871325..872704 1 NC_008686.1 Tig; RopA; peptidyl-prolyl cis/trans isomerase; promotes folding of newly synthesized proteins; binds ribosomal 50S subunit; forms a homodimer; trigger factor 872704 tig 4578565 tig Paracoccus denitrificans PD1222 trigger factor YP_914694.1 871325 D 318586 CDS YP_914695.1 119383639 4578566 complement(872907..873701) 1 NC_008686.1 KEGG: afm:Afu1g11690 hypothetical protein; hypothetical protein 873701 4578566 Pden_0888 Paracoccus denitrificans PD1222 hypothetical protein YP_914695.1 872907 R 318586 CDS YP_914696.1 119383640 4578567 complement(873862..874446) 1 NC_008686.1 in Escherichia coli this protein is wrapped around the base of the L1 stalk; 50S ribosomal protein L9 874446 rplI 4578567 rplI Paracoccus denitrificans PD1222 50S ribosomal protein L9 YP_914696.1 873862 R 318586 CDS YP_914697.1 119383641 4578568 complement(874459..874686) 1 NC_008686.1 binds as a heterodimer with protein S6 to the central domain of the 16S rRNA; helps stabilize the platform of the 30S subunit; 30S ribosomal protein S18 874686 rpsR 4578568 rpsR Paracoccus denitrificans PD1222 30S ribosomal protein S18 YP_914697.1 874459 R 318586 CDS YP_914698.1 119383642 4578569 complement(874705..875100) 1 NC_008686.1 binds cooperatively with S18 to the S15-16S complex, allowing platform assembly to continue with S11 and S21; 30S ribosomal protein S6 875100 rpsF 4578569 rpsF Paracoccus denitrificans PD1222 30S ribosomal protein S6 YP_914698.1 874705 R 318586 CDS YP_914699.1 119383643 4578570 875389..875970 1 NC_008686.1 PFAM: YceI family protein; KEGG: sil:SPO2279 hypothetical protein; hypothetical protein 875970 4578570 Pden_0892 Paracoccus denitrificans PD1222 hypothetical protein YP_914699.1 875389 D 318586 CDS YP_914700.1 119383644 4578571 complement(876043..877065) 1 NC_008686.1 PFAM: Di-haem cytochrome c peroxidase; KEGG: sil:SPO0330 cytochrome c peroxidase; cytochrome-c peroxidase 877065 4578571 Pden_0893 Paracoccus denitrificans PD1222 cytochrome-c peroxidase YP_914700.1 876043 R 318586 CDS YP_914701.1 119383645 4578572 877258..878313 1 NC_008686.1 recognizes the termination signals UAG and UAA during protein translation a specificity which is dependent on amino acid residues residing in loops of the L-shaped tRNA-like molecule of RF1; this protein is similar to release factor 2; peptide chain release factor 1 878313 prfA 4578572 prfA Paracoccus denitrificans PD1222 peptide chain release factor 1 YP_914701.1 877258 D 318586 CDS YP_914702.1 119383646 4578573 878318..879145 1 NC_008686.1 TIGRFAM: modification methylase, HemK family; PFAM: methyltransferase small; ribosomal L11 methyltransferase; Methyltransferase type 11; Methyltransferase type 12; KEGG: rsp:RSP_2906 methylase; HemK family modification methylase 879145 4578573 Pden_0895 Paracoccus denitrificans PD1222 HemK family modification methylase YP_914702.1 878318 D 318586 CDS YP_914703.1 119383647 4578574 879393..880181 1 NC_008686.1 KEGG: rsp:RSP_6078 hypothetical protein; hypothetical protein 880181 4578574 Pden_0896 Paracoccus denitrificans PD1222 hypothetical protein YP_914703.1 879393 D 318586 CDS YP_914704.1 119383648 4578575 complement(880185..881033) 1 NC_008686.1 catalyzes the transfer of a total of four methyl groups from S-adenosyl-l-methionine (S-AdoMet) to two adjacent adenosine bases A1518 and A1519 in 16S rRNA; mutations in ksgA causes resistance to the translation initiation inhibitor kasugamycin; dimethyladenosine transferase 881033 ksgA 4578575 ksgA Paracoccus denitrificans PD1222 dimethyladenosine transferase YP_914704.1 880185 R 318586 CDS YP_914705.1 119383649 4578576 complement(881030..881998) 1 NC_008686.1 catalyzes oxidation of 4-(phosphohydroxy)-L-threonine into 2-amino-3-oxo-4-(phosphohydroxy)butyric acid which decarboxylates to form 1-amino-3-(phosphohydroxy)propan-2-one (3-amino-2-oxopropyl phosphate); 4-hydroxythreonine-4-phosphate dehydrogenase 881998 pdxA 4578576 pdxA Paracoccus denitrificans PD1222 4-hydroxythreonine-4-phosphate dehydrogenase YP_914705.1 881030 R 318586 CDS YP_914706.1 119383650 4578577 complement(882066..883337) 1 NC_008686.1 PFAM: PpiC-type peptidyl-prolyl cis-trans isomerase; KEGG: rsp:RSP_2903 probable PpiC-type peptidyl-prolyl cis-trans isomerase; PpiC-type peptidyl-prolyl cis-trans isomerase 883337 4578577 Pden_0899 Paracoccus denitrificans PD1222 PpiC-type peptidyl-prolyl cis-trans isomerase YP_914706.1 882066 R 318586 CDS YP_914707.1 119383651 4578578 complement(883369..885783) 1 NC_008686.1 PFAM: Organic solvent tolerance protein; KEGG: rsp:RSP_2902 organic solvent tolerance protein; organic solvent tolerance protein 885783 4578578 Pden_0900 Paracoccus denitrificans PD1222 organic solvent tolerance protein YP_914707.1 883369 R 318586 CDS YP_914708.1 119383652 4578579 complement(885783..886904) 1 NC_008686.1 PFAM: permease YjgP/YjgQ family protein; KEGG: rsp:RSP_2901 permease; YjgP/YjgQ family permease 886904 4578579 Pden_0901 Paracoccus denitrificans PD1222 YjgP/YjgQ family permease YP_914708.1 885783 R 318586 CDS YP_914709.1 119383653 4578580 complement(886901..888049) 1 NC_008686.1 PFAM: permease YjgP/YjgQ family protein; KEGG: rsp:RSP_2900 predicted permease; YjgP/YjgQ family permease 888049 4578580 Pden_0902 Paracoccus denitrificans PD1222 YjgP/YjgQ family permease YP_914709.1 886901 R 318586 CDS YP_914710.1 119383654 4578581 888179..889780 1 NC_008686.1 catalyzes the removal of N-terminal amino acids preferably leucine from various peptides; leucyl aminopeptidase 889780 4578581 Pden_0903 Paracoccus denitrificans PD1222 leucyl aminopeptidase YP_914710.1 888179 D 318586 CDS YP_914711.1 119383655 4578582 889780..890229 1 NC_008686.1 binds to single-strand binding (SSB) protein and acts as a bridge between the DnaX clamp loader complex and the SSB; DNA polymerase III subunit chi 890229 4578582 Pden_0904 Paracoccus denitrificans PD1222 DNA polymerase III subunit chi YP_914711.1 889780 D 318586 CDS YP_914712.1 119383656 4578583 complement(890283..890858) 1 NC_008686.1 KEGG: sit:TM1040_0952 conserved hypothetical protein; hypothetical protein 890858 4578583 Pden_0905 Paracoccus denitrificans PD1222 hypothetical protein YP_914712.1 890283 R 318586 CDS YP_914713.1 119383657 4579055 complement(890858..891469) 1 NC_008686.1 PFAM: multiple antibiotic resistance (MarC)-related proteins; KEGG: rsp:RSP_2896 multiple antibiotic transporter; multiple antibiotic resistance (MarC)-like proteins 891469 4579055 Pden_0906 Paracoccus denitrificans PD1222 multiple antibiotic resistance (MarC)-like proteins YP_914713.1 890858 R 318586 CDS YP_914714.1 119383658 4579056 891636..891914 1 NC_008686.1 PFAM: sec-independent translocation protein mttA/Hcf106; KEGG: rde:RD1_3255 twin-arginine translocation protein, TatA/E family; sec-independent translocation protein mttA/Hcf106 891914 4579056 Pden_0907 Paracoccus denitrificans PD1222 sec-independent translocation protein mttA/Hcf106 YP_914714.1 891636 D 318586 CDS YP_914715.1 119383659 4579057 891933..892436 1 NC_008686.1 TIGRFAM: twin-arginine translocation protein, TatB subunit; PFAM: sec-independent translocation protein mttA/Hcf106; KEGG: rsp:RSP_6059 twin-arginine translocation system protein, TatB; twin-arginine translocation protein subunit TatB 892436 4579057 Pden_0908 Paracoccus denitrificans PD1222 twin-arginine translocation protein subunit TatB YP_914715.1 891933 D 318586 CDS YP_914716.1 119383660 4579058 892437..893279 1 NC_008686.1 TIGRFAM: Sec-independent protein translocase, TatC subunit; PFAM: Sec-independent periplasmic protein translocase; KEGG: rsp:RSP_2541 twin-arginine translocation system protein, TatC; Sec-independent protein translocase subunit TatC 893279 4579058 Pden_0909 Paracoccus denitrificans PD1222 Sec-independent protein translocase subunit TatC YP_914716.1 892437 D 318586 CDS YP_914717.1 119383661 4579059 893272..894114 1 NC_008686.1 PFAM: protein of unknown function DUF815; KEGG: rsp:RSP_2542 ATPase; hypothetical protein 894114 4579059 Pden_0910 Paracoccus denitrificans PD1222 hypothetical protein YP_914717.1 893272 D 318586 CDS YP_914718.1 119383662 4579060 complement(894663..895712) 1 NC_008686.1 PFAM: Choloylglycine hydrolase; KEGG: atc:AGR_L_573 probable hydrolase VCA0877; choloylglycine hydrolase 895712 4579060 Pden_0911 Paracoccus denitrificans PD1222 choloylglycine hydrolase YP_914718.1 894663 R 318586 CDS YP_914719.1 119383663 4579061 complement(895740..896078) 1 NC_008686.1 hypothetical protein 896078 4579061 Pden_0912 Paracoccus denitrificans PD1222 hypothetical protein YP_914719.1 895740 R 318586 CDS YP_914720.1 119383664 4579062 complement(896404..897765) 1 NC_008686.1 An oxygenase that acts to open the ring of homogentisate formingmaleylacetoacetate as part of the catabolism of L-tyrosine and L-phenylalanine; homogentisate 1,2-dioxygenase 897765 4579062 Pden_0913 Paracoccus denitrificans PD1222 homogentisate 1,2-dioxygenase YP_914720.1 896404 R 318586 CDS YP_914721.1 119383665 4579063 897908..898339 1 NC_008686.1 PFAM: regulatory protein, MarR; KEGG: rde:RD1_3650 transcriptional regulator MarR/EmrR family; MarR family transcriptional regulator 898339 4579063 Pden_0914 Paracoccus denitrificans PD1222 MarR family transcriptional regulator YP_914721.1 897908 D 318586 CDS YP_914722.1 119383666 4579064 complement(898445..898843) 1 NC_008686.1 PFAM: Entericidin EcnAB; entericidin A/B 898843 4579064 Pden_0915 Paracoccus denitrificans PD1222 entericidin A/B YP_914722.1 898445 R 318586 CDS YP_914723.1 119383667 4579065 898903..899223 1 NC_008686.1 KEGG: rde:RD1_1084 hypothetical protein; TraR/DksA family transcriptional regulator 899223 4579065 Pden_0916 Paracoccus denitrificans PD1222 TraR/DksA family transcriptional regulator YP_914723.1 898903 D 318586 CDS YP_914724.1 119383668 4579066 complement(899233..899382) 1 NC_008686.1 PFAM: Entericidin EcnAB; KEGG: rsp:RSP_6220 hypothetical protein; entericidin EcnAB 899382 4579066 Pden_0917 Paracoccus denitrificans PD1222 entericidin EcnAB YP_914724.1 899233 R 318586 CDS YP_914725.1 119383669 4579067 complement(899825..900592) 1 NC_008686.1 PFAM: alpha/beta hydrolase fold; Thioesterase; PGAP1 family protein; KEGG: rsp:RSP_0821 esterase/lipase/thioesterase; alpha/beta hydrolase 900592 4579067 Pden_0918 Paracoccus denitrificans PD1222 alpha/beta hydrolase YP_914725.1 899825 R 318586 CDS YP_914726.1 119383670 4579068 900663..901046 1 NC_008686.1 KEGG: rsp:RSP_0822 hypothetical protein; hypothetical protein 901046 4579068 Pden_0919 Paracoccus denitrificans PD1222 hypothetical protein YP_914726.1 900663 D 318586 CDS YP_914727.1 119383671 4579069 complement(901497..902780) 1 NC_008686.1 catalyzes the reaction of glycine with 5,10-methylenetetrahydrofolate to form L-serine and tetrahydrofolate; serine hydroxymethyltransferase 902780 glyA 4579069 glyA Paracoccus denitrificans PD1222 serine hydroxymethyltransferase YP_914727.1 901497 R 318586 CDS YP_914728.1 119383672 4579070 902924..903673 1 NC_008686.1 catalyzes the phosphorylation of NAD to NADP; inorganic polyphosphate/ATP-NAD kinase 903673 ppnK 4579070 ppnK Paracoccus denitrificans PD1222 inorganic polyphosphate/ATP-NAD kinase YP_914728.1 902924 D 318586 CDS YP_914729.1 119383673 4579071 903740..905335 1 NC_008686.1 TIGRFAM: peptide chain release factor 3; small GTP-binding protein; PFAM: protein synthesis factor, GTP-binding; elongation factor Tu, domain 2 protein; KEGG: rsp:RSP_2537 probable peptide chain release factor RF3; peptide chain release factor 3 905335 4579071 Pden_0922 Paracoccus denitrificans PD1222 peptide chain release factor 3 YP_914729.1 903740 D 318586 CDS YP_914730.1 119383674 4579072 905484..905984 1 NC_008686.1 hypothetical protein 905984 4579072 Pden_0923 Paracoccus denitrificans PD1222 hypothetical protein YP_914730.1 905484 D 318586 CDS YP_914731.1 119383675 4579073 complement(906075..906497) 1 NC_008686.1 PFAM: OsmC family protein; KEGG: rpa:RPA4194 osmotically inducible protein OsmC; OsmC family protein 906497 4579073 Pden_0924 Paracoccus denitrificans PD1222 OsmC family protein YP_914731.1 906075 R 318586 CDS YP_914732.1 119383676 4579399 906605..907498 1 NC_008686.1 PFAM: protein of unknown function DUF6, transmembrane; KEGG: bmb:BruAb2_0942 hypothetical membrane protein; hypothetical protein 907498 4579399 Pden_0925 Paracoccus denitrificans PD1222 hypothetical protein YP_914732.1 906605 D 318586 CDS YP_914733.1 119383677 4579400 907568..907921 1 NC_008686.1 PFAM: protein of unknown function DUF305; KEGG: mes:Meso_3895 protein of unknown function DUF305; hypothetical protein 907921 4579400 Pden_0926 Paracoccus denitrificans PD1222 hypothetical protein YP_914733.1 907568 D 318586 CDS YP_914734.1 119383678 4579401 complement(907993..909129) 1 NC_008686.1 KEGG: rsp:RSP_2659 deoxyguanosinetriphosphate triphosphohydrolase; TIGRFAM: deoxyguanosinetriphosphate triphosphohydrolase; PFAM: metal-dependent phosphohydrolase, HD sub domain; SMART: metal-dependent phosphohydrolase, HD region; deoxyguanosinetriphosphate triphosphohydrolase 909129 4579401 Pden_0927 Paracoccus denitrificans PD1222 deoxyguanosinetriphosphate triphosphohydrolase YP_914734.1 907993 R 318586 CDS YP_914735.1 119383679 4579402 909205..909540 1 NC_008686.1 TIGRFAM: iron-sulfur cluster assembly accessory protein; PFAM: HesB/YadR/YfhF-family protein; KEGG: jan:Jann_1504 HesB/YadR/YfhF; iron-sulfur cluster assembly accessory protein 909540 4579402 Pden_0928 Paracoccus denitrificans PD1222 iron-sulfur cluster assembly accessory protein YP_914735.1 909205 D 318586 CDS YP_914736.1 119383680 4579403 909579..910364 1 NC_008686.1 TIGRFAM: exodeoxyribonuclease III; exodeoxyribonuclease III Xth; PFAM: Endonuclease/exonuclease/phosphatase; KEGG: rsp:RSP_2657 exodeoxyribonuclease III; exodeoxyribonuclease III 910364 4579403 Pden_0929 Paracoccus denitrificans PD1222 exodeoxyribonuclease III YP_914736.1 909579 D 318586 CDS YP_914737.1 119383681 4579404 complement(910464..910817) 1 NC_008686.1 hypothetical protein 910817 4579404 Pden_0930 Paracoccus denitrificans PD1222 hypothetical protein YP_914737.1 910464 R 318586 CDS YP_914738.1 119383682 4579405 complement(910948..912804) 1 NC_008686.1 PFAM: extracellular solute-binding protein, family 5; KEGG: rsp:RSP_2856 oligopeptide ABC transporter, periplasmic-binding protein; extracellular solute-binding protein 912804 4579405 Pden_0931 Paracoccus denitrificans PD1222 extracellular solute-binding protein YP_914738.1 910948 R 318586 CDS YP_914739.1 119383683 4579406 913215..913997 1 NC_008686.1 TIGRFAM: 3-hydroxybutyrate dehydrogenase; PFAM: short-chain dehydrogenase/reductase SDR; KR; KEGG: rde:RD1_2738 D-beta-hydroxybutyrate dehydrogenase; 3-hydroxybutyrate dehydrogenase 913997 4579406 Pden_0932 Paracoccus denitrificans PD1222 3-hydroxybutyrate dehydrogenase YP_914739.1 913215 D 318586 CDS YP_914740.1 119383684 4579407 complement(914019..915005) 1 NC_008686.1 PFAM: basic membrane lipoprotein; KEGG: rha:RHA1_ro04986 hypothetical protein; basic membrane lipoprotein 915005 4579407 Pden_0933 Paracoccus denitrificans PD1222 basic membrane lipoprotein YP_914740.1 914019 R 318586 CDS YP_914741.1 119383685 4579408 complement(915121..916053) 1 NC_008686.1 flavin dependent thymidylate synthase; ThyX; thymidylate synthase complementing protein; catalyzes the formation of dTMP and tetrahydrofolate from dUMP and methylenetetrahydrofolate; the enzyme from Mycobacterium tuberculosis forms homotetramers; uses FAD as a cofactor; FAD-dependent thymidylate synthase 916053 thyX 4579408 thyX Paracoccus denitrificans PD1222 FAD-dependent thymidylate synthase YP_914741.1 915121 R 318586 CDS YP_914742.1 119383686 4579409 916203..916631 1 NC_008686.1 PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase; KEGG: rde:RD1_1872 lactoylglutathione lyase; glyoxalase/bleomycin resistance protein/dioxygenase 916631 4579409 Pden_0935 Paracoccus denitrificans PD1222 glyoxalase/bleomycin resistance protein/dioxygenase YP_914742.1 916203 D 318586 CDS YP_914743.1 119383687 4579410 complement(916811..917329) 1 NC_008686.1 PFAM: regulatory protein, MarR; KEGG: sil:SPO1267 transcriptional regulator, MarR family; MarR family transcriptional regulator 917329 4579410 Pden_0936 Paracoccus denitrificans PD1222 MarR family transcriptional regulator YP_914743.1 916811 R 318586 CDS YP_914744.1 119383688 4579411 complement(917421..917666) 1 NC_008686.1 PFAM: protein of unknown function DUF339; KEGG: rsp:RSP_0761 hypothetical protein; hypothetical protein 917666 4579411 Pden_0937 Paracoccus denitrificans PD1222 hypothetical protein YP_914744.1 917421 R 318586 CDS YP_914745.1 119383689 4579412 917772..918974 1 NC_008686.1 PFAM: aminotransferase, class I and II; KEGG: rsp:RSP_0763 aspartate aminotransferase; class I and II aminotransferase 918974 4579412 Pden_0938 Paracoccus denitrificans PD1222 class I and II aminotransferase YP_914745.1 917772 D 318586 CDS YP_914746.1 119383690 4579413 complement(919032..920438) 1 NC_008686.1 catalyzes the formation of fumarate from aspartate; aspartate ammonia-lyase 920438 aspA 4579413 aspA Paracoccus denitrificans PD1222 aspartate ammonia-lyase YP_914746.1 919032 R 318586 CDS YP_914747.1 119383691 4579414 complement(920599..921495) 1 NC_008686.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: sil:SPO2668 transcriptional regulator, LysR family; LysR family transcriptional regulator 921495 4579414 Pden_0940 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_914747.1 920599 R 318586 CDS YP_914748.1 119383692 4579415 921708..922742 1 NC_008686.1 PFAM: Malate/L-lactate dehydrogenase; KEGG: atc:AGR_L_410 probable L-malate dehydrogenase; malate/L-lactate dehydrogenase 922742 4579415 Pden_0941 Paracoccus denitrificans PD1222 malate/L-lactate dehydrogenase YP_914748.1 921708 D 318586 CDS YP_914749.1 119383693 4579416 complement(922739..923203) 1 NC_008686.1 PFAM: regulatory protein, AsnC/Lrp family; KEGG: jan:Jann_3495 transcriptional regulator, AsnC family; AsnC family transcriptional regulator 923203 4579416 Pden_0942 Paracoccus denitrificans PD1222 AsnC family transcriptional regulator YP_914749.1 922739 R 318586 CDS YP_914750.1 119383694 4579417 923313..926732 1 NC_008686.1 proline utilization protein A; multifunctional protein that functions in proline catabolism in the first two enzymatic steps resulting in the conversion of proline to glutamate; in Escherichia coli this protein self regulates transcription via a DNA-binding domain at the N-terminus but the protein from Pseudomonas does not have this domain; bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase 926732 4579417 Pden_0943 Paracoccus denitrificans PD1222 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase YP_914750.1 923313 D 318586 CDS YP_914751.1 119383695 4579418 926862..927233 1 NC_008686.1 KEGG: rsp:RSP_3680 transcriptional regulator, TetR family; TetR family transcriptional regulator 927233 4579418 Pden_0944 Paracoccus denitrificans PD1222 TetR family transcriptional regulator YP_914751.1 926862 D 318586 CDS YP_914752.1 119383696 4579656 927765..928766 1 NC_008686.1 PFAM: Substrate-binding region of ABC-type glycine betaine transport system; KEGG: sme:SMc02378 periplasmic binding transmembrane protein; substrate-binding region of ABC-type glycine betaine transport system 928766 4579656 Pden_0945 Paracoccus denitrificans PD1222 substrate-binding region of ABC-type glycine betaine transport system YP_914752.1 927765 D 318586 CDS YP_914753.1 119383697 4579657 928843..929733 1 NC_008686.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: sme:SMc02379 permease protein; binding-protein-dependent transport system inner membrane protein 929733 4579657 Pden_0946 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_914753.1 928843 D 318586 CDS YP_914754.1 119383698 4579658 929726..930772 1 NC_008686.1 KEGG: ret:RHE_PF00412 probable amino acid ABC transporter, ATP-binding protein; TIGRFAM: glycine betaine/L-proline ABC transporter, ATPase subunit; PFAM: ABC transporter related; SMART: AAA ATPase; glycine betaine/L-proline ABC transporter ATPase 930772 4579658 Pden_0947 Paracoccus denitrificans PD1222 glycine betaine/L-proline ABC transporter ATPase YP_914754.1 929726 D 318586 CDS YP_914755.1 119383699 4579659 930853..932481 1 NC_008686.1 PFAM: acyl-CoA dehydrogenase domain protein; Acyl-CoA dehydrogenase, type 2, C-terminal domain; KEGG: csa:Csal_2827 acyl-CoA dehydrogenase-like protein; acyl-CoA dehydrogenase 932481 4579659 Pden_0948 Paracoccus denitrificans PD1222 acyl-CoA dehydrogenase YP_914755.1 930853 D 318586 CDS YP_914756.1 119383700 4579660 complement(932488..933501) 1 NC_008686.1 PFAM: DNA/RNA non-specific endonuclease; KEGG: rha:RHA1_ro05345 hypothetical protein; DNA/RNA non-specific endonuclease 933501 4579660 Pden_0949 Paracoccus denitrificans PD1222 DNA/RNA non-specific endonuclease YP_914756.1 932488 R 318586 CDS YP_914757.1 119383701 4579661 complement(933691..935244) 1 NC_008686.1 PFAM: peptidase S8 and S53, subtilisin, kexin, sedolisin; KEGG: bha:BH0684 prepro-alkaline protease; peptidase S8/S53 subtilisin kexin sedolisin 935244 4579661 Pden_0950 Paracoccus denitrificans PD1222 peptidase S8/S53 subtilisin kexin sedolisin YP_914757.1 933691 R 318586 CDS YP_914758.1 119383702 4579662 complement(935339..937603) 1 NC_008686.1 TIGRFAM: ribonucleoside-diphosphate reductase, adenosylcobalamin-dependent; PFAM: ribonucleotide reductase large subunit; Ribonucleotide reductase large subunit, N terminal domain protein; KEGG: rsp:RSP_3547 ribonucleotide reductase; ribonucleoside-diphosphate reductase 937603 4579662 Pden_0951 Paracoccus denitrificans PD1222 ribonucleoside-diphosphate reductase YP_914758.1 935339 R 318586 CDS YP_914759.1 119383703 4579663 complement(937769..938428) 1 NC_008686.1 PFAM: DSBA oxidoreductase; KEGG: rsp:RSP_2852 predicted polyketide biosynthesis associated protein; DSBA oxidoreductase 938428 4579663 Pden_0952 Paracoccus denitrificans PD1222 DSBA oxidoreductase YP_914759.1 937769 R 318586 CDS YP_914760.1 119383704 4579664 complement(938429..939892) 1 NC_008686.1 PFAM: AMP-dependent synthetase and ligase; KEGG: sil:SPO2069 benzoate-coenzyme A ligase; AMP-dependent synthetase/ligase 939892 4579664 Pden_0953 Paracoccus denitrificans PD1222 AMP-dependent synthetase/ligase YP_914760.1 938429 R 318586 CDS YP_914761.1 119383705 4579665 complement(940098..940304) 1 NC_008686.1 PFAM: Cold-shock protein, DNA-binding; SMART: Cold shock protein; KEGG: rsp:RSP_0386 cold-shock DNA-binding domain protein; cold-shock DNA-binding domain-containing protein 940304 4579665 Pden_0954 Paracoccus denitrificans PD1222 cold-shock DNA-binding domain-containing protein YP_914761.1 940098 R 318586 CDS YP_914762.1 119383706 4579666 complement(940532..942478) 1 NC_008686.1 catalyzes a two-step reaction, first charging a threonine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; catalyzes the formation of threonyl-tRNA(Thr) from threonine and tRNA(Thr); threonyl-tRNA synthetase 942478 thrS 4579666 thrS Paracoccus denitrificans PD1222 threonyl-tRNA synthetase YP_914762.1 940532 R 318586 CDS YP_914763.1 119383707 4579667 942649..943398 1 NC_008686.1 KEGG: sit:TM1040_1720 conserved hypothetical protein; hypothetical protein 943398 4579667 Pden_0956 Paracoccus denitrificans PD1222 hypothetical protein YP_914763.1 942649 D 318586 CDS YP_914764.1 119383708 4579668 complement(943441..944784) 1 NC_008686.1 TIGRFAM: polyhydroxyalkanoate depolymerase, intracellular; PFAM: PHB de-polymerase domain protein; KEGG: rde:RD1_1887 polyhydroxyalkanoate depolymerase, intracellular; polyhydroxyalkanoate depolymerase 944784 4579668 Pden_0957 Paracoccus denitrificans PD1222 polyhydroxyalkanoate depolymerase YP_914764.1 943441 R 318586 CDS YP_914765.1 119383709 4579669 944898..947219 1 NC_008686.1 TIGRFAM: poly(R)-hydroxyalkanoic acid synthase, class I; PFAM: Poly-beta-hydroxybutyrate polymerase domain protein; KEGG: rde:RD1_1888 poly(3-hydroxyalkanoate) polymerase; poly(R)-hydroxyalkanoic acid synthase 947219 4579669 Pden_0958 Paracoccus denitrificans PD1222 poly(R)-hydroxyalkanoic acid synthase YP_914765.1 944898 D 318586 CDS YP_914766.1 119383710 4579670 947333..947806 1 NC_008686.1 KEGG: rsp:RSP_0381 hypothetical protein; hypothetical protein 947806 4579670 Pden_0959 Paracoccus denitrificans PD1222 hypothetical protein YP_914766.1 947333 D 318586 CDS YP_914767.1 119383711 4579671 947955..948542 1 NC_008686.1 TIGRFAM: polyhydroxyalkanoate synthesis repressor PhaR; PFAM: PHB accumulation regulatory domain protein; PHA accumulation regulator DNA-binding protein; KEGG: rsp:RSP_0380 hypothetical protein; polyhydroxyalkonate synthesis repressor PhaR 948542 4579671 Pden_0960 Paracoccus denitrificans PD1222 polyhydroxyalkonate synthesis repressor PhaR YP_914767.1 947955 D 318586 CDS YP_914768.1 119383712 4579672 complement(948709..949788) 1 NC_008686.1 PFAM: phage integrase family protein; KEGG: rsp:RSP_1662 integrase/recombinase; phage integrase family protein 949788 4579672 Pden_0961 Paracoccus denitrificans PD1222 phage integrase family protein YP_914768.1 948709 R 318586 CDS YP_914769.1 119383713 4579673 complement(949785..950018) 1 NC_008686.1 KEGG: rsp:RSP_6015 hypothetical protein; hypothetical protein 950018 4579673 Pden_0962 Paracoccus denitrificans PD1222 hypothetical protein YP_914769.1 949785 R 318586 CDS YP_914770.1 119383714 4579674 complement(950015..950743) 1 NC_008686.1 KEGG: rsp:RSP_3624 hypothetical protein; hypothetical protein 950743 4579674 Pden_0963 Paracoccus denitrificans PD1222 hypothetical protein YP_914770.1 950015 R 318586 CDS YP_914771.1 119383715 4579538 complement(950740..951180) 1 NC_008686.1 hypothetical protein 951180 4579538 Pden_0964 Paracoccus denitrificans PD1222 hypothetical protein YP_914771.1 950740 R 318586 CDS YP_914772.1 119383716 4579539 complement(951170..951442) 1 NC_008686.1 hypothetical protein 951442 4579539 Pden_0965 Paracoccus denitrificans PD1222 hypothetical protein YP_914772.1 951170 R 318586 CDS YP_914773.1 119383717 4579540 complement(951442..952170) 1 NC_008686.1 hypothetical protein 952170 4579540 Pden_0966 Paracoccus denitrificans PD1222 hypothetical protein YP_914773.1 951442 R 318586 CDS YP_914774.1 119383718 4579541 complement(952167..952967) 1 NC_008686.1 KEGG: ecc:c1524 hypothetical protein; hypothetical protein 952967 4579541 Pden_0967 Paracoccus denitrificans PD1222 hypothetical protein YP_914774.1 952167 R 318586 CDS YP_914775.1 119383719 4579542 complement(952964..953392) 1 NC_008686.1 KEGG: bxe:Bxe_A3103 bacteriophage hypothetical protein; hypothetical protein 953392 4579542 Pden_0968 Paracoccus denitrificans PD1222 hypothetical protein YP_914775.1 952964 R 318586 CDS YP_914776.1 119383720 4579543 complement(953392..956043) 1 NC_008686.1 PFAM: DNA methylase N-4/N-6 domain protein; KEGG: mes:Meso_1199 helicase-like; DNA methylase N-4/N-6 domain-containing protein 956043 4579543 Pden_0969 Paracoccus denitrificans PD1222 DNA methylase N-4/N-6 domain-containing protein YP_914776.1 953392 R 318586 CDS YP_914777.1 119383721 4579544 complement(956047..957165) 1 NC_008686.1 KEGG: jan:Jann_0002 DNA polymerase III, beta subunit; TIGRFAM: DNA polymerase III, beta subunit; PFAM: DNA polymerase III, beta chain; DNA polymerase III subunit beta 957165 4579544 Pden_0970 Paracoccus denitrificans PD1222 DNA polymerase III subunit beta YP_914777.1 956047 R 318586 CDS YP_914778.1 119383722 4579545 complement(957302..957514) 1 NC_008686.1 hypothetical protein 957514 4579545 Pden_0971 Paracoccus denitrificans PD1222 hypothetical protein YP_914778.1 957302 R 318586 CDS YP_914779.1 119383723 4579546 complement(957514..957774) 1 NC_008686.1 hypothetical protein 957774 4579546 Pden_0972 Paracoccus denitrificans PD1222 hypothetical protein YP_914779.1 957514 R 318586 CDS YP_914780.1 119383724 4579547 958079..958315 1 NC_008686.1 hypothetical protein 958315 4579547 Pden_0973 Paracoccus denitrificans PD1222 hypothetical protein YP_914780.1 958079 D 318586 CDS YP_914781.1 119383725 4579548 complement(958305..958832) 1 NC_008686.1 hypothetical protein 958832 4579548 Pden_0974 Paracoccus denitrificans PD1222 hypothetical protein YP_914781.1 958305 R 318586 CDS YP_914782.1 119383726 4579549 complement(959004..959615) 1 NC_008686.1 PFAM: helix-turn-helix domain protein; peptidase S24, S26A and S26B; KEGG: rsp:RSP_3771 hypothetical protein; phage repressor 959615 4579549 Pden_0975 Paracoccus denitrificans PD1222 phage repressor YP_914782.1 959004 R 318586 CDS YP_914783.1 119383727 4579550 complement(959622..959930) 1 NC_008686.1 hypothetical protein 959930 4579550 Pden_0976 Paracoccus denitrificans PD1222 hypothetical protein YP_914783.1 959622 R 318586 CDS YP_914784.1 119383728 4579551 959968..960303 1 NC_008686.1 hypothetical protein 960303 4579551 Pden_0977 Paracoccus denitrificans PD1222 hypothetical protein YP_914784.1 959968 D 318586 CDS YP_914785.1 119383729 4579552 complement(960623..960958) 1 NC_008686.1 hypothetical protein 960958 4579552 Pden_0978 Paracoccus denitrificans PD1222 hypothetical protein YP_914785.1 960623 R 318586 CDS YP_914786.1 119383730 4579553 961090..961365 1 NC_008686.1 hypothetical protein 961365 4579553 Pden_0979 Paracoccus denitrificans PD1222 hypothetical protein YP_914786.1 961090 D 318586 CDS YP_914787.1 119383731 4579554 961362..961556 1 NC_008686.1 hypothetical protein 961556 4579554 Pden_0980 Paracoccus denitrificans PD1222 hypothetical protein YP_914787.1 961362 D 318586 CDS YP_914788.1 119383732 4579555 961553..962695 1 NC_008686.1 KEGG: sit:TM1040_1631 hypothetical protein; hypothetical protein 962695 4579555 Pden_0981 Paracoccus denitrificans PD1222 hypothetical protein YP_914788.1 961553 D 318586 CDS YP_914789.1 119383733 4579556 962688..962936 1 NC_008686.1 hypothetical protein 962936 4579556 Pden_0982 Paracoccus denitrificans PD1222 hypothetical protein YP_914789.1 962688 D 318586 CDS YP_914790.1 119383734 4579557 962933..964771 1 NC_008686.1 TIGRFAM: phage/plasmid primase, P4 family; PFAM: Poxvirus D5 protein; KEGG: lin:lin2587 similar to bacteriophage protein; P4 family phage/plasmid primase 964771 4579557 Pden_0983 Paracoccus denitrificans PD1222 P4 family phage/plasmid primase YP_914790.1 962933 D 318586 CDS YP_914791.1 119383735 4578760 965147..965905 1 NC_008686.1 KEGG: rsp:RSP_3778 hypothetical protein; hypothetical protein 965905 4578760 Pden_0984 Paracoccus denitrificans PD1222 hypothetical protein YP_914791.1 965147 D 318586 CDS YP_914792.1 119383736 4578761 966075..966425 1 NC_008686.1 PFAM: HNH endonuclease; SMART: HNH nuclease; KEGG: rsp:RSP_2072 phage-related holin protein; HNH endonuclease 966425 4578761 Pden_0985 Paracoccus denitrificans PD1222 HNH endonuclease YP_914792.1 966075 D 318586 CDS YP_914793.1 119383737 4578762 966475..966735 1 NC_008686.1 hypothetical protein 966735 4578762 Pden_0986 Paracoccus denitrificans PD1222 hypothetical protein YP_914793.1 966475 D 318586 CDS YP_914794.1 119383738 4578763 966910..967413 1 NC_008686.1 PFAM: Resolvase helix-turn-helix domain protein; KEGG: sit:TM1040_1626 hypothetical protein; resolvase domain-containing protein 967413 4578763 Pden_0987 Paracoccus denitrificans PD1222 resolvase domain-containing protein YP_914794.1 966910 D 318586 CDS YP_914795.1 119383739 4578764 967403..969124 1 NC_008686.1 PFAM: phage Terminase; KEGG: rsp:RSP_2070 phage-related terminase; phage terminase 969124 4578764 Pden_0988 Paracoccus denitrificans PD1222 phage terminase YP_914795.1 967403 D 318586 CDS YP_914796.1 119383740 4578765 969124..970461 1 NC_008686.1 TIGRFAM: phage portal protein, HK97 family; PFAM: phage portal protein; KEGG: rsp:RSP_2069 phage portal protein, HK97 family; HK97 family phage portal protein 970461 4578765 Pden_0989 Paracoccus denitrificans PD1222 HK97 family phage portal protein YP_914796.1 969124 D 318586 CDS YP_914797.1 119383741 4578766 970448..971290 1 NC_008686.1 PFAM: peptidase S14, ClpP; KEGG: rsp:RSP_2068 ClpP-like protease; peptidase S14, ClpP 971290 4578766 Pden_0990 Paracoccus denitrificans PD1222 peptidase S14, ClpP YP_914797.1 970448 D 318586 CDS YP_914798.1 119383742 4578767 971302..972651 1 NC_008686.1 TIGRFAM: phage major capsid protein, HK97 family; KEGG: rsp:RSP_2067 prophage LambdaSo, major capsid protein, HK97 family; HK97 family phage major capsid protein 972651 4578767 Pden_0991 Paracoccus denitrificans PD1222 HK97 family phage major capsid protein YP_914798.1 971302 D 318586 CDS YP_914799.1 119383743 4578768 972709..973017 1 NC_008686.1 hypothetical protein 973017 4578768 Pden_0992 Paracoccus denitrificans PD1222 hypothetical protein YP_914799.1 972709 D 318586 CDS YP_914800.1 119383744 4578769 973059..973553 1 NC_008686.1 hypothetical protein 973553 4578769 Pden_0993 Paracoccus denitrificans PD1222 hypothetical protein YP_914800.1 973059 D 318586 CDS YP_914801.1 119383745 4578770 973522..974070 1 NC_008686.1 KEGG: sit:TM1040_1619 phage conserved hypothetical protein, phiE125 gp8; hypothetical protein 974070 4578770 Pden_0994 Paracoccus denitrificans PD1222 hypothetical protein YP_914801.1 973522 D 318586 CDS YP_914802.1 119383746 4578771 974064..974414 1 NC_008686.1 KEGG: sit:TM1040_1666 conserved hypothetical protein; hypothetical protein 974414 4578771 Pden_0995 Paracoccus denitrificans PD1222 hypothetical protein YP_914802.1 974064 D 318586 CDS YP_914803.1 119383747 4578772 974411..974818 1 NC_008686.1 KEGG: rpa:RPA1898 homologue of rhodobacter capsulatus gene transfer agent (GTA) orfg8 (32% identity); hypothetical protein 974818 4578772 Pden_0996 Paracoccus denitrificans PD1222 hypothetical protein YP_914803.1 974411 D 318586 CDS YP_914804.1 119383748 4578773 975002..975460 1 NC_008686.1 TIGRFAM: phage protein, HK97 gp10 family; PFAM: TP901-1 ORF40 family protein; KEGG: mes:Meso_1888 phage protein, HK97 GP10 family; HK97 family phage protein 975460 4578773 Pden_0997 Paracoccus denitrificans PD1222 HK97 family phage protein YP_914804.1 975002 D 318586 CDS YP_914805.1 119383749 4578774 975521..975982 1 NC_008686.1 hypothetical protein 975982 4578774 Pden_0998 Paracoccus denitrificans PD1222 hypothetical protein YP_914805.1 975521 D 318586 CDS YP_914806.1 119383750 4578775 975982..976437 1 NC_008686.1 hypothetical protein 976437 4578775 Pden_0999 Paracoccus denitrificans PD1222 hypothetical protein YP_914806.1 975982 D 318586 CDS YP_914807.1 119383751 4578776 976763..979738 1 NC_008686.1 TIGRFAM: phage tape measure protein; KEGG: rso:RSc0873 bacteriophage-related transmembrane protein; phage tape measure protein 979738 4578776 Pden_1000 Paracoccus denitrificans PD1222 phage tape measure protein YP_914807.1 976763 D 318586 CDS YP_914808.1 119383752 4578777 979738..980418 1 NC_008686.1 hypothetical protein 980418 4578777 Pden_1001 Paracoccus denitrificans PD1222 hypothetical protein YP_914808.1 979738 D 318586 CDS YP_914809.1 119383753 4578778 980415..980981 1 NC_008686.1 hypothetical protein 980981 4578778 Pden_1002 Paracoccus denitrificans PD1222 hypothetical protein YP_914809.1 980415 D 318586 CDS YP_914810.1 119383754 4579752 980966..981337 1 NC_008686.1 KEGG: mes:Meso_1234 hypothetical protein; hypothetical protein 981337 4579752 Pden_1003 Paracoccus denitrificans PD1222 hypothetical protein YP_914810.1 980966 D 318586 CDS YP_914811.1 119383755 4579753 981337..983379 1 NC_008686.1 KEGG: nar:Saro_2739 hypothetical protein; hypothetical protein 983379 4579753 Pden_1004 Paracoccus denitrificans PD1222 hypothetical protein YP_914811.1 981337 D 318586 CDS YP_914812.1 119383756 4579754 983443..983823 1 NC_008686.1 hypothetical protein 983823 4579754 Pden_1005 Paracoccus denitrificans PD1222 hypothetical protein YP_914812.1 983443 D 318586 CDS YP_914813.1 119383757 4579755 complement(983811..984200) 1 NC_008686.1 PFAM: transposase, IS4 family protein; KEGG: sit:TM1040_0174 transposase, IS4; transposase, IS4 family protein 984200 4579755 Pden_1006 Paracoccus denitrificans PD1222 transposase, IS4 family protein YP_914813.1 983811 R 318586 CDS YP_914814.1 119383758 4579756 complement(984197..984568) 1 NC_008686.1 KEGG: nar:Saro_2759 transposase orfA IS5 family element; IS5 family transposase OrfA 984568 4579756 Pden_1007 Paracoccus denitrificans PD1222 IS5 family transposase OrfA YP_914814.1 984197 R 318586 CDS YP_914815.1 119383759 4579757 complement(984674..985630) 1 NC_008686.1 KEGG: rsp:RSP_4009 phosphate acetyl/butaryl transferase; TIGRFAM: phosphate acetyltransferase; PFAM: phosphate acetyl/butaryl transferase; phosphate acetyltransferase 985630 4579757 Pden_1008 Paracoccus denitrificans PD1222 phosphate acetyltransferase YP_914815.1 984674 R 318586 CDS YP_914816.1 119383760 4579758 complement(985643..986659) 1 NC_008686.1 PFAM: conserved hypothetical protein 698; KEGG: rsp:RSP_4010 conserved hypothetical protein 698; hypothetical protein 986659 4579758 Pden_1009 Paracoccus denitrificans PD1222 hypothetical protein YP_914816.1 985643 R 318586 CDS YP_914817.1 119383761 4579759 complement(986933..988714) 1 NC_008686.1 catalyzes the formation of acetyl phosphate and sulfite from 2-sulfoacetaldehyde; is active when grown on taurine as a sole carbon source; sulfoacetaldehyde acetyltransferase 988714 4579759 Pden_1010 Paracoccus denitrificans PD1222 sulfoacetaldehyde acetyltransferase YP_914817.1 986933 R 318586 CDS YP_914818.1 119383762 4579760 complement(988911..990215) 1 NC_008686.1 PFAM: major facilitator superfamily MFS_1; KEGG: bja:bll6038 hypothetical transport protein; major facilitator superfamily transporter 990215 4579760 Pden_1011 Paracoccus denitrificans PD1222 major facilitator superfamily transporter YP_914818.1 988911 R 318586 CDS YP_914819.1 119383763 4579761 complement(990373..991899) 1 NC_008686.1 PFAM: AMP-dependent synthetase and ligase; KEGG: rde:RD1_2917 hypothetical protein; AMP-dependent synthetase/ligase 991899 4579761 Pden_1012 Paracoccus denitrificans PD1222 AMP-dependent synthetase/ligase YP_914819.1 990373 R 318586 CDS YP_914820.1 119383764 4579762 complement(991896..993305) 1 NC_008686.1 KEGG: jan:Jann_1566 aldehyde dehydrogenase; succinate-semialdehyde dehydrogenase (NAD(P)(+)) 993305 4579762 Pden_1013 Paracoccus denitrificans PD1222 succinate-semialdehyde dehydrogenase (NAD(P)(+)) YP_914820.1 991896 R 318586 CDS YP_914821.1 119383765 4579763 993512..994546 1 NC_008686.1 PFAM: regulatory protein, LacI; periplasmic binding protein/LacI transcriptional regulator; KEGG: rde:RD1_2923 transcriptional regulator, LacI family; periplasmic binding protein/LacI transcriptional regulator 994546 4579763 Pden_1014 Paracoccus denitrificans PD1222 periplasmic binding protein/LacI transcriptional regulator YP_914821.1 993512 D 318586 CDS YP_914822.1 119383766 4579764 complement(994548..994751) 1 NC_008686.1 KEGG: ccr:CC2592 ISCc1, transposase OrfB; ISCc1, transposase OrfB 994751 4579764 Pden_1015 Paracoccus denitrificans PD1222 ISCc1, transposase OrfB YP_914822.1 994548 R 318586 CDS YP_914823.1 119383767 4579765 complement(994798..995172) 1 NC_008686.1 hypothetical protein 995172 4579765 Pden_1016 Paracoccus denitrificans PD1222 hypothetical protein YP_914823.1 994798 R 318586 CDS YP_914824.1 119383768 4579766 995578..996606 1 NC_008686.1 PFAM: transposase, IS111A/IS1328/IS1533; transposase IS116/IS110/IS902 family protein; KEGG: nha:Nham_3955 transposase IS116/IS110/IS902; transposase IS116/IS110/IS902 family protein 996606 4579766 Pden_1017 Paracoccus denitrificans PD1222 transposase IS116/IS110/IS902 family protein YP_914824.1 995578 D 318586 CDS YP_914825.1 119383769 4579767 997017..998231 1 NC_008686.1 PFAM: creatinase; peptidase M24; KEGG: ppu:PP_3667 creatinase; creatinase 998231 4579767 Pden_1018 Paracoccus denitrificans PD1222 creatinase YP_914825.1 997017 D 318586 CDS YP_914826.1 119383770 4579768 complement(998293..999084) 1 NC_008686.1 PFAM: Creatininase; KEGG: rxy:Rxyl_0459 creatininase; creatininase 999084 4579768 Pden_1019 Paracoccus denitrificans PD1222 creatininase YP_914826.1 998293 R 318586 CDS YP_914827.1 119383771 4579769 999184..1000077 1 NC_008686.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: rde:RD1_2370 transcriptional regulator, LysR family; LysR family transcriptional regulator 1000077 4579769 Pden_1020 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_914827.1 999184 D 318586 CDS YP_914828.1 119383772 4579770 1000194..1001321 1 NC_008686.1 KEGG: rde:RD1_2369 spermidine/putrescine ABC transporter, periplasmic binding protein; spermidine/putrescine ABC transporter, periplasmic binding protein 1001321 4579770 Pden_1021 Paracoccus denitrificans PD1222 spermidine/putrescine ABC transporter, periplasmic binding protein YP_914828.1 1000194 D 318586 CDS YP_914829.1 119383773 4579771 1001379..1002224 1 NC_008686.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: rde:RD1_2368 putrescine ABC transporter, permease protein; binding-protein-dependent transport system inner membrane protein 1002224 4579771 Pden_1022 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_914829.1 1001379 D 318586 CDS YP_914830.1 119383774 4579578 1002221..1003039 1 NC_008686.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: rde:RD1_2367 spermidine/putrescine transport system, permease protein; binding-protein-dependent transport system inner membrane protein 1003039 4579578 Pden_1023 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_914830.1 1002221 D 318586 CDS YP_914831.1 119383775 4579579 1003043..1004131 1 NC_008686.1 PFAM: ABC transporter related; TOBE domain protein; Transport-associated OB domain protein; SMART: AAA ATPase; KEGG: rde:RD1_2364 spermidine/putrescine ABC transporter, ATP-binding protein; ABC transporter 1004131 4579579 Pden_1024 Paracoccus denitrificans PD1222 ABC transporter YP_914831.1 1003043 D 318586 CDS YP_914832.1 119383776 4579580 1004440..1005285 1 NC_008686.1 PFAM: extracellular solute-binding protein, family 3; KEGG: atc:AGR_L_407 probable binding protein component of ABC transporter; extracellular solute-binding protein 1005285 4579580 Pden_1025 Paracoccus denitrificans PD1222 extracellular solute-binding protein YP_914832.1 1004440 D 318586 CDS YP_914833.1 119383777 4579581 1005295..1005960 1 NC_008686.1 TIGRFAM: polar amino acid ABC transporter, inner membrane subunit; PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: sme:SMb20264 amino acid ABC transporter permease protein; polar amino acid ABC transporter inner membrane subunit 1005960 4579581 Pden_1026 Paracoccus denitrificans PD1222 polar amino acid ABC transporter inner membrane subunit YP_914833.1 1005295 D 318586 CDS YP_914834.1 119383778 4579582 1005950..1006621 1 NC_008686.1 TIGRFAM: polar amino acid ABC transporter, inner membrane subunit; PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: pau:PA14_47950 amino acid ABC transporter permease; polar amino acid ABC transporter inner membrane subunit 1006621 4579582 Pden_1027 Paracoccus denitrificans PD1222 polar amino acid ABC transporter inner membrane subunit YP_914834.1 1005950 D 318586 CDS YP_914835.1 119383779 4579583 1006618..1007340 1 NC_008686.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sme:SMb20266 amino acid ABC transporter ATP-binding protein; ABC transporter 1007340 4579583 Pden_1028 Paracoccus denitrificans PD1222 ABC transporter YP_914835.1 1006618 D 318586 CDS YP_914836.1 119383780 4579584 1007353..1007610 1 NC_008686.1 hypothetical protein 1007610 4579584 Pden_1029 Paracoccus denitrificans PD1222 hypothetical protein YP_914836.1 1007353 D 318586 CDS YP_914837.1 119383781 4579585 1007692..1008927 1 NC_008686.1 PFAM: major facilitator superfamily MFS_1; KEGG: rru:Rru_A1180 major facilitator superfamily MFS_1; major facilitator superfamily transporter 1008927 4579585 Pden_1030 Paracoccus denitrificans PD1222 major facilitator superfamily transporter YP_914837.1 1007692 D 318586 CDS YP_914838.1 119383782 4579586 1009116..1010735 1 NC_008686.1 PFAM: glucose-methanol-choline oxidoreductase; GMC oxidoreductase; KEGG: mes:Meso_3754 glucose-methanol-choline oxidoreductase; glucose-methanol-choline oxidoreductase 1010735 4579586 Pden_1031 Paracoccus denitrificans PD1222 glucose-methanol-choline oxidoreductase YP_914838.1 1009116 D 318586 CDS YP_914839.1 119383783 4579587 1010907..1011980 1 NC_008686.1 PFAM: periplasmic binding protein/LacI transcriptional regulator; KEGG: rha:RHA1_ro00226 ABC sugar transporter, periplasmic solute-binding protein; periplasmic binding protein/LacI transcriptional regulator 1011980 4579587 Pden_1032 Paracoccus denitrificans PD1222 periplasmic binding protein/LacI transcriptional regulator YP_914839.1 1010907 D 318586 CDS YP_914840.1 119383784 4579588 1012013..1012810 1 NC_008686.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sco:SCO6010 probable ABC-transport system ATP binding protein; ABC transporter 1012810 4579588 Pden_1033 Paracoccus denitrificans PD1222 ABC transporter YP_914840.1 1012013 D 318586 CDS YP_914841.1 119383785 4579589 1012803..1014017 1 NC_008686.1 PFAM: inner-membrane translocator; KEGG: tfu:Tfu_1920 ABC transporter transmembrane transport protein; inner-membrane translocator 1014017 4579589 Pden_1034 Paracoccus denitrificans PD1222 inner-membrane translocator YP_914841.1 1012803 D 318586 CDS YP_914842.1 119383786 4579590 complement(1014024..1014977) 1 NC_008686.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: bms:BR1086 transcriptional regulator, LysR family; LysR family transcriptional regulator 1014977 4579590 Pden_1035 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_914842.1 1014024 R 318586 CDS YP_914843.1 119383787 4579591 1015071..1016027 1 NC_008686.1 PFAM: amidohydrolase 2; KEGG: mlo:mll5767 hypothetical protein; amidohydrolase 1016027 4579591 Pden_1036 Paracoccus denitrificans PD1222 amidohydrolase YP_914843.1 1015071 D 318586 CDS YP_914844.1 119383788 4579592 1016024..1017241 1 NC_008686.1 PFAM: amidohydrolase; Amidohydrolase 3; KEGG: mes:Meso_4503 amidohydrolase; amidohydrolase 1017241 4579592 Pden_1037 Paracoccus denitrificans PD1222 amidohydrolase YP_914844.1 1016024 D 318586 CDS YP_914845.1 119383789 4579593 complement(1017249..1018118) 1 NC_008686.1 PFAM: protein of unknown function DUF6, transmembrane; KEGG: mlo:mlr0545 hypothetical protein; hypothetical protein 1018118 4579593 Pden_1038 Paracoccus denitrificans PD1222 hypothetical protein YP_914845.1 1017249 R 318586 CDS YP_914846.1 119383790 4579594 complement(1018118..1018432) 1 NC_008686.1 PFAM: NIPSNAP family containing protein; KEGG: bbr:BB1741 hypothetical protein; NIPSNAP family protein 1018432 4579594 Pden_1039 Paracoccus denitrificans PD1222 NIPSNAP family protein YP_914846.1 1018118 R 318586 CDS YP_914847.1 119383791 4579595 complement(1018437..1019198) 1 NC_008686.1 PFAM: short-chain dehydrogenase/reductase SDR; KR; KEGG: bbr:BB1748 short chain dehydrogenase; short chain dehydrogenase 1019198 4579595 Pden_1040 Paracoccus denitrificans PD1222 short chain dehydrogenase YP_914847.1 1018437 R 318586 CDS YP_914848.1 119383792 4579596 complement(1019202..1019999) 1 NC_008686.1 PFAM: aspartate dehydrogenase; homoserine dehydrogenase, NAD-binding; KEGG: rso:RS01727 L-aspartate dehydrogenase; aspartate dehydrogenase 1019999 4579596 Pden_1041 Paracoccus denitrificans PD1222 aspartate dehydrogenase YP_914848.1 1019202 R 318586 CDS YP_914849.1 119383793 4578623 complement(1019996..1020793) 1 NC_008686.1 PFAM: alpha/beta hydrolase fold; KEGG: bbr:BB1746 hydrolase; alpha/beta hydrolase 1020793 4578623 Pden_1042 Paracoccus denitrificans PD1222 alpha/beta hydrolase YP_914849.1 1019996 R 318586 CDS YP_914850.1 119383794 4578624 complement(1020799..1021344) 1 NC_008686.1 PFAM: Cupin 2, conserved barrel domain protein; KEGG: bpa:BPP2288 hypothetical protein; cupin 1021344 4578624 Pden_1043 Paracoccus denitrificans PD1222 cupin YP_914850.1 1020799 R 318586 CDS YP_914851.1 119383795 4578625 complement(1021341..1023008) 1 NC_008686.1 PFAM: glucose-methanol-choline oxidoreductase; GMC oxidoreductase; KEGG: pfo:Pfl_5244 choline dehydrogenase; glucose-methanol-choline oxidoreductase 1023008 4578625 Pden_1044 Paracoccus denitrificans PD1222 glucose-methanol-choline oxidoreductase YP_914851.1 1021341 R 318586 CDS YP_914852.1 119383796 4578626 complement(1023021..1024043) 1 NC_008686.1 PFAM: proline racemase; KEGG: rha:RHA1_ro05288 probable proline racemase; proline racemase 1024043 4578626 Pden_1045 Paracoccus denitrificans PD1222 proline racemase YP_914852.1 1023021 R 318586 CDS YP_914853.1 119383797 4578627 complement(1024119..1025192) 1 NC_008686.1 PFAM: regulatory protein, LacI; periplasmic binding protein/LacI transcriptional regulator; KEGG: sil:SPO0590 transcriptional regulator, LacI family; regulatory protein, LacI 1025192 4578627 Pden_1046 Paracoccus denitrificans PD1222 regulatory protein, LacI YP_914853.1 1024119 R 318586 CDS YP_914854.1 119383798 4578628 1025338..1026639 1 NC_008686.1 PFAM: extracellular solute-binding protein, family 1; KEGG: rxy:Rxyl_0062 extracellular solute-binding protein, family 1; extracellular solute-binding protein 1026639 4578628 Pden_1047 Paracoccus denitrificans PD1222 extracellular solute-binding protein YP_914854.1 1025338 D 318586 CDS YP_914855.1 119383799 4578629 1026700..1027626 1 NC_008686.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: bja:bll2730 probable ABC transporter permease protein; binding-protein-dependent transport system inner membrane protein 1027626 4578629 Pden_1048 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_914855.1 1026700 D 318586 CDS YP_914856.1 119383800 4578630 1027639..1028481 1 NC_008686.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: rfr:Rfer_0952 binding-protein-dependent transport systems inner membrane component; binding-protein-dependent transport system inner membrane protein 1028481 4578630 Pden_1049 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_914856.1 1027639 D 318586 CDS YP_914857.1 119383801 4578631 1028486..1029556 1 NC_008686.1 PFAM: ABC transporter related; Transport-associated OB domain protein; SMART: AAA ATPase; KEGG: sth:STH1782 sugar ABC transportor ATP-binding protein; ABC transporter 1029556 4578631 Pden_1050 Paracoccus denitrificans PD1222 ABC transporter YP_914857.1 1028486 D 318586 CDS YP_914858.1 119383802 4578632 1029578..1031062 1 NC_008686.1 PFAM: aldehyde dehydrogenase; KEGG: mlo:mll1015 aldehyde dehydrogenase; aldehyde dehydrogenase 1031062 4578632 Pden_1051 Paracoccus denitrificans PD1222 aldehyde dehydrogenase YP_914858.1 1029578 D 318586 CDS YP_914859.1 119383803 4578634 1032328..1033653 1 NC_008686.1 PFAM: aldehyde dehydrogenase; KEGG: jan:Jann_3747 aldehyde dehydrogenase; aldehyde dehydrogenase 1033653 4578634 Pden_1054 Paracoccus denitrificans PD1222 aldehyde dehydrogenase YP_914859.1 1032328 D 318586 CDS YP_914860.1 119383804 4578635 complement(1033801..1034103) 1 NC_008686.1 hypothetical protein 1034103 4578635 Pden_1055 Paracoccus denitrificans PD1222 hypothetical protein YP_914860.1 1033801 R 318586 CDS YP_914861.1 119383805 4578636 1034464..1035075 1 NC_008686.1 KEGG: nha:Nham_3600 AMP-dependent synthetase and ligase; hypothetical protein 1035075 4578636 Pden_1056 Paracoccus denitrificans PD1222 hypothetical protein YP_914861.1 1034464 D 318586 CDS YP_914862.1 119383806 4578637 complement(1035142..1036530) 1 NC_008686.1 metallo-dependent hydrolase superfamily; deaminase with metallo-dependent hydrolase domain; deaminase 1036530 4578637 Pden_1057 Paracoccus denitrificans PD1222 deaminase YP_914862.1 1035142 R 318586 CDS YP_914863.1 119383807 4578638 1036643..1037509 1 NC_008686.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: pau:PA14_32360 LysR-family transcriptional regulator; LysR family transcriptional regulator 1037509 4578638 Pden_1058 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_914863.1 1036643 D 318586 CDS YP_914864.1 119383808 4578639 1037570..1037839 1 NC_008686.1 hypothetical protein 1037839 4578639 Pden_1059 Paracoccus denitrificans PD1222 hypothetical protein YP_914864.1 1037570 D 318586 CDS YP_914865.1 119383809 4578640 complement(1037869..1038864) 1 NC_008686.1 KEGG: sil:SPO0875 glyceraldehyde-3-phosphate dehydrogenase, type I; TIGRFAM: glyceraldehyde-3-phosphate dehydrogenase, type I; PFAM: glyceraldehyde 3-phosphate dehydrogenase; glyceraldehyde-3-phosphate dehydrogenase, type I 1038864 4578640 Pden_1060 Paracoccus denitrificans PD1222 glyceraldehyde-3-phosphate dehydrogenase, type I YP_914865.1 1037869 R 318586 CDS YP_914866.1 119383810 4578641 complement(1038928..1039539) 1 NC_008686.1 PFAM: protein of unknown function DUF224, cysteine-rich region domain protein; KEGG: bja:blr6041 glycolate oxidase; hypothetical protein 1039539 4578641 Pden_1061 Paracoccus denitrificans PD1222 hypothetical protein YP_914866.1 1038928 R 318586 CDS YP_914867.1 119383811 4578642 complement(1039892..1040434) 1 NC_008686.1 PFAM: flavin reductase domain protein, FMN-binding; KEGG: dar:Daro_1187 hypothetical protein; flavin reductase domain-containing protein 1040434 4578642 Pden_1062 Paracoccus denitrificans PD1222 flavin reductase domain-containing protein YP_914867.1 1039892 R 318586 CDS YP_914868.1 119383812 4580262 1040964..1041296 1 NC_008686.1 KEGG: atc:AGR_L_3474 hypothetical protein; aspartate racemase 1041296 4580262 Pden_1063 Paracoccus denitrificans PD1222 aspartate racemase YP_914868.1 1040964 D 318586 CDS YP_914869.1 119383813 4580263 complement(1041329..1042243) 1 NC_008686.1 PFAM: helix-turn-helix- domain containing protein, AraC type; AraC-type transcriptional regulator domain protein; KEGG: eca:ECA3213 AraC-family transcriptional regulator; AraC family transcriptional regulator 1042243 4580263 Pden_1064 Paracoccus denitrificans PD1222 AraC family transcriptional regulator YP_914869.1 1041329 R 318586 CDS YP_914870.1 119383814 4580264 1042377..1043132 1 NC_008686.1 PFAM: short-chain dehydrogenase/reductase SDR; KR; KEGG: eca:ECA3214 probable short chain dehydrogenase; short-chain dehydrogenase/reductase SDR 1043132 4580264 Pden_1065 Paracoccus denitrificans PD1222 short-chain dehydrogenase/reductase SDR YP_914870.1 1042377 D 318586 CDS YP_914871.1 119383815 4580265 complement(1043153..1043650) 1 NC_008686.1 KEGG: atc:AGR_C_479 hypothetical protein; hypothetical protein 1043650 4580265 Pden_1066 Paracoccus denitrificans PD1222 hypothetical protein YP_914871.1 1043153 R 318586 CDS YP_914872.1 119383816 4580266 complement(1043791..1044216) 1 NC_008686.1 PFAM: OsmC family protein; KEGG: gbe:GbCGDNIH1_0067 organic hydroperoxide resistance protein; OsmC family protein 1044216 4580266 Pden_1067 Paracoccus denitrificans PD1222 OsmC family protein YP_914872.1 1043791 R 318586 CDS YP_914873.1 119383817 4580267 1044336..1044779 1 NC_008686.1 PFAM: regulatory protein, MarR; KEGG: mlo:mlr2690 probable transcriptional regulator; MarR family transcriptional regulator 1044779 4580267 Pden_1068 Paracoccus denitrificans PD1222 MarR family transcriptional regulator YP_914873.1 1044336 D 318586 CDS YP_914874.1 119383818 4580268 1044898..1045320 1 NC_008686.1 KEGG: aba:Acid345_1171 hypothetical protein; hypothetical protein 1045320 4580268 Pden_1069 Paracoccus denitrificans PD1222 hypothetical protein YP_914874.1 1044898 D 318586 CDS YP_914875.1 119383819 4580269 1045344..1045961 1 NC_008686.1 PFAM: regulatory proteins, IclR; KEGG: bja:bll3094 transcriptional regulatory protein; regulatory proteins, IclR 1045961 4580269 Pden_1070 Paracoccus denitrificans PD1222 regulatory proteins, IclR YP_914875.1 1045344 D 318586 CDS YP_914876.1 119383820 4580270 1046186..1047334 1 NC_008686.1 PFAM: aminotransferase, class V; KEGG: bja:blr3095 probable aminotransferase; class V aminotransferase 1047334 4580270 Pden_1071 Paracoccus denitrificans PD1222 class V aminotransferase YP_914876.1 1046186 D 318586 CDS YP_914877.1 119383821 4580271 1047405..1048292 1 NC_008686.1 PFAM: extracellular solute-binding protein, family 3; KEGG: bja:blr3096 ABC transporter substrate-binding protein; extracellular solute-binding protein 1048292 4580271 Pden_1072 Paracoccus denitrificans PD1222 extracellular solute-binding protein YP_914877.1 1047405 D 318586 CDS YP_914878.1 119383822 4580272 1048349..1049110 1 NC_008686.1 TIGRFAM: polar amino acid ABC transporter, inner membrane subunit; PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: bja:blr3097 ABC transporter permease protein; polar amino acid ABC transporter inner membrane subunit 1049110 4580272 Pden_1073 Paracoccus denitrificans PD1222 polar amino acid ABC transporter inner membrane subunit YP_914878.1 1048349 D 318586 CDS YP_914879.1 119383823 4580273 1049107..1049799 1 NC_008686.1 TIGRFAM: polar amino acid ABC transporter, inner membrane subunit; PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: bja:blr3098 ABC transporter permease protein; polar amino acid ABC transporter inner membrane subunit 1049799 4580273 Pden_1074 Paracoccus denitrificans PD1222 polar amino acid ABC transporter inner membrane subunit YP_914879.1 1049107 D 318586 CDS YP_914880.1 119383824 4580274 1049814..1050566 1 NC_008686.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: psp:PSPPH_1133 amino acid ABC transporter, ATP-binding protein; ABC transporter 1050566 4580274 Pden_1075 Paracoccus denitrificans PD1222 ABC transporter YP_914880.1 1049814 D 318586 CDS YP_914881.1 119383825 4580275 complement(1050707..1051222) 1 NC_008686.1 PFAM: protein of unknown function DUF1697; KEGG: bja:bll4334 hypothetical protein; hypothetical protein 1051222 4580275 Pden_1076 Paracoccus denitrificans PD1222 hypothetical protein YP_914881.1 1050707 R 318586 CDS YP_914882.1 119383826 4580276 1051385..1052533 1 NC_008686.1 PFAM: ABC transporter related; Transport-associated OB domain protein; SMART: AAA ATPase; KEGG: mlo:mll3624 ATP-binding component of transport system; ABC transporter 1052533 4580276 Pden_1077 Paracoccus denitrificans PD1222 ABC transporter YP_914882.1 1051385 D 318586 CDS YP_914883.1 119383827 4580277 1052524..1053492 1 NC_008686.1 PFAM: extracellular solute-binding protein, family 1; KEGG: sit:TM1040_0544 extracellular solute-binding protein, family 1; extracellular solute-binding protein 1053492 4580277 Pden_1078 Paracoccus denitrificans PD1222 extracellular solute-binding protein YP_914883.1 1052524 D 318586 CDS YP_914884.1 119383828 4580278 1053498..1055225 1 NC_008686.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: mlo:mll3625 ABC transport system permease protein; binding-protein-dependent transport system inner membrane protein 1055225 4580278 Pden_1079 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_914884.1 1053498 D 318586 CDS YP_914885.1 119383829 4580279 1055213..1056331 1 NC_008686.1 PFAM: beta-lactamase domain protein; KEGG: sit:TM1040_0541 beta-lactamase-like; beta-lactamase domain-containing protein 1056331 4580279 Pden_1080 Paracoccus denitrificans PD1222 beta-lactamase domain-containing protein YP_914885.1 1055213 D 318586 CDS YP_914886.1 119383830 4580280 1056489..1056848 1 NC_008686.1 KEGG: sme:SMb20160 hypothetical protein; dual specificity protein phosphatase 1056848 4580280 Pden_1081 Paracoccus denitrificans PD1222 dual specificity protein phosphatase YP_914886.1 1056489 D 318586 CDS YP_914887.1 119383831 4578779 1056891..1057169 1 NC_008686.1 hypothetical protein 1057169 4578779 Pden_1082 Paracoccus denitrificans PD1222 hypothetical protein YP_914887.1 1056891 D 318586 CDS YP_914888.1 119383832 4578780 1057189..1058175 1 NC_008686.1 PFAM: beta-lactamase; KEGG: rsp:RSP_2235 hypothetical protein; beta-lactamase 1058175 4578780 Pden_1083 Paracoccus denitrificans PD1222 beta-lactamase YP_914888.1 1057189 D 318586 CDS YP_914889.1 119383833 4578781 1058320..1058490 1 NC_008686.1 KEGG: mes:Meso_0502 conjugal transfer protein; conjugal transfer protein 1058490 4578781 Pden_1084 Paracoccus denitrificans PD1222 conjugal transfer protein YP_914889.1 1058320 D 318586 CDS YP_914890.1 119383834 4578782 complement(1058907..1060412) 1 NC_008686.1 PFAM: glucose-methanol-choline oxidoreductase; KEGG: mlo:mlr6655 similar to dehydrogenase subunit; glucose-methanol-choline oxidoreductase 1060412 4578782 Pden_1086 Paracoccus denitrificans PD1222 glucose-methanol-choline oxidoreductase YP_914890.1 1058907 R 318586 CDS YP_914891.1 119383835 4578783 complement(1060420..1061517) 1 NC_008686.1 PFAM: ABC transporter related; TOBE domain protein; Transport-associated OB domain protein; SMART: AAA ATPase; KEGG: mlo:mlr6654 ABC transporter, ATP-binding component; ABC transporter 1061517 4578783 Pden_1087 Paracoccus denitrificans PD1222 ABC transporter YP_914891.1 1060420 R 318586 CDS YP_914892.1 119383836 4578784 complement(1061523..1062401) 1 NC_008686.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: mlo:mlr6653 ABC transporter (permease protein); binding-protein-dependent transport system inner membrane protein 1062401 4578784 Pden_1088 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_914892.1 1061523 R 318586 CDS YP_914893.1 119383837 4578785 complement(1062391..1063287) 1 NC_008686.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: mlo:mlr6652 ABC transporter (permease protein); binding-protein-dependent transport system inner membrane protein 1063287 4578785 Pden_1089 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_914893.1 1062391 R 318586 CDS YP_914894.1 119383838 4578786 complement(1063371..1064624) 1 NC_008686.1 PFAM: extracellular solute-binding protein, family 1; KEGG: mlo:mlr6651 ABC transporter (substrate-binding protein); extracellular solute-binding protein 1064624 4578786 Pden_1090 Paracoccus denitrificans PD1222 extracellular solute-binding protein YP_914894.1 1063371 R 318586 CDS YP_914895.1 119383839 4578787 complement(1064693..1066000) 1 NC_008686.1 catalyzes the oxidation of L-histidinol to L-histidinaldehyde and then to L-histidine in histidine biosynthesis; functions as a dimer; histidinol dehydrogenase 1066000 4578787 Pden_1091 Paracoccus denitrificans PD1222 histidinol dehydrogenase YP_914895.1 1064693 R 318586 CDS YP_914896.1 119383840 4578788 complement(1066114..1067916) 1 NC_008686.1 PFAM: thiamine pyrophosphate enzyme domain protein TPP-binding; thiamine pyrophosphate enzyme, central region; thiamine pyrophosphate enzyme TPP binding domain protein; KEGG: mlo:mlr6648 acetolactate synthase large subunit; thiamine pyrophosphate binding domain-containing protein 1067916 4578788 Pden_1092 Paracoccus denitrificans PD1222 thiamine pyrophosphate binding domain-containing protein YP_914896.1 1066114 R 318586 CDS YP_914897.1 119383841 4578789 1068069..1068911 1 NC_008686.1 SMART: helix-turn-helix domain protein; KEGG: mlo:mlr6646 hypothetical protein; XRE family transcriptional regulator 1068911 4578789 Pden_1093 Paracoccus denitrificans PD1222 XRE family transcriptional regulator YP_914897.1 1068069 D 318586 CDS YP_914898.1 119383842 4578790 1068972..1069730 1 NC_008686.1 KEGG: mlo:mll6647 hypothetical protein; hypothetical protein 1069730 4578790 Pden_1094 Paracoccus denitrificans PD1222 hypothetical protein YP_914898.1 1068972 D 318586 CDS YP_914899.1 119383843 4578791 1069750..1071117 1 NC_008686.1 PFAM: fumarate lyase; KEGG: bms:BR1958 aspartate ammonia-lyase; aspartate ammonia-lyase 1071117 4578791 Pden_1095 Paracoccus denitrificans PD1222 aspartate ammonia-lyase YP_914899.1 1069750 D 318586 CDS YP_914900.1 119383844 4578792 1071142..1072143 1 NC_008686.1 PFAM: glycoside hydrolase, family 3 domain protein; KEGG: bcn:Bcen_1514 glycoside hydrolase, family 3-like; glycoside hydrolase family protein 1072143 4578792 Pden_1096 Paracoccus denitrificans PD1222 glycoside hydrolase family protein YP_914900.1 1071142 D 318586 CDS YP_914901.1 119383845 4578793 complement(1072164..1072523) 1 NC_008686.1 KEGG: mlo:mlr6657 hypothetical protein; hypothetical protein 1072523 4578793 Pden_1097 Paracoccus denitrificans PD1222 hypothetical protein YP_914901.1 1072164 R 318586 CDS YP_914902.1 119383846 4578794 complement(1072561..1074150) 1 NC_008686.1 PFAM: glucose-methanol-choline oxidoreductase; FAD dependent oxidoreductase; GMC oxidoreductase; KEGG: mlo:mlr6656 dehydrogenase; glucose-methanol-choline oxidoreductase 1074150 4578794 Pden_1098 Paracoccus denitrificans PD1222 glucose-methanol-choline oxidoreductase YP_914902.1 1072561 R 318586 CDS YP_914903.1 119383847 4578795 1074342..1075223 1 NC_008686.1 PFAM: Xylose isomerase domain protein TIM barrel; KEGG: bcn:Bcen_1508 xylose isomerase-like TIM barrel; xylose isomerase domain-containing protein 1075223 4578795 Pden_1099 Paracoccus denitrificans PD1222 xylose isomerase domain-containing protein YP_914903.1 1074342 D 318586 CDS YP_914904.1 119383848 4578796 1075249..1076409 1 NC_008686.1 PFAM: major facilitator superfamily MFS_1; KEGG: rha:RHA1_ro01579 possible transporter, MFS superfamily; major facilitator superfamily transporter 1076409 4578796 Pden_1100 Paracoccus denitrificans PD1222 major facilitator superfamily transporter YP_914904.1 1075249 D 318586 CDS YP_914905.1 119383849 4578797 complement(1076527..1076964) 1 NC_008686.1 KEGG: sme:SMb20276 transcriptional regulator protein; RpiR family transcriptional regulator 1076964 4578797 Pden_1101 Paracoccus denitrificans PD1222 RpiR family transcriptional regulator YP_914905.1 1076527 R 318586 CDS YP_914906.1 119383850 4578798 complement(1077084..1077986) 1 NC_008686.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: gvi:glr2986 LysR family transcriptional regulatory protein; LysR family transcriptional regulator 1077986 4578798 Pden_1102 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_914906.1 1077084 R 318586 CDS YP_914907.1 119383851 4580437 1078420..1079778 1 NC_008686.1 PFAM: General substrate transporter; major facilitator superfamily MFS_1; KEGG: ppu:PP_2411 major facilitator family transporter; major facilitator superfamily transporter 1079778 4580437 Pden_1103 Paracoccus denitrificans PD1222 major facilitator superfamily transporter YP_914907.1 1078420 D 318586 CDS YP_914908.1 119383852 4580438 1079858..1080391 1 NC_008686.1 PFAM: 4-vinyl reductase, 4VR; KEGG: reu:Reut_B4820 4-vinyl reductase, 4VR; 4-vinyl reductase, 4VR 1080391 4580438 Pden_1104 Paracoccus denitrificans PD1222 4-vinyl reductase, 4VR YP_914908.1 1079858 D 318586 CDS YP_914909.1 119383853 4580439 1080449..1081447 1 NC_008686.1 PFAM: peptidase M19, renal dipeptidase; KEGG: cps:CPS_4019 peptidase, M19 family; peptidase M19 1081447 4580439 Pden_1105 Paracoccus denitrificans PD1222 peptidase M19 YP_914909.1 1080449 D 318586 CDS YP_914910.1 119383854 4580440 1082126..1082881 1 NC_008686.1 PFAM: regulatory protein GntR, HTH; GntR domain protein; KEGG: sil:SPO1912 transcriptional regulator, GntR family; GntR family transcriptional regulator 1082881 4580440 Pden_1106 Paracoccus denitrificans PD1222 GntR family transcriptional regulator YP_914910.1 1082126 D 318586 CDS YP_914911.1 119383855 4580441 1082878..1083873 1 NC_008686.1 PFAM: Alcohol dehydrogenase, zinc-binding domain protein; Alcohol dehydrogenase GroES domain protein; KEGG: pol:Bpro_2634 alcohol dehydrogenase, zinc-binding; alcohol dehydrogenase 1083873 4580441 Pden_1107 Paracoccus denitrificans PD1222 alcohol dehydrogenase YP_914911.1 1082878 D 318586 CDS YP_914912.1 119383856 4580442 complement(1083927..1085582) 1 NC_008686.1 activates fatty acids by binding to coenzyme A; acyl-CoA synthetase 1085582 4580442 Pden_1108 Paracoccus denitrificans PD1222 acyl-CoA synthetase YP_914912.1 1083927 R 318586 CDS YP_914913.1 119383857 4580443 complement(1085622..1085837) 1 NC_008686.1 KEGG: mes:Meso_2537 rhodanese-like; rhodanese-like protein 1085837 4580443 Pden_1109 Paracoccus denitrificans PD1222 rhodanese-like protein YP_914913.1 1085622 R 318586 CDS YP_914914.1 119383858 4580444 complement(1086247..1086537) 1 NC_008686.1 PFAM: protein of unknown function DUF1330; KEGG: mes:Meso_0684 protein of unknown function DUF1330; hypothetical protein 1086537 4580444 Pden_1110 Paracoccus denitrificans PD1222 hypothetical protein YP_914914.1 1086247 R 318586 CDS YP_914915.1 119383859 4580445 complement(1086592..1088076) 1 NC_008686.1 TIGRFAM: NCS1 nucleoside transporter family; PFAM: permease for cytosine/purines, uracil, thiamine, allantoin; KEGG: sit:TM1040_0338 NCS1 nucleoside transporter family; NCS1 nucleoside transporter 1088076 4580445 Pden_1111 Paracoccus denitrificans PD1222 NCS1 nucleoside transporter YP_914915.1 1086592 R 318586 CDS YP_914916.1 119383860 4580446 complement(1088170..1089639) 1 NC_008686.1 catalyzes the hydrolytic cleavage of hydantoin with aromatic side chains at the 5'position; phenylhydantoinase 1089639 4580446 Pden_1112 Paracoccus denitrificans PD1222 phenylhydantoinase YP_914916.1 1088170 R 318586 CDS YP_914917.1 119383861 4580447 complement(1089636..1090886) 1 NC_008686.1 allantoate amidohydrolase and N-carbamoyl-L-amino acid amidohydrolase are very similar; the allantoate amidohydrolase from Escherichia coli forms a dimer and binds zinc ions for catalytic activity and catalyzes the conversion of allantoate to (S)-ureidoglycolate and ammonia; carbamoyl amidohydrolase from Bacillus sp. converts N-carbamoyl amino acids to amino acids, ammonia, and carbon dioxide; allantoate amidohydrolase 1090886 4580447 Pden_1113 Paracoccus denitrificans PD1222 allantoate amidohydrolase YP_914917.1 1089636 R 318586 CDS YP_914918.1 119383862 4580448 1091275..1092417 1 NC_008686.1 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase subunit 1; catalyzes radical-mediated transfer of hydroxybenzyl group from 4-hydroxyphenylpyruvate (HPP) to 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione to form 7,8-didemethyl-8-hydroxy-5-deazariboflavin (FO); functions in F420 biosynthesis along with cofH; FO synthase subunit 1 1092417 cofG 4580448 cofG Paracoccus denitrificans PD1222 FO synthase subunit 1 YP_914918.1 1091275 D 318586 CDS YP_914919.1 119383863 4580449 1092414..1093670 1 NC_008686.1 PFAM: Radical SAM domain protein; SMART: Elongator protein 3/MiaB/NifB; KEGG: cps:CPS_4048 conserved hypothetical protein TIGR00423; radical SAM domain-containing protein 1093670 4580449 Pden_1115 Paracoccus denitrificans PD1222 radical SAM domain-containing protein YP_914919.1 1092414 D 318586 CDS YP_914920.1 119383864 4580450 1093667..1094620 1 NC_008686.1 catalyzes the formation of the L-lactyl phosphodiester of 7,8-didemethyl-8-hydroxy-5-deazariboflavin (F420-0) and GMP from actyl (2) diphospho-(5')guanosine (LPPG) to 7,8-didemethyl-8-hydroxy-5-deazariboflavin (FO); LPPG:FO 2-phospho-L-lactate transferase 1094620 4580450 Pden_1116 Paracoccus denitrificans PD1222 LPPG:FO 2-phospho-L-lactate transferase YP_914920.1 1093667 D 318586 CDS YP_914921.1 119383865 4580451 1094617..1095267 1 NC_008686.1 PFAM: protein of unknown function DUF121; KEGG: cps:CPS_4046 hypothetical protein; hypothetical protein 1095267 4580451 Pden_1117 Paracoccus denitrificans PD1222 hypothetical protein YP_914921.1 1094617 D 318586 CDS YP_914922.1 119383866 4580452 1095264..1096037 1 NC_008686.1 TIGRFAM: F420-dependent oxidoreductase, PFAM: protein of unknown function DUF129; KEGG: cps:CPS_4045 F420-dependent oxidoreductase; F420-dependent oxidoreductase 1096037 4580452 Pden_1118 Paracoccus denitrificans PD1222 F420-dependent oxidoreductase YP_914922.1 1095264 D 318586 CDS YP_914923.1 119383867 4580453 1096034..1096702 1 NC_008686.1 TIGRFAM: NADPH-dependent F420 reductase; PFAM: NADP oxidoreductase, coenzyme F420-dependent; NAD-dependent glycerol-3-phosphate dehydrogenase domain protein; KEGG: cps:CPS_4044 NADPH-dependent F420 reductase; NADPH-dependent F420 reductase 1096702 4580453 Pden_1119 Paracoccus denitrificans PD1222 NADPH-dependent F420 reductase YP_914923.1 1096034 D 318586 CDS YP_914924.1 119383868 4580454 1096737..1097738 1 NC_008686.1 PFAM: luciferase family protein; KEGG: cps:CPS_4043 methylenetetrahydromethanopterin reductase; luciferase family protein 1097738 4580454 Pden_1120 Paracoccus denitrificans PD1222 luciferase family protein YP_914924.1 1096737 D 318586 CDS YP_914925.1 119383869 4580455 1097832..1098497 1 NC_008686.1 PFAM: regulatory protein, TetR; Tetracycline transcriptional regulator YcdC, C-terminal domain protein; KEGG: mlo:mlr1634 probable transcriptional regulator; TetR family transcriptional regulator 1098497 4580455 Pden_1121 Paracoccus denitrificans PD1222 TetR family transcriptional regulator YP_914925.1 1097832 D 318586 CDS YP_914926.1 119383870 4578857 complement(1098969..1099472) 1 NC_008686.1 PFAM: protein of unknown function DUF336; KEGG: atc:AGR_C_2067 hypothetical protein; hypothetical protein 1099472 4578857 Pden_1122 Paracoccus denitrificans PD1222 hypothetical protein YP_914926.1 1098969 R 318586 CDS YP_914927.1 119383871 4578858 complement(1099543..1100151) 1 NC_008686.1 PFAM: regulatory protein, LuxR; response regulator receiver; Sigma-70, region 4 type 2; KEGG: atc:AGR_C_2066 hypothetical protein; Fis family transcriptional regulator 1100151 4578858 Pden_1123 Paracoccus denitrificans PD1222 Fis family transcriptional regulator YP_914927.1 1099543 R 318586 CDS YP_914928.1 119383872 4578859 complement(1100148..1101599) 1 NC_008686.1 PFAM: ATP-binding region, ATPase domain protein domain protein; histidine kinase A domain protein domain protein; KEGG: atc:AGR_C_2063 hypothetical protein; histidine kinase 1101599 4578859 Pden_1124 Paracoccus denitrificans PD1222 histidine kinase YP_914928.1 1100148 R 318586 CDS YP_914929.1 119383873 4578860 1101981..1102979 1 NC_008686.1 PFAM: ATPase associated with various cellular activities, AAA_3; ATPase associated with various cellular activities, AAA_5; SMART: AAA ATPase; KEGG: rsp:RSP_3275 MoxR-like ATPase; ATPase 1102979 4578860 Pden_1125 Paracoccus denitrificans PD1222 ATPase YP_914929.1 1101981 D 318586 CDS YP_914930.1 119383874 4578861 1103117..1103815 1 NC_008686.1 KEGG: rsp:RSP_3276 hypothetical protein; hypothetical protein 1103815 4578861 Pden_1126 Paracoccus denitrificans PD1222 hypothetical protein YP_914930.1 1103117 D 318586 CDS YP_914931.1 119383875 4578862 1103802..1104131 1 NC_008686.1 KEGG: rsp:RSP_6252 hypothetical protein; hypothetical protein 1104131 4578862 Pden_1127 Paracoccus denitrificans PD1222 hypothetical protein YP_914931.1 1103802 D 318586 CDS YP_914932.1 119383876 4578863 1104128..1104976 1 NC_008686.1 PFAM: von Willebrand factor, type A; KEGG: rsp:RSP_3278 Von Willebrand domain containing protein; von Willebrand factor type A domain-containing protein 1104976 4578863 Pden_1128 Paracoccus denitrificans PD1222 von Willebrand factor type A domain-containing protein YP_914932.1 1104128 D 318586 CDS YP_914933.1 119383877 4578864 1104973..1105920 1 NC_008686.1 PFAM: von Willebrand factor, type A; KEGG: rsp:RSP_3280 hypothetical protein; von Willebrand factor A 1105920 4578864 Pden_1129 Paracoccus denitrificans PD1222 von Willebrand factor A YP_914933.1 1104973 D 318586 CDS YP_914934.1 119383878 4578865 1105917..1106528 1 NC_008686.1 KEGG: rsp:RSP_3281 hypothetical protein; hypothetical protein 1106528 4578865 Pden_1130 Paracoccus denitrificans PD1222 hypothetical protein YP_914934.1 1105917 D 318586 CDS YP_914935.1 119383879 4578866 1106522..1107718 1 NC_008686.1 KEGG: rsp:RSP_3282 hypothetical protein; hypothetical protein 1107718 4578866 Pden_1131 Paracoccus denitrificans PD1222 hypothetical protein YP_914935.1 1106522 D 318586 CDS YP_914936.1 119383880 4578867 complement(1107943..1108827) 1 NC_008686.1 KEGG: mes:Meso_3101 PRC-barrel; PRC-barrel containing protein 1108827 4578867 Pden_1132 Paracoccus denitrificans PD1222 PRC-barrel containing protein YP_914936.1 1107943 R 318586 CDS YP_914937.1 119383881 4578868 complement(1108967..1109188) 1 NC_008686.1 KEGG: rsp:RSP_2379 hypothetical protein; hypothetical protein 1109188 4578868 Pden_1133 Paracoccus denitrificans PD1222 hypothetical protein YP_914937.1 1108967 R 318586 CDS YP_914938.1 119383882 4578869 complement(1109204..1110061) 1 NC_008686.1 PFAM: short-chain dehydrogenase/reductase SDR; KR; KEGG: ret:RHE_PE00299 oxidoreductase protein, short-chain dehydrogenase reductase (SDR)family; short-chain dehydrogenase/reductase SDR 1110061 4578869 Pden_1134 Paracoccus denitrificans PD1222 short-chain dehydrogenase/reductase SDR YP_914938.1 1109204 R 318586 CDS YP_914939.1 119383883 4578870 complement(1110058..1110744) 1 NC_008686.1 KEGG: sme:SMb20339 hypothetical protein; hypothetical protein 1110744 4578870 Pden_1135 Paracoccus denitrificans PD1222 hypothetical protein YP_914939.1 1110058 R 318586 CDS YP_914940.1 119383884 4578871 1110901..1111398 1 NC_008686.1 PFAM: protein of unknown function DUF892; KEGG: sme:SMc00371 hypothetical protein; hypothetical protein 1111398 4578871 Pden_1136 Paracoccus denitrificans PD1222 hypothetical protein YP_914940.1 1110901 D 318586 CDS YP_914941.1 119383885 4578872 complement(1111575..1112048) 1 NC_008686.1 PFAM: sigma-70 region 2 domain protein; sigma-70 region 4 domain protein; Sigma-70, region 4 type 2; KEGG: rsp:RSP_2681 sigma factor, RpoE; ECF subfamily RNA polymerase sigma-24 factor 1112048 4578872 Pden_1137 Paracoccus denitrificans PD1222 ECF subfamily RNA polymerase sigma-24 factor YP_914941.1 1111575 R 318586 CDS YP_914942.1 119383886 4578873 1112662..1113549 1 NC_008686.1 PFAM: helix-turn-helix- domain containing protein, AraC type; KEGG: sme:SMc01610 transcription regulator protein; helix-turn-helix domain-containing protein 1113549 4578873 Pden_1138 Paracoccus denitrificans PD1222 helix-turn-helix domain-containing protein YP_914942.1 1112662 D 318586 CDS YP_914943.1 119383887 4578874 1113565..1115775 1 NC_008686.1 TIGRFAM: TonB-dependent siderophore receptor; PFAM: TonB-dependent receptor; TonB-dependent receptor, plug; KEGG: rsp:RSP_1440 TonB dependent, hydroxamate-type ferrisiderophore, outer membrane receptor; TonB-dependent siderophore receptor 1115775 4578874 Pden_1139 Paracoccus denitrificans PD1222 TonB-dependent siderophore receptor YP_914943.1 1113565 D 318586 CDS YP_914944.1 119383888 4578875 1115769..1116647 1 NC_008686.1 PFAM: periplasmic binding protein; KEGG: rsp:RSP_1439 ABC Fe+3 hydroxamate (ferrichrome) transporter, periplasmic siderophore binding protein; periplasmic binding protein 1116647 4578875 Pden_1140 Paracoccus denitrificans PD1222 periplasmic binding protein YP_914944.1 1115769 D 318586 CDS YP_914945.1 119383889 4578876 1116644..1118614 1 NC_008686.1 part of the FhuBCD ATP-dependent iron (III) hydroxamate transporter involved in the high-affinity transport of Fe(3+)-ferrichrome; iron-hydroxamate transporter permease subunit 1118614 4578876 Pden_1141 Paracoccus denitrificans PD1222 iron-hydroxamate transporter permease subunit YP_914945.1 1116644 D 318586 CDS YP_914946.1 119383890 4580456 1118611..1119378 1 NC_008686.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rsp:RSP_1437 ABC Fe+3 hydroxamate (ferrichrome) transporter, ATPase subunit; ABC transporter 1119378 4580456 Pden_1142 Paracoccus denitrificans PD1222 ABC transporter YP_914946.1 1118611 D 318586 CDS YP_914947.1 119383891 4580457 1119400..1121097 1 NC_008686.1 PFAM: ABC transporter, transmembrane region; ABC transporter related; SMART: AAA ATPase; KEGG: rsp:RSP_3081 ABC multidrug efflux transporter, fused ATPase and inner membrane subunits; ABC transporter 1121097 4580457 Pden_1143 Paracoccus denitrificans PD1222 ABC transporter YP_914947.1 1119400 D 318586 CDS YP_914948.1 119383892 4580458 complement(1121215..1121577) 1 NC_008686.1 KEGG: ret:RHE_CH03726 hypothetical protein; hypothetical protein 1121577 4580458 Pden_1144 Paracoccus denitrificans PD1222 hypothetical protein YP_914948.1 1121215 R 318586 CDS YP_914949.1 119383893 4580459 complement(1121604..1122161) 1 NC_008686.1 TIGRFAM: intracellular protease, PfpI family; PFAM: ThiJ/PfpI domain protein; KEGG: ret:RHE_CH03725 hypothetical protein; PfpI family intracellular peptidase 1122161 4580459 Pden_1145 Paracoccus denitrificans PD1222 PfpI family intracellular peptidase YP_914949.1 1121604 R 318586 CDS YP_914950.1 119383894 4580460 complement(1122331..1123320) 1 NC_008686.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: bmb:BruAb1_1927 transcriptional regulator, LysR family; LysR family transcriptional regulator 1123320 4580460 Pden_1146 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_914950.1 1122331 R 318586 CDS YP_914951.1 119383895 4580461 1123561..1124403 1 NC_008686.1 PFAM: extracellular solute-binding protein, family 3; KEGG: bmb:BruAb1_1929 amino acid ABC transporter, periplasmic amino acid-binding protein; extracellular solute-binding protein 1124403 4580461 Pden_1147 Paracoccus denitrificans PD1222 extracellular solute-binding protein YP_914951.1 1123561 D 318586 CDS YP_914952.1 119383896 4580462 1124465..1125124 1 NC_008686.1 TIGRFAM: polar amino acid ABC transporter, inner membrane subunit; PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: bme:BMEI0113 asparagine transport system permease protein; polar amino acid ABC transporter inner membrane subunit 1125124 4580462 Pden_1148 Paracoccus denitrificans PD1222 polar amino acid ABC transporter inner membrane subunit YP_914952.1 1124465 D 318586 CDS YP_914953.1 119383897 4580463 1125128..1125850 1 NC_008686.1 TIGRFAM: polar amino acid ABC transporter, inner membrane subunit; PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: bmb:BruAb1_1931 amino acid ABC transporter, permease protein; polar amino acid ABC transporter inner membrane subunit 1125850 4580463 Pden_1149 Paracoccus denitrificans PD1222 polar amino acid ABC transporter inner membrane subunit YP_914953.1 1125128 D 318586 CDS YP_914954.1 119383898 4580464 1125898..1126653 1 NC_008686.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: bmb:BruAb1_1932 amino acid ABC transporter, ATP-binding protein; ABC transporter 1126653 4580464 Pden_1150 Paracoccus denitrificans PD1222 ABC transporter YP_914954.1 1125898 D 318586 CDS YP_914955.1 119383899 4580465 1126673..1127662 1 NC_008686.1 PFAM: Arginase/agmatinase/formiminoglutamase; KEGG: bms:BR1957 arginase family protein; arginase 1127662 4580465 Pden_1151 Paracoccus denitrificans PD1222 arginase YP_914955.1 1126673 D 318586 CDS YP_914956.1 119383900 4580466 1127743..1128501 1 NC_008686.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: bms:BR1959 amino acid ABC transporter, ATP-binding protein; ABC transporter 1128501 4580466 Pden_1152 Paracoccus denitrificans PD1222 ABC transporter YP_914956.1 1127743 D 318586 CDS YP_914957.1 119383901 4580467 1128513..1129523 1 NC_008686.1 PFAM: Asparaginase/glutaminase; KEGG: bmb:BruAb1_1936 L-asparaginase type II, hypothetical; asparaginase/glutaminase 1129523 4580467 Pden_1153 Paracoccus denitrificans PD1222 asparaginase/glutaminase YP_914957.1 1128513 D 318586 CDS YP_914958.1 119383902 4580468 1129819..1130460 1 NC_008686.1 KEGG: mag:amb4044 site-specific recombinase; hypothetical protein 1130460 4580468 Pden_1154 Paracoccus denitrificans PD1222 hypothetical protein YP_914958.1 1129819 D 318586 CDS YP_914959.1 119383903 4580469 1130501..1130773 1 NC_008686.1 hypothetical protein 1130773 4580469 Pden_1155 Paracoccus denitrificans PD1222 hypothetical protein YP_914959.1 1130501 D 318586 CDS YP_914960.1 119383904 4580470 1131251..1131565 1 NC_008686.1 KEGG: swo:Swol_1691 periplasmic binding protein; periplasmic binding protein 1131565 4580470 Pden_1157 Paracoccus denitrificans PD1222 periplasmic binding protein YP_914960.1 1131251 D 318586 CDS YP_914961.1 119383905 4580471 1131562..1132419 1 NC_008686.1 KEGG: mta:Moth_1420 hypothetical protein; hypothetical protein 1132419 4580471 Pden_1158 Paracoccus denitrificans PD1222 hypothetical protein YP_914961.1 1131562 D 318586 CDS YP_914962.1 119383906 4580472 1132445..1132687 1 NC_008686.1 KEGG: nwi:Nwi_2070 hypothetical protein; hypothetical protein 1132687 4580472 Pden_1159 Paracoccus denitrificans PD1222 hypothetical protein YP_914962.1 1132445 D 318586 CDS YP_914963.1 119383907 4580473 complement(1132706..1133068) 1 NC_008686.1 PFAM: HPP family protein+B94; KEGG: son:SO1392 hypothetical protein; HPP family protein 1133068 4580473 Pden_1160 Paracoccus denitrificans PD1222 HPP family protein YP_914963.1 1132706 R 318586 CDS YP_914964.1 119383908 4580474 complement(1133256..1134461) 1 NC_008686.1 Catalyzes the reversible two-electron oxidation of formate to carbon dioxide. It allows the assimilation of carbon dioxide and provides energy for growth through oxidative phosphorylation coupled to the reduction of oxygen, nitrate, sulphate or fumarate; formate dehydrogenase 1134461 4580474 Pden_1161 Paracoccus denitrificans PD1222 formate dehydrogenase YP_914964.1 1133256 R 318586 CDS YP_914965.1 119383909 4579928 1134577..1135359 1 NC_008686.1 PFAM: Arginase/agmatinase/formiminoglutamase; KEGG: csa:Csal_1087 arginase/agmatinase/formiminoglutamase; arginase 1135359 4579928 Pden_1162 Paracoccus denitrificans PD1222 arginase YP_914965.1 1134577 D 318586 CDS YP_914966.1 119383910 4579929 complement(1135367..1135786) 1 NC_008686.1 PFAM: NUDIX hydrolase; KEGG: pfl:PFL_4894 hydrolase, NUDIX family; NUDIX hydrolase 1135786 4579929 Pden_1163 Paracoccus denitrificans PD1222 NUDIX hydrolase YP_914966.1 1135367 R 318586 CDS YP_914967.1 119383911 4579931 1136932..1138197 1 NC_008686.1 PFAM: major facilitator superfamily MFS_1; KEGG: rsp:RSP_4025 major facilitator superfamily, fosmidomycin resistant protein; major facilitator superfamily transporter 1138197 4579931 Pden_1166 Paracoccus denitrificans PD1222 major facilitator superfamily transporter YP_914967.1 1136932 D 318586 CDS YP_914968.1 119383912 4579932 complement(1138212..1138949) 1 NC_008686.1 TIGRFAM: molybdenum ABC transporter, periplasmic molybdate-binding protein; KEGG: ava:Ava_4058 hypothetical protein; molybdenum ABC transporter periplasmic molybdate-binding protein 1138949 4579932 Pden_1167 Paracoccus denitrificans PD1222 molybdenum ABC transporter periplasmic molybdate-binding protein YP_914968.1 1138212 R 318586 CDS YP_914969.1 119383913 4579933 1139024..1140085 1 NC_008686.1 PFAM: periplasmic binding protein; KEGG: hin:HI1472 iron transport system substrate-binding protein; periplasmic binding protein 1140085 4579933 Pden_1168 Paracoccus denitrificans PD1222 periplasmic binding protein YP_914969.1 1139024 D 318586 CDS YP_914970.1 119383914 4579934 1140148..1141122 1 NC_008686.1 PFAM: transport system permease protein; KEGG: eca:ECA3095 ABC transporter permease protein; transport system permease 1141122 4579934 Pden_1169 Paracoccus denitrificans PD1222 transport system permease YP_914970.1 1140148 D 318586 CDS YP_914971.1 119383915 4579935 1141115..1141867 1 NC_008686.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rpa:RPA2310 iron ABC transporter ATP-binding protein; ABC transporter 1141867 4579935 Pden_1170 Paracoccus denitrificans PD1222 ABC transporter YP_914971.1 1141115 D 318586 CDS YP_914972.1 119383916 4579936 complement(1141928..1144021) 1 NC_008686.1 PFAM: TonB-dependent receptor; TonB-dependent receptor, plug; KEGG: nha:Nham_3366 TonB-dependent receptor; TonB-dependent receptor 1144021 4579936 Pden_1171 Paracoccus denitrificans PD1222 TonB-dependent receptor YP_914972.1 1141928 R 318586 CDS YP_914973.1 119383917 4579937 1144375..1144584 1 NC_008686.1 PFAM: TOBE domain protein; KEGG: mlo:msr1466 molybdo-pterin binding protein; TOBE domain-containing protein 1144584 4579937 Pden_1172 Paracoccus denitrificans PD1222 TOBE domain-containing protein YP_914973.1 1144375 D 318586 CDS YP_914974.1 119383918 4579938 complement(1144701..1145660) 1 NC_008686.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: bpm:BURPS1710b_A0985 transcriptional regulator CatR; LysR family transcriptional regulator 1145660 4579938 Pden_1173 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_914974.1 1144701 R 318586 CDS YP_914975.1 119383919 4579939 1145826..1147016 1 NC_008686.1 KEGG: bam:Bamb_6587 muconate and chloromuconate cycloisomerases; TIGRFAM: muconate and chloromuconate cycloisomerases; PFAM: Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein; Mandelate racemase/muconate lactonizing enzyme, C-terminal domain protein; muconate and chloromuconate cycloisomerase 1147016 4579939 Pden_1174 Paracoccus denitrificans PD1222 muconate and chloromuconate cycloisomerase YP_914975.1 1145826 D 318586 CDS YP_914976.1 119383920 4579940 1147019..1147309 1 NC_008686.1 PFAM: Muconolactone delta-isomerase; KEGG: bam:Bamb_6586 muconolactone delta-isomerase; muconolactone delta-isomerase 1147309 4579940 Pden_1175 Paracoccus denitrificans PD1222 muconolactone delta-isomerase YP_914976.1 1147019 D 318586 CDS YP_914977.1 119383921 4579941 1147377..1148315 1 NC_008686.1 TIGRFAM: catechol 1,2-dioxygenase; PFAM: intradiol ring-cleavage dioxygenase; Catechol dioxygenase, N-terminal domain protein; KEGG: aci:ACIAD1442 catechol 1,2-dioxygenase; catechol 1,2-dioxygenase 1148315 4579941 Pden_1176 Paracoccus denitrificans PD1222 catechol 1,2-dioxygenase YP_914977.1 1147377 D 318586 CDS YP_914978.1 119383922 4579942 1148433..1149791 1 NC_008686.1 PFAM: ring hydroxylating dioxygenase, alpha subunit; Rieske [2Fe-2S] domain protein; KEGG: bur:Bcep18194_C7046 ring hydroxylating dioxygenase, alpha subunit; Rieske (2Fe-2S) domain-containing protein 1149791 4579942 Pden_1177 Paracoccus denitrificans PD1222 Rieske (2Fe-2S) domain-containing protein YP_914978.1 1148433 D 318586 CDS YP_914979.1 119383923 4579943 1149788..1150276 1 NC_008686.1 PFAM: aromatic-ring-hydroxylating dioxygenase, beta subunit; KEGG: bur:Bcep18194_C7047 2-chlorobenzoate 1,2-dioxygenase; 2-chlorobenzoate 1,2-dioxygenase 1150276 4579943 Pden_1178 Paracoccus denitrificans PD1222 2-chlorobenzoate 1,2-dioxygenase YP_914979.1 1149788 D 318586 CDS YP_914980.1 119383924 4579944 1150318..1151346 1 NC_008686.1 PFAM: ferredoxin; oxidoreductase FAD/NAD(P)-binding domain protein; Oxidoreductase FAD-binding domain protein; FAD-binding 9, siderophore-interacting domain protein; KEGG: bam:Bamb_6582 oxidoreductase FAD/NAD(P)-binding domain protein; oxidoreductase FAD/NAD(P)-binding subunit 1151346 4579944 Pden_1179 Paracoccus denitrificans PD1222 oxidoreductase FAD/NAD(P)-binding subunit YP_914980.1 1150318 D 318586 CDS YP_914981.1 119383925 4579945 1151343..1152128 1 NC_008686.1 catalyzes the degradation of 2-hydro-1,2-dihydroxy benzoate to catechol; 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase 1152128 benD 4579945 benD Paracoccus denitrificans PD1222 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase YP_914981.1 1151343 D 318586 CDS YP_914982.1 119383926 4579946 1152170..1153501 1 NC_008686.1 PFAM: General substrate transporter; major facilitator superfamily MFS_1; KEGG: ppu:PP_3165 benzoate MFS transporter BenK; major facilitator superfamily transporter 1153501 4579946 Pden_1181 Paracoccus denitrificans PD1222 major facilitator superfamily transporter YP_914982.1 1152170 D 318586 CDS YP_914983.1 119383927 4579947 1153562..1154359 1 NC_008686.1 TIGRFAM: 3-oxoadipate enol-lactonase; PFAM: alpha/beta hydrolase fold; KEGG: xcb:XC_0382 b-ketoadipate enol-lactone hydrolase; 3-oxoadipate enol-lactonase 1154359 4579947 Pden_1182 Paracoccus denitrificans PD1222 3-oxoadipate enol-lactonase YP_914983.1 1153562 D 318586 CDS YP_914984.1 119383928 4580066 complement(1154430..1155110) 1 NC_008686.1 PFAM: regulatory protein GntR, HTH; GntR domain protein; KEGG: pau:PA14_47820 transcriptional regulator; GntR family transcriptional regulator 1155110 4580066 Pden_1183 Paracoccus denitrificans PD1222 GntR family transcriptional regulator YP_914984.1 1154430 R 318586 CDS YP_914985.1 119383929 4580067 1155325..1156353 1 NC_008686.1 PFAM: proline racemase; KEGG: bmb:BruAb1_0363 hypothetical proline racemase; proline racemase 1156353 4580067 Pden_1184 Paracoccus denitrificans PD1222 proline racemase YP_914985.1 1155325 D 318586 CDS YP_914986.1 119383930 4580068 1156370..1157320 1 NC_008686.1 PFAM: ornithine cyclodeaminase/mu-crystallin; Shikimate/quinate 5-dehydrogenase; KEGG: rsp:RSP_0854 predicted ornithine cyclodeaminase; ornithine cyclodeaminase/mu-crystallin 1157320 4580068 Pden_1185 Paracoccus denitrificans PD1222 ornithine cyclodeaminase/mu-crystallin YP_914986.1 1156370 D 318586 CDS YP_914987.1 119383931 4580069 complement(1157466..1158650) 1 NC_008686.1 PFAM: Alcohol dehydrogenase, zinc-binding domain protein; Alcohol dehydrogenase GroES domain protein; KEGG: atc:AGR_C_2885 hypothetical protein; alcohol dehydrogenase 1158650 4580069 Pden_1186 Paracoccus denitrificans PD1222 alcohol dehydrogenase YP_914987.1 1157466 R 318586 CDS YP_914988.1 119383932 4580070 complement(1158682..1159791) 1 NC_008686.1 PFAM: Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein; Mandelate racemase/muconate lactonizing enzyme, C-terminal domain protein; KEGG: rsp:RSP_4007 mandelate racemase/muconate lactonizing enzyme; mandelate racemase 1159791 4580070 Pden_1187 Paracoccus denitrificans PD1222 mandelate racemase YP_914988.1 1158682 R 318586 CDS YP_914989.1 119383933 4580071 complement(1159855..1160922) 1 NC_008686.1 PFAM: ferredoxin; oxidoreductase FAD/NAD(P)-binding domain protein; Oxidoreductase FAD-binding domain protein; KEGG: sme:SMa0752 possible dioxygenase reductase subunit; ferredoxin 1160922 4580071 Pden_1188 Paracoccus denitrificans PD1222 ferredoxin YP_914989.1 1159855 R 318586 CDS YP_914990.1 119383934 4580072 complement(1160925..1162277) 1 NC_008686.1 PFAM: Rieske [2Fe-2S] domain protein; KEGG: sme:SMa0751 aromatic-ring hydroxylating dioxygenase, alpha-subunit; Rieske (2Fe-2S) domain-containing protein 1162277 4580072 Pden_1189 Paracoccus denitrificans PD1222 Rieske (2Fe-2S) domain-containing protein YP_914990.1 1160925 R 318586 CDS YP_914991.1 119383935 4580073 1162292..1163167 1 NC_008686.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: sme:SMa0750 probable LysR-family transcriptional activator; LysR family transcriptional regulator 1163167 4580073 Pden_1190 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_914991.1 1162292 D 318586 CDS YP_914992.1 119383936 4580074 complement(1163174..1164652) 1 NC_008686.1 PFAM: FAD dependent oxidoreductase; KEGG: mes:Meso_1861 FAD dependent oxidoreductase; FAD dependent oxidoreductase 1164652 4580074 Pden_1191 Paracoccus denitrificans PD1222 FAD dependent oxidoreductase YP_914992.1 1163174 R 318586 CDS YP_914993.1 119383937 4580075 complement(1164649..1165437) 1 NC_008686.1 PFAM: NADP oxidoreductase, coenzyme F420-dependent; KEGG: ret:RHE_PF00409 pyrroline-5-carboxylate reductase protein; NADP oxidoreductase, coenzyme F420-dependent 1165437 4580075 Pden_1192 Paracoccus denitrificans PD1222 NADP oxidoreductase, coenzyme F420-dependent YP_914993.1 1164649 R 318586 CDS YP_914994.1 119383938 4580076 complement(1165434..1166477) 1 NC_008686.1 KEGG: ret:RHE_PF00412 probable amino acid ABC transporter, ATP-binding protein; TIGRFAM: glycine betaine/L-proline ABC transporter, ATPase subunit; PFAM: ABC transporter related; SMART: AAA ATPase; glycine betaine/L-proline ABC transporter ATPase 1166477 4580076 Pden_1193 Paracoccus denitrificans PD1222 glycine betaine/L-proline ABC transporter ATPase YP_914994.1 1165434 R 318586 CDS YP_914995.1 119383939 4580077 complement(1166470..1167360) 1 NC_008686.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: sme:SMc02379 permease protein; binding-protein-dependent transport system inner membrane protein 1167360 4580077 Pden_1194 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_914995.1 1166470 R 318586 CDS YP_914996.1 119383940 4580078 complement(1167437..1168438) 1 NC_008686.1 PFAM: Substrate-binding region of ABC-type glycine betaine transport system; KEGG: sme:SMc02378 periplasmic binding transmembrane protein; substrate-binding region of ABC-type glycine betaine transport system 1168438 4580078 Pden_1195 Paracoccus denitrificans PD1222 substrate-binding region of ABC-type glycine betaine transport system YP_914996.1 1167437 R 318586 CDS YP_914997.1 119383941 4580079 complement(1168970..1169614) 1 NC_008686.1 PFAM: regulatory protein, TetR; KEGG: rsp:RSP_3680 transcriptional regulator, TetR family; TetR family transcriptional regulator 1169614 4580079 Pden_1196 Paracoccus denitrificans PD1222 TetR family transcriptional regulator YP_914997.1 1168970 R 318586 CDS YP_914998.1 119383942 4580080 1169763..1171799 1 NC_008686.1 PFAM: NADH:flavin oxidoreductase/NADH oxidase; FAD-dependent pyridine nucleotide-disulphide oxidoreductase; KEGG: ppu:PP_4753 N-methylproline demethylase; NADH:flavin oxidoreductase 1171799 4580080 Pden_1197 Paracoccus denitrificans PD1222 NADH:flavin oxidoreductase YP_914998.1 1169763 D 318586 CDS YP_914999.1 119383943 4580081 complement(1172410..1172922) 1 NC_008686.1 PFAM: regulatory protein, MarR; KEGG: sil:SPO1261 transcriptional regulator, MarR family; MarR family transcriptional regulator 1172922 4580081 Pden_1198 Paracoccus denitrificans PD1222 MarR family transcriptional regulator YP_914999.1 1172410 R 318586 CDS YP_915000.1 119383944 4580082 1173049..1174212 1 NC_008686.1 KEGG: sil:SPO1214 hippurate hydrolase; TIGRFAM: amidohydrolase; PFAM: peptidase M20; peptidase dimerisation domain protein; amidohydrolase 1174212 4580082 Pden_1199 Paracoccus denitrificans PD1222 amidohydrolase YP_915000.1 1173049 D 318586 CDS YP_915001.1 119383945 4580083 1174251..1174988 1 NC_008686.1 KEGG: oih:OB0951 hypothetical protein; hypothetical protein 1174988 4580083 Pden_1200 Paracoccus denitrificans PD1222 hypothetical protein YP_915001.1 1174251 D 318586 CDS YP_915002.1 119383946 4580084 1175013..1175708 1 NC_008686.1 KEGG: oih:OB0952 hypothetical protein; hypothetical protein 1175708 4580084 Pden_1201 Paracoccus denitrificans PD1222 hypothetical protein YP_915002.1 1175013 D 318586 CDS YP_915003.1 119383947 4578584 complement(1176020..1176604) 1 NC_008686.1 PFAM: Resolvase, N-terminal domain; KEGG: bpm:BURPS1710b_2172 recombinase; resolvase domain-containing protein 1176604 4578584 Pden_1202 Paracoccus denitrificans PD1222 resolvase domain-containing protein YP_915003.1 1176020 R 318586 CDS YP_915004.1 119383948 4578585 1176837..1177217 1 NC_008686.1 hypothetical protein 1177217 4578585 Pden_1203 Paracoccus denitrificans PD1222 hypothetical protein YP_915004.1 1176837 D 318586 CDS YP_915005.1 119383949 4578586 complement(1177372..1178277) 1 NC_008686.1 KEGG: mes:Meso_2004 D-alanine--D-alanine ligase; TIGRFAM: D-alanine--D-alanine ligase; PFAM: D-alanine--D-alanine ligase domain protein; D-alanine--D-alanine ligase 1178277 4578586 Pden_1204 Paracoccus denitrificans PD1222 D-alanine--D-alanine ligase YP_915005.1 1177372 R 318586 CDS YP_915006.1 119383950 4578587 complement(1178651..1179286) 1 NC_008686.1 TIGRFAM: urease accessory protein UreG; PFAM: cobalamin synthesis protein, P47K; KEGG: rsp:RSP_0302 urease accessory protein G; urease accessory protein UreG 1179286 4578587 Pden_1205 Paracoccus denitrificans PD1222 urease accessory protein UreG YP_915006.1 1178651 R 318586 CDS YP_915007.1 119383951 4578588 complement(1179283..1179930) 1 NC_008686.1 PFAM: Urease accessory protein UreF; KEGG: rsp:RSP_0303 urease accessory protein UreF; urease accessory protein UreF 1179930 4578588 Pden_1206 Paracoccus denitrificans PD1222 urease accessory protein UreF YP_915007.1 1179283 R 318586 CDS YP_915008.1 119383952 4578589 complement(1179911..1180375) 1 NC_008686.1 PFAM: UreE urease accessory domain protein domain protein; UreE urease accessory domain protein; KEGG: rsp:RSP_0304 urease accessory protein UreE; UreE urease accessory domain-containing protein 1180375 4578589 Pden_1207 Paracoccus denitrificans PD1222 UreE urease accessory domain-containing protein YP_915008.1 1179911 R 318586 CDS YP_915009.1 119383953 4578590 complement(1180388..1182076) 1 NC_008686.1 ureases catalyze the hydrolysis of urea into ammonia and carbon dioxide; in Helicobacter pylori the ammonia released plays a key role in bacterial survival by neutralizing acids when colonizing the gastric mucosa; the holoenzyme is composed of 3 ureC (alpha) and 3 ureAB (gamma/beta) subunits; urease subunit alpha 1182076 ureC 4578590 ureC Paracoccus denitrificans PD1222 urease subunit alpha YP_915009.1 1180388 R 318586 CDS YP_915010.1 119383954 4578591 complement(1182076..1182393) 1 NC_008686.1 KEGG: sme:SMc01939 urease beta subunit protein; TIGRFAM: urease, beta subunit; PFAM: Urease, beta subunit; urease subunit beta 1182393 4578591 Pden_1209 Paracoccus denitrificans PD1222 urease subunit beta YP_915010.1 1182076 R 318586 CDS YP_915011.1 119383955 4578592 complement(1182394..1182954) 1 NC_008686.1 PFAM: HupE/UreJ protein; KEGG: pst:PSPTO_4912 urease accessory protein; HupE/UreJ protein 1182954 4578592 Pden_1210 Paracoccus denitrificans PD1222 HupE/UreJ protein YP_915011.1 1182394 R 318586 CDS YP_915012.1 119383956 4578593 complement(1182955..1183266) 1 NC_008686.1 KEGG: rsp:RSP_0309 urease, gamma subunit; TIGRFAM: urease, gamma subunit; PFAM: Urease, gamma subunit region; urease subunit gamma 1183266 4578593 Pden_1211 Paracoccus denitrificans PD1222 urease subunit gamma YP_915012.1 1182955 R 318586 CDS YP_915013.1 119383957 4578594 complement(1183268..1184107) 1 NC_008686.1 PFAM: Urease accessory protein UreD; KEGG: rsp:RSP_0310 urease accessory protein UreD; urease accessory protein UreD 1184107 4578594 Pden_1212 Paracoccus denitrificans PD1222 urease accessory protein UreD YP_915013.1 1183268 R 318586 CDS YP_915014.1 119383958 4578595 complement(1184112..1184393) 1 NC_008686.1 hypothetical protein 1184393 4578595 Pden_1213 Paracoccus denitrificans PD1222 hypothetical protein YP_915014.1 1184112 R 318586 CDS YP_915015.1 119383959 4578596 1184520..1184873 1 NC_008686.1 PFAM: regulatory protein, ArsR; KEGG: atc:AGR_L_3580 hypothetical protein; regulatory protein ArsR 1184873 4578596 Pden_1214 Paracoccus denitrificans PD1222 regulatory protein ArsR YP_915015.1 1184520 D 318586 CDS YP_915016.1 119383960 4578597 1184870..1185346 1 NC_008686.1 PFAM: Activator of Hsp90 ATPase 1 family protein; KEGG: jan:Jann_2413 hypothetical protein; activator of Hsp90 ATPase 1 family protein 1185346 4578597 Pden_1215 Paracoccus denitrificans PD1222 activator of Hsp90 ATPase 1 family protein YP_915016.1 1184870 D 318586 CDS YP_915017.1 119383961 4578598 1185343..1186215 1 NC_008686.1 PFAM: Activator of Hsp90 ATPase 1 family protein; KEGG: atc:AGR_L_3582 hypothetical protein; activator of Hsp90 ATPase 1 family protein 1186215 4578598 Pden_1216 Paracoccus denitrificans PD1222 activator of Hsp90 ATPase 1 family protein YP_915017.1 1185343 D 318586 CDS YP_915018.1 119383962 4578599 1186313..1186939 1 NC_008686.1 KEGG: ccr:CC1241 hypothetical protein; hypothetical protein 1186939 4578599 Pden_1217 Paracoccus denitrificans PD1222 hypothetical protein YP_915018.1 1186313 D 318586 CDS YP_915019.1 119383963 4578600 1186983..1187225 1 NC_008686.1 hypothetical protein 1187225 4578600 Pden_1218 Paracoccus denitrificans PD1222 hypothetical protein YP_915019.1 1186983 D 318586 CDS YP_915020.1 119383964 4578601 complement(1187344..1188015) 1 NC_008686.1 hypothetical protein 1188015 4578601 Pden_1219 Paracoccus denitrificans PD1222 hypothetical protein YP_915020.1 1187344 R 318586 CDS YP_915021.1 119383965 4578602 1188064..1188312 1 NC_008686.1 hypothetical protein 1188312 4578602 Pden_1220 Paracoccus denitrificans PD1222 hypothetical protein YP_915021.1 1188064 D 318586 CDS YP_915022.1 119383966 4578603 complement(1188554..1188940) 1 NC_008686.1 PFAM: transposase, IS4 family protein; KEGG: nmu:Nmul_A2650 transposase, IS4; transposase, IS4 family protein 1188940 4578603 Pden_1221 Paracoccus denitrificans PD1222 transposase, IS4 family protein YP_915022.1 1188554 R 318586 CDS YP_915023.1 119383967 4581076 complement(1188937..1189305) 1 NC_008686.1 KEGG: mag:amb0408 transposase and inactivated derivative; transposase and inactivated derivative 1189305 4581076 Pden_1222 Paracoccus denitrificans PD1222 transposase and inactivated derivative YP_915023.1 1188937 R 318586 CDS YP_915024.1 119383968 4581077 1189396..1190604 1 NC_008686.1 PFAM: phage integrase family protein; KEGG: rpc:RPC_3658 phage integrase; phage integrase family protein 1190604 4581077 Pden_1223 Paracoccus denitrificans PD1222 phage integrase family protein YP_915024.1 1189396 D 318586 CDS YP_915025.1 119383969 4581078 1190595..1190783 1 NC_008686.1 hypothetical protein 1190783 4581078 Pden_1224 Paracoccus denitrificans PD1222 hypothetical protein YP_915025.1 1190595 D 318586 CDS YP_915026.1 119383970 4581079 1190776..1191063 1 NC_008686.1 hypothetical protein 1191063 4581079 Pden_1225 Paracoccus denitrificans PD1222 hypothetical protein YP_915026.1 1190776 D 318586 CDS YP_915027.1 119383971 4581080 1191160..1191747 1 NC_008686.1 hypothetical protein 1191747 4581080 Pden_1226 Paracoccus denitrificans PD1222 hypothetical protein YP_915027.1 1191160 D 318586 CDS YP_915028.1 119383972 4581081 1191719..1192684 1 NC_008686.1 KEGG: rpc:RPC_3654 hypothetical protein; hypothetical protein 1192684 4581081 Pden_1227 Paracoccus denitrificans PD1222 hypothetical protein YP_915028.1 1191719 D 318586 CDS YP_915029.1 119383973 4581082 complement(1192946..1193203) 1 NC_008686.1 PFAM: helix-turn-helix domain protein; KEGG: rde:RD1_0810 DNA-binding protein; XRE family transcriptional regulator 1193203 4581082 Pden_1228 Paracoccus denitrificans PD1222 XRE family transcriptional regulator YP_915029.1 1192946 R 318586 CDS YP_915030.1 119383974 4581083 1193452..1193832 1 NC_008686.1 KEGG: ilo:IL2080 hypothetical protein; hypothetical protein 1193832 4581083 Pden_1229 Paracoccus denitrificans PD1222 hypothetical protein YP_915030.1 1193452 D 318586 CDS YP_915031.1 119383975 4581084 1193829..1194254 1 NC_008686.1 hypothetical protein 1194254 4581084 Pden_1230 Paracoccus denitrificans PD1222 hypothetical protein YP_915031.1 1193829 D 318586 CDS YP_915032.1 119383976 4581085 1194291..1194746 1 NC_008686.1 KEGG: ath:At4g01985 expressed protein; hypothetical protein 1194746 4581085 Pden_1231 Paracoccus denitrificans PD1222 hypothetical protein YP_915032.1 1194291 D 318586 CDS YP_915033.1 119383977 4581086 1195187..1196395 1 NC_008686.1 PFAM: HI0933 family protein; FAD dependent oxidoreductase; FAD-dependent pyridine nucleotide-disulphide oxidoreductase; KEGG: ccr:CC1477 hypothetical protein; hypothetical protein 1196395 4581086 Pden_1232 Paracoccus denitrificans PD1222 hypothetical protein YP_915033.1 1195187 D 318586 CDS YP_915034.1 119383978 4581087 complement(1196396..1197229) 1 NC_008686.1 catalyzes the formation of 2-dehydro-3-deoxy-D-octonate 8-phosphate from phosphoenolpyruvate and D-arabinose 5-phosphate in LPS biosynthesis; 2-dehydro-3-deoxyphosphooctonate aldolase 1197229 4581087 Pden_1233 Paracoccus denitrificans PD1222 2-dehydro-3-deoxyphosphooctonate aldolase YP_915034.1 1196396 R 318586 CDS YP_915035.1 119383979 4581088 complement(1197226..1198965) 1 NC_008686.1 KEGG: jan:Jann_3657 capsule polysaccharide export protein-like; capsule polysaccharide export protein 1198965 4581088 Pden_1234 Paracoccus denitrificans PD1222 capsule polysaccharide export protein YP_915035.1 1197226 R 318586 CDS YP_915036.1 119383980 4581089 complement(1198949..1199602) 1 NC_008686.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: jan:Jann_3656 ABC transporter related; ABC transporter 1199602 4581089 Pden_1235 Paracoccus denitrificans PD1222 ABC transporter YP_915036.1 1198949 R 318586 CDS YP_915037.1 119383981 4581090 1199757..1200419 1 NC_008686.1 PFAM: Uracil-DNA glycosylase superfamily; KEGG: sil:SPO0950 uracil-DNA glycosylase; uracil-DNA glycosylase 1200419 4581090 Pden_1236 Paracoccus denitrificans PD1222 uracil-DNA glycosylase YP_915037.1 1199757 D 318586 CDS YP_915038.1 119383982 4581091 1200403..1201155 1 NC_008686.1 KEGG: sil:SPO0951 hypothetical protein; hypothetical protein 1201155 4581091 Pden_1237 Paracoccus denitrificans PD1222 hypothetical protein YP_915038.1 1200403 D 318586 CDS YP_915039.1 119383983 4581092 complement(1201248..1201808) 1 NC_008686.1 PFAM: protein of unknown function DUF882; Peptidase M15A; KEGG: rsp:RSP_2773 hypothetical protein; hypothetical protein 1201808 4581092 Pden_1238 Paracoccus denitrificans PD1222 hypothetical protein YP_915039.1 1201248 R 318586 CDS YP_915040.1 119383984 4581093 1201891..1202133 1 NC_008686.1 hypothetical protein 1202133 4581093 Pden_1239 Paracoccus denitrificans PD1222 hypothetical protein YP_915040.1 1201891 D 318586 CDS YP_915041.1 119383985 4581094 1202142..1203749 1 NC_008686.1 PFAM: Peptidoglycan-binding domain 1 protein; KEGG: rsp:RSP_2774 hypothetical protein; peptidoglycan binding domain-containing protein 1203749 4581094 Pden_1240 Paracoccus denitrificans PD1222 peptidoglycan binding domain-containing protein YP_915041.1 1202142 D 318586 CDS YP_915042.1 119383986 4580007 1203776..1204870 1 NC_008686.1 TIGRFAM: UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; KEGG: rsp:RSP_2775 UDP-3-O-(3-hydroxymyristoyl) glucosamine N-acyltransferase; UDP-3-O-(3-hydroxymyristoyl) glucosamine N-acyltransferase 1204870 4580007 Pden_1241 Paracoccus denitrificans PD1222 UDP-3-O-(3-hydroxymyristoyl) glucosamine N-acyltransferase YP_915042.1 1203776 D 318586 CDS YP_915043.1 119383987 4580008 1204965..1205177 1 NC_008686.1 KEGG: jan:Jann_2147 phosphopantetheine-binding; phosphopantetheine-binding protein 1205177 4580008 Pden_1242 Paracoccus denitrificans PD1222 phosphopantetheine-binding protein YP_915043.1 1204965 D 318586 CDS YP_915044.1 119383988 4580009 1205174..1206523 1 NC_008686.1 PFAM: beta-ketoacyl synthase; KEGG: rsp:RSP_2777 3-oxoacyl-(acyl-carrier-protein) synthase; beta-ketoacyl synthase 1206523 4580009 Pden_1243 Paracoccus denitrificans PD1222 beta-ketoacyl synthase YP_915044.1 1205174 D 318586 CDS YP_915045.1 119383989 4580010 complement(1206615..1207841) 1 NC_008686.1 PFAM: major facilitator superfamily MFS_1; KEGG: rsp:RSP_2726 multidrug/metabolite efflux pump, major facilitator superfamily (MFS); major facilitator superfamily transporter 1207841 4580010 Pden_1244 Paracoccus denitrificans PD1222 major facilitator superfamily transporter YP_915045.1 1206615 R 318586 CDS YP_915046.1 119383990 4580011 complement(1207849..1208487) 1 NC_008686.1 KEGG: sil:SPO3031 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase; TIGRFAM: 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase; PFAM: KDPG and KHG aldolase; 2-dehydro-3-deoxyphosphooctonate aldolase 1208487 4580011 Pden_1245 Paracoccus denitrificans PD1222 2-dehydro-3-deoxyphosphooctonate aldolase YP_915046.1 1207849 R 318586 CDS YP_915047.1 119383991 4580012 complement(1208672..1209292) 1 NC_008686.1 KEGG: rsp:RSP_3425 hypothetical protein; hypothetical protein 1209292 4580012 Pden_1246 Paracoccus denitrificans PD1222 hypothetical protein YP_915047.1 1208672 R 318586 CDS YP_915048.1 119383992 4580013 complement(1209295..1210518) 1 NC_008686.1 PFAM: glutathionylspermidine synthase; KEGG: rsp:RSP_3426 hypothetical protein; glutathionylspermidine synthase 1210518 4580013 Pden_1247 Paracoccus denitrificans PD1222 glutathionylspermidine synthase YP_915048.1 1209295 R 318586 CDS YP_915049.1 119383993 4580014 1210724..1212337 1 NC_008686.1 PFAM: extracellular solute-binding protein, family 5; KEGG: sit:TM1040_0038 extracellular solute-binding protein, family 5; extracellular solute-binding protein 1212337 4580014 Pden_1248 Paracoccus denitrificans PD1222 extracellular solute-binding protein YP_915049.1 1210724 D 318586 CDS YP_915050.1 119383994 4580015 1212380..1213438 1 NC_008686.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: sil:SPO1544 peptide/opine/nickel uptake family ABC transporter, permease protein; binding-protein-dependent transport system inner membrane protein 1213438 4580015 Pden_1249 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_915050.1 1212380 D 318586 CDS YP_915051.1 119383995 4580016 1213435..1214340 1 NC_008686.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: sit:TM1040_0036 binding-protein-dependent transport systems inner membrane component; binding-protein-dependent transport system inner membrane protein 1214340 4580016 Pden_1250 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_915051.1 1213435 D 318586 CDS YP_915052.1 119383996 4580017 1214337..1215191 1 NC_008686.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sit:TM1040_0035 ABC transporter related; ABC transporter 1215191 4580017 Pden_1251 Paracoccus denitrificans PD1222 ABC transporter YP_915052.1 1214337 D 318586 CDS YP_915053.1 119383997 4580018 1215238..1215993 1 NC_008686.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sil:SPO1547 peptide/opine/nickel uptake family ABC transporter, ATP-binding protein; ABC transporter 1215993 4580018 Pden_1252 Paracoccus denitrificans PD1222 ABC transporter YP_915053.1 1215238 D 318586 CDS YP_915054.1 119383998 4580019 complement(1215990..1216697) 1 NC_008686.1 PFAM: protein of unknown function DUF125, transmembrane; KEGG: sit:TM1040_3365 protein of unknown function DUF125, transmembrane; hypothetical protein 1216697 4580019 Pden_1253 Paracoccus denitrificans PD1222 hypothetical protein YP_915054.1 1215990 R 318586 CDS YP_915055.1 119383999 4580020 1216822..1218267 1 NC_008686.1 PFAM: aldehyde dehydrogenase; KEGG: bxe:Bxe_A3401 betaine-aldehyde dehydrogenase; aldehyde dehydrogenase 1218267 4580020 Pden_1254 Paracoccus denitrificans PD1222 aldehyde dehydrogenase YP_915055.1 1216822 D 318586 CDS YP_915056.1 119384000 4580021 1218294..1219037 1 NC_008686.1 Catalyzes the first of the two reduction steps in the elongation cycle of fatty acid synthesis; 3-ketoacyl-ACP reductase 1219037 fabG 4580021 fabG Paracoccus denitrificans PD1222 3-ketoacyl-ACP reductase YP_915056.1 1218294 D 318586 CDS YP_915057.1 119384001 4580022 complement(1219069..1219899) 1 NC_008686.1 PFAM: ABC-3 protein; KEGG: rsp:RSP_0908 ABC Mn+2/Fe+2 transporter, inner membrane subunit SitD; ABC-3 protein 1219899 4580022 Pden_1256 Paracoccus denitrificans PD1222 ABC-3 protein YP_915057.1 1219069 R 318586 CDS YP_915058.1 119384002 4580023 complement(1219899..1220759) 1 NC_008686.1 PFAM: transport system permease protein; ABC-3 protein; KEGG: sme:SMc02507 iron transport system membrane ABC transporter protein; ABC-3 protein 1220759 4580023 Pden_1257 Paracoccus denitrificans PD1222 ABC-3 protein YP_915058.1 1219899 R 318586 CDS YP_915059.1 119384003 4580024 complement(1220756..1221625) 1 NC_008686.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sme:SMc02508 iron transport ATP-binding ABC transporter protein; ABC transporter 1221625 4580024 Pden_1258 Paracoccus denitrificans PD1222 ABC transporter YP_915059.1 1220756 R 318586 CDS YP_915060.1 119384004 4580025 complement(1221618..1222523) 1 NC_008686.1 PFAM: periplasmic solute binding protein; KEGG: rsp:RSP_0904 ABC Mn+2/Fe+2 transporter, periplasmic substrate-binding protein SitA; periplasmic solute binding protein 1222523 4580025 Pden_1259 Paracoccus denitrificans PD1222 periplasmic solute binding protein YP_915060.1 1221618 R 318586 CDS YP_915061.1 119384005 4580026 1222629..1223051 1 NC_008686.1 PFAM: ferric-uptake regulator; KEGG: sme:SMc02510 probable ferric uptake regulation protein; ferric uptake regulator family protein 1223051 4580026 Pden_1260 Paracoccus denitrificans PD1222 ferric uptake regulator family protein YP_915061.1 1222629 D 318586 CDS YP_915062.1 119384006 4580300 1223048..1223422 1 NC_008686.1 PFAM: protein of unknown function UPF0029; KEGG: rde:RD1_4095 hypothetical protein; hypothetical protein 1223422 4580300 Pden_1261 Paracoccus denitrificans PD1222 hypothetical protein YP_915062.1 1223048 D 318586 CDS YP_915063.1 119384007 4580301 complement(1223419..1223793) 1 NC_008686.1 KEGG: sil:SPO0809 hypothetical protein; hypothetical protein 1223793 4580301 Pden_1262 Paracoccus denitrificans PD1222 hypothetical protein YP_915063.1 1223419 R 318586 CDS YP_915064.1 119384008 4580302 complement(1223795..1224847) 1 NC_008686.1 KEGG: sme:SMc03928 hypothetical protein; hypothetical protein 1224847 4580302 Pden_1263 Paracoccus denitrificans PD1222 hypothetical protein YP_915064.1 1223795 R 318586 CDS YP_915065.1 119384009 4580303 complement(1224844..1225551) 1 NC_008686.1 Enables the recycling of peptidyl-tRNAs produced at termination of translation; peptidyl-tRNA hydrolase 1225551 4580303 Pden_1264 Paracoccus denitrificans PD1222 peptidyl-tRNA hydrolase YP_915065.1 1224844 R 318586 CDS YP_915066.1 119384010 4580304 1225747..1226376 1 NC_008686.1 hydrolyzes proteins to small peptides; with the ATPase subunits ClpA or ClpX, ClpP degrades specific substrates; ATP-dependent Clp protease proteolytic subunit 1226376 clpP 4580304 clpP Paracoccus denitrificans PD1222 ATP-dependent Clp protease proteolytic subunit YP_915066.1 1225747 D 318586 CDS YP_915067.1 119384011 4580305 1226538..1227803 1 NC_008686.1 binds and unfolds substrates as part of the ClpXP protease; ATP-dependent protease ATP-binding subunit ClpX 1227803 clpX 4580305 clpX Paracoccus denitrificans PD1222 ATP-dependent protease ATP-binding subunit ClpX YP_915067.1 1226538 D 318586 CDS YP_915068.1 119384012 4580306 1228027..1228401 1 NC_008686.1 Provides the input to the respiratory chain from the NAD-linked dehydrogenases of the citric acid cycle. The complex couples the oxidation of NADH and the reduction of ubiquinone, to the generation of a proton gradient which is then used for ATP synthesis; NADH dehydrogenase 1228401 4580306 Pden_1267 Paracoccus denitrificans PD1222 NADH dehydrogenase YP_915068.1 1228027 D 318586 CDS YP_915069.1 119384013 4580307 1228406..1228873 1 NC_008686.1 PFAM: Mammalian cell entry related domain protein; KEGG: rsp:RSP_0194 possible ABC transporter, substrate-binding protein; hypothetical protein 1228873 4580307 Pden_1268 Paracoccus denitrificans PD1222 hypothetical protein YP_915069.1 1228406 D 318586 CDS YP_915070.1 119384014 4580308 1228870..1229361 1 NC_008686.1 KEGG: sil:SPO1008 hypothetical protein; hypothetical protein 1229361 4580308 Pden_1269 Paracoccus denitrificans PD1222 hypothetical protein YP_915070.1 1228870 D 318586 CDS YP_915071.1 119384015 4580309 complement(1229325..1229963) 1 NC_008686.1 leucyltransferase; phenylalanyltransferse; functions in the N-end rule pathway; transfers Leu, Phe, Met, from aminoacyl-tRNAs to N-terminal of proteins with Arg or Lys; leucyl/phenylalanyl-tRNA--protein transferase 1229963 aat 4580309 aat Paracoccus denitrificans PD1222 leucyl/phenylalanyl-tRNA--protein transferase YP_915071.1 1229325 R 318586 CDS YP_915072.1 119384016 4580310 complement(1229999..1231351) 1 NC_008686.1 an AccC homodimer forms the biotin carboxylase subunit of the acetyl CoA carboxylase, an enzyme that catalyzes the formation of malonyl-CoA, which in turn controls the rate of fatty acid metabolism; acetyl-CoA carboxylase biotin carboxylase subunit 1231351 4580310 Pden_1271 Paracoccus denitrificans PD1222 acetyl-CoA carboxylase biotin carboxylase subunit YP_915072.1 1229999 R 318586 CDS YP_915073.1 119384017 4580311 complement(1231359..1231880) 1 NC_008686.1 TIGRFAM: acetyl-CoA carboxylase, biotin carboxyl carrier protein; PFAM: biotin/lipoyl attachment domain-containing protein; KEGG: rsp:RSP_0190 biotin carboxyl carrier protein, AccB; acetyl-CoA carboxylase, biotin carboxyl carrier protein 1231880 4580311 Pden_1272 Paracoccus denitrificans PD1222 acetyl-CoA carboxylase, biotin carboxyl carrier protein YP_915073.1 1231359 R 318586 CDS YP_915074.1 119384018 4580312 complement(1231984..1232874) 1 NC_008686.1 PFAM: lipid A biosynthesis acyltransferase; KEGG: rsp:RSP_2219 lipid A biosynthesis lauroyl acyltransferase; lipid A biosynthesis acyltransferase 1232874 4580312 Pden_1273 Paracoccus denitrificans PD1222 lipid A biosynthesis acyltransferase YP_915074.1 1231984 R 318586 CDS YP_915075.1 119384019 4580313 complement(1232900..1233826) 1 NC_008686.1 PFAM: protein of unknown function DUF6, transmembrane; KEGG: jan:Jann_2643 protein of unknown function DUF6, transmembrane; hypothetical protein 1233826 4580313 Pden_1274 Paracoccus denitrificans PD1222 hypothetical protein YP_915075.1 1232900 R 318586 CDS YP_915076.1 119384020 4580314 complement(1234011..1236029) 1 NC_008686.1 catalyzes the formation of ribose 5-phosphate and xylulose 5-phosphate from sedoheptulose 7-phosphate and glyceraldehyde 3-phosphate; can transfer ketol groups between several groups; in Escherichia coli there are two tkt genes, tktA expressed during exponential growth and the tktB during stationary phase; transketolase 1236029 4580314 Pden_1275 Paracoccus denitrificans PD1222 transketolase YP_915076.1 1234011 R 318586 CDS YP_915077.1 119384021 4580315 1236124..1238088 1 NC_008686.1 hypothetical protein 1238088 4580315 Pden_1276 Paracoccus denitrificans PD1222 hypothetical protein YP_915077.1 1236124 D 318586 CDS YP_915078.1 119384022 4580316 1238179..1239669 1 NC_008686.1 TIGRFAM: uracil-xanthine permease; PFAM: Xanthine/uracil/vitamin C permease; KEGG: sme:SMc02512 permease transmembrane protein; uracil-xanthine permease 1239669 4580316 Pden_1277 Paracoccus denitrificans PD1222 uracil-xanthine permease YP_915078.1 1238179 D 318586 CDS YP_915079.1 119384023 4580317 complement(1239663..1241015) 1 NC_008686.1 PFAM: CBS domain containing protein; protein of unknown function DUF21; transporter-associated region; KEGG: rsp:RSP_2814 hypothetical protein with CBS domain; hypothetical protein 1241015 4580317 Pden_1278 Paracoccus denitrificans PD1222 hypothetical protein YP_915079.1 1239663 R 318586 CDS YP_915080.1 119384024 4580318 complement(1241012..1241983) 1 NC_008686.1 PFAM: phage integrase family protein; phage integrase domain protein SAM domain protein; KEGG: rsp:RSP_2815 probable integrase/recombinase XerD; phage integrase family protein 1241983 4580318 Pden_1279 Paracoccus denitrificans PD1222 phage integrase family protein YP_915080.1 1241012 R 318586 CDS YP_915081.1 119384025 4580899 complement(1241980..1243602) 1 NC_008686.1 KEGG: rsp:RSP_2816 hypothetical protein; hypothetical protein 1243602 4580899 Pden_1280 Paracoccus denitrificans PD1222 hypothetical protein YP_915081.1 1241980 R 318586 CDS YP_915082.1 119384026 4580900 complement(1243589..1243846) 1 NC_008686.1 hypothetical protein 1243846 4580900 Pden_1281 Paracoccus denitrificans PD1222 hypothetical protein YP_915082.1 1243589 R 318586 CDS YP_915083.1 119384027 4580901 1243974..1244510 1 NC_008686.1 PFAM: shikimate kinase; KEGG: rsp:RSP_2817 shikimate kinase; shikimate kinase 1244510 4580901 Pden_1282 Paracoccus denitrificans PD1222 shikimate kinase YP_915083.1 1243974 D 318586 CDS YP_915084.1 119384028 4580902 1244507..1245610 1 NC_008686.1 catalyzes the formation of 3-dehydroquinate from 3-deoxy-arabino-heptulonate 7-phosphate; functions in aromatic amino acid biosynthesis; 3-dehydroquinate synthase 1245610 aroB 4580902 aroB Paracoccus denitrificans PD1222 3-dehydroquinate synthase YP_915084.1 1244507 D 318586 CDS YP_915085.1 119384029 4580903 complement(1245607..1246029) 1 NC_008686.1 TIGRFAM: monovalent cation/proton antiporter, MnhG/PhaG subunit; PFAM: Na+/H+ antiporter subunit; KEGG: rsp:RSP_3710 multicomponent K+:H+ antiporter subunit G; monovalent cation/proton antiporter subunit MnhG/PhaG 1246029 4580903 Pden_1284 Paracoccus denitrificans PD1222 monovalent cation/proton antiporter subunit MnhG/PhaG YP_915085.1 1245607 R 318586 CDS YP_915086.1 119384030 4580904 complement(1246026..1246307) 1 NC_008686.1 subunit F of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; in S. meliloti it is known to be involved specifically with K+ transport; monovalent cation/H+ antiporter subunit F 1246307 4580904 Pden_1285 Paracoccus denitrificans PD1222 monovalent cation/H+ antiporter subunit F YP_915086.1 1246026 R 318586 CDS YP_915087.1 119384031 4580905 complement(1246304..1246792) 1 NC_008686.1 PFAM: cation antiporter; KEGG: rsp:RSP_3712 hypothetical protein; cation antiporter 1246792 4580905 Pden_1286 Paracoccus denitrificans PD1222 cation antiporter YP_915087.1 1246304 R 318586 CDS YP_915088.1 119384032 4580906 complement(1246789..1248519) 1 NC_008686.1 subunit D of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; contains an oxidoreductase domain; catalyzes the transfer of electrons from NADH to ubiquinone; monovalent cation/H+ antiporter subunit D 1248519 4580906 Pden_1287 Paracoccus denitrificans PD1222 monovalent cation/H+ antiporter subunit D YP_915088.1 1246789 R 318586 CDS YP_915089.1 119384033 4580907 complement(1248519..1248863) 1 NC_008686.1 subunit C of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; monovalent cation/H+ antiporter subunit C 1248863 4580907 Pden_1288 Paracoccus denitrificans PD1222 monovalent cation/H+ antiporter subunit C YP_915089.1 1248519 R 318586 CDS YP_915090.1 119384034 4580908 complement(1248863..1251742) 1 NC_008686.1 subunit A of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; in S. meliloti it is known to be involved with K+; monovalent cation/H+ antiporter subunit A 1251742 4580908 Pden_1289 Paracoccus denitrificans PD1222 monovalent cation/H+ antiporter subunit A YP_915090.1 1248863 R 318586 CDS YP_915091.1 119384035 4580909 complement(1251889..1253133) 1 NC_008686.1 PFAM: Orn/DAP/Arg decarboxylase 2; KEGG: aeh:Mlg_0126 Orn/DAP/Arg decarboxylase 2; Orn/DAP/Arg decarboxylase 2 1253133 4580909 Pden_1290 Paracoccus denitrificans PD1222 Orn/DAP/Arg decarboxylase 2 YP_915091.1 1251889 R 318586 CDS YP_915092.1 119384036 4580910 complement(1253114..1253350) 1 NC_008686.1 hypothetical protein 1253350 4580910 Pden_1291 Paracoccus denitrificans PD1222 hypothetical protein YP_915092.1 1253114 R 318586 CDS YP_915093.1 119384037 4580911 complement(1253370..1254941) 1 NC_008686.1 PFAM: AMP-dependent synthetase and ligase; KEGG: nmu:Nmul_A2670 AMP-dependent synthetase and ligase; AMP-dependent synthetase/ligase 1254941 4580911 Pden_1292 Paracoccus denitrificans PD1222 AMP-dependent synthetase/ligase YP_915093.1 1253370 R 318586 CDS YP_915094.1 119384038 4580912 complement(1254934..1255476) 1 NC_008686.1 KEGG: mca:MCA1436 serine acetyltransferase CysE; serine acetyltransferase CysE 1255476 4580912 Pden_1293 Paracoccus denitrificans PD1222 serine acetyltransferase CysE YP_915094.1 1254934 R 318586 CDS YP_915095.1 119384039 4580913 complement(1255559..1256623) 1 NC_008686.1 KEGG: pen:PSEEN2951 hypothetical protein; hypothetical protein 1256623 4580913 Pden_1294 Paracoccus denitrificans PD1222 hypothetical protein YP_915095.1 1255559 R 318586 CDS YP_915096.1 119384040 4580914 complement(1256696..1257868) 1 NC_008686.1 KEGG: ccr:CC2454 lipase/acylhydrolase; lipase/acylhydrolase 1257868 4580914 Pden_1295 Paracoccus denitrificans PD1222 lipase/acylhydrolase YP_915096.1 1256696 R 318586 CDS YP_915097.1 119384041 4580915 complement(1257917..1259086) 1 NC_008686.1 PFAM: DegT/DnrJ/EryC1/StrS aminotransferase; KEGG: cps:CPS_4201 polysaccharide biosynthesis protein; DegT/DnrJ/EryC1/StrS aminotransferase 1259086 4580915 Pden_1296 Paracoccus denitrificans PD1222 DegT/DnrJ/EryC1/StrS aminotransferase YP_915097.1 1257917 R 318586 CDS YP_915098.1 119384042 4580916 complement(1259083..1260006) 1 NC_008686.1 PFAM: NAD-dependent epimerase/dehydratase; 3-beta hydroxysteroid dehydrogenase/isomerase; dTDP-4-dehydrorhamnose reductase; KEGG: cps:CPS_4200 NAD-dependent epimerase/dehydratase family protein; NAD-dependent epimerase/dehydratase 1260006 4580916 Pden_1297 Paracoccus denitrificans PD1222 NAD-dependent epimerase/dehydratase YP_915098.1 1259083 R 318586 CDS YP_915099.1 119384043 4580917 complement(1260007..1261131) 1 NC_008686.1 TIGRFAM: GDP-mannose 4,6-dehydratase; PFAM: NAD-dependent epimerase/dehydratase; KEGG: sit:TM1040_1482 GDP-mannose 4,6-dehydratase; GDP-mannose 4,6-dehydratase 1261131 4580917 Pden_1298 Paracoccus denitrificans PD1222 GDP-mannose 4,6-dehydratase YP_915099.1 1260007 R 318586 CDS YP_915100.1 119384044 4580918 complement(1261338..1262690) 1 NC_008686.1 catalyzes the formation of prolyl-tRNA(Pro) from proline and tRNA(Pro); prolyl-tRNA synthetase 1262690 4580918 Pden_1299 Paracoccus denitrificans PD1222 prolyl-tRNA synthetase YP_915100.1 1261338 R 318586 CDS YP_915101.1 119384045 4579481 1262820..1264124 1 NC_008686.1 PFAM: protein of unknown function UPF0118; KEGG: jan:Jann_1056 protein of unknown function UPF0118; hypothetical protein 1264124 4579481 Pden_1300 Paracoccus denitrificans PD1222 hypothetical protein YP_915101.1 1262820 D 318586 CDS YP_915102.1 119384046 4579482 1264128..1264817 1 NC_008686.1 KEGG: rsp:RSP_0780 hypothetical protein with ATP/GTP-binding site; hypothetical protein 1264817 4579482 Pden_1301 Paracoccus denitrificans PD1222 hypothetical protein YP_915102.1 1264128 D 318586 CDS YP_915103.1 119384047 4579483 1264849..1267014 1 NC_008686.1 catalyzes the reversible transfer of the terminal phosphate of ATP to form a long chain polyphosphate; polyphosphate kinase 1267014 4579483 Pden_1302 Paracoccus denitrificans PD1222 polyphosphate kinase YP_915103.1 1264849 D 318586 CDS YP_915104.1 119384048 4579484 1267083..1268624 1 NC_008686.1 PFAM: Ppx/GppA phosphatase; KEGG: rsp:RSP_0782 Ppx/GppA phosphatase; Ppx/GppA phosphatase 1268624 4579484 Pden_1303 Paracoccus denitrificans PD1222 Ppx/GppA phosphatase YP_915104.1 1267083 D 318586 CDS YP_915105.1 119384049 4579485 complement(1268835..1269884) 1 NC_008686.1 PFAM: peptidase M19, renal dipeptidase; KEGG: rsp:RSP_0802 dipeptidase; peptidase M19 1269884 4579485 Pden_1304 Paracoccus denitrificans PD1222 peptidase M19 YP_915105.1 1268835 R 318586 CDS YP_915106.1 119384050 4579486 1270069..1270392 1 NC_008686.1 PFAM: Antibiotic biosynthesis monooxygenase; KEGG: sil:SPO0462 antibiotic biosynthesis monooxygenase domain protein; antibiotic biosynthesis monooxygenase 1270392 4579486 Pden_1305 Paracoccus denitrificans PD1222 antibiotic biosynthesis monooxygenase YP_915106.1 1270069 D 318586 CDS YP_915107.1 119384051 4579487 1270495..1271130 1 NC_008686.1 PFAM: Cobyrinic acid a,c-diamide synthase; KEGG: sil:SPO0461 ParA family protein; cobyrinic acid a,c-diamide synthase 1271130 4579487 Pden_1306 Paracoccus denitrificans PD1222 cobyrinic acid a,c-diamide synthase YP_915107.1 1270495 D 318586 CDS YP_915108.1 119384052 4579488 1271230..1271517 1 NC_008686.1 KEGG: pol:Bpro_1343 hypothetical protein; hypothetical protein 1271517 4579488 Pden_1307 Paracoccus denitrificans PD1222 hypothetical protein YP_915108.1 1271230 D 318586 CDS YP_915109.1 119384053 4579489 complement(1271560..1273785) 1 NC_008686.1 The UvrABC repair system catalyzes the recognition and processing of DNA lesions. The beta-hairpin of the Uvr-B subunit is inserted between the strands, where it probes for the presence of a lesion; excinuclease ABC subunit B 1273785 4579489 Pden_1308 Paracoccus denitrificans PD1222 excinuclease ABC subunit B YP_915109.1 1271560 R 318586 CDS YP_915110.1 119384054 4579490 1273934..1274245 1 NC_008686.1 PFAM: ETC complex I subunit conserved region; KEGG: sil:SPO0482 NADH-ubiquinone oxidoreductase family protein; ETC complex I subunit region 1274245 4579490 Pden_1309 Paracoccus denitrificans PD1222 ETC complex I subunit region YP_915110.1 1273934 D 318586 CDS YP_915111.1 119384055 4579491 complement(1274539..1275879) 1 NC_008686.1 PFAM: ATP-binding region, ATPase domain protein domain protein; KEGG: rpe:RPE_1965 periplasmic sensor signal transduction histidine kinase; integral membrane sensor signal transduction histidine kinase 1275879 4579491 Pden_1310 Paracoccus denitrificans PD1222 integral membrane sensor signal transduction histidine kinase YP_915111.1 1274539 R 318586 CDS YP_915112.1 119384056 4579492 complement(1275876..1276538) 1 NC_008686.1 PFAM: response regulator receiver; transcriptional regulator domain protein; KEGG: mes:Meso_0894 two component transcriptional regulator, winged helix family; two component transcriptional regulator 1276538 4579492 Pden_1311 Paracoccus denitrificans PD1222 two component transcriptional regulator YP_915112.1 1275876 R 318586 CDS YP_915113.1 119384057 4579493 complement(1276535..1276933) 1 NC_008686.1 hypothetical protein 1276933 4579493 Pden_1312 Paracoccus denitrificans PD1222 hypothetical protein YP_915113.1 1276535 R 318586 CDS YP_915114.1 119384058 4579494 1277063..1277941 1 NC_008686.1 hypothetical protein 1277941 4579494 Pden_1313 Paracoccus denitrificans PD1222 hypothetical protein YP_915114.1 1277063 D 318586 CDS YP_915115.1 119384059 4579495 1278128..1279726 1 NC_008686.1 involved in the biosynthesis of osmoregulated periplasmic glucans; required for the assembly of the polyglucose structure of glucan; glucan biosynthesis protein G 1279726 mdoG 4579495 mdoG Paracoccus denitrificans PD1222 glucan biosynthesis protein G YP_915115.1 1278128 D 318586 CDS YP_915116.1 119384060 4579496 1279723..1281897 1 NC_008686.1 necessary for biosynthesis of osmoregulated periplasmic glucans possibly involved in the transfer to the periplasmic space; glucosyltransferase MdoH 1281897 4579496 Pden_1315 Paracoccus denitrificans PD1222 glucosyltransferase MdoH YP_915116.1 1279723 D 318586 CDS YP_915117.1 119384061 4579497 1281894..1283027 1 NC_008686.1 KEGG: rme:Rmet_4886 hypothetical protein; hypothetical protein 1283027 4579497 Pden_1316 Paracoccus denitrificans PD1222 hypothetical protein YP_915117.1 1281894 D 318586 CDS YP_915118.1 119384062 4579498 1283098..1284765 1 NC_008686.1 catalyzes the formation of 10-formyltetrahydrofolate from formate and tetrahydrofolate; formate--tetrahydrofolate ligase 1284765 4579498 Pden_1317 Paracoccus denitrificans PD1222 formate--tetrahydrofolate ligase YP_915118.1 1283098 D 318586 CDS YP_915119.1 119384063 4579499 1284769..1285371 1 NC_008686.1 transfers an adenyl group from ATP to NaMN to form nicotinic acid adenine dinucleotide (NaAD) which is then converted to the ubiquitous compound NAD by NAD synthetase; essential enzyme in bacteria; nicotinic acid mononucleotide adenylyltransferase 1285371 nadD 4579499 nadD Paracoccus denitrificans PD1222 nicotinic acid mononucleotide adenylyltransferase YP_915119.1 1284769 D 318586 CDS YP_915120.1 119384064 4579422 1285371..1286825 1 NC_008686.1 PFAM: peptidase S13, D-Ala-D-Ala carboxypeptidase C; KEGG: sil:SPO0451 D-alanyl-D-alanine carboxypeptidase/D-alanyl-D-alanine-endopeptidase; peptidase S13, D-Ala-D-Ala carboxypeptidase C 1286825 4579422 Pden_1319 Paracoccus denitrificans PD1222 peptidase S13, D-Ala-D-Ala carboxypeptidase C YP_915120.1 1285371 D 318586 CDS YP_915121.1 119384065 4579423 complement(1286836..1287258) 1 NC_008686.1 KEGG: rsp:RSP_0583 hypothetical protein; hypothetical protein 1287258 4579423 Pden_1320 Paracoccus denitrificans PD1222 hypothetical protein YP_915121.1 1286836 R 318586 CDS YP_915122.1 119384066 4579424 1287350..1288942 1 NC_008686.1 class I; LysRS1; catalyzes a two-step reaction, first charging a lysine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; in Methanosarcina barkeri this enzyme charges both tRNA molecules for lysine that exist in this organism (but the tRNALysUUU very poorly) and in the presence of LysRS2 can charge tRNAPyl with lysine; lysyl-tRNA synthetase 1288942 lysK 4579424 lysK Paracoccus denitrificans PD1222 lysyl-tRNA synthetase YP_915122.1 1287350 D 318586 CDS YP_915123.1 119384067 4579425 1289083..1291377 1 NC_008686.1 KEGG: sil:SPO0459 hypothetical protein; hypothetical protein 1291377 4579425 Pden_1322 Paracoccus denitrificans PD1222 hypothetical protein YP_915123.1 1289083 D 318586 CDS YP_915124.1 119384068 4579426 complement(1291414..1291899) 1 NC_008686.1 PFAM: pyridoxamine 5'-phosphate oxidase-related, FMN-binding; KEGG: ret:RHE_CH03088 hypothetical protein; pyridoxamine 5'-phosphate oxidase-like FMN-binding protein 1291899 4579426 Pden_1323 Paracoccus denitrificans PD1222 pyridoxamine 5'-phosphate oxidase-like FMN-binding protein YP_915124.1 1291414 R 318586 CDS YP_915125.1 119384069 4579427 complement(1291957..1292970) 1 NC_008686.1 KEGG: vvy:VV1207 ABC-type oligopeptide transport system, ATPase component; TIGRFAM: oligopeptide/dipeptide ABC transporter, ATPase subunit; PFAM: ABC transporter related; Oligopeptide/dipeptide ABC transporter, C-terminal domain protein; SMART: AAA ATPase; oligopeptide/dipeptide ABC transporter ATPase 1292970 4579427 Pden_1324 Paracoccus denitrificans PD1222 oligopeptide/dipeptide ABC transporter ATPase YP_915125.1 1291957 R 318586 CDS YP_915126.1 119384070 4579428 complement(1292967..1294022) 1 NC_008686.1 KEGG: vpa:VP2088 oligopeptide ABC transporter, ATP-binding protein; TIGRFAM: oligopeptide/dipeptide ABC transporter, ATPase subunit; PFAM: ABC transporter related; Oligopeptide/dipeptide ABC transporter, C-terminal domain protein; SMART: AAA ATPase; oligopeptide/dipeptide ABC transporter ATPase 1294022 4579428 Pden_1325 Paracoccus denitrificans PD1222 oligopeptide/dipeptide ABC transporter ATPase YP_915126.1 1292967 R 318586 CDS YP_915127.1 119384071 4579429 complement(1294024..1294947) 1 NC_008686.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: jan:Jann_3052 binding-protein-dependent transport systems inner membrane component; binding-protein-dependent transport system inner membrane protein 1294947 4579429 Pden_1326 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_915127.1 1294024 R 318586 CDS YP_915128.1 119384072 4579430 complement(1294951..1295868) 1 NC_008686.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: jan:Jann_3051 binding-protein-dependent transport systems inner membrane component; binding-protein-dependent transport system inner membrane protein 1295868 4579430 Pden_1327 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_915128.1 1294951 R 318586 CDS YP_915129.1 119384073 4579431 complement(1295935..1297539) 1 NC_008686.1 PFAM: extracellular solute-binding protein, family 5; KEGG: jan:Jann_3050 extracellular solute-binding protein, family 5; extracellular solute-binding protein 1297539 4579431 Pden_1328 Paracoccus denitrificans PD1222 extracellular solute-binding protein YP_915129.1 1295935 R 318586 CDS YP_915130.1 119384074 4579432 1297935..1298813 1 NC_008686.1 KEGG: nph:NP3544A thioredoxin reductase homolog; thioredoxin reductase 1298813 4579432 Pden_1329 Paracoccus denitrificans PD1222 thioredoxin reductase YP_915130.1 1297935 D 318586 CDS YP_915131.1 119384075 4579433 1298865..1299239 1 NC_008686.1 KEGG: gbe:GbCGDNIH1_1136 cysteinyl-tRNA synthetase; cysteinyl-tRNA synthetase 1299239 4579433 Pden_1330 Paracoccus denitrificans PD1222 cysteinyl-tRNA synthetase YP_915131.1 1298865 D 318586 CDS YP_915132.1 119384076 4579434 1299236..1300336 1 NC_008686.1 PFAM: cobalamin synthesis protein, P47K; cobalamin synthesis CobW domain protein; KEGG: atc:AGR_L_3251 hypothetical protein; cobalamin synthesis protein, P47K 1300336 4579434 Pden_1331 Paracoccus denitrificans PD1222 cobalamin synthesis protein, P47K YP_915132.1 1299236 D 318586 CDS YP_915133.1 119384077 4579435 1300377..1300775 1 NC_008686.1 PFAM: helix-turn-helix- domain containing protein, AraC type; KEGG: bpm:BURPS1710b_A0955 DarR; helix-turn-helix domain-containing protein 1300775 4579435 Pden_1332 Paracoccus denitrificans PD1222 helix-turn-helix domain-containing protein YP_915133.1 1300377 D 318586 CDS YP_915134.1 119384078 4579436 complement(1300801..1302015) 1 NC_008686.1 PFAM: cobalamin synthesis protein, P47K; cobalamin synthesis CobW domain protein; KEGG: eci:UTI89_C1131 hypothetical protein; cobalamin synthesis protein, P47K 1302015 4579436 Pden_1333 Paracoccus denitrificans PD1222 cobalamin synthesis protein, P47K YP_915134.1 1300801 R 318586 CDS YP_915135.1 119384079 4579437 complement(1302041..1302259) 1 NC_008686.1 KEGG: xcb:XC_2473 hypothetical protein; hypothetical protein 1302259 4579437 Pden_1334 Paracoccus denitrificans PD1222 hypothetical protein YP_915135.1 1302041 R 318586 CDS YP_915136.1 119384080 4579438 complement(1302268..1302927) 1 NC_008686.1 KEGG: rpc:RPC_2661 riboflavin biosynthesis protein RibD; TIGRFAM: riboflavin biosynthesis protein RibD; PFAM: CMP/dCMP deaminase, zinc-binding; riboflavin biosynthesis protein RibD 1302927 4579438 Pden_1335 Paracoccus denitrificans PD1222 riboflavin biosynthesis protein RibD YP_915136.1 1302268 R 318586 CDS YP_915137.1 119384081 4579439 complement(1302938..1303402) 1 NC_008686.1 PR-AMP cyclohydrolase; functions in histidine biosynthesis from PRPP; converts 1-(5-phosphoribosyl)-AMP to 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino]imidazole-4- carboxyamide during the histidine biosynthesis pathway; binds zinc and magnesium; forms homodimers; phosphoribosyl-AMP cyclohydrolase 1303402 hisI 4579439 hisI Paracoccus denitrificans PD1222 phosphoribosyl-AMP cyclohydrolase YP_915137.1 1302938 R 318586 CDS YP_915138.1 119384082 4579440 complement(1303421..1303873) 1 NC_008686.1 KEGG: ppu:PP_3321 hypothetical protein; hypothetical protein 1303873 4579440 Pden_1337 Paracoccus denitrificans PD1222 hypothetical protein YP_915138.1 1303421 R 318586 CDS YP_915139.1 119384083 4579441 1304019..1305242 1 NC_008686.1 PFAM: cobalamin synthesis protein, P47K; cobalamin synthesis CobW domain protein; KEGG: rde:RD1_1856 cobalamin synthesis protein; cobalamin synthesis protein, P47K 1305242 4579441 Pden_1338 Paracoccus denitrificans PD1222 cobalamin synthesis protein, P47K YP_915139.1 1304019 D 318586 CDS YP_915140.1 119384084 4580593 1305333..1306001 1 NC_008686.1 KEGG: jan:Jann_2253 hypothetical protein; hypothetical protein 1306001 4580593 Pden_1339 Paracoccus denitrificans PD1222 hypothetical protein YP_915140.1 1305333 D 318586 CDS YP_915141.1 119384085 4580594 1306001..1306318 1 NC_008686.1 KEGG: rde:RD1_1858 hypothetical protein; hypothetical protein 1306318 4580594 Pden_1340 Paracoccus denitrificans PD1222 hypothetical protein YP_915141.1 1306001 D 318586 CDS YP_915142.1 119384086 4580595 1306419..1307921 1 NC_008686.1 PFAM: extracellular solute-binding protein, family 5; KEGG: mfa:Mfla_2388 extracellular solute-binding protein, family 5; extracellular solute-binding protein 1307921 4580595 Pden_1341 Paracoccus denitrificans PD1222 extracellular solute-binding protein YP_915142.1 1306419 D 318586 CDS YP_915143.1 119384087 4580596 1307918..1308856 1 NC_008686.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: vch:VCA1099 peptide transport system permease protein; binding-protein-dependent transport system inner membrane protein 1308856 4580596 Pden_1342 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_915143.1 1307918 D 318586 CDS YP_915144.1 119384088 4580597 1308853..1309677 1 NC_008686.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: mfa:Mfla_2390 binding-protein-dependent transport systems inner membrane component; binding-protein-dependent transport system inner membrane protein 1309677 4580597 Pden_1343 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_915144.1 1308853 D 318586 CDS YP_915145.1 119384089 4580598 1309674..1311110 1 NC_008686.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: vch:VCA1101 peptide transport system ATP-binding protein; ABC transporter 1311110 4580598 Pden_1344 Paracoccus denitrificans PD1222 ABC transporter YP_915145.1 1309674 D 318586 CDS YP_915146.1 119384090 4580599 complement(1312023..1312937) 1 NC_008686.1 TIGRFAM: methylisocitrate lyase; KEGG: rpa:RPA2395 carboxyphosphonoenolpyruvate phosphonomutase; methylisocitrate lyase 1312937 4580599 Pden_1346 Paracoccus denitrificans PD1222 methylisocitrate lyase YP_915146.1 1312023 R 318586 CDS YP_915147.1 119384091 4580600 complement(1312934..1314103) 1 NC_008686.1 catalyzes the synthesis of 2-methylcitrate from propionyl-CoA and oxaloacetate; also catalyzes the condensation of oxaloacetate with acetyl-CoA but with a lower specificity; methylcitrate synthase 1314103 4580600 Pden_1347 Paracoccus denitrificans PD1222 methylcitrate synthase YP_915147.1 1312934 R 318586 CDS YP_915148.1 119384092 4580601 complement(1314114..1315637) 1 NC_008686.1 PFAM: MmgE/PrpD family protein; KEGG: rpc:RPC_3512 2-methylcitrate dehydratase; 2-methylcitrate dehydratase 1315637 4580601 Pden_1348 Paracoccus denitrificans PD1222 2-methylcitrate dehydratase YP_915148.1 1314114 R 318586 CDS YP_915149.1 119384093 4580602 complement(1315624..1316025) 1 NC_008686.1 PFAM: thioesterase superfamily protein; KEGG: rpc:RPC_3513 thioesterase superfamily; thioesterase 1316025 4580602 Pden_1349 Paracoccus denitrificans PD1222 thioesterase YP_915149.1 1315624 R 318586 CDS YP_915150.1 119384094 4580603 1316144..1317529 1 NC_008686.1 PFAM: helix-turn-helix domain protein; protein of unknown function DUF955; KEGG: rru:Rru_A2316 transcriptional regulator, XRE family; hypothetical protein 1317529 4580603 Pden_1350 Paracoccus denitrificans PD1222 hypothetical protein YP_915150.1 1316144 D 318586 CDS YP_915151.1 119384095 4580604 complement(1317508..1318200) 1 NC_008686.1 PFAM: LysR, substrate-binding; KEGG: atc:AGR_L_2015 transcription regulator MetR; LysR family transcriptional regulator 1318200 4580604 Pden_1351 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_915151.1 1317508 R 318586 CDS YP_915152.1 119384096 4580606 1320063..1321046 1 NC_008686.1 KEGG: bur:Bcep18194_C7370 hypothetical protein; hypothetical protein 1321046 4580606 Pden_1354 Paracoccus denitrificans PD1222 hypothetical protein YP_915152.1 1320063 D 318586 CDS YP_915153.1 119384097 4580607 1321075..1322112 1 NC_008686.1 catalyzes the formation of tetrahydropteroyl-L-glutamate and methionine from L-homocysteine and 5-methyltetrahydropteroyltri-L-glutamate; 5- methyltetrahydropteroyltriglutamate/homocysteine S-methyltransferase 1322112 4580607 Pden_1355 Paracoccus denitrificans PD1222 5- methyltetrahydropteroyltriglutamate/homocysteine S-methyltransferase YP_915153.1 1321075 D 318586 CDS YP_915154.1 119384098 4580608 complement(1323389..1323796) 1 NC_008686.1 hypothetical protein 1323796 4580608 Pden_1357 Paracoccus denitrificans PD1222 hypothetical protein YP_915154.1 1323389 R 318586 CDS YP_915155.1 119384099 4580609 complement(1323995..1324810) 1 NC_008686.1 PFAM: UbiE/COQ5 methyltransferase; Methyltransferase type 11; Methyltransferase type 12; KEGG: sme:SMb21433 methyl-transferase, S-adenosyl-L-methionine (SAM)-MTase protein; type 11 methyltransferase 1324810 4580609 Pden_1358 Paracoccus denitrificans PD1222 type 11 methyltransferase YP_915155.1 1323995 R 318586 CDS YP_915156.1 119384100 4580610 complement(1324827..1325252) 1 NC_008686.1 TIGRFAM: pseudoazurin; PFAM: blue (type 1) copper domain protein; KEGG: rru:Rru_A1139 blue (type 1) copper subtype; pseudoazurin 1325252 4580610 Pden_1359 Paracoccus denitrificans PD1222 pseudoazurin YP_915156.1 1324827 R 318586 CDS YP_915157.1 119384101 4580611 complement(1325264..1326034) 1 NC_008686.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sme:SMb20058 ABC transporter ATP-binding protein; ABC transporter 1326034 4580611 Pden_1360 Paracoccus denitrificans PD1222 ABC transporter YP_915157.1 1325264 R 318586 CDS YP_915158.1 119384102 4579792 complement(1326031..1327104) 1 NC_008686.1 PFAM: transport system permease protein; KEGG: psp:PSPPH_3007 iron ABC transporter, permease protein; transport system permease 1327104 4579792 Pden_1361 Paracoccus denitrificans PD1222 transport system permease YP_915158.1 1326031 R 318586 CDS YP_915159.1 119384103 4579793 complement(1327101..1328108) 1 NC_008686.1 PFAM: periplasmic binding protein; KEGG: rru:Rru_A1136 periplasmic binding protein; periplasmic binding protein 1328108 4579793 Pden_1362 Paracoccus denitrificans PD1222 periplasmic binding protein YP_915159.1 1327101 R 318586 CDS YP_915160.1 119384104 4579794 complement(1328565..1330172) 1 NC_008686.1 Catalyzes the first step in the glyoxalate cycle, which converts lipids to carbohydrates; isocitrate lyase 1330172 4579794 Pden_1363 Paracoccus denitrificans PD1222 isocitrate lyase YP_915160.1 1328565 R 318586 CDS YP_915161.1 119384105 4579795 complement(1330296..1331918) 1 NC_008686.1 Catalyzes the aldol condensation of glyoxylate with acetyl-CoA to form malate as part of the second step of the glyoxylate bypass and an alternative to the tricarboxylic acid cycle; malate synthase 1331918 4579795 Pden_1364 Paracoccus denitrificans PD1222 malate synthase YP_915161.1 1330296 R 318586 CDS YP_915162.1 119384106 4579796 1332053..1333486 1 NC_008686.1 PFAM: helix-turn-helix domain protein; protein of unknown function DUF955; KEGG: hne:HNE_1237 DNA-binding protein; hypothetical protein 1333486 4579796 Pden_1365 Paracoccus denitrificans PD1222 hypothetical protein YP_915162.1 1332053 D 318586 CDS YP_915163.1 119384107 4579797 complement(1333483..1334499) 1 NC_008686.1 KEGG: rru:Rru_A1617 protein of unknown function DUF1289; hypothetical protein 1334499 4579797 Pden_1366 Paracoccus denitrificans PD1222 hypothetical protein YP_915163.1 1333483 R 318586 CDS YP_915164.1 119384108 4579798 complement(1334483..1335343) 1 NC_008686.1 PFAM: periplasmic binding protein; KEGG: rsp:RSP_2403 ABC cobalamin/Fe3+-siderophore transporter, periplasmic substrate-binding subunit; periplasmic binding protein 1335343 4579798 Pden_1367 Paracoccus denitrificans PD1222 periplasmic binding protein YP_915164.1 1334483 R 318586 CDS YP_915165.1 119384109 4579799 complement(1335337..1337220) 1 NC_008686.1 PFAM: TonB-dependent receptor; TonB-dependent receptor, plug; KEGG: rru:Rru_A0488 TonB-dependent receptor; TonB-dependent receptor 1337220 4579799 Pden_1368 Paracoccus denitrificans PD1222 TonB-dependent receptor YP_915165.1 1335337 R 318586 CDS YP_915166.1 119384110 4579800 complement(1337561..1337956) 1 NC_008686.1 hypothetical protein 1337956 4579800 Pden_1369 Paracoccus denitrificans PD1222 hypothetical protein YP_915166.1 1337561 R 318586 CDS YP_915167.1 119384111 4579801 1338220..1338939 1 NC_008686.1 hypothetical protein 1338939 4579801 Pden_1370 Paracoccus denitrificans PD1222 hypothetical protein YP_915167.1 1338220 D 318586 CDS YP_915168.1 119384112 4579802 1338995..1339444 1 NC_008686.1 hypothetical protein 1339444 4579802 Pden_1371 Paracoccus denitrificans PD1222 hypothetical protein YP_915168.1 1338995 D 318586 CDS YP_915169.1 119384113 4579803 complement(1339398..1340204) 1 NC_008686.1 KEGG: sme:SMb20398 hypothetical protein; phosphoesterase or phosphohydrolase-like protein 1340204 4579803 Pden_1372 Paracoccus denitrificans PD1222 phosphoesterase or phosphohydrolase-like protein YP_915169.1 1339398 R 318586 CDS YP_915170.1 119384114 4579804 complement(1340206..1341507) 1 NC_008686.1 KEGG: rde:RD1_4059 Lon protease; ATP-dependent Lon protease 1341507 4579804 Pden_1373 Paracoccus denitrificans PD1222 ATP-dependent Lon protease YP_915170.1 1340206 R 318586 CDS YP_915171.1 119384115 4579805 complement(1341954..1342742) 1 NC_008686.1 PFAM: metallophosphoesterase; KEGG: nha:Nham_1359 metallophosphoesterase; metallophosphoesterase 1342742 4579805 Pden_1374 Paracoccus denitrificans PD1222 metallophosphoesterase YP_915171.1 1341954 R 318586 CDS YP_915172.1 119384116 4579806 complement(1342739..1343188) 1 NC_008686.1 hypothetical protein 1343188 4579806 Pden_1375 Paracoccus denitrificans PD1222 hypothetical protein YP_915172.1 1342739 R 318586 CDS YP_915173.1 119384117 4579807 complement(1343653..1344600) 1 NC_008686.1 catalyzes the radical-mediated insertion of two sulfur atoms into an acyl carrier protein (ACP) bound to an octanoyl group to produce a lipoyl group; lipoyl synthase 1344600 4579807 Pden_1376 Paracoccus denitrificans PD1222 lipoyl synthase YP_915173.1 1343653 R 318586 CDS YP_915174.1 119384118 4579808 1344725..1345291 1 NC_008686.1 PFAM: alkyl hydroperoxide reductase/ Thiol specific antioxidant/ Mal allergen; Redoxin domain protein; KEGG: rsp:RSP_2781 peroxiredoxin/glutaredoxin family protein; redoxin domain-containing protein 1345291 4579808 Pden_1377 Paracoccus denitrificans PD1222 redoxin domain-containing protein YP_915174.1 1344725 D 318586 CDS YP_915175.1 119384119 4579809 complement(1345362..1346516) 1 NC_008686.1 KEGG: rsp:RSP_6073 hypothetical protein; hypothetical protein 1346516 4579809 Pden_1378 Paracoccus denitrificans PD1222 hypothetical protein YP_915175.1 1345362 R 318586 CDS YP_915176.1 119384120 4579810 1346729..1347061 1 NC_008686.1 KEGG: rsp:RSP_6226 hypothetical protein; hypothetical protein 1347061 4579810 Pden_1379 Paracoccus denitrificans PD1222 hypothetical protein YP_915176.1 1346729 D 318586 CDS YP_915177.1 119384121 4579811 complement(1347048..1348622) 1 NC_008686.1 PFAM: protein of unknown function DUF853, NPT hydrolase KEGG: sil:SPO1934 hypothetical protein; hypothetical protein 1348622 4579811 Pden_1380 Paracoccus denitrificans PD1222 hypothetical protein YP_915177.1 1347048 R 318586 CDS YP_915178.1 119384122 4581304 1349084..1349872 1 NC_008686.1 PFAM: Invasion associated locus B family protein; KEGG: rsp:RSP_2778 hypothetical protein; invasion associated locus B family protein 1349872 4581304 Pden_1381 Paracoccus denitrificans PD1222 invasion associated locus B family protein YP_915178.1 1349084 D 318586 CDS YP_915179.1 119384123 4581305 complement(1349947..1351491) 1 NC_008686.1 TIGRFAM: protease Do; PFAM: peptidase S1 and S6, chymotrypsin/Hap; PDZ/DHR/GLGF domain protein; KEGG: rsp:RSP_0355 possible serine protease; protease Do 1351491 4581305 Pden_1382 Paracoccus denitrificans PD1222 protease Do YP_915179.1 1349947 R 318586 CDS YP_915180.1 119384124 4581306 complement(1351705..1351956) 1 NC_008686.1 hypothetical protein 1351956 4581306 Pden_1383 Paracoccus denitrificans PD1222 hypothetical protein YP_915180.1 1351705 R 318586 CDS YP_915181.1 119384125 4581307 complement(1352030..1355647) 1 NC_008686.1 Catalyzes the rate-limiting step in dNTP synthesis; ribonucleotide-diphosphate reductase subunit alpha 1355647 4581307 Pden_1384 Paracoccus denitrificans PD1222 ribonucleotide-diphosphate reductase subunit alpha YP_915181.1 1352030 R 318586 CDS YP_915182.1 119384126 4581308 complement(1356043..1356627) 1 NC_008686.1 PFAM: 5-formyltetrahydrofolate cyclo-ligase; KEGG: rsp:RSP_1898 5-formyltetrahydrofolate cyclo-ligase; 5-formyltetrahydrofolate cyclo-ligase 1356627 4581308 Pden_1385 Paracoccus denitrificans PD1222 5-formyltetrahydrofolate cyclo-ligase YP_915182.1 1356043 R 318586 CDS YP_915183.1 119384127 4581309 complement(1356612..1358069) 1 NC_008686.1 TIGRFAM: magnesium transporter; PFAM: CBS domain containing protein; MgtE integral membrane region; MgtE intracellular region; KEGG: rsp:RSP_1897 Mg/Co/Ni transporter, MgtE; magnesium transporter 1358069 4581309 Pden_1386 Paracoccus denitrificans PD1222 magnesium transporter YP_915183.1 1356612 R 318586 CDS YP_915184.1 119384128 4581310 complement(1358090..1358905) 1 NC_008686.1 PFAM: inositol monophosphatase; KEGG: rde:RD1_2006 inositol monophosphatase family protein; inositol monophosphatase 1358905 4581310 Pden_1387 Paracoccus denitrificans PD1222 inositol monophosphatase YP_915184.1 1358090 R 318586 CDS YP_915185.1 119384129 4581311 complement(1358986..1359345) 1 NC_008686.1 PFAM: helix-turn-helix domain protein; KEGG: rsp:RSP_1892 Cro/CI transcriptional regulator; XRE family transcriptional regulator 1359345 4581311 Pden_1388 Paracoccus denitrificans PD1222 XRE family transcriptional regulator YP_915185.1 1358986 R 318586 CDS YP_915186.1 119384130 4581312 1359524..1360492 1 NC_008686.1 PFAM: Alcohol dehydrogenase, zinc-binding domain protein; Alcohol dehydrogenase GroES domain protein; KEGG: jan:Jann_1231 alcohol dehydrogenase, zinc-binding; alcohol dehydrogenase 1360492 4581312 Pden_1389 Paracoccus denitrificans PD1222 alcohol dehydrogenase YP_915186.1 1359524 D 318586 CDS YP_915187.1 119384131 4581313 1360615..1361385 1 NC_008686.1 PFAM: protein of unknown function UPF0005; KEGG: sil:SPO2963 membrane protein; hypothetical protein 1361385 4581313 Pden_1390 Paracoccus denitrificans PD1222 hypothetical protein YP_915187.1 1360615 D 318586 CDS YP_915188.1 119384132 4581314 1361653..1361895 1 NC_008686.1 PFAM: BolA family protein; KEGG: rsp:RSP_2952 BolA-like protein; BolA family protein 1361895 4581314 Pden_1391 Paracoccus denitrificans PD1222 BolA family protein YP_915188.1 1361653 D 318586 CDS YP_915189.1 119384133 4581315 1361947..1362309 1 NC_008686.1 TIGRFAM: glutaredoxin-like protein; PFAM: glutaredoxin; KEGG: sil:SPO1868 glutaredoxin-related protein; glutaredoxin-like protein 1362309 4581315 Pden_1392 Paracoccus denitrificans PD1222 glutaredoxin-like protein YP_915189.1 1361947 D 318586 CDS YP_915190.1 119384134 4581316 complement(1362397..1363092) 1 NC_008686.1 hypothetical protein 1363092 4581316 Pden_1393 Paracoccus denitrificans PD1222 hypothetical protein YP_915190.1 1362397 R 318586 CDS YP_915191.1 119384135 4581317 complement(1363100..1363528) 1 NC_008686.1 PFAM: protein of unknown function DUF883, ElaB; KEGG: rha:RHA1_ro00971 hypothetical protein; hypothetical protein 1363528 4581317 Pden_1394 Paracoccus denitrificans PD1222 hypothetical protein YP_915191.1 1363100 R 318586 CDS YP_915192.1 119384136 4581318 complement(1363627..1364754) 1 NC_008686.1 PFAM: aminotransferase, class V; KEGG: rsp:RSP_1868 serine-pyruvate aminotransferase; class V aminotransferase 1364754 4581318 Pden_1395 Paracoccus denitrificans PD1222 class V aminotransferase YP_915192.1 1363627 R 318586 CDS YP_915193.1 119384137 4581319 1364894..1365610 1 NC_008686.1 PFAM: glutamine amidotransferase class-I; KEGG: rsp:RSP_0376 glutamine amidotransferase class-I; glutamine amidotransferase 1365610 4581319 Pden_1396 Paracoccus denitrificans PD1222 glutamine amidotransferase YP_915193.1 1364894 D 318586 CDS YP_915194.1 119384138 4581320 1365607..1366965 1 NC_008686.1 PFAM: glutamine synthetase, catalytic region; KEGG: rsp:RSP_0377 probable glutamine synthetase; glutamate--ammonia ligase 1366965 4581320 Pden_1397 Paracoccus denitrificans PD1222 glutamate--ammonia ligase YP_915194.1 1365607 D 318586 CDS YP_915195.1 119384139 4581321 1367038..1368348 1 NC_008686.1 PFAM: FAD dependent oxidoreductase; KEGG: rsp:RSP_0378 hypothetical protein; FAD dependent oxidoreductase 1368348 4581321 Pden_1398 Paracoccus denitrificans PD1222 FAD dependent oxidoreductase YP_915195.1 1367038 D 318586 CDS YP_915196.1 119384140 4581322 complement(1368345..1369001) 1 NC_008686.1 KEGG: rsp:RSP_1671 hypothetical protein; hypothetical protein 1369001 4581322 Pden_1399 Paracoccus denitrificans PD1222 hypothetical protein YP_915196.1 1368345 R 318586 CDS YP_915197.1 119384141 4581265 complement(1369014..1371131) 1 NC_008686.1 KEGG: rsp:RSP_1670 RelA/SpoT family protein; TIGRFAM: RelA/SpoT family protein; PFAM: amino acid-binding ACT domain protein; TGS domain protein; metal-dependent phosphohydrolase, HD sub domain; RelA/SpoT domain protein; SMART: metal-dependent phosphohydrolase, HD region; (p)ppGpp synthetase I SpoT/RelA 1371131 4581265 Pden_1400 Paracoccus denitrificans PD1222 (p)ppGpp synthetase I SpoT/RelA YP_915197.1 1369014 R 318586 CDS YP_915198.1 119384142 4581266 complement(1371154..1371510) 1 NC_008686.1 Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits; DNA-directed RNA polymerase subunit omega 1371510 4581266 Pden_1401 Paracoccus denitrificans PD1222 DNA-directed RNA polymerase subunit omega YP_915198.1 1371154 R 318586 CDS YP_915199.1 119384143 4581267 complement(1371581..1372072) 1 NC_008686.1 TIGRFAM: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase; PFAM: 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase, HPPK; KEGG: sil:SPO3205 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase; 2-amino-4-hydroxy-6- hydroxymethyldihydropteridine pyrophosphokinase 1372072 4581267 Pden_1402 Paracoccus denitrificans PD1222 2-amino-4-hydroxy-6- hydroxymethyldihydropteridine pyrophosphokinase YP_915199.1 1371581 R 318586 CDS YP_915200.1 119384144 4581268 1372187..1372738 1 NC_008686.1 PFAM: protein of unknown function DUF88; KEGG: rsp:RSP_1667 hypothetical protein; hypothetical protein 1372738 4581268 Pden_1403 Paracoccus denitrificans PD1222 hypothetical protein YP_915200.1 1372187 D 318586 CDS YP_915201.1 119384145 4581269 complement(1372781..1374172) 1 NC_008686.1 PFAM: OmpA/MotB domain protein; KEGG: rsp:RSP_2289 flagellar motor protein; hypothetical protein 1374172 4581269 Pden_1404 Paracoccus denitrificans PD1222 hypothetical protein YP_915201.1 1372781 R 318586 CDS YP_915202.1 119384146 4581270 complement(1374162..1375871) 1 NC_008686.1 KEGG: rsp:RSP_2288 hypothetical protein; hypothetical protein 1375871 4581270 Pden_1405 Paracoccus denitrificans PD1222 hypothetical protein YP_915202.1 1374162 R 318586 CDS YP_915203.1 119384147 4581271 complement(1375897..1376451) 1 NC_008686.1 PFAM: ChaC family protein; KEGG: rsp:RSP_2287 ChaC-like protein; ChaC family protein 1376451 4581271 Pden_1406 Paracoccus denitrificans PD1222 ChaC family protein YP_915203.1 1375897 R 318586 CDS YP_915204.1 119384148 4581272 1376502..1377551 1 NC_008686.1 KEGG: rsp:RSP_2286 hypothetical protein; hypothetical protein 1377551 4581272 Pden_1407 Paracoccus denitrificans PD1222 hypothetical protein YP_915204.1 1376502 D 318586 CDS YP_915205.1 119384149 4581273 complement(1377548..1378483) 1 NC_008686.1 dual function enzyme catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate and the formation of tyrosine from arogenate; cyclohexadienyl dehydrogenase 1378483 4581273 Pden_1408 Paracoccus denitrificans PD1222 cyclohexadienyl dehydrogenase YP_915205.1 1377548 R 318586 CDS YP_915206.1 119384150 4581274 complement(1378483..1379586) 1 NC_008686.1 catalyzes the formation of L-histidinol phosphate from imidazole-acetol phosphate and glutamate in histidine biosynthesis; histidinol-phosphate aminotransferase 1379586 4581274 Pden_1409 Paracoccus denitrificans PD1222 histidinol-phosphate aminotransferase YP_915206.1 1378483 R 318586 CDS YP_915207.1 119384151 4581275 complement(1379784..1380302) 1 NC_008686.1 TIGRFAM: periplasmic protein thiol--disulphide oxidoreductase DsbE; PFAM: Redoxin domain protein; KEGG: rde:RD1_2551 thiol:disulfide interchange protein CycY; periplasmic protein thiol--disulfide oxidoreductase DsbE 1380302 4581275 Pden_1410 Paracoccus denitrificans PD1222 periplasmic protein thiol--disulfide oxidoreductase DsbE YP_915207.1 1379784 R 318586 CDS YP_915208.1 119384152 4581276 complement(1380456..1381181) 1 NC_008686.1 TIGRFAM: heme exporter protein CcmC; PFAM: cytochrome c assembly protein; KEGG: rsp:RSP_1803 ABC heme exporter, inner membrane subunit CcmC; heme exporter protein CcmC 1381181 4581276 Pden_1411 Paracoccus denitrificans PD1222 heme exporter protein CcmC YP_915208.1 1380456 R 318586 CDS YP_915209.1 119384153 4581277 complement(1381234..1381890) 1 NC_008686.1 TIGRFAM: heme exporter protein CcmB; PFAM: cytochrome c-type biogenesis protein CcmB; KEGG: rsp:RSP_1802 ABC heme exporter, inner membrane subunit CcmB; heme exporter protein CcmB 1381890 4581277 Pden_1412 Paracoccus denitrificans PD1222 heme exporter protein CcmB YP_915209.1 1381234 R 318586 CDS YP_915210.1 119384154 4581278 complement(1381901..1382533) 1 NC_008686.1 ATP-binding protein; required for proper cytochrome c maturation; cytochrome c biogenesis protein CcmA 1382533 4581278 Pden_1413 Paracoccus denitrificans PD1222 cytochrome c biogenesis protein CcmA YP_915210.1 1381901 R 318586 CDS YP_915211.1 119384155 4581279 complement(1382530..1382886) 1 NC_008686.1 PFAM: protein of unknown function DUF498; KEGG: rsp:RSP_1800 hypothetical protein; hypothetical protein 1382886 4581279 Pden_1414 Paracoccus denitrificans PD1222 hypothetical protein YP_915211.1 1382530 R 318586 CDS YP_915212.1 119384156 4581280 complement(1382886..1383878) 1 NC_008686.1 forms a complex with SecD and YajC; SecDFyajC stimulates the proton motive force-driven protein translocation; seems to modulate the cycling of SecA by stabilizing its membrane-inserted state and appears to be required for the release of mature proteins from the extracytoplasmic side of the membrane; in some organisms, such as Bacillus subtilis, SecD is fused to SecF; preprotein translocase subunit SecF 1383878 secF 4581280 secF Paracoccus denitrificans PD1222 preprotein translocase subunit SecF YP_915212.1 1382886 R 318586 CDS YP_915213.1 119384157 4581281 complement(1383891..1385555) 1 NC_008686.1 part of the preprotein secretory system; when complexed with proteins SecF and YajC, SecDFyajC stimulates the proton motive force-driven protein translocation, and appears to be required for the release of mature proteins from the extracytoplasmic side of the membrane; preprotein translocase subunit SecD 1385555 secD 4581281 secD Paracoccus denitrificans PD1222 preprotein translocase subunit SecD YP_915213.1 1383891 R 318586 CDS YP_915214.1 119384158 4581282 complement(1385572..1385904) 1 NC_008686.1 TIGRFAM: preprotein translocase, YajC subunit; PFAM: YajC family protein; KEGG: rsp:RSP_1797 preprotein translocase subunit YajC; preprotein translocase subunit YajC 1385904 4581282 Pden_1417 Paracoccus denitrificans PD1222 preprotein translocase subunit YajC YP_915214.1 1385572 R 318586 CDS YP_915215.1 119384159 4581283 1386096..1386947 1 NC_008686.1 functions in degradation of stringent response intracellular messenger ppGpp; in Escherichia coli this gene is co-transcribed with the toxin/antitoxin genes mazEF; activity of MazG is inhibited by MazEF in vitro; ppGpp inhibits mazEF expression; MazG thus works in limiting the toxic activity of the MazF toxin induced during starvation; MazG also interacts with the GTPase protein Era; nucleoside triphosphate pyrophosphohydrolase 1386947 mazG 4581283 mazG Paracoccus denitrificans PD1222 nucleoside triphosphate pyrophosphohydrolase YP_915215.1 1386096 D 318586 CDS YP_915216.1 119384160 4581284 1386952..1387857 1 NC_008686.1 hypothetical protein 1387857 4581284 Pden_1419 Paracoccus denitrificans PD1222 hypothetical protein YP_915216.1 1386952 D 318586 CDS YP_915217.1 119384161 4580475 complement(1387841..1388830) 1 NC_008686.1 PFAM: dihydrouridine synthase, DuS; KEGG: sil:SPO2374 tRNA-dihydrouridine synthase A; tRNA-dihydrouridine synthase A 1388830 4580475 Pden_1420 Paracoccus denitrificans PD1222 tRNA-dihydrouridine synthase A YP_915217.1 1387841 R 318586 CDS YP_915218.1 119384162 4580476 1388943..1389998 1 NC_008686.1 PFAM: phage integrase family protein; KEGG: hne:HNE_0292 site-specific recombinase, phage integrase family; phage integrase family protein 1389998 4580476 Pden_1421 Paracoccus denitrificans PD1222 phage integrase family protein YP_915218.1 1388943 D 318586 CDS YP_915219.1 119384163 4580477 complement(1390072..1390542) 1 NC_008686.1 PFAM: protein of unknown function UPF0074; Helix-turn-helix, type 11 domain protein; KEGG: bte:BTH_II1478 transcriptional regulator family; BadM/Rrf2 family transcriptional regulator 1390542 4580477 Pden_1422 Paracoccus denitrificans PD1222 BadM/Rrf2 family transcriptional regulator YP_915219.1 1390072 R 318586 CDS YP_915220.1 119384164 4580478 1390665..1391582 1 NC_008686.1 PFAM: HI0933 family protein; FAD-dependent pyridine nucleotide-disulphide oxidoreductase; KEGG: bpm:BURPS1710b_A2517 pyridine nucleotide-disulphide oxidoreductase; FAD-dependent pyridine nucleotide-disulfide oxidoreductase 1391582 4580478 Pden_1423 Paracoccus denitrificans PD1222 FAD-dependent pyridine nucleotide-disulfide oxidoreductase YP_915220.1 1390665 D 318586 CDS YP_915221.1 119384165 4580479 1391595..1392215 1 NC_008686.1 PFAM: Tellurite resistance protein TehB; thiopurine S-methyltransferase; Methyltransferase type 11; Methyltransferase type 12; KEGG: mmc:Mmcs_3339 methyltransferase type 12; type 11 methyltransferase 1392215 4580479 Pden_1424 Paracoccus denitrificans PD1222 type 11 methyltransferase YP_915221.1 1391595 D 318586 CDS YP_915222.1 119384166 4580480 complement(1392368..1395784) 1 NC_008686.1 PFAM: ABC transporter, transmembrane region; SMC domain protein; ABC transporter related; SMART: AAA ATPase; KEGG: gvi:gll0322 HlyB/MsbA family ABC transporter; ABC transporter 1395784 4580480 Pden_1425 Paracoccus denitrificans PD1222 ABC transporter YP_915222.1 1392368 R 318586 CDS YP_915223.1 119384167 4580481 complement(1395781..1396800) 1 NC_008686.1 KEGG: mes:Meso_0337 major facilitator superfamily MFS_1; major facilitator superfamily transporter 1396800 4580481 Pden_1426 Paracoccus denitrificans PD1222 major facilitator superfamily transporter YP_915223.1 1395781 R 318586 CDS YP_915224.1 119384168 4580482 complement(1396961..1399102) 1 NC_008686.1 PFAM: TonB-dependent receptor; TonB-dependent receptor, plug; KEGG: pau:PA14_55050 possible TonB-dependent receptor; TonB-dependent receptor 1399102 4580482 Pden_1427 Paracoccus denitrificans PD1222 TonB-dependent receptor YP_915224.1 1396961 R 318586 CDS YP_915225.1 119384169 4580483 complement(1399197..1400186) 1 NC_008686.1 PFAM: helix-turn-helix- domain containing protein, AraC type; KEGG: pae:PA2281 probable transcriptional regulator; helix-turn-helix domain-containing protein 1400186 4580483 Pden_1428 Paracoccus denitrificans PD1222 helix-turn-helix domain-containing protein YP_915225.1 1399197 R 318586 CDS YP_915226.1 119384170 4580484 1400353..1400946 1 NC_008686.1 PFAM: Lysine exporter protein (LYSE/YGGA); KEGG: ret:RHE_CH02787 probable amino acid efflux protein, LysE family; lysine exporter protein LysE/YggA 1400946 4580484 Pden_1429 Paracoccus denitrificans PD1222 lysine exporter protein LysE/YggA YP_915226.1 1400353 D 318586 CDS YP_915227.1 119384171 4580485 1400925..1401488 1 NC_008686.1 hypothetical protein 1401488 4580485 Pden_1430 Paracoccus denitrificans PD1222 hypothetical protein YP_915227.1 1400925 D 318586 CDS YP_915228.1 119384172 4580486 1401527..1402195 1 NC_008686.1 PFAM: regulatory protein GntR, HTH; GntR domain protein; KEGG: rsp:RSP_1925 transcriptional regulator, GntR family; GntR family transcriptional regulator 1402195 4580486 Pden_1431 Paracoccus denitrificans PD1222 GntR family transcriptional regulator YP_915228.1 1401527 D 318586 CDS YP_915229.1 119384173 4580487 1402280..1402837 1 NC_008686.1 PFAM: BioY protein; KEGG: rsp:RSP_1924 BioY family protein; BioY protein 1402837 4580487 Pden_1432 Paracoccus denitrificans PD1222 BioY protein YP_915229.1 1402280 D 318586 CDS YP_915230.1 119384174 4580488 1402834..1403808 1 NC_008686.1 KEGG: rsp:RSP_1923 biotin synthase; TIGRFAM: biotin synthase; PFAM: Radical SAM domain protein; biotin and thiamin synthesis associated; SMART: Elongator protein 3/MiaB/NifB; biotin synthase 1403808 4580488 Pden_1433 Paracoccus denitrificans PD1222 biotin synthase YP_915230.1 1402834 D 318586 CDS YP_915231.1 119384175 4580489 complement(1403811..1405253) 1 NC_008686.1 PFAM: regulatory protein GntR, HTH; aminotransferase, class I and II; KEGG: rsp:RSP_1922 transcriptional regulator, GntR family, with aminotransferase domain; GntR family transcriptional regulator 1405253 4580489 Pden_1434 Paracoccus denitrificans PD1222 GntR family transcriptional regulator YP_915231.1 1403811 R 318586 CDS YP_915232.1 119384176 4580490 1405317..1406012 1 NC_008686.1 PFAM: glutamine amidotransferase class-I; KEGG: rru:Rru_A3512 glutamine amidotransferase class-I; glutamine amidotransferase 1406012 4580490 Pden_1435 Paracoccus denitrificans PD1222 glutamine amidotransferase YP_915232.1 1405317 D 318586 CDS YP_915233.1 119384177 4580491 1406009..1406689 1 NC_008686.1 PFAM: 3-alpha; MOSC domain containing protein; KEGG: rsp:RSP_1921 MOSC domain protein; MOSC domain-containing protein 1406689 4580491 Pden_1436 Paracoccus denitrificans PD1222 MOSC domain-containing protein YP_915233.1 1406009 D 318586 CDS YP_915234.1 119384178 4580492 1406686..1407534 1 NC_008686.1 TIGRFAM: pyridoxal kinase; PFAM: Phosphomethylpyrimidine kinase type-1; KEGG: rsp:RSP_1920 pyridoxal/pyridoxine/pyridoxamine kinase; pyridoxal kinase 1407534 4580492 Pden_1437 Paracoccus denitrificans PD1222 pyridoxal kinase YP_915234.1 1406686 D 318586 CDS YP_915235.1 119384179 4580493 complement(1407734..1409686) 1 NC_008686.1 KEGG: bte:BTH_I2719 pathogenesis-related protein; pathogenesis-like protein 1409686 4580493 Pden_1438 Paracoccus denitrificans PD1222 pathogenesis-like protein YP_915235.1 1407734 R 318586 CDS YP_915236.1 119384180 4580223 complement(1409683..1411917) 1 NC_008686.1 KEGG: bte:BTH_I2720 hypothetical protein; hypothetical protein 1411917 4580223 Pden_1439 Paracoccus denitrificans PD1222 hypothetical protein YP_915236.1 1409683 R 318586 CDS YP_915237.1 119384181 4580224 1412139..1412408 1 NC_008686.1 hypothetical protein 1412408 4580224 Pden_1440 Paracoccus denitrificans PD1222 hypothetical protein YP_915237.1 1412139 D 318586 CDS YP_915238.1 119384182 4580225 1412411..1412872 1 NC_008686.1 TIGRFAM: uncharacterized domain 1; PFAM: thioesterase superfamily protein; KEGG: hne:HNE_1462 thioesterase family protein; hypothetical protein 1412872 4580225 Pden_1441 Paracoccus denitrificans PD1222 hypothetical protein YP_915238.1 1412411 D 318586 CDS YP_915239.1 119384183 4580226 complement(1412869..1413117) 1 NC_008686.1 hypothetical protein 1413117 4580226 Pden_1442 Paracoccus denitrificans PD1222 hypothetical protein YP_915239.1 1412869 R 318586 CDS YP_915240.1 119384184 4580227 1413275..1413652 1 NC_008686.1 KEGG: hne:HNE_1461 conserved hypothetical protein TIGR02246; hypothetical protein 1413652 4580227 Pden_1443 Paracoccus denitrificans PD1222 hypothetical protein YP_915240.1 1413275 D 318586 CDS YP_915241.1 119384185 4580228 1413649..1414047 1 NC_008686.1 PFAM: Cupin 2, conserved barrel domain protein; KEGG: xcb:XC_1877 hypothetical protein; cupin 1414047 4580228 Pden_1444 Paracoccus denitrificans PD1222 cupin YP_915241.1 1413649 D 318586 CDS YP_915242.1 119384186 4580229 1414120..1414404 1 NC_008686.1 hypothetical protein 1414404 4580229 Pden_1445 Paracoccus denitrificans PD1222 hypothetical protein YP_915242.1 1414120 D 318586 CDS YP_915243.1 119384187 4580230 1414397..1415647 1 NC_008686.1 PFAM: major facilitator superfamily MFS_1; KEGG: reu:Reut_A2630 major facilitator superfamily MFS_1; major facilitator superfamily transporter 1415647 4580230 Pden_1446 Paracoccus denitrificans PD1222 major facilitator superfamily transporter YP_915243.1 1414397 D 318586 CDS YP_915244.1 119384188 4580231 1415738..1416283 1 NC_008686.1 PFAM: PEBP family protein; KEGG: rpa:RPA0709 hypothetical protein; PEBP family protein 1416283 4580231 Pden_1447 Paracoccus denitrificans PD1222 PEBP family protein YP_915244.1 1415738 D 318586 CDS YP_915245.1 119384189 4580232 1416302..1417177 1 NC_008686.1 TIGRFAM: phenazine biosynthesis protein PhzF family; PFAM: Phenazine biosynthesis PhzC/PhzF protein; KEGG: zmo:ZMO1945 predicted epimerase; PhzF family phenazine biosynthesis protein 1417177 4580232 Pden_1448 Paracoccus denitrificans PD1222 PhzF family phenazine biosynthesis protein YP_915245.1 1416302 D 318586 CDS YP_915246.1 119384190 4580233 complement(1417178..1417720) 1 NC_008686.1 KEGG: rsp:RSP_1919 hypothetical protein; hypothetical protein 1417720 4580233 Pden_1449 Paracoccus denitrificans PD1222 hypothetical protein YP_915246.1 1417178 R 318586 CDS YP_915247.1 119384191 4580234 complement(1417876..1418190) 1 NC_008686.1 KEGG: rsp:RSP_1918 predicted alpha/beta hydrolase; alpha/beta hydrolase 1418190 4580234 Pden_1450 Paracoccus denitrificans PD1222 alpha/beta hydrolase YP_915247.1 1417876 R 318586 CDS YP_915248.1 119384192 4580235 complement(1418685..1418975) 1 NC_008686.1 PFAM: protein of unknown function DUF1330; KEGG: mmc:Mmcs_0720 protein of unknown function DUF1330; hypothetical protein 1418975 4580235 Pden_1452 Paracoccus denitrificans PD1222 hypothetical protein YP_915248.1 1418685 R 318586 CDS YP_915249.1 119384193 4580236 1419245..1420051 1 NC_008686.1 KEGG: jan:Jann_1547 DNA polymerase, beta-like; DNA polymerase, beta-like 1420051 4580236 Pden_1453 Paracoccus denitrificans PD1222 DNA polymerase, beta-like YP_915249.1 1419245 D 318586 CDS YP_915250.1 119384194 4580237 1420288..1421376 1 NC_008686.1 KEGG: rme:Rmet_1656 glutathione S-transferase-like protein; glutathione S-transferase-like protein 1421376 4580237 Pden_1454 Paracoccus denitrificans PD1222 glutathione S-transferase-like protein YP_915250.1 1420288 D 318586 CDS YP_915251.1 119384195 4580238 complement(1421594..1422829) 1 NC_008686.1 PFAM: protein of unknown function DUF1228; major facilitator superfamily MFS_1; KEGG: rpe:RPE_0479 major facilitator superfamily MFS_1; major facilitator superfamily transporter 1422829 4580238 Pden_1455 Paracoccus denitrificans PD1222 major facilitator superfamily transporter YP_915251.1 1421594 R 318586 CDS YP_915252.1 119384196 4580239 1422907..1423398 1 NC_008686.1 PFAM: helix-turn-helix, HxlR type; KEGG: sit:TM1040_2008 transcriptional regulator, HxlR family; HxlR family transcriptional regulator 1423398 4580239 Pden_1456 Paracoccus denitrificans PD1222 HxlR family transcriptional regulator YP_915252.1 1422907 D 318586 CDS YP_915253.1 119384197 4580240 complement(1423406..1424317) 1 NC_008686.1 KEGG: rsp:RSP_1918 predicted alpha/beta hydrolase; alpha/beta hydrolase 1424317 4580240 Pden_1457 Paracoccus denitrificans PD1222 alpha/beta hydrolase YP_915253.1 1423406 R 318586 CDS YP_915254.1 119384198 4580241 1424485..1425009 1 NC_008686.1 PFAM: Cupin 2, conserved barrel domain protein; KEGG: rsp:RSP_1917 hypothetical protein; cupin 1425009 4580241 Pden_1458 Paracoccus denitrificans PD1222 cupin YP_915254.1 1424485 D 318586 CDS YP_915255.1 119384199 4580242 1425006..1425662 1 NC_008686.1 PFAM: DSBA oxidoreductase; KEGG: rsp:RSP_1916 possible 2-hydroxychromene-2-carboxylate isomerase; DSBA oxidoreductase 1425662 4580242 Pden_1459 Paracoccus denitrificans PD1222 DSBA oxidoreductase YP_915255.1 1425006 D 318586 CDS YP_915256.1 119384200 4580281 1425659..1426087 1 NC_008686.1 PFAM: GCN5-related N-acetyltransferase; KEGG: rsp:RSP_6026 acetyltransferase; N-acetyltransferase 1426087 4580281 Pden_1460 Paracoccus denitrificans PD1222 N-acetyltransferase YP_915256.1 1425659 D 318586 CDS YP_915257.1 119384201 4580282 complement(1426069..1426521) 1 NC_008686.1 PFAM: GCN5-related N-acetyltransferase; KEGG: rru:Rru_A3458 GCN5-related N-acetyltransferase; N-acetyltransferase 1426521 4580282 Pden_1461 Paracoccus denitrificans PD1222 N-acetyltransferase YP_915257.1 1426069 R 318586 CDS YP_915258.1 119384202 4580283 1426766..1427152 1 NC_008686.1 PFAM: GCN5-related N-acetyltransferase; KEGG: ret:RHE_CH02190 probable acetyltransferase protein; N-acetyltransferase 1427152 4580283 Pden_1462 Paracoccus denitrificans PD1222 N-acetyltransferase YP_915258.1 1426766 D 318586 CDS YP_915259.1 119384203 4580284 complement(1427197..1428117) 1 NC_008686.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: rsp:RSP_1915 transcriptional regulator, LysR family; LysR family transcriptional regulator 1428117 4580284 Pden_1463 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_915259.1 1427197 R 318586 CDS YP_915260.1 119384204 4580285 1428263..1429180 1 NC_008686.1 PFAM: aminotransferase, class IV; KEGG: rru:Rru_A2223 branched-chain amino acid aminotransferase I; aminotransferase, class IV 1429180 4580285 Pden_1464 Paracoccus denitrificans PD1222 aminotransferase, class IV YP_915260.1 1428263 D 318586 CDS YP_915261.1 119384205 4580286 complement(1429171..1429911) 1 NC_008686.1 KEGG: atc:AGR_C_4899 hypothetical transmembrane protein; hypothetical protein 1429911 4580286 Pden_1465 Paracoccus denitrificans PD1222 hypothetical protein YP_915261.1 1429171 R 318586 CDS YP_915262.1 119384206 4580287 1430186..1430767 1 NC_008686.1 SMART: helix-turn-helix- domain containing protein, AraC type; KEGG: cvi:CV1825 probable transcriptional regulator, AraC family; helix-turn-helix domain-containing protein 1430767 4580287 Pden_1466 Paracoccus denitrificans PD1222 helix-turn-helix domain-containing protein YP_915262.1 1430186 D 318586 CDS YP_915263.1 119384207 4580288 complement(1430770..1431402) 1 NC_008686.1 PFAM: Lysine exporter protein (LYSE/YGGA); KEGG: gbe:GbCGDNIH1_1691 transporter, LysE family; lysine exporter protein LysE/YggA 1431402 4580288 Pden_1467 Paracoccus denitrificans PD1222 lysine exporter protein LysE/YggA YP_915263.1 1430770 R 318586 CDS YP_915264.1 119384208 4580289 complement(1431405..1431950) 1 NC_008686.1 PFAM: protein of unknown function DUF1234; KEGG: bur:Bcep18194_B2508 protein of unknown function DUF1234; hypothetical protein 1431950 4580289 Pden_1468 Paracoccus denitrificans PD1222 hypothetical protein YP_915264.1 1431405 R 318586 CDS YP_915265.1 119384209 4580290 1432068..1432523 1 NC_008686.1 PFAM: regulatory protein, AsnC/Lrp family; KEGG: bur:Bcep18194_B2509 transcriptional regulator, AsnC family; AsnC family transcriptional regulator 1432523 4580290 Pden_1469 Paracoccus denitrificans PD1222 AsnC family transcriptional regulator YP_915265.1 1432068 D 318586 CDS YP_915266.1 119384210 4580291 1432553..1433176 1 NC_008686.1 PFAM: Lysine exporter protein (LYSE/YGGA); KEGG: jan:Jann_1597 lysine exporter protein (LysE/YggA); lysine exporter protein LysE/YggA 1433176 4580291 Pden_1470 Paracoccus denitrificans PD1222 lysine exporter protein LysE/YggA YP_915266.1 1432553 D 318586 CDS YP_915267.1 119384211 4580292 1433351..1434349 1 NC_008686.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: mes:Meso_3862 transcriptional regulator, LysR family; LysR family transcriptional regulator 1434349 4580292 Pden_1471 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_915267.1 1433351 D 318586 CDS YP_915268.1 119384212 4580293 1434342..1435595 1 NC_008686.1 PFAM: TPR repeat-containing protein; Tetratricopeptide TPR_2 repeat protein; Methyltransferase type 11; Methyltransferase type 12; SMART: Tetratricopeptide domain protein; KEGG: mag:amb4019 predicted methyltransferase; type 12 methyltransferase 1435595 4580293 Pden_1472 Paracoccus denitrificans PD1222 type 12 methyltransferase YP_915268.1 1434342 D 318586 CDS YP_915269.1 119384213 4580294 complement(1435611..1436129) 1 NC_008686.1 PFAM: MaoC domain protein dehydratase; KEGG: mag:amb1218 acyl dehydratase; dehydratase 1436129 4580294 Pden_1473 Paracoccus denitrificans PD1222 dehydratase YP_915269.1 1435611 R 318586 CDS YP_915270.1 119384214 4580295 complement(1436263..1436496) 1 NC_008686.1 KEGG: gbe:GbCGDNIH1_1065 hypothetical protein; hypothetical protein 1436496 4580295 Pden_1474 Paracoccus denitrificans PD1222 hypothetical protein YP_915270.1 1436263 R 318586 CDS YP_915271.1 119384215 4580296 complement(1436499..1437620) 1 NC_008686.1 PFAM: conjugation TrbI family protein; KEGG: mes:Meso_0500 conjugation TrbI-like protein; conjugation TrbI family protein 1437620 4580296 Pden_1475 Paracoccus denitrificans PD1222 conjugation TrbI family protein YP_915271.1 1436499 R 318586 CDS YP_915272.1 119384216 4580297 complement(1437617..1438645) 1 NC_008686.1 PFAM: Conjugal transfer protein TrbG/VirB9/CagX; KEGG: mes:Meso_0501 conjugal transfer protein TrbG/VirB9/CagX; conjugal transfer protein TrbG/VirB9/CagX 1438645 4580297 Pden_1476 Paracoccus denitrificans PD1222 conjugal transfer protein TrbG/VirB9/CagX YP_915272.1 1437617 R 318586 CDS YP_915273.1 119384217 4580298 complement(1438642..1439331) 1 NC_008686.1 PFAM: Conjugal transfer protein; KEGG: mes:Meso_0502 conjugal transfer protein; conjugal transfer protein TrbF 1439331 4580298 Pden_1477 Paracoccus denitrificans PD1222 conjugal transfer protein TrbF YP_915273.1 1438642 R 318586 CDS YP_915274.1 119384218 4580299 complement(1439328..1440680) 1 NC_008686.1 type IV secretion VirB6 family; conjugal transfer protein TrbL 1440680 4580299 Pden_1478 Paracoccus denitrificans PD1222 conjugal transfer protein TrbL YP_915274.1 1439328 R 318586 CDS YP_915275.1 119384219 4580319 complement(1440684..1440971) 1 NC_008686.1 KEGG: mes:Meso_2319 hypothetical protein; hypothetical protein 1440971 4580319 Pden_1479 Paracoccus denitrificans PD1222 hypothetical protein YP_915275.1 1440684 R 318586 CDS YP_915276.1 119384220 4580320 complement(1440989..1441771) 1 NC_008686.1 KEGG: mes:Meso_3855 conjugal transfer protein TrbJ; conjugal transfer protein TrbJ 1441771 4580320 Pden_1480 Paracoccus denitrificans PD1222 conjugal transfer protein TrbJ YP_915276.1 1440989 R 318586 CDS YP_915277.1 119384221 4580321 complement(1441768..1444278) 1 NC_008686.1 type IV secretion system VirB4 family; conjugal transfer ATPase TrbE 1444278 4580321 Pden_1481 Paracoccus denitrificans PD1222 conjugal transfer ATPase TrbE YP_915277.1 1441768 R 318586 CDS YP_915278.1 119384222 4580322 complement(1444285..1444578) 1 NC_008686.1 KEGG: mlo:mll9611 conjugal transfer protein trbB; conjugal transfer protein trbB 1444578 4580322 Pden_1482 Paracoccus denitrificans PD1222 conjugal transfer protein trbB YP_915278.1 1444285 R 318586 CDS YP_915279.1 119384223 4580323 complement(1444645..1444977) 1 NC_008686.1 PFAM: Conjugal transfer protein TrbC; KEGG: mes:Meso_2323 conjugal transfer protein TrbC; conjugal transfer protein TrbC 1444977 4580323 Pden_1483 Paracoccus denitrificans PD1222 conjugal transfer protein TrbC YP_915279.1 1444645 R 318586 CDS YP_915280.1 119384224 4580324 complement(1444974..1445972) 1 NC_008686.1 PFAM: type II secretion system protein E; KEGG: mes:Meso_2324 type II secretion system protein E; type II secretion system protein E 1445972 4580324 Pden_1484 Paracoccus denitrificans PD1222 type II secretion system protein E YP_915280.1 1444974 R 318586 CDS YP_915281.1 119384225 4580325 1446345..1447265 1 NC_008686.1 PFAM: helix-turn-helix- domain containing protein, AraC type; KEGG: rru:Rru_A1456 transcriptional regulator, AraC family; helix-turn-helix domain-containing protein 1447265 4580325 Pden_1485 Paracoccus denitrificans PD1222 helix-turn-helix domain-containing protein YP_915281.1 1446345 D 318586 CDS YP_915282.1 119384226 4580326 1447354..1449435 1 NC_008686.1 PFAM: TonB-dependent receptor; TonB-dependent receptor, plug; KEGG: rru:Rru_A1458 TonB-dependent receptor; TonB-dependent receptor 1449435 4580326 Pden_1486 Paracoccus denitrificans PD1222 TonB-dependent receptor YP_915282.1 1447354 D 318586 CDS YP_915283.1 119384227 4580327 1449435..1450445 1 NC_008686.1 PFAM: Methyltransferase type 11; Methyltransferase type 12; KEGG: rru:Rru_A1457 O-methyltransferase, family 2; type 12 methyltransferase 1450445 4580327 Pden_1487 Paracoccus denitrificans PD1222 type 12 methyltransferase YP_915283.1 1449435 D 318586 CDS YP_915284.1 119384228 4580328 1450447..1451349 1 NC_008686.1 KEGG: atc:AGR_L_928 sulfonate/nitrate transport system substrate-binding protein; sulfonate/nitrate transport system substrate-binding protein 1451349 4580328 Pden_1488 Paracoccus denitrificans PD1222 sulfonate/nitrate transport system substrate-binding protein YP_915284.1 1450447 D 318586 CDS YP_915285.1 119384229 4580329 1451349..1452080 1 NC_008686.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: rpc:RPC_1932 binding-protein-dependent transport systems inner membrane component; binding-protein-dependent transport system inner membrane protein 1452080 4580329 Pden_1489 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_915285.1 1451349 D 318586 CDS YP_915286.1 119384230 4580330 1452077..1452658 1 NC_008686.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: swo:Swol_0339 sulfonate transport system ATP-binding protein; ABC transporter 1452658 4580330 Pden_1490 Paracoccus denitrificans PD1222 ABC transporter YP_915286.1 1452077 D 318586 CDS YP_915287.1 119384231 4580331 complement(1452668..1453366) 1 NC_008686.1 PFAM: regulatory protein, TetR; KEGG: nfa:nfa16940 transcriptional regulator; TetR family transcriptional regulator 1453366 4580331 Pden_1491 Paracoccus denitrificans PD1222 TetR family transcriptional regulator YP_915287.1 1452668 R 318586 CDS YP_915288.1 119384232 4580332 complement(1453406..1455184) 1 NC_008686.1 PFAM: ABC transporter, transmembrane region; ABC transporter related; SMART: AAA ATPase; KEGG: cdi:DIP2158 ABC transport protein; ABC transporter 1455184 4580332 Pden_1492 Paracoccus denitrificans PD1222 ABC transporter YP_915288.1 1453406 R 318586 CDS YP_915289.1 119384233 4580333 complement(1455181..1457001) 1 NC_008686.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: gvi:gll0322 HlyB/MsbA family ABC transporter; ABC transporter 1457001 4580333 Pden_1493 Paracoccus denitrificans PD1222 ABC transporter YP_915289.1 1455181 R 318586 CDS YP_915290.1 119384234 4580334 complement(1457084..1458244) 1 NC_008686.1 PFAM: monooxygenase, FAD-binding; KEGG: sme:SMc02891 oxidoreductase transmembrane protein; FAD-binding monooxygenase 1458244 4580334 Pden_1494 Paracoccus denitrificans PD1222 FAD-binding monooxygenase YP_915290.1 1457084 R 318586 CDS YP_915291.1 119384235 4580335 complement(1458248..1460236) 1 NC_008686.1 PFAM: TonB-dependent receptor; TonB-dependent receptor, plug; KEGG: sme:SMc02890 outer membrane receptor protein; TonB-dependent receptor 1460236 4580335 Pden_1495 Paracoccus denitrificans PD1222 TonB-dependent receptor YP_915291.1 1458248 R 318586 CDS YP_915292.1 119384236 4580336 complement(1460233..1461420) 1 NC_008686.1 PFAM: major facilitator superfamily MFS_1; KEGG: sme:SMc02889 transport protein; major facilitator superfamily transporter 1461420 4580336 Pden_1496 Paracoccus denitrificans PD1222 major facilitator superfamily transporter YP_915292.1 1460233 R 318586 CDS YP_915293.1 119384237 4580337 1461579..1462580 1 NC_008686.1 PFAM: helix-turn-helix- domain containing protein, AraC type; KEGG: sme:SMc02888 transcription regulator protein; helix-turn-helix domain-containing protein 1462580 4580337 Pden_1497 Paracoccus denitrificans PD1222 helix-turn-helix domain-containing protein YP_915293.1 1461579 D 318586 CDS YP_915294.1 119384238 4580338 complement(1462601..1463827) 1 NC_008686.1 PFAM: major facilitator superfamily MFS_1; KEGG: rru:Rru_A2336 major facilitator superfamily MFS_1; major facilitator superfamily transporter 1463827 4580338 Pden_1498 Paracoccus denitrificans PD1222 major facilitator superfamily transporter YP_915294.1 1462601 R 318586 CDS YP_915295.1 119384239 4581095 complement(1463830..1465779) 1 NC_008686.1 PFAM: TonB-dependent receptor; TonB-dependent receptor, plug; KEGG: rru:Rru_A2337 TonB-dependent receptor; TonB-dependent receptor 1465779 4581095 Pden_1499 Paracoccus denitrificans PD1222 TonB-dependent receptor YP_915295.1 1463830 R 318586 CDS YP_915296.1 119384240 4581096 1466069..1467028 1 NC_008686.1 PFAM: helix-turn-helix- domain containing protein, AraC type; KEGG: yps:YPTB1597 transcriptional regulator YbtA; helix-turn-helix domain-containing protein 1467028 4581096 Pden_1500 Paracoccus denitrificans PD1222 helix-turn-helix domain-containing protein YP_915296.1 1466069 D 318586 CDS YP_915297.1 119384241 4581097 complement(1467357..1467746) 1 NC_008686.1 PFAM: protein of unknown function DUF454; KEGG: nha:Nham_3232 protein of unknown function DUF454; hypothetical protein 1467746 4581097 Pden_1501 Paracoccus denitrificans PD1222 hypothetical protein YP_915297.1 1467357 R 318586 CDS YP_915298.1 119384242 4581098 complement(1467733..1468083) 1 NC_008686.1 KEGG: mxa:MXAN_7409 hypothetical protein; hypothetical protein 1468083 4581098 Pden_1502 Paracoccus denitrificans PD1222 hypothetical protein YP_915298.1 1467733 R 318586 CDS YP_915299.1 119384243 4581099 complement(1468070..1469287) 1 NC_008686.1 PFAM: monooxygenase, FAD-binding; KEGG: nwi:Nwi_2327 hypothetical protein; hypothetical protein 1469287 4581099 Pden_1503 Paracoccus denitrificans PD1222 hypothetical protein YP_915299.1 1468070 R 318586 CDS YP_915300.1 119384244 4581100 complement(1469486..1470022) 1 NC_008686.1 hypothetical protein 1470022 4581100 Pden_1504 Paracoccus denitrificans PD1222 hypothetical protein YP_915300.1 1469486 R 318586 CDS YP_915301.1 119384245 4581101 complement(1470456..1470884) 1 NC_008686.1 KEGG: mlo:mlr9748 hypothetical protein; hypothetical protein 1470884 4581101 Pden_1505 Paracoccus denitrificans PD1222 hypothetical protein YP_915301.1 1470456 R 318586 CDS YP_915302.1 119384246 4581102 complement(1470887..1472872) 1 NC_008686.1 type IV secretion VirD4 coupling protein family; conjugal transfer coupling protein TraG 1472872 4581102 Pden_1506 Paracoccus denitrificans PD1222 conjugal transfer coupling protein TraG YP_915302.1 1470887 R 318586 CDS YP_915303.1 119384247 4581103 complement(1472899..1474653) 1 NC_008686.1 KEGG: bja:bll0044 hypothetical protein; hypothetical protein 1474653 4581103 Pden_1507 Paracoccus denitrificans PD1222 hypothetical protein YP_915303.1 1472899 R 318586 CDS YP_915304.1 119384248 4581104 complement(1474897..1475661) 1 NC_008686.1 PFAM: Lytic transglycosylase, catalytic; KEGG: mes:Meso_2331 lytic transglycosylase, catalytic; lytic transglycosylase, catalytic 1475661 4581104 Pden_1508 Paracoccus denitrificans PD1222 lytic transglycosylase, catalytic YP_915304.1 1474897 R 318586 CDS YP_915305.1 119384249 4581105 complement(1475664..1475999) 1 NC_008686.1 PFAM: protein of unknown function DUF736; KEGG: mes:Meso_2332 protein of unknown function DUF736; hypothetical protein 1475999 4581105 Pden_1509 Paracoccus denitrificans PD1222 hypothetical protein YP_915305.1 1475664 R 318586 CDS YP_915306.1 119384250 4581106 complement(1476066..1476608) 1 NC_008686.1 KEGG: mes:Meso_2333 conjugal transfer protein precursor; conjugal transfer protein precursor 1476608 4581106 Pden_1510 Paracoccus denitrificans PD1222 conjugal transfer protein precursor YP_915306.1 1476066 R 318586 CDS YP_915307.1 119384251 4581107 complement(1476605..1477126) 1 NC_008686.1 KEGG: rpc:RPC_3907 hypothetical protein; hypothetical protein 1477126 4581107 Pden_1511 Paracoccus denitrificans PD1222 hypothetical protein YP_915307.1 1476605 R 318586 CDS YP_915308.1 119384252 4581108 complement(1477126..1478298) 1 NC_008686.1 KEGG: mlo:mlr9740 replication protein A; replication protein A 1478298 4581108 Pden_1512 Paracoccus denitrificans PD1222 replication protein A YP_915308.1 1477126 R 318586 CDS YP_915309.1 119384253 4581109 complement(1478317..1478598) 1 NC_008686.1 KEGG: mlo:msr9739 hypothetical protein; hypothetical protein 1478598 4581109 Pden_1513 Paracoccus denitrificans PD1222 hypothetical protein YP_915309.1 1478317 R 318586 CDS YP_915310.1 119384254 4581110 complement(1478736..1479131) 1 NC_008686.1 KEGG: mes:Meso_0525 hypothetical protein; hypothetical protein 1479131 4581110 Pden_1514 Paracoccus denitrificans PD1222 hypothetical protein YP_915310.1 1478736 R 318586 CDS YP_915311.1 119384255 4581111 complement(1479202..1479561) 1 NC_008686.1 KEGG: mes:Meso_3837 hypothetical protein; hypothetical protein 1479561 4581111 Pden_1515 Paracoccus denitrificans PD1222 hypothetical protein YP_915311.1 1479202 R 318586 CDS YP_915312.1 119384256 4581112 complement(1479617..1479880) 1 NC_008686.1 KEGG: mes:Meso_0527 hypothetical protein; hypothetical protein 1479880 4581112 Pden_1516 Paracoccus denitrificans PD1222 hypothetical protein YP_915312.1 1479617 R 318586 CDS YP_915313.1 119384257 4581113 complement(1479986..1480243) 1 NC_008686.1 KEGG: mes:Meso_0528 transcriptional regulator, XRE family; XRE family transcriptional regulator 1480243 4581113 Pden_1517 Paracoccus denitrificans PD1222 XRE family transcriptional regulator YP_915313.1 1479986 R 318586 CDS YP_915314.1 119384258 4578976 complement(1480430..1480753) 1 NC_008686.1 PFAM: protein of unknown function DUF736; KEGG: mes:Meso_0529 protein of unknown function DUF736; hypothetical protein 1480753 4578976 Pden_1518 Paracoccus denitrificans PD1222 hypothetical protein YP_915314.1 1480430 R 318586 CDS YP_915315.1 119384259 4578977 1480790..1481251 1 NC_008686.1 hypothetical protein 1481251 4578977 Pden_1519 Paracoccus denitrificans PD1222 hypothetical protein YP_915315.1 1480790 D 318586 CDS YP_915316.1 119384260 4578978 complement(1481310..1481747) 1 NC_008686.1 KEGG: mes:Meso_2343 hypothetical protein; hypothetical protein 1481747 4578978 Pden_1520 Paracoccus denitrificans PD1222 hypothetical protein YP_915316.1 1481310 R 318586 CDS YP_915317.1 119384261 4578979 1481913..1482437 1 NC_008686.1 KEGG: bcz:BCZK2630 2'-5' RNA ligase; hypothetical protein 1482437 4578979 Pden_1521 Paracoccus denitrificans PD1222 hypothetical protein YP_915317.1 1481913 D 318586 CDS YP_915318.1 119384262 4578980 1482485..1482733 1 NC_008686.1 hypothetical protein 1482733 4578980 Pden_1522 Paracoccus denitrificans PD1222 hypothetical protein YP_915318.1 1482485 D 318586 CDS YP_915319.1 119384263 4578981 complement(1482702..1483478) 1 NC_008686.1 KEGG: gox:GOX1507 restriction endonuclease; restriction endonuclease 1483478 4578981 Pden_1523 Paracoccus denitrificans PD1222 restriction endonuclease YP_915319.1 1482702 R 318586 CDS YP_915320.1 119384264 4578982 complement(1483478..1485439) 1 NC_008686.1 KEGG: gox:GOX1506 chromosome segregation SMC protein; chromosome segregation protein SMC 1485439 4578982 Pden_1524 Paracoccus denitrificans PD1222 chromosome segregation protein SMC YP_915320.1 1483478 R 318586 CDS YP_915321.1 119384265 4578983 complement(1485429..1489808) 1 NC_008686.1 KEGG: gox:GOX1505 type II DNA modification enzyme; hypothetical protein 1489808 4578983 Pden_1525 Paracoccus denitrificans PD1222 hypothetical protein YP_915321.1 1485429 R 318586 CDS YP_915322.1 119384266 4578984 complement(1489811..1492582) 1 NC_008686.1 PFAM: SNF2-related protein; helicase domain protein; SMART: DEAD-like helicases-like; KEGG: gox:GOX1504 ATP-dependent helicase HepA; helicase 1492582 4578984 Pden_1526 Paracoccus denitrificans PD1222 helicase YP_915322.1 1489811 R 318586 CDS YP_915323.1 119384267 4578985 complement(1492584..1497761) 1 NC_008686.1 PFAM: helicase domain protein; DEAD/DEAH box helicase domain protein; SMART: DEAD-like helicases-like; KEGG: gox:GOX1503 probable ATP-dependent helicase Lhr; DEAD/DEAH box helicase 1497761 4578985 Pden_1527 Paracoccus denitrificans PD1222 DEAD/DEAH box helicase YP_915323.1 1492584 R 318586 CDS YP_915324.1 119384268 4578986 complement(1497762..1499684) 1 NC_008686.1 PFAM: protein of unknown function DUF262; KEGG: rha:RHA1_ro01680 hypothetical protein; hypothetical protein 1499684 4578986 Pden_1528 Paracoccus denitrificans PD1222 hypothetical protein YP_915324.1 1497762 R 318586 CDS YP_915325.1 119384269 4578987 complement(1499748..1500635) 1 NC_008686.1 KEGG: nar:Saro_2176 hypothetical protein; hypothetical protein 1500635 4578987 Pden_1529 Paracoccus denitrificans PD1222 hypothetical protein YP_915325.1 1499748 R 318586 CDS YP_915326.1 119384270 4578988 1501056..1501295 1 NC_008686.1 KEGG: rsp:RSP_3007 hypothetical protein; hypothetical protein 1501295 4578988 Pden_1530 Paracoccus denitrificans PD1222 hypothetical protein YP_915326.1 1501056 D 318586 CDS YP_915327.1 119384271 4578989 complement(1501625..1502551) 1 NC_008686.1 KEGG: mes:Meso_0533 hypothetical protein; hypothetical protein 1502551 4578989 Pden_1531 Paracoccus denitrificans PD1222 hypothetical protein YP_915327.1 1501625 R 318586 CDS YP_915328.1 119384272 4578990 complement(1502908..1503942) 1 NC_008686.1 KEGG: nwi:Nwi_2129 hypothetical protein; hypothetical protein 1503942 4578990 Pden_1532 Paracoccus denitrificans PD1222 hypothetical protein YP_915328.1 1502908 R 318586 CDS YP_915329.1 119384273 4578991 complement(1503942..1508264) 1 NC_008686.1 KEGG: mes:Meso_3828 probably methylase/helicase; methylase/helicase 1508264 4578991 Pden_1533 Paracoccus denitrificans PD1222 methylase/helicase YP_915329.1 1503942 R 318586 CDS YP_915330.1 119384274 4578992 1508430..1510043 1 NC_008686.1 PFAM: filamentation induced by cAMP protein Fic; KEGG: rpc:RPC_1039 filamentation induced by cAMP protein Fic; Fic family protein 1510043 4578992 Pden_1534 Paracoccus denitrificans PD1222 Fic family protein YP_915330.1 1508430 D 318586 CDS YP_915331.1 119384275 4578993 complement(1510055..1510699) 1 NC_008686.1 KEGG: mes:Meso_0536 hypothetical protein; hypothetical protein 1510699 4578993 Pden_1535 Paracoccus denitrificans PD1222 hypothetical protein YP_915331.1 1510055 R 318586 CDS YP_915332.1 119384276 4578994 complement(1510692..1511108) 1 NC_008686.1 KEGG: mes:Meso_3827 hypothetical protein; hypothetical protein 1511108 4578994 Pden_1536 Paracoccus denitrificans PD1222 hypothetical protein YP_915332.1 1510692 R 318586 CDS YP_915333.1 119384277 4578995 complement(1511174..1511731) 1 NC_008686.1 KEGG: net:Neut_0078 hypothetical protein; hypothetical protein 1511731 4578995 Pden_1537 Paracoccus denitrificans PD1222 hypothetical protein YP_915333.1 1511174 R 318586 CDS YP_915334.1 119384278 4581285 complement(1511923..1512180) 1 NC_008686.1 KEGG: mlo:msr9708 hypothetical protein; hypothetical protein 1512180 4581285 Pden_1538 Paracoccus denitrificans PD1222 hypothetical protein YP_915334.1 1511923 R 318586 CDS YP_915335.1 119384279 4581286 complement(1512503..1512808) 1 NC_008686.1 hypothetical protein 1512808 4581286 Pden_1539 Paracoccus denitrificans PD1222 hypothetical protein YP_915335.1 1512503 R 318586 CDS YP_915336.1 119384280 4581287 complement(1512910..1515234) 1 NC_008686.1 KEGG: sil:SPO2244 hypothetical protein; hypothetical protein 1515234 4581287 Pden_1540 Paracoccus denitrificans PD1222 hypothetical protein YP_915336.1 1512910 R 318586 CDS YP_915337.1 119384281 4581288 complement(1515718..1517844) 1 NC_008686.1 TIGRFAM: parB-like partition proteins; PFAM: ParB domain protein nuclease; KEGG: mes:Meso_0538 ParB-like partition proteins; parB-like partition proteins 1517844 4581288 Pden_1541 Paracoccus denitrificans PD1222 parB-like partition proteins YP_915337.1 1515718 R 318586 CDS YP_915338.1 119384282 4581289 complement(1517961..1518449) 1 NC_008686.1 PFAM: DNA repair protein RadC; KEGG: rsp:RSP_1171 DNA repair protein; DNA repair protein RadC 1518449 4581289 Pden_1542 Paracoccus denitrificans PD1222 DNA repair protein RadC YP_915338.1 1517961 R 318586 CDS YP_915339.1 119384283 4581290 complement(1518561..1518956) 1 NC_008686.1 KEGG: nwi:Nwi_2122 hypothetical protein; hypothetical protein 1518956 4581290 Pden_1543 Paracoccus denitrificans PD1222 hypothetical protein YP_915339.1 1518561 R 318586 CDS YP_915340.1 119384284 4581291 complement(1518953..1519915) 1 NC_008686.1 PFAM: domain of unknown function DUF1738; KEGG: nwi:Nwi_2121 antirestriction protein; ArdC; hypothetical protein 1519915 4581291 Pden_1544 Paracoccus denitrificans PD1222 hypothetical protein YP_915340.1 1518953 R 318586 CDS YP_915341.1 119384285 4581292 1520277..1520594 1 NC_008686.1 PFAM: histone family protein nucleoid-structuring protein H-NS; KEGG: rsp:RSP_4056 histone-like nucleoid-structuring protein H-NS; histone family protein nucleoid-structuring protein H-NS 1520594 4581292 Pden_1545 Paracoccus denitrificans PD1222 histone family protein nucleoid-structuring protein H-NS YP_915341.1 1520277 D 318586 CDS YP_915342.1 119384286 4581293 1520610..1521227 1 NC_008686.1 similar to plasmid pRiA4b; PFAM: plasmid pRiA4b ORF-3 family protein; KEGG: sme:SMa0896 hypothetical protein; ORF-3 family protein 1521227 4581293 Pden_1546 Paracoccus denitrificans PD1222 ORF-3 family protein YP_915342.1 1520610 D 318586 CDS YP_915343.1 119384287 4581294 1521563..1521871 1 NC_008686.1 PFAM: helix-turn-helix domain protein; KEGG: rpb:RPB_0688 transcriptional regulator, XRE family; XRE family transcriptional regulator 1521871 4581294 Pden_1547 Paracoccus denitrificans PD1222 XRE family transcriptional regulator YP_915343.1 1521563 D 318586 CDS YP_915344.1 119384288 4581295 1521861..1523102 1 NC_008686.1 PFAM: HipA domain protein; KEGG: rpb:RPB_0687 HipA-like protein; HipA domain-containing protein 1523102 4581295 Pden_1548 Paracoccus denitrificans PD1222 HipA domain-containing protein YP_915344.1 1521861 D 318586 CDS YP_915345.1 119384289 4581296 1523662..1523889 1 NC_008686.1 KEGG: rsp:RSP_6129 hypothetical protein; hypothetical protein 1523889 4581296 Pden_1549 Paracoccus denitrificans PD1222 hypothetical protein YP_915345.1 1523662 D 318586 CDS YP_915346.1 119384290 4581297 complement(1523870..1524346) 1 NC_008686.1 PFAM: protein of unknown function DUF1052; KEGG: sil:SPO1766 hypothetical protein; hypothetical protein 1524346 4581297 Pden_1550 Paracoccus denitrificans PD1222 hypothetical protein YP_915346.1 1523870 R 318586 CDS YP_915347.1 119384291 4581298 complement(1524673..1525593) 1 NC_008686.1 PFAM: protein of unknown function DUF481; KEGG: rsp:RSP_0753 salt-stress induced outer membrane protein; hypothetical protein 1525593 4581298 Pden_1551 Paracoccus denitrificans PD1222 hypothetical protein YP_915347.1 1524673 R 318586 CDS YP_915348.1 119384292 4581299 complement(1526019..1526324) 1 NC_008686.1 KEGG: rsp:RSP_0754 hypothetical protein; hypothetical protein 1526324 4581299 Pden_1552 Paracoccus denitrificans PD1222 hypothetical protein YP_915348.1 1526019 R 318586 CDS YP_915349.1 119384293 4581300 complement(1526439..1526939) 1 NC_008686.1 TIGRFAM: transcription antitermination factor NusB; PFAM: NusB/RsmB/TIM44; KEGG: jan:Jann_3412 NusB antitermination factor; NusB antitermination factor 1526939 4581300 Pden_1553 Paracoccus denitrificans PD1222 NusB antitermination factor YP_915349.1 1526439 R 318586 CDS YP_915350.1 119384294 4581301 complement(1526936..1527487) 1 NC_008686.1 RibE; 6,7-diimethyl-8-ribityllumazine synthase; DMRL synthase; lumazine synthase; beta subunit of riboflavin synthase; condenses 5-amino-6-(1'-D)-ribityl-amino-2,4(1H,3H)-pyrimidinedione with L-3,4-dihydrohy-2-butanone-4-phosphate to generate 6,6-dimethyl-8-lumazine (DMRL); riboflavin synthase then uses 2 molecules of DMRL to produce riboflavin (vitamin B12); involved in the last steps of riboflavin biosynthesis; forms a 60mer (icosahedral shell) in both Bacillus subtilis and Escherichia coli; in Bacillus subtilis this 60mer is associated with the riboflavin synthase subunit (alpha) while in Escherichia coli it is not; 6,7-dimethyl-8-ribityllumazine synthase 1527487 ribH 4581301 ribH Paracoccus denitrificans PD1222 6,7-dimethyl-8-ribityllumazine synthase YP_915350.1 1526936 R 318586 CDS YP_915351.1 119384295 4581302 complement(1527492..1528610) 1 NC_008686.1 PFAM: 3,4-dihydroxy-2-butanone 4-phosphate synthase; GTP cyclohydrolase II; KEGG: jan:Jann_3414 3,4-dihydroxy-2-butanone 4-phosphate synthase; 3,4-dihydroxy-2-butanone 4-phosphate synthase 1528610 4581302 Pden_1555 Paracoccus denitrificans PD1222 3,4-dihydroxy-2-butanone 4-phosphate synthase YP_915351.1 1527492 R 318586 CDS YP_915352.1 119384296 4581303 complement(1528600..1529178) 1 NC_008686.1 KEGG: sil:SPO1760 hypothetical protein; hypothetical protein 1529178 4581303 Pden_1556 Paracoccus denitrificans PD1222 hypothetical protein YP_915352.1 1528600 R 318586 CDS YP_915353.1 119384297 4580859 complement(1529178..1529771) 1 NC_008686.1 catalyzes the formation of riboflavin from 6,7-dimethyl-8-(1-D-ribityl)lumazine; riboflavin synthase subunit alpha 1529771 4580859 Pden_1557 Paracoccus denitrificans PD1222 riboflavin synthase subunit alpha YP_915353.1 1529178 R 318586 CDS YP_915354.1 119384298 4580860 1530081..1531403 1 NC_008686.1 PFAM: Capsule polysaccharide biosynthesis; KEGG: sil:SPO1757 capsular polysaccharide export protein KpsS; capsule polysaccharide biosynthesis 1531403 4580860 Pden_1558 Paracoccus denitrificans PD1222 capsule polysaccharide biosynthesis YP_915354.1 1530081 D 318586 CDS YP_915355.1 119384299 4580861 1531502..1532680 1 NC_008686.1 PFAM: polysaccharide export protein; KEGG: sit:TM1040_2133 polysaccharide export protein; polysaccharide export protein 1532680 4580861 Pden_1559 Paracoccus denitrificans PD1222 polysaccharide export protein YP_915355.1 1531502 D 318586 CDS YP_915356.1 119384300 4580862 1532685..1534676 1 NC_008686.1 PFAM: Capsule polysaccharide biosynthesis; KEGG: sil:SPO1755 capsular polysaccharide export protein KpsC; capsule polysaccharide biosynthesis 1534676 4580862 Pden_1560 Paracoccus denitrificans PD1222 capsule polysaccharide biosynthesis YP_915356.1 1532685 D 318586 CDS YP_915357.1 119384301 4580863 complement(1534673..1535650) 1 NC_008686.1 TIGRFAM: riboflavin biosynthesis protein RibD; PFAM: CMP/dCMP deaminase, zinc-binding; bifunctional deaminase-reductase domain protein; KEGG: sit:TM1040_2135 riboflavin biosynthesis protein RibD; riboflavin biosynthesis protein RibD 1535650 4580863 Pden_1561 Paracoccus denitrificans PD1222 riboflavin biosynthesis protein RibD YP_915357.1 1534673 R 318586 CDS YP_915358.1 119384302 4580864 complement(1535665..1536129) 1 NC_008686.1 PFAM: ATP-cone domain protein; KEGG: rsp:RSP_0394 hypothetical protein; transcriptional regulator NrdR 1536129 nrdR 4580864 nrdR Paracoccus denitrificans PD1222 transcriptional regulator NrdR YP_915358.1 1535665 R 318586 CDS YP_915359.1 119384303 4580865 1536368..1537492 1 NC_008686.1 PFAM: TRAP dicarboxylate transporter- DctP subunit; KEGG: rsp:RSP_0097 TRAP-T family sorbitol/mannitol transporter, periplasmic binding protein, SmoM; TRAP dicarboxylate transporter- DctP subunit 1537492 4580865 Pden_1563 Paracoccus denitrificans PD1222 TRAP dicarboxylate transporter- DctP subunit YP_915359.1 1536368 D 318586 CDS YP_915360.1 119384304 4580866 complement(1537598..1539490) 1 NC_008686.1 TIGRFAM: TRAP dicarboxylate transporter, DctM subunit; PFAM: TRAP C4-dicarboxylate transport system permease DctM subunit; KEGG: rsp:RSP_6094 TRAP-T family sorbitol/mannitol transporter, DctM (12TMs) subunit; TRAP dicarboxylate transporter subunit DctM 1539490 4580866 Pden_1564 Paracoccus denitrificans PD1222 TRAP dicarboxylate transporter subunit DctM YP_915360.1 1537598 R 318586 CDS YP_915361.1 119384305 4580867 complement(1539487..1540110) 1 NC_008686.1 PFAM: Tripartite ATP-independent periplasmic transporter, DctQ component; KEGG: rsp:RSP_0099 TRAP-T family sorbitol/mannitol transporter, DctQ (4TMs) subunit; tripartite ATP-independent periplasmic transporter DctQ 1540110 4580867 Pden_1565 Paracoccus denitrificans PD1222 tripartite ATP-independent periplasmic transporter DctQ YP_915361.1 1539487 R 318586 CDS YP_915362.1 119384306 4580868 complement(1540248..1541015) 1 NC_008686.1 TIGRFAM: cobalamin 5'-phosphate synthase; PFAM: cobalamin-5-phosphate synthase CobS; KEGG: bja:bll3255 cobalamin (5'-phosphate) synthase; cobalamin 5'-phosphate synthase 1541015 4580868 Pden_1566 Paracoccus denitrificans PD1222 cobalamin 5'-phosphate synthase YP_915362.1 1540248 R 318586 CDS YP_915363.1 119384307 4580869 complement(1541008..1541964) 1 NC_008686.1 PFAM: Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase; KEGG: sil:SPO1423 nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase; nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase 1541964 4580869 Pden_1567 Paracoccus denitrificans PD1222 nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase YP_915363.1 1541008 R 318586 CDS YP_915364.1 119384308 4580870 complement(1541961..1542494) 1 NC_008686.1 PFAM: cobalbumin biosynthesis enzyme; KEGG: bja:bll3256 cobinamide kinase / conamide phosphate guanylyltransferase; adenosylcobinamide kinase 1542494 4580870 Pden_1568 Paracoccus denitrificans PD1222 adenosylcobinamide kinase YP_915364.1 1541961 R 318586 CDS YP_915365.1 119384309 4580871 1542634..1544238 1 NC_008686.1 PFAM: extracellular solute-binding protein, family 5; KEGG: jan:Jann_3050 extracellular solute-binding protein, family 5; extracellular solute-binding protein 1544238 4580871 Pden_1569 Paracoccus denitrificans PD1222 extracellular solute-binding protein YP_915365.1 1542634 D 318586 CDS YP_915366.1 119384310 4580872 1544305..1545222 1 NC_008686.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: jan:Jann_3051 binding-protein-dependent transport systems inner membrane component; binding-protein-dependent transport system inner membrane protein 1545222 4580872 Pden_1570 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_915366.1 1544305 D 318586 CDS YP_915367.1 119384311 4580873 1545226..1546149 1 NC_008686.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: jan:Jann_3052 binding-protein-dependent transport systems inner membrane component; binding-protein-dependent transport system inner membrane protein 1546149 4580873 Pden_1571 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_915367.1 1545226 D 318586 CDS YP_915368.1 119384312 4580874 1546151..1547206 1 NC_008686.1 KEGG: vpa:VP2088 oligopeptide ABC transporter, ATP-binding protein; TIGRFAM: oligopeptide/dipeptide ABC transporter, ATPase subunit; PFAM: ABC transporter related; Oligopeptide/dipeptide ABC transporter, C-terminal domain protein; SMART: AAA ATPase; oligopeptide/dipeptide ABC transporter ATPase 1547206 4580874 Pden_1572 Paracoccus denitrificans PD1222 oligopeptide/dipeptide ABC transporter ATPase YP_915368.1 1546151 D 318586 CDS YP_915369.1 119384313 4580875 1547203..1548216 1 NC_008686.1 KEGG: vvy:VV1207 ABC-type oligopeptide transport system, ATPase component; TIGRFAM: oligopeptide/dipeptide ABC transporter, ATPase subunit; PFAM: ABC transporter related; Oligopeptide/dipeptide ABC transporter, C-terminal domain protein; SMART: AAA ATPase; oligopeptide/dipeptide ABC transporter ATPase 1548216 4580875 Pden_1573 Paracoccus denitrificans PD1222 oligopeptide/dipeptide ABC transporter ATPase YP_915369.1 1547203 D 318586 CDS YP_915370.1 119384314 4580876 1548274..1548759 1 NC_008686.1 PFAM: pyridoxamine 5'-phosphate oxidase-related, FMN-binding; KEGG: ret:RHE_CH03088 hypothetical protein; pyridoxamine 5'-phosphate oxidase-like FMN-binding protein 1548759 4580876 Pden_1574 Paracoccus denitrificans PD1222 pyridoxamine 5'-phosphate oxidase-like FMN-binding protein YP_915370.1 1548274 D 318586 CDS YP_915371.1 119384315 4580877 complement(1548796..1551090) 1 NC_008686.1 KEGG: sil:SPO0459 hypothetical protein; hypothetical protein 1551090 4580877 Pden_1575 Paracoccus denitrificans PD1222 hypothetical protein YP_915371.1 1548796 R 318586 CDS YP_915372.1 119384316 4580878 complement(1551231..1552823) 1 NC_008686.1 class I; LysRS1; catalyzes a two-step reaction, first charging a lysine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; in Methanosarcina barkeri this enzyme charges both tRNA molecules for lysine that exist in this organism (but the tRNALysUUU very poorly) and in the presence of LysRS2 can charge tRNAPyl with lysine; lysyl-tRNA synthetase 1552823 lysK 4580878 lysK Paracoccus denitrificans PD1222 lysyl-tRNA synthetase YP_915372.1 1551231 R 318586 CDS YP_915373.1 119384317 4580840 1552915..1553337 1 NC_008686.1 KEGG: rsp:RSP_0583 hypothetical protein; hypothetical protein 1553337 4580840 Pden_1577 Paracoccus denitrificans PD1222 hypothetical protein YP_915373.1 1552915 D 318586 CDS YP_915374.1 119384318 4580841 complement(1553348..1554802) 1 NC_008686.1 PFAM: peptidase S13, D-Ala-D-Ala carboxypeptidase C; KEGG: sil:SPO0451 D-alanyl-D-alanine carboxypeptidase/D-alanyl-D-alanine-endopeptidase; peptidase S13, D-Ala-D-Ala carboxypeptidase C 1554802 4580841 Pden_1578 Paracoccus denitrificans PD1222 peptidase S13, D-Ala-D-Ala carboxypeptidase C YP_915374.1 1553348 R 318586 CDS YP_915375.1 119384319 4580842 complement(1554802..1555404) 1 NC_008686.1 transfers an adenyl group from ATP to NaMN to form nicotinic acid adenine dinucleotide (NaAD) which is then converted to the ubiquitous compound NAD by NAD synthetase; essential enzyme in bacteria; nicotinic acid mononucleotide adenylyltransferase 1555404 nadD 4580842 nadD Paracoccus denitrificans PD1222 nicotinic acid mononucleotide adenylyltransferase YP_915375.1 1554802 R 318586 CDS YP_915376.1 119384320 4580843 complement(1555408..1557075) 1 NC_008686.1 catalyzes the formation of 10-formyltetrahydrofolate from formate and tetrahydrofolate; formate--tetrahydrofolate ligase 1557075 4580843 Pden_1580 Paracoccus denitrificans PD1222 formate--tetrahydrofolate ligase YP_915376.1 1555408 R 318586 CDS YP_915377.1 119384321 4580844 complement(1557146..1558279) 1 NC_008686.1 KEGG: rme:Rmet_4886 hypothetical protein; hypothetical protein 1558279 4580844 Pden_1581 Paracoccus denitrificans PD1222 hypothetical protein YP_915377.1 1557146 R 318586 CDS YP_915378.1 119384322 4580845 complement(1558276..1560450) 1 NC_008686.1 necessary for biosynthesis of osmoregulated periplasmic glucans possibly involved in the transfer to the periplasmic space; glucosyltransferase MdoH 1560450 4580845 Pden_1582 Paracoccus denitrificans PD1222 glucosyltransferase MdoH YP_915378.1 1558276 R 318586 CDS YP_915379.1 119384323 4580846 complement(1560447..1562045) 1 NC_008686.1 involved in the biosynthesis of osmoregulated periplasmic glucans; required for the assembly of the polyglucose structure of glucan; glucan biosynthesis protein G 1562045 mdoG 4580846 mdoG Paracoccus denitrificans PD1222 glucan biosynthesis protein G YP_915379.1 1560447 R 318586 CDS YP_915380.1 119384324 4580847 1562157..1563164 1 NC_008686.1 hypothetical protein 1563164 4580847 Pden_1584 Paracoccus denitrificans PD1222 hypothetical protein YP_915380.1 1562157 D 318586 CDS YP_915381.1 119384325 4580848 1563635..1564297 1 NC_008686.1 PFAM: response regulator receiver; transcriptional regulator domain protein; KEGG: mes:Meso_0894 two component transcriptional regulator, winged helix family; two component transcriptional regulator 1564297 4580848 Pden_1585 Paracoccus denitrificans PD1222 two component transcriptional regulator YP_915381.1 1563635 D 318586 CDS YP_915382.1 119384326 4580849 1564294..1565634 1 NC_008686.1 PFAM: ATP-binding region, ATPase domain protein domain protein; KEGG: mmr:Mmar10_0937 periplasmic sensor signal transduction histidine kinase; integral membrane sensor signal transduction histidine kinase 1565634 4580849 Pden_1586 Paracoccus denitrificans PD1222 integral membrane sensor signal transduction histidine kinase YP_915382.1 1564294 D 318586 CDS YP_915383.1 119384327 4580850 complement(1565928..1566239) 1 NC_008686.1 PFAM: ETC complex I subunit conserved region; KEGG: sil:SPO0482 NADH-ubiquinone oxidoreductase family protein; ETC complex I subunit region 1566239 4580850 Pden_1587 Paracoccus denitrificans PD1222 ETC complex I subunit region YP_915383.1 1565928 R 318586 CDS YP_915384.1 119384328 4580851 1566388..1568613 1 NC_008686.1 The UvrABC repair system catalyzes the recognition and processing of DNA lesions. The beta-hairpin of the Uvr-B subunit is inserted between the strands, where it probes for the presence of a lesion; excinuclease ABC subunit B 1568613 4580851 Pden_1588 Paracoccus denitrificans PD1222 excinuclease ABC subunit B YP_915384.1 1566388 D 318586 CDS YP_915385.1 119384329 4580852 complement(1568656..1568943) 1 NC_008686.1 KEGG: pol:Bpro_1343 hypothetical protein; hypothetical protein 1568943 4580852 Pden_1589 Paracoccus denitrificans PD1222 hypothetical protein YP_915385.1 1568656 R 318586 CDS YP_915386.1 119384330 4580853 complement(1569043..1569678) 1 NC_008686.1 PFAM: Cobyrinic acid a,c-diamide synthase; KEGG: sil:SPO0461 ParA family protein; cobyrinic acid a,c-diamide synthase 1569678 4580853 Pden_1590 Paracoccus denitrificans PD1222 cobyrinic acid a,c-diamide synthase YP_915386.1 1569043 R 318586 CDS YP_915387.1 119384331 4580854 complement(1569781..1570104) 1 NC_008686.1 PFAM: Antibiotic biosynthesis monooxygenase; KEGG: sil:SPO0462 antibiotic biosynthesis monooxygenase domain protein; antibiotic biosynthesis monooxygenase 1570104 4580854 Pden_1591 Paracoccus denitrificans PD1222 antibiotic biosynthesis monooxygenase YP_915387.1 1569781 R 318586 CDS YP_915388.1 119384332 4580855 1570289..1571338 1 NC_008686.1 PFAM: peptidase M19, renal dipeptidase; KEGG: rsp:RSP_0802 dipeptidase; peptidase M19 1571338 4580855 Pden_1592 Paracoccus denitrificans PD1222 peptidase M19 YP_915388.1 1570289 D 318586 CDS YP_915389.1 119384333 4580856 complement(1571549..1573090) 1 NC_008686.1 PFAM: Ppx/GppA phosphatase; KEGG: rsp:RSP_0782 Ppx/GppA phosphatase; Ppx/GppA phosphatase 1573090 4580856 Pden_1593 Paracoccus denitrificans PD1222 Ppx/GppA phosphatase YP_915389.1 1571549 R 318586 CDS YP_915390.1 119384334 4580857 complement(1573159..1574460) 1 NC_008686.1 PFAM: Polyphosphate kinase; KEGG: rde:RD1_2042 polyphosphate kinase; polyphosphate kinase 1574460 4580857 Pden_1594 Paracoccus denitrificans PD1222 polyphosphate kinase YP_915390.1 1573159 R 318586 CDS YP_915391.1 119384335 4580858 1574589..1575380 1 NC_008686.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: mlo:mll8315 ABC transporter, ATP-binding protein; ABC transporter 1575380 4580858 Pden_1595 Paracoccus denitrificans PD1222 ABC transporter YP_915391.1 1574589 D 318586 CDS YP_915392.1 119384336 4580203 1575380..1576246 1 NC_008686.1 PFAM: ABC-3 protein; KEGG: mlo:mll8314 ABC transporter, permease protein; ABC-3 protein 1576246 4580203 Pden_1596 Paracoccus denitrificans PD1222 ABC-3 protein YP_915392.1 1575380 D 318586 CDS YP_915393.1 119384337 4580204 1576266..1577195 1 NC_008686.1 PFAM: periplasmic solute binding protein; KEGG: atc:AGR_L_3262 adhesin, probable; periplasmic solute binding protein 1577195 4580204 Pden_1597 Paracoccus denitrificans PD1222 periplasmic solute binding protein YP_915393.1 1576266 D 318586 CDS YP_915394.1 119384338 4580205 1577267..1578493 1 NC_008686.1 KEGG: mes:Meso_4007 hypothetical protein; hypothetical protein 1578493 4580205 Pden_1598 Paracoccus denitrificans PD1222 hypothetical protein YP_915394.1 1577267 D 318586 CDS YP_915395.1 119384339 4580206 complement(1578721..1579401) 1 NC_008686.1 PFAM: Glutathione S-transferase, N-terminal domain; KEGG: sme:SMc00594 beta-etherase (beta-aryl ether cleaving enzyme) protein; glutathione S-transferase domain-containing protein 1579401 4580206 Pden_1599 Paracoccus denitrificans PD1222 glutathione S-transferase domain-containing protein YP_915395.1 1578721 R 318586 CDS YP_915396.1 119384340 4580207 complement(1579401..1580333) 1 NC_008686.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: cvi:CV3061 probable transcriptional regulator, LysR family; LysR family transcriptional regulator 1580333 4580207 Pden_1600 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_915396.1 1579401 R 318586 CDS YP_915397.1 119384341 4580208 complement(1580445..1581911) 1 NC_008686.1 PFAM: major facilitator superfamily MFS_1; KEGG: sme:SMc02892 transport protein; major facilitator superfamily transporter 1581911 4580208 Pden_1601 Paracoccus denitrificans PD1222 major facilitator superfamily transporter YP_915397.1 1580445 R 318586 CDS YP_915398.1 119384342 4580209 complement(1581989..1583947) 1 NC_008686.1 PFAM: TonB-dependent receptor; TonB-dependent receptor, plug; KEGG: ilo:IL0069 outer membrane protein; TonB-dependent receptor, plug 1583947 4580209 Pden_1602 Paracoccus denitrificans PD1222 TonB-dependent receptor, plug YP_915398.1 1581989 R 318586 CDS YP_915399.1 119384343 4580210 complement(1584109..1585242) 1 NC_008686.1 PFAM: biotin/lipoyl attachment domain-containing protein; catalytic domain of components of various dehydrogenase complexes; E3 binding domain protein; KEGG: sme:SMb20019 dihydrolipoamide succinyltransferase protein; dihydrolipoyllysine-residue succinyltransferase 1585242 4580210 Pden_1603 Paracoccus denitrificans PD1222 dihydrolipoyllysine-residue succinyltransferase YP_915399.1 1584109 R 318586 CDS YP_915400.1 119384344 4580211 complement(1585243..1587324) 1 NC_008686.1 PFAM: dehydrogenase, E1 component; Transketolase, central region; Transketolase domain protein; KEGG: sme:SMb20020 pyruvate dehydrogenase E1 component,alpha and beta subunits protein; transketolase, central region 1587324 4580211 Pden_1604 Paracoccus denitrificans PD1222 transketolase, central region YP_915400.1 1585243 R 318586 CDS YP_915401.1 119384345 4580212 complement(1587353..1587946) 1 NC_008686.1 PFAM: flavoprotein; KEGG: bcl:ABC3557 lantibiotic biosynthesis protein, flavoprotein; flavoprotein 1587946 4580212 Pden_1605 Paracoccus denitrificans PD1222 flavoprotein YP_915401.1 1587353 R 318586 CDS YP_915402.1 119384346 4580213 complement(1587959..1588795) 1 NC_008686.1 PFAM: Methyltransferase type 12; KEGG: cps:CPS_2928 hypothetical protein; type 12 methyltransferase 1588795 4580213 Pden_1606 Paracoccus denitrificans PD1222 type 12 methyltransferase YP_915402.1 1587959 R 318586 CDS YP_915403.1 119384347 4580214 1588977..1590524 1 NC_008686.1 PFAM: MaoC domain protein dehydratase; KEGG: nha:Nham_0934 phenylacetic acid degradation protein PaaN; dehydratase 1590524 4580214 Pden_1607 Paracoccus denitrificans PD1222 dehydratase YP_915403.1 1588977 D 318586 CDS YP_915404.1 119384348 4580215 1590526..1592076 1 NC_008686.1 PFAM: extracellular solute-binding protein, family 5; KEGG: wsu:WS1160 oligopeptide binding protein; extracellular solute-binding protein 1592076 4580215 Pden_1608 Paracoccus denitrificans PD1222 extracellular solute-binding protein YP_915404.1 1590526 D 318586 CDS YP_915405.1 119384349 4580216 1592073..1593071 1 NC_008686.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: dsy:DSY3210 hypothetical protein; binding-protein-dependent transport system inner membrane protein 1593071 4580216 Pden_1609 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_915405.1 1592073 D 318586 CDS YP_915406.1 119384350 4580217 1593071..1593844 1 NC_008686.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: mac:MA0843 dipeptide ABC transporter, permease; binding-protein-dependent transport system inner membrane protein 1593844 4580217 Pden_1610 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_915406.1 1593071 D 318586 CDS YP_915407.1 119384351 4580218 1593841..1595223 1 NC_008686.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sma:SAV3045 ABC transporter ATP-binding protein; ABC transporter 1595223 4580218 Pden_1611 Paracoccus denitrificans PD1222 ABC transporter YP_915407.1 1593841 D 318586 CDS YP_915408.1 119384352 4580219 complement(1595224..1595760) 1 NC_008686.1 PFAM: ChaC family protein; KEGG: rsp:RSP_2287 ChaC-like protein; ChaC family protein 1595760 4580219 Pden_1612 Paracoccus denitrificans PD1222 ChaC family protein YP_915408.1 1595224 R 318586 CDS YP_915409.1 119384353 4580220 complement(1595760..1596941) 1 NC_008686.1 PFAM: acyl-CoA dehydrogenase domain protein; Acyl-CoA dehydrogenase, type 2, C-terminal domain; KEGG: bca:BCE_5473 acyl-CoA dehydrogenase; acyl-CoA dehydrogenase 1596941 4580220 Pden_1613 Paracoccus denitrificans PD1222 acyl-CoA dehydrogenase YP_915409.1 1595760 R 318586 CDS YP_915410.1 119384354 4580221 complement(1596964..1597413) 1 NC_008686.1 PFAM: thioesterase superfamily protein; KEGG: sth:STH878 hypothetical protein; thioesterase 1597413 4580221 Pden_1614 Paracoccus denitrificans PD1222 thioesterase YP_915410.1 1596964 R 318586 CDS YP_915411.1 119384355 4580222 complement(1597420..1598061) 1 NC_008686.1 KEGG: bld:BLi04239 YwfB; hypothetical protein 1598061 4580222 Pden_1615 Paracoccus denitrificans PD1222 hypothetical protein YP_915411.1 1597420 R 318586 CDS YP_915412.1 119384356 4580998 complement(1599137..1599460) 1 NC_008686.1 PFAM: transposase IS3/IS911 family protein; KEGG: nwi:Nwi_2119 transposase IS3/IS911; transposase IS3/IS911 family protein 1599460 4580998 Pden_1617 Paracoccus denitrificans PD1222 transposase IS3/IS911 family protein YP_915412.1 1599137 R 318586 CDS YP_915413.1 119384357 4580999 complement(1599713..1600507) 1 NC_008686.1 KEGG: sil:SPO3456 flagellar protein; flagellar protein 1600507 4580999 Pden_1618 Paracoccus denitrificans PD1222 flagellar protein YP_915413.1 1599713 R 318586 CDS YP_915414.1 119384358 4581000 complement(1600823..1601188) 1 NC_008686.1 PFAM: flagellar FlaF family protein; KEGG: rde:RD1_0159 flagellar protein; flagellar FlaF family protein 1601188 4581000 Pden_1619 Paracoccus denitrificans PD1222 flagellar FlaF family protein YP_915414.1 1600823 R 318586 CDS YP_915415.1 119384359 4581001 complement(1601253..1602107) 1 NC_008686.1 PFAM: flagellin domain protein; KEGG: sit:TM1040_3134 flagellin-like; flagellin domain-containing protein 1602107 4581001 Pden_1620 Paracoccus denitrificans PD1222 flagellin domain-containing protein YP_915415.1 1601253 R 318586 CDS YP_915416.1 119384360 4581002 complement(1602260..1602574) 1 NC_008686.1 hypothetical protein 1602574 4581002 Pden_1621 Paracoccus denitrificans PD1222 hypothetical protein YP_915416.1 1602260 R 318586 CDS YP_915417.1 119384361 4581003 1602940..1604133 1 NC_008686.1 KEGG: rde:RD1_0163 flagellar hook-length control protein; hypothetical protein 1604133 4581003 Pden_1622 Paracoccus denitrificans PD1222 hypothetical protein YP_915417.1 1602940 D 318586 CDS YP_915418.1 119384362 4581004 1604147..1604812 1 NC_008686.1 acts as a scaffold for the assembly of hook proteins onto the flagellar basal body rod; Rhodobacter sphaeroides has 2 copies of many flagellar genes; the Rhodobacter protein in this cluster is associated with a set of flagellar genes acquired by lateral gene transfer; these genes are not normally expressed; flagellar basal body rod modification protein 1604812 flgD 4581004 flgD Paracoccus denitrificans PD1222 flagellar basal body rod modification protein YP_915418.1 1604147 D 318586 CDS YP_915419.1 119384363 4581005 1605044..1605415 1 NC_008686.1 PFAM: transposase IS3/IS911 family protein; KEGG: ret:RHE_CH03058 probable insertion sequence transposase protein; transposase IS3/IS911 family protein 1605415 4581005 Pden_1624 Paracoccus denitrificans PD1222 transposase IS3/IS911 family protein YP_915419.1 1605044 D 318586 CDS YP_915420.1 119384364 4581006 complement(1606371..1606682) 1 NC_008686.1 hypothetical protein 1606682 4581006 Pden_1626 Paracoccus denitrificans PD1222 hypothetical protein YP_915420.1 1606371 R 318586 CDS YP_915421.1 119384365 4581007 complement(1606847..1608202) 1 NC_008686.1 KEGG: stm:STM1586 periplasmic protein; hypothetical protein 1608202 4581007 Pden_1627 Paracoccus denitrificans PD1222 hypothetical protein YP_915421.1 1606847 R 318586 CDS YP_915422.1 119384366 4581008 complement(1608270..1610312) 1 NC_008686.1 PFAM: TonB-dependent receptor; TonB-dependent receptor, plug; KEGG: bbr:BB4761 exogenous ferric siderophore receptor; TonB-dependent receptor, plug 1610312 4581008 Pden_1628 Paracoccus denitrificans PD1222 TonB-dependent receptor, plug YP_915422.1 1608270 R 318586 CDS YP_915423.1 119384367 4581009 1610564..1611091 1 NC_008686.1 PFAM: sigma-70 region 2 domain protein; sigma-70 region 4 domain protein; Sigma-70, region 4 type 2; KEGG: pfo:Pfl_0929 sigma-24 (FecI); ECF subfamily RNA polymerase sigma-24 factor 1611091 4581009 Pden_1629 Paracoccus denitrificans PD1222 ECF subfamily RNA polymerase sigma-24 factor YP_915423.1 1610564 D 318586 CDS YP_915424.1 119384368 4581010 1611103..1612077 1 NC_008686.1 PFAM: FecR protein; KEGG: nwi:Nwi_2882 FecR protein; FecR protein 1612077 4581010 Pden_1630 Paracoccus denitrificans PD1222 FecR protein YP_915424.1 1611103 D 318586 CDS YP_915425.1 119384369 4581011 1612232..1614451 1 NC_008686.1 PFAM: TonB-dependent receptor; TonB-dependent receptor, plug; KEGG: csa:Csal_2678 TonB-dependent siderophore receptor; TonB-dependent receptor, plug 1614451 4581011 Pden_1631 Paracoccus denitrificans PD1222 TonB-dependent receptor, plug YP_915425.1 1612232 D 318586 CDS YP_915426.1 119384370 4581012 1614613..1614864 1 NC_008686.1 hypothetical protein 1614864 4581012 Pden_1632 Paracoccus denitrificans PD1222 hypothetical protein YP_915426.1 1614613 D 318586 CDS YP_915427.1 119384371 4581013 1614861..1615991 1 NC_008686.1 ATP-dependent carboxylate-amine ligase; carboxylate-amine ligase 1615991 4581013 Pden_1633 Paracoccus denitrificans PD1222 carboxylate-amine ligase YP_915427.1 1614861 D 318586 CDS YP_915428.1 119384372 4581014 1616089..1616586 1 NC_008686.1 PFAM: superoxide dismutase, copper/zinc binding; KEGG: ret:RHE_CH01400 superoxide dismutase protein; superoxide dismutase, copper/zinc binding 1616586 4581014 Pden_1634 Paracoccus denitrificans PD1222 superoxide dismutase, copper/zinc binding YP_915428.1 1616089 D 318586 CDS YP_915429.1 119384373 4581015 complement(1616616..1617704) 1 NC_008686.1 PFAM: HWE histidine kinase; KEGG: mes:Meso_0180 signal transduction histidine kinase; signal transduction histidine kinase 1617704 4581015 Pden_1635 Paracoccus denitrificans PD1222 signal transduction histidine kinase YP_915429.1 1616616 R 318586 CDS YP_915430.1 119384374 4581016 1617928..1618539 1 NC_008686.1 PFAM: isochorismatase hydrolase; KEGG: mlo:mlr6855 hypothetical protein; isochorismatase hydrolase 1618539 4581016 Pden_1636 Paracoccus denitrificans PD1222 isochorismatase hydrolase YP_915430.1 1617928 D 318586 CDS YP_915431.1 119384375 4580820 1618639..1618875 1 NC_008686.1 KEGG: rsp:RSP_2671 hypothetical protein; hypothetical protein 1618875 4580820 Pden_1637 Paracoccus denitrificans PD1222 hypothetical protein YP_915431.1 1618639 D 318586 CDS YP_915432.1 119384376 4580821 complement(1619053..1619235) 1 NC_008686.1 KEGG: bbr:BB2396 hypothetical protein; hypothetical protein 1619235 4580821 Pden_1638 Paracoccus denitrificans PD1222 hypothetical protein YP_915432.1 1619053 R 318586 CDS YP_915433.1 119384377 4580822 complement(1619984..1620940) 1 NC_008686.1 KEGG: rsp:RSP_4009 phosphate acetyl/butaryl transferase; TIGRFAM: phosphate acetyltransferase; PFAM: phosphate acetyl/butaryl transferase; phosphate acetyltransferase 1620940 4580822 Pden_1640 Paracoccus denitrificans PD1222 phosphate acetyltransferase YP_915433.1 1619984 R 318586 CDS YP_915434.1 119384378 4580823 complement(1620953..1621969) 1 NC_008686.1 PFAM: conserved hypothetical protein 698; KEGG: rsp:RSP_4010 conserved hypothetical protein 698; hypothetical protein 1621969 4580823 Pden_1641 Paracoccus denitrificans PD1222 hypothetical protein YP_915434.1 1620953 R 318586 CDS YP_915435.1 119384379 4580824 complement(1622243..1624024) 1 NC_008686.1 catalyzes the formation of acetyl phosphate and sulfite from 2-sulfoacetaldehyde; is active when grown on taurine as a sole carbon source; sulfoacetaldehyde acetyltransferase 1624024 4580824 Pden_1642 Paracoccus denitrificans PD1222 sulfoacetaldehyde acetyltransferase YP_915435.1 1622243 R 318586 CDS YP_915436.1 119384380 4580825 complement(1624037..1625428) 1 NC_008686.1 PFAM: FAD dependent oxidoreductase; KEGG: rsp:RSP_4012 FAD dependent oxidoreductase; FAD dependent oxidoreductase 1625428 4580825 Pden_1643 Paracoccus denitrificans PD1222 FAD dependent oxidoreductase YP_915436.1 1624037 R 318586 CDS YP_915437.1 119384381 4580826 complement(1625437..1625856) 1 NC_008686.1 PFAM: protein of unknown function DUF1486; KEGG: rsp:RSP_4013 hypothetical protein; hypothetical protein 1625856 4580826 Pden_1644 Paracoccus denitrificans PD1222 hypothetical protein YP_915437.1 1625437 R 318586 CDS YP_915438.1 119384382 4580827 complement(1625871..1627211) 1 NC_008686.1 TIGRFAM: TRAP dicarboxylate transporter, DctM subunit; PFAM: TRAP C4-dicarboxylate transport system permease DctM subunit; KEGG: rsp:RSP_4014 TRAP-T family transporter, large inner membrane subunit DctM; TRAP dicarboxylate transporter subunit DctM 1627211 4580827 Pden_1645 Paracoccus denitrificans PD1222 TRAP dicarboxylate transporter subunit DctM YP_915438.1 1625871 R 318586 CDS YP_915439.1 119384383 4580828 complement(1627208..1627768) 1 NC_008686.1 PFAM: Tripartite ATP-independent periplasmic transporter, DctQ component; KEGG: rsp:RSP_4015 TRAP-T family transporter, periplasmic ligand binding protein, DctQ; tripartite ATP-independent periplasmic transporter DctQ 1627768 4580828 Pden_1646 Paracoccus denitrificans PD1222 tripartite ATP-independent periplasmic transporter DctQ YP_915439.1 1627208 R 318586 CDS YP_915440.1 119384384 4580829 complement(1627853..1628863) 1 NC_008686.1 TIGRFAM: TRAP dicarboxylate transporter, DctP subunit; PFAM: TRAP dicarboxylate transporter- DctP subunit; KEGG: rsp:RSP_4016 TRAP-T family transporter, DctP subunit; TRAP dicarboxylate transporter subunit DctP 1628863 4580829 Pden_1647 Paracoccus denitrificans PD1222 TRAP dicarboxylate transporter subunit DctP YP_915440.1 1627853 R 318586 CDS YP_915441.1 119384385 4580830 1628978..1630465 1 NC_008686.1 PFAM: regulatory protein GntR, HTH; aminotransferase, class I and II; KEGG: rsp:RSP_4017 transcriptional regulator, GntR family; GntR family transcriptional regulator 1630465 4580830 Pden_1648 Paracoccus denitrificans PD1222 GntR family transcriptional regulator YP_915441.1 1628978 D 318586 CDS YP_915442.1 119384386 4580831 1630782..1631291 1 NC_008686.1 catalyzes the dehydration of (3R)-3-hydroxydecanoyl-ACP to 2,3-decenoyl-ACP or 3,4-decenoyl-ACP; 3-hydroxydecanoyl-ACP dehydratase 1631291 4580831 Pden_1649 Paracoccus denitrificans PD1222 3-hydroxydecanoyl-ACP dehydratase YP_915442.1 1630782 D 318586 CDS YP_915443.1 119384387 4580832 1631313..1632542 1 NC_008686.1 PFAM: beta-ketoacyl synthase; KEGG: rsp:RSP_3177 3-oxoacyl-(acyl-carrier-protein) synthase; beta-ketoacyl synthase 1632542 4580832 Pden_1650 Paracoccus denitrificans PD1222 beta-ketoacyl synthase YP_915443.1 1631313 D 318586 CDS YP_915444.1 119384388 4580833 1632562..1633350 1 NC_008686.1 PFAM: short-chain dehydrogenase/reductase SDR; KEGG: rsp:RSP_3176 enoyl-(acyl-carrier protein) reductase (NADH); short-chain dehydrogenase/reductase SDR 1633350 4580833 Pden_1651 Paracoccus denitrificans PD1222 short-chain dehydrogenase/reductase SDR YP_915444.1 1632562 D 318586 CDS YP_915445.1 119384389 4580834 1633350..1634177 1 NC_008686.1 KEGG: rsp:RSP_2253 predicted hydrolase or acyltransferase; hydrolase 1634177 4580834 Pden_1652 Paracoccus denitrificans PD1222 hydrolase YP_915445.1 1633350 D 318586 CDS YP_915446.1 119384390 4580835 complement(1634531..1635805) 1 NC_008686.1 TIGRFAM: lytic murein transglycosylase; PFAM: Peptidoglycan-binding domain 1 protein; KEGG: rsp:RSP_1125 membrane bound lytic murein transglycosylase B; lytic murein transglycosylase 1635805 4580835 Pden_1653 Paracoccus denitrificans PD1222 lytic murein transglycosylase YP_915446.1 1634531 R 318586 CDS YP_915447.1 119384391 4580836 complement(1635960..1637006) 1 NC_008686.1 PFAM: tRNA synthetase, class II (D, K and N); KEGG: rsp:RSP_0478 lysyl-tRNA synthetase; lysine--tRNA ligase 1637006 4580836 Pden_1654 Paracoccus denitrificans PD1222 lysine--tRNA ligase YP_915447.1 1635960 R 318586 CDS YP_915448.1 119384392 4580837 1637085..1637708 1 NC_008686.1 Involved in peptide bond synthesis; alters the affinity of the ribosome for aminoacyl-tRNA; elongation factor P 1637708 4580837 Pden_1655 Paracoccus denitrificans PD1222 elongation factor P YP_915448.1 1637085 D 318586 CDS YP_915449.1 119384393 4580838 complement(1638090..1639118) 1 NC_008686.1 catalyzes the reduction of N-acetyl-5-glutamyl phosphate to N-acetyl-L-glutamate 5-semialdehyde in arginine biosynthesis and the reduction of N-acetyl-gamma-aminoadipyl-phosphate to N-acetyl-L-aminoadipate-semialdehyde in lysine biosynthesis; involved in both the arginine and lysine biosynthetic pathways; lysine is produced via the AAA pathway, lysine from alpha-aminoadipate; N-acetyl-gamma-glutamyl-phosphate reductase 1639118 argC 4580838 argC Paracoccus denitrificans PD1222 N-acetyl-gamma-glutamyl-phosphate reductase YP_915449.1 1638090 R 318586 CDS YP_915450.1 119384394 4580839 1639582..1640412 1 NC_008686.1 catalyzes the formation of tetrahydrofolate and 2-dehydropantoate from 5,10-methylenetetrahydrofolate and 3-methyl-2-oxobutanoate; 3-methyl-2-oxobutanoate hydroxymethyltransferase 1640412 panB 4580839 panB Paracoccus denitrificans PD1222 3-methyl-2-oxobutanoate hydroxymethyltransferase YP_915450.1 1639582 D 318586 CDS YP_915451.1 119384395 4579812 1640409..1641257 1 NC_008686.1 catalyzes the formation of (R)-pantothenate from pantoate and beta-alanine; pantoate--beta-alanine ligase 1641257 panC 4579812 panC Paracoccus denitrificans PD1222 pantoate--beta-alanine ligase YP_915451.1 1640409 D 318586 CDS YP_915452.1 119384396 4579813 complement(1641303..1642682) 1 NC_008686.1 PFAM: ATP-binding region, ATPase domain protein domain protein; histidine kinase A domain protein domain protein; KEGG: rsp:RSP_3512 periplasmic sensor signal transduction histidine kinase; integral membrane sensor signal transduction histidine kinase 1642682 4579813 Pden_1659 Paracoccus denitrificans PD1222 integral membrane sensor signal transduction histidine kinase YP_915452.1 1641303 R 318586 CDS YP_915453.1 119384397 4579814 complement(1642679..1643362) 1 NC_008686.1 PFAM: response regulator receiver; transcriptional regulator domain protein; KEGG: rsp:RSP_3511 two component transcriptional regulator, winged helix family family; two component transcriptional regulator 1643362 4579814 Pden_1660 Paracoccus denitrificans PD1222 two component transcriptional regulator YP_915453.1 1642679 R 318586 CDS YP_915454.1 119384398 4579815 complement(1643362..1643676) 1 NC_008686.1 PFAM: Propeptide, PepSY amd peptidase M4; KEGG: rsp:RSP_3510 hypothetical protein; peptidase 1643676 4579815 Pden_1661 Paracoccus denitrificans PD1222 peptidase YP_915454.1 1643362 R 318586 CDS YP_915455.1 119384399 4579816 1643855..1644637 1 NC_008686.1 PFAM: Hemolysin-type calcium-binding region; KEGG: rsp:RSP_3509 hemolysin-type calcium-binding region, RTX; hemolysin-type calcium-binding protein 1644637 4579816 Pden_1662 Paracoccus denitrificans PD1222 hemolysin-type calcium-binding protein YP_915455.1 1643855 D 318586 CDS YP_915456.1 119384400 4579817 complement(1644768..1645124) 1 NC_008686.1 PFAM: Rieske [2Fe-2S] domain protein; KEGG: gbe:GbCGDNIH1_0274 rieske (2Fe-2S) domain protein; Rieske (2Fe-2S) domain-containing protein 1645124 4579817 Pden_1663 Paracoccus denitrificans PD1222 Rieske (2Fe-2S) domain-containing protein YP_915456.1 1644768 R 318586 CDS YP_915457.1 119384401 4579818 complement(1645128..1646240) 1 NC_008686.1 KEGG: sme:SMc03211 4-hydroxyphenylpyruvate dioxygenase protein; TIGRFAM: 4-hydroxyphenylpyruvate dioxygenase; PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase; 4-hydroxyphenylpyruvate dioxygenase 1646240 4579818 Pden_1664 Paracoccus denitrificans PD1222 4-hydroxyphenylpyruvate dioxygenase YP_915457.1 1645128 R 318586 CDS YP_915458.1 119384402 4579819 1646362..1646832 1 NC_008686.1 PFAM: regulatory protein, AsnC/Lrp family; KEGG: rpa:RPA0006 transcriptional regulator, AsnC family; AsnC family transcriptional regulator 1646832 4579819 Pden_1665 Paracoccus denitrificans PD1222 AsnC family transcriptional regulator YP_915458.1 1646362 D 318586 CDS YP_915459.1 119384403 4579820 1646854..1647954 1 NC_008686.1 TIGRFAM: lysine 2,3-aminomutase YodO family protein; PFAM: Radical SAM domain protein; KEGG: rsp:RSP_3227 lysine 2,3-aminomutase; lysine 2,3-aminomutase YodO family protein 1647954 4579820 Pden_1666 Paracoccus denitrificans PD1222 lysine 2,3-aminomutase YodO family protein YP_915459.1 1646854 D 318586 CDS YP_915460.1 119384404 4579821 complement(1648040..1648891) 1 NC_008686.1 PFAM: ABC transporter related; Oligopeptide/dipeptide ABC transporter, C-terminal domain protein; SMART: AAA ATPase; KEGG: atc:AGR_L_1474 probable ATP-binding component of ABC dipeptide transporter; ABC transporter 1648891 4579821 Pden_1667 Paracoccus denitrificans PD1222 ABC transporter YP_915460.1 1648040 R 318586 CDS YP_915461.1 119384405 4579822 complement(1648888..1649727) 1 NC_008686.1 PFAM: ABC transporter related; Oligopeptide/dipeptide ABC transporter, C-terminal domain protein; SMART: AAA ATPase; KEGG: atc:AGR_L_1475 probable ATP-binding component of ABC transporter; ABC transporter 1649727 4579822 Pden_1668 Paracoccus denitrificans PD1222 ABC transporter YP_915461.1 1648888 R 318586 CDS YP_915462.1 119384406 4579823 complement(1649731..1650633) 1 NC_008686.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: atc:AGR_L_1477 probable permease of ABC transporter; binding-protein-dependent transport system inner membrane protein 1650633 4579823 Pden_1669 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_915462.1 1649731 R 318586 CDS YP_915463.1 119384407 4579824 complement(1650630..1651637) 1 NC_008686.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: atc:AGR_L_1478 dipeptide transport system permease protein DppB; binding-protein-dependent transport system inner membrane protein 1651637 4579824 Pden_1670 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_915463.1 1650630 R 318586 CDS YP_915464.1 119384408 4579825 complement(1651711..1653327) 1 NC_008686.1 PFAM: extracellular solute-binding protein, family 5; KEGG: atc:AGR_L_1481 dipeptide transport protein; extracellular solute-binding protein 1653327 4579825 Pden_1671 Paracoccus denitrificans PD1222 extracellular solute-binding protein YP_915464.1 1651711 R 318586 CDS YP_915465.1 119384409 4579826 complement(1653521..1654327) 1 NC_008686.1 PFAM: Myo-inositol catabolism IolB domain protein; KEGG: bmb:BruAb2_0514 IolB protein; myo-inositol catabolism IolB domain-containing protein 1654327 4579826 Pden_1672 Paracoccus denitrificans PD1222 myo-inositol catabolism IolB domain-containing protein YP_915465.1 1653521 R 318586 CDS YP_915466.1 119384410 4579827 complement(1654324..1654509) 1 NC_008686.1 KEGG: ret:RHE_CH03169 hypothetical protein; hypothetical protein 1654509 4579827 Pden_1673 Paracoccus denitrificans PD1222 hypothetical protein YP_915466.1 1654324 R 318586 CDS YP_915467.1 119384411 4579828 complement(1654519..1655415) 1 NC_008686.1 PFAM: Xylose isomerase domain protein TIM barrel; KEGG: atc:AGR_L_177GM iolE protein; xylose isomerase domain-containing protein 1655415 4579828 Pden_1674 Paracoccus denitrificans PD1222 xylose isomerase domain-containing protein YP_915467.1 1654519 R 318586 CDS YP_915468.1 119384412 4579829 complement(1655427..1657256) 1 NC_008686.1 PFAM: thiamine pyrophosphate enzyme domain protein TPP-binding; thiamine pyrophosphate enzyme, central region; thiamine pyrophosphate enzyme TPP binding domain protein; KEGG: rsp:RSP_3284 acetolactate synthase; thiamine pyrophosphate binding domain-containing protein 1657256 4579829 Pden_1675 Paracoccus denitrificans PD1222 thiamine pyrophosphate binding domain-containing protein YP_915468.1 1655427 R 318586 CDS YP_915469.1 119384413 4579830 complement(1657333..1659240) 1 NC_008686.1 PFAM: PfkB domain protein; KEGG: bmb:BruAb2_0517 IolC myo-catabolism protein; ribokinase-like domain-containing protein 1659240 4579830 Pden_1676 Paracoccus denitrificans PD1222 ribokinase-like domain-containing protein YP_915469.1 1657333 R 318586 CDS YP_915470.1 119384414 4580085 complement(1659244..1660044) 1 NC_008686.1 PFAM: Xylose isomerase domain protein TIM barrel; KEGG: atc:AGR_L_627 IolI protein; xylose isomerase domain-containing protein 1660044 4580085 Pden_1677 Paracoccus denitrificans PD1222 xylose isomerase domain-containing protein YP_915470.1 1659244 R 318586 CDS YP_915471.1 119384415 4580086 complement(1660053..1661063) 1 NC_008686.1 PFAM: oxidoreductase domain protein; Oxidoreductase, C-terminal domain; KEGG: atc:AGR_L_628 myo-inositol 2-dehydrogenase; inositol 2-dehydrogenase 1661063 4580086 Pden_1678 Paracoccus denitrificans PD1222 inositol 2-dehydrogenase YP_915471.1 1660053 R 318586 CDS YP_915472.1 119384416 4580087 complement(1661066..1661968) 1 NC_008686.1 PFAM: Xylose isomerase domain protein TIM barrel; KEGG: atc:AGR_pAT_639 myo-inositol catabolism; xylose isomerase domain-containing protein 1661968 4580087 Pden_1679 Paracoccus denitrificans PD1222 xylose isomerase domain-containing protein YP_915472.1 1661066 R 318586 CDS YP_915473.1 119384417 4580088 complement(1661976..1663094) 1 NC_008686.1 PFAM: oxidoreductase domain protein; Oxidoreductase, C-terminal domain; KEGG: psb:Psyr_2455 oxidoreductase, N-terminal:oxidoreductase, C-terminal; oxidoreductase domain-containing protein 1663094 4580088 Pden_1680 Paracoccus denitrificans PD1222 oxidoreductase domain-containing protein YP_915473.1 1661976 R 318586 CDS YP_915474.1 119384418 4580089 complement(1663100..1664020) 1 NC_008686.1 PFAM: periplasmic binding protein/LacI transcriptional regulator; KEGG: atc:AGR_L_632 rhizopine-binding protein precursor; periplasmic binding protein/LacI transcriptional regulator 1664020 4580089 Pden_1681 Paracoccus denitrificans PD1222 periplasmic binding protein/LacI transcriptional regulator YP_915474.1 1663100 R 318586 CDS YP_915475.1 119384419 4580090 complement(1664032..1665042) 1 NC_008686.1 PFAM: inner-membrane translocator; KEGG: sme:SMb20714 sugar uptake ABC transporter permease protein; inner-membrane translocator 1665042 4580090 Pden_1682 Paracoccus denitrificans PD1222 inner-membrane translocator YP_915475.1 1664032 R 318586 CDS YP_915476.1 119384420 4580091 complement(1665055..1666566) 1 NC_008686.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: atc:AGR_L_2903 D-galactose transport system ATP-binding protein; ABC transporter 1666566 4580091 Pden_1683 Paracoccus denitrificans PD1222 ABC transporter YP_915476.1 1665055 R 318586 CDS YP_915477.1 119384421 4580092 complement(1666620..1667561) 1 NC_008686.1 PFAM: periplasmic binding protein/LacI transcriptional regulator; KEGG: atc:AGR_L_634 rhizopine-binding protein precursor; periplasmic binding protein/LacI transcriptional regulator 1667561 4580092 Pden_1684 Paracoccus denitrificans PD1222 periplasmic binding protein/LacI transcriptional regulator YP_915477.1 1666620 R 318586 CDS YP_915478.1 119384422 4580093 complement(1667791..1668795) 1 NC_008686.1 PFAM: regulatory protein, LacI; KEGG: atc:AGR_L_636 hypothetical protein; regulatory protein, LacI 1668795 4580093 Pden_1685 Paracoccus denitrificans PD1222 regulatory protein, LacI YP_915478.1 1667791 R 318586 CDS YP_915479.1 119384423 4580094 complement(1668901..1669575) 1 NC_008686.1 KEGG: bja:blr7843 hypothetical protein; hypothetical protein 1669575 4580094 Pden_1686 Paracoccus denitrificans PD1222 hypothetical protein YP_915479.1 1668901 R 318586 CDS YP_915480.1 119384424 4580095 complement(1669663..1670700) 1 NC_008686.1 PFAM: helix-turn-helix- domain containing protein, AraC type; ThiJ/PfpI domain protein; KEGG: sil:SPO1002 transcriptional regulator, AraC family; AraC family transcriptional regulator 1670700 4580095 Pden_1687 Paracoccus denitrificans PD1222 AraC family transcriptional regulator YP_915480.1 1669663 R 318586 CDS YP_915481.1 119384425 4580096 complement(1670911..1671375) 1 NC_008686.1 KEGG: nmu:Nmul_A2076 hypothetical protein; hypothetical protein 1671375 4580096 Pden_1688 Paracoccus denitrificans PD1222 hypothetical protein YP_915481.1 1670911 R 318586 CDS YP_915482.1 119384426 4580097 complement(1671389..1672597) 1 NC_008686.1 flavohemoprotein; catalyzes the formation of nitrate from nitric oxide; can also catalyze the reduction of dihydropteridine; nitric oxide dioxygenase 1672597 4580097 Pden_1689 Paracoccus denitrificans PD1222 nitric oxide dioxygenase YP_915482.1 1671389 R 318586 CDS YP_915483.1 119384427 4580098 1672723..1673166 1 NC_008686.1 TIGRFAM: transcriptional regulator, Rrf2 family; PFAM: protein of unknown function UPF0074; KEGG: neu:NE0928 hypothetical protein; BadM/Rrf2 family transcriptional regulator 1673166 4580098 Pden_1690 Paracoccus denitrificans PD1222 BadM/Rrf2 family transcriptional regulator YP_915483.1 1672723 D 318586 CDS YP_915484.1 119384428 4580099 complement(1673173..1674075) 1 NC_008686.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: atc:AGR_C_2527 hypothetical protein; LysR family transcriptional regulator 1674075 4580099 Pden_1691 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_915484.1 1673173 R 318586 CDS YP_915485.1 119384429 4580100 1674196..1675422 1 NC_008686.1 PFAM: creatinase; peptidase M24; KEGG: rxy:Rxyl_0461 creatinase; creatinase 1675422 4580100 Pden_1692 Paracoccus denitrificans PD1222 creatinase YP_915485.1 1674196 D 318586 CDS YP_915486.1 119384430 4580101 1675567..1676901 1 NC_008686.1 PFAM: General substrate transporter; major facilitator superfamily MFS_1; KEGG: ppu:PP_3666 metabolite MFS transporter, MHS family; major facilitator superfamily transporter 1676901 4580101 Pden_1693 Paracoccus denitrificans PD1222 major facilitator superfamily transporter YP_915486.1 1675567 D 318586 CDS YP_915487.1 119384431 4580102 complement(1676951..1677880) 1 NC_008686.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: rsp:RSP_1286 RuBisCO operon transcriptional regulator, CbbR; LysR family transcriptional regulator 1677880 4580102 Pden_1694 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_915487.1 1676951 R 318586 CDS YP_915488.1 119384432 4580103 1677976..1678968 1 NC_008686.1 PFAM: Inositol phosphatase/fructose-1,6-bisphosphatase; KEGG: rsp:RSP_1285 fructose-1,6-bisphosphatase I; inositol phosphatase/fructose-1,6-bisphosphatase 1678968 4580103 Pden_1695 Paracoccus denitrificans PD1222 inositol phosphatase/fructose-1,6-bisphosphatase YP_915488.1 1677976 D 318586 CDS YP_915489.1 119384433 4580104 1678991..1679863 1 NC_008686.1 PFAM: phosphoribulokinase/uridine kinase; KEGG: rsp:RSP_1284 phosphoribulokinase; phosphoribulokinase 1679863 4580104 Pden_1696 Paracoccus denitrificans PD1222 phosphoribulokinase YP_915489.1 1678991 D 318586 CDS YP_915490.1 119384434 4581323 1679875..1681881 1 NC_008686.1 catalyzes the formation of ribose 5-phosphate and xylulose 5-phosphate from sedoheptulose 7-phosphate and glyceraldehyde 3-phosphate; can transfer ketol groups between several groups; in Escherichia coli there are two tkt genes, tktA expressed during exponential growth and the tktB during stationary phase; transketolase 1681881 4581323 Pden_1697 Paracoccus denitrificans PD1222 transketolase YP_915490.1 1679875 D 318586 CDS YP_915491.1 119384435 4581324 1681881..1682960 1 NC_008686.1 class II aldolase; catalyzes the reversible aldol condensation of dihydroxyacetonephosphate and glyceraldehyde 3-phosphate in the Calvin cycle, glycolysis and gluconeogenesis; fructose-1,6-bisphosphate aldolase 1682960 4581324 Pden_1698 Paracoccus denitrificans PD1222 fructose-1,6-bisphosphate aldolase YP_915491.1 1681881 D 318586 CDS YP_915492.1 119384436 4581325 1682975..1684438 1 NC_008686.1 type III RuBisCO; involved in carbon fixation; ribulose bisophosphate carboxylase 1684438 rbcL 4581325 rbcL Paracoccus denitrificans PD1222 ribulose bisophosphate carboxylase YP_915492.1 1682975 D 318586 CDS YP_915493.1 119384437 4581326 1684450..1684839 1 NC_008686.1 PFAM: ribulose bisphosphate carboxylase, small chain; KEGG: rpa:RPA1560 ribulose-bisphosphate carboxylase small chain; ribulose-bisphosphate carboxylase 1684839 4581326 Pden_1700 Paracoccus denitrificans PD1222 ribulose-bisphosphate carboxylase YP_915493.1 1684450 D 318586 CDS YP_915494.1 119384438 4581327 1684912..1685838 1 NC_008686.1 PFAM: AAA ATPase, central domain protein; SMART: AAA ATPase; KEGG: rsp:RSP_1280 CbbX protein; ATPase central domain-containing protein 1685838 4581327 Pden_1701 Paracoccus denitrificans PD1222 ATPase central domain-containing protein YP_915494.1 1684912 D 318586 CDS YP_915495.1 119384439 4581328 complement(1686315..1687565) 1 NC_008686.1 KEGG: pfl:PFL_4132 PimS2 protein; PimS2 protein 1687565 4581328 Pden_1702 Paracoccus denitrificans PD1222 PimS2 protein YP_915495.1 1686315 R 318586 CDS YP_915496.1 119384440 4581329 1687776..1689314 1 NC_008686.1 KEGG: pfo:Pfl_2975 quinohemoprotein amine dehydrogenase, 60 kDa subunit; quinohemoprotein amine dehydrogenase, 60 kDa subunit 1689314 4581329 Pden_1703 Paracoccus denitrificans PD1222 quinohemoprotein amine dehydrogenase, 60 kDa subunit YP_915496.1 1687776 D 318586 CDS YP_915497.1 119384441 4581330 1689319..1690776 1 NC_008686.1 PFAM: Radical SAM domain protein; KEGG: pfo:Pfl_2974 radical SAM; radical SAM domain-containing protein 1690776 4581330 Pden_1704 Paracoccus denitrificans PD1222 radical SAM domain-containing protein YP_915497.1 1689319 D 318586 CDS YP_915498.1 119384442 4581331 1690773..1691105 1 NC_008686.1 KEGG: pfo:Pfl_2973 hypothetical protein; hypothetical protein 1691105 4581331 Pden_1705 Paracoccus denitrificans PD1222 hypothetical protein YP_915498.1 1690773 D 318586 CDS YP_915499.1 119384443 4581332 1691105..1692181 1 NC_008686.1 KEGG: pfo:Pfl_2972 quinohemoprotein amine dehydrogenase, subunit beta; quinohemoprotein amine dehydrogenase subunit beta 1692181 4581332 Pden_1706 Paracoccus denitrificans PD1222 quinohemoprotein amine dehydrogenase subunit beta YP_915499.1 1691105 D 318586 CDS YP_915500.1 119384444 4581333 1692183..1692851 1 NC_008686.1 KEGG: pfo:Pfl_2971 hypothetical protein; hypothetical protein 1692851 4581333 Pden_1707 Paracoccus denitrificans PD1222 hypothetical protein YP_915500.1 1692183 D 318586 CDS YP_915501.1 119384445 4581334 1692844..1694565 1 NC_008686.1 PFAM: ABC transporter, transmembrane region; ABC transporter related; SMART: AAA ATPase; KEGG: pfl:PFL_4134 ABC transporter, ATP-binding protein, MsbA family; ABC transporter 1694565 4581334 Pden_1708 Paracoccus denitrificans PD1222 ABC transporter YP_915501.1 1692844 D 318586 CDS YP_915502.1 119384446 4581335 complement(1694469..1695449) 1 NC_008686.1 PFAM: helix-turn-helix- domain containing protein, AraC type; KEGG: nar:Saro_2605 transcriptional regulator, AraC family; Fis family transcriptional regulator 1695449 4581335 Pden_1709 Paracoccus denitrificans PD1222 Fis family transcriptional regulator YP_915502.1 1694469 R 318586 CDS YP_915503.1 119384447 4581336 1695772..1697175 1 NC_008686.1 PFAM: aldehyde dehydrogenase; KEGG: nar:Saro_1692 aldehyde dehydrogenase; betaine aldehyde dehydrogenase 1697175 4581336 Pden_1710 Paracoccus denitrificans PD1222 betaine aldehyde dehydrogenase YP_915503.1 1695772 D 318586 CDS YP_915504.1 119384448 4581337 complement(1697230..1697835) 1 NC_008686.1 KEGG: nwi:Nwi_2052 hypothetical protein; hypothetical protein 1697835 4581337 Pden_1711 Paracoccus denitrificans PD1222 hypothetical protein YP_915504.1 1697230 R 318586 CDS YP_915505.1 119384449 4581338 complement(1697832..1699442) 1 NC_008686.1 PFAM: glucose-methanol-choline oxidoreductase; GMC oxidoreductase; KEGG: rsp:RSP_3292 glucose-methanol-choline oxidoreductase; glucose-methanol-choline oxidoreductase 1699442 4581338 Pden_1712 Paracoccus denitrificans PD1222 glucose-methanol-choline oxidoreductase YP_915505.1 1697832 R 318586 CDS YP_915506.1 119384450 4581339 complement(1699474..1700472) 1 NC_008686.1 PFAM: inner-membrane translocator; KEGG: rsp:RSP_3293 ABC branched-chain amino acid transporter, inner membrane subunit; inner-membrane translocator 1700472 4581339 Pden_1713 Paracoccus denitrificans PD1222 inner-membrane translocator YP_915506.1 1699474 R 318586 CDS YP_915507.1 119384451 4581340 complement(1700474..1701361) 1 NC_008686.1 PFAM: inner-membrane translocator; KEGG: rsp:RSP_3294 ABC branched-chain amino acid transporter, inner membrane subunit; inner-membrane translocator 1701361 4581340 Pden_1714 Paracoccus denitrificans PD1222 inner-membrane translocator YP_915507.1 1700474 R 318586 CDS YP_915508.1 119384452 4581341 complement(1701363..1702067) 1 NC_008686.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rsp:RSP_3295 ABC branched-chain amino acid transporter, ATPase subunit; ABC transporter 1702067 4581341 Pden_1715 Paracoccus denitrificans PD1222 ABC transporter YP_915508.1 1701363 R 318586 CDS YP_915509.1 119384453 4580978 complement(1702064..1702840) 1 NC_008686.1 PFAM: ABC transporter related; KEGG: rsp:RSP_3296 ABC branched-chain amino acid transporter, ATPase subunit; ABC transporter 1702840 4580978 Pden_1716 Paracoccus denitrificans PD1222 ABC transporter YP_915509.1 1702064 R 318586 CDS YP_915510.1 119384454 4580979 complement(1702840..1704039) 1 NC_008686.1 KEGG: rsp:RSP_3297 ABC branched-chain amino acid transporter, periplasmic binding protein; branched chain amino acid ABC transporter substrate-binding protein 1704039 4580979 Pden_1717 Paracoccus denitrificans PD1222 branched chain amino acid ABC transporter substrate-binding protein YP_915510.1 1702840 R 318586 CDS YP_915511.1 119384455 4580980 1704227..1705144 1 NC_008686.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: rsp:RSP_3298 transcriptional regulator, LysR family; LysR family transcriptional regulator 1705144 4580980 Pden_1718 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_915511.1 1704227 D 318586 CDS YP_915512.1 119384456 4580981 complement(1705314..1706825) 1 NC_008686.1 catalyzes the formation of malonyl-CoA from malonate and CoA; malonyl-CoA synthase 1706825 4580981 Pden_1719 Paracoccus denitrificans PD1222 malonyl-CoA synthase YP_915512.1 1705314 R 318586 CDS YP_915513.1 119384457 4580982 complement(1706842..1708212) 1 NC_008686.1 PFAM: Malonyl-CoA decarboxylase; KEGG: rpb:RPB_0704 malonyl-CoA decarboxylase; malonyl-CoA decarboxylase 1708212 4580982 Pden_1720 Paracoccus denitrificans PD1222 malonyl-CoA decarboxylase YP_915513.1 1706842 R 318586 CDS YP_915514.1 119384458 4580983 complement(1708247..1709629) 1 NC_008686.1 PFAM: Citrate transporter; Dicarboxylate carrier MatC domain protein; KEGG: rha:RHA1_ro02937 possible dicarboxylate carrier protein; dicarboxylate carrier MatC domain-containing protein 1709629 4580983 Pden_1721 Paracoccus denitrificans PD1222 dicarboxylate carrier MatC domain-containing protein YP_915514.1 1708247 R 318586 CDS YP_915515.1 119384459 4580984 1709821..1710477 1 NC_008686.1 PFAM: regulatory protein GntR, HTH; GntR domain protein; KEGG: dar:Daro_4024 regulatory protein GntR, HTH:GntR, C-terminal; GntR family transcriptional regulator 1710477 4580984 Pden_1722 Paracoccus denitrificans PD1222 GntR family transcriptional regulator YP_915515.1 1709821 D 318586 CDS YP_915516.1 119384460 4580985 1710559..1711242 1 NC_008686.1 KEGG: bxe:Bxe_C1278 hypothetical protein; hypothetical protein 1711242 4580985 Pden_1723 Paracoccus denitrificans PD1222 hypothetical protein YP_915516.1 1710559 D 318586 CDS YP_915517.1 119384461 4580986 1711267..1712628 1 NC_008686.1 KEGG: bbr:BB1601 hypothetical protein; hypothetical protein 1712628 4580986 Pden_1724 Paracoccus denitrificans PD1222 hypothetical protein YP_915517.1 1711267 D 318586 CDS YP_915518.1 119384462 4580987 complement(1712600..1713151) 1 NC_008686.1 hypothetical protein 1713151 4580987 Pden_1725 Paracoccus denitrificans PD1222 hypothetical protein YP_915518.1 1712600 R 318586 CDS YP_915519.1 119384463 4580988 complement(1713148..1713696) 1 NC_008686.1 KEGG: sme:SMc02592 hypothetical protein; hypothetical protein 1713696 4580988 Pden_1726 Paracoccus denitrificans PD1222 hypothetical protein YP_915519.1 1713148 R 318586 CDS YP_915520.1 119384464 4580989 complement(1713693..1714220) 1 NC_008686.1 KEGG: sme:SMc02593 hypothetical protein; hypothetical protein 1714220 4580989 Pden_1727 Paracoccus denitrificans PD1222 hypothetical protein YP_915520.1 1713693 R 318586 CDS YP_915521.1 119384465 4580990 1714648..1716132 1 NC_008686.1 PFAM: CHAD domain containing protein; adenylate cyclase; KEGG: mlo:mll9114 hypothetical protein; CHAD domain-containing protein 1716132 4580990 Pden_1728 Paracoccus denitrificans PD1222 CHAD domain-containing protein YP_915521.1 1714648 D 318586 CDS YP_915522.1 119384466 4580991 complement(1716154..1717272) 1 NC_008686.1 TIGRFAM: alanine dehydrogenase; PFAM: D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding; alanine dehydrogenase/PNT domain protein; KEGG: sit:TM1040_3628 alanine dehydrogenase; alanine dehydrogenase 1717272 4580991 Pden_1729 Paracoccus denitrificans PD1222 alanine dehydrogenase YP_915522.1 1716154 R 318586 CDS YP_915523.1 119384467 4580992 1717674..1718153 1 NC_008686.1 hypothetical protein 1718153 4580992 Pden_1730 Paracoccus denitrificans PD1222 hypothetical protein YP_915523.1 1717674 D 318586 CDS YP_915524.1 119384468 4580993 1718248..1720026 1 NC_008686.1 TIGRFAM: sulfate transporter; PFAM: Sulfate transporter/antisigma-factor antagonist STAS; sulphate transporter; KEGG: sit:TM1040_3648 sulfate permease; sulfate transporter 1720026 4580993 Pden_1731 Paracoccus denitrificans PD1222 sulfate transporter YP_915524.1 1718248 D 318586 CDS YP_915525.1 119384469 4580994 1720321..1721295 1 NC_008686.1 KEGG: sil:SPO3222 glutathione S-transferase; glutathione S-transferase 1721295 4580994 Pden_1732 Paracoccus denitrificans PD1222 glutathione S-transferase YP_915525.1 1720321 D 318586 CDS YP_915526.1 119384470 4580995 1721402..1722316 1 NC_008686.1 PFAM: iron permease FTR1; KEGG: rru:Rru_A2597 iron permease FTR1; iron permease 1722316 4580995 Pden_1733 Paracoccus denitrificans PD1222 iron permease YP_915526.1 1721402 D 318586 CDS YP_915527.1 119384471 4580996 1722313..1723470 1 NC_008686.1 PFAM: protein of unknown function DUF451; KEGG: rru:Rru_A2598 hypothetical protein; hypothetical protein 1723470 4580996 Pden_1734 Paracoccus denitrificans PD1222 hypothetical protein YP_915527.1 1722313 D 318586 CDS YP_915528.1 119384472 4580997 1723472..1724776 1 NC_008686.1 TIGRFAM: Dyp-type peroxidase family; PFAM: Dyp-type peroxidase; KEGG: rru:Rru_A2599 Tat-translocated enzyme; Dyp-type peroxidase family protein 1724776 4580997 Pden_1735 Paracoccus denitrificans PD1222 Dyp-type peroxidase family protein YP_915528.1 1723472 D 318586 CDS YP_915529.1 119384473 4581246 1724819..1725646 1 NC_008686.1 PFAM: protein of unknown function DUF451; KEGG: rru:Rru_A2600 protein of unknown function DUF451; hypothetical protein 1725646 4581246 Pden_1736 Paracoccus denitrificans PD1222 hypothetical protein YP_915529.1 1724819 D 318586 CDS YP_915530.1 119384474 4581247 complement(1726093..1726992) 1 NC_008686.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: ret:RHE_CH00925 probable transcriptional regulator protein, LysR family; LysR family transcriptional regulator 1726992 4581247 Pden_1737 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_915530.1 1726093 R 318586 CDS YP_915531.1 119384475 4581248 1727097..1728326 1 NC_008686.1 PFAM: creatinase; peptidase M24; KEGG: rxy:Rxyl_0461 creatinase; creatinase 1728326 4581248 Pden_1738 Paracoccus denitrificans PD1222 creatinase YP_915531.1 1727097 D 318586 CDS YP_915532.1 119384476 4581249 1728497..1729609 1 NC_008686.1 KEGG: rsp:RSP_1883 ABC polyamine/opine transporter, periplasmic substrate-binding protein; polyamine/opine ABC transporter substrate-binding protein 1729609 4581249 Pden_1739 Paracoccus denitrificans PD1222 polyamine/opine ABC transporter substrate-binding protein YP_915532.1 1728497 D 318586 CDS YP_915533.1 119384477 4581250 complement(1729955..1730197) 1 NC_008686.1 KEGG: rde:RD1_2835 hypothetical protein; hypothetical protein 1730197 4581250 Pden_1740 Paracoccus denitrificans PD1222 hypothetical protein YP_915533.1 1729955 R 318586 CDS YP_915534.1 119384478 4581251 1730480..1730707 1 NC_008686.1 KEGG: sit:TM1040_1503 conserved hypothetical protein; hypothetical protein 1730707 4581251 Pden_1741 Paracoccus denitrificans PD1222 hypothetical protein YP_915534.1 1730480 D 318586 CDS YP_915535.1 119384479 4581252 1730709..1731158 1 NC_008686.1 hydrolyzes D-tyrosyl-tRNA(Tyr) into D-tyrosine and free tRNA(Tyr); possible defense mechanism against a harmful effect of D-tyrosine; D-tyrosyl-tRNA(Tyr) deacylase 1731158 4581252 Pden_1742 Paracoccus denitrificans PD1222 D-tyrosyl-tRNA(Tyr) deacylase YP_915535.1 1730709 D 318586 CDS YP_915536.1 119384480 4581253 1731341..1732780 1 NC_008686.1 PFAM: helicase domain protein; DEAD/DEAH box helicase domain protein; SMART: DEAD-like helicases-like; KEGG: rsp:RSP_0819 DEAD/DEAH box helicase; DEAD/DEAH box helicase 1732780 4581253 Pden_1743 Paracoccus denitrificans PD1222 DEAD/DEAH box helicase YP_915536.1 1731341 D 318586 CDS YP_915537.1 119384481 4581254 1732864..1733442 1 NC_008686.1 catalyzes the formation of thymidine 5'-phosphate from thymidine; thymidine kinase 1733442 4581254 Pden_1744 Paracoccus denitrificans PD1222 thymidine kinase YP_915537.1 1732864 D 318586 CDS YP_915538.1 119384482 4581255 1733439..1734659 1 NC_008686.1 PFAM: YceI family protein; cytochrome B561; KEGG: sit:TM1040_1049 cytochrome b561; cytochrome B561 1734659 4581255 Pden_1745 Paracoccus denitrificans PD1222 cytochrome B561 YP_915538.1 1733439 D 318586 CDS YP_915539.1 119384483 4581256 complement(1734782..1735204) 1 NC_008686.1 catalyzes the formation of nucleoside triphosphate from ATP and nucleoside diphosphate; nucleoside diphosphate kinase 1735204 ndk 4581256 ndk Paracoccus denitrificans PD1222 nucleoside diphosphate kinase YP_915539.1 1734782 R 318586 CDS YP_915540.1 119384484 4581257 1735334..1737181 1 NC_008686.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rsp:RSP_2895 ABC transporter, fused ATPase subunits; ABC transporter 1737181 4581257 Pden_1747 Paracoccus denitrificans PD1222 ABC transporter YP_915540.1 1735334 D 318586 CDS YP_915541.1 119384485 4581258 1737281..1738009 1 NC_008686.1 PFAM: MltA-interacting MipA family protein; KEGG: rpc:RPC_0793 MltA-interacting MipA; MltA-interacting MipA family protein 1738009 4581258 Pden_1748 Paracoccus denitrificans PD1222 MltA-interacting MipA family protein YP_915541.1 1737281 D 318586 CDS YP_915542.1 119384486 4581259 1738074..1738433 1 NC_008686.1 PFAM: protein of unknown function DUF59; KEGG: rde:RD1_2957 hypothetical protein; hypothetical protein 1738433 4581259 Pden_1749 Paracoccus denitrificans PD1222 hypothetical protein YP_915542.1 1738074 D 318586 CDS YP_915543.1 119384487 4581260 1738430..1738978 1 NC_008686.1 PFAM: transferase hexapeptide repeat containing protein; KEGG: rde:RD1_2959 maltose O-acetyltransferase; hexapaptide repeat-containing transferase 1738978 4581260 Pden_1750 Paracoccus denitrificans PD1222 hexapaptide repeat-containing transferase YP_915543.1 1738430 D 318586 CDS YP_915544.1 119384488 4581261 complement(1738985..1739554) 1 NC_008686.1 PFAM: Phosphoglycerate mutase; KEGG: rde:RD1_2834 phosphoglycerate mutase; phosphoglycerate mutase 1739554 4581261 Pden_1751 Paracoccus denitrificans PD1222 phosphoglycerate mutase YP_915544.1 1738985 R 318586 CDS YP_915545.1 119384489 4581262 complement(1739545..1740405) 1 NC_008686.1 catalyzes the conversion of the propionic acid groups of rings I and III to vinyl groups during heme synthesis; coproporphyrinogen III oxidase 1740405 4581262 Pden_1752 Paracoccus denitrificans PD1222 coproporphyrinogen III oxidase YP_915545.1 1739545 R 318586 CDS YP_915546.1 119384490 4581263 1740461..1740901 1 NC_008686.1 KEGG: rsp:RSP_0683 hypothetical protein; hypothetical protein 1740901 4581263 Pden_1753 Paracoccus denitrificans PD1222 hypothetical protein YP_915546.1 1740461 D 318586 CDS YP_915547.1 119384491 4581264 complement(1740906..1741715) 1 NC_008686.1 PFAM: short-chain dehydrogenase/reductase SDR; KEGG: rsp:RSP_0684 possible oxidoreductase; short-chain dehydrogenase/reductase SDR; short-chain dehydrogenase/reductase SDR 1741715 4581264 Pden_1754 Paracoccus denitrificans PD1222 short-chain dehydrogenase/reductase SDR YP_915547.1 1740906 R 318586 CDS YP_915548.1 119384492 4580919 complement(1741712..1742746) 1 NC_008686.1 PFAM: methyltransferase small; KEGG: rsp:RSP_0685 possible ribosomal RNA small subunit methyltransferase C RsmC; methyltransferase small 1742746 4580919 Pden_1755 Paracoccus denitrificans PD1222 methyltransferase small YP_915548.1 1741712 R 318586 CDS YP_915549.1 119384493 4580920 complement(1742750..1743067) 1 NC_008686.1 PFAM: ATP-dependent Clp protease adaptor protein ClpS; KEGG: sit:TM1040_2534 ATP-dependent Clp protease adaptor protein ClpS; ATP-dependent Clp protease adaptor protein ClpS 1743067 4580920 Pden_1756 Paracoccus denitrificans PD1222 ATP-dependent Clp protease adaptor protein ClpS YP_915549.1 1742750 R 318586 CDS YP_915550.1 119384494 4580921 1743278..1744984 1 NC_008686.1 PFAM: beta-lactamase; peptidase S11, D-alanyl-D-alanine carboxypeptidase 1; KEGG: rsp:RSP_0688 probable penicillin-binding protein; serine-type D-Ala-D-Ala carboxypeptidase 1744984 4580921 Pden_1757 Paracoccus denitrificans PD1222 serine-type D-Ala-D-Ala carboxypeptidase YP_915550.1 1743278 D 318586 CDS YP_915551.1 119384495 4580922 complement(1745177..1745638) 1 NC_008686.1 PFAM: regulatory protein, AsnC/Lrp family; KEGG: rsp:RSP_1867 transcriptional regulator, AsnC family; AsnC family transcriptional regulator 1745638 4580922 Pden_1758 Paracoccus denitrificans PD1222 AsnC family transcriptional regulator YP_915551.1 1745177 R 318586 CDS YP_915552.1 119384496 4580923 complement(1745635..1746090) 1 NC_008686.1 PFAM: regulatory protein, AsnC/Lrp family; Helix-turn-helix, type 11 domain protein; KEGG: rsp:RSP_1866 transcriptional regulator, AsnC family; AsnC family transcriptional regulator 1746090 4580923 Pden_1759 Paracoccus denitrificans PD1222 AsnC family transcriptional regulator YP_915552.1 1745635 R 318586 CDS YP_915553.1 119384497 4580924 1746218..1747240 1 NC_008686.1 catalyzes the formation of (R)-2,3-dihydroxy-3-methylbutanoate from (S)-2-hydroxy-2-methyl-3-oxobutanoate in valine and isoleucine biosynthesis; ketol-acid reductoisomerase 1747240 4580924 Pden_1760 Paracoccus denitrificans PD1222 ketol-acid reductoisomerase YP_915553.1 1746218 D 318586 CDS YP_915554.1 119384498 4580925 1747542..1748414 1 NC_008686.1 PFAM: protein of unknown function DUF6, transmembrane; KEGG: rsp:RSP_1649 possible transporter, DMT superfamily; hypothetical protein 1748414 4580925 Pden_1761 Paracoccus denitrificans PD1222 hypothetical protein YP_915554.1 1747542 D 318586 CDS YP_915555.1 119384499 4580926 complement(1748469..1751939) 1 NC_008686.1 catalyzes DNA-template-directed extension of the 3'- end of a DNA strand by one nucleotide at a time; main replicative polymerase; DNA polymerase III subunit alpha 1751939 dnaE 4580926 dnaE Paracoccus denitrificans PD1222 DNA polymerase III subunit alpha YP_915555.1 1748469 R 318586 CDS YP_915556.1 119384500 4580927 1752032..1753546 1 NC_008686.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rde:RD1_4071 sugar ABC transporter, ATP-binding protein; ABC transporter 1753546 4580927 Pden_1763 Paracoccus denitrificans PD1222 ABC transporter YP_915556.1 1752032 D 318586 CDS YP_915557.1 119384501 4580928 1753533..1754603 1 NC_008686.1 PFAM: inner-membrane translocator; KEGG: sit:TM1040_0495 inner-membrane translocator; inner-membrane translocator 1754603 4580928 Pden_1764 Paracoccus denitrificans PD1222 inner-membrane translocator YP_915557.1 1753533 D 318586 CDS YP_915558.1 119384502 4580929 1754600..1755490 1 NC_008686.1 PFAM: inner-membrane translocator; KEGG: sil:SPO0649 sugar ABC transporter, permease protein; inner-membrane translocator 1755490 4580929 Pden_1765 Paracoccus denitrificans PD1222 inner-membrane translocator YP_915558.1 1754600 D 318586 CDS YP_915559.1 119384503 4580930 1755514..1756590 1 NC_008686.1 PFAM: basic membrane lipoprotein; KEGG: rsp:RSP_3560 possible ABC transporter, periplasmic binding protein; basic membrane lipoprotein 1756590 4580930 Pden_1766 Paracoccus denitrificans PD1222 basic membrane lipoprotein YP_915559.1 1755514 D 318586 CDS YP_915560.1 119384504 4580931 complement(1756646..1757119) 1 NC_008686.1 PFAM: Ferritin, Dps family protein; KEGG: gbe:GbCGDNIH1_0685 ferroxidase; ferritin 1757119 4580931 Pden_1767 Paracoccus denitrificans PD1222 ferritin YP_915560.1 1756646 R 318586 CDS YP_915561.1 119384505 4580932 complement(1757265..1757498) 1 NC_008686.1 carries the fatty acid chain in fatty acid biosynthesis; acyl carrier protein 1757498 acpP 4580932 acpP Paracoccus denitrificans PD1222 acyl carrier protein YP_915561.1 1757265 R 318586 CDS YP_915562.1 119384506 4580933 complement(1757635..1758372) 1 NC_008686.1 TIGRFAM: 3-oxoacyl-(acyl-carrier-protein) reductase; PFAM: short-chain dehydrogenase/reductase SDR; KR; KEGG: sit:TM1040_1051 3-oxoacyl-(acyl-carrier-protein) reductase; 3-oxoacyl-(acyl-carrier-protein) reductase 1758372 4580933 Pden_1769 Paracoccus denitrificans PD1222 3-oxoacyl-(acyl-carrier-protein) reductase YP_915562.1 1757635 R 318586 CDS YP_915563.1 119384507 4580934 complement(1758436..1759362) 1 NC_008686.1 TIGRFAM: malonyl CoA-acyl carrier protein transacylase; PFAM: acyl transferase domain protein; KEGG: sit:TM1040_1050 malonyl CoA-acyl carrier protein transacylase; malonyl CoA-ACP transacylase 1759362 4580934 Pden_1770 Paracoccus denitrificans PD1222 malonyl CoA-ACP transacylase YP_915563.1 1758436 R 318586 CDS YP_915564.1 119384508 4580935 complement(1759435..1760772) 1 NC_008686.1 PFAM: ATP-binding region, ATPase domain protein domain protein; histidine kinase, HAMP region domain protein; histidine kinase A domain protein domain protein; KEGG: sil:SPO2173 sensor histidine kinase; integral membrane sensor signal transduction histidine kinase 1760772 4580935 Pden_1771 Paracoccus denitrificans PD1222 integral membrane sensor signal transduction histidine kinase YP_915564.1 1759435 R 318586 CDS YP_915565.1 119384509 4580936 1760831..1761697 1 NC_008686.1 PFAM: beta-lactamase domain protein; KEGG: sil:SPO2174 metallo-beta-lactamase family protein; beta-lactamase domain-containing protein 1761697 4580936 Pden_1772 Paracoccus denitrificans PD1222 beta-lactamase domain-containing protein YP_915565.1 1760831 D 318586 CDS YP_915566.1 119384510 4580937 complement(1762154..1763218) 1 NC_008686.1 PFAM: Siderophore-interacting protein; FAD-binding 9, siderophore-interacting domain protein; KEGG: mes:Meso_0336 siderophore-interacting protein; siderophore-interacting protein 1763218 4580937 Pden_1773 Paracoccus denitrificans PD1222 siderophore-interacting protein YP_915566.1 1762154 R 318586 CDS YP_915567.1 119384511 4580938 complement(1763222..1764313) 1 NC_008686.1 KEGG: rpc:RPC_3611 periplasmic binding protein; periplasmic binding protein 1764313 4580938 Pden_1774 Paracoccus denitrificans PD1222 periplasmic binding protein YP_915567.1 1763222 R 318586 CDS YP_915568.1 119384512 4580959 complement(1764315..1766480) 1 NC_008686.1 TIGRFAM: TonB-dependent siderophore receptor; PFAM: TonB-dependent receptor; TonB-dependent receptor, plug; KEGG: neu:NE1097 TonB-dependent receptor protein; TonB-dependent siderophore receptor 1766480 4580959 Pden_1775 Paracoccus denitrificans PD1222 TonB-dependent siderophore receptor YP_915568.1 1764315 R 318586 CDS YP_915569.1 119384513 4580960 1766649..1767638 1 NC_008686.1 PFAM: helix-turn-helix- domain containing protein, AraC type; KEGG: bam:Bamb_1692 transcriptional regulator, AraC family; helix-turn-helix domain-containing protein 1767638 4580960 Pden_1776 Paracoccus denitrificans PD1222 helix-turn-helix domain-containing protein YP_915569.1 1766649 D 318586 CDS YP_915570.1 119384514 4580961 1767766..1769595 1 NC_008686.1 PFAM: Citrate transporter; TrkA-C domain protein; TRAP C4-dicarboxylate transport system permease DctM subunit; KEGG: pau:PA14_14360 sodium/sulphate transporter; citrate transporter 1769595 4580961 Pden_1777 Paracoccus denitrificans PD1222 citrate transporter YP_915570.1 1767766 D 318586 CDS YP_915571.1 119384515 4580962 complement(1769921..1771135) 1 NC_008686.1 TIGRFAM: drug resistance transporter, Bcr/CflA subfamily; PFAM: major facilitator superfamily MFS_1; KEGG: rsp:RSP_2851 multidrug (bicyclomycin) efflux pump, major facilitator superfamily (MFS); Bcr/CflA subfamily drug resistance transporter 1771135 4580962 Pden_1778 Paracoccus denitrificans PD1222 Bcr/CflA subfamily drug resistance transporter YP_915571.1 1769921 R 318586 CDS YP_915572.1 119384516 4580963 1771246..1771668 1 NC_008686.1 PFAM: Uncharacterized conserved protein UCP032025; KEGG: rsp:RSP_3548 hypothetical protein; hypothetical protein 1771668 4580963 Pden_1779 Paracoccus denitrificans PD1222 hypothetical protein YP_915572.1 1771246 D 318586 CDS YP_915573.1 119384517 4580964 1772014..1773369 1 NC_008686.1 TIGRFAM: efflux transporter, RND family, MFP subunit; PFAM: secretion protein HlyD family protein; KEGG: rsp:RSP_3321 cation/multidrug efflux pump, membrane-fusion protein; RND family efflux transporter MFP subunit 1773369 4580964 Pden_1780 Paracoccus denitrificans PD1222 RND family efflux transporter MFP subunit YP_915573.1 1772014 D 318586 CDS YP_915574.1 119384518 4580965 1773407..1775482 1 NC_008686.1 TIGRFAM: transporter, hydrophobe/amphiphile efflux-1 (HAE1) family; PFAM: acriflavin resistance protein; KEGG: rsp:RSP_3318 cation/multidrug efflux pump, RND family; hydrophobe/amphiphile efflux-1 (HAE1) family protein 1775482 4580965 Pden_1781 Paracoccus denitrificans PD1222 hydrophobe/amphiphile efflux-1 (HAE1) family protein YP_915574.1 1773407 D 318586 CDS YP_915575.1 119384519 4580966 1775454..1776539 1 NC_008686.1 KEGG: rsp:RSP_3318 cation/multidrug efflux pump, RND family; cation efflux transporter 1776539 4580966 Pden_1782 Paracoccus denitrificans PD1222 cation efflux transporter YP_915575.1 1775454 D 318586 CDS YP_915576.1 119384520 4580967 1776681..1778087 1 NC_008686.1 PFAM: ATP-binding region, ATPase domain protein domain protein; histidine kinase, HAMP region domain protein; histidine kinase, dimerisation and phosphoacceptor region; KEGG: rpe:RPE_2819 signal transduction histidine kinase, glucose-6-phosphate specific; integral membrane sensor signal transduction histidine kinase 1778087 4580967 Pden_1783 Paracoccus denitrificans PD1222 integral membrane sensor signal transduction histidine kinase YP_915576.1 1776681 D 318586 CDS YP_915577.1 119384521 4580968 1778084..1778758 1 NC_008686.1 PFAM: regulatory protein, LuxR; response regulator receiver; KEGG: rpe:RPE_3142 two component transcriptional regulator, LuxR family; LuxR family transcriptional regulator 1778758 4580968 Pden_1784 Paracoccus denitrificans PD1222 LuxR family transcriptional regulator YP_915577.1 1778084 D 318586 CDS YP_915578.1 119384522 4580969 1778762..1780048 1 NC_008686.1 PFAM: helix-turn-helix domain protein; KEGG: rsp:RSP_0172 predicted transcriptional regulators; helix-turn-helix domain-containing protein 1780048 4580969 Pden_1785 Paracoccus denitrificans PD1222 helix-turn-helix domain-containing protein YP_915578.1 1778762 D 318586 CDS YP_915579.1 119384523 4580970 1780107..1780469 1 NC_008686.1 PFAM: response regulator receiver; KEGG: rde:RD1_2841 response regulator receiver domain protein; response regulator receiver protein 1780469 4580970 Pden_1786 Paracoccus denitrificans PD1222 response regulator receiver protein YP_915579.1 1780107 D 318586 CDS YP_915580.1 119384524 4580971 1780478..1780720 1 NC_008686.1 KEGG: rsp:RSP_0170 hypothetical protein; hypothetical protein 1780720 4580971 Pden_1787 Paracoccus denitrificans PD1222 hypothetical protein YP_915580.1 1780478 D 318586 CDS YP_915581.1 119384525 4580972 1780710..1783367 1 NC_008686.1 PFAM: ATP-binding region, ATPase domain protein domain protein; histidine kinase A domain protein domain protein; KEGG: rsp:RSP_0169 Na+/solute symporter; integral membrane sensor signal transduction histidine kinase 1783367 4580972 Pden_1788 Paracoccus denitrificans PD1222 integral membrane sensor signal transduction histidine kinase YP_915581.1 1780710 D 318586 CDS YP_915582.1 119384526 4580973 1783427..1784605 1 NC_008686.1 PFAM: surface presentation of antigens (SPOA) protein; KEGG: rsp:RSP_6099 possible flagellar switch protein FliM; surface presentation of antigens (SPOA) protein 1784605 4580973 Pden_1789 Paracoccus denitrificans PD1222 surface presentation of antigens (SPOA) protein YP_915582.1 1783427 D 318586 CDS YP_915583.1 119384527 4580974 1784790..1785008 1 NC_008686.1 stimulates the activities of the other two initiation factors, IF-2 and IF-3; translation initiation factor IF-1 1785008 infA 4580974 infA Paracoccus denitrificans PD1222 translation initiation factor IF-1 YP_915583.1 1784790 D 318586 CDS YP_915584.1 119384528 4580975 1785037..1785678 1 NC_008686.1 TIGRFAM: maf protein; PFAM: Maf family protein; KEGG: rsp:RSP_0625 Maf-like protein; maf protein 1785678 4580975 Pden_1791 Paracoccus denitrificans PD1222 maf protein YP_915584.1 1785037 D 318586 CDS YP_915585.1 119384529 4580976 1785675..1786736 1 NC_008686.1 KEGG: rsp:RSP_0624 ribonuclease; ribonuclease 1786736 4580976 Pden_1792 Paracoccus denitrificans PD1222 ribonuclease YP_915585.1 1785675 D 318586 CDS YP_915586.1 119384530 4580977 1786733..1786882 1 NC_008686.1 PFAM: protein of unknown function DUF329; KEGG: rpe:RPE_4479 protein of unknown function DUF329; hypothetical protein 1786882 4580977 Pden_1793 Paracoccus denitrificans PD1222 hypothetical protein YP_915586.1 1786733 D 318586 CDS YP_915587.1 119384531 4580494 complement(1787121..1787453) 1 NC_008686.1 hypothetical protein 1787453 4580494 Pden_1794 Paracoccus denitrificans PD1222 hypothetical protein YP_915587.1 1787121 R 318586 CDS YP_915588.1 119384532 4580495 complement(1787522..1788787) 1 NC_008686.1 PFAM: Allergen V5/Tpx-1 family protein; Hemolysin-type calcium-binding region; KEGG: eba:ebA7184 hypothetical protein; Allergen V5/Tpx-1 family protein 1788787 4580495 Pden_1795 Paracoccus denitrificans PD1222 Allergen V5/Tpx-1 family protein YP_915588.1 1787522 R 318586 CDS YP_915589.1 119384533 4580496 complement(1789095..1789577) 1 NC_008686.1 PFAM: GCN5-related N-acetyltransferase; KEGG: rsp:RSP_2081 acetyltransferase, GNAT family; N-acetyltransferase 1789577 4580496 Pden_1796 Paracoccus denitrificans PD1222 N-acetyltransferase YP_915589.1 1789095 R 318586 CDS YP_915590.1 119384534 4580497 1789856..1790971 1 NC_008686.1 KEGG: rsp:RSP_3696 ABC sulfate/thiosulfate transporter, ATPase subunit CysA; TIGRFAM: sulfate ABC transporter, ATPase subunit; PFAM: ABC transporter related; SMART: AAA ATPase; sulfate ABC transporter ATPase 1790971 4580497 Pden_1797 Paracoccus denitrificans PD1222 sulfate ABC transporter ATPase YP_915590.1 1789856 D 318586 CDS YP_915591.1 119384535 4580498 1790968..1791966 1 NC_008686.1 TIGRFAM: sulfate ABC transporter, periplasmic sulfate-binding protein; KEGG: rsp:RSP_3697 ABC sulfate/thiosulfate transporter, periplasmic binding protein CysP; sulfate ABC transporter substrate-binding protein 1791966 4580498 Pden_1798 Paracoccus denitrificans PD1222 sulfate ABC transporter substrate-binding protein YP_915591.1 1790968 D 318586 CDS YP_915592.1 119384536 4580499 1791963..1792808 1 NC_008686.1 TIGRFAM: sulfate ABC transporter, inner membrane subunit; sulfate ABC transporter, inner membrane subunit CysT; PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: rsp:RSP_3698 ABC sulfate/thiosulfate transporter, inner membrane subunit CysT; sulfate ABC transporter inner membrane subunit CysT 1792808 4580499 Pden_1799 Paracoccus denitrificans PD1222 sulfate ABC transporter inner membrane subunit CysT YP_915592.1 1791963 D 318586 CDS YP_915593.1 119384537 4580500 1792805..1793632 1 NC_008686.1 TIGRFAM: sulfate ABC transporter, inner membrane subunit; sulfate ABC transporter, inner membrane subunit CysW; PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: rsp:RSP_3699 ABC sulfate/thiosulfate transporter, inner membrane subunit CysW; sulfate ABC transporter inner membrane subunit CysW 1793632 4580500 Pden_1800 Paracoccus denitrificans PD1222 sulfate ABC transporter inner membrane subunit CysW YP_915593.1 1792805 D 318586 CDS YP_915594.1 119384538 4580501 1793695..1794420 1 NC_008686.1 PFAM: heat shock protein DnaJ domain protein; KEGG: rsp:RSP_0785 heat shock protein DnaJ; molecular chaperone DnaJ 1794420 4580501 Pden_1801 Paracoccus denitrificans PD1222 molecular chaperone DnaJ YP_915594.1 1793695 D 318586 CDS YP_915595.1 119384539 4580502 1794477..1794962 1 NC_008686.1 KEGG: rsp:RSP_6229 hypothetical protein; hypothetical protein 1794962 4580502 Pden_1802 Paracoccus denitrificans PD1222 hypothetical protein YP_915595.1 1794477 D 318586 CDS YP_915596.1 119384540 4580503 complement(1794959..1796176) 1 NC_008686.1 PFAM: glycosyl transferase, group 1; KEGG: rsp:RSP_0700 probable glycosyltransferase; group 1 glycosyl transferase 1796176 4580503 Pden_1803 Paracoccus denitrificans PD1222 group 1 glycosyl transferase YP_915596.1 1794959 R 318586 CDS YP_915597.1 119384541 4580504 complement(1796176..1797789) 1 NC_008686.1 PFAM: ABC transporter related; Oligopeptide/dipeptide ABC transporter, C-terminal domain protein; SMART: AAA ATPase; KEGG: rsp:RSP_0701 ABC peptide transporter, fused ATPase domains; ABC transporter 1797789 4580504 Pden_1804 Paracoccus denitrificans PD1222 ABC transporter YP_915597.1 1796176 R 318586 CDS YP_915598.1 119384542 4580505 complement(1797786..1798892) 1 NC_008686.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: rsp:RSP_0702 ABC peptide transporter, inner membrane subunit; binding-protein-dependent transport system inner membrane protein 1798892 4580505 Pden_1805 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_915598.1 1797786 R 318586 CDS YP_915599.1 119384543 4580506 complement(1798892..1800031) 1 NC_008686.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: rde:RD1_1264 peptide ABC transporter, permease protein; binding-protein-dependent transport system inner membrane protein 1800031 4580506 Pden_1806 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_915599.1 1798892 R 318586 CDS YP_915600.1 119384544 4580507 complement(1800075..1802072) 1 NC_008686.1 PFAM: extracellular solute-binding protein, family 5; KEGG: rsp:RSP_0704 ABC peptide transporter, substrate binding protein; ABC transporter substrate-binding protein 1802072 4580507 Pden_1807 Paracoccus denitrificans PD1222 ABC transporter substrate-binding protein YP_915600.1 1800075 R 318586 CDS YP_915601.1 119384545 4580508 complement(1802128..1802658) 1 NC_008686.1 PFAM: cytochrome c, class I; KEGG: sil:SPO3538 cytochrome c552; cytochrome c, class I 1802658 4580508 Pden_1808 Paracoccus denitrificans PD1222 cytochrome c, class I YP_915601.1 1802128 R 318586 CDS YP_915602.1 119384546 4580509 1802822..1803709 1 NC_008686.1 catalyzes the formation of phenylpyruvate from prephenate in phenylalanine biosynthesis; prephenate dehydratase 1803709 4580509 Pden_1809 Paracoccus denitrificans PD1222 prephenate dehydratase YP_915602.1 1802822 D 318586 CDS YP_915603.1 119384547 4580510 complement(1803749..1804210) 1 NC_008686.1 KEGG: sit:TM1040_0171 conserved hypothetical protein; hypothetical protein 1804210 4580510 Pden_1810 Paracoccus denitrificans PD1222 hypothetical protein YP_915603.1 1803749 R 318586 CDS YP_915604.1 119384548 4580511 1804328..1806226 1 NC_008686.1 PFAM: metallophosphoesterase; 5'-Nucleotidase domain protein; KEGG: sit:TM1040_1036 twin-arginine translocation pathway signal; 5'-nucleotidase 1806226 4580511 Pden_1811 Paracoccus denitrificans PD1222 5'-nucleotidase YP_915604.1 1804328 D 318586 CDS YP_915605.1 119384549 4580512 1806435..1807340 1 NC_008686.1 PFAM: PfkB domain protein; KEGG: sil:SPO2060 kinase, PfkB family; ribokinase-like domain-containing protein 1807340 4580512 Pden_1812 Paracoccus denitrificans PD1222 ribokinase-like domain-containing protein YP_915605.1 1806435 D 318586 CDS YP_915606.1 119384550 4580513 1807328..1808242 1 NC_008686.1 PFAM: Indigoidine synthase A family protein; KEGG: rsp:RSP_2858 IndA involved in pigment biosynthesis; indigoidine synthase A family protein 1808242 4580513 Pden_1813 Paracoccus denitrificans PD1222 indigoidine synthase A family protein YP_915606.1 1807328 D 318586 CDS YP_915607.1 119384551 4578526 complement(1808239..1809294) 1 NC_008686.1 PFAM: Patatin; KEGG: jan:Jann_2313 patatin; patatin 1809294 4578526 Pden_1814 Paracoccus denitrificans PD1222 patatin YP_915607.1 1808239 R 318586 CDS YP_915608.1 119384552 4578527 complement(1809473..1810681) 1 NC_008686.1 recognizes the termination signals UGA and UAA during protein translation a specificity which is dependent on amino acid residues residing in loops of the L-shaped tRNA-like molecule of RF2; in some organisms control of PrfB protein levels is maintained through a +1 ribosomal frameshifting mechanism; this protein is similar to release factor 1; peptide chain release factor 2 1810681 prfB 4578527 prfB Paracoccus denitrificans PD1222 peptide chain release factor 2 YP_915608.1 1809473 R 318586 CDS YP_915609.1 119384553 4578528 complement(1810689..1813226) 1 NC_008686.1 KEGG: rsp:RSP_2978 penicillin-binding protein 1A (PBP-1a); TIGRFAM: penicillin-binding protein, 1A family; PFAM: glycosyl transferase, family 51; penicillin-binding protein, transpeptidase; 1A family penicillin-binding protein 1813226 4578528 Pden_1816 Paracoccus denitrificans PD1222 1A family penicillin-binding protein YP_915609.1 1810689 R 318586 CDS YP_915610.1 119384554 4578529 complement(1813297..1814532) 1 NC_008686.1 PFAM: cell wall hydrolase/autolysin; KEGG: sil:SPO2588 N-acetylmuramoyl-L-alanine amidase, family 3; N-acetylmuramoyl-L-alanine amidase 1814532 4578529 Pden_1817 Paracoccus denitrificans PD1222 N-acetylmuramoyl-L-alanine amidase YP_915610.1 1813297 R 318586 CDS YP_915611.1 119384555 4578530 complement(1814529..1815665) 1 NC_008686.1 PFAM: aminotransferase, class I and II; KEGG: rsp:RSP_2980 aspartate aminotransferase A; class I and II aminotransferase 1815665 4578530 Pden_1818 Paracoccus denitrificans PD1222 class I and II aminotransferase YP_915611.1 1814529 R 318586 CDS YP_915612.1 119384556 4578531 1815801..1816553 1 NC_008686.1 PFAM: DSBA oxidoreductase; KEGG: rde:RD1_2824 outer membrane protein; DSBA oxidoreductase 1816553 4578531 Pden_1819 Paracoccus denitrificans PD1222 DSBA oxidoreductase YP_915612.1 1815801 D 318586 CDS YP_915613.1 119384557 4578532 complement(1816643..1817767) 1 NC_008686.1 catalyzes the conversion of 2C-methyl-D-erythritol 2,4-cyclodiphosphate into 4-hydroxy-3-methyl-2-en-1-yl diphosphate; involved in isoprenoid synthesis; 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase 1817767 ispG 4578532 ispG Paracoccus denitrificans PD1222 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase YP_915613.1 1816643 R 318586 CDS YP_915614.1 119384558 4578533 complement(1817894..1819114) 1 NC_008686.1 KEGG: rsp:RSP_2983 hypothetical protein; hypothetical protein 1819114 4578533 Pden_1821 Paracoccus denitrificans PD1222 hypothetical protein YP_915614.1 1817894 R 318586 CDS YP_915615.1 119384559 4578534 complement(1819224..1820498) 1 NC_008686.1 catalyzes the formation of 5-aminolevulinate from succinyl-CoA and glycine; 5-aminolevulinate synthase 1820498 4578534 Pden_1822 Paracoccus denitrificans PD1222 5-aminolevulinate synthase YP_915615.1 1819224 R 318586 CDS YP_915616.1 119384560 4578535 1820623..1822008 1 NC_008686.1 PFAM: peptidase M20; peptidase dimerisation domain protein; KEGG: rsp:RSP_2986 hypothetical protein; hypothetical protein 1822008 4578535 Pden_1823 Paracoccus denitrificans PD1222 hypothetical protein YP_915616.1 1820623 D 318586 CDS YP_915617.1 119384561 4578536 1822158..1822733 1 NC_008686.1 KEGG: rpa:RPA2196 hypothetical protein; hypothetical protein 1822733 4578536 Pden_1824 Paracoccus denitrificans PD1222 hypothetical protein YP_915617.1 1822158 D 318586 CDS YP_915618.1 119384562 4578537 complement(1822871..1823380) 1 NC_008686.1 PFAM: transcription factor CarD; KEGG: rsp:RSP_2425 CarD-like transcriptional regulator; CarD family transcriptional regulator 1823380 4578537 Pden_1825 Paracoccus denitrificans PD1222 CarD family transcriptional regulator YP_915618.1 1822871 R 318586 CDS YP_915619.1 119384563 4578538 complement(1823834..1824172) 1 NC_008686.1 PFAM: 4Fe-4S ferredoxin, iron-sulfur binding domain protein; KEGG: sit:TM1040_0575 4Fe-4S ferredoxin, iron-sulfur binding; 4Fe-4S ferredoxin 1824172 4578538 Pden_1826 Paracoccus denitrificans PD1222 4Fe-4S ferredoxin YP_915619.1 1823834 R 318586 CDS YP_915620.1 119384564 4578539 complement(1824335..1824604) 1 NC_008686.1 PFAM: RNA-binding S4 domain protein; KEGG: sil:SPO1418 S4 domain protein; RNA-binding S4 domain-containing protein 1824604 4578539 Pden_1827 Paracoccus denitrificans PD1222 RNA-binding S4 domain-containing protein YP_915620.1 1824335 R 318586 CDS YP_915621.1 119384565 4578540 complement(1824601..1827528) 1 NC_008686.1 PFAM: helicase domain protein; KEGG: rsp:RSP_2422 ATP-dependent helicase, MgpS; helicase 1827528 4578540 Pden_1828 Paracoccus denitrificans PD1222 helicase YP_915621.1 1824601 R 318586 CDS YP_915622.1 119384566 4578541 complement(1827530..1828267) 1 NC_008686.1 PFAM: TPR repeat-containing protein; Tetratricopeptide TPR_2 repeat protein; SMART: Tetratricopeptide domain protein; KEGG: rsp:RSP_2421 hypothetical protein; hypothetical protein 1828267 4578541 Pden_1829 Paracoccus denitrificans PD1222 hypothetical protein YP_915622.1 1827530 R 318586 CDS YP_915623.1 119384567 4578542 1828317..1828601 1 NC_008686.1 PFAM: Sterol-binding domain protein; KEGG: jan:Jann_3313 sterol-binding; sterol-binding domain-containing protein 1828601 4578542 Pden_1830 Paracoccus denitrificans PD1222 sterol-binding domain-containing protein YP_915623.1 1828317 D 318586 CDS YP_915624.1 119384568 4578543 1828605..1829549 1 NC_008686.1 PFAM: alpha/beta hydrolase fold; KEGG: sil:SPO1414 hydrolase, alpha/beta fold family; alpha/beta hydrolase 1829549 4578543 Pden_1831 Paracoccus denitrificans PD1222 alpha/beta hydrolase YP_915624.1 1828605 D 318586 CDS YP_915625.1 119384569 4578544 1829638..1831500 1 NC_008686.1 TIGRFAM: oligoendopeptidase, pepF/M3 family; PFAM: peptidase M3A and M3B, thimet/oligopeptidase F; Oligopeptidase F; KEGG: rsp:RSP_2412 oligoendopeptidase F; pepF/M3 family oligoendopeptidase 1831500 4578544 Pden_1832 Paracoccus denitrificans PD1222 pepF/M3 family oligoendopeptidase YP_915625.1 1829638 D 318586 CDS YP_915626.1 119384570 4581017 1831685..1832866 1 NC_008686.1 PFAM: peptidase M19, renal dipeptidase; KEGG: sit:TM1040_0564 peptidase M19, renal dipeptidase; peptidase M19 1832866 4581017 Pden_1833 Paracoccus denitrificans PD1222 peptidase M19 YP_915626.1 1831685 D 318586 CDS YP_915627.1 119384571 4581018 1832903..1833562 1 NC_008686.1 PFAM: Glutathione S-transferase, N-terminal domain; Glutathione S-transferase, C-terminal domain; KEGG: atc:AGR_C_1530 structure of glutathione S-transferase III in apo form; glutathione S-transferase domain-containing protein 1833562 4581018 Pden_1834 Paracoccus denitrificans PD1222 glutathione S-transferase domain-containing protein YP_915627.1 1832903 D 318586 CDS YP_915628.1 119384572 4581019 complement(1833725..1834747) 1 NC_008686.1 PFAM: protein of unknown function DUF344; KEGG: rsp:RSP_0766 hypothetical protein; hypothetical protein 1834747 4581019 Pden_1835 Paracoccus denitrificans PD1222 hypothetical protein YP_915628.1 1833725 R 318586 CDS YP_915629.1 119384573 4581020 1834978..1836948 1 NC_008686.1 decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling; DNA topoisomerase IV subunit B 1836948 4581020 Pden_1836 Paracoccus denitrificans PD1222 DNA topoisomerase IV subunit B YP_915629.1 1834978 D 318586 CDS YP_915630.1 119384574 4581021 1836945..1837280 1 NC_008686.1 PFAM: protein of unknown function UPF0060; KEGG: mag:amb3269 hypothetical protein; hypothetical protein 1837280 4581021 Pden_1837 Paracoccus denitrificans PD1222 hypothetical protein YP_915630.1 1836945 D 318586 CDS YP_915631.1 119384575 4581022 complement(1837363..1837866) 1 NC_008686.1 PFAM: phosphoesterase, PA-phosphatase related; KEGG: cch:Cag_0961 phosphoesterase, PA-phosphatase related; PA-phosphatase-like phosphoesterase 1837866 4581022 Pden_1838 Paracoccus denitrificans PD1222 PA-phosphatase-like phosphoesterase YP_915631.1 1837363 R 318586 CDS YP_915632.1 119384576 4581023 complement(1837863..1838525) 1 NC_008686.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rsp:RSP_0776 ABC lipoprotein efflux transporter, ATPase subunit, LolD; ABC transporter 1838525 4581023 Pden_1839 Paracoccus denitrificans PD1222 ABC transporter YP_915632.1 1837863 R 318586 CDS YP_915633.1 119384577 4581024 complement(1838518..1839819) 1 NC_008686.1 TIGRFAM: lipoprotein releasing system, transmembrane protein, LolC/E family; PFAM: protein of unknown function DUF214; KEGG: sit:TM1040_1846 lipoprotein releasing system, transmembrane protein, LolC/E family; LolC/E family lipoprotein releasing system, transmembrane protein 1839819 4581024 Pden_1840 Paracoccus denitrificans PD1222 LolC/E family lipoprotein releasing system, transmembrane protein YP_915633.1 1838518 R 318586 CDS YP_915634.1 119384578 4581025 complement(1839899..1840057) 1 NC_008686.1 TIGRFAM: cytochrome oxidase maturation protein, cbb3-type; PFAM: cytochrome oxidase maturation protein cbb3-type; KEGG: sit:TM1040_2537 cytochrome oxidase maturation protein, cbb3-type; cbb3-type cytochrome oxidase maturation protein 1840057 4581025 Pden_1841 Paracoccus denitrificans PD1222 cbb3-type cytochrome oxidase maturation protein YP_915634.1 1839899 R 318586 CDS YP_915635.1 119384579 4581026 complement(1840067..1842265) 1 NC_008686.1 TIGRFAM: ATPase, P-type (transporting), HAD superfamily, subfamily IC; copper-translocating P-type ATPase; heavy metal translocating P-type ATPase; PFAM: Haloacid dehalogenase domain protein hydrolase; Heavy metal transport/detoxification protein; E1-E2 ATPase-associated domain protein; KEGG: rsp:RSP_0690 copper-translocating P-type ATPase, RdxI; heavy metal translocating P-type ATPase 1842265 4581026 Pden_1842 Paracoccus denitrificans PD1222 heavy metal translocating P-type ATPase YP_915635.1 1840067 R 318586 CDS YP_915636.1 119384580 4581027 complement(1842267..1842731) 1 NC_008686.1 PFAM: FixH family protein; KEGG: rsp:RSP_0691 RdxH; nitrogen fixation protein FixH 1842731 4581027 Pden_1843 Paracoccus denitrificans PD1222 nitrogen fixation protein FixH YP_915636.1 1842267 R 318586 CDS YP_915637.1 119384581 4581028 complement(1842731..1844188) 1 NC_008686.1 TIGRFAM: 4Fe-4S ferredoxin, iron-sulfur binding domain protein; KEGG: rsp:RSP_0692 iron-sulfur cluster-binding protein; 4Fe-4S ferredoxin 1844188 4581028 Pden_1844 Paracoccus denitrificans PD1222 4Fe-4S ferredoxin YP_915637.1 1842731 R 318586 CDS YP_915638.1 119384582 4581029 complement(1844464..1845513) 1 NC_008686.1 TIGRFAM: cytochrome c oxidase, cbb3-type, subunit III; PFAM: cytochrome c, class I; KEGG: rsp:RSP_0693 Cbb3-type cytochrome c oxidase CcoP subunit; cytochrome c oxidase, cbb3-type subunit III 1845513 4581029 Pden_1845 Paracoccus denitrificans PD1222 cytochrome c oxidase, cbb3-type subunit III YP_915638.1 1844464 R 318586 CDS YP_915639.1 119384583 4581030 complement(1845513..1845701) 1 NC_008686.1 PFAM: Cbb3-type cytochrome oxidase component; KEGG: sit:TM1040_2543 Cbb3-type cytochrome oxidase component; cbb3-type cytochrome oxidase subunit 1845701 4581030 Pden_1846 Paracoccus denitrificans PD1222 cbb3-type cytochrome oxidase subunit YP_915639.1 1845513 R 318586 CDS YP_915640.1 119384584 4581031 complement(1845710..1846435) 1 NC_008686.1 CcoO; FixO; cbb3-type cytochrome c oxidase subunit II 1846435 4581031 Pden_1847 Paracoccus denitrificans PD1222 cbb3-type cytochrome c oxidase subunit II YP_915640.1 1845710 R 318586 CDS YP_915641.1 119384585 4581032 complement(1846445..1848064) 1 NC_008686.1 CcoN; FixN; cbb3-type cytochrome c oxidase subunit I 1848064 4581032 Pden_1848 Paracoccus denitrificans PD1222 cbb3-type cytochrome c oxidase subunit I YP_915641.1 1846445 R 318586 CDS YP_915642.1 119384586 4581033 1848315..1849148 1 NC_008686.1 PFAM: UspA domain protein; KEGG: sil:SPO3527 universal stress protein family protein; UspA domain-containing protein 1849148 4581033 Pden_1849 Paracoccus denitrificans PD1222 UspA domain-containing protein YP_915642.1 1848315 D 318586 CDS YP_915643.1 119384587 4581034 complement(1849236..1849871) 1 NC_008686.1 PFAM: cyclic nucleotide-binding; regulatory protein, Crp; KEGG: rde:RD1_1268 transcriptional activator protein FnrL; Crp/Fnr family transcriptional regulator 1849871 4581034 Pden_1850 Paracoccus denitrificans PD1222 Crp/Fnr family transcriptional regulator YP_915643.1 1849236 R 318586 CDS YP_915644.1 119384588 4581035 1850034..1851389 1 NC_008686.1 catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III; coproporphyrinogen III oxidase 1851389 4581035 Pden_1851 Paracoccus denitrificans PD1222 coproporphyrinogen III oxidase YP_915644.1 1850034 D 318586 CDS YP_915645.1 119384589 4581036 complement(1851392..1852327) 1 NC_008686.1 TIGRFAM: cation diffusion facilitator family transporter; PFAM: cation efflux protein; KEGG: sil:SPO1387 cation efflux system protein; cation diffusion facilitator family transporter 1852327 4581036 Pden_1852 Paracoccus denitrificans PD1222 cation diffusion facilitator family transporter YP_915645.1 1851392 R 318586 CDS YP_915646.1 119384590 4579112 complement(1852399..1855221) 1 NC_008686.1 has 3'-5' exonuclease, 5'-3' exonuclease and 5'-3'polymerase activities, primarily functions to fill gaps during DNA replication and repair; DNA polymerase I 1855221 4579112 Pden_1853 Paracoccus denitrificans PD1222 DNA polymerase I YP_915646.1 1852399 R 318586 CDS YP_915647.1 119384591 4579113 complement(1855405..1855593) 1 NC_008686.1 KEGG: rsp:RSP_1027 hypothetical protein; hypothetical protein 1855593 4579113 Pden_1854 Paracoccus denitrificans PD1222 hypothetical protein YP_915647.1 1855405 R 318586 CDS YP_915648.1 119384592 4579114 1855663..1856622 1 NC_008686.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sil:SPO3847 ABC transporter, ATP-binding protein; ABC transporter 1856622 4579114 Pden_1855 Paracoccus denitrificans PD1222 ABC transporter YP_915648.1 1855663 D 318586 CDS YP_915649.1 119384593 4579115 complement(1856610..1856984) 1 NC_008686.1 PFAM: histidine triad (HIT) protein; KEGG: rsp:RSP_1029 possible histidine triad (HIT) protein; histidine triad (HIT) protein 1856984 4579115 Pden_1856 Paracoccus denitrificans PD1222 histidine triad (HIT) protein YP_915649.1 1856610 R 318586 CDS YP_915650.1 119384594 4579116 complement(1856995..1858584) 1 NC_008686.1 PFAM: glycosyl transferase, family 14; KEGG: sil:SPO3319 EpsK domain protein; glycosyl transferase family protein 1858584 4579116 Pden_1857 Paracoccus denitrificans PD1222 glycosyl transferase family protein YP_915650.1 1856995 R 318586 CDS YP_915651.1 119384595 4579117 1858734..1859552 1 NC_008686.1 KEGG: sit:TM1040_2487 conserved hypothetical protein; hypothetical protein 1859552 4579117 Pden_1858 Paracoccus denitrificans PD1222 hypothetical protein YP_915651.1 1858734 D 318586 CDS YP_915652.1 119384596 4579118 1859826..1860032 1 NC_008686.1 some L32 proteins have zinc finger motifs consisting of CXXC while others do not; 50S ribosomal protein L32 1860032 rpmF 4579118 rpmF Paracoccus denitrificans PD1222 50S ribosomal protein L32 YP_915652.1 1859826 D 318586 CDS YP_915653.1 119384597 4579119 1860050..1861162 1 NC_008686.1 involved in acylation of glycerol-3-phosphate to form 1-acyl-glycerol-3 phosphate for use in phospholipid biosynthesis; functions with PlsY; glycerol-3-phosphate acyltransferase PlsX 1861162 4579119 Pden_1860 Paracoccus denitrificans PD1222 glycerol-3-phosphate acyltransferase PlsX YP_915653.1 1860050 D 318586 CDS YP_915654.1 119384598 4579120 1861162..1862133 1 NC_008686.1 KEGG: rsp:RSP_2612 3-oxoacyl-(acyl-carrier-protein) synthase III; TIGRFAM: 3-oxoacyl-(acyl-carrier-protein) synthase III; PFAM: 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal domain protein; 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III; 3-oxoacyl-ACP synthase 1862133 4579120 Pden_1861 Paracoccus denitrificans PD1222 3-oxoacyl-ACP synthase YP_915654.1 1861162 D 318586 CDS YP_915655.1 119384599 4579121 complement(1862142..1862417) 1 NC_008686.1 PFAM: zinc finger, DksA/TraR C4-type; KEGG: sil:SPO1411 C4-type zinc finger protein, DksA/TraR family; hypothetical protein 1862417 4579121 Pden_1862 Paracoccus denitrificans PD1222 hypothetical protein YP_915655.1 1862142 R 318586 CDS YP_915656.1 119384600 4579122 1862630..1862938 1 NC_008686.1 This protein is one of the two subunits of integration host factor, a specific DNA-binding protein that functions in genetic recombination as well as in transcriptional and translational control; integration host factor subunit alpha 1862938 ihfA 4579122 ihfA Paracoccus denitrificans PD1222 integration host factor subunit alpha YP_915656.1 1862630 D 318586 CDS YP_915657.1 119384601 4579123 1862938..1863543 1 NC_008686.1 PFAM: regulatory protein, MerR; KEGG: sil:SPO2496 transcriptional regulator, MerR family; MerR family transcriptional regulator 1863543 4579123 Pden_1864 Paracoccus denitrificans PD1222 MerR family transcriptional regulator YP_915657.1 1862938 D 318586 CDS YP_915658.1 119384602 4579124 1863788..1864873 1 NC_008686.1 Catalyzes the deamination of dCTP to form dUTP; 2'-deoxycytidine 5'-triphosphate deaminase 1864873 4579124 Pden_1865 Paracoccus denitrificans PD1222 2'-deoxycytidine 5'-triphosphate deaminase YP_915658.1 1863788 D 318586 CDS YP_915659.1 119384603 4579125 complement(1865120..1865785) 1 NC_008686.1 TIGRFAM: segregation and condensation protein B; PFAM: chromosome segregation and condensation protein ScpB; KEGG: rsp:RSP_2939 predicted transcriptional regulator containing the HTH domain; transcriptional regulator 1865785 4579125 Pden_1866 Paracoccus denitrificans PD1222 transcriptional regulator YP_915659.1 1865120 R 318586 CDS YP_915660.1 119384604 4579126 complement(1865782..1866636) 1 NC_008686.1 PFAM: chromosome segregation and condensation protein ScpA; KEGG: rde:RD1_3162 hypothetical protein; chromosome segregation and condensation protein ScpA 1866636 4579126 Pden_1867 Paracoccus denitrificans PD1222 chromosome segregation and condensation protein ScpA YP_915660.1 1865782 R 318586 CDS YP_915661.1 119384605 4579127 complement(1866682..1867668) 1 NC_008686.1 PFAM: glycoside hydrolase, family 3 domain protein; KEGG: rsp:RSP_2941 glycoside hydrolase; beta-N-acetylhexosaminidase 1867668 4579127 Pden_1868 Paracoccus denitrificans PD1222 beta-N-acetylhexosaminidase YP_915661.1 1866682 R 318586 CDS YP_915662.1 119384606 4579128 complement(1867678..1868847) 1 NC_008686.1 PFAM: Sporulation domain protein; KEGG: rde:RD1_3164 hypothetical protein; sporulation domain-containing protein 1868847 4579128 Pden_1869 Paracoccus denitrificans PD1222 sporulation domain-containing protein YP_915662.1 1867678 R 318586 CDS YP_915663.1 119384607 4579129 complement(1868916..1870661) 1 NC_008686.1 catalyzes a two-step reaction, first charging an arginine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; class-I aminoacyl-tRNA synthetase; arginyl-tRNA synthetase 1870661 argS 4579129 argS Paracoccus denitrificans PD1222 arginyl-tRNA synthetase YP_915663.1 1868916 R 318586 CDS YP_915664.1 119384608 4579130 1874653..1875819 1 NC_008686.1 catalyzes the formation of S-adenosylmethionine from methionine and ATP; methionine adenosyltransferase; S-adenosylmethionine synthetase 1875819 4579130 Pden_1873 Paracoccus denitrificans PD1222 S-adenosylmethionine synthetase YP_915664.1 1874653 D 318586 CDS YP_915665.1 119384609 4580533 complement(1875928..1876554) 1 NC_008686.1 PFAM: heat shock protein DnaJ domain protein; KEGG: rsp:RSP_1978 molecular chaperone, DnaJ family; molecular chaperone DnaJ 1876554 4580533 Pden_1874 Paracoccus denitrificans PD1222 molecular chaperone DnaJ YP_915665.1 1875928 R 318586 CDS YP_915666.1 119384610 4580534 1876624..1876875 1 NC_008686.1 PFAM: BolA family protein; KEGG: sil:SPO2849 BolA protein, truncation; BolA family protein 1876875 4580534 Pden_1875 Paracoccus denitrificans PD1222 BolA family protein YP_915666.1 1876624 D 318586 CDS YP_915667.1 119384611 4580535 1876957..1877922 1 NC_008686.1 type II fructose 1,6-bisphosphatae; in Escherichia coli this protein forms a dimer and binds manganese; fructose 1,6-bisphosphatase II 1877922 glpX 4580535 glpX Paracoccus denitrificans PD1222 fructose 1,6-bisphosphatase II YP_915667.1 1876957 D 318586 CDS YP_915668.1 119384612 4580536 1877974..1879716 1 NC_008686.1 TIGRFAM: single-stranded-DNA-specific exonuclease RecJ; PFAM: phosphoesterase, RecJ domain protein; phosphoesterase, DHHA1; KEGG: rsp:RSP_0405 probable single-stranded DNA-specific exonuclease; single-stranded-DNA-specific exonuclease RecJ 1879716 4580536 Pden_1877 Paracoccus denitrificans PD1222 single-stranded-DNA-specific exonuclease RecJ YP_915668.1 1877974 D 318586 CDS YP_915669.1 119384613 4580537 1880002..1880325 1 NC_008686.1 hypothetical protein 1880325 4580537 Pden_1878 Paracoccus denitrificans PD1222 hypothetical protein YP_915669.1 1880002 D 318586 CDS YP_915670.1 119384614 4580538 complement(1880355..1883687) 1 NC_008686.1 four CarB-CarA dimers form the carbamoyl phosphate synthetase holoenzyme that catalyzes the production of carbamoyl phosphate; CarB is responsible for the amidotransferase activity; carbamoyl phosphate synthase large subunit 1883687 carB 4580538 carB Paracoccus denitrificans PD1222 carbamoyl phosphate synthase large subunit YP_915670.1 1880355 R 318586 CDS YP_915671.1 119384615 4580539 complement(1883878..1884402) 1 NC_008686.1 PFAM: Uncharacterized protein UPF0114; KEGG: ccr:CC1036 hypothetical protein; hypothetical protein 1884402 4580539 Pden_1880 Paracoccus denitrificans PD1222 hypothetical protein YP_915671.1 1883878 R 318586 CDS YP_915672.1 119384616 4580540 complement(1884716..1885078) 1 NC_008686.1 PFAM: protein of unknown function DUF710; KEGG: rde:RD1_2980 hypothetical protein; hypothetical protein 1885078 4580540 Pden_1881 Paracoccus denitrificans PD1222 hypothetical protein YP_915672.1 1884716 R 318586 CDS YP_915673.1 119384617 4580541 complement(1885082..1885717) 1 NC_008686.1 KEGG: rde:RD1_2981 hypothetical protein; hypothetical protein 1885717 4580541 Pden_1882 Paracoccus denitrificans PD1222 hypothetical protein YP_915673.1 1885082 R 318586 CDS YP_915674.1 119384618 4580542 1885895..1886482 1 NC_008686.1 catalyzes the dehydration of D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate to 3-(imidazol-4-yl)-2-oxopropyl phosphate in histidine biosynthesis; imidazoleglycerol-phosphate dehydratase 1886482 hisB 4580542 hisB Paracoccus denitrificans PD1222 imidazoleglycerol-phosphate dehydratase YP_915674.1 1885895 D 318586 CDS YP_915675.1 119384619 4580543 1886482..1887111 1 NC_008686.1 with HisF IGPS catalyzes the conversion of phosphoribulosyl-formimino-5-aminoimidazole-4-carboxamide ribonucleotide phosphate and glutamine to imidazole-glycerol phosphate, 5-aminoimidazol-4-carboxamide ribonucleotide, and glutamate in histidine biosynthesis; the HisH subunit provides the glutamine amidotransferase activity that produces the ammonia necessary to HisF for the synthesis of imidazole-glycerol phosphate and 5-aminoimidazol-4-carboxamide ribonucleotide; imidazole glycerol phosphate synthase subunit HisH 1887111 hisH 4580543 hisH Paracoccus denitrificans PD1222 imidazole glycerol phosphate synthase subunit HisH YP_915675.1 1886482 D 318586 CDS YP_915676.1 119384620 4580544 complement(1887211..1887597) 1 NC_008686.1 KEGG: rsp:RSP_2244 hypothetical protein; hypothetical protein 1887597 4580544 Pden_1885 Paracoccus denitrificans PD1222 hypothetical protein YP_915676.1 1887211 R 318586 CDS YP_915677.1 119384621 4580545 1887757..1888473 1 NC_008686.1 catalyzes the formation of 5-(5-phospho-1-deoxyribulos-1-ylamino)methylideneamino-l- (5-phosphoribosyl)imidazole-4-carboxamide from 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide; 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase 1888473 4580545 Pden_1886 Paracoccus denitrificans PD1222 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase YP_915677.1 1887757 D 318586 CDS YP_915678.1 119384622 4580546 1888501..1889262 1 NC_008686.1 catalyzes the conversion of 5-[(5-phospho-1-deoxyribulos-1-ylamino)methylideneamino]- 1-(5-phosphoribosyl)imidazole-4-carboxamideand glutamine to imidazole-glycerol phosphate, 5-aminoimidazol-4-carboxamideribonucleotide and glutamate; the HisF subunit acts as a cyclase; imidazole glycerol phosphate synthase subunit HisF 1889262 4580546 Pden_1887 Paracoccus denitrificans PD1222 imidazole glycerol phosphate synthase subunit HisF YP_915678.1 1888501 D 318586 CDS YP_915679.1 119384623 4580547 1889259..1889585 1 NC_008686.1 catalyzes the formation of 1-(5-phosphoribosyl)-AMP from 1-(5-phosphoribolsyl)-ATP in histidine biosynthesis; phosphoribosyl-ATP pyrophosphatase 1889585 hisE 4580547 hisE Paracoccus denitrificans PD1222 phosphoribosyl-ATP pyrophosphatase YP_915679.1 1889259 D 318586 CDS YP_915680.1 119384624 4580548 1889590..1890090 1 NC_008686.1 PFAM: MgtC/SapB transporter; KEGG: mes:Meso_3446 MgtC/SapB transporter; MgtC/SapB transporter 1890090 4580548 Pden_1889 Paracoccus denitrificans PD1222 MgtC/SapB transporter YP_915680.1 1889590 D 318586 CDS YP_915681.1 119384625 4580549 complement(1890087..1891292) 1 NC_008686.1 TIGRFAM: ribonuclease D; PFAM: HRDC domain protein; 3'-5' exonuclease; KEGG: rsp:RSP_1971 ribonuclease D; ribonuclease D 1891292 4580549 Pden_1890 Paracoccus denitrificans PD1222 ribonuclease D YP_915681.1 1890087 R 318586 CDS YP_915682.1 119384626 4580550 complement(1891381..1892523) 1 NC_008686.1 Exchanges the guanine residue with 7-aminomethyl-7-deazaguanine in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr); queuine tRNA-ribosyltransferase 1892523 tgt 4580550 tgt Paracoccus denitrificans PD1222 queuine tRNA-ribosyltransferase YP_915682.1 1891381 R 318586 CDS YP_915683.1 119384627 4580551 complement(1892555..1893310) 1 NC_008686.1 KEGG: rsp:RSP_2618 hemolysin; hemolysin 1893310 4580551 Pden_1892 Paracoccus denitrificans PD1222 hemolysin YP_915683.1 1892555 R 318586 CDS YP_915684.1 119384628 4580552 1893409..1893801 1 NC_008686.1 KEGG: sme:SMc00117 peptide methionine sulfoxide reductase; TIGRFAM: methionine-R-sulfoxide reductase; PFAM: Methionine sulfoxide reductase B; methionine-R-sulfoxide reductase 1893801 4580552 Pden_1893 Paracoccus denitrificans PD1222 methionine-R-sulfoxide reductase YP_915684.1 1893409 D 318586 CDS YP_915685.1 119384629 4581114 complement(1893837..1894292) 1 NC_008686.1 KEGG: rsp:RSP_2616 hypothetical protein; hypothetical protein 1894292 4581114 Pden_1894 Paracoccus denitrificans PD1222 hypothetical protein YP_915685.1 1893837 R 318586 CDS YP_915686.1 119384630 4581115 1894407..1894934 1 NC_008686.1 PFAM: protein of unknown function DUF177; KEGG: rsp:RSP_2615 hypothetical protein; hypothetical protein 1894934 4581115 Pden_1895 Paracoccus denitrificans PD1222 hypothetical protein YP_915686.1 1894407 D 318586 CDS YP_915687.1 119384631 4581116 complement(1894936..1896588) 1 NC_008686.1 catalyzes the oxidation of choline to betaine aldehyde and betain aldehyde to glycine betaine; choline dehydrogenase 1896588 4581116 Pden_1896 Paracoccus denitrificans PD1222 choline dehydrogenase YP_915687.1 1894936 R 318586 CDS YP_915688.1 119384632 4581117 complement(1896670..1898115) 1 NC_008686.1 catalyzes the formation of betaine from betaine aldehyde; betaine aldehyde dehydrogenase 1898115 4581117 Pden_1897 Paracoccus denitrificans PD1222 betaine aldehyde dehydrogenase YP_915688.1 1896670 R 318586 CDS YP_915689.1 119384633 4581118 complement(1898112..1898681) 1 NC_008686.1 HTH-type; bet1; Repressor involved in choline regulation of the bet genes; transcriptional regulator BetI 1898681 4581118 Pden_1898 Paracoccus denitrificans PD1222 transcriptional regulator BetI YP_915689.1 1898112 R 318586 CDS YP_915690.1 119384634 4581119 1898812..1899765 1 NC_008686.1 PFAM: Substrate-binding region of ABC-type glycine betaine transport system; KEGG: sme:SMc02737 glycine betaine-binding ABC transporter protein; substrate-binding region of ABC-type glycine betaine transport system 1899765 4581119 Pden_1899 Paracoccus denitrificans PD1222 substrate-binding region of ABC-type glycine betaine transport system YP_915690.1 1898812 D 318586 CDS YP_915691.1 119384635 4581120 1899930..1900781 1 NC_008686.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: rsp:RSP_2180 ABC glycine betaine/L-proline transporter, inner membrane subunit; binding-protein-dependent transport system inner membrane protein 1900781 4581120 Pden_1900 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_915691.1 1899930 D 318586 CDS YP_915692.1 119384636 4581121 1900774..1901832 1 NC_008686.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rsp:RSP_2179 ABC glycine betaine/L-proline tranporter, ATPase subunit, ProV; ABC transporter 1901832 4581121 Pden_1901 Paracoccus denitrificans PD1222 ABC transporter YP_915692.1 1900774 D 318586 CDS YP_915693.1 119384637 4581122 complement(1901854..1902780) 1 NC_008686.1 PFAM: protein of unknown function DUF6, transmembrane; KEGG: rsp:RSP_0654 possible transporter, DMT superfamily; hypothetical protein 1902780 4581122 Pden_1902 Paracoccus denitrificans PD1222 hypothetical protein YP_915693.1 1901854 R 318586 CDS YP_915694.1 119384638 4581123 complement(1902808..1903407) 1 NC_008686.1 PFAM: Lysine exporter protein (LYSE/YGGA); KEGG: rru:Rru_A0657 lysine exporter protein (LysE/YggA); lysine exporter protein LysE/YggA 1903407 4581123 Pden_1903 Paracoccus denitrificans PD1222 lysine exporter protein LysE/YggA YP_915694.1 1902808 R 318586 CDS YP_915695.1 119384639 4581124 1903489..1904358 1 NC_008686.1 specific inhibitor of chromosomal initiation of replication in vitro; binds the three 13-mers in the origin (oriC) to block initiation of replication; also controls genes involved in arginine transport; chromosome replication initiation inhibitor protein 1904358 4581124 Pden_1904 Paracoccus denitrificans PD1222 chromosome replication initiation inhibitor protein YP_915695.1 1903489 D 318586 CDS YP_915696.1 119384640 4581125 complement(1904398..1905138) 1 NC_008686.1 PFAM: protein of unknown function DUF28; KEGG: rsp:RSP_0655 hypothetical protein; hypothetical protein 1905138 4581125 Pden_1905 Paracoccus denitrificans PD1222 hypothetical protein YP_915696.1 1904398 R 318586 CDS YP_915697.1 119384641 4581126 complement(1905203..1905478) 1 NC_008686.1 KEGG: mes:Meso_1983 hypothetical protein; hypothetical protein 1905478 4581126 Pden_1906 Paracoccus denitrificans PD1222 hypothetical protein YP_915697.1 1905203 R 318586 CDS YP_915698.1 119384642 4581127 complement(1905465..1905674) 1 NC_008686.1 KEGG: rsp:RSP_2137 hypothetical protein; hypothetical protein 1905674 4581127 Pden_1907 Paracoccus denitrificans PD1222 hypothetical protein YP_915698.1 1905465 R 318586 CDS YP_915699.1 119384643 4581128 complement(1905677..1907074) 1 NC_008686.1 class II family (does not require metal); tetrameric enzyme; fumarase C; reversibly converts (S)-malate to fumarate and water; functions in the TCA cycle; fumarate hydratase 1907074 fumC 4581128 fumC Paracoccus denitrificans PD1222 fumarate hydratase YP_915699.1 1905677 R 318586 CDS YP_915700.1 119384644 4581129 complement(1907167..1907628) 1 NC_008686.1 PFAM: protein of unknown function DUF1321; KEGG: rsp:RSP_2139 hypothetical protein; hypothetical protein 1907628 4581129 Pden_1909 Paracoccus denitrificans PD1222 hypothetical protein YP_915700.1 1907167 R 318586 CDS YP_915701.1 119384645 4581130 complement(1908117..1908446) 1 NC_008686.1 KEGG: mes:Meso_3101 PRC-barrel; hypothetical protein 1908446 4581130 Pden_1911 Paracoccus denitrificans PD1222 hypothetical protein YP_915701.1 1908117 R 318586 CDS YP_915702.1 119384646 4581131 complement(1909112..1910221) 1 NC_008686.1 catalyzes hydrolysis of 1,6-anhydro bond of anyhydro-N-acetylmuramic acid (anhMurNAc) and phosphorylates anhMurNAc to produce N-acetyl-muramate-6-phosphate; involved in murein recycling; anhydro-N-acetylmuramic acid kinase 1910221 anmK 4581131 anmK Paracoccus denitrificans PD1222 anhydro-N-acetylmuramic acid kinase YP_915702.1 1909112 R 318586 CDS YP_915703.1 119384647 4581132 1910277..1911521 1 NC_008686.1 KEGG: rsp:RSP_4041 tyrosyl-tRNA synthetase, class Ib; TIGRFAM: tyrosyl-tRNA synthetase; PFAM: aminoacyl-tRNA synthetase, class Ib; RNA-binding S4 domain protein; tyrosyl-tRNA synthetase 1911521 4581132 Pden_1913 Paracoccus denitrificans PD1222 tyrosyl-tRNA synthetase YP_915703.1 1910277 D 318586 CDS YP_915704.1 119384648 4580573 complement(1911566..1912147) 1 NC_008686.1 KEGG: mlo:mll5005 hypothetical protein; hypothetical protein 1912147 4580573 Pden_1914 Paracoccus denitrificans PD1222 hypothetical protein YP_915704.1 1911566 R 318586 CDS YP_915705.1 119384649 4580574 complement(1912182..1912637) 1 NC_008686.1 PFAM: protein of unknown function DUF188; KEGG: rde:RD1_0321 YaiI/YqxD family protein; hypothetical protein 1912637 4580574 Pden_1915 Paracoccus denitrificans PD1222 hypothetical protein YP_915705.1 1912182 R 318586 CDS YP_915706.1 119384650 4580575 complement(1912702..1913295) 1 NC_008686.1 PFAM: peptidyl-prolyl cis-trans isomerase, cyclophilin type; KEGG: rsp:RSP_4042 peptidyl-prolyl cis-trans isomerase, cyclophilin type; cyclophilin type peptidyl-prolyl cis-trans isomerase 1913295 4580575 Pden_1916 Paracoccus denitrificans PD1222 cyclophilin type peptidyl-prolyl cis-trans isomerase YP_915706.1 1912702 R 318586 CDS YP_915707.1 119384651 4580576 complement(1913285..1913794) 1 NC_008686.1 PFAM: peptidyl-prolyl cis-trans isomerase, cyclophilin type; KEGG: sit:TM1040_1085 peptidyl-prolyl cis-trans isomerase, cyclophilin type; cyclophilin type peptidyl-prolyl cis-trans isomerase 1913794 4580576 Pden_1917 Paracoccus denitrificans PD1222 cyclophilin type peptidyl-prolyl cis-trans isomerase YP_915707.1 1913285 R 318586 CDS YP_915708.1 119384652 4580577 1913972..1915168 1 NC_008686.1 Converts 3-phospho-D-glycerate to 3-phospho-D-glyceroyl phosphate during the glycolysis pathway; phosphoglycerate kinase 1915168 pgk 4580577 pgk Paracoccus denitrificans PD1222 phosphoglycerate kinase YP_915708.1 1913972 D 318586 CDS YP_915709.1 119384653 4580578 complement(1915409..1915624) 1 NC_008686.1 hypothetical protein 1915624 4580578 Pden_1919 Paracoccus denitrificans PD1222 hypothetical protein YP_915709.1 1915409 R 318586 CDS YP_915710.1 119384654 4580579 1915751..1916680 1 NC_008686.1 catalyzes the formation of glycerone phosphate and D-glyceraldehyde 3-phosphate from D-fructose 1,6-bisphosphate; fructose-bisphosphate aldolase 1916680 4580579 Pden_1920 Paracoccus denitrificans PD1222 fructose-bisphosphate aldolase YP_915710.1 1915751 D 318586 CDS YP_915711.1 119384655 4580580 1916810..1917850 1 NC_008686.1 KEGG: rsp:RSP_1843 signal recognition particle-docking protein FtsY; TIGRFAM: signal recognition particle-docking protein FtsY; PFAM: GTP-binding signal recognition particle SRP54, G- domain; GTP-binding signal recognition particle SRP54, helical bundle; SMART: AAA ATPase; signal recognition particle-docking protein FtsY 1917850 4580580 Pden_1921 Paracoccus denitrificans PD1222 signal recognition particle-docking protein FtsY YP_915711.1 1916810 D 318586 CDS YP_915712.1 119384656 4580581 complement(1917907..1918275) 1 NC_008686.1 KEGG: rsp:RSP_2037 hypothetical protein; hypothetical protein 1918275 4580581 Pden_1922 Paracoccus denitrificans PD1222 hypothetical protein YP_915712.1 1917907 R 318586 CDS YP_915713.1 119384657 4580582 complement(1918330..1919007) 1 NC_008686.1 short form of enzyme; requires HisZ for function; catalyzes the formation of N'-5'-phosphoribosyl-ATP from phosphoribosyl pyrophosphate; crucial role in histidine biosynthesis; forms heteromultimer of HisG and HisZ; ATP phosphoribosyltransferase 1919007 hisG 4580582 hisG Paracoccus denitrificans PD1222 ATP phosphoribosyltransferase YP_915713.1 1918330 R 318586 CDS YP_915714.1 119384658 4580583 complement(1919004..1920086) 1 NC_008686.1 May allow the feedback regulation of ATP phosphoribosyltransferase activity by histidine; ATP phosphoribosyltransferase 1920086 hisZ 4580583 hisZ Paracoccus denitrificans PD1222 ATP phosphoribosyltransferase YP_915714.1 1919004 R 318586 CDS YP_915715.1 119384659 4580584 complement(1920083..1921567) 1 NC_008686.1 catalyzes a two-step reaction, first charging a histidine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; class II aminoacyl-tRNA synthetase; forms homodimers; some organisms have a paralogous gene, hisZ, that is similar to hisS and produces a protein that performs the first step in histidine biosynthesis along with HisG; histidyl-tRNA synthetase 1921567 hisS 4580584 hisS Paracoccus denitrificans PD1222 histidyl-tRNA synthetase YP_915715.1 1920083 R 318586 CDS YP_915716.1 119384660 4580585 1921616..1921831 1 NC_008686.1 KEGG: rde:RD1_4066 hypothetical protein; hypothetical protein 1921831 4580585 Pden_1926 Paracoccus denitrificans PD1222 hypothetical protein YP_915716.1 1921616 D 318586 CDS YP_915717.1 119384661 4580586 complement(1921901..1922392) 1 NC_008686.1 KEGG: rsp:RSP_1985 hypothetical protein; hypothetical protein 1922392 4580586 Pden_1927 Paracoccus denitrificans PD1222 hypothetical protein YP_915717.1 1921901 R 318586 CDS YP_915718.1 119384662 4580587 complement(1922493..1923002) 1 NC_008686.1 PFAM: cell wall hydrolase, SleB; KEGG: rsp:RSP_2496 hypothetical protein; cell wall hydrolase SleB 1923002 4580587 Pden_1928 Paracoccus denitrificans PD1222 cell wall hydrolase SleB YP_915718.1 1922493 R 318586 CDS YP_915719.1 119384663 4580588 complement(1923126..1924640) 1 NC_008686.1 allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases; reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA; aspartyl/glutamyl-tRNA amidotransferase subunit B 1924640 gatB 4580588 gatB Paracoccus denitrificans PD1222 aspartyl/glutamyl-tRNA amidotransferase subunit B YP_915719.1 1923126 R 318586 CDS YP_915720.1 119384664 4580589 complement(1925055..1928345) 1 NC_008686.1 KEGG: rsp:RSP_6052 hypothetical protein; hypothetical protein 1928345 4580589 Pden_1931 Paracoccus denitrificans PD1222 hypothetical protein YP_915720.1 1925055 R 318586 CDS YP_915721.1 119384665 4580590 1928360..1929205 1 NC_008686.1 PFAM: protein of unknown function DUF541; KEGG: rsp:RSP_2430 hypothetical protein; hypothetical protein 1929205 4580590 Pden_1932 Paracoccus denitrificans PD1222 hypothetical protein YP_915721.1 1928360 D 318586 CDS YP_915722.1 119384666 4580591 complement(1929274..1930560) 1 NC_008686.1 KEGG: sit:TM1040_0585 O-acetylhomoserine/O-acetylserine sulfhydrylase; TIGRFAM: O-acetylhomoserine/O-acetylserine sulfhydrylase; PFAM: Cys/Met metabolism pyridoxal-phosphate-dependent enzymes; O-acetylhomoserine/O-acetylserine sulfhydrylase 1930560 4580591 Pden_1933 Paracoccus denitrificans PD1222 O-acetylhomoserine/O-acetylserine sulfhydrylase YP_915722.1 1929274 R 318586 CDS YP_915723.1 119384667 4580592 complement(1930887..1931267) 1 NC_008686.1 KEGG: rsp:RSP_7183 translation initiation factor 2, gamma subunit, GTPase; translation initiation factor 2 subunit gamma, GTPase 1931267 4580592 Pden_1934 Paracoccus denitrificans PD1222 translation initiation factor 2 subunit gamma, GTPase YP_915723.1 1930887 R 318586 CDS YP_915724.1 119384668 4581057 complement(1931703..1935455) 1 NC_008686.1 one of two methionine synthases in Escherichia coli; MetH catalyzes a methyl transfer reaction from methyltetrahydrofolate to homocysteine to create methionine; requires zinc for activity; B12-dependent methionine synthase 1935455 metH 4581057 metH Paracoccus denitrificans PD1222 B12-dependent methionine synthase YP_915724.1 1931703 R 318586 CDS YP_915725.1 119384669 4581058 1935600..1936256 1 NC_008686.1 lipoyl-[acyl-carrier protein]-protein-N-lipoyltransferse; lipoate-protein ligase B; transfers lipoate to apolipoproteins; involved in lipoate metabolism; lipoyltransferase 1936256 lipB 4581058 lipB Paracoccus denitrificans PD1222 lipoyltransferase YP_915725.1 1935600 D 318586 CDS YP_915726.1 119384670 4581059 1936399..1936866 1 NC_008686.1 PFAM: cytochrome c, class I; KEGG: sil:SPO0130 cytochrome c family protein; cytochrome c, class I 1936866 4581059 Pden_1937 Paracoccus denitrificans PD1222 cytochrome c, class I YP_915726.1 1936399 D 318586 CDS YP_915727.1 119384671 4581060 1937038..1938714 1 NC_008686.1 PFAM: cytochrome c oxidase, subunit I; KEGG: rsp:RSP_1877 cytochrome c oxidase, aa3 type, subunit I; cytochrome-c oxidase 1938714 4581060 Pden_1938 Paracoccus denitrificans PD1222 cytochrome-c oxidase YP_915727.1 1937038 D 318586 CDS YP_915728.1 119384672 4581061 1938734..1939228 1 NC_008686.1 KEGG: rsp:RSP_1876 hypothetical protein; hypothetical protein 1939228 4581061 Pden_1939 Paracoccus denitrificans PD1222 hypothetical protein YP_915728.1 1938734 D 318586 CDS YP_915729.1 119384673 4581062 complement(1939823..1942315) 1 NC_008686.1 PFAM: FAD dependent oxidoreductase; glycine cleavage T protein (aminomethyl transferase); Glycine cleavage T-protein, C-terminal barrel; KEGG: rsp:RSP_3566 dimethylglycine dehydrogenase; FAD dependent oxidoreductase 1942315 4581062 Pden_1940 Paracoccus denitrificans PD1222 FAD dependent oxidoreductase YP_915729.1 1939823 R 318586 CDS YP_915730.1 119384674 4581063 complement(1942478..1943488) 1 NC_008686.1 PFAM: D-isomer specific 2-hydroxyacid dehydrogenase, catalytic region; D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding; KEGG: jan:Jann_0915 glycolate reductase; glyoxylate reductase 1943488 4581063 Pden_1941 Paracoccus denitrificans PD1222 glyoxylate reductase YP_915730.1 1942478 R 318586 CDS YP_915731.1 119384675 4581064 1943580..1944182 1 NC_008686.1 PFAM: protein of unknown function DUF1058; KEGG: rsp:RSP_2312 hypothetical protein; hypothetical protein 1944182 4581064 Pden_1942 Paracoccus denitrificans PD1222 hypothetical protein YP_915731.1 1943580 D 318586 CDS YP_915732.1 119384676 4581065 complement(1944200..1945057) 1 NC_008686.1 KEGG: syw:SYNW2410 hypothetical protein; hypothetical protein 1945057 4581065 Pden_1943 Paracoccus denitrificans PD1222 hypothetical protein YP_915732.1 1944200 R 318586 CDS YP_915733.1 119384677 4581066 complement(1945211..1947247) 1 NC_008686.1 PFAM: peptidase M3A and M3B, thimet/oligopeptidase F; KEGG: rsp:RSP_0596 peptidyl-dipeptidase; peptidyl-dipeptidase Dcp 1947247 4581066 Pden_1944 Paracoccus denitrificans PD1222 peptidyl-dipeptidase Dcp YP_915733.1 1945211 R 318586 CDS YP_915734.1 119384678 4581067 complement(1947281..1948333) 1 NC_008686.1 PFAM: UBA/THIF-type NAD/FAD binding protein; MoeZ/MoeB domain protein; KEGG: rsp:RSP_0597 probable molybdopterin biosynthesis protein; UBA/THIF-type NAD/FAD binding protein 1948333 4581067 Pden_1945 Paracoccus denitrificans PD1222 UBA/THIF-type NAD/FAD binding protein YP_915734.1 1947281 R 318586 CDS YP_915735.1 119384679 4581068 complement(1948338..1948799) 1 NC_008686.1 KEGG: sil:SPO0409 deoxyuridine 5'-triphosphate nucleotidohydrolase; TIGRFAM: deoxyuridine 5'-triphosphate nucleotidohydrolase Dut; PFAM: deoxyUTP pyrophosphatase; deoxyuridine 5'-triphosphate nucleotidohydrolase Dut 1948799 4581068 Pden_1946 Paracoccus denitrificans PD1222 deoxyuridine 5'-triphosphate nucleotidohydrolase Dut YP_915735.1 1948338 R 318586 CDS YP_915736.1 119384680 4581069 1950168..1951043 1 NC_008686.1 KEGG: sit:TM1040_0184 conserved hypothetical protein; hypothetical protein 1951043 4581069 Pden_1948 Paracoccus denitrificans PD1222 hypothetical protein YP_915736.1 1950168 D 318586 CDS YP_915737.1 119384681 4581070 complement(1951059..1952348) 1 NC_008686.1 KEGG: rsp:RSP_3072 L-sorbosone dehydrogenase; L-sorbosone dehydrogenase 1952348 4581070 Pden_1949 Paracoccus denitrificans PD1222 L-sorbosone dehydrogenase YP_915737.1 1951059 R 318586 CDS YP_915738.1 119384682 4581071 complement(1952489..1954090) 1 NC_008686.1 functions in sugar metabolism in glycolysis and the Embden-Meyerhof pathways (EMP) and in gluconeogenesis; catalyzes reversible isomerization of glucose-6-phosphate to fructose-6-phosphate; member of PGI family; glucose-6-phosphate isomerase 1954090 pgi 4581071 pgi Paracoccus denitrificans PD1222 glucose-6-phosphate isomerase YP_915738.1 1952489 R 318586 CDS YP_915739.1 119384683 4581072 complement(1954092..1954766) 1 NC_008686.1 TIGRFAM: 6-phosphogluconolactonase; KEGG: rsp:RSP_2735 6-phosphogluconolactonase; 6-phosphogluconolactonase 1954766 4581072 Pden_1951 Paracoccus denitrificans PD1222 6-phosphogluconolactonase YP_915739.1 1954092 R 318586 CDS YP_915740.1 119384684 4581073 complement(1954763..1956265) 1 NC_008686.1 catalyzes the formation of D-glucono-1,5-lactone 6-phosphate from D-glucose 6-phosphate; glucose-6-phosphate 1-dehydrogenase 1956265 4581073 Pden_1952 Paracoccus denitrificans PD1222 glucose-6-phosphate 1-dehydrogenase YP_915740.1 1954763 R 318586 CDS YP_915741.1 119384685 4581074 complement(1956291..1956884) 1 NC_008686.1 KEGG: jan:Jann_2688 hypothetical protein; hypothetical protein 1956884 4581074 Pden_1953 Paracoccus denitrificans PD1222 hypothetical protein YP_915741.1 1956291 R 318586 CDS YP_915742.1 119384686 4581075 complement(1956881..1958077) 1 NC_008686.1 KEGG: rsp:RSP_2647 predicted SAM-dependent methyltransferase; SAM-dependent methyltransferase 1958077 4581075 Pden_1954 Paracoccus denitrificans PD1222 SAM-dependent methyltransferase YP_915742.1 1956881 R 318586 CDS YP_915743.1 119384687 4578721 1958193..1959995 1 NC_008686.1 catalyzes the formation of 2-dehydro-3-deoxy-6-phospho-D-gluconate from 6-phospho-D-gluconate; phosphogluconate dehydratase 1959995 4578721 Pden_1955 Paracoccus denitrificans PD1222 phosphogluconate dehydratase YP_915743.1 1958193 D 318586 CDS YP_915744.1 119384688 4578722 complement(1960034..1960564) 1 NC_008686.1 TIGRFAM: PAS sensor protein; PFAM: PAS fold domain protein; KEGG: mca:MCA2070 sensory box protein; PAS/PAC sensor protein 1960564 4578722 Pden_1956 Paracoccus denitrificans PD1222 PAS/PAC sensor protein YP_915744.1 1960034 R 318586 CDS YP_915745.1 119384689 4578723 complement(1960643..1961101) 1 NC_008686.1 PFAM: low molecular weight phosphotyrosine protein phosphatase; KEGG: rsp:RSP_0630 hypothetical protein; protein tyrosine phosphatase 1961101 4578723 Pden_1957 Paracoccus denitrificans PD1222 protein tyrosine phosphatase YP_915745.1 1960643 R 318586 CDS YP_915746.1 119384690 4578724 complement(1961105..1961593) 1 NC_008686.1 PFAM: Uncharacterized conserved protein UCP032146; KEGG: rde:RD1_1069 hypothetical protein; hypothetical protein 1961593 4578724 Pden_1958 Paracoccus denitrificans PD1222 hypothetical protein YP_915746.1 1961105 R 318586 CDS YP_915747.1 119384691 4578725 complement(1961590..1962900) 1 NC_008686.1 catalyzes the oxidation of L-histidinol to L-histidinaldehyde and then to L-histidine in histidine biosynthesis; functions as a dimer; histidinol dehydrogenase 1962900 hisD 4578725 hisD Paracoccus denitrificans PD1222 histidinol dehydrogenase YP_915747.1 1961590 R 318586 CDS YP_915748.1 119384692 4578726 complement(1963111..1963590) 1 NC_008686.1 KEGG: sit:TM1040_3566 conserved hypothetical protein; hypothetical protein 1963590 4578726 Pden_1960 Paracoccus denitrificans PD1222 hypothetical protein YP_915748.1 1963111 R 318586 CDS YP_915749.1 119384693 4578727 complement(1963583..1964863) 1 NC_008686.1 adds enolpyruvyl to UDP-N-acetylglucosamine as a component of cell wall formation; gram-positive bacteria have 2 copies of MurA which are active; UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1964863 4578727 Pden_1961 Paracoccus denitrificans PD1222 UDP-N-acetylglucosamine 1-carboxyvinyltransferase YP_915749.1 1963583 R 318586 CDS YP_915750.1 119384694 4578728 1965483..1965734 1 NC_008686.1 KEGG: mca:MCA2639 hypothetical protein; hypothetical protein 1965734 4578728 Pden_1962 Paracoccus denitrificans PD1222 hypothetical protein YP_915750.1 1965483 D 318586 CDS YP_915751.1 119384695 4578729 complement(1965805..1966104) 1 NC_008686.1 TIGRFAM: addiction module antidote protein, HigA family; PFAM: helix-turn-helix domain protein; KEGG: sme:SMc02151 hypothetical virulence associated protein homologue; XRE family transcriptional regulator 1966104 4578729 Pden_1963 Paracoccus denitrificans PD1222 XRE family transcriptional regulator YP_915751.1 1965805 R 318586 CDS YP_915752.1 119384696 4578730 complement(1966566..1967483) 1 NC_008686.1 KEGG: shm:Shewmr7_0348 hypothetical protein; hypothetical protein 1967483 4578730 Pden_1964 Paracoccus denitrificans PD1222 hypothetical protein YP_915752.1 1966566 R 318586 CDS YP_915753.1 119384697 4578731 complement(1967473..1968294) 1 NC_008686.1 KEGG: mes:Meso_4610 hypothetical protein; hypothetical protein 1968294 4578731 Pden_1965 Paracoccus denitrificans PD1222 hypothetical protein YP_915753.1 1967473 R 318586 CDS YP_915754.1 119384698 4578732 complement(1968478..1968774) 1 NC_008686.1 hypothetical protein 1968774 4578732 Pden_1966 Paracoccus denitrificans PD1222 hypothetical protein YP_915754.1 1968478 R 318586 CDS YP_915755.1 119384699 4578733 1968801..1969079 1 NC_008686.1 hypothetical protein 1969079 4578733 Pden_1967 Paracoccus denitrificans PD1222 hypothetical protein YP_915755.1 1968801 D 318586 CDS YP_915756.1 119384700 4578734 complement(1969222..1969740) 1 NC_008686.1 hypothetical protein 1969740 4578734 Pden_1968 Paracoccus denitrificans PD1222 hypothetical protein YP_915756.1 1969222 R 318586 CDS YP_915757.1 119384701 4578735 complement(1969844..1970968) 1 NC_008686.1 KEGG: bxe:Bxe_A0083 hypothetical protein; hypothetical protein 1970968 4578735 Pden_1969 Paracoccus denitrificans PD1222 hypothetical protein YP_915757.1 1969844 R 318586 CDS YP_915758.1 119384702 4578736 complement(1970958..1971539) 1 NC_008686.1 KEGG: psp:PSPPH_0608 pancortin-3; pancortin-3 1971539 4578736 Pden_1970 Paracoccus denitrificans PD1222 pancortin-3 YP_915758.1 1970958 R 318586 CDS YP_915759.1 119384703 4578737 1971910..1972491 1 NC_008686.1 KEGG: bja:blr1827 transposase; hypothetical protein 1972491 4578737 Pden_1971 Paracoccus denitrificans PD1222 hypothetical protein YP_915759.1 1971910 D 318586 CDS YP_915760.1 119384704 4578738 1972763..1974499 1 NC_008686.1 PFAM: Resolvase, N-terminal domain; Recombinase; KEGG: nha:Nham_3864 recombinase; recombinase 1974499 4578738 Pden_1972 Paracoccus denitrificans PD1222 recombinase YP_915760.1 1972763 D 318586 CDS YP_915761.1 119384705 4578739 1979926..1980246 1 NC_008686.1 KEGG: rsp:RSP_3837 hypothetical protein; hypothetical protein 1980246 4578739 Pden_1973 Paracoccus denitrificans PD1222 hypothetical protein YP_915761.1 1979926 D 318586 CDS YP_915762.1 119384706 4578740 1980668..1980853 1 NC_008686.1 KEGG: mag:amb1768 Mu-like prophage major head subunit gpT; Mu-like prophage major head subunit gpT 1980853 4578740 Pden_1974 Paracoccus denitrificans PD1222 Mu-like prophage major head subunit gpT YP_915762.1 1980668 D 318586 CDS YP_915763.1 119384707 4581133 complement(1980891..1981145) 1 NC_008686.1 hypothetical protein 1981145 4581133 Pden_1975 Paracoccus denitrificans PD1222 hypothetical protein YP_915763.1 1980891 R 318586 CDS YP_915764.1 119384708 4581134 1981241..1981540 1 NC_008686.1 hypothetical protein 1981540 4581134 Pden_1976 Paracoccus denitrificans PD1222 hypothetical protein YP_915764.1 1981241 D 318586 CDS YP_915765.1 119384709 4581135 1981544..1981885 1 NC_008686.1 hypothetical protein 1981885 4581135 Pden_1977 Paracoccus denitrificans PD1222 hypothetical protein YP_915765.1 1981544 D 318586 CDS YP_915766.1 119384710 4581136 1982268..1983287 1 NC_008686.1 PFAM: regulatory protein, LacI; periplasmic binding protein/LacI transcriptional regulator; KEGG: rsp:RSP_1663 transcriptional regulator, LacI family; periplasmic binding protein/LacI transcriptional regulator 1983287 4581136 Pden_1978 Paracoccus denitrificans PD1222 periplasmic binding protein/LacI transcriptional regulator YP_915766.1 1982268 D 318586 CDS YP_915767.1 119384711 4581137 complement(1983453..1984283) 1 NC_008686.1 TIGRFAM: methionine aminopeptidase, type I; PFAM: peptidase M24; KEGG: rsp:RSP_0923 methionine aminopeptidase, subfamily 1; methionine aminopeptidase 1984283 4581137 Pden_1979 Paracoccus denitrificans PD1222 methionine aminopeptidase YP_915767.1 1983453 R 318586 CDS YP_915768.1 119384712 4581138 1984370..1985110 1 NC_008686.1 PFAM: molybdopterin binding domain; KEGG: sit:TM1040_2467 molybdopterin binding domain; molybdopterin binding domain-containing protein 1985110 4581138 Pden_1980 Paracoccus denitrificans PD1222 molybdopterin binding domain-containing protein YP_915768.1 1984370 D 318586 CDS YP_915769.1 119384713 4581139 1985107..1985826 1 NC_008686.1 PFAM: GCN5-related N-acetyltransferase; KEGG: rsp:RSP_0925 acetyl transferase; N-acetyltransferase 1985826 4581139 Pden_1981 Paracoccus denitrificans PD1222 N-acetyltransferase YP_915769.1 1985107 D 318586 CDS YP_915770.1 119384714 4581140 complement(1985841..1986227) 1 NC_008686.1 KEGG: sit:TM1040_2681 conserved hypothetical protein; hypothetical protein 1986227 4581140 Pden_1982 Paracoccus denitrificans PD1222 hypothetical protein YP_915770.1 1985841 R 318586 CDS YP_915771.1 119384715 4581141 complement(1986242..1987042) 1 NC_008686.1 KEGG: sil:SPO3814 hypothetical protein; hypothetical protein 1987042 4581141 Pden_1983 Paracoccus denitrificans PD1222 hypothetical protein YP_915771.1 1986242 R 318586 CDS YP_915772.1 119384716 4581142 complement(1987039..1988772) 1 NC_008686.1 catalyzes the dehydration of 2,3-dihydroxy-3-methylbutanoate to 3-methyl-2-oxobutanoate in valine and isoleucine biosynthesis; dihydroxy-acid dehydratase 1988772 4581142 Pden_1984 Paracoccus denitrificans PD1222 dihydroxy-acid dehydratase YP_915772.1 1987039 R 318586 CDS YP_915773.1 119384717 4581143 complement(1988851..1989174) 1 NC_008686.1 PFAM: transcriptional coactivator/pterin dehydratase; KEGG: mca:MCA0497 pterin-4-alpha-carbinolamine dehydratase; transcriptional coactivator/pterin dehydratase 1989174 4581143 Pden_1985 Paracoccus denitrificans PD1222 transcriptional coactivator/pterin dehydratase YP_915773.1 1988851 R 318586 CDS YP_915774.1 119384718 4581144 complement(1989186..1990613) 1 NC_008686.1 PFAM: phospholipase D/Transphosphatidylase; KEGG: rba:RB9533 cardiolipin synthase; phospholipase D/transphosphatidylase 1990613 4581144 Pden_1986 Paracoccus denitrificans PD1222 phospholipase D/transphosphatidylase YP_915774.1 1989186 R 318586 CDS YP_915775.1 119384719 4581145 1990702..1991643 1 NC_008686.1 TIGRFAM: acetyl-CoA carboxylase, carboxyl transferase, beta subunit; KEGG: sit:TM1040_2676 acetyl-CoA carboxylase, carboxyl transferase, beta subunit; acetyl-CoA carboxylase, carboxyl transferase subunit beta 1991643 4581145 Pden_1987 Paracoccus denitrificans PD1222 acetyl-CoA carboxylase, carboxyl transferase subunit beta YP_915775.1 1990702 D 318586 CDS YP_915776.1 119384720 4581146 1991660..1992928 1 NC_008686.1 KEGG: rsp:RSP_0930 folylpolyglutamate synthetase; TIGRFAM: FolC bifunctional protein; PFAM: Mur ligase, middle domain protein; bifunctional folylpolyglutamate synthase/dihydrofolate synthase 1992928 4581146 Pden_1988 Paracoccus denitrificans PD1222 bifunctional folylpolyglutamate synthase/dihydrofolate synthase YP_915776.1 1991660 D 318586 CDS YP_915777.1 119384721 4581147 complement(1992946..1994052) 1 NC_008686.1 PFAM: AFG1-family ATPase; KEGG: rsp:RSP_1349 hypothetical protein; AFG1 family ATPase 1994052 4581147 Pden_1989 Paracoccus denitrificans PD1222 AFG1 family ATPase YP_915777.1 1992946 R 318586 CDS YP_915778.1 119384722 4581148 complement(1994137..1994742) 1 NC_008686.1 KEGG: jan:Jann_2690 hypothetical protein; hypothetical protein 1994742 4581148 Pden_1990 Paracoccus denitrificans PD1222 hypothetical protein YP_915778.1 1994137 R 318586 CDS YP_915779.1 119384723 4581149 1994943..1996325 1 NC_008686.1 PFAM: aldehyde dehydrogenase; KEGG: rme:Rmet_0158 aldehyde dehydrogenase; aldehyde dehydrogenase 1996325 4581149 Pden_1991 Paracoccus denitrificans PD1222 aldehyde dehydrogenase YP_915779.1 1994943 D 318586 CDS YP_915780.1 119384724 4581150 complement(1996322..1997632) 1 NC_008686.1 PFAM: General substrate transporter; major facilitator superfamily MFS_1; KEGG: atc:AGR_C_4107 hypothetical protein; major facilitator superfamily transporter 1997632 4581150 Pden_1992 Paracoccus denitrificans PD1222 major facilitator superfamily transporter YP_915780.1 1996322 R 318586 CDS YP_915781.1 119384725 4581151 1997908..1999521 1 NC_008686.1 KEGG: ade:Adeh_0560 hypothetical protein; hypothetical protein 1999521 4581151 Pden_1993 Paracoccus denitrificans PD1222 hypothetical protein YP_915781.1 1997908 D 318586 CDS YP_915782.1 119384726 4578663 complement(1999629..2000324) 1 NC_008686.1 KEGG: hsa:729099 hypothetical protein LOC729099; hypothetical protein 2000324 4578663 Pden_1994 Paracoccus denitrificans PD1222 hypothetical protein YP_915782.1 1999629 R 318586 CDS YP_915783.1 119384727 4578664 complement(2000815..2002605) 1 NC_008686.1 PFAM: HemY domain protein; KEGG: rsp:RSP_1508 uncharacterized HemY-like membrane protein; HemY domain-containing protein 2002605 4578664 Pden_1995 Paracoccus denitrificans PD1222 HemY domain-containing protein YP_915783.1 2000815 R 318586 CDS YP_915784.1 119384728 4578665 complement(2002568..2004139) 1 NC_008686.1 KEGG: jan:Jann_4082 hypothetical protein; hypothetical protein 2004139 4578665 Pden_1996 Paracoccus denitrificans PD1222 hypothetical protein YP_915784.1 2002568 R 318586 CDS YP_915785.1 119384729 4578666 complement(2004193..2004867) 1 NC_008686.1 KEGG: rsp:RSP_6208 uroporphyrinogen-III synthase; uroporphyrinogen-III synthase 2004867 4578666 Pden_1997 Paracoccus denitrificans PD1222 uroporphyrinogen-III synthase YP_915785.1 2004193 R 318586 CDS YP_915786.1 119384730 4578667 2004932..2006002 1 NC_008686.1 in most organisms, only the N-terminal domain is present in a single polypeptide; in some archaea this domain is fused to a kinase domain; this gene is essential for growth in Escherichia coli and Bacillus subtilis; the secreted glycoprotease from Pasteurella haemolytica showed specificity for O-sialoglycosylated proteins; the Pyrococcus structure shows DNA-binding properties, iron-binding, ATP-binding, and AP endonuclease activity; DNA-binding/iron metalloprotein/AP endonuclease 2006002 4578667 Pden_1998 Paracoccus denitrificans PD1222 DNA-binding/iron metalloprotein/AP endonuclease YP_915786.1 2004932 D 318586 CDS YP_915787.1 119384731 4578668 2005999..2006943 1 NC_008686.1 catalyzes the NAD(P)H-dependent reduction of glycerol 3-phosphate to glycerone phosphate; NAD(P)H-dependent glycerol-3-phosphate dehydrogenase 2006943 gpsA 4578668 gpsA Paracoccus denitrificans PD1222 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase YP_915787.1 2005999 D 318586 CDS YP_915788.1 119384732 4578669 2006940..2007215 1 NC_008686.1 PFAM: YCII-related; KEGG: rsp:RSP_1511 hypothetical protein; hypothetical protein 2007215 4578669 Pden_2000 Paracoccus denitrificans PD1222 hypothetical protein YP_915788.1 2006940 D 318586 CDS YP_915789.1 119384733 4578670 2007215..2007640 1 NC_008686.1 PFAM: protein of unknown function DUF55; KEGG: rsp:RSP_1512 hypothetical protein; hypothetical protein 2007640 4578670 Pden_2001 Paracoccus denitrificans PD1222 hypothetical protein YP_915789.1 2007215 D 318586 CDS YP_915790.1 119384734 4578671 2007683..2009476 1 NC_008686.1 KEGG: rsp:RSP_2254 ABC efflux transporter, fused ATPase and inner membrane subunits; TIGRFAM: lipid A ABC exporter family, fused ATPase and inner membrane subunits; PFAM: ABC transporter, transmembrane region; ABC transporter related; SMART: AAA ATPase; lipid ABC transporter ATPase/inner membrane protein 2009476 4578671 Pden_2002 Paracoccus denitrificans PD1222 lipid ABC transporter ATPase/inner membrane protein YP_915790.1 2007683 D 318586 CDS YP_915791.1 119384735 4578672 complement(2009604..2010026) 1 NC_008686.1 PFAM: Allergen V5/Tpx-1 family protein; KEGG: fra:Francci3_3457 allergen V5/TPX-1 related; Allergen V5/Tpx-1 family protein 2010026 4578672 Pden_2003 Paracoccus denitrificans PD1222 Allergen V5/Tpx-1 family protein YP_915791.1 2009604 R 318586 CDS YP_915792.1 119384736 4578673 2010277..2010762 1 NC_008686.1 PFAM: Peptidoglycan-binding LysM; transport-associated; KEGG: sil:SPO3004 LysM/phospholipid-binding domain protein; LysM domain/BON superfamily protein 2010762 4578673 Pden_2004 Paracoccus denitrificans PD1222 LysM domain/BON superfamily protein YP_915792.1 2010277 D 318586 CDS YP_915793.1 119384737 4578674 2010891..2012780 1 NC_008686.1 activates fatty acids by binding to coenzyme A; AMP-binding protein 2012780 4578674 Pden_2005 Paracoccus denitrificans PD1222 AMP-binding protein YP_915793.1 2010891 D 318586 CDS YP_915794.1 119384738 4578675 2012982..2014001 1 NC_008686.1 KEGG: sit:TM1040_2837 conserved hypothetical protein; hypothetical protein 2014001 4578675 Pden_2006 Paracoccus denitrificans PD1222 hypothetical protein YP_915794.1 2012982 D 318586 CDS YP_915795.1 119384739 4578676 2014058..2015065 1 NC_008686.1 KEGG: sil:SPO3503 hypothetical protein; hypothetical protein 2015065 4578676 Pden_2007 Paracoccus denitrificans PD1222 hypothetical protein YP_915795.1 2014058 D 318586 CDS YP_915796.1 119384740 4578677 complement(2015124..2016779) 1 NC_008686.1 ChvD; in Agrobacterium tumefaciens, mutations in both Walker boxes were found to affect virulence; ABC transporter ATP-binding protein 2016779 4578677 Pden_2008 Paracoccus denitrificans PD1222 ABC transporter ATP-binding protein YP_915796.1 2015124 R 318586 CDS YP_915797.1 119384741 4578678 complement(2016852..2017709) 1 NC_008686.1 PFAM: sulfotransferase; KEGG: syg:sync_0226 hypothetical protein; sulfotransferase 2017709 4578678 Pden_2009 Paracoccus denitrificans PD1222 sulfotransferase YP_915797.1 2016852 R 318586 CDS YP_915798.1 119384742 4578679 complement(2017786..2019177) 1 NC_008686.1 catalyzes the methylthiolation of an aspartic acid residue of the S12 protein of the 30S ribosomal subunit; 30S ribosomal protein S12 methylthiotransferase 2019177 rimO 4578679 rimO Paracoccus denitrificans PD1222 30S ribosomal protein S12 methylthiotransferase YP_915798.1 2017786 R 318586 CDS YP_915799.1 119384743 4578680 2019275..2019745 1 NC_008686.1 hypothetical protein 2019745 4578680 Pden_2011 Paracoccus denitrificans PD1222 hypothetical protein YP_915799.1 2019275 D 318586 CDS YP_915800.1 119384744 4578681 2019730..2020119 1 NC_008686.1 hypothetical protein 2020119 4578681 Pden_2012 Paracoccus denitrificans PD1222 hypothetical protein YP_915800.1 2019730 D 318586 CDS YP_915801.1 119384745 4578682 complement(2020124..2020885) 1 NC_008686.1 PFAM: ABC-2 type transporter; KEGG: sit:TM1040_2524 ABC-2 type transporter; ABC transporter 2020885 4578682 Pden_2013 Paracoccus denitrificans PD1222 ABC transporter YP_915801.1 2020124 R 318586 CDS YP_915802.1 119384746 4580398 complement(2020882..2021811) 1 NC_008686.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: jan:Jann_0746 ABC transporter related; ABC transporter 2021811 4580398 Pden_2014 Paracoccus denitrificans PD1222 ABC transporter YP_915802.1 2020882 R 318586 CDS YP_915803.1 119384747 4580399 complement(2021929..2022711) 1 NC_008686.1 PFAM: phospholipid/glycerol acyltransferase; KEGG: rde:RD1_1601 acyltransferase; phospholipid/glycerol acyltransferase 2022711 4580399 Pden_2015 Paracoccus denitrificans PD1222 phospholipid/glycerol acyltransferase YP_915803.1 2021929 R 318586 CDS YP_915804.1 119384748 4580400 complement(2022711..2023640) 1 NC_008686.1 PFAM: protein of unknown function DUF214; KEGG: rsp:RSP_0734 cell division protein FtsX; hypothetical protein 2023640 4580400 Pden_2016 Paracoccus denitrificans PD1222 hypothetical protein YP_915804.1 2022711 R 318586 CDS YP_915805.1 119384749 4580401 complement(2023637..2024311) 1 NC_008686.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sil:SPO0337 cell division ATP-binding protein FtsE; ABC transporter 2024311 4580401 Pden_2017 Paracoccus denitrificans PD1222 ABC transporter YP_915805.1 2023637 R 318586 CDS YP_915806.1 119384750 4580402 2024436..2025395 1 NC_008686.1 TIGRFAM: MJ0042 family finger-like protein; KEGG: rsp:RSP_0732 hypothetical protein; Zinc finger-domain-containing protein 2025395 4580402 Pden_2018 Paracoccus denitrificans PD1222 Zinc finger-domain-containing protein YP_915806.1 2024436 D 318586 CDS YP_915807.1 119384751 4580403 complement(2025475..2027979) 1 NC_008686.1 KEGG: rsp:RSP_0730 hypothetical protein; hypothetical protein 2027979 4580403 Pden_2019 Paracoccus denitrificans PD1222 hypothetical protein YP_915807.1 2025475 R 318586 CDS YP_915808.1 119384752 4580404 complement(2028070..2029335) 1 NC_008686.1 TIGRFAM: diaminopimelate decarboxylase; PFAM: Orn/DAP/Arg decarboxylase 2; KEGG: rsp:RSP_0729 Orn/DAP/Arg decarboxylase, family 2; diaminopimelate decarboxylase 2029335 4580404 Pden_2020 Paracoccus denitrificans PD1222 diaminopimelate decarboxylase YP_915808.1 2028070 R 318586 CDS YP_915809.1 119384753 4580405 complement(2029335..2029610) 1 NC_008686.1 KEGG: rsp:RSP_0728 hypothetical protein; hypothetical protein 2029610 4580405 Pden_2021 Paracoccus denitrificans PD1222 hypothetical protein YP_915809.1 2029335 R 318586 CDS YP_915810.1 119384754 4580406 complement(2029755..2031164) 1 NC_008686.1 catalyzes the formation of arginine from (N-L-arginino)succinate; argininosuccinate lyase 2031164 4580406 Pden_2022 Paracoccus denitrificans PD1222 argininosuccinate lyase YP_915810.1 2029755 R 318586 CDS YP_915811.1 119384755 4580407 2031256..2031741 1 NC_008686.1 PFAM: Redoxin domain protein; Thioredoxin domain; KEGG: rsp:RSP_0725 thioredoxin, thioldisulfide interchange protein; redoxin domain-containing protein 2031741 4580407 Pden_2023 Paracoccus denitrificans PD1222 redoxin domain-containing protein YP_915811.1 2031256 D 318586 CDS YP_915812.1 119384756 4580408 complement(2031719..2032303) 1 NC_008686.1 KEGG: rsp:RSP_0744 DNA-3-methyladenine glycosylase I; TIGRFAM: DNA-3-methyladenine glycosylase I; PFAM: methyladenine glycosylase; DNA-3-methyladenine glycosylase I 2032303 4580408 Pden_2024 Paracoccus denitrificans PD1222 DNA-3-methyladenine glycosylase I YP_915812.1 2031719 R 318586 CDS YP_915813.1 119384757 4580409 2032396..2033223 1 NC_008686.1 PFAM: EAL domain protein; KEGG: jan:Jann_0494 diguanylate phosphodiesterase; diguanylate phosphodiesterase 2033223 4580409 Pden_2025 Paracoccus denitrificans PD1222 diguanylate phosphodiesterase YP_915813.1 2032396 D 318586 CDS YP_915814.1 119384758 4580410 2033477..2034652 1 NC_008686.1 Catalyzes the synthesis of acetoacetyl coenzyme A from two molecules of acetyl coenzyme A. It can also act as a thiolase, catalyzing the reverse reaction and generating two-carbon units from the four-carbon product of fatty acid oxidation; in Rhizobia and Ralstonia is involved in PHB biosynthesis; acetyl-CoA acetyltransferase 2034652 4580410 Pden_2026 Paracoccus denitrificans PD1222 acetyl-CoA acetyltransferase YP_915814.1 2033477 D 318586 CDS YP_915815.1 119384759 4580411 2034739..2035464 1 NC_008686.1 TIGRFAM: acetoacetyl-CoA reductase; PFAM: short-chain dehydrogenase/reductase SDR; KR; KEGG: rsp:RSP_0747 short-chain dehydrogenase/reductase; acetoacetyl-CoA reductase 2035464 4580411 Pden_2027 Paracoccus denitrificans PD1222 acetoacetyl-CoA reductase YP_915815.1 2034739 D 318586 CDS YP_915816.1 119384760 4580412 complement(2035563..2035781) 1 NC_008686.1 PFAM: protein of unknown function DUF465; KEGG: rde:RD1_3398 hypothetical protein; hypothetical protein 2035781 4580412 Pden_2028 Paracoccus denitrificans PD1222 hypothetical protein YP_915816.1 2035563 R 318586 CDS YP_915817.1 119384761 4580413 complement(2035786..2036544) 1 NC_008686.1 PFAM: methyltransferase small; Methyltransferase type 11; KEGG: rsp:RSP_0748 N-6 adenine-specific DNA methylase; methyltransferase small 2036544 4580413 Pden_2029 Paracoccus denitrificans PD1222 methyltransferase small YP_915817.1 2035786 R 318586 CDS YP_915818.1 119384762 4580414 complement(2036537..2036749) 1 NC_008686.1 KEGG: rsp:RSP_0749 hypothetical protein; hypothetical protein 2036749 4580414 Pden_2030 Paracoccus denitrificans PD1222 hypothetical protein YP_915818.1 2036537 R 318586 CDS YP_915819.1 119384763 4580415 2036825..2037826 1 NC_008686.1 PFAM: Polyprenyl synthetase; KEGG: sit:TM1040_3742 farnesyltranstransferase; trans-hexaprenyltranstransferase 2037826 4580415 Pden_2031 Paracoccus denitrificans PD1222 trans-hexaprenyltranstransferase YP_915819.1 2036825 D 318586 CDS YP_915820.1 119384764 4580416 complement(2037929..2039377) 1 NC_008686.1 TIGRFAM: ammonium transporter; PFAM: Rh family protein/ammonium transporter; KEGG: mca:MCA2136 ammonium transporter; ammonium transporter 2039377 4580416 Pden_2032 Paracoccus denitrificans PD1222 ammonium transporter YP_915820.1 2037929 R 318586 CDS YP_915821.1 119384765 4580417 2039634..2041964 1 NC_008686.1 KEGG: rsp:RSP_0887 glycosyl transferase, family 51; TIGRFAM: penicillin-binding protein, 1A family; PFAM: glycosyl transferase, family 51; penicillin-binding protein, transpeptidase; 1A family penicillin-binding protein 2041964 4580417 Pden_2033 Paracoccus denitrificans PD1222 1A family penicillin-binding protein YP_915821.1 2039634 D 318586 CDS YP_915822.1 119384766 4580418 complement(2042017..2042622) 1 NC_008686.1 PFAM: toluene tolerance family protein; KEGG: rsp:RSP_0890 possible protein YrbC precursor; toluene tolerance family protein 2042622 4580418 Pden_2034 Paracoccus denitrificans PD1222 toluene tolerance family protein YP_915822.1 2042017 R 318586 CDS YP_915823.1 119384767 4580419 complement(2042603..2043328) 1 NC_008686.1 PFAM: VacJ family lipoprotein; KEGG: sil:SPO3727 VacJ lipoprotein; VacJ family lipoprotein 2043328 4580419 Pden_2035 Paracoccus denitrificans PD1222 VacJ family lipoprotein YP_915823.1 2042603 R 318586 CDS YP_915824.1 119384768 4580420 2043489..2045231 1 NC_008686.1 KEGG: rsp:RSP_0892 ABC protein toxin exporter, fused ATPase and inner membrane domain; TIGRFAM: type I secretion system ATPase; PFAM: ABC transporter related; SMART: AAA ATPase; type I secretion system ATPase 2045231 4580420 Pden_2036 Paracoccus denitrificans PD1222 type I secretion system ATPase YP_915824.1 2043489 D 318586 CDS YP_915825.1 119384769 4580421 2045228..2046661 1 NC_008686.1 TIGRFAM: type I secretion membrane fusion protein, HlyD family; PFAM: secretion protein HlyD family protein; KEGG: rsp:RSP_0893 RTX secretion protein D, HlyD family; HlyD family type I secretion membrane fusion protein 2046661 4580421 Pden_2037 Paracoccus denitrificans PD1222 HlyD family type I secretion membrane fusion protein YP_915825.1 2045228 D 318586 CDS YP_915826.1 119384770 4580422 2046692..2046952 1 NC_008686.1 hypothetical protein 2046952 4580422 Pden_2038 Paracoccus denitrificans PD1222 hypothetical protein YP_915826.1 2046692 D 318586 CDS YP_915827.1 119384771 4580423 complement(2047060..2047986) 1 NC_008686.1 catalyzes the formation of L-citrulline from carbamoyl phosphate and L-ornithine in arginine biosynthesis and degradation; ornithine carbamoyltransferase 2047986 4580423 Pden_2039 Paracoccus denitrificans PD1222 ornithine carbamoyltransferase YP_915827.1 2047060 R 318586 CDS YP_915828.1 119384772 4580424 complement(2048084..2048560) 1 NC_008686.1 PFAM: GCN5-related N-acetyltransferase; KEGG: mlo:mll5006 aminoglycoside 6'-N-acetyltransferase; N-acetyltransferase 2048560 4580424 Pden_2040 Paracoccus denitrificans PD1222 N-acetyltransferase YP_915828.1 2048084 R 318586 CDS YP_915829.1 119384773 4580425 complement(2048553..2049725) 1 NC_008686.1 DapATase; functions in arginine biosynthetic pathway; catalyzes the formation of N-acetyl-L-glutamate 5-semialdehyde from 2-oxoglutarate and N(2)-acetyl-L-ornithine; acetylornithine transaminase protein 2049725 argD 4580425 argD Paracoccus denitrificans PD1222 acetylornithine transaminase protein YP_915829.1 2048553 R 318586 CDS YP_915830.1 119384774 4580426 complement(2049899..2050720) 1 NC_008686.1 PFAM: ABC-2 type transporter; KEGG: sil:SPO0957 ABC transporter, permease protein; ABC transporter 2050720 4580426 Pden_2042 Paracoccus denitrificans PD1222 ABC transporter YP_915830.1 2049899 R 318586 CDS YP_915831.1 119384775 4580427 2050852..2051457 1 NC_008686.1 PFAM: GcrA cell cycle regulator; KEGG: rsp:RSP_2007 conservd hypothetical protein; GcrA cell cycle regulator 2051457 4580427 Pden_2043 Paracoccus denitrificans PD1222 GcrA cell cycle regulator YP_915831.1 2050852 D 318586 CDS YP_915832.1 119384776 4580428 2051458..2051901 1 NC_008686.1 PFAM: NUDIX hydrolase; KEGG: sit:TM1040_3067 NUDIX hydrolase; NUDIX hydrolase 2051901 4580428 Pden_2044 Paracoccus denitrificans PD1222 NUDIX hydrolase YP_915832.1 2051458 D 318586 CDS YP_915833.1 119384777 4580429 2052010..2053728 1 NC_008686.1 methionine--tRNA ligase; MetRS; adds methionine to tRNA(Met) with cleavage of ATP to AMP and diphosphate; some MetRS enzymes form dimers depending on a C-terminal domain that is also found in other proteins such as Trbp111 in Aquifex aeolicus and the cold-shock protein CsaA from Bacillus subtilis while others do not; four subfamilies exist based on sequence motifs and zinc content; methionyl-tRNA synthetase 2053728 4580429 Pden_2045 Paracoccus denitrificans PD1222 methionyl-tRNA synthetase YP_915833.1 2052010 D 318586 CDS YP_915834.1 119384778 4580430 2053922..2056063 1 NC_008686.1 PFAM: TonB-dependent receptor; TonB-dependent receptor, plug; KEGG: atc:AGR_L_1858 outer membrane protein irgA precursor; TonB-dependent receptor 2056063 4580430 Pden_2046 Paracoccus denitrificans PD1222 TonB-dependent receptor YP_915834.1 2053922 D 318586 CDS YP_915835.1 119384779 4580431 2056156..2057076 1 NC_008686.1 TIGRFAM: arginase; PFAM: Arginase/agmatinase/formiminoglutamase; KEGG: rsp:RSP_2632 arginase; arginase 2057076 4580431 Pden_2047 Paracoccus denitrificans PD1222 arginase YP_915835.1 2056156 D 318586 CDS YP_915836.1 119384780 4580432 complement(2057392..2057754) 1 NC_008686.1 hypothetical protein 2057754 4580432 Pden_2048 Paracoccus denitrificans PD1222 hypothetical protein YP_915836.1 2057392 R 318586 CDS YP_915837.1 119384781 4580433 complement(2057841..2058308) 1 NC_008686.1 hypothetical protein 2058308 4580433 Pden_2049 Paracoccus denitrificans PD1222 hypothetical protein YP_915837.1 2057841 R 318586 CDS YP_915838.1 119384782 4580434 complement(2059246..2059770) 1 NC_008686.1 hypothetical protein 2059770 4580434 Pden_2050 Paracoccus denitrificans PD1222 hypothetical protein YP_915838.1 2059246 R 318586 CDS YP_915839.1 119384783 4580435 complement(2059763..2060041) 1 NC_008686.1 hypothetical protein 2060041 4580435 Pden_2051 Paracoccus denitrificans PD1222 hypothetical protein YP_915839.1 2059763 R 318586 CDS YP_915840.1 119384784 4580436 2060592..2060891 1 NC_008686.1 hypothetical protein 2060891 4580436 Pden_2052 Paracoccus denitrificans PD1222 hypothetical protein YP_915840.1 2060592 D 318586 CDS YP_915841.1 119384785 4578917 2060891..2061109 1 NC_008686.1 hypothetical protein 2061109 4578917 Pden_2053 Paracoccus denitrificans PD1222 hypothetical protein YP_915841.1 2060891 D 318586 CDS YP_915842.1 119384786 4578918 2061405..2062328 1 NC_008686.1 KEGG: nha:Nham_2360 hypothetical protein; hypothetical protein 2062328 4578918 Pden_2054 Paracoccus denitrificans PD1222 hypothetical protein YP_915842.1 2061405 D 318586 CDS YP_915843.1 119384787 4578919 2063243..2063758 1 NC_008686.1 hypothetical protein 2063758 4578919 Pden_2055 Paracoccus denitrificans PD1222 hypothetical protein YP_915843.1 2063243 D 318586 CDS YP_915844.1 119384788 4578920 complement(2063766..2065175) 1 NC_008686.1 KEGG: xft:PD1844 hypothetical protein; hypothetical protein 2065175 4578920 Pden_2056 Paracoccus denitrificans PD1222 hypothetical protein YP_915844.1 2063766 R 318586 CDS YP_915845.1 119384789 4578921 2065343..2065744 1 NC_008686.1 hypothetical protein 2065744 4578921 Pden_2057 Paracoccus denitrificans PD1222 hypothetical protein YP_915845.1 2065343 D 318586 CDS YP_915846.1 119384790 4578922 complement(2065737..2066510) 1 NC_008686.1 KEGG: jan:Jann_0233 hypothetical protein; hypothetical protein 2066510 4578922 Pden_2058 Paracoccus denitrificans PD1222 hypothetical protein YP_915846.1 2065737 R 318586 CDS YP_915847.1 119384791 4578923 complement(2066523..2066894) 1 NC_008686.1 KEGG: nar:Saro_2759 transposase orfA IS5 family element; IS5 family transposase OrfA 2066894 4578923 Pden_2059 Paracoccus denitrificans PD1222 IS5 family transposase OrfA YP_915847.1 2066523 R 318586 CDS YP_915848.1 119384792 4578924 2067123..2067452 1 NC_008686.1 PFAM: HNH endonuclease; SMART: HNH nuclease; KEGG: reu:Reut_A0008 HNH endonuclease; HNH endonuclease 2067452 4578924 Pden_2060 Paracoccus denitrificans PD1222 HNH endonuclease YP_915848.1 2067123 D 318586 CDS YP_915849.1 119384793 4578925 complement(2067435..2068970) 1 NC_008686.1 TIGRFAM: DNA-cytosine methyltransferase; PFAM: C-5 cytosine-specific DNA methylase; KEGG: jan:Jann_2858 DNA-cytosine methyltransferase; DNA-cytosine methyltransferase 2068970 4578925 Pden_2061 Paracoccus denitrificans PD1222 DNA-cytosine methyltransferase YP_915849.1 2067435 R 318586 CDS YP_915850.1 119384794 4578926 2069038..2069502 1 NC_008686.1 PFAM: DNA mismatch endonuclease vsr; KEGG: dvu:DVU2843 DNA mismatch endonuclease Vsr; DNA mismatch endonuclease vsr 2069502 4578926 Pden_2062 Paracoccus denitrificans PD1222 DNA mismatch endonuclease vsr YP_915850.1 2069038 D 318586 CDS YP_915851.1 119384795 4578927 complement(2069678..2070169) 1 NC_008686.1 KEGG: son:SO2967 hypothetical phage terminase large subunit; phage terminase large subunit 2070169 4578927 Pden_2063 Paracoccus denitrificans PD1222 phage terminase large subunit YP_915851.1 2069678 R 318586 CDS YP_915852.1 119384796 4578928 complement(2070153..2070623) 1 NC_008686.1 TIGRFAM: phage terminase, small subunit, , P27 family; PFAM: phage terminase, small subunit, , P27; KEGG: dvu:DVU1504 terminase, small subunit; P27 family phage terminase small subunit 2070623 4578928 Pden_2064 Paracoccus denitrificans PD1222 P27 family phage terminase small subunit YP_915852.1 2070153 R 318586 CDS YP_915853.1 119384797 4578929 2070830..2071036 1 NC_008686.1 PFAM: Cold-shock protein, DNA-binding; SMART: Cold shock protein; KEGG: rsp:RSP_3621 cold-shock DNA-binding protein; cold-shock DNA-binding domain-containing protein 2071036 4578929 Pden_2065 Paracoccus denitrificans PD1222 cold-shock DNA-binding domain-containing protein YP_915853.1 2070830 D 318586 CDS YP_915854.1 119384798 4578930 2071116..2071421 1 NC_008686.1 KEGG: rsp:RSP_3622 hypothetical protein; hypothetical protein 2071421 4578930 Pden_2066 Paracoccus denitrificans PD1222 hypothetical protein YP_915854.1 2071116 D 318586 CDS YP_915855.1 119384799 4578931 complement(2071691..2071915) 1 NC_008686.1 KEGG: mag:amb1162 hypothetical protein; hypothetical protein 2071915 4578931 Pden_2067 Paracoccus denitrificans PD1222 hypothetical protein YP_915855.1 2071691 R 318586 CDS YP_915856.1 119384800 4578932 complement(2071912..2073303) 1 NC_008686.1 PFAM: DNA methylase N-4/N-6 domain protein; ParB domain protein nuclease; KEGG: mag:amb0363 modification methylase DpnIIB; nuclease 2073303 4578932 Pden_2068 Paracoccus denitrificans PD1222 nuclease YP_915856.1 2071912 R 318586 CDS YP_915857.1 119384801 4578933 complement(2073402..2073797) 1 NC_008686.1 PFAM: HNH endonuclease; SMART: HNH nuclease; KEGG: rso:RSc1680 probable phage PHI-105 holin-like protein; HNH endonuclease 2073797 4578933 Pden_2069 Paracoccus denitrificans PD1222 HNH endonuclease YP_915857.1 2073402 R 318586 CDS YP_915858.1 119384802 4578934 complement(2073885..2074262) 1 NC_008686.1 KEGG: hch:HCH_05683 hypothetical protein; hypothetical protein 2074262 4578934 Pden_2070 Paracoccus denitrificans PD1222 hypothetical protein YP_915858.1 2073885 R 318586 CDS YP_915859.1 119384803 4578935 complement(2074255..2074743) 1 NC_008686.1 KEGG: mag:amb0360 hypothetical protein; hypothetical protein 2074743 4578935 Pden_2071 Paracoccus denitrificans PD1222 hypothetical protein YP_915859.1 2074255 R 318586 CDS YP_915860.1 119384804 4578936 complement(2074747..2076405) 1 NC_008686.1 KEGG: ade:Adeh_1681 PE-PGRS family protein; hypothetical protein 2076405 4578936 Pden_2072 Paracoccus denitrificans PD1222 hypothetical protein YP_915860.1 2074747 R 318586 CDS YP_915861.1 119384805 4578937 complement(2076402..2076602) 1 NC_008686.1 hypothetical protein 2076602 4578937 Pden_2073 Paracoccus denitrificans PD1222 hypothetical protein YP_915861.1 2076402 R 318586 CDS YP_915862.1 119384806 4578938 2076726..2076965 1 NC_008686.1 KEGG: bbr:BB2472 plasmid stability protein; plasmid stability protein 2076965 4578938 Pden_2074 Paracoccus denitrificans PD1222 plasmid stability protein YP_915862.1 2076726 D 318586 CDS YP_915863.1 119384807 4578939 2076962..2077396 1 NC_008686.1 PFAM: PilT protein domain protein; KEGG: gox:GOX2696 plasmid stabilization protein; twitching motility protein PilT 2077396 4578939 Pden_2075 Paracoccus denitrificans PD1222 twitching motility protein PilT YP_915863.1 2076962 D 318586 CDS YP_915864.1 119384808 4578940 complement(2077384..2078100) 1 NC_008686.1 KEGG: mxa:MXAN_1879 hypothetical protein; ECF subfamily RNA polymerase sigma-24 factor 2078100 4578940 Pden_2076 Paracoccus denitrificans PD1222 ECF subfamily RNA polymerase sigma-24 factor YP_915864.1 2077384 R 318586 CDS YP_915865.1 119384809 4578941 complement(2078198..2078431) 1 NC_008686.1 hypothetical protein 2078431 4578941 Pden_2077 Paracoccus denitrificans PD1222 hypothetical protein YP_915865.1 2078198 R 318586 CDS YP_915866.1 119384810 4578942 complement(2078525..2080687) 1 NC_008686.1 KEGG: rso:RSc3240 hypothetical protein; hypothetical protein 2080687 4578942 Pden_2078 Paracoccus denitrificans PD1222 hypothetical protein YP_915866.1 2078525 R 318586 CDS YP_915867.1 119384811 4578943 2080770..2081024 1 NC_008686.1 hypothetical protein 2081024 4578943 Pden_2079 Paracoccus denitrificans PD1222 hypothetical protein YP_915867.1 2080770 D 318586 CDS YP_915868.1 119384812 4578944 2081021..2081476 1 NC_008686.1 KEGG: nwi:Nwi_1952 hypothetical protein; hypothetical protein 2081476 4578944 Pden_2080 Paracoccus denitrificans PD1222 hypothetical protein YP_915868.1 2081021 D 318586 CDS YP_915869.1 119384813 4578945 2081476..2082801 1 NC_008686.1 PFAM: Resolvase, N-terminal domain; Recombinase; KEGG: nwi:Nwi_1951 resolvase; recombinase 2082801 4578945 Pden_2081 Paracoccus denitrificans PD1222 recombinase YP_915869.1 2081476 D 318586 CDS YP_915870.1 119384814 4578946 2082798..2083181 1 NC_008686.1 KEGG: nwi:Nwi_2834 hypothetical protein; hypothetical protein 2083181 4578946 Pden_2082 Paracoccus denitrificans PD1222 hypothetical protein YP_915870.1 2082798 D 318586 CDS YP_915871.1 119384815 4578947 complement(2083185..2084021) 1 NC_008686.1 KEGG: rsp:RSP_3808 hypothetical protein; hypothetical protein 2084021 4578947 Pden_2083 Paracoccus denitrificans PD1222 hypothetical protein YP_915871.1 2083185 R 318586 CDS YP_915872.1 119384816 4578948 complement(2084031..2084288) 1 NC_008686.1 hypothetical protein 2084288 4578948 Pden_2084 Paracoccus denitrificans PD1222 hypothetical protein YP_915872.1 2084031 R 318586 CDS YP_915873.1 119384817 4578949 2084523..2085431 1 NC_008686.1 KEGG: nar:Saro_2176 hypothetical protein; hypothetical protein 2085431 4578949 Pden_2085 Paracoccus denitrificans PD1222 hypothetical protein YP_915873.1 2084523 D 318586 CDS YP_915874.1 119384818 4578950 2085415..2087601 1 NC_008686.1 PFAM: Ankyrin; sigma-70 region 2 domain protein; sigma-70 region 4 domain protein; KEGG: tpa:TP0493 RNA polymerase sigma-70 factor; RNA polymerase sigma-32 subunit RpoH 2087601 4578950 Pden_2086 Paracoccus denitrificans PD1222 RNA polymerase sigma-32 subunit RpoH YP_915874.1 2085415 D 318586 CDS YP_915875.1 119384819 4578951 2087606..2089108 1 NC_008686.1 KEGG: rfr:Rfer_3071 hypothetical protein; hypothetical protein 2089108 4578951 Pden_2087 Paracoccus denitrificans PD1222 hypothetical protein YP_915875.1 2087606 D 318586 CDS YP_915876.1 119384820 4578952 2089105..2091972 1 NC_008686.1 KEGG: rfr:Rfer_3072 endonuclease; endonuclease 2091972 4578952 Pden_2088 Paracoccus denitrificans PD1222 endonuclease YP_915876.1 2089105 D 318586 CDS YP_915877.1 119384821 4578953 2091956..2092960 1 NC_008686.1 KEGG: rfr:Rfer_3073 hypothetical protein; hypothetical protein 2092960 4578953 Pden_2089 Paracoccus denitrificans PD1222 hypothetical protein YP_915877.1 2091956 D 318586 CDS YP_915878.1 119384822 4578954 2092962..2094764 1 NC_008686.1 KEGG: rfr:Rfer_3074 hypothetical protein; hypothetical protein 2094764 4578954 Pden_2090 Paracoccus denitrificans PD1222 hypothetical protein YP_915878.1 2092962 D 318586 CDS YP_915879.1 119384823 4578955 2094772..2095239 1 NC_008686.1 hypothetical protein 2095239 4578955 Pden_2091 Paracoccus denitrificans PD1222 hypothetical protein YP_915879.1 2094772 D 318586 CDS YP_915880.1 119384824 4579889 complement(2095223..2095783) 1 NC_008686.1 PFAM: transposase, IS4 family protein; KEGG: sil:SPOA0134 ISSpo7, transposase; transposase, IS4 family protein 2095783 4579889 Pden_2092 Paracoccus denitrificans PD1222 transposase, IS4 family protein YP_915880.1 2095223 R 318586 CDS YP_915881.1 119384825 4579890 2096063..2097922 1 NC_008686.1 KEGG: rsp:RSP_1461 3-deoxy-D-manno-octulosonic-acid transferase; 3-deoxy-D-manno-octulosonic-acid transferase 2097922 4579890 Pden_2093 Paracoccus denitrificans PD1222 3-deoxy-D-manno-octulosonic-acid transferase YP_915881.1 2096063 D 318586 CDS YP_915882.1 119384826 4579891 2097919..2098908 1 NC_008686.1 transfers the gamma-phosphate of ATP to the 4' position of a tetraacyldisaccharide 1-phosphate intermediate to form tetraacyldisaccharide 1,4'-bis-phosphate; tetraacyldisaccharide 4'-kinase 2098908 lpxK 4579891 lpxK Paracoccus denitrificans PD1222 tetraacyldisaccharide 4'-kinase YP_915882.1 2097919 D 318586 CDS YP_915883.1 119384827 4579892 complement(2098948..2099619) 1 NC_008686.1 PFAM: DSBA oxidoreductase; KEGG: sit:TM1040_2643 thiol:disulfide interchange protein, DsbA family; DSBA oxidoreductase 2099619 4579892 Pden_2095 Paracoccus denitrificans PD1222 DSBA oxidoreductase YP_915883.1 2098948 R 318586 CDS YP_915884.1 119384828 4579893 complement(2099616..2100158) 1 NC_008686.1 PFAM: protein of unknown function DUF1159; KEGG: rsp:RSP_1465 hypothetical protein; hypothetical protein 2100158 4579893 Pden_2096 Paracoccus denitrificans PD1222 hypothetical protein YP_915884.1 2099616 R 318586 CDS YP_915885.1 119384829 4579894 2100310..2101296 1 NC_008686.1 PFAM: helix-hairpin-helix motif; HhH-GPD family protein; SMART: iron-sulfur cluster loop; KEGG: rsp:RSP_1466 MutY, A/G-specific adenine glycosylase; HhH-GPD family protein 2101296 4579894 Pden_2097 Paracoccus denitrificans PD1222 HhH-GPD family protein YP_915885.1 2100310 D 318586 CDS YP_915886.1 119384830 4579895 2101374..2102516 1 NC_008686.1 PFAM: fatty acid desaturase; KEGG: sit:TM1040_2646 alkane-1 monooxygenase; alkane 1-monooxygenase 2102516 4579895 Pden_2098 Paracoccus denitrificans PD1222 alkane 1-monooxygenase YP_915886.1 2101374 D 318586 CDS YP_915887.1 119384831 4579896 complement(2102511..2103296) 1 NC_008686.1 hypothetical protein 2103296 4579896 Pden_2099 Paracoccus denitrificans PD1222 hypothetical protein YP_915887.1 2102511 R 318586 CDS YP_915888.1 119384832 4579897 complement(2103293..2104414) 1 NC_008686.1 KEGG: jan:Jann_1007 hypothetical protein; hypothetical protein 2104414 4579897 Pden_2100 Paracoccus denitrificans PD1222 hypothetical protein YP_915888.1 2103293 R 318586 CDS YP_915889.1 119384833 4579898 complement(2104472..2105602) 1 NC_008686.1 PFAM: DNA methylase N-4/N-6 domain protein; KEGG: rsp:RSP_1468 site-specific DNA-methyltransferase; DNA methylase N-4/N-6 domain-containing protein 2105602 4579898 Pden_2101 Paracoccus denitrificans PD1222 DNA methylase N-4/N-6 domain-containing protein YP_915889.1 2104472 R 318586 CDS YP_915890.1 119384834 4579899 complement(2105691..2106323) 1 NC_008686.1 RNH2; RNase HII; binds manganese; endonuclease which specifically degrades the RNA of RNA-DNA hybrids; ribonuclease HII 2106323 rnhB 4579899 rnhB Paracoccus denitrificans PD1222 ribonuclease HII YP_915890.1 2105691 R 318586 CDS YP_915891.1 119384835 4579900 complement(2106320..2106799) 1 NC_008686.1 PFAM: Ureidoglycolate hydrolase; KEGG: sit:TM1040_3474 ureidoglycolate hydrolase; ureidoglycolate hydrolase 2106799 4579900 Pden_2103 Paracoccus denitrificans PD1222 ureidoglycolate hydrolase YP_915891.1 2106320 R 318586 CDS YP_915892.1 119384836 4579901 complement(2106857..2108032) 1 NC_008686.1 PFAM: major facilitator superfamily MFS_1; KEGG: mlo:mlr2687 probable fosmidomycin resistance protein; major facilitator superfamily transporter 2108032 4579901 Pden_2104 Paracoccus denitrificans PD1222 major facilitator superfamily transporter YP_915892.1 2106857 R 318586 CDS YP_915893.1 119384837 4579902 2108324..2109073 1 NC_008686.1 PFAM: regulatory protein GntR, HTH; UbiC transcription regulator-associated domain protein; KEGG: sil:SPO1369 transcriptional regulator, GntR family; UbiC transcription regulator-associated domain-containing protein 2109073 4579902 Pden_2105 Paracoccus denitrificans PD1222 UbiC transcription regulator-associated domain-containing protein YP_915893.1 2108324 D 318586 CDS YP_915894.1 119384838 4579903 2109183..2110664 1 NC_008686.1 PFAM: Peptidoglycan-binding domain 1 protein; ErfK/YbiS/YcfS/YnhG family protein; KEGG: ret:RHE_CH01741 hypothetical protein; ErfK/YbiS/YcfS/YnhG family protein 2110664 4579903 Pden_2106 Paracoccus denitrificans PD1222 ErfK/YbiS/YcfS/YnhG family protein YP_915894.1 2109183 D 318586 CDS YP_915895.1 119384839 4579904 2110666..2111502 1 NC_008686.1 PFAM: Extensin family protein; KEGG: sme:SMc02727 hypothetical protein; extensin family protein 2111502 4579904 Pden_2107 Paracoccus denitrificans PD1222 extensin family protein YP_915895.1 2110666 D 318586 CDS YP_915896.1 119384840 4579905 complement(2111506..2112237) 1 NC_008686.1 PFAM: cyclic nucleotide-binding; regulatory protein, Crp; KEGG: mlo:mll3135 transcriptional regulator, Fnr-type; Crp/Fnr family transcriptional regulator 2112237 4579905 Pden_2108 Paracoccus denitrificans PD1222 Crp/Fnr family transcriptional regulator YP_915896.1 2111506 R 318586 CDS YP_915897.1 119384841 4579906 complement(2112344..2113678) 1 NC_008686.1 KEGG: rsp:RSP_1332 H+-transporting two-sector ATPase, alpha/beta subunit; TIGRFAM: ATPase, FliI/YscN family; PFAM: H+-transporting two-sector ATPase, alpha/beta subunit, central region; SMART: AAA ATPase; FliI/YscN family ATPase 2113678 4579906 Pden_2109 Paracoccus denitrificans PD1222 FliI/YscN family ATPase YP_915897.1 2112344 R 318586 CDS YP_915898.1 119384842 4579907 2113787..2114176 1 NC_008686.1 with FlgF and C makes up the proximal portion of the flagellar basal body rod; flagellar basal-body rod protein FlgB 2114176 flgB 4579907 flgB Paracoccus denitrificans PD1222 flagellar basal-body rod protein FlgB YP_915898.1 2113787 D 318586 CDS YP_915899.1 119384843 4579908 2114188..2114580 1 NC_008686.1 with FlgF and B makes up the proximal portion of the flagellar basal body rod; flagellar basal body rod protein FlgC 2114580 flgC 4579908 flgC Paracoccus denitrificans PD1222 flagellar basal body rod protein FlgC YP_915899.1 2114188 D 318586 CDS YP_915900.1 119384844 4579909 2114592..2114870 1 NC_008686.1 PFAM: flagellar hook-basal body complex protein FliE; KEGG: rsp:RSP_1329 flagellar hook-basal body complex protein; flagellar hook-basal body complex protein FliE 2114870 4579909 Pden_2112 Paracoccus denitrificans PD1222 flagellar hook-basal body complex protein FliE YP_915900.1 2114592 D 318586 CDS YP_915901.1 119384845 4579910 2114881..2115147 1 NC_008686.1 PFAM: export protein FliQ, family 3; KEGG: rsp:RSP_1328 flagellar biosynthetic protein FliQ; export protein FliQ 2115147 4579910 Pden_2113 Paracoccus denitrificans PD1222 export protein FliQ YP_915901.1 2114881 D 318586 CDS YP_915902.1 119384846 4579911 2115151..2115867 1 NC_008686.1 FlgF, with FlgB and C, makes up the proximal portion of the flagellar basal body rod; Rhodobacter sphaeroides has 2 copies of this and other flagella genes; flagellar basal body rod protein FlgF 2115867 flgF 4579911 flgF Paracoccus denitrificans PD1222 flagellar basal body rod protein FlgF YP_915902.1 2115151 D 318586 CDS YP_915903.1 119384847 4579912 2115879..2116664 1 NC_008686.1 makes up the distal portion of the flagellar basal body rod; Bradyrhizobium has one thick flagellum and several thin flagella; the Bradyrhizobium protein in this cluster is associated with the thick flagella; flagellar basal body rod protein FlgG 2116664 flgG 4579912 flgG Paracoccus denitrificans PD1222 flagellar basal body rod protein FlgG YP_915903.1 2115879 D 318586 CDS YP_915904.1 119384848 4579913 2116664..2117080 1 NC_008686.1 required for the assembly of the flagellar basal body P-ring; flagellar basal body P-ring biosynthesis protein FlgA 2117080 flgA 4579913 flgA Paracoccus denitrificans PD1222 flagellar basal body P-ring biosynthesis protein FlgA YP_915904.1 2116664 D 318586 CDS YP_915905.1 119384849 4579914 2117091..2117843 1 NC_008686.1 part of the flagellar basal body which consists of four rings L,P, S and M mounted on a central rod; flagellar basal body L-ring protein 2117843 flgH 4579914 flgH Paracoccus denitrificans PD1222 flagellar basal body L-ring protein YP_915905.1 2117091 D 318586 CDS YP_915906.1 119384850 4579915 2117857..2118390 1 NC_008686.1 KEGG: jan:Jann_4190 hypothetical protein; hypothetical protein 2118390 4579915 Pden_2118 Paracoccus denitrificans PD1222 hypothetical protein YP_915906.1 2117857 D 318586 CDS YP_915907.1 119384851 4579916 complement(2119104..2120006) 1 NC_008686.1 TIGRFAM: glucose-1-phosphate thymidylyltransferase; PFAM: Nucleotidyl transferase; KEGG: sit:TM1040_3859 glucose-1-phosphate thymidylyltransferase; glucose-1-phosphate thymidylyltransferase 2120006 4579916 Pden_2119 Paracoccus denitrificans PD1222 glucose-1-phosphate thymidylyltransferase YP_915907.1 2119104 R 318586 CDS YP_915908.1 119384852 4579917 complement(2120003..2120854) 1 NC_008686.1 PFAM: NAD-dependent epimerase/dehydratase; dTDP-4-dehydrorhamnose reductase; Male sterility C-terminal domain; KEGG: rde:RD1_B0018 dTDP-4-dehydrorhamnose reductase; dTDP-4-dehydrorhamnose reductase 2120854 4579917 Pden_2120 Paracoccus denitrificans PD1222 dTDP-4-dehydrorhamnose reductase YP_915908.1 2120003 R 318586 CDS YP_915909.1 119384853 4579918 complement(2120851..2121888) 1 NC_008686.1 TIGRFAM: dTDP-glucose 4,6-dehydratase; PFAM: NAD-dependent epimerase/dehydratase; short-chain dehydrogenase/reductase SDR; 3-beta hydroxysteroid dehydrogenase/isomerase; polysaccharide biosynthesis protein CapD; dTDP-4-dehydrorhamnose reductase; Male sterility C-terminal domain; KEGG: rde:RD1_B0019 dTDP-glucose 4,6-dehydratase; dTDP-glucose 4,6-dehydratase 2121888 4579918 Pden_2121 Paracoccus denitrificans PD1222 dTDP-glucose 4,6-dehydratase YP_915909.1 2120851 R 318586 CDS YP_915910.1 119384854 4579919 complement(2121885..2122466) 1 NC_008686.1 KEGG: sit:TM1040_3863 dTDP-4-dehydrorhamnose 3,5-epimerase; TIGRFAM: dTDP-4-dehydrorhamnose 3,5-epimerase; PFAM: dTDP-4-dehydrorhamnose 3,5-epimerase related; dTDP-4-dehydrorhamnose 3,5-epimerase 2122466 4579919 Pden_2122 Paracoccus denitrificans PD1222 dTDP-4-dehydrorhamnose 3,5-epimerase YP_915910.1 2121885 R 318586 CDS YP_915911.1 119384855 4579920 2122642..2123313 1 NC_008686.1 hypothetical protein 2123313 4579920 Pden_2123 Paracoccus denitrificans PD1222 hypothetical protein YP_915911.1 2122642 D 318586 CDS YP_915912.1 119384856 4579921 2123332..2126172 1 NC_008686.1 PFAM: Hemolysin-type calcium-binding region; KEGG: ter:Tery_2034 RTX toxins and related Ca2+-binding protein; hemolysin-type calcium-binding protein 2126172 4579921 Pden_2124 Paracoccus denitrificans PD1222 hemolysin-type calcium-binding protein YP_915912.1 2123332 D 318586 CDS YP_915913.1 119384857 4579922 complement(2126169..2126921) 1 NC_008686.1 PFAM: ABC-2 type transporter; KEGG: sme:SMb20833 cell surface polysaccharide export ABC-2 transporter permease protein, close relative of Y20822wzm2; ABC transporter 2126921 4579922 Pden_2125 Paracoccus denitrificans PD1222 ABC transporter YP_915913.1 2126169 R 318586 CDS YP_915914.1 119384858 4579923 2127145..2129103 1 NC_008686.1 KEGG: mes:Meso_2756 capsule polysaccharide export protein-like; capsule polysaccharide export protein 2129103 4579923 Pden_2126 Paracoccus denitrificans PD1222 capsule polysaccharide export protein YP_915914.1 2127145 D 318586 CDS YP_915915.1 119384859 4579924 2129108..2129785 1 NC_008686.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sme:SMb20832 cell surface polysaccharide export ABC-2 transporter ATP-binding protein; ABC transporter 2129785 4579924 Pden_2127 Paracoccus denitrificans PD1222 ABC transporter YP_915915.1 2129108 D 318586 CDS YP_915916.1 119384860 4579925 2129883..2130284 1 NC_008686.1 PFAM: protein of unknown function DUF1486; KEGG: rsp:RSP_0629 hypothetical protein; hypothetical protein 2130284 4579925 Pden_2128 Paracoccus denitrificans PD1222 hypothetical protein YP_915916.1 2129883 D 318586 CDS YP_915917.1 119384861 4579926 2130281..2130862 1 NC_008686.1 KEGG: rsp:RSP_0628 hypothetical protein; hypothetical protein 2130862 4579926 Pden_2129 Paracoccus denitrificans PD1222 hypothetical protein YP_915917.1 2130281 D 318586 CDS YP_915918.1 119384862 4579927 2130871..2131728 1 NC_008686.1 PFAM: Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase; KEGG: rsp:RSP_0627 amidohydrolase; nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase 2131728 4579927 Pden_2130 Paracoccus denitrificans PD1222 nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase YP_915918.1 2130871 D 318586 CDS YP_915919.1 119384863 4579948 complement(2131809..2132297) 1 NC_008686.1 PFAM: GCN5-related N-acetyltransferase; KEGG: bbr:BB0980 GnaT-family acetyltransferase; N-acetyltransferase 2132297 4579948 Pden_2131 Paracoccus denitrificans PD1222 N-acetyltransferase YP_915919.1 2131809 R 318586 CDS YP_915920.1 119384864 4579949 complement(2132432..2133934) 1 NC_008686.1 with component II, the glutamine amidotransferase, catalyzes the formation of anthranilate from chorismate and glutamine; anthranilate synthase component I 2133934 4579949 Pden_2132 Paracoccus denitrificans PD1222 anthranilate synthase component I YP_915920.1 2132432 R 318586 CDS YP_915921.1 119384865 4579950 complement(2133934..2135892) 1 NC_008686.1 KEGG: rsp:RSP_2005 possible peptidyl-prolyl cis-trans isomerse; peptidyl-prolyl cis-trans isomerse 2135892 4579950 Pden_2133 Paracoccus denitrificans PD1222 peptidyl-prolyl cis-trans isomerse YP_915921.1 2133934 R 318586 CDS YP_915922.1 119384866 4579951 complement(2136018..2137193) 1 NC_008686.1 PFAM: aminotransferase, class V; aminotransferase, class I and II; KEGG: rsp:RSP_2341 hypothetical protein; hypothetical protein 2137193 4579951 Pden_2134 Paracoccus denitrificans PD1222 hypothetical protein YP_915922.1 2136018 R 318586 CDS YP_915923.1 119384867 4579952 complement(2137203..2137916) 1 NC_008686.1 KEGG: cel:ZK84.1 Hypothetical protein ZK84.1; hypothetical protein 2137916 4579952 Pden_2135 Paracoccus denitrificans PD1222 hypothetical protein YP_915923.1 2137203 R 318586 CDS YP_915924.1 119384868 4579953 2138071..2138661 1 NC_008686.1 TIGRFAM: glutamine amidotransferase of anthranilate synthase; PFAM: glutamine amidotransferase class-I; KEGG: rsp:RSP_2002 anthranilate synthase component II; glutamine amidotransferase of anthranilate synthase 2138661 4579953 Pden_2136 Paracoccus denitrificans PD1222 glutamine amidotransferase of anthranilate synthase YP_915924.1 2138071 D 318586 CDS YP_915925.1 119384869 4579954 2138658..2139695 1 NC_008686.1 Catalyzes the conversion of N-(5-phospho-D-ribosyl)-anthranilate and diphosphate to anthranilate and 5-phospho-alpha-D-ribose 1-diphosphate; anthranilate phosphoribosyltransferase 2139695 trpD 4579954 trpD Paracoccus denitrificans PD1222 anthranilate phosphoribosyltransferase YP_915925.1 2138658 D 318586 CDS YP_915926.1 119384870 4579955 2139688..2140356 1 NC_008686.1 TIGRFAM: uracil-DNA glycosylase; PFAM: Uracil-DNA glycosylase superfamily; KEGG: sit:TM1040_1139 uracil-DNA glycosylase; uracil-DNA glycosylase 2140356 4579955 Pden_2138 Paracoccus denitrificans PD1222 uracil-DNA glycosylase YP_915926.1 2139688 D 318586 CDS YP_915927.1 119384871 4579956 2140366..2141157 1 NC_008686.1 PFAM: Indole-3-glycerol phosphate synthase; KEGG: sil:SPO2151 indole-3-glycerol phosphate synthase; indole-3-glycerol phosphate synthase 2141157 4579956 Pden_2139 Paracoccus denitrificans PD1222 indole-3-glycerol phosphate synthase YP_915927.1 2140366 D 318586 CDS YP_915928.1 119384872 4579957 2141154..2141627 1 NC_008686.1 TIGRFAM: molybdenum cofactor biosynthesis protein C; PFAM: molybdopterin cofactor biosynthesis MoaC region; KEGG: rsp:RSP_2000 molybdenum cofactor biosynthesis protein C; molybdenum cofactor biosynthesis protein C 2141627 4579957 Pden_2140 Paracoccus denitrificans PD1222 molybdenum cofactor biosynthesis protein C YP_915928.1 2141154 D 318586 CDS YP_915929.1 119384873 4579958 2141638..2142810 1 NC_008686.1 TIGRFAM: molybdenum cofactor synthesis domain; PFAM: molybdopterin binding domain; MoeA domain protein, domain I and II; MoeA domain protein, domain IV; KEGG: rsp:RSP_1998 molybdenum cofactor biosynthesis protein A; molybdenum cofactor synthesis domain-containing protein 2142810 4579958 Pden_2141 Paracoccus denitrificans PD1222 molybdenum cofactor synthesis domain-containing protein YP_915929.1 2141638 D 318586 CDS YP_915930.1 119384874 4579959 2142920..2143618 1 NC_008686.1 Represses a number of genes involved in the response to DNA damage; LexA repressor 2143618 4579959 Pden_2142 Paracoccus denitrificans PD1222 LexA repressor YP_915930.1 2142920 D 318586 CDS YP_915931.1 119384875 4579960 2143743..2144900 1 NC_008686.1 PFAM: peptidase S11, D-alanyl-D-alanine carboxypeptidase 1; Penicillin-binding protein 5 domain protein; KEGG: rsp:RSP_0550 D-alanyl-D-alanine carboxypeptidase; serine-type D-Ala-D-Ala carboxypeptidase 2144900 4579960 Pden_2143 Paracoccus denitrificans PD1222 serine-type D-Ala-D-Ala carboxypeptidase YP_915931.1 2143743 D 318586 CDS YP_915932.1 119384876 4579961 2144912..2145511 1 NC_008686.1 PFAM: thymidylate kinase; KEGG: sil:SPO2740 thymidylate kinase; dTMP kinase 2145511 4579961 Pden_2144 Paracoccus denitrificans PD1222 dTMP kinase YP_915932.1 2144912 D 318586 CDS YP_915933.1 119384877 4579962 2145508..2146605 1 NC_008686.1 catalyzes the DNA-template-directed extension of the 3'-end of a DNA strand; the delta' subunit seems to interact with the gamma subunit to transfer the beta subunit on the DNA; DNA polymerase III subunit delta' 2146605 4579962 Pden_2145 Paracoccus denitrificans PD1222 DNA polymerase III subunit delta' YP_915933.1 2145508 D 318586 CDS YP_915934.1 119384878 4579963 2146618..2147415 1 NC_008686.1 TIGRFAM: hydrolase, TatD family; PFAM: TatD-related deoxyribonuclease; amidohydrolase 2; KEGG: rsp:RSP_0675 TatD-related deoxyribonuclease; TatD family hydrolase 2147415 4579963 Pden_2146 Paracoccus denitrificans PD1222 TatD family hydrolase YP_915934.1 2146618 D 318586 CDS YP_915935.1 119384879 4579964 2147412..2148212 1 NC_008686.1 PFAM: beta-lactamase domain protein; KEGG: rsp:RSP_0676 PhnP-like protein; beta-lactamase domain-containing protein 2148212 4579964 Pden_2147 Paracoccus denitrificans PD1222 beta-lactamase domain-containing protein YP_915935.1 2147412 D 318586 CDS YP_915936.1 119384880 4579965 2148209..2149153 1 NC_008686.1 PFAM: Auxin Efflux Carrier; KEGG: rsp:RSP_0677 malonate transporter, MdcF, AEC family; auxin efflux carrier 2149153 4579965 Pden_2148 Paracoccus denitrificans PD1222 auxin efflux carrier YP_915936.1 2148209 D 318586 CDS YP_915937.1 119384881 4579966 complement(2149189..2150142) 1 NC_008686.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: rsp:RSP_1886 ABC polyamine/opine transporter, inner membrane subunit; binding-protein-dependent transport system inner membrane protein 2150142 4579966 Pden_2149 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_915937.1 2149189 R 318586 CDS YP_915938.1 119384882 4579967 complement(2150148..2151449) 1 NC_008686.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: rsp:RSP_1884 ABC polyamine/opine transporter, inner membrane subunit; binding-protein-dependent transport system inner membrane protein 2151449 4579967 Pden_2150 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_915938.1 2150148 R 318586 CDS YP_915939.1 119384883 4579968 complement(2151524..2152603) 1 NC_008686.1 KEGG: sil:SPO3473 polyamine ABC trasnporter, periplasmic polyamine-binding protein; polyamine ABC transporter periplasmic substrate-binding protein 2152603 4579968 Pden_2151 Paracoccus denitrificans PD1222 polyamine ABC transporter periplasmic substrate-binding protein YP_915939.1 2151524 R 318586 CDS YP_915940.1 119384884 4579969 complement(2152702..2153784) 1 NC_008686.1 PFAM: extracellular solute-binding protein, family 1; KEGG: rsp:RSP_0161 spermidine/putrescine-binding periplasmic protein; extracellular solute-binding protein 2153784 4579969 Pden_2152 Paracoccus denitrificans PD1222 extracellular solute-binding protein YP_915940.1 2152702 R 318586 CDS YP_915941.1 119384885 4579970 complement(2153814..2154917) 1 NC_008686.1 KEGG: rsp:RSP_1882 ABC polyamine/opine transporter, ATPase subunit; TIGRFAM: spermidine/putrescine ABC transporter ATPase subunit; PFAM: ABC transporter related; Transport-associated OB domain protein; SMART: AAA ATPase; spermidine/putrescine ABC transporter ATPase 2154917 4579970 Pden_2153 Paracoccus denitrificans PD1222 spermidine/putrescine ABC transporter ATPase YP_915941.1 2153814 R 318586 CDS YP_915942.1 119384886 4579971 complement(2155122..2155688) 1 NC_008686.1 PFAM: protein of unknown function DUF421; KEGG: rsp:RSP_1130 hypothetical membrane protein; hypothetical protein 2155688 4579971 Pden_2154 Paracoccus denitrificans PD1222 hypothetical protein YP_915942.1 2155122 R 318586 CDS YP_915943.1 119384887 4579972 complement(2155791..2156528) 1 NC_008686.1 PFAM: short-chain dehydrogenase/reductase SDR; KR; KEGG: atc:AGR_L_1073 short chain dehydrogenase; short chain dehydrogenase 2156528 4579972 Pden_2155 Paracoccus denitrificans PD1222 short chain dehydrogenase YP_915943.1 2155791 R 318586 CDS YP_915944.1 119384888 4579973 complement(2156531..2158153) 1 NC_008686.1 TIGRFAM: FGGY-family pentulose kinase; PFAM: carbohydrate kinase, FGGY; KEGG: atc:AGR_L_1075 D-ribulokinase; FGGY-family pentulose kinase 2158153 4579973 Pden_2156 Paracoccus denitrificans PD1222 FGGY-family pentulose kinase YP_915944.1 2156531 R 318586 CDS YP_915945.1 119384889 4579974 complement(2158182..2158913) 1 NC_008686.1 PFAM: short-chain dehydrogenase/reductase SDR; KEGG: atc:AGR_L_1076 ribitol 2-dehydrogenase; short-chain dehydrogenase/reductase SDR 2158913 4579974 Pden_2157 Paracoccus denitrificans PD1222 short-chain dehydrogenase/reductase SDR YP_915945.1 2158182 R 318586 CDS YP_915946.1 119384890 4579975 complement(2158950..2159927) 1 NC_008686.1 PFAM: inner-membrane translocator; KEGG: atc:AGR_L_1078 ribose ABC transporter (permease); inner-membrane translocator 2159927 4579975 Pden_2158 Paracoccus denitrificans PD1222 inner-membrane translocator YP_915946.1 2158950 R 318586 CDS YP_915947.1 119384891 4579976 complement(2159917..2161419) 1 NC_008686.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: atu:Atu4321 ABC transporter, nucleotide binding/ATPase protein [ribose]; ABC transporter 2161419 4579976 Pden_2159 Paracoccus denitrificans PD1222 ABC transporter YP_915947.1 2159917 R 318586 CDS YP_915948.1 119384892 4579977 complement(2161490..2162395) 1 NC_008686.1 PFAM: periplasmic binding protein/LacI transcriptional regulator; KEGG: atc:AGR_L_1084 periplasmic ribose-binding protein of ABC transport system; periplasmic binding protein/LacI transcriptional regulator 2162395 4579977 Pden_2160 Paracoccus denitrificans PD1222 periplasmic binding protein/LacI transcriptional regulator YP_915948.1 2161490 R 318586 CDS YP_915949.1 119384893 4579978 complement(2162495..2163379) 1 NC_008686.1 PFAM: helix-turn-helix- domain containing protein, AraC type; KEGG: atc:AGR_L_1086 hypothetical protein; helix-turn-helix domain-containing protein 2163379 4579978 Pden_2161 Paracoccus denitrificans PD1222 helix-turn-helix domain-containing protein YP_915949.1 2162495 R 318586 CDS YP_915950.1 119384894 4579979 complement(2163630..2165087) 1 NC_008686.1 TIGRFAM: xylulokinase; PFAM: carbohydrate kinase, FGGY; KEGG: mlo:mlr5033 xylulokinase; xylulokinase 2165087 4579979 Pden_2162 Paracoccus denitrificans PD1222 xylulokinase YP_915950.1 2163630 R 318586 CDS YP_915951.1 119384895 4579980 complement(2165092..2166129) 1 NC_008686.1 PFAM: Alcohol dehydrogenase, zinc-binding domain protein; Alcohol dehydrogenase GroES domain protein; KEGG: atc:AGR_L_1091 xylitol dehydrogenase; alcohol dehydrogenase 2166129 4579980 Pden_2163 Paracoccus denitrificans PD1222 alcohol dehydrogenase YP_915951.1 2165092 R 318586 CDS YP_915952.1 119384896 4579981 complement(2166333..2166797) 1 NC_008686.1 PFAM: GatB/Yqey domain protein; KEGG: rsp:RSP_1875 hypothetical protein; GatB/Yqey domain-containing protein 2166797 4579981 Pden_2164 Paracoccus denitrificans PD1222 GatB/Yqey domain-containing protein YP_915952.1 2166333 R 318586 CDS YP_915953.1 119384897 4579982 2166966..2168114 1 NC_008686.1 catalyzes production of carbamoyl phosphate from bicarbonate and glutamine in pyrimidine and arginine biosynthesis pathways; forms an octamer composed of four CarAB dimers; carbamoyl phosphate synthase small subunit 2168114 4579982 Pden_2165 Paracoccus denitrificans PD1222 carbamoyl phosphate synthase small subunit YP_915953.1 2166966 D 318586 CDS YP_915954.1 119384898 4579983 2168202..2170298 1 NC_008686.1 PFAM: glycosyl transferase, family 2; General secretory system II, protein E domain protein; KEGG: rsp:RSP_1872 glycosyl transferase, family 2; general secretion pathway protein E 2170298 4579983 Pden_2166 Paracoccus denitrificans PD1222 general secretion pathway protein E YP_915954.1 2168202 D 318586 CDS YP_915955.1 119384899 4579984 complement(2170435..2173236) 1 NC_008686.1 PFAM: glutamate-ammonia ligase adenylyltransferase; KEGG: rsp:RSP_2643 glutamate-ammonia-ligase adenylyltransferase; (glutamate--ammonia-ligase) adenylyltransferase 2173236 4579984 Pden_2167 Paracoccus denitrificans PD1222 (glutamate--ammonia-ligase) adenylyltransferase YP_915955.1 2170435 R 318586 CDS YP_915956.1 119384900 4579985 2173462..2174307 1 NC_008686.1 Conjugates Arg from its aminoacyl-tRNA to the N-termini of proteins containing an N-terminal aspartate or glutamate; arginyl-tRNA-protein transferase 2174307 4579985 Pden_2168 Paracoccus denitrificans PD1222 arginyl-tRNA-protein transferase YP_915956.1 2173462 D 318586 CDS YP_915957.1 119384901 4579986 2174500..2176227 1 NC_008686.1 TIGRFAM: acetolactate synthase, large subunit, biosynthetic type; PFAM: thiamine pyrophosphate enzyme domain protein TPP-binding; thiamine pyrophosphate enzyme, central region; thiamine pyrophosphate enzyme TPP binding domain protein; KEGG: sit:TM1040_0875 acetolactate synthase, large subunit, biosynthetic type; acetolactate synthase 3 catalytic subunit 2176227 4579986 Pden_2169 Paracoccus denitrificans PD1222 acetolactate synthase 3 catalytic subunit YP_915957.1 2174500 D 318586 CDS YP_915958.1 119384902 4579146 2176242..2176802 1 NC_008686.1 with IlvI catalyzes the formation of 2-acetolactate from pyruvate, the small subunit is required for full activity and valine sensitivity; E.coli produces 3 isoenzymes of acetolactate synthase which differ in specificity to substrates, valine sensitivity and affinity for cofactors; also known as acetolactate synthase 3 small subunit; acetolactate synthase 3 regulatory subunit 2176802 ilvH 4579146 ilvH Paracoccus denitrificans PD1222 acetolactate synthase 3 regulatory subunit YP_915958.1 2176242 D 318586 CDS YP_915959.1 119384903 4579147 complement(2176808..2177149) 1 NC_008686.1 KEGG: rde:RD1_2814 hypothetical protein; hypothetical protein 2177149 4579147 Pden_2171 Paracoccus denitrificans PD1222 hypothetical protein YP_915959.1 2176808 R 318586 CDS YP_915960.1 119384904 4579148 complement(2177401..2178204) 1 NC_008686.1 PFAM: peptidase M48, Ste24p; KEGG: rde:RD1_1656 peptidase, M48 family; peptidase M48, Ste24p 2178204 4579148 Pden_2172 Paracoccus denitrificans PD1222 peptidase M48, Ste24p YP_915960.1 2177401 R 318586 CDS YP_915961.1 119384905 4579149 2178277..2178528 1 NC_008686.1 KEGG: rsp:RSP_6045 hypothetical protein; hypothetical protein 2178528 4579149 Pden_2173 Paracoccus denitrificans PD1222 hypothetical protein YP_915961.1 2178277 D 318586 CDS YP_915962.1 119384906 4579150 complement(2178525..2178773) 1 NC_008686.1 PFAM: protein of unknown function DUF167; KEGG: sil:SPO0937 hypothetical protein; hypothetical protein 2178773 4579150 Pden_2174 Paracoccus denitrificans PD1222 hypothetical protein YP_915962.1 2178525 R 318586 CDS YP_915963.1 119384907 4579151 2178879..2179445 1 NC_008686.1 PFAM: nitroreductase; KEGG: jan:Jann_3161 nitroreductase; nitroreductase 2179445 4579151 Pden_2175 Paracoccus denitrificans PD1222 nitroreductase YP_915963.1 2178879 D 318586 CDS YP_915964.1 119384908 4579152 2179445..2180137 1 NC_008686.1 KEGG: rsp:RSP_0810 hypothetical protein; hypothetical protein 2180137 4579152 Pden_2176 Paracoccus denitrificans PD1222 hypothetical protein YP_915964.1 2179445 D 318586 CDS YP_915965.1 119384909 4579153 complement(2180103..2180363) 1 NC_008686.1 PFAM: protein of unknown function DUF1467; KEGG: rsp:RSP_0811 hypothetical protein; hypothetical protein 2180363 4579153 Pden_2177 Paracoccus denitrificans PD1222 hypothetical protein YP_915965.1 2180103 R 318586 CDS YP_915966.1 119384910 4579154 complement(2180363..2180767) 1 NC_008686.1 PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase; KEGG: sit:TM1040_0637 glyoxalase/bleomycin resistance protein/dioxygenase; glyoxalase/bleomycin resistance protein/dioxygenase 2180767 4579154 Pden_2178 Paracoccus denitrificans PD1222 glyoxalase/bleomycin resistance protein/dioxygenase YP_915966.1 2180363 R 318586 CDS YP_915967.1 119384911 4579155 2180904..2181632 1 NC_008686.1 PFAM: response regulator receiver; KEGG: sil:SPO0931 response regulator; response regulator receiver protein 2181632 4579155 Pden_2179 Paracoccus denitrificans PD1222 response regulator receiver protein YP_915967.1 2180904 D 318586 CDS YP_915968.1 119384912 4579156 complement(2181637..2182377) 1 NC_008686.1 PFAM: GCN5-related N-acetyltransferase; KEGG: rsp:RSP_0814 acetyltransferase; N-acetyltransferase 2182377 4579156 Pden_2180 Paracoccus denitrificans PD1222 N-acetyltransferase YP_915968.1 2181637 R 318586 CDS YP_915969.1 119384913 4579157 complement(2182398..2183579) 1 NC_008686.1 PFAM: protein of unknown function DUF1501; KEGG: ret:RHE_CH02550 hypothetical protein; hypothetical protein 2183579 4579157 Pden_2181 Paracoccus denitrificans PD1222 hypothetical protein YP_915969.1 2182398 R 318586 CDS YP_915970.1 119384914 4579158 complement(2183589..2184956) 1 NC_008686.1 KEGG: ret:RHE_CH02551 hypothetical protein; hypothetical protein 2184956 4579158 Pden_2182 Paracoccus denitrificans PD1222 hypothetical protein YP_915970.1 2183589 R 318586 CDS YP_915971.1 119384915 4579159 complement(2185083..2186858) 1 NC_008686.1 catalyzes a two-step reaction, first charging an aspartate molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; contains discriminating and non-discriminating subtypes; aspartyl-tRNA synthetase 2186858 aspS 4579159 aspS Paracoccus denitrificans PD1222 aspartyl-tRNA synthetase YP_915971.1 2185083 R 318586 CDS YP_915972.1 119384916 4579160 complement(2186919..2187575) 1 NC_008686.1 PFAM: Abortive infection protein; KEGG: pat:Patl_3840 abortive infection protein; abortive infection protein 2187575 4579160 Pden_2184 Paracoccus denitrificans PD1222 abortive infection protein YP_915972.1 2186919 R 318586 CDS YP_915973.1 119384917 4579161 complement(2187551..2188333) 1 NC_008686.1 PFAM: glycoside hydrolase, family 25; KEGG: sil:SPO3258 glycosyl hydrolase, family 25; glycoside hydrolase 2188333 4579161 Pden_2185 Paracoccus denitrificans PD1222 glycoside hydrolase YP_915973.1 2187551 R 318586 CDS YP_915974.1 119384918 4579162 2188538..2188897 1 NC_008686.1 hypothetical protein 2188897 4579162 Pden_2186 Paracoccus denitrificans PD1222 hypothetical protein YP_915974.1 2188538 D 318586 CDS YP_915975.1 119384919 4579163 complement(2188967..2190346) 1 NC_008686.1 PFAM: FAD linked oxidase domain protein; KEGG: rsp:RSP_2120 D-lactate dehydrogenase (cytochrome), FAD/FMN-containing oxidoreductase; D-lactate dehydrogenase 2190346 4579163 Pden_2187 Paracoccus denitrificans PD1222 D-lactate dehydrogenase YP_915975.1 2188967 R 318586 CDS YP_915976.1 119384920 4579164 complement(2190412..2191380) 1 NC_008686.1 PFAM: protein of unknown function DUF808; KEGG: jan:Jann_1699 protein of unknown function DUF808; hypothetical protein 2191380 4579164 Pden_2188 Paracoccus denitrificans PD1222 hypothetical protein YP_915976.1 2190412 R 318586 CDS YP_915977.1 119384921 4579165 2191536..2192510 1 NC_008686.1 KEGG: rsp:RSP_1977 cobalt chelatase, CobS small subunit; TIGRFAM: cobalt chelatase, pCobS small subunit; PFAM: ATPase associated with various cellular activities, AAA_5; cobalt chelatase small subunit 2192510 4579165 Pden_2189 Paracoccus denitrificans PD1222 cobalt chelatase small subunit YP_915977.1 2191536 D 318586 CDS YP_915978.1 119384922 4579166 2192507..2192944 1 NC_008686.1 hypothetical protein 2192944 4579166 Pden_2190 Paracoccus denitrificans PD1222 hypothetical protein YP_915978.1 2192507 D 318586 CDS YP_915979.1 119384923 4579167 2193033..2194895 1 NC_008686.1 KEGG: rde:RD1_3340 aerobic cobaltochelatase CobT subunit; TIGRFAM: cobalt chelatase, pCobT subunit; PFAM: Cobalt chelatase, CobT subunit; SMART: von Willebrand factor, type A; cobalt chelatase large subunit 2194895 4579167 Pden_2191 Paracoccus denitrificans PD1222 cobalt chelatase large subunit YP_915979.1 2193033 D 318586 CDS YP_915980.1 119384924 4579168 2194934..2196247 1 NC_008686.1 PFAM: glycosyl transferase, group 1; KEGG: mxa:MXAN_7445 glycosyl transferase, group 1 family protein; group 1 glycosyl transferase 2196247 4579168 Pden_2192 Paracoccus denitrificans PD1222 group 1 glycosyl transferase YP_915980.1 2194934 D 318586 CDS YP_915981.1 119384925 4579169 2196275..2198092 1 NC_008686.1 PFAM: peptidase M24; KEGG: rsp:RSP_1975 aminopeptidase P; peptidase M24 2198092 4579169 Pden_2193 Paracoccus denitrificans PD1222 peptidase M24 YP_915981.1 2196275 D 318586 CDS YP_915982.1 119384926 4579170 complement(2198283..2199329) 1 NC_008686.1 PFAM: protein of unknown function DUF475; KEGG: rsp:RSP_0459 hypothetical protein; hypothetical protein 2199329 4579170 Pden_2194 Paracoccus denitrificans PD1222 hypothetical protein YP_915982.1 2198283 R 318586 CDS YP_915983.1 119384927 4579171 complement(2199445..2200671) 1 NC_008686.1 PFAM: MOFRL domain protein; KEGG: sit:TM1040_3471 hydroxypyruvate reductase; hydroxypyruvate reductase 2200671 4579171 Pden_2195 Paracoccus denitrificans PD1222 hydroxypyruvate reductase YP_915983.1 2199445 R 318586 CDS YP_915984.1 119384928 4579172 complement(2200671..2201621) 1 NC_008686.1 PFAM: 6-phosphogluconate dehydrogenase, NAD-binding; D-isomer specific 2-hydroxyacid dehydrogenase, catalytic region; D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding; KEGG: sil:SPO0913 D-isomer specific 2-hydroxyacid dehydrogenase family protein; D-isomer specific 2-hydroxyacid dehydrogenase 2201621 4579172 Pden_2196 Paracoccus denitrificans PD1222 D-isomer specific 2-hydroxyacid dehydrogenase YP_915984.1 2200671 R 318586 CDS YP_915985.1 119384929 4579173 complement(2201621..2201962) 1 NC_008686.1 TIGRFAM: export-related chaperone CsaA; PFAM: t-RNA-binding domain protein; KEGG: rsp:RSP_3365 protein secretion chaperonine; export-related chaperone CsaA 2201962 4579173 Pden_2197 Paracoccus denitrificans PD1222 export-related chaperone CsaA YP_915985.1 2201621 R 318586 CDS YP_915986.1 119384930 4579174 complement(2201959..2202762) 1 NC_008686.1 catalyzes the formation of L-proline from pyrroline-5-carboxylate; pyrroline-5-carboxylate reductase 2202762 4579174 Pden_2198 Paracoccus denitrificans PD1222 pyrroline-5-carboxylate reductase YP_915986.1 2201959 R 318586 CDS YP_915987.1 119384931 4579175 complement(2202801..2203301) 1 NC_008686.1 KEGG: jan:Jann_3330 hypothetical protein; hypothetical protein 2203301 4579175 Pden_2199 Paracoccus denitrificans PD1222 hypothetical protein YP_915987.1 2202801 R 318586 CDS YP_915988.1 119384932 4579176 2203527..2204489 1 NC_008686.1 PFAM: aminotransferase, class I and II; KEGG: rsp:RSP_0789 aminotransferase, class-I; class I and II aminotransferase 2204489 4579176 Pden_2200 Paracoccus denitrificans PD1222 class I and II aminotransferase YP_915988.1 2203527 D 318586 CDS YP_915989.1 119384933 4579177 complement(2204473..2205516) 1 NC_008686.1 With PurE catalyzes the conversion of aminoimidazole ribonucleotide to carboxyaminoimidazole ribonucleotide in the de novo purine nucleotide biosynthetic pathway; phosphoribosylaminoimidazole carboxylase ATPase subunit 2205516 4579177 Pden_2201 Paracoccus denitrificans PD1222 phosphoribosylaminoimidazole carboxylase ATPase subunit YP_915989.1 2204473 R 318586 CDS YP_915990.1 119384934 4579178 complement(2205509..2206006) 1 NC_008686.1 KEGG: rsp:RSP_1571 phosphoribosylaminoimidazole carboxylase, catalytic subunit; TIGRFAM: phosphoribosylaminoimidazole carboxylase, catalytic subunit; PFAM: 1-(5-phosphoribosyl)-5-amino-4-imidazole-carboxylate (AIR) carboxylase; phosphoribosylaminoimidazole carboxylase catalytic subunit 2206006 4579178 Pden_2202 Paracoccus denitrificans PD1222 phosphoribosylaminoimidazole carboxylase catalytic subunit YP_915990.1 2205509 R 318586 CDS YP_915991.1 119384935 4579179 complement(2206059..2206277) 1 NC_008686.1 PFAM: protein of unknown function DUF465; KEGG: jan:Jann_3351 protein of unknown function DUF465; hypothetical protein 2206277 4579179 Pden_2203 Paracoccus denitrificans PD1222 hypothetical protein YP_915991.1 2206059 R 318586 CDS YP_915992.1 119384936 4579180 2206440..2207036 1 NC_008686.1 KEGG: jan:Jann_2350 hypothetical protein; hypothetical protein 2207036 4579180 Pden_2204 Paracoccus denitrificans PD1222 hypothetical protein YP_915992.1 2206440 D 318586 CDS YP_915993.1 119384937 4579181 2207159..2207569 1 NC_008686.1 PFAM: heat shock protein Hsp20; KEGG: jan:Jann_3350 heat shock protein HSP20; heat shock protein Hsp20 2207569 4579181 Pden_2205 Paracoccus denitrificans PD1222 heat shock protein Hsp20 YP_915993.1 2207159 D 318586 CDS YP_915994.1 119384938 4579182 2207583..2207810 1 NC_008686.1 PFAM: protein of unknown function DUF1150; KEGG: rsp:RSP_1573 hypothetical protein; hypothetical protein 2207810 4579182 Pden_2206 Paracoccus denitrificans PD1222 hypothetical protein YP_915994.1 2207583 D 318586 CDS YP_915995.1 119384939 4579183 complement(2207975..2208787) 1 NC_008686.1 KEGG: rsp:RSP_1575 binfunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; binfunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein 2208787 4579183 Pden_2207 Paracoccus denitrificans PD1222 binfunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein YP_915995.1 2207975 R 318586 CDS YP_915996.1 119384940 4579184 complement(2208807..2209823) 1 NC_008686.1 TIGRFAM: thioredoxin reductase; PFAM: FAD-dependent pyridine nucleotide-disulphide oxidoreductase; glucose-inhibited division protein A; KEGG: rsp:RSP_1576 thioredoxin reductase; thioredoxin reductase 2209823 4579184 Pden_2208 Paracoccus denitrificans PD1222 thioredoxin reductase YP_915996.1 2208807 R 318586 CDS YP_915997.1 119384941 4579185 2209988..2210488 1 NC_008686.1 PFAM: regulatory protein, AsnC/Lrp family; KEGG: rsp:RSP_1577 proline dehydrogenase transcriptional activator; AsnC family transcriptional regulator 2210488 4579185 Pden_2209 Paracoccus denitrificans PD1222 AsnC family transcriptional regulator YP_915997.1 2209988 D 318586 CDS YP_915998.1 119384942 4579186 2210569..2211006 1 NC_008686.1 hypothetical protein 2211006 4579186 Pden_2210 Paracoccus denitrificans PD1222 hypothetical protein YP_915998.1 2210569 D 318586 CDS YP_915999.1 119384943 4579187 complement(2211103..2211867) 1 NC_008686.1 PFAM: protein of unknown function DUF152; KEGG: rde:RD1_3503 hypothetical protein; hypothetical protein 2211867 4579187 Pden_2211 Paracoccus denitrificans PD1222 hypothetical protein YP_915999.1 2211103 R 318586 CDS YP_916000.1 119384944 4579188 complement(2211851..2212918) 1 NC_008686.1 PFAM: protein of unknown function DUF185; KEGG: sil:SPO0907 hypothetical protein; hypothetical protein 2212918 4579188 Pden_2212 Paracoccus denitrificans PD1222 hypothetical protein YP_916000.1 2211851 R 318586 CDS YP_916001.1 119384945 4579189 complement(2212915..2213805) 1 NC_008686.1 transfers the N-acyl diglyceride moiety to the prospective N-terminal cysteine in prolipoprotein; prolipoprotein diacylglyceryl transferase 2213805 4579189 Pden_2213 Paracoccus denitrificans PD1222 prolipoprotein diacylglyceryl transferase YP_916001.1 2212915 R 318586 CDS YP_916002.1 119384946 4579190 2213932..2214186 1 NC_008686.1 PFAM: protein of unknown function DUF526; KEGG: sit:TM1040_0621 protein of unknown function DUF526; hypothetical protein 2214186 4579190 Pden_2214 Paracoccus denitrificans PD1222 hypothetical protein YP_916002.1 2213932 D 318586 CDS YP_916003.1 119384947 4579191 2214481..2215506 1 NC_008686.1 TIGRFAM: pseudouridine synthase, RluA family; PFAM: pseudouridine synthase; KEGG: rsp:RSP_2409 pseudouridine synthase, Rlu; RluA family pseudouridine synthase 2215506 4579191 Pden_2215 Paracoccus denitrificans PD1222 RluA family pseudouridine synthase YP_916003.1 2214481 D 318586 CDS YP_916004.1 119384948 4579192 2215573..2216478 1 NC_008686.1 binds with the catalytic core of RNA polymerase to produce the holoenzyme; this sigma factor is responsible for the expression of heat shock promoters; RNA polymerase factor sigma-32 2216478 4579192 Pden_2216 Paracoccus denitrificans PD1222 RNA polymerase factor sigma-32 YP_916004.1 2215573 D 318586 CDS YP_916005.1 119384949 4579193 2216845..2217864 1 NC_008686.1 KEGG: rsp:RSP_6009 hypothetical protein; hypothetical protein 2217864 4579193 Pden_2217 Paracoccus denitrificans PD1222 hypothetical protein YP_916005.1 2216845 D 318586 CDS YP_916006.1 119384950 4579194 complement(2217872..2218921) 1 NC_008686.1 PFAM: Sporulation domain protein; KEGG: rsp:RSP_6008 hypothetical protein; sporulation domain-containing protein 2218921 4579194 Pden_2218 Paracoccus denitrificans PD1222 sporulation domain-containing protein YP_916006.1 2217872 R 318586 CDS YP_916007.1 119384951 4579195 complement(2218991..2219626) 1 NC_008686.1 Catalyzes the formation of uracil and 5-phospho-alpha-D-ribosy 1-diphosphate from UMP and diphosphate; uracil phosphoribosyltransferase 2219626 upp 4579195 upp Paracoccus denitrificans PD1222 uracil phosphoribosyltransferase YP_916007.1 2218991 R 318586 CDS YP_916008.1 119384952 4579196 complement(2219623..2220591) 1 NC_008686.1 catalyzes the formation of inosine from adenosine; adenosine deaminase 2220591 4579196 Pden_2220 Paracoccus denitrificans PD1222 adenosine deaminase YP_916008.1 2219623 R 318586 CDS YP_916009.1 119384953 4579197 complement(2220588..2221772) 1 NC_008686.1 catalyzes the transfer of phosphate between the C1 and C5 carbons of pentose; phosphopentomutase 2221772 4579197 Pden_2221 Paracoccus denitrificans PD1222 phosphopentomutase YP_916009.1 2220588 R 318586 CDS YP_916010.1 119384954 4579198 complement(2221769..2223061) 1 NC_008686.1 Catalyzes the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate; thymidine phosphorylase 2223061 deoA 4579198 deoA Paracoccus denitrificans PD1222 thymidine phosphorylase YP_916010.1 2221769 R 318586 CDS YP_916011.1 119384955 4579199 complement(2223058..2223453) 1 NC_008686.1 TIGRFAM: cytidine deaminase; PFAM: CMP/dCMP deaminase, zinc-binding; KEGG: sil:SPO2930 cytidine deaminase; cytidine deaminase 2223453 4579199 Pden_2223 Paracoccus denitrificans PD1222 cytidine deaminase YP_916011.1 2223058 R 318586 CDS YP_916012.1 119384956 4579200 2223617..2225896 1 NC_008686.1 NAD-dependent; catalyzes the oxidative decarboxylation of malate to form pyruvate; does not decarboxylate oxaloacetate; malic enzyme 2225896 4579200 Pden_2224 Paracoccus denitrificans PD1222 malic enzyme YP_916012.1 2223617 D 318586 CDS YP_916013.1 119384957 4579201 2226148..2228052 1 NC_008686.1 PFAM: AMP-dependent synthetase and ligase; KEGG: rsp:RSP_1592 possible acyl-CoA sythetase; AMP-dependent synthetase/ligase 2228052 4579201 Pden_2225 Paracoccus denitrificans PD1222 AMP-dependent synthetase/ligase YP_916013.1 2226148 D 318586 CDS YP_916014.1 119384958 4579202 complement(2228138..2229469) 1 NC_008686.1 catalyzes the formation of 5-O-(1-carboxyvinyl)-3-phosphoshikimate from phosphoenolpyruvate and 3-phosphoshikimate in tryptophan biosynthesis; 3-phosphoshikimate 1-carboxyvinyltransferase 2229469 4579202 Pden_2226 Paracoccus denitrificans PD1222 3-phosphoshikimate 1-carboxyvinyltransferase YP_916014.1 2228138 R 318586 CDS YP_916015.1 119384959 4579203 complement(2229547..2230248) 1 NC_008686.1 tRNA (guanine-N(7)-)-methyltransferase; catalyzes the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA by transferring the methyl residue from S-adenosyl-L-methionine; tRNA (guanine-N(7)-)-methyltransferase 2230248 trmB 4579203 trmB Paracoccus denitrificans PD1222 tRNA (guanine-N(7)-)-methyltransferase YP_916015.1 2229547 R 318586 CDS YP_916016.1 119384960 4579282 complement(2230270..2231946) 1 NC_008686.1 PFAM: beta-lactamase domain protein; RNA-metabolising metallo-beta-lactamase; KEGG: rsp:RSP_2534 predicted hydrolase of the metallo-beta-lactamase superfamily; beta-lactamase domain-containing protein 2231946 4579282 Pden_2228 Paracoccus denitrificans PD1222 beta-lactamase domain-containing protein YP_916016.1 2230270 R 318586 CDS YP_916017.1 119384961 4579283 complement(2231939..2232718) 1 NC_008686.1 type III; catalyzes the formation of (R)-4'-phosphopantothenate from (R)-pantothenate in coenzyme A biosynthesis; type III pantothenate kinases are not subject to feedback inhibition from coenzyme A and have a high Km for ATP; pantothenate kinase 2232718 4579283 Pden_2229 Paracoccus denitrificans PD1222 pantothenate kinase YP_916017.1 2231939 R 318586 CDS YP_916018.1 119384962 4579284 complement(2232722..2233480) 1 NC_008686.1 KEGG: sil:SPO2762 biotin--acetyl-CoA-carboxylase ligase; TIGRFAM: biotin--acetyl-CoA-carboxylase ligase; PFAM: biotin protein ligase domain protein; biotin/lipoate A/B protein ligase; biotin--acetyl-CoA-carboxylase ligase 2233480 4579284 Pden_2230 Paracoccus denitrificans PD1222 biotin--acetyl-CoA-carboxylase ligase YP_916018.1 2232722 R 318586 CDS YP_916019.1 119384963 4579285 complement(2233473..2234972) 1 NC_008686.1 Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit N 2234972 4579285 Pden_2231 Paracoccus denitrificans PD1222 NADH dehydrogenase subunit N YP_916019.1 2233473 R 318586 CDS YP_916020.1 119384964 4579286 complement(2234982..2236523) 1 NC_008686.1 Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit M 2236523 4579286 Pden_2232 Paracoccus denitrificans PD1222 NADH dehydrogenase subunit M YP_916020.1 2234982 R 318586 CDS YP_916021.1 119384965 4579287 complement(2236525..2238636) 1 NC_008686.1 Catalyzes the transfer of electrons from NADH to ubiquinone; NADH dehydrogenase subunit L 2238636 4579287 Pden_2233 Paracoccus denitrificans PD1222 NADH dehydrogenase subunit L YP_916021.1 2236525 R 318586 CDS YP_916022.1 119384966 4579288 complement(2238643..2238948) 1 NC_008686.1 PFAM: NADH-ubiquinone oxidoreductase, chain 4L; KEGG: sit:TM1040_0757 NADH-ubiquinone oxidoreductase, chain 4L; NADH-ubiquinone oxidoreductase, chain 4L 2238948 4579288 Pden_2234 Paracoccus denitrificans PD1222 NADH-ubiquinone oxidoreductase, chain 4L YP_916022.1 2238643 R 318586 CDS YP_916023.1 119384967 4579289 complement(2239048..2239647) 1 NC_008686.1 Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit J 2239647 4579289 Pden_2235 Paracoccus denitrificans PD1222 NADH dehydrogenase subunit J YP_916023.1 2239048 R 318586 CDS YP_916024.1 119384968 4579290 complement(2239647..2240051) 1 NC_008686.1 PFAM: Carboxymuconolactone decarboxylase; KEGG: rsp:RSP_2524 possible carboxymuconolactone decarboxylase family protein; carboxymuconolactone decarboxylase 2240051 4579290 Pden_2236 Paracoccus denitrificans PD1222 carboxymuconolactone decarboxylase YP_916024.1 2239647 R 318586 CDS YP_916025.1 119384969 4579291 complement(2240048..2240440) 1 NC_008686.1 PFAM: Carboxymuconolactone decarboxylase; KEGG: jan:Jann_1188 carboxymuconolactone decarboxylase; carboxymuconolactone decarboxylase 2240440 4579291 Pden_2237 Paracoccus denitrificans PD1222 carboxymuconolactone decarboxylase YP_916025.1 2240048 R 318586 CDS YP_916026.1 119384970 4579292 complement(2240437..2240928) 1 NC_008686.1 Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit I 2240928 4579292 Pden_2238 Paracoccus denitrificans PD1222 NADH dehydrogenase subunit I YP_916026.1 2240437 R 318586 CDS YP_916027.1 119384971 4579293 complement(2241114..2242151) 1 NC_008686.1 Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit H 2242151 4579293 Pden_2239 Paracoccus denitrificans PD1222 NADH dehydrogenase subunit H YP_916027.1 2241114 R 318586 CDS YP_916028.1 119384972 4579294 complement(2242170..2242937) 1 NC_008686.1 KEGG: jan:Jann_1184 lipoprotein; hypothetical protein 2242937 4579294 Pden_2240 Paracoccus denitrificans PD1222 hypothetical protein YP_916028.1 2242170 R 318586 CDS YP_916029.1 119384973 4579295 complement(2242943..2244967) 1 NC_008686.1 Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit G 2244967 4579295 Pden_2241 Paracoccus denitrificans PD1222 NADH dehydrogenase subunit G YP_916029.1 2242943 R 318586 CDS YP_916030.1 119384974 4579296 complement(2245247..2245813) 1 NC_008686.1 KEGG: sil:SPO2775 hypothetical protein; hypothetical protein 2245813 4579296 Pden_2242 Paracoccus denitrificans PD1222 hypothetical protein YP_916030.1 2245247 R 318586 CDS YP_916031.1 119384975 4579297 complement(2245820..2247115) 1 NC_008686.1 part of NADH-ubiquinone oxidoreductase complex I; shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain; NuoF is part of the soluble NADH dehydrogenase fragment, which represents the electron input part of NADH dehydrogenase; NADH dehydrogenase I subunit F 2247115 4579297 Pden_2243 Paracoccus denitrificans PD1222 NADH dehydrogenase I subunit F YP_916031.1 2245820 R 318586 CDS YP_916032.1 119384976 4579298 complement(2247120..2247383) 1 NC_008686.1 KEGG: jan:Jann_1178 hypothetical protein; hypothetical protein 2247383 4579298 Pden_2244 Paracoccus denitrificans PD1222 hypothetical protein YP_916032.1 2247120 R 318586 CDS YP_916033.1 119384977 4579299 complement(2247383..2248027) 1 NC_008686.1 KEGG: jan:Jann_1177 hypothetical protein; hypothetical protein 2248027 4579299 Pden_2245 Paracoccus denitrificans PD1222 hypothetical protein YP_916033.1 2247383 R 318586 CDS YP_916034.1 119384978 4579300 complement(2248052..2248771) 1 NC_008686.1 Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit E 2248771 4579300 Pden_2246 Paracoccus denitrificans PD1222 NADH dehydrogenase subunit E YP_916034.1 2248052 R 318586 CDS YP_916035.1 119384979 4579301 complement(2248771..2250009) 1 NC_008686.1 Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit D 2250009 4579301 Pden_2247 Paracoccus denitrificans PD1222 NADH dehydrogenase subunit D YP_916035.1 2248771 R 318586 CDS YP_916036.1 119384980 4579302 complement(2250063..2250689) 1 NC_008686.1 Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit C 2250689 4579302 Pden_2248 Paracoccus denitrificans PD1222 NADH dehydrogenase subunit C YP_916036.1 2250063 R 318586 CDS YP_916037.1 119384981 4579303 complement(2250693..2251220) 1 NC_008686.1 The point of entry for the majority of electrons that traverse the respiratory chain eventually resulting in the reduction of oxygen; NADH dehydrogenase subunit B 2251220 4579303 Pden_2249 Paracoccus denitrificans PD1222 NADH dehydrogenase subunit B YP_916037.1 2250693 R 318586 CDS YP_916038.1 119384982 4579304 complement(2251217..2251582) 1 NC_008686.1 Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit A 2251582 4579304 Pden_2250 Paracoccus denitrificans PD1222 NADH dehydrogenase subunit A YP_916038.1 2251217 R 318586 CDS YP_916039.1 119384983 4579305 complement(2251761..2252132) 1 NC_008686.1 KEGG: sit:TM1040_0660 conserved hypothetical protein; hypothetical protein 2252132 4579305 Pden_2251 Paracoccus denitrificans PD1222 hypothetical protein YP_916039.1 2251761 R 318586 CDS YP_916040.1 119384984 4579306 complement(2252129..2255008) 1 NC_008686.1 The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrA is an ATPase and a DNA-binding protein. A damage recognition complex composed of 2 uvrA and 2 uvrB subunits scans DNA for abnormalities. When the presence of a lesion has been verified by uvrB, the uvrA molecules dissociate; excinuclease ABC subunit A 2255008 uvrA 4579306 uvrA Paracoccus denitrificans PD1222 excinuclease ABC subunit A YP_916040.1 2252129 R 318586 CDS YP_916041.1 119384985 4579307 2255154..2255507 1 NC_008686.1 PFAM: glutathione-dependent formaldehyde-activating, GFA; KEGG: atc:AGR_C_4363 hypothetical protein; glutathione-dependent formaldehyde-activating protein 2255507 4579307 Pden_2253 Paracoccus denitrificans PD1222 glutathione-dependent formaldehyde-activating protein YP_916041.1 2255154 D 318586 CDS YP_916042.1 119384986 4579308 complement(2255504..2256538) 1 NC_008686.1 together with moaC, is involved in the conversion of a guanosine derivative (GXP) into molybdopterin precursor Z; molybdenum cofactor biosynthesis protein A 2256538 moaA 4579308 moaA Paracoccus denitrificans PD1222 molybdenum cofactor biosynthesis protein A YP_916042.1 2255504 R 318586 CDS YP_916043.1 119384987 4579309 2256663..2257166 1 NC_008686.1 KEGG: rsp:RSP_6106 hypothetical protein; hypothetical protein 2257166 4579309 Pden_2255 Paracoccus denitrificans PD1222 hypothetical protein YP_916043.1 2256663 D 318586 CDS YP_916044.1 119384988 4579310 complement(2257154..2257858) 1 NC_008686.1 KEGG: sil:SPO2798 hypothetical protein; hypothetical protein 2257858 4579310 Pden_2256 Paracoccus denitrificans PD1222 hypothetical protein YP_916044.1 2257154 R 318586 CDS YP_916045.1 119384989 4579311 2258143..2259615 1 NC_008686.1 KEGG: rsp:RSP_1012 succinate-semialdehyde dehdyrogenase; TIGRFAM: succinic semialdehyde dehydrogenase; PFAM: aldehyde dehydrogenase; succinate-semialdehyde dehydrogenase 2259615 4579311 Pden_2257 Paracoccus denitrificans PD1222 succinate-semialdehyde dehydrogenase YP_916045.1 2258143 D 318586 CDS YP_916046.1 119384990 4579312 complement(2259661..2260407) 1 NC_008686.1 PFAM: protein of unknown function DUF1013; KEGG: rsp:RSP_0714 hypothetical protein; hypothetical protein 2260407 4579312 Pden_2258 Paracoccus denitrificans PD1222 hypothetical protein YP_916046.1 2259661 R 318586 CDS YP_916047.1 119384991 4579313 2260568..2261188 1 NC_008686.1 PFAM: ribonuclease T2; KEGG: sit:TM1040_2631 ribonuclease T2; ribonuclease T2 2261188 4579313 Pden_2259 Paracoccus denitrificans PD1222 ribonuclease T2 YP_916047.1 2260568 D 318586 CDS YP_916048.1 119384992 4579314 2261370..2261852 1 NC_008686.1 hypothetical protein 2261852 4579314 Pden_2260 Paracoccus denitrificans PD1222 hypothetical protein YP_916048.1 2261370 D 318586 CDS YP_916049.1 119384993 4579315 complement(2261861..2262172) 1 NC_008686.1 PFAM: TM2 domain containing protein+B7201; KEGG: pau:PA14_53630 hypothetical protein; TM2 domain-containing protein 2262172 4579315 Pden_2261 Paracoccus denitrificans PD1222 TM2 domain-containing protein YP_916049.1 2261861 R 318586 CDS YP_916050.1 119384994 4579316 2262355..2264742 1 NC_008686.1 catalyzes a two-step reaction, first charging a phenylalanine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; forms a tetramer of alpha(2)beta(2); binds two magnesium ions per tetramer; type 2 subfamily; phenylalanyl-tRNA synthetase subunit beta 2264742 pheT 4579316 pheT Paracoccus denitrificans PD1222 phenylalanyl-tRNA synthetase subunit beta YP_916050.1 2262355 D 318586 CDS YP_916051.1 119384995 4579317 2264921..2265478 1 NC_008686.1 hypothetical protein 2265478 4579317 Pden_2263 Paracoccus denitrificans PD1222 hypothetical protein YP_916051.1 2264921 D 318586 CDS YP_916052.1 119384996 4579318 complement(2265660..2266376) 1 NC_008686.1 PFAM: Glutathione S-transferase, N-terminal domain; KEGG: bxe:Bxe_A3350 glutathione S-transferase; glutathione S-transferase domain-containing protein 2266376 4579318 Pden_2264 Paracoccus denitrificans PD1222 glutathione S-transferase domain-containing protein YP_916052.1 2265660 R 318586 CDS YP_916053.1 119384997 4579319 2266459..2266896 1 NC_008686.1 TIGRFAM: large conductance mechanosensitive channel protein; PFAM: large-conductance mechanosensitive channel; KEGG: sil:SPO3495 large conductance mechanosensitive channel protein; large conductance mechanosensitive channel protein 2266896 4579319 Pden_2265 Paracoccus denitrificans PD1222 large conductance mechanosensitive channel protein YP_916053.1 2266459 D 318586 CDS YP_916054.1 119384998 4579320 2267048..2267509 1 NC_008686.1 PFAM: regulatory protein, AsnC/Lrp family; KEGG: rsp:RSP_0722 transcriptional regulator, AsnC family; AsnC family transcriptional regulator 2267509 4579320 Pden_2266 Paracoccus denitrificans PD1222 AsnC family transcriptional regulator YP_916054.1 2267048 D 318586 CDS YP_916055.1 119384999 4579321 complement(2267563..2267769) 1 NC_008686.1 a small basic protein that is one of the last in the subunit assembly; omission does not prevent assembly but the subunit is inactive; binds central domain of 16S rRNA; 30S ribosomal protein S21 2267769 rpsU 4579321 rpsU Paracoccus denitrificans PD1222 30S ribosomal protein S21 YP_916055.1 2267563 R 318586 CDS YP_916056.1 119385000 4579322 2267894..2268580 1 NC_008686.1 TIGRFAM: rpsU-divergently transcribed protein; PFAM: COQ9 domain protein; KEGG: sil:SPO0230 hypothetical protein; rpsU-divergently transcribed protein 2268580 4579322 Pden_2268 Paracoccus denitrificans PD1222 rpsU-divergently transcribed protein YP_916056.1 2267894 D 318586 CDS YP_916057.1 119385001 4579323 2268592..2269569 1 NC_008686.1 PFAM: Alcohol dehydrogenase, zinc-binding domain protein; Alcohol dehydrogenase GroES domain protein; KEGG: rsp:RSP_0716 NADPH/quinone reductase and related Zn-dependent oxidoreductase; alcohol dehydrogenase 2269569 4579323 Pden_2269 Paracoccus denitrificans PD1222 alcohol dehydrogenase YP_916057.1 2268592 D 318586 CDS YP_916058.1 119385002 4579324 complement(2269677..2270759) 1 NC_008686.1 catalyzes a two-step reaction, first charging a phenylalanine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; forms a heterotetramer of alpha(2)beta(2); binds two magnesium ions per tetramer; type 1 subfamily; phenylalanyl-tRNA synthetase subunit alpha 2270759 pheS 4579324 pheS Paracoccus denitrificans PD1222 phenylalanyl-tRNA synthetase subunit alpha YP_916058.1 2269677 R 318586 CDS YP_916059.1 119385003 4579325 complement(2270818..2271162) 1 NC_008686.1 TIGRFAM: arsenate reductase; PFAM: arsenate reductase and related; KEGG: hne:HNE_0991 arsenate reductase; arsenate reductase 2271162 4579325 Pden_2271 Paracoccus denitrificans PD1222 arsenate reductase YP_916059.1 2270818 R 318586 CDS YP_916060.1 119385004 4579326 complement(2271194..2272555) 1 NC_008686.1 PFAM: cytochrome P450; KEGG: rde:RD1_1394 cytochrome P450; cytochrome P450 2272555 4579326 Pden_2272 Paracoccus denitrificans PD1222 cytochrome P450 YP_916060.1 2271194 R 318586 CDS YP_916061.1 119385005 4579327 complement(2272794..2273153) 1 NC_008686.1 binds directly to 23S ribosomal RNA prior to in vitro assembly of the 50S ribosomal subunit; 50S ribosomal protein L20 2273153 rplT 4579327 rplT Paracoccus denitrificans PD1222 50S ribosomal protein L20 YP_916061.1 2272794 R 318586 CDS YP_916062.1 119385006 4579328 complement(2273166..2273366) 1 NC_008686.1 PFAM: ribosomal protein L35; KEGG: rsp:RSP_1765 50S ribosomal protein L35; 50S ribosomal protein L35 2273366 rpmI 4579328 rpmI Paracoccus denitrificans PD1222 50S ribosomal protein L35 YP_916062.1 2273166 R 318586 CDS YP_916063.1 119385007 4579329 complement(2273475..2273864) 1 NC_008686.1 hypothetical protein 2273864 4579329 Pden_2275 Paracoccus denitrificans PD1222 hypothetical protein YP_916063.1 2273475 R 318586 CDS YP_916064.1 119385008 4579330 complement(2273905..2275350) 1 NC_008686.1 PFAM: pyruvate kinase; KEGG: sil:SPO3600 pyruvate kinase; pyruvate kinase 2275350 4579330 Pden_2276 Paracoccus denitrificans PD1222 pyruvate kinase YP_916064.1 2273905 R 318586 CDS YP_916065.1 119385009 4579331 2275471..2276211 1 NC_008686.1 PFAM: N-formylglutamate amidohydrolase; KEGG: rsp:RSP_1767 possible N-formylglutamate amidohydrolase; N-formylglutamate amidohydrolase 2276211 4579331 Pden_2277 Paracoccus denitrificans PD1222 N-formylglutamate amidohydrolase YP_916065.1 2275471 D 318586 CDS YP_916066.1 119385010 4579332 complement(2276961..2277200) 1 NC_008686.1 hypothetical protein 2277200 4579332 Pden_2278 Paracoccus denitrificans PD1222 hypothetical protein YP_916066.1 2276961 R 318586 CDS YP_916067.1 119385011 4579333 complement(2277297..2277767) 1 NC_008686.1 hypothetical protein 2277767 4579333 Pden_2279 Paracoccus denitrificans PD1222 hypothetical protein YP_916067.1 2277297 R 318586 CDS YP_916068.1 119385012 4579334 2277814..2278233 1 NC_008686.1 hypothetical protein 2278233 4579334 Pden_2280 Paracoccus denitrificans PD1222 hypothetical protein YP_916068.1 2277814 D 318586 CDS YP_916069.1 119385013 4579335 2278522..2279088 1 NC_008686.1 PFAM: Arc domain protein DNA binding domain protein; Arc domain-containing protein 2279088 4579335 Pden_2281 Paracoccus denitrificans PD1222 Arc domain-containing protein YP_916069.1 2278522 D 318586 CDS YP_916070.1 119385014 4579336 complement(2279485..2280549) 1 NC_008686.1 PFAM: TPR repeat-containing protein; Tetratricopeptide TPR_2 repeat protein; SMART: Tetratricopeptide domain protein; KEGG: mca:MCA1751 hypothetical protein; hypothetical protein 2280549 4579336 Pden_2282 Paracoccus denitrificans PD1222 hypothetical protein YP_916070.1 2279485 R 318586 CDS YP_916071.1 119385015 4579337 complement(2280660..2281010) 1 NC_008686.1 hypothetical protein 2281010 4579337 Pden_2283 Paracoccus denitrificans PD1222 hypothetical protein YP_916071.1 2280660 R 318586 CDS YP_916072.1 119385016 4579338 2281578..2282513 1 NC_008686.1 PFAM: Substrate-binding region of ABC-type glycine betaine transport system; KEGG: atc:AGR_L_470 hypothetical protein; substrate-binding region of ABC-type glycine betaine transport system 2282513 4579338 Pden_2285 Paracoccus denitrificans PD1222 substrate-binding region of ABC-type glycine betaine transport system YP_916072.1 2281578 D 318586 CDS YP_916073.1 119385017 4579339 2282514..2284010 1 NC_008686.1 PFAM: sulfatase; KEGG: rsp:RSP_0594 choline sulfatase; sulfatase 2284010 4579339 Pden_2286 Paracoccus denitrificans PD1222 sulfatase YP_916073.1 2282514 D 318586 CDS YP_916074.1 119385018 4579340 2284145..2284726 1 NC_008686.1 PFAM: membrane protein of uknown function UCP014873; KEGG: gvi:gll1598 hypothetical protein; hypothetical protein 2284726 4579340 Pden_2287 Paracoccus denitrificans PD1222 hypothetical protein YP_916074.1 2284145 D 318586 CDS YP_916075.1 119385019 4579341 2284766..2285524 1 NC_008686.1 TIGRFAM: monofunctional biosynthetic peptidoglycan transglycosylase; PFAM: glycosyl transferase, family 51; KEGG: sil:SPO3766 monofunctional biosynthetic peptidoglycan transglycosylase; monofunctional biosynthetic peptidoglycan transglycosylase 2285524 4579341 Pden_2288 Paracoccus denitrificans PD1222 monofunctional biosynthetic peptidoglycan transglycosylase YP_916075.1 2284766 D 318586 CDS YP_916076.1 119385020 4579342 2285541..2286299 1 NC_008686.1 PFAM: Glutathione S-transferase, N-terminal domain; KEGG: jan:Jann_0275 glutathione S-transferase-like; glutathione S-transferase domain-containing protein 2286299 4579342 Pden_2289 Paracoccus denitrificans PD1222 glutathione S-transferase domain-containing protein YP_916076.1 2285541 D 318586 CDS YP_916077.1 119385021 4579343 2286280..2287323 1 NC_008686.1 PFAM: 4Fe-4S ferredoxin, iron-sulfur binding domain protein; domain of unknown function DUF1730; KEGG: rsp:RSP_1143 4Fe-4S ferredoxin, iron-sulfur cluster binding protein; hypothetical protein 2287323 4579343 Pden_2290 Paracoccus denitrificans PD1222 hypothetical protein YP_916077.1 2286280 D 318586 CDS YP_916078.1 119385022 4579344 2287320..2288261 1 NC_008686.1 PFAM: protein of unknown function DUF6, transmembrane; KEGG: rsp:RSP_0987 transporter, RarD family, DMT superfamily; hypothetical protein 2288261 4579344 Pden_2291 Paracoccus denitrificans PD1222 hypothetical protein YP_916078.1 2287320 D 318586 CDS YP_916079.1 119385023 4579345 complement(2288274..2289668) 1 NC_008686.1 KEGG: sit:TM1040_0020 conserved hypothetical protein; hypothetical protein 2289668 4579345 Pden_2292 Paracoccus denitrificans PD1222 hypothetical protein YP_916079.1 2288274 R 318586 CDS YP_916080.1 119385024 4579346 complement(2289665..2291365) 1 NC_008686.1 PFAM: glycosyl transferase, family 14; KEGG: sit:TM1040_0019 glycosyl transferase, family 14; glycosyl transferase family protein 2291365 4579346 Pden_2293 Paracoccus denitrificans PD1222 glycosyl transferase family protein YP_916080.1 2289665 R 318586 CDS YP_916081.1 119385025 4579347 complement(2291362..2292387) 1 NC_008686.1 KEGG: jan:Jann_0220 hypothetical protein; hypothetical protein 2292387 4579347 Pden_2294 Paracoccus denitrificans PD1222 hypothetical protein YP_916081.1 2291362 R 318586 CDS YP_916082.1 119385026 4579348 complement(2292415..2293653) 1 NC_008686.1 PFAM: glycosyl transferase, group 1; KEGG: jan:Jann_0219 glycosyl transferase, group 1; group 1 glycosyl transferase 2293653 4579348 Pden_2295 Paracoccus denitrificans PD1222 group 1 glycosyl transferase YP_916082.1 2292415 R 318586 CDS YP_916083.1 119385027 4579349 complement(2293643..2294641) 1 NC_008686.1 TIGRFAM: UDP-glucose 4-epimerase; PFAM: NAD-dependent epimerase/dehydratase; short-chain dehydrogenase/reductase SDR; 3-beta hydroxysteroid dehydrogenase/isomerase; polysaccharide biosynthesis protein CapD; dTDP-4-dehydrorhamnose reductase; KEGG: sit:TM1040_0016 UDP-glucose 4-epimerase; UDP-glucose 4-epimerase 2294641 4579349 Pden_2296 Paracoccus denitrificans PD1222 UDP-glucose 4-epimerase YP_916083.1 2293643 R 318586 CDS YP_916084.1 119385028 4579350 complement(2294647..2295537) 1 NC_008686.1 PFAM: Nucleotidyl transferase; KEGG: rsp:RSP_1159 UDP-glucose pyrophosphate; nucleotidyl transferase 2295537 4579350 Pden_2297 Paracoccus denitrificans PD1222 nucleotidyl transferase YP_916084.1 2294647 R 318586 CDS YP_916085.1 119385029 4579351 complement(2295684..2296892) 1 NC_008686.1 PFAM: glycosyl transferase, family 2; KEGG: jan:Jann_0217 glycosyl transferase, family 2; glycosyl transferase family protein 2296892 4579351 Pden_2298 Paracoccus denitrificans PD1222 glycosyl transferase family protein YP_916085.1 2295684 R 318586 CDS YP_916086.1 119385030 4579352 complement(2296892..2297692) 1 NC_008686.1 CMP-2-keto-3-deoxyoctulosonic acid synthetase; catalyzes the formation of CMP-3-deoxy-D-manno-octulosonate from CTP and 3-deoxy-D-manno-octulosonate which is incorporated into LPS; 3-deoxy-manno-octulosonate cytidylyltransferase 2297692 4579352 Pden_2299 Paracoccus denitrificans PD1222 3-deoxy-manno-octulosonate cytidylyltransferase YP_916086.1 2296892 R 318586 CDS YP_916087.1 119385031 4579353 complement(2297697..2298494) 1 NC_008686.1 TIGRFAM: 3'(2'),5'-bisphosphate nucleotidase; PFAM: inositol monophosphatase; KEGG: rsp:RSP_1161 3'-phosphadenosine 5'-phosphosulfate 3'-phosphatase; 3'(2'),5'-bisphosphate nucleotidase 2298494 4579353 Pden_2300 Paracoccus denitrificans PD1222 3'(2'),5'-bisphosphate nucleotidase YP_916087.1 2297697 R 318586 CDS YP_916088.1 119385032 4579354 2298636..2299457 1 NC_008686.1 PFAM: ABC-2 type transporter; KEGG: sil:SPO0040 ABC transporter, permease protein; ABC transporter 2299457 4579354 Pden_2301 Paracoccus denitrificans PD1222 ABC transporter YP_916088.1 2298636 D 318586 CDS YP_916089.1 119385033 4579355 2299715..2301631 1 NC_008686.1 heat shock protein 70; assists in folding of nascent polypeptide chains; refolding of misfolded proteins; utilizes ATPase activity to help fold; co-chaperones are DnaJ and GrpE; multiple copies in some bacteria; molecular chaperone DnaK 2301631 dnaK 4579355 dnaK Paracoccus denitrificans PD1222 molecular chaperone DnaK YP_916089.1 2299715 D 318586 CDS YP_916090.1 119385034 4579356 2301713..2302867 1 NC_008686.1 chaperone Hsp40; co-chaperone with DnaK; Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins and by disaggregating proteins, also in an autonomous, dnaK-independent fashion; molecular chaperone DnaJ 2302867 4579356 Pden_2303 Paracoccus denitrificans PD1222 molecular chaperone DnaJ YP_916090.1 2301713 D 318586 CDS YP_916091.1 119385035 4579357 2302913..2303704 1 NC_008686.1 Involved in DNA double-strand break repair and recombination. Promotes the annealing of complementary single-stranded DNA and by simulation of RAD51 recombinase; DNA repair protein RadC 2303704 radC 4579357 radC Paracoccus denitrificans PD1222 DNA repair protein RadC YP_916091.1 2302913 D 318586 CDS YP_916092.1 119385036 4579358 2303887..2304474 1 NC_008686.1 TIGRFAM: ubiquinol-cytochrome c reductase, iron-sulfur subunit; PFAM: Rieske [2Fe-2S] domain protein; KEGG: sit:TM1040_2814 ubiquinol-cytochrome c reductase, iron-sulfur subunit; ubiquinol-cytochrome c reductase, iron-sulfur subunit 2304474 4579358 Pden_2305 Paracoccus denitrificans PD1222 ubiquinol-cytochrome c reductase, iron-sulfur subunit YP_916092.1 2303887 D 318586 CDS YP_916093.1 119385037 4579359 2304485..2305807 1 NC_008686.1 PFAM: Cytochrome b/b6, N-terminal domain; Cytochrome b/b6, C-terminal domain; KEGG: sit:TM1040_2813 cytochrome b/b6-like; cytochrome b/b6 domain-containing protein 2305807 4579359 Pden_2306 Paracoccus denitrificans PD1222 cytochrome b/b6 domain-containing protein YP_916093.1 2304485 D 318586 CDS YP_916094.1 119385038 4579360 2305820..2307172 1 NC_008686.1 PFAM: cytochrome c1; KEGG: rde:RD1_0565 cytochrome c1; cytochrome c1 2307172 4579360 Pden_2307 Paracoccus denitrificans PD1222 cytochrome c1 YP_916094.1 2305820 D 318586 CDS YP_916095.1 119385039 4579361 2307311..2308180 1 NC_008686.1 PFAM: PfkB domain protein; KEGG: rsp:RSP_1216 RbsK, carbohydrate kinase, ribokinase family; ribokinase 2308180 4579361 Pden_2308 Paracoccus denitrificans PD1222 ribokinase YP_916095.1 2307311 D 318586 CDS YP_916096.1 119385040 4579362 2308220..2309023 1 NC_008686.1 PFAM: peptidase S49; KEGG: sil:SPO3640 peptidase, family S49; peptidase S49 2309023 4579362 Pden_2309 Paracoccus denitrificans PD1222 peptidase S49 YP_916096.1 2308220 D 318586 CDS YP_916097.1 119385041 4579363 2309020..2309130 1 NC_008686.1 hypothetical protein 2309130 4579363 Pden_2310 Paracoccus denitrificans PD1222 hypothetical protein YP_916097.1 2309020 D 318586 CDS YP_916098.1 119385042 4579364 2309127..2309897 1 NC_008686.1 PFAM: short-chain dehydrogenase/reductase SDR; KR; KEGG: jan:Jann_3920 short-chain dehydrogenase/reductase SDR; short chain dehydrogenase 2309897 4579364 Pden_2311 Paracoccus denitrificans PD1222 short chain dehydrogenase YP_916098.1 2309127 D 318586 CDS YP_916099.1 119385043 4579365 2310199..2312070 1 NC_008686.1 The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrC both incises the 5' and 3' sides of the lesion. The N-terminal half is responsible for the 3' incision and the C-terminal half is responsible for the 5' incision; excinuclease ABC subunit C 2312070 uvrC 4579365 uvrC Paracoccus denitrificans PD1222 excinuclease ABC subunit C YP_916099.1 2310199 D 318586 CDS YP_916100.1 119385044 4579366 2312083..2312514 1 NC_008686.1 KEGG: atc:AGR_C_2408 hypothetical protein; hypothetical protein 2312514 4579366 Pden_2313 Paracoccus denitrificans PD1222 hypothetical protein YP_916100.1 2312083 D 318586 CDS YP_916101.1 119385045 4579367 complement(2312521..2313147) 1 NC_008686.1 KEGG: rsp:RSP_2812 hypothetical protein; hypothetical protein 2313147 4579367 Pden_2314 Paracoccus denitrificans PD1222 hypothetical protein YP_916101.1 2312521 R 318586 CDS YP_916102.1 119385046 4579368 complement(2313159..2314460) 1 NC_008686.1 PFAM: Mammalian cell entry related domain protein; KEGG: rsp:RSP_2811 ABC transporter, periplasmic substrate-binding protein; hypothetical protein 2314460 4579368 Pden_2315 Paracoccus denitrificans PD1222 hypothetical protein YP_916102.1 2313159 R 318586 CDS YP_916103.1 119385047 4579369 complement(2314465..2315241) 1 NC_008686.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rsp:RSP_2810 ABC transporter, ATPase subunit; ABC transporter 2315241 4579369 Pden_2316 Paracoccus denitrificans PD1222 ABC transporter YP_916103.1 2314465 R 318586 CDS YP_916104.1 119385048 4579370 complement(2315238..2316332) 1 NC_008686.1 PFAM: protein of unknown function DUF140; KEGG: rsp:RSP_2809 ABC transporter, inner membrane subunit; hypothetical protein 2316332 4579370 Pden_2317 Paracoccus denitrificans PD1222 hypothetical protein YP_916104.1 2315238 R 318586 CDS YP_916105.1 119385049 4579371 complement(2316776..2317693) 1 NC_008686.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: jan:Jann_1027 transcriptional regulator, LysR family; LysR family transcriptional regulator 2317693 4579371 Pden_2318 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_916105.1 2316776 R 318586 CDS YP_916106.1 119385050 4579372 2317784..2318647 1 NC_008686.1 TIGRFAM: 5,10-methylenetetrahydrofolate reductase; PFAM: methylenetetrahydrofolate reductase; KEGG: rsp:RSP_2172 5,10-methylenetetrahydrofolate reductase; 5,10-methylenetetrahydrofolate reductase 2318647 4579372 Pden_2319 Paracoccus denitrificans PD1222 5,10-methylenetetrahydrofolate reductase YP_916106.1 2317784 D 318586 CDS YP_916107.1 119385051 4579373 complement(2318675..2319826) 1 NC_008686.1 KEGG: sil:SPO3018 hypothetical protein; hypothetical protein 2319826 4579373 Pden_2320 Paracoccus denitrificans PD1222 hypothetical protein YP_916107.1 2318675 R 318586 CDS YP_916108.1 119385052 4579374 complement(2319868..2321031) 1 NC_008686.1 PFAM: Orn/DAP/Arg decarboxylase 2; KEGG: rsp:RSP_1991 ornithine decarboxylase; Orn/DAP/Arg decarboxylase 2 2321031 4579374 Pden_2321 Paracoccus denitrificans PD1222 Orn/DAP/Arg decarboxylase 2 YP_916108.1 2319868 R 318586 CDS YP_916109.1 119385053 4579375 2321165..2321596 1 NC_008686.1 PFAM: regulatory protein, AsnC/Lrp family; KEGG: rsp:RSP_1990 transcriptional regulator, AsnC family; AsnC family transcriptional regulator 2321596 4579375 Pden_2322 Paracoccus denitrificans PD1222 AsnC family transcriptional regulator YP_916109.1 2321165 D 318586 CDS YP_916110.1 119385054 4579376 complement(2321563..2322159) 1 NC_008686.1 TIGRFAM: methyltransferase; PFAM: conserved hypothetical protein 95; KEGG: rsp:RSP_0901 N-6 adenine-specific DNA methylase; methyltransferase 2322159 4579376 Pden_2323 Paracoccus denitrificans PD1222 methyltransferase YP_916110.1 2321563 R 318586 CDS YP_916111.1 119385055 4579377 complement(2322156..2323352) 1 NC_008686.1 PFAM: FAD-dependent pyridine nucleotide-disulphide oxidoreductase; KEGG: rsp:RSP_0900 FAD-dependent pyridine nucleotide-disulphide oxidoreductase; FAD-dependent pyridine nucleotide-disulfide oxidoreductase 2323352 4579377 Pden_2324 Paracoccus denitrificans PD1222 FAD-dependent pyridine nucleotide-disulfide oxidoreductase YP_916111.1 2322156 R 318586 CDS YP_916112.1 119385056 4579378 2323408..2323914 1 NC_008686.1 PFAM: Redoxin domain protein; KEGG: sit:TM1040_2472 redoxin; redoxin domain-containing protein 2323914 4579378 Pden_2325 Paracoccus denitrificans PD1222 redoxin domain-containing protein YP_916112.1 2323408 D 318586 CDS YP_916113.1 119385057 4579379 complement(2323848..2324561) 1 NC_008686.1 PFAM: helix-turn-helix, HxlR type; KEGG: bpa:BPP3401 transcriptional regulator; HxlR family transcriptional regulator 2324561 4579379 Pden_2326 Paracoccus denitrificans PD1222 HxlR family transcriptional regulator YP_916113.1 2323848 R 318586 CDS YP_916114.1 119385058 4579380 2324650..2325006 1 NC_008686.1 PFAM: protein of unknown function DUF1428; KEGG: hne:HNE_1019 hypothetical protein; hypothetical protein 2325006 4579380 Pden_2327 Paracoccus denitrificans PD1222 hypothetical protein YP_916114.1 2324650 D 318586 CDS YP_916115.1 119385059 4579381 2325203..2325805 1 NC_008686.1 PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase; KEGG: sme:SMc04054 hypothetical protein; glyoxalase/bleomycin resistance protein/dioxygenase 2325805 4579381 Pden_2328 Paracoccus denitrificans PD1222 glyoxalase/bleomycin resistance protein/dioxygenase YP_916115.1 2325203 D 318586 CDS YP_916116.1 119385060 4579382 2325802..2326437 1 NC_008686.1 PFAM: YceI family protein; KEGG: bma:BMAA0007 YceI like family protein; hypothetical protein 2326437 4579382 Pden_2329 Paracoccus denitrificans PD1222 hypothetical protein YP_916116.1 2325802 D 318586 CDS YP_916117.1 119385061 4579383 2326441..2327073 1 NC_008686.1 PFAM: Glutathione S-transferase, N-terminal domain; Glutathione S-transferase, C-terminal domain; KEGG: bja:blr5350 glutathione S-transferase; glutathione S-transferase domain-containing protein 2327073 4579383 Pden_2330 Paracoccus denitrificans PD1222 glutathione S-transferase domain-containing protein YP_916117.1 2326441 D 318586 CDS YP_916118.1 119385062 4579384 2327364..2330456 1 NC_008686.1 valine--tRNA ligase; ValRS; converts valine ATP and tRNA(Val) to AMP PPi and valyl-tRNA(Val); class-I aminoacyl-tRNA synthetase type 1 subfamily; has a posttransfer editing process to hydrolyze mischarged Thr-tRNA(Val) which is done by the editing domain; valyl-tRNA synthetase 2330456 valS 4579384 valS Paracoccus denitrificans PD1222 valyl-tRNA synthetase YP_916118.1 2327364 D 318586 CDS YP_916119.1 119385063 4579385 complement(2330519..2331211) 1 NC_008686.1 PFAM: cobalamin (vitamin B12) biosynthesis CbiX protein; KEGG: sil:SPO2745 hypothetical protein; cobalamin (vitamin B12) biosynthesis CbiX protein 2331211 4579385 Pden_2332 Paracoccus denitrificans PD1222 cobalamin (vitamin B12) biosynthesis CbiX protein YP_916119.1 2330519 R 318586 CDS YP_916120.1 119385064 4579386 complement(2331204..2331767) 1 NC_008686.1 KEGG: sil:SPOA0324 hypothetical protein; hypothetical protein 2331767 4579386 Pden_2333 Paracoccus denitrificans PD1222 hypothetical protein YP_916120.1 2331204 R 318586 CDS YP_916121.1 119385065 4579387 2331856..2332365 1 NC_008686.1 PFAM: NnrUfamily protein; KEGG: rpe:RPE_1287 NnrU family protein; NnrU family protein 2332365 4579387 Pden_2334 Paracoccus denitrificans PD1222 NnrU family protein YP_916121.1 2331856 D 318586 CDS YP_916122.1 119385066 4579388 complement(2332349..2333365) 1 NC_008686.1 PFAM: FAD dependent oxidoreductase; KEGG: jan:Jann_0139 FAD dependent oxidoreductase; FAD dependent oxidoreductase 2333365 4579388 Pden_2335 Paracoccus denitrificans PD1222 FAD dependent oxidoreductase YP_916122.1 2332349 R 318586 CDS YP_916123.1 119385067 4579389 2333413..2334069 1 NC_008686.1 PFAM: protein of unknown function DUF752; KEGG: sil:SPO3553 hypothetical protein; hypothetical protein 2334069 4579389 Pden_2336 Paracoccus denitrificans PD1222 hypothetical protein YP_916123.1 2333413 D 318586 CDS YP_916124.1 119385068 4579390 complement(2334066..2334782) 1 NC_008686.1 PFAM: Rhomboid family protein; KEGG: jan:Jann_3255 rhomboid-like protein; rhomboid family protein 2334782 4579390 Pden_2337 Paracoccus denitrificans PD1222 rhomboid family protein YP_916124.1 2334066 R 318586 CDS YP_916125.1 119385069 4579391 2334887..2336155 1 NC_008686.1 catalyzes the formation of succinate semialdehyde and glutamate from 4-aminobutanoate and 2-oxoglutarate; 4-aminobutyrate aminotransferase 2336155 4579391 Pden_2338 Paracoccus denitrificans PD1222 4-aminobutyrate aminotransferase YP_916125.1 2334887 D 318586 CDS YP_916126.1 119385070 4579392 complement(2336443..2337399) 1 NC_008686.1 catalyzes the carboxylation of acetyl-CoA to malonyl-CoA; forms a tetramer composed of two alpha (AccA) and two beta (AccD) subunits; one of the two catalytic subunits that can form the acetyl CoA carboxylase enzyme together with a carrier protein; acetyl-CoA carboxylase carboxyltransferase subunit alpha 2337399 4579392 Pden_2339 Paracoccus denitrificans PD1222 acetyl-CoA carboxylase carboxyltransferase subunit alpha YP_916126.1 2336443 R 318586 CDS YP_916127.1 119385071 4579393 complement(2337468..2337908) 1 NC_008686.1 PFAM: molybdopterin biosynthesis MoaE; KEGG: sit:TM1040_3633 molybdopterin biosynthesis MoaE; molybdopterin biosynthesis MoaE 2337908 4579393 Pden_2340 Paracoccus denitrificans PD1222 molybdopterin biosynthesis MoaE YP_916127.1 2337468 R 318586 CDS YP_916128.1 119385072 4579394 complement(2337910..2338161) 1 NC_008686.1 TIGRFAM: molybdopterin converting factor, subunit 1; PFAM: thiamineS protein; KEGG: sit:TM1040_3632 molybdopterin converting factor, subunit 1; molybdopterin converting factor subunit 1 2338161 4579394 Pden_2341 Paracoccus denitrificans PD1222 molybdopterin converting factor subunit 1 YP_916128.1 2337910 R 318586 CDS YP_916129.1 119385073 4579395 complement(2338151..2338780) 1 NC_008686.1 TIGRFAM: CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase; PFAM: CDP-alcohol phosphatidyltransferase; KEGG: rsp:RSP_1073 phosphatidylglycerol phosphate synthase; CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase 2338780 4579395 Pden_2342 Paracoccus denitrificans PD1222 CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase YP_916129.1 2338151 R 318586 CDS YP_916130.1 119385074 4579396 complement(2338840..2339280) 1 NC_008686.1 PFAM: regulatory protein, MerR; KEGG: rsp:RSP_1790 probable transcriptional regulator; MerR family transcriptional regulator 2339280 4579396 Pden_2343 Paracoccus denitrificans PD1222 MerR family transcriptional regulator YP_916130.1 2338840 R 318586 CDS YP_916131.1 119385075 4579397 2339369..2341567 1 NC_008686.1 TIGRFAM: ATPase, P-type (transporting), HAD superfamily, subfamily IC; cadmium-translocating P-type ATPase; heavy metal translocating P-type ATPase; PFAM: Haloacid dehalogenase domain protein hydrolase; Heavy metal transport/detoxification protein; E1-E2 ATPase-associated domain protein; KEGG: rsp:RSP_1791 heavy metal-(Cd/Co/Hg/Pb/Zn)-translocating P-type ATPase; heavy metal translocating P-type ATPase 2341567 4579397 Pden_2344 Paracoccus denitrificans PD1222 heavy metal translocating P-type ATPase YP_916131.1 2339369 D 318586 CDS YP_916132.1 119385076 4579398 complement(2341915..2344743) 1 NC_008686.1 acts in conjunction with GvcH to form H-protein-S-aminomethyldihydrolipoyllysine from glycine; glycine dehydrogenase 2344743 4579398 Pden_2346 Paracoccus denitrificans PD1222 glycine dehydrogenase YP_916132.1 2341915 R 318586 CDS YP_916133.1 119385077 4579204 complement(2344903..2345259) 1 NC_008686.1 TIGRFAM: glycine cleavage system H protein; PFAM: glycine cleavage H-protein; KEGG: rde:RD1_1223 glycine cleavage system H protein; glycine cleavage system H protein 2345259 4579204 Pden_2347 Paracoccus denitrificans PD1222 glycine cleavage system H protein YP_916133.1 2344903 R 318586 CDS YP_916134.1 119385078 4579205 complement(2345270..2346382) 1 NC_008686.1 TIGRFAM: glycine cleavage system T protein; PFAM: glycine cleavage T protein (aminomethyl transferase); Glycine cleavage T-protein, C-terminal barrel; KEGG: rsp:RSP_2193 predicted aminomethyltransferase, tetrahydrofolate dependent; glycine cleavage system T protein 2346382 4579205 Pden_2348 Paracoccus denitrificans PD1222 glycine cleavage system T protein YP_916134.1 2345270 R 318586 CDS YP_916135.1 119385079 4579206 complement(2346659..2347441) 1 NC_008686.1 PFAM: short-chain dehydrogenase/reductase SDR; KEGG: sil:SPO2692 oxidoreductase, short chain dehydrogenase/reductase family; short-chain dehydrogenase/reductase SDR 2347441 4579206 Pden_2349 Paracoccus denitrificans PD1222 short-chain dehydrogenase/reductase SDR YP_916135.1 2346659 R 318586 CDS YP_916136.1 119385080 4579207 complement(2347500..2347838) 1 NC_008686.1 KEGG: rde:RD1_0883 hypothetical protein; hypothetical protein 2347838 4579207 Pden_2350 Paracoccus denitrificans PD1222 hypothetical protein YP_916136.1 2347500 R 318586 CDS YP_916137.1 119385081 4579208 complement(2347835..2348449) 1 NC_008686.1 KEGG: rsp:RSP_2594 hypothetical protein; hypothetical protein 2348449 4579208 Pden_2351 Paracoccus denitrificans PD1222 hypothetical protein YP_916137.1 2347835 R 318586 CDS YP_916138.1 119385082 4579209 complement(2348533..2349858) 1 NC_008686.1 PFAM: response regulator receiver; ATP-binding region, ATPase domain protein domain protein; histidine kinase A domain protein domain protein; KEGG: rsp:RSP_2593 hybrid histidine kinase; histidine kinase 2349858 4579209 Pden_2352 Paracoccus denitrificans PD1222 histidine kinase YP_916138.1 2348533 R 318586 CDS YP_916139.1 119385083 4579210 complement(2349862..2351043) 1 NC_008686.1 PFAM: domain of unknown function DUF1745; KEGG: rsp:RSP_2592 hypothetical protein; hypothetical protein 2351043 4579210 Pden_2353 Paracoccus denitrificans PD1222 hypothetical protein YP_916139.1 2349862 R 318586 CDS YP_916140.1 119385084 4579211 complement(2351040..2351750) 1 NC_008686.1 PFAM: regulatory protein, LuxR; response regulator receiver; Sigma-70, region 4 type 2; KEGG: rsp:RSP_2591 two component transcriptional regulator, LuxR family family; LuxR family transcriptional regulator 2351750 4579211 Pden_2354 Paracoccus denitrificans PD1222 LuxR family transcriptional regulator YP_916140.1 2351040 R 318586 CDS YP_916141.1 119385085 4579212 2351939..2352928 1 NC_008686.1 KEGG: sme:SMb20181 ABC transporter periplasmic solute-binding protein; ABC transporter periplasmic solute-binding protein 2352928 4579212 Pden_2355 Paracoccus denitrificans PD1222 ABC transporter periplasmic solute-binding protein YP_916141.1 2351939 D 318586 CDS YP_916142.1 119385086 4579213 2352936..2353718 1 NC_008686.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: sme:SMb20182 ABC transporter protein; binding-protein-dependent transport system inner membrane protein 2353718 4579213 Pden_2356 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_916142.1 2352936 D 318586 CDS YP_916143.1 119385087 4579214 2353708..2354298 1 NC_008686.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rde:RD1_0904 ABC transporter; ABC transporter 2354298 4579214 Pden_2357 Paracoccus denitrificans PD1222 ABC transporter YP_916143.1 2353708 D 318586 CDS YP_916144.1 119385088 4579215 complement(2354286..2355056) 1 NC_008686.1 KEGG: rsp:RSP_2590 hypothetical protein; hypothetical protein 2355056 4579215 Pden_2358 Paracoccus denitrificans PD1222 hypothetical protein YP_916144.1 2354286 R 318586 CDS YP_916145.1 119385089 4579216 complement(2355053..2356189) 1 NC_008686.1 KEGG: rde:RD1_1150 coenzyme PQQ biosynthesis protein E; TIGRFAM: coenzyme PQQ biosynthesis protein E; PFAM: Radical SAM domain protein; SMART: Elongator protein 3/MiaB/NifB; pyrroloquinoline quinone biosynthesis protein PqqE 2356189 4579216 Pden_2359 Paracoccus denitrificans PD1222 pyrroloquinoline quinone biosynthesis protein PqqE YP_916145.1 2355053 R 318586 CDS YP_916146.1 119385090 4579217 complement(2356186..2356494) 1 NC_008686.1 PFAM: coenzyme PQQ synthesis D; KEGG: rde:RD1_1151 coenzyme PQQ synthesis protein D; coenzyme PQQ biosynthesis protein PqqD 2356494 4579217 Pden_2360 Paracoccus denitrificans PD1222 coenzyme PQQ biosynthesis protein PqqD YP_916146.1 2356186 R 318586 CDS YP_916147.1 119385091 4579218 complement(2356491..2357285) 1 NC_008686.1 Required in the synthesis of PPQ, but its exact function is unknown; pyrroloquinoline quinone biosynthesis protein PqqC 2357285 4579218 Pden_2361 Paracoccus denitrificans PD1222 pyrroloquinoline quinone biosynthesis protein PqqC YP_916147.1 2356491 R 318586 CDS YP_916148.1 119385092 4579219 complement(2357282..2358172) 1 NC_008686.1 possibly involved in transport of pyrroloquinoline quinone transport; pyrroloquinoline quinone biosynthesis protein PqqB 2358172 4579219 Pden_2362 Paracoccus denitrificans PD1222 pyrroloquinoline quinone biosynthesis protein PqqB YP_916148.1 2357282 R 318586 CDS YP_916149.1 119385093 4579220 2358471..2359526 1 NC_008686.1 PFAM: beta-lactamase domain protein; KEGG: rsp:RSP_2589 hypothetical protein; beta-lactamase domain-containing protein 2359526 4579220 Pden_2363 Paracoccus denitrificans PD1222 beta-lactamase domain-containing protein YP_916149.1 2358471 D 318586 CDS YP_916150.1 119385094 4579221 2359584..2365085 1 NC_008686.1 PFAM: alpha-2-macroglobulin domain protein; N/apple PAN domain protein; alpha-2-macroglobulin domain protein 2; Tetratricopeptide TPR_2 repeat protein; KEGG: rsp:RSP_1356 hypothetical protein; alpha-2-macroglobulin domain-containing protein 2365085 4579221 Pden_2364 Paracoccus denitrificans PD1222 alpha-2-macroglobulin domain-containing protein YP_916150.1 2359584 D 318586 CDS YP_916151.1 119385095 4579222 2365153..2366238 1 NC_008686.1 PFAM: helix-turn-helix, Fis-type; GAF domain protein; KEGG: sit:TM1040_3622 GAF sensor protein; Fis family transcriptional regulator 2366238 4579222 Pden_2365 Paracoccus denitrificans PD1222 Fis family transcriptional regulator YP_916151.1 2365153 D 318586 CDS YP_916152.1 119385096 4579223 2366345..2367871 1 NC_008686.1 PFAM: aldehyde dehydrogenase; KEGG: sme:SMc02689 probable aldehyde dehydrogenase protein; aldehyde dehydrogenase 2367871 4579223 Pden_2366 Paracoccus denitrificans PD1222 aldehyde dehydrogenase YP_916152.1 2366345 D 318586 CDS YP_916153.1 119385097 4579224 2367955..2368989 1 NC_008686.1 PFAM: Alcohol dehydrogenase, zinc-binding domain protein; Alcohol dehydrogenase GroES domain protein; KEGG: bmb:BruAb1_0198 alcohol dehydrogenase, zinc-containing; alcohol dehydrogenase 2368989 4579224 Pden_2367 Paracoccus denitrificans PD1222 alcohol dehydrogenase YP_916153.1 2367955 D 318586 CDS YP_916154.1 119385098 4579225 2368992..2369348 1 NC_008686.1 PFAM: protein of unknown function DUF779; KEGG: mlo:mll6637 hypothetical protein; hypothetical protein 2369348 4579225 Pden_2368 Paracoccus denitrificans PD1222 hypothetical protein YP_916154.1 2368992 D 318586 CDS YP_916155.1 119385099 4579226 complement(2369402..2369593) 1 NC_008686.1 PFAM: protein of unknown function DUF343; KEGG: sit:TM1040_0056 protein of unknown function DUF343; hypothetical protein 2369593 4579226 Pden_2369 Paracoccus denitrificans PD1222 hypothetical protein YP_916155.1 2369402 R 318586 CDS YP_916156.1 119385100 4579227 complement(2369590..2370228) 1 NC_008686.1 PFAM: peptidase S16, lon domain protein; KEGG: sit:TM1040_0055 peptidase S16, lon-like; peptidase S16, lon domain-containing protein 2370228 4579227 Pden_2370 Paracoccus denitrificans PD1222 peptidase S16, lon domain-containing protein YP_916156.1 2369590 R 318586 CDS YP_916157.1 119385101 4579228 complement(2370230..2371141) 1 NC_008686.1 PFAM: Thioredoxin domain; KEGG: rsp:RSP_1489 protein containing thioredoxin domain; thioredoxin 2371141 4579228 Pden_2371 Paracoccus denitrificans PD1222 thioredoxin YP_916157.1 2370230 R 318586 CDS YP_916158.1 119385102 4579229 complement(2371232..2372017) 1 NC_008686.1 TIGRFAM: exodeoxyribonuclease III Xth; PFAM: Endonuclease/exonuclease/phosphatase; KEGG: sit:TM1040_0053 exodeoxyribonuclease III; exodeoxyribonuclease III 2372017 4579229 Pden_2372 Paracoccus denitrificans PD1222 exodeoxyribonuclease III YP_916158.1 2371232 R 318586 CDS YP_916159.1 119385103 4579230 2372110..2372355 1 NC_008686.1 hypothetical protein 2372355 4579230 Pden_2373 Paracoccus denitrificans PD1222 hypothetical protein YP_916159.1 2372110 D 318586 CDS YP_916160.1 119385104 4579231 complement(2372321..2373007) 1 NC_008686.1 PFAM: response regulator receiver; transcriptional regulator domain protein; KEGG: jan:Jann_0417 two component transcriptional regulator, winged helix family; two component transcriptional regulator 2373007 4579231 Pden_2374 Paracoccus denitrificans PD1222 two component transcriptional regulator YP_916160.1 2372321 R 318586 CDS YP_916161.1 119385105 4579232 2373141..2374202 1 NC_008686.1 PFAM: GTP cyclohydrolase II; KEGG: jan:Jann_0416 GTP cyclohydrolase II; GTP cyclohydrolase II 2374202 4579232 Pden_2375 Paracoccus denitrificans PD1222 GTP cyclohydrolase II YP_916161.1 2373141 D 318586 CDS YP_916162.1 119385106 4579233 2374211..2374735 1 NC_008686.1 KEGG: sil:SPO3428 hypothetical protein; hypothetical protein 2374735 4579233 Pden_2376 Paracoccus denitrificans PD1222 hypothetical protein YP_916162.1 2374211 D 318586 CDS YP_916163.1 119385107 4579234 complement(2374740..2375489) 1 NC_008686.1 PFAM: short-chain dehydrogenase/reductase SDR; KR; KEGG: mes:Meso_2224 short-chain dehydrogenase/reductase SDR; short-chain dehydrogenase/reductase SDR 2375489 4579234 Pden_2377 Paracoccus denitrificans PD1222 short-chain dehydrogenase/reductase SDR YP_916163.1 2374740 R 318586 CDS YP_916164.1 119385108 4579235 complement(2375591..2376790) 1 NC_008686.1 PFAM: RNA methylase; KEGG: sit:TM1040_2415 RNA methylase; RNA methylase 2376790 4579235 Pden_2378 Paracoccus denitrificans PD1222 RNA methylase YP_916164.1 2375591 R 318586 CDS YP_916165.1 119385109 4579236 2376954..2377748 1 NC_008686.1 PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase; KEGG: mes:Meso_1284 glyoxalase/bleomycin resistance protein/dioxygenase; glyoxalase/bleomycin resistance protein/dioxygenase 2377748 4579236 Pden_2379 Paracoccus denitrificans PD1222 glyoxalase/bleomycin resistance protein/dioxygenase YP_916165.1 2376954 D 318586 CDS YP_916166.1 119385110 4579237 complement(2377750..2378538) 1 NC_008686.1 PFAM: metallophosphoesterase; KEGG: rsp:RSP_0337 possible phospodiesterase; metallophosphoesterase 2378538 4579237 Pden_2380 Paracoccus denitrificans PD1222 metallophosphoesterase YP_916166.1 2377750 R 318586 CDS YP_916167.1 119385111 4579238 complement(2378535..2379515) 1 NC_008686.1 PFAM: diacylglycerol kinase, catalytic region; KEGG: rsp:RSP_0338 hypothetical protein; diacylglycerol kinase catalytic subunit 2379515 4579238 Pden_2381 Paracoccus denitrificans PD1222 diacylglycerol kinase catalytic subunit YP_916167.1 2378535 R 318586 CDS YP_916168.1 119385112 4579239 2379864..2381087 1 NC_008686.1 TIGRFAM: isochorismate synthases; PFAM: Anthranilate synthase component I and chorismate binding protein; KEGG: tfu:Tfu_1872 isochorismate synthase; isochorismate synthase 2381087 4579239 Pden_2382 Paracoccus denitrificans PD1222 isochorismate synthase YP_916168.1 2379864 D 318586 CDS YP_916169.1 119385113 4579240 2381087..2381743 1 NC_008686.1 PFAM: isochorismatase hydrolase; KEGG: bsu:BG11241 isochorismatase (2,3 dihydro-2,3 dihydroxybenzoate synthase); isochorismatase 2381743 4579240 Pden_2383 Paracoccus denitrificans PD1222 isochorismatase YP_916169.1 2381087 D 318586 CDS YP_916170.1 119385114 4579241 2381734..2382504 1 NC_008686.1 PFAM: NAD-dependent epimerase/dehydratase; short-chain dehydrogenase/reductase SDR; Male sterility C-terminal domain; KR; KEGG: hch:HCH_06575 short-chain alcohol dehydrogenase-like protein; short-chain dehydrogenase/reductase SDR 2382504 4579241 Pden_2384 Paracoccus denitrificans PD1222 short-chain dehydrogenase/reductase SDR YP_916170.1 2381734 D 318586 CDS YP_916171.1 119385115 4579242 complement(2382798..2384420) 1 NC_008686.1 bifunctional 2,3-dihydroxybenzoate-AMP ligase/S-dihydroxybenzoyltransferase; activates the carboxylate group of 2,3-dihydroxy-benzoate forming (2,3-dihydroxybenzoyl)adenylate then catalyzes the acylation of holo-entB with 2,3-dihydroxy-benzoate adenylate; enterobactin synthase subunit E 2384420 entE 4579242 entE Paracoccus denitrificans PD1222 enterobactin synthase subunit E YP_916171.1 2382798 R 318586 CDS YP_916172.1 119385116 4579243 2384608..2385957 1 NC_008686.1 PFAM: condensation domain protein; KEGG: bmb:BruAb2_0017 hypothetical enterobactin synthetase, component F; condensation domain-containing protein 2385957 4579243 Pden_2387 Paracoccus denitrificans PD1222 condensation domain-containing protein YP_916172.1 2384608 D 318586 CDS YP_916173.1 119385117 4579244 2386014..2386469 1 NC_008686.1 PFAM: GCN5-related N-acetyltransferase; KEGG: pfl:PFL_4020 acetyltransferase, GNAT family; N-acetyltransferase 2386469 4579244 Pden_2388 Paracoccus denitrificans PD1222 N-acetyltransferase YP_916173.1 2386014 D 318586 CDS YP_916174.1 119385118 4579245 complement(2386466..2386900) 1 NC_008686.1 KEGG: hne:HNE_2962 hypothetical protein; hypothetical protein 2386900 4579245 Pden_2389 Paracoccus denitrificans PD1222 hypothetical protein YP_916174.1 2386466 R 318586 CDS YP_916175.1 119385119 4579246 complement(2386893..2387513) 1 NC_008686.1 KEGG: hne:HNE_2963 hypothetical protein; hypothetical protein 2387513 4579246 Pden_2390 Paracoccus denitrificans PD1222 hypothetical protein YP_916175.1 2386893 R 318586 CDS YP_916176.1 119385120 4579247 2388052..2389314 1 NC_008686.1 PFAM: Cyclopropane-fatty-acyl-phospholipid synthase; Methyltransferase type 11; Methyltransferase type 12; KEGG: pol:Bpro_3190 cyclopropane-fatty-acyl-phospholipid synthase; cyclopropane-fatty-acyl-phospholipid synthase 2389314 4579247 Pden_2392 Paracoccus denitrificans PD1222 cyclopropane-fatty-acyl-phospholipid synthase YP_916176.1 2388052 D 318586 CDS YP_916177.1 119385121 4579248 2389473..2390873 1 NC_008686.1 catalyzes the formation of D-ribulose 5-phosphate from 6-phospho-D-gluconate; 6-phosphogluconate dehydrogenase 2390873 4579248 Pden_2393 Paracoccus denitrificans PD1222 6-phosphogluconate dehydrogenase YP_916177.1 2389473 D 318586 CDS YP_916178.1 119385122 4579249 2391447..2392544 1 NC_008686.1 KEGG: ret:RHE_PB00165 plasmid replication protein RepCb; hypothetical protein 2392544 4579249 Pden_2394 Paracoccus denitrificans PD1222 hypothetical protein YP_916178.1 2391447 D 318586 CDS YP_916179.1 119385123 4579250 2392537..2393898 1 NC_008686.1 hypothetical protein 2393898 4579250 Pden_2395 Paracoccus denitrificans PD1222 hypothetical protein YP_916179.1 2392537 D 318586 CDS YP_916180.1 119385124 4579251 2394003..2394248 1 NC_008686.1 TIGRFAM: addiction module antidote protein, CC2985 family; PFAM: protein of unknown function UPF0156; KEGG: xfa:XF2071 conserved hypothetical protein; CopG family transcriptional regulator 2394248 4579251 Pden_2396 Paracoccus denitrificans PD1222 CopG family transcriptional regulator YP_916180.1 2394003 D 318586 CDS YP_916181.1 119385125 4579252 2394370..2394717 1 NC_008686.1 hypothetical protein 2394717 4579252 Pden_2397 Paracoccus denitrificans PD1222 hypothetical protein YP_916181.1 2394370 D 318586 CDS YP_916182.1 119385126 4579253 complement(2394938..2396110) 1 NC_008686.1 KEGG: mlo:mlr9349 hypothetical protein; hypothetical protein 2396110 4579253 Pden_2398 Paracoccus denitrificans PD1222 hypothetical protein YP_916182.1 2394938 R 318586 CDS YP_916183.1 119385127 4579254 complement(2396435..2396644) 1 NC_008686.1 hypothetical protein 2396644 4579254 Pden_2399 Paracoccus denitrificans PD1222 hypothetical protein YP_916183.1 2396435 R 318586 CDS YP_916184.1 119385128 4579255 complement(2396780..2397058) 1 NC_008686.1 hypothetical protein 2397058 4579255 Pden_2400 Paracoccus denitrificans PD1222 hypothetical protein YP_916184.1 2396780 R 318586 CDS YP_916185.1 119385129 4579256 complement(2397055..2397564) 1 NC_008686.1 hypothetical protein 2397564 4579256 Pden_2401 Paracoccus denitrificans PD1222 hypothetical protein YP_916185.1 2397055 R 318586 CDS YP_916186.1 119385130 4579257 complement(2397740..2398063) 1 NC_008686.1 hypothetical protein 2398063 4579257 Pden_2402 Paracoccus denitrificans PD1222 hypothetical protein YP_916186.1 2397740 R 318586 CDS YP_916187.1 119385131 4579258 2398139..2398366 1 NC_008686.1 PFAM: helix-turn-helix domain protein; KEGG: ngo:NGO0797 transcriptional regulator; XRE family transcriptional regulator 2398366 4579258 Pden_2403 Paracoccus denitrificans PD1222 XRE family transcriptional regulator YP_916187.1 2398139 D 318586 CDS YP_916188.1 119385132 4579259 2398439..2399194 1 NC_008686.1 KEGG: ccr:CC1796 hypothetical protein; hypothetical protein 2399194 4579259 Pden_2404 Paracoccus denitrificans PD1222 hypothetical protein YP_916188.1 2398439 D 318586 CDS YP_916189.1 119385133 4579260 2399178..2399603 1 NC_008686.1 KEGG: ccr:CC1796 hypothetical protein; hypothetical protein 2399603 4579260 Pden_2405 Paracoccus denitrificans PD1222 hypothetical protein YP_916189.1 2399178 D 318586 CDS YP_916190.1 119385134 4579261 2399885..2400790 1 NC_008686.1 KEGG: mes:Meso_2004 D-alanine--D-alanine ligase; TIGRFAM: D-alanine--D-alanine ligase; PFAM: D-alanine--D-alanine ligase domain protein; D-alanine--D-alanine ligase 2400790 4579261 Pden_2406 Paracoccus denitrificans PD1222 D-alanine--D-alanine ligase YP_916190.1 2399885 D 318586 CDS YP_916191.1 119385135 4579262 complement(2400950..2404012) 1 NC_008686.1 PFAM: cytoplasmic peptidoglycan synthetases domain protein; Mur ligase, middle domain protein; KEGG: sil:SPO1183 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Mur ligase middle domain-containing protein 2404012 4579262 Pden_2407 Paracoccus denitrificans PD1222 Mur ligase middle domain-containing protein YP_916191.1 2400950 R 318586 CDS YP_916192.1 119385136 4580742 complement(2404009..2405817) 1 NC_008686.1 hypothetical protein 2405817 4580742 Pden_2408 Paracoccus denitrificans PD1222 hypothetical protein YP_916192.1 2404009 R 318586 CDS YP_916193.1 119385137 4580743 complement(2405814..2406701) 1 NC_008686.1 hypothetical protein 2406701 4580743 Pden_2409 Paracoccus denitrificans PD1222 hypothetical protein YP_916193.1 2405814 R 318586 CDS YP_916194.1 119385138 4580744 complement(2406704..2408428) 1 NC_008686.1 KEGG: bcl:ABC0984 hypothetical protein; hypothetical protein 2408428 4580744 Pden_2410 Paracoccus denitrificans PD1222 hypothetical protein YP_916194.1 2406704 R 318586 CDS YP_916195.1 119385139 4580745 complement(2408431..2409807) 1 NC_008686.1 PFAM: outer membrane efflux protein; KEGG: spt:SPA2549 type I secretion protein; outer membrane efflux protein 2409807 4580745 Pden_2411 Paracoccus denitrificans PD1222 outer membrane efflux protein YP_916195.1 2408431 R 318586 CDS YP_916196.1 119385140 4580746 complement(2409815..2411014) 1 NC_008686.1 TIGRFAM: type I secretion membrane fusion protein, HlyD family; PFAM: secretion protein HlyD family protein; KEGG: ppu:PP_0803 protein secretion ABC efflux system, membrane fusion protein; HlyD family type I secretion membrane fusion protein 2411014 4580746 Pden_2412 Paracoccus denitrificans PD1222 HlyD family type I secretion membrane fusion protein YP_916196.1 2409815 R 318586 CDS YP_916197.1 119385141 4580747 complement(2411014..2413311) 1 NC_008686.1 PFAM: ABC transporter, transmembrane region; ABC transporter related; SMART: AAA ATPase; KEGG: aeh:Mlg_2167 ABC transporter related; ABC transporter 2413311 4580747 Pden_2413 Paracoccus denitrificans PD1222 ABC transporter YP_916197.1 2411014 R 318586 CDS YP_916198.1 119385142 4580748 2419791..2420072 1 NC_008686.1 hypothetical protein 2420072 4580748 Pden_2414 Paracoccus denitrificans PD1222 hypothetical protein YP_916198.1 2419791 D 318586 CDS YP_916199.1 119385143 4580749 complement(2420089..2420415) 1 NC_008686.1 PFAM: helix-turn-helix domain protein; KEGG: hne:HNE_0388 DNA-binding protein; XRE family transcriptional regulator 2420415 4580749 Pden_2415 Paracoccus denitrificans PD1222 XRE family transcriptional regulator YP_916199.1 2420089 R 318586 CDS YP_916200.1 119385144 4580750 complement(2421784..2421978) 1 NC_008686.1 KEGG: sme:SMa2171 hypothetical protein; hypothetical protein 2421978 4580750 Pden_2416 Paracoccus denitrificans PD1222 hypothetical protein YP_916200.1 2421784 R 318586 CDS YP_916201.1 119385145 4580751 complement(2422041..2422346) 1 NC_008686.1 PFAM: IS66 Orf2 family protein; KEGG: sme:SMa1613 hypothetical protein; IS66 Orf2 family protein 2422346 4580751 Pden_2417 Paracoccus denitrificans PD1222 IS66 Orf2 family protein YP_916201.1 2422041 R 318586 CDS YP_916202.1 119385146 4580752 2422453..2423145 1 NC_008686.1 PFAM: phage integrase family protein; KEGG: sit:TM1040_1328 phage integrase; phage integrase family protein 2423145 4580752 Pden_2418 Paracoccus denitrificans PD1222 phage integrase family protein YP_916202.1 2422453 D 318586 CDS YP_916203.1 119385147 4580753 complement(2423384..2424307) 1 NC_008686.1 PFAM: phage integrase family protein; KEGG: sit:TM1040_1328 phage integrase; phage integrase family protein 2424307 4580753 Pden_2419 Paracoccus denitrificans PD1222 phage integrase family protein YP_916203.1 2423384 R 318586 CDS YP_916204.1 119385148 4580754 complement(2424334..2424609) 1 NC_008686.1 hypothetical protein 2424609 4580754 Pden_2420 Paracoccus denitrificans PD1222 hypothetical protein YP_916204.1 2424334 R 318586 CDS YP_916205.1 119385149 4580755 2424703..2425491 1 NC_008686.1 PFAM: helix-turn-helix domain protein; XRE family transcriptional regulator 2425491 4580755 Pden_2421 Paracoccus denitrificans PD1222 XRE family transcriptional regulator YP_916205.1 2424703 D 318586 CDS YP_916206.1 119385150 4580756 complement(2426535..2427872) 1 NC_008686.1 hypothetical protein 2427872 4580756 Pden_2423 Paracoccus denitrificans PD1222 hypothetical protein YP_916206.1 2426535 R 318586 CDS YP_916207.1 119385151 4580757 2428012..2428923 1 NC_008686.1 TIGRFAM: RarD protein, DMT superfamily transporter; PFAM: protein of unknown function DUF6, transmembrane; KEGG: sil:SPO2338 RarD; transporter DMT superfamily protein 2428923 4580757 Pden_2424 Paracoccus denitrificans PD1222 transporter DMT superfamily protein YP_916207.1 2428012 D 318586 CDS YP_916208.1 119385152 4580758 2428920..2429660 1 NC_008686.1 KEGG: sil:SPO2330 hypothetical protein; hypothetical protein 2429660 4580758 Pden_2425 Paracoccus denitrificans PD1222 hypothetical protein YP_916208.1 2428920 D 318586 CDS YP_916209.1 119385153 4580759 2429742..2431064 1 NC_008686.1 PFAM: Pyrrolo-quinoline quinone; KEGG: rsp:RSP_2698 quinoprotein; Pyrrolo-quinoline quinone 2431064 4580759 Pden_2426 Paracoccus denitrificans PD1222 Pyrrolo-quinoline quinone YP_916209.1 2429742 D 318586 CDS YP_916210.1 119385154 4580760 2431061..2432530 1 NC_008686.1 EngA; essential Neisserial GTPase; synchronizes cellular events by interacting with multiple targets with tandem G-domains; overexpression in Escherichia coli suppresses rrmJ mutation; structural analysis of the Thermotoga maritima ortholog shows different nucleotide binding affinities in the two binding domains; GTP-binding protein EngA 2432530 engA 4580760 engA Paracoccus denitrificans PD1222 GTP-binding protein EngA YP_916210.1 2431061 D 318586 CDS YP_916211.1 119385155 4580761 complement(2432540..2433400) 1 NC_008686.1 KEGG: sil:SPO1487 hypothetical protein; hypothetical protein 2433400 4580761 Pden_2428 Paracoccus denitrificans PD1222 hypothetical protein YP_916211.1 2432540 R 318586 CDS YP_916212.1 119385156 4580762 complement(2433457..2434749) 1 NC_008686.1 catalyzes a two-step reaction, first charging a serine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; seryl-tRNA synthetase 2434749 4580762 Pden_2429 Paracoccus denitrificans PD1222 seryl-tRNA synthetase YP_916212.1 2433457 R 318586 CDS YP_916213.1 119385157 4580763 complement(2434831..2435190) 1 NC_008686.1 KEGG: rde:RD1_1508 SoxS; SoxS protein 2435190 4580763 Pden_2430 Paracoccus denitrificans PD1222 SoxS protein YP_916213.1 2434831 R 318586 CDS YP_916214.1 119385158 4580764 2435333..2436346 1 NC_008686.1 functions in transport of arginine/ornithine; inner membrane ATPase that cleaves ATP and phosphorylates two periplasmic proteins that function as two distinct transport systems, the AO (arginine and ornithine) and LAO (lysine, arginine, and ornithine) periplasmic binding proteins; arginine/ornithine transport system ATPase 2436346 4580764 Pden_2431 Paracoccus denitrificans PD1222 arginine/ornithine transport system ATPase YP_916214.1 2435333 D 318586 CDS YP_916215.1 119385159 4580765 2436330..2436920 1 NC_008686.1 TIGRFAM: methylated-DNA--protein-cysteine methyltransferase; PFAM: methylated-DNA-[protein]-cysteine S-methyltransferase; KEGG: sil:SPO3311 ADA regulatory protein; methylated-DNA--protein-cysteine methyltransferase 2436920 4580765 Pden_2432 Paracoccus denitrificans PD1222 methylated-DNA--protein-cysteine methyltransferase YP_916215.1 2436330 D 318586 CDS YP_916216.1 119385160 4580766 2437076..2437351 1 NC_008686.1 required for 70S ribosome assembly; 50S ribosomal protein L28 2437351 rpmB 4580766 rpmB Paracoccus denitrificans PD1222 50S ribosomal protein L28 YP_916216.1 2437076 D 318586 CDS YP_916217.1 119385161 4580767 2437625..2438041 1 NC_008686.1 KEGG: mlo:mll2356 hypothetical protein; hypothetical protein 2438041 4580767 Pden_2434 Paracoccus denitrificans PD1222 hypothetical protein YP_916217.1 2437625 D 318586 CDS YP_916218.1 119385162 4580768 2438041..2438394 1 NC_008686.1 KEGG: mlo:mll2355 hypothetical protein; hypothetical protein 2438394 4580768 Pden_2435 Paracoccus denitrificans PD1222 hypothetical protein YP_916218.1 2438041 D 318586 CDS YP_916219.1 119385163 4580769 complement(2438382..2439323) 1 NC_008686.1 hypothetical protein 2439323 4580769 Pden_2436 Paracoccus denitrificans PD1222 hypothetical protein YP_916219.1 2438382 R 318586 CDS YP_916220.1 119385164 4580770 complement(2439316..2440302) 1 NC_008686.1 KEGG: mlo:mlr2353 hypothetical protein; hypothetical protein 2440302 4580770 Pden_2437 Paracoccus denitrificans PD1222 hypothetical protein YP_916220.1 2439316 R 318586 CDS YP_916221.1 119385165 4580771 complement(2440299..2441363) 1 NC_008686.1 catalyzes a condensation reaction in fatty acid biosynthesis: addition of an acyl acceptor of two carbons from malonyl-ACP; 3-oxoacyl-ACP synthase 2441363 4580771 Pden_2438 Paracoccus denitrificans PD1222 3-oxoacyl-ACP synthase YP_916221.1 2440299 R 318586 CDS YP_916222.1 119385166 4580772 complement(2441360..2442460) 1 NC_008686.1 KEGG: mlo:mlr2351 hypothetical protein; hypothetical protein 2442460 4580772 Pden_2439 Paracoccus denitrificans PD1222 hypothetical protein YP_916222.1 2441360 R 318586 CDS YP_916223.1 119385167 4580773 complement(2442469..2445216) 1 NC_008686.1 PFAM: AAA ATPase, central domain protein; Clp N terminal domain protein; ATPase associated with various cellular activities, AAA_5; ATPase AAA-2 domain protein; SMART: AAA ATPase; KEGG: rsp:RSP_3474 hypothetical protein; ATPase 2445216 4580773 Pden_2440 Paracoccus denitrificans PD1222 ATPase YP_916223.1 2442469 R 318586 CDS YP_916224.1 119385168 4580774 2445389..2447494 1 NC_008686.1 PFAM: protein kinase; SMART: tyrosine protein kinase; serine/threonine protein kinase; KEGG: rsp:RSP_3475 serine/threonine protein kinase; protein kinase 2447494 4580774 Pden_2441 Paracoccus denitrificans PD1222 protein kinase YP_916224.1 2445389 D 318586 CDS YP_916225.1 119385169 4580775 2447625..2448755 1 NC_008686.1 PFAM: ImpA domain protein; KEGG: rsp:RSP_3476 hypothetical protein; ImpA domain-containing protein 2448755 4580775 Pden_2442 Paracoccus denitrificans PD1222 ImpA domain-containing protein YP_916225.1 2447625 D 318586 CDS YP_916226.1 119385170 4580776 2448813..2449355 1 NC_008686.1 PFAM: Uncharacterized conserved protein UCP028301; KEGG: rsp:RSP_3477 hypothetical protein; hypothetical protein 2449355 4580776 Pden_2443 Paracoccus denitrificans PD1222 hypothetical protein YP_916226.1 2448813 D 318586 CDS YP_916227.1 119385171 4580777 2449359..2450873 1 NC_008686.1 PFAM: protein of unknown function DUF877; KEGG: rsp:RSP_3478 hypothetical protein; hypothetical protein 2450873 4580777 Pden_2444 Paracoccus denitrificans PD1222 hypothetical protein YP_916227.1 2449359 D 318586 CDS YP_916228.1 119385172 4580778 2451018..2451506 1 NC_008686.1 PFAM: protein of unknown function DUF796; KEGG: rsp:RSP_3479 hypothetical protein; hypothetical protein 2451506 4580778 Pden_2445 Paracoccus denitrificans PD1222 hypothetical protein YP_916228.1 2451018 D 318586 CDS YP_916229.1 119385173 4580779 2451532..2452278 1 NC_008686.1 PFAM: protein of unknown function DUF1316; KEGG: rsp:RSP_3480 hypothetical protein; hypothetical protein 2452278 4580779 Pden_2446 Paracoccus denitrificans PD1222 hypothetical protein YP_916229.1 2451532 D 318586 CDS YP_916230.1 119385174 4580780 2452278..2454140 1 NC_008686.1 PFAM: protein of unknown function DUF879; KEGG: rsp:RSP_3481 hypothetical protein; hypothetical protein 2454140 4580780 Pden_2447 Paracoccus denitrificans PD1222 hypothetical protein YP_916230.1 2452278 D 318586 CDS YP_916231.1 119385175 4580781 2454104..2455141 1 NC_008686.1 PFAM: protein of unknown function DUF1305; KEGG: mlo:mlr2343 hypothetical protein; hypothetical protein 2455141 4580781 Pden_2448 Paracoccus denitrificans PD1222 hypothetical protein YP_916231.1 2454104 D 318586 CDS YP_916232.1 119385176 4580782 2455141..2456376 1 NC_008686.1 PFAM: Forkhead-associated protein; KEGG: rsp:RSP_3483 FHA domain-containing protein; FHA domain-containing protein 2456376 4580782 Pden_2449 Paracoccus denitrificans PD1222 FHA domain-containing protein YP_916232.1 2455141 D 318586 CDS YP_916233.1 119385177 4580783 2456373..2456846 1 NC_008686.1 KEGG: rsp:RSP_3484 hypothetical protein; hypothetical protein 2456846 4580783 Pden_2450 Paracoccus denitrificans PD1222 hypothetical protein YP_916233.1 2456373 D 318586 CDS YP_916234.1 119385178 4580784 2456858..2458192 1 NC_008686.1 PFAM: protein of unknown function DUF876; KEGG: rsp:RSP_3485 hypothetical protein; hypothetical protein 2458192 4580784 Pden_2451 Paracoccus denitrificans PD1222 hypothetical protein YP_916234.1 2456858 D 318586 CDS YP_916235.1 119385179 4580785 2458202..2459593 1 NC_008686.1 PFAM: OmpA/MotB domain protein; KEGG: rsp:RSP_3486 possible outer membrane protein, OmpA family; OmpA/MotB domain-containing protein 2459593 4580785 Pden_2452 Paracoccus denitrificans PD1222 OmpA/MotB domain-containing protein YP_916235.1 2458202 D 318586 CDS YP_916236.1 119385180 4580786 2459594..2463124 1 NC_008686.1 PFAM: ImcF domain protein; protein of unknown function DUF1215; KEGG: rsp:RSP_3487 hypothetical protein; ImcF domain-containing protein 2463124 4580786 Pden_2453 Paracoccus denitrificans PD1222 ImcF domain-containing protein YP_916236.1 2459594 D 318586 CDS YP_916237.1 119385181 4580787 2463106..2463621 1 NC_008686.1 KEGG: rsp:RSP_3488 hypothetical protein; hypothetical protein 2463621 4580787 Pden_2454 Paracoccus denitrificans PD1222 hypothetical protein YP_916237.1 2463106 D 318586 CDS YP_916238.1 119385182 4580788 complement(2463608..2465959) 1 NC_008686.1 PFAM: Rhs element Vgr protein; Gp5 domain protein; KEGG: rsp:RSP_3489 hypothetical protein; Rhs element Vgr protein 2465959 4580788 Pden_2455 Paracoccus denitrificans PD1222 Rhs element Vgr protein YP_916238.1 2463608 R 318586 CDS YP_916239.1 119385183 4580789 complement(2466042..2468447) 1 NC_008686.1 PFAM: protein of unknown function DUF1215; KEGG: rsp:RSP_3490 hypothetical protein; hypothetical protein 2468447 4580789 Pden_2456 Paracoccus denitrificans PD1222 hypothetical protein YP_916239.1 2466042 R 318586 CDS YP_916240.1 119385184 4580790 complement(2468423..2469370) 1 NC_008686.1 KEGG: rsp:RSP_3491 hypothetical protein; hypothetical protein 2469370 4580790 Pden_2457 Paracoccus denitrificans PD1222 hypothetical protein YP_916240.1 2468423 R 318586 CDS YP_916241.1 119385185 4580791 complement(2469372..2470148) 1 NC_008686.1 PFAM: protein phosphatase 2C domain protein; Stage II sporulation E family protein; KEGG: rsp:RSP_3492 protein phosphatase 2C-like; protein phosphatase 2C 2470148 4580791 Pden_2458 Paracoccus denitrificans PD1222 protein phosphatase 2C YP_916241.1 2469372 R 318586 CDS YP_916242.1 119385186 4580792 2470233..2470826 1 NC_008686.1 PFAM: OmpA/MotB domain protein; KEGG: rsp:RSP_3494 OmpA/MotB domain protein; OmpA/MotB domain-containing protein 2470826 4580792 Pden_2459 Paracoccus denitrificans PD1222 OmpA/MotB domain-containing protein YP_916242.1 2470233 D 318586 CDS YP_916243.1 119385187 4580793 2470943..2472706 1 NC_008686.1 PFAM: Polypeptide-transport-associated domain protein, ShlB-type; KEGG: pau:PA14_61190 hemolysin activation/secretion protein; polypeptide-transport-associated domain-containing protein 2472706 4580793 Pden_2460 Paracoccus denitrificans PD1222 polypeptide-transport-associated domain-containing protein YP_916243.1 2470943 D 318586 CDS YP_916244.1 119385188 4580794 2472753..2477666 1 NC_008686.1 TIGRFAM: filamentous haemagglutinin family outer membrane protein; PFAM: filamentous haemagglutinin domain protein; GLUG domain protein; KEGG: pau:PA14_61200 hypothetical protein; filamentous hemagglutinin 2477666 4580794 Pden_2461 Paracoccus denitrificans PD1222 filamentous hemagglutinin YP_916244.1 2472753 D 318586 CDS YP_916245.1 119385189 4580795 2477635..2479584 1 NC_008686.1 PFAM: Sel1 domain protein repeat-containing protein; peptidase C14, caspase catalytic subunit p20; SMART: peptidase C14, caspase precursor p45; KEGG: mlo:mlr2366 hypothetical protein; peptidase C14, caspase catalytic subunit p20 2479584 4580795 Pden_2462 Paracoccus denitrificans PD1222 peptidase C14, caspase catalytic subunit p20 YP_916245.1 2477635 D 318586 CDS YP_916246.1 119385190 4580796 complement(2479845..2480135) 1 NC_008686.1 hypothetical protein 2480135 4580796 Pden_2463 Paracoccus denitrificans PD1222 hypothetical protein YP_916246.1 2479845 R 318586 CDS YP_916247.1 119385191 4580797 complement(2480226..2480945) 1 NC_008686.1 KEGG: bms:BRA0423 outer membrane protein, 31 kDa; hypothetical protein 2480945 4580797 Pden_2464 Paracoccus denitrificans PD1222 hypothetical protein YP_916247.1 2480226 R 318586 CDS YP_916248.1 119385192 4580798 complement(2480963..2482648) 1 NC_008686.1 PFAM: Hemolysin-type calcium-binding region; KEGG: sil:SPO1617 type I secretion target repeat protein; hemolysin-type calcium-binding protein 2482648 4580798 Pden_2465 Paracoccus denitrificans PD1222 hemolysin-type calcium-binding protein YP_916248.1 2480963 R 318586 CDS YP_916249.1 119385193 4580799 complement(2482759..2483106) 1 NC_008686.1 hypothetical protein 2483106 4580799 Pden_2466 Paracoccus denitrificans PD1222 hypothetical protein YP_916249.1 2482759 R 318586 CDS YP_916250.1 119385194 4580105 complement(2483174..2484091) 1 NC_008686.1 PFAM: LytTr DNA-binding region; KEGG: sil:SPO1616 transcriptional regulator; response regulator receiver protein 2484091 4580105 Pden_2467 Paracoccus denitrificans PD1222 response regulator receiver protein YP_916250.1 2483174 R 318586 CDS YP_916251.1 119385195 4580106 2484647..2485534 1 NC_008686.1 TIGRFAM: cation diffusion facilitator family transporter; PFAM: cation efflux protein; KEGG: rsp:RSP_0463 cation efflux transporter, CDF family; cation diffusion facilitator family transporter 2485534 4580106 Pden_2468 Paracoccus denitrificans PD1222 cation diffusion facilitator family transporter YP_916251.1 2484647 D 318586 CDS YP_916252.1 119385196 4580107 complement(2485531..2486523) 1 NC_008686.1 PFAM: ABC transporter related; Transport-associated OB domain protein; SMART: AAA ATPase; KEGG: sme:SMc02869 ATP-binding ABC transporter protein; ABC transporter 2486523 4580107 Pden_2469 Paracoccus denitrificans PD1222 ABC transporter YP_916252.1 2485531 R 318586 CDS YP_916253.1 119385197 4580108 complement(2486561..2487400) 1 NC_008686.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: mes:Meso_2708 binding-protein-dependent transport systems inner membrane component; binding-protein-dependent transport system inner membrane protein 2487400 4580108 Pden_2470 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_916253.1 2486561 R 318586 CDS YP_916254.1 119385198 4580109 complement(2487410..2488327) 1 NC_008686.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: jan:Jann_1355 binding-protein-dependent transport systems inner membrane component; binding-protein-dependent transport system inner membrane protein 2488327 4580109 Pden_2471 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_916254.1 2487410 R 318586 CDS YP_916255.1 119385199 4580110 complement(2488422..2489681) 1 NC_008686.1 PFAM: extracellular solute-binding protein, family 1; KEGG: mes:Meso_2706 extracellular solute-binding protein, family 1; extracellular solute-binding protein 2489681 4580110 Pden_2472 Paracoccus denitrificans PD1222 extracellular solute-binding protein YP_916255.1 2488422 R 318586 CDS YP_916256.1 119385200 4580111 complement(2489730..2490608) 1 NC_008686.1 catalyzes the cleavage of the lactyl ether moiety of N-acetylmuramic acid-6-phosphate (MurNAc-6-P) to form N-acetylglucosamine-6-phosphate (GlcNAc-6-P) and lactate; involved in MurNAc dissimilation pathway; N-acetylmuramic acid 6-phosphate etherase 2490608 murQ 4580111 murQ Paracoccus denitrificans PD1222 N-acetylmuramic acid 6-phosphate etherase YP_916256.1 2489730 R 318586 CDS YP_916257.1 119385201 4580112 2490761..2491594 1 NC_008686.1 PFAM: ATPase, BadF/BadG/BcrA/BcrD type; KEGG: mes:Meso_2705 ATPase, BadF/BadG/BcrA/BcrD type; BadF/BadG/BcrA/BcrD type ATPase 2491594 4580112 Pden_2474 Paracoccus denitrificans PD1222 BadF/BadG/BcrA/BcrD type ATPase YP_916257.1 2490761 D 318586 CDS YP_916258.1 119385202 4580113 2491594..2492361 1 NC_008686.1 PFAM: regulatory protein GntR, HTH; UbiC transcription regulator-associated domain protein; KEGG: mlo:mll4768 transcriptional regulator, (GntR family); UbiC transcription regulator-associated domain-containing protein 2492361 4580113 Pden_2475 Paracoccus denitrificans PD1222 UbiC transcription regulator-associated domain-containing protein YP_916258.1 2491594 D 318586 CDS YP_916259.1 119385203 4580114 2492361..2493386 1 NC_008686.1 PFAM: sugar isomerase (SIS); KEGG: mlo:mll4767 glucosamine-fructose-6-phosphate aminotransferase; glutamine--fructose-6-phosphate transaminase (isomerizing) 2493386 4580114 Pden_2476 Paracoccus denitrificans PD1222 glutamine--fructose-6-phosphate transaminase (isomerizing) YP_916259.1 2492361 D 318586 CDS YP_916260.1 119385204 4580115 2493386..2494507 1 NC_008686.1 KEGG: rsp:RSP_1296 N-acetylglucosamine-6-phosphate deacetylase; TIGRFAM: N-acetylglucosamine-6-phosphate deacetylase; PFAM: amidohydrolase; N-acetylglucosamine-6-phosphate deacetylase 2494507 4580115 Pden_2477 Paracoccus denitrificans PD1222 N-acetylglucosamine-6-phosphate deacetylase YP_916260.1 2493386 D 318586 CDS YP_916261.1 119385205 4580116 2494525..2495274 1 NC_008686.1 PFAM: cyclic nucleotide-binding; SMART: regulatory protein, Crp; KEGG: sil:SPOA0323 cyclic nucleotide-binding protein; Crp/Fnr family transcriptional regulator 2495274 4580116 Pden_2478 Paracoccus denitrificans PD1222 Crp/Fnr family transcriptional regulator YP_916261.1 2494525 D 318586 CDS YP_916262.1 119385206 4580117 complement(2495469..2495702) 1 NC_008686.1 hypothetical protein 2495702 4580117 Pden_2479 Paracoccus denitrificans PD1222 hypothetical protein YP_916262.1 2495469 R 318586 CDS YP_916263.1 119385207 4580118 complement(2495706..2496242) 1 NC_008686.1 PFAM: cytochrome c oxidase, subunit III; KEGG: sil:SPOA0213 nitric oxide reductase E protein; cytochrome c oxidase subunit III 2496242 4580118 Pden_2480 Paracoccus denitrificans PD1222 cytochrome c oxidase subunit III YP_916263.1 2495706 R 318586 CDS YP_916264.1 119385208 4580119 complement(2496242..2498158) 1 NC_008686.1 PFAM: von Willebrand factor, type A; KEGG: sil:SPOA0214 nitric oxide reductase D protein; von Willebrand factor A 2498158 4580119 Pden_2481 Paracoccus denitrificans PD1222 von Willebrand factor A YP_916264.1 2496242 R 318586 CDS YP_916265.1 119385209 4580120 complement(2498170..2498982) 1 NC_008686.1 PFAM: ATPase associated with various cellular activities, AAA_5; CbbQ/NirQ/NorQ C-terminal domain protein; KEGG: sil:SPOA0215 nitric oxide reductase Q protein; ATPase 2498982 4580120 Pden_2482 Paracoccus denitrificans PD1222 ATPase YP_916265.1 2498170 R 318586 CDS YP_916266.1 119385210 4580121 complement(2498986..2500374) 1 NC_008686.1 PFAM: cytochrome c oxidase, subunit I; KEGG: sil:SPOA0216 nitric oxide reductase, large subunit; cytochrome c oxidase subunit I 2500374 4580121 Pden_2483 Paracoccus denitrificans PD1222 cytochrome c oxidase subunit I YP_916266.1 2498986 R 318586 CDS YP_916267.1 119385211 4580122 complement(2500388..2500840) 1 NC_008686.1 KEGG: sil:SPOA0217 nitric oxide reductase, small subunit; nitric-oxide reductase 2500840 4580122 Pden_2484 Paracoccus denitrificans PD1222 nitric-oxide reductase YP_916267.1 2500388 R 318586 CDS YP_916268.1 119385212 4580123 complement(2500915..2501829) 1 NC_008686.1 PFAM: ApbE family lipoprotein; KEGG: rde:RD1_1552 nitrous-oxide reductase protein NosX; ApbE family lipoprotein 2501829 4580123 Pden_2485 Paracoccus denitrificans PD1222 ApbE family lipoprotein YP_916268.1 2500915 R 318586 CDS YP_916269.1 119385213 4580124 complement(2501826..2503871) 1 NC_008686.1 PFAM: FMN-binding domain protein; KEGG: rde:RD1_1564 nitrous oxide reductase regulatory protein NosR; FMN-binding domain-containing protein 2503871 4580124 Pden_2486 Paracoccus denitrificans PD1222 FMN-binding domain-containing protein YP_916269.1 2501826 R 318586 CDS YP_916270.1 119385214 4580125 2503999..2505789 1 NC_008686.1 PFAM: cytochrome c, class I; cytochrome d1, heme region; KEGG: sil:SPOA0220 cytochrome cd1 nitrite reductase; hydroxylamine reductase 2505789 4580125 Pden_2487 Paracoccus denitrificans PD1222 hydroxylamine reductase YP_916270.1 2503999 D 318586 CDS YP_916271.1 119385215 4580126 2505861..2506724 1 NC_008686.1 TIGRFAM: uroporphyrin-III C-methyltransferase; PFAM: Uroporphyrin-III C/tetrapyrrole (Corrin/Porphyrin) methyltransferase; KEGG: rde:RD1_1566 uroporphyrin-III C-methyltransferase; uroporphyrin-III C-methyltransferase 2506724 4580126 Pden_2488 Paracoccus denitrificans PD1222 uroporphyrin-III C-methyltransferase YP_916271.1 2505861 D 318586 CDS YP_916272.1 119385216 4580127 2506717..2507028 1 NC_008686.1 KEGG: rde:RD1_1567 cytochrome c (c55X); cytochrome c (c55X) 2507028 4580127 Pden_2489 Paracoccus denitrificans PD1222 cytochrome c (c55X) YP_916272.1 2506717 D 318586 CDS YP_916273.1 119385217 4580128 2507025..2508179 1 NC_008686.1 PFAM: cytochrome d1, heme region; KEGG: sil:SPOA0223 cytochrome cd1 nitrite reductase; cytochrome d1, heme region 2508179 4580128 Pden_2490 Paracoccus denitrificans PD1222 cytochrome d1, heme region YP_916273.1 2507025 D 318586 CDS YP_916274.1 119385218 4580129 2508182..2509153 1 NC_008686.1 KEGG: sil:SPOA0224 nitrite reductase heme biosynthesis D/L protein; AsnC family transcriptional regulator 2509153 4580129 Pden_2491 Paracoccus denitrificans PD1222 AsnC family transcriptional regulator YP_916274.1 2508182 D 318586 CDS YP_916275.1 119385219 4580130 2509150..2509623 1 NC_008686.1 KEGG: rde:RD1_1570 nitrite reductase heme biosynthesis G; AsnC family transcriptional regulator 2509623 4580130 Pden_2492 Paracoccus denitrificans PD1222 AsnC family transcriptional regulator YP_916275.1 2509150 D 318586 CDS YP_916276.1 119385220 4580131 2509620..2510102 1 NC_008686.1 KEGG: sil:SPOA0226 nitrite reductase heme biosynthesis H protein; AsnC family transcriptional regulator 2510102 4580131 Pden_2493 Paracoccus denitrificans PD1222 AsnC family transcriptional regulator YP_916276.1 2509620 D 318586 CDS YP_916277.1 119385221 4580132 2510116..2511339 1 NC_008686.1 PFAM: Radical SAM domain protein; SMART: Elongator protein 3/MiaB/NifB; KEGG: sil:SPOA0227 nitrite reductase heme biosynthesis J protein; radical SAM domain-containing protein 2511339 4580132 Pden_2494 Paracoccus denitrificans PD1222 radical SAM domain-containing protein YP_916277.1 2510116 D 318586 CDS YP_916278.1 119385222 4580133 2511314..2512768 1 NC_008686.1 PFAM: cytochrome d1, heme region; KEGG: sil:SPOA0228 nitrite reductase protein N; cytochrome d1, heme region 2512768 4580133 Pden_2495 Paracoccus denitrificans PD1222 cytochrome d1, heme region YP_916278.1 2511314 D 318586 CDS YP_916279.1 119385223 4580134 2512725..2512991 1 NC_008686.1 KEGG: rde:RD1_1575 hypothetical protein; hypothetical protein 2512991 4580134 Pden_2496 Paracoccus denitrificans PD1222 hypothetical protein YP_916279.1 2512725 D 318586 CDS YP_916280.1 119385224 4580135 2513247..2515424 1 NC_008686.1 KEGG: atc:AGR_L_481 catalase; TIGRFAM: catalase/peroxidase HPI; PFAM: Haem peroxidase; catalase/peroxidase HPI 2515424 4580135 Pden_2497 Paracoccus denitrificans PD1222 catalase/peroxidase HPI YP_916280.1 2513247 D 318586 CDS YP_916281.1 119385225 4580136 complement(2515560..2517761) 1 NC_008686.1 binding of PriA to forked DNA starts the assembly of the primosome, also possesses 3'-5' helicase activity; primosome assembly protein PriA 2517761 4580136 Pden_2498 Paracoccus denitrificans PD1222 primosome assembly protein PriA YP_916281.1 2515560 R 318586 CDS YP_916282.1 119385226 4580137 2518051..2518704 1 NC_008686.1 similar to novel fructose-6-phosphate aldolase from Escherichia coli; enzyme from Methanocaldococcus janaschii shows transaldolase activity; translaldolase 2518704 4580137 Pden_2499 Paracoccus denitrificans PD1222 translaldolase YP_916282.1 2518051 D 318586 CDS YP_916283.1 119385227 4580138 2518704..2519414 1 NC_008686.1 KEGG: rsp:RSP_0562 hypothetical protein; hypothetical protein 2519414 4580138 Pden_2500 Paracoccus denitrificans PD1222 hypothetical protein YP_916283.1 2518704 D 318586 CDS YP_916284.1 119385228 4580139 2519411..2520349 1 NC_008686.1 site-specific tyrosine recombinase which cuts and rejoins DNA molecules; binds cooperatively to specific DNA consensus sites; forms a heterotetrameric complex with XerC; XerCD exhibit similar sequences; essential to convert chromosome dimers to monomers during cell division and functions during plasmid segregation; cell division protein FtsK may regulate the XerCD complex; enzyme from Streptococcus group has unusual active site motifs; site-specific tyrosine recombinase XerC 2520349 xerC 4580139 xerC Paracoccus denitrificans PD1222 site-specific tyrosine recombinase XerC YP_916284.1 2519411 D 318586 CDS YP_916285.1 119385229 4580140 2520515..2521273 1 NC_008686.1 PFAM: protein of unknown function DUF81; KEGG: sit:TM1040_3018 protein of unknown function DUF81; hypothetical protein 2521273 4580140 Pden_2502 Paracoccus denitrificans PD1222 hypothetical protein YP_916285.1 2520515 D 318586 CDS YP_916286.1 119385230 4580141 complement(2521311..2522297) 1 NC_008686.1 PFAM: L-asparaginase II; KEGG: rsp:RSP_1384 hypothetical protein; L-asparaginase II 2522297 4580141 Pden_2503 Paracoccus denitrificans PD1222 L-asparaginase II YP_916286.1 2521311 R 318586 CDS YP_916287.1 119385231 4580142 2522449..2522976 1 NC_008686.1 KEGG: rsp:RSP_1383 hypothetical protein; hypothetical protein 2522976 4580142 Pden_2504 Paracoccus denitrificans PD1222 hypothetical protein YP_916287.1 2522449 D 318586 CDS YP_916288.1 119385232 4580143 2523082..2524257 1 NC_008686.1 TIGRFAM: radical SAM enzyme, Cfr family; PFAM: Radical SAM domain protein; KEGG: rsp:RSP_1382 radical SAM superfamily protein; radical SAM protein 2524257 4580143 Pden_2505 Paracoccus denitrificans PD1222 radical SAM protein YP_916288.1 2523082 D 318586 CDS YP_916289.1 119385233 4580144 2524476..2525999 1 NC_008686.1 catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate; phosphoglyceromutase 2525999 4580144 Pden_2506 Paracoccus denitrificans PD1222 phosphoglyceromutase YP_916289.1 2524476 D 318586 CDS YP_916290.1 119385234 4580145 2525996..2527231 1 NC_008686.1 PFAM: peptidase M23B; KEGG: rsp:RSP_0933 hypothetical protein; peptidase M23B 2527231 4580145 Pden_2507 Paracoccus denitrificans PD1222 peptidase M23B YP_916290.1 2525996 D 318586 CDS YP_916291.1 119385235 4580146 2527228..2528643 1 NC_008686.1 KEGG: sil:SPO3812 carboxyl-terminal protease family protein; TIGRFAM: carboxyl-terminal protease; PFAM: PDZ/DHR/GLGF domain protein; peptidase S41; carboxyl-terminal protease 2528643 4580146 Pden_2508 Paracoccus denitrificans PD1222 carboxyl-terminal protease YP_916291.1 2527228 D 318586 CDS YP_916292.1 119385236 4580147 2528640..2529131 1 NC_008686.1 hydrolyzes diadenosine polyphosphate; dinucleoside polyphosphate hydrolase 2529131 4580147 Pden_2509 Paracoccus denitrificans PD1222 dinucleoside polyphosphate hydrolase YP_916292.1 2528640 D 318586 CDS YP_916293.1 119385237 4580148 complement(2529222..2530475) 1 NC_008686.1 TIGRFAM: lytic murein transglycosylase; PFAM: Peptidoglycan-binding domain 1 protein; KEGG: rsp:RSP_1125 membrane bound lytic murein transglycosylase B; lytic murein transglycosylase 2530475 4580148 Pden_2510 Paracoccus denitrificans PD1222 lytic murein transglycosylase YP_916293.1 2529222 R 318586 CDS YP_916294.1 119385238 4580149 complement(2530564..2530881) 1 NC_008686.1 KEGG: sil:SPO3336 hypothetical protein; hypothetical protein 2530881 4580149 Pden_2511 Paracoccus denitrificans PD1222 hypothetical protein YP_916294.1 2530564 R 318586 CDS YP_916295.1 119385239 4580150 2530938..2531408 1 NC_008686.1 PFAM: YbaK/prolyl-tRNA synthetase associated region; KEGG: jan:Jann_2447 YbaK/prolyl-tRNA synthetase associated protein; prolyl-tRNA synthetase 2531408 4580150 Pden_2512 Paracoccus denitrificans PD1222 prolyl-tRNA synthetase YP_916295.1 2530938 D 318586 CDS YP_916296.1 119385240 4580151 complement(2531453..2531704) 1 NC_008686.1 PFAM: Transglycosylase-associated protein; KEGG: jan:Jann_0350 transglycosylase-associated protein; transglycosylase-associated protein 2531704 4580151 Pden_2513 Paracoccus denitrificans PD1222 transglycosylase-associated protein YP_916296.1 2531453 R 318586 CDS YP_916297.1 119385241 4580152 complement(2531809..2532633) 1 NC_008686.1 catalyzes the formation of N-succinyl-2-amino-6-ketopimelate from succinyl-CoA and tetrahydrodipicolinate in the lysine biosynthetic pathway; 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase 2532633 dapD 4580152 dapD Paracoccus denitrificans PD1222 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase YP_916297.1 2531809 R 318586 CDS YP_916298.1 119385242 4580153 2532699..2533553 1 NC_008686.1 PFAM: conserved hypothetical protein 730; KEGG: rsp:RSP_1132 hypothetical protein; hypothetical protein 2533553 4580153 Pden_2515 Paracoccus denitrificans PD1222 hypothetical protein YP_916298.1 2532699 D 318586 CDS YP_916299.1 119385243 4580154 complement(2533772..2534299) 1 NC_008686.1 hypothetical protein 2534299 4580154 Pden_2516 Paracoccus denitrificans PD1222 hypothetical protein YP_916299.1 2533772 R 318586 CDS YP_916300.1 119385244 4580155 complement(2534412..2534879) 1 NC_008686.1 SPOUT methyltransferase family protein; crystal structure shows homodimer; in Escherichia coli this protein methylates pseudouridine at position 1915 of the 23S ribosomal RNA; rRNA large subunit methyltransferase 2534879 4580155 Pden_2517 Paracoccus denitrificans PD1222 rRNA large subunit methyltransferase YP_916300.1 2534412 R 318586 CDS YP_916301.1 119385245 4580156 complement(2534883..2535215) 1 NC_008686.1 TIGRFAM: iojap-like protein; PFAM: Iojap-related protein; KEGG: rsp:RSP_0865 hypothetical protein; iojap family protein 2535215 4580156 Pden_2518 Paracoccus denitrificans PD1222 iojap family protein YP_916301.1 2534883 R 318586 CDS YP_916302.1 119385246 4580157 complement(2535414..2535647) 1 NC_008686.1 hypothetical protein 2535647 4580157 Pden_2519 Paracoccus denitrificans PD1222 hypothetical protein YP_916302.1 2535414 R 318586 CDS YP_916303.1 119385247 4580158 2535943..2537379 1 NC_008686.1 dehydratase component, catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; isopropylmalate isomerase large subunit 2537379 4580158 Pden_2520 Paracoccus denitrificans PD1222 isopropylmalate isomerase large subunit YP_916303.1 2535943 D 318586 CDS YP_916304.1 119385248 4580159 complement(2537397..2537981) 1 NC_008686.1 hypothetical protein 2537981 4580159 Pden_2521 Paracoccus denitrificans PD1222 hypothetical protein YP_916304.1 2537397 R 318586 CDS YP_916305.1 119385249 4580160 2538074..2538679 1 NC_008686.1 catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate in leucine biosynthesis; forms a heterodimer of LeuC/D; isopropylmalate isomerase small subunit 2538679 leuD 4580160 leuD Paracoccus denitrificans PD1222 isopropylmalate isomerase small subunit YP_916305.1 2538074 D 318586 CDS YP_916306.1 119385250 4580161 2538670..2539722 1 NC_008686.1 KEGG: sil:SPO0213 hypothetical protein; hypothetical protein 2539722 4580161 Pden_2523 Paracoccus denitrificans PD1222 hypothetical protein YP_916306.1 2538670 D 318586 CDS YP_916307.1 119385251 4580162 2540009..2540185 1 NC_008686.1 KEGG: sil:SPO2875 hypothetical protein; hypothetical protein 2540185 4580162 Pden_2524 Paracoccus denitrificans PD1222 hypothetical protein YP_916307.1 2540009 D 318586 CDS YP_916308.1 119385252 4580163 2540187..2540885 1 NC_008686.1 TIGRFAM: cobalt transporter, subunit CbtA; KEGG: sit:TM1040_2222 cobalt transporter subunit CbtA; cobalt transporter subunit CbtA 2540885 4580163 Pden_2525 Paracoccus denitrificans PD1222 cobalt transporter subunit CbtA YP_916308.1 2540187 D 318586 CDS YP_916309.1 119385253 4579831 2540955..2541488 1 NC_008686.1 KEGG: sit:TM1040_2223 conserved hypothetical protein; hypothetical protein 2541488 4579831 Pden_2526 Paracoccus denitrificans PD1222 hypothetical protein YP_916309.1 2540955 D 318586 CDS YP_916310.1 119385254 4579832 2541488..2542111 1 NC_008686.1 KEGG: rde:RD1_3815 cobalamin biosynthesis protein BluB; TIGRFAM: cob(II)yrinic acid a,c-diamide reductase; PFAM: nitroreductase; cob(II)yrinic acid a,c-diamide reductase 2542111 4579832 Pden_2527 Paracoccus denitrificans PD1222 cob(II)yrinic acid a,c-diamide reductase YP_916310.1 2541488 D 318586 CDS YP_916311.1 119385255 4579833 complement(2542115..2542531) 1 NC_008686.1 KEGG: bbr:BB2359 hypothetical protein; hypothetical protein 2542531 4579833 Pden_2528 Paracoccus denitrificans PD1222 hypothetical protein YP_916311.1 2542115 R 318586 CDS YP_916312.1 119385256 4579834 complement(2542536..2543147) 1 NC_008686.1 catalyzes the formation of adenosylcob(III)yrinic acid a,c-diamide from cob(I)yrinic acid a,c-diamide; cob(I)yrinic acid a,c-diamide adenosyltransferase 2543147 4579834 Pden_2529 Paracoccus denitrificans PD1222 cob(I)yrinic acid a,c-diamide adenosyltransferase YP_916312.1 2542536 R 318586 CDS YP_916313.1 119385257 4579835 2543463..2543816 1 NC_008686.1 PFAM: protein of unknown function DUF1636; KEGG: rsp:RSP_2829 hypothetical protein; hypothetical protein 2543816 4579835 Pden_2530 Paracoccus denitrificans PD1222 hypothetical protein YP_916313.1 2543463 D 318586 CDS YP_916314.1 119385258 4579836 2543820..2544854 1 NC_008686.1 TIGRFAM: cobalamin biosynthesis protein CobW; PFAM: cobalamin synthesis protein, P47K; cobalamin synthesis CobW domain protein; KEGG: sit:TM1040_2209 cobalamin (vitamin B12) biosynthesis CobW; cobalamin biosynthesis protein CobW 2544854 4579836 Pden_2531 Paracoccus denitrificans PD1222 cobalamin biosynthesis protein CobW YP_916314.1 2543820 D 318586 CDS YP_916315.1 119385259 4579837 2544858..2548028 1 NC_008686.1 with CobST catalyzes the formation of cobyrinic acid a,c-diamide from hydrogenobyrinic acid a,c-diamide in an ATP-dependent manner; involved in porphyrin and chlorophyll metabolism; vitamin B12 metabolism; cobaltochelatase subunit CobN 2548028 cobN 4579837 cobN Paracoccus denitrificans PD1222 cobaltochelatase subunit CobN YP_916315.1 2544858 D 318586 CDS YP_916316.1 119385260 4579838 2548025..2549188 1 NC_008686.1 TIGRFAM: precorrin-3B synthase; PFAM: nitrite/sulfite reductase, hemoprotein beta-component, ferrodoxin domain protein; KEGG: sit:TM1040_2211 precorrin-3B synthase; precorrin-3B synthase 2549188 4579838 Pden_2533 Paracoccus denitrificans PD1222 precorrin-3B synthase YP_916316.1 2548025 D 318586 CDS YP_916317.1 119385261 4579839 2549232..2549861 1 NC_008686.1 catalyzes the interconversion of precorrin-8X and hydrogenobyrinate; precorrin-8X methylmutase 2549861 cobH 4579839 cobH Paracoccus denitrificans PD1222 precorrin-8X methylmutase YP_916317.1 2549232 D 318586 CDS YP_916318.1 119385262 4579840 2549864..2550625 1 NC_008686.1 TIGRFAM: precorrin-2 C20-methyltransferase; PFAM: Uroporphyrin-III C/tetrapyrrole (Corrin/Porphyrin) methyltransferase; KEGG: rsp:RSP_2826 precorrin-2 C20-methyltransferase; precorrin-2 C(20)-methyltransferase 2550625 4579840 Pden_2535 Paracoccus denitrificans PD1222 precorrin-2 C(20)-methyltransferase YP_916318.1 2549864 D 318586 CDS YP_916319.1 119385263 4579841 2550622..2551350 1 NC_008686.1 TIGRFAM: precorrin-3B C17-methyltransferase; PFAM: Uroporphyrin-III C/tetrapyrrole (Corrin/Porphyrin) methyltransferase; KEGG: rsp:RSP_2824 precorrin-3B C17-methyltransferase; precorrin-3B C(17)-methyltransferase 2551350 4579841 Pden_2536 Paracoccus denitrificans PD1222 precorrin-3B C(17)-methyltransferase YP_916319.1 2550622 D 318586 CDS YP_916320.1 119385264 4579842 complement(2551326..2552018) 1 NC_008686.1 PFAM: Precorrin-6x reductase CbiJ/CobK; KEGG: rsp:RSP_2825 precorrin-6x reductase; precorrin-6A reductase 2552018 4579842 Pden_2537 Paracoccus denitrificans PD1222 precorrin-6A reductase YP_916320.1 2551326 R 318586 CDS YP_916321.1 119385265 4579843 2552062..2553234 1 NC_008686.1 KEGG: rsp:RSP_2823 precorrin-6y C5,15-methyltransferase; TIGRFAM: precorrin-6y C5,15-methyltransferase (decarboxylating), CbiE subunit; precorrin-6Y C5,15-methyltransferase (decarboxylating), CbiT subunit; PFAM: Uroporphyrin-III C/tetrapyrrole (Corrin/Porphyrin) methyltransferase; precorrin-6y C5,15-methyltransferase subunit CbiE 2553234 4579843 Pden_2538 Paracoccus denitrificans PD1222 precorrin-6y C5,15-methyltransferase subunit CbiE YP_916321.1 2552062 D 318586 CDS YP_916322.1 119385266 4579844 2553231..2553581 1 NC_008686.1 KEGG: bja:blr3270 precorrin methylase; precorrin methylase 2553581 4579844 Pden_2539 Paracoccus denitrificans PD1222 precorrin methylase YP_916322.1 2553231 D 318586 CDS YP_916323.1 119385267 4579845 2553578..2554351 1 NC_008686.1 TIGRFAM: precorrin-4 C11-methyltransferase; PFAM: Uroporphyrin-III C/tetrapyrrole (Corrin/Porphyrin) methyltransferase; KEGG: rsp:RSP_2821 precorrin-4 C11-methyltransferase; precorrin-4 C(11)-methyltransferase 2554351 4579845 Pden_2540 Paracoccus denitrificans PD1222 precorrin-4 C(11)-methyltransferase YP_916323.1 2553578 D 318586 CDS YP_916324.1 119385268 4579846 2554348..2555637 1 NC_008686.1 responsible for the amidation of carboxylic groups at position A and C of cobyrinic acid or hydrogenobrynic acid; cobyrinic acid a,c-diamide synthase 2555637 4579846 Pden_2541 Paracoccus denitrificans PD1222 cobyrinic acid a,c-diamide synthase YP_916324.1 2554348 D 318586 CDS YP_916325.1 119385269 4579847 2555634..2556383 1 NC_008686.1 catalyzes the formation of precorrin 6x from precorrin 5; precorrin 6A synthase 2556383 4579847 Pden_2542 Paracoccus denitrificans PD1222 precorrin 6A synthase YP_916325.1 2555634 D 318586 CDS YP_916326.1 119385270 4579848 2556368..2556676 1 NC_008686.1 KEGG: sil:SPO2878 hypothetical protein; hypothetical protein 2556676 4579848 Pden_2543 Paracoccus denitrificans PD1222 hypothetical protein YP_916326.1 2556368 D 318586 CDS YP_916327.1 119385271 4579849 2557025..2557504 1 NC_008686.1 PFAM: cytochrome c, class II; KEGG: rsp:RSP_0474 cytochrome c'; cytochrome c, class II 2557504 4579849 Pden_2544 Paracoccus denitrificans PD1222 cytochrome c, class II YP_916327.1 2557025 D 318586 CDS YP_916328.1 119385272 4579850 2557504..2558085 1 NC_008686.1 PFAM: cytochrome B561; KEGG: rsp:RSP_0475 cytochrome b; cytochrome B561 2558085 4579850 Pden_2545 Paracoccus denitrificans PD1222 cytochrome B561 YP_916328.1 2557504 D 318586 CDS YP_916329.1 119385273 4579851 complement(2558375..2560618) 1 NC_008686.1 decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling; DNA topoisomerase IV subunit A 2560618 4579851 Pden_2546 Paracoccus denitrificans PD1222 DNA topoisomerase IV subunit A YP_916329.1 2558375 R 318586 CDS YP_916330.1 119385274 4579852 2560721..2561539 1 NC_008686.1 PFAM: short-chain dehydrogenase/reductase SDR; KR; KEGG: rsp:RSP_1694 probable short-chain dehydrogenase/reductase; short-chain dehydrogenase/reductase SDR 2561539 4579852 Pden_2547 Paracoccus denitrificans PD1222 short-chain dehydrogenase/reductase SDR YP_916330.1 2560721 D 318586 CDS YP_916331.1 119385275 4579853 2561564..2561764 1 NC_008686.1 KEGG: rsp:RSP_6016 hypothetical protein; hypothetical protein 2561764 4579853 Pden_2548 Paracoccus denitrificans PD1222 hypothetical protein YP_916331.1 2561564 D 318586 CDS YP_916332.1 119385276 4579854 2561764..2562336 1 NC_008686.1 TIGRFAM: ATP--cobalamin adenosyltransferase; PFAM: cobalamin adenosyltransferase; KEGG: jan:Jann_0549 cobalamin adenosyltransferase; ATP--cobalamin adenosyltransferase 2562336 4579854 Pden_2549 Paracoccus denitrificans PD1222 ATP--cobalamin adenosyltransferase YP_916332.1 2561764 D 318586 CDS YP_916333.1 119385277 4579855 2562457..2563215 1 NC_008686.1 PFAM: electron transfer flavoprotein beta-subunit; KEGG: sit:TM1040_2427 electron transfer flavoprotein beta-subunit; electron transfer flavoprotein subunit beta 2563215 4579855 Pden_2550 Paracoccus denitrificans PD1222 electron transfer flavoprotein subunit beta YP_916333.1 2562457 D 318586 CDS YP_916334.1 119385278 4579856 2563215..2564141 1 NC_008686.1 PFAM: electron transfer flavoprotein beta-subunit; electron transfer flavoprotein, alpha subunit; KEGG: sit:TM1040_2426 electron transfer flavoprotein, alpha subunit; electron transfer flavoprotein subunit alpha 2564141 4579856 Pden_2551 Paracoccus denitrificans PD1222 electron transfer flavoprotein subunit alpha YP_916334.1 2563215 D 318586 CDS YP_916335.1 119385279 4579857 2564340..2565215 1 NC_008686.1 converts (S)-3-hydroxybutanoyl-CoA to 3-acetoacetyl-CoA; 3-hydroxybutyryl-CoA dehydrogenase 2565215 4579857 Pden_2552 Paracoccus denitrificans PD1222 3-hydroxybutyryl-CoA dehydrogenase YP_916335.1 2564340 D 318586 CDS YP_916336.1 119385280 4579858 complement(2565291..2565875) 1 NC_008686.1 PFAM: protein of unknown function DUF205; KEGG: rsp:RSP_1004 hypothetical protein; hypothetical protein 2565875 4579858 Pden_2553 Paracoccus denitrificans PD1222 hypothetical protein YP_916336.1 2565291 R 318586 CDS YP_916337.1 119385281 4579859 complement(2565872..2567143) 1 NC_008686.1 TIGRFAM: dihydroorotase, multifunctional complex type; PFAM: amidohydrolase; KEGG: rsp:RSP_1003 dihydroorotase and related cyclic amidohydrolase; dihydroorotase, multifunctional complex type 2567143 4579859 Pden_2554 Paracoccus denitrificans PD1222 dihydroorotase, multifunctional complex type YP_916337.1 2565872 R 318586 CDS YP_916338.1 119385282 4579860 complement(2567140..2568099) 1 NC_008686.1 catalyzes the transfer of the carbamoyl moiety from carbamoyl phosphate to L- aspartate in pyrimidine biosynthesis; aspartate carbamoyltransferase 2568099 pyrB 4579860 pyrB Paracoccus denitrificans PD1222 aspartate carbamoyltransferase YP_916338.1 2567140 R 318586 CDS YP_916339.1 119385283 4579861 2568202..2568936 1 NC_008686.1 catalyzes 2 sequential methylations, the formation of precorrin-1 and S-adenosyl-L-homocysteine from S-adenosyl-L-methionine and uroporphyrin III, and the formation of precorrin-2 and S-adenosyl-L-homocysteine from S-adenosyl-L-methionine and precorrin-1; uroporphyrin-III C-methyltransferase 2568936 4579861 Pden_2556 Paracoccus denitrificans PD1222 uroporphyrin-III C-methyltransferase YP_916339.1 2568202 D 318586 CDS YP_916340.1 119385284 4579862 2569020..2569535 1 NC_008686.1 KEGG: sil:SPO1135 hypothetical protein; hypothetical protein 2569535 4579862 Pden_2557 Paracoccus denitrificans PD1222 hypothetical protein YP_916340.1 2569020 D 318586 CDS YP_916341.1 119385285 4579863 2569538..2569780 1 NC_008686.1 PFAM: SirA family protein; KEGG: sil:SPO1895 SirA family protein; SirA family protein 2569780 4579863 Pden_2558 Paracoccus denitrificans PD1222 SirA family protein YP_916341.1 2569538 D 318586 CDS YP_916342.1 119385286 4579864 2569780..2570709 1 NC_008686.1 PFAM: Auxin Efflux Carrier; KEGG: rsp:RSP_0851 transporter, AEC family; auxin efflux carrier 2570709 4579864 Pden_2559 Paracoccus denitrificans PD1222 auxin efflux carrier YP_916342.1 2569780 D 318586 CDS YP_916343.1 119385287 4579865 2570713..2571519 1 NC_008686.1 Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA; enoyl-CoA hydratase 2571519 4579865 Pden_2560 Paracoccus denitrificans PD1222 enoyl-CoA hydratase YP_916343.1 2570713 D 318586 CDS YP_916344.1 119385288 4579866 2571625..2572569 1 NC_008686.1 PFAM: protein of unknown function DUF6, transmembrane; KEGG: atc:AGR_C_3767 hypothetical protein; hypothetical protein 2572569 4579866 Pden_2561 Paracoccus denitrificans PD1222 hypothetical protein YP_916344.1 2571625 D 318586 CDS YP_916345.1 119385289 4579867 complement(2572609..2572944) 1 NC_008686.1 KEGG: sit:TM1040_3453 conserved hypothetical protein; hypothetical protein 2572944 4579867 Pden_2562 Paracoccus denitrificans PD1222 hypothetical protein YP_916345.1 2572609 R 318586 CDS YP_916346.1 119385290 4579868 complement(2573003..2573602) 1 NC_008686.1 PFAM: cytochrome B561; KEGG: rde:RD1_3654 cytochrome b561; cytochrome B561 2573602 4579868 Pden_2563 Paracoccus denitrificans PD1222 cytochrome B561 YP_916346.1 2573003 R 318586 CDS YP_916347.1 119385291 4579869 2573716..2577630 1 NC_008686.1 with EntB, EntD, and EntE forms the multienzyme complex enterobactin synthase; EntF is the serine activating enzyme which catalyzes the formation of the amide and ester bonds of the cyclic enterobactin; enterobactin synthase subunit F 2577630 entF 4579869 entF Paracoccus denitrificans PD1222 enterobactin synthase subunit F YP_916347.1 2573716 D 318586 CDS YP_916348.1 119385292 4579870 complement(2577850..2578683) 1 NC_008686.1 PFAM: esterase; KEGG: ppu:PP_0532 hypothetical protein; esterase 2578683 4579870 Pden_2565 Paracoccus denitrificans PD1222 esterase YP_916348.1 2577850 R 318586 CDS YP_916349.1 119385293 4579871 2578835..2580241 1 NC_008686.1 KEGG: tac:Ta1322 surface antigen genes (Methanosarcina mazei) related protein; hypothetical protein 2580241 4579871 Pden_2566 Paracoccus denitrificans PD1222 hypothetical protein YP_916349.1 2578835 D 318586 CDS YP_916350.1 119385294 4579872 2580301..2581398 1 NC_008686.1 PFAM: periplasmic binding protein; KEGG: rpb:RPB_2696 periplasmic binding protein; periplasmic binding protein 2581398 4579872 Pden_2567 Paracoccus denitrificans PD1222 periplasmic binding protein YP_916350.1 2580301 D 318586 CDS YP_916351.1 119385295 4579873 2581395..2582429 1 NC_008686.1 PFAM: transport system permease protein; KEGG: pfl:PFL_3501 heme/hemin ABC transporter, permease protein; transport system permease 2582429 4579873 Pden_2568 Paracoccus denitrificans PD1222 transport system permease YP_916351.1 2581395 D 318586 CDS YP_916352.1 119385296 4579874 2582429..2583205 1 NC_008686.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rpb:RPB_2698 ABC transporter related; ABC transporter 2583205 4579874 Pden_2569 Paracoccus denitrificans PD1222 ABC transporter YP_916352.1 2582429 D 318586 CDS YP_916353.1 119385297 4579875 complement(2583236..2583655) 1 NC_008686.1 PFAM: protein of unknown function DUF1178; KEGG: rsp:RSP_2387 hypothetical protein; hypothetical protein 2583655 4579875 Pden_2570 Paracoccus denitrificans PD1222 hypothetical protein YP_916353.1 2583236 R 318586 CDS YP_916354.1 119385298 4579876 complement(2583696..2584895) 1 NC_008686.1 PFAM: Three-deoxy-D-manno-octulosonic-acid transferase domain protein; KEGG: rsp:RSP_2394 3-deoxy-D-manno-octulosonic-acid transferase (KDO transferase); 3-deoxy-D-manno-octulosonic-acid transferase 2584895 4579876 Pden_2571 Paracoccus denitrificans PD1222 3-deoxy-D-manno-octulosonic-acid transferase YP_916354.1 2583696 R 318586 CDS YP_916355.1 119385299 4579877 complement(2584892..2585626) 1 NC_008686.1 PFAM: ribulose-phosphate 3-epimerase; KEGG: rsp:RSP_2864 pentose-5-phosphate-3-epimerase; ribulose-phosphate 3-epimerase 2585626 4579877 Pden_2572 Paracoccus denitrificans PD1222 ribulose-phosphate 3-epimerase YP_916355.1 2584892 R 318586 CDS YP_916356.1 119385300 4579878 2585807..2586832 1 NC_008686.1 PFAM: Hsp33 protein; KEGG: sil:SPO0024 chaperonin, 33 kDa; heat shock protein 33 2586832 4579878 Pden_2573 Paracoccus denitrificans PD1222 heat shock protein 33 YP_916356.1 2585807 D 318586 CDS YP_916357.1 119385301 4579879 2586829..2587416 1 NC_008686.1 PFAM: NUDIX hydrolase; KEGG: rde:RD1_0410 hydrolase; NUDIX hydrolase 2587416 4579879 Pden_2574 Paracoccus denitrificans PD1222 NUDIX hydrolase YP_916357.1 2586829 D 318586 CDS YP_916358.1 119385302 4579880 2587413..2588579 1 NC_008686.1 PFAM: Polynucleotide adenylyltransferase region; KEGG: rsp:RSP_1205 poly A polymerase family protein; polynucleotide adenylyltransferase 2588579 4579880 Pden_2575 Paracoccus denitrificans PD1222 polynucleotide adenylyltransferase YP_916358.1 2587413 D 318586 CDS YP_916359.1 119385303 4579881 2588579..2590441 1 NC_008686.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rsp:RSP_1203 ABC multidrug efflux pump, fused ATPase and inner membrane subunits; ABC transporter 2590441 4579881 Pden_2576 Paracoccus denitrificans PD1222 ABC transporter YP_916359.1 2588579 D 318586 CDS YP_916360.1 119385304 4579882 2590438..2591658 1 NC_008686.1 PFAM: (Uracil-5)-methyltransferase; KEGG: sil:SPO0029 23S rRNA (uracil-5-)-methyltransferase RumA; (uracil-5)-methyltransferase 2591658 4579882 Pden_2577 Paracoccus denitrificans PD1222 (uracil-5)-methyltransferase YP_916360.1 2590438 D 318586 CDS YP_916361.1 119385305 4579883 2591724..2592239 1 NC_008686.1 KEGG: rsp:RSP_1201 hypothetical protein; hypothetical protein 2592239 4579883 Pden_2578 Paracoccus denitrificans PD1222 hypothetical protein YP_916361.1 2591724 D 318586 CDS YP_916362.1 119385306 4579884 complement(2592340..2592993) 1 NC_008686.1 PFAM: Glutathione S-transferase, N-terminal domain; KEGG: bja:blr5350 glutathione S-transferase; glutathione S-transferase domain-containing protein 2592993 4579884 Pden_2579 Paracoccus denitrificans PD1222 glutathione S-transferase domain-containing protein YP_916362.1 2592340 R 318586 CDS YP_916363.1 119385307 4579885 complement(2593137..2593736) 1 NC_008686.1 PFAM: Allergen V5/Tpx-1 family protein; KEGG: rsp:RSP_1200 hypothetical protein; Allergen V5/Tpx-1 family protein 2593736 4579885 Pden_2580 Paracoccus denitrificans PD1222 Allergen V5/Tpx-1 family protein YP_916363.1 2593137 R 318586 CDS YP_916364.1 119385308 4579886 2593932..2594585 1 NC_008686.1 PFAM: ErfK/YbiS/YcfS/YnhG family protein; KEGG: sil:SPO0075 ErfK/YbiS/YcfS/YnhG family protein/Tat domain protein; ErfK/YbiS/YcfS/YnhG family protein 2594585 4579886 Pden_2581 Paracoccus denitrificans PD1222 ErfK/YbiS/YcfS/YnhG family protein YP_916364.1 2593932 D 318586 CDS YP_916365.1 119385309 4579887 2594774..2595289 1 NC_008686.1 hypothetical protein 2595289 4579887 Pden_2582 Paracoccus denitrificans PD1222 hypothetical protein YP_916365.1 2594774 D 318586 CDS YP_916366.1 119385310 4579888 complement(2595317..2596348) 1 NC_008686.1 protoheme ferro-lyase; catalyzes the insertion of a ferrous ion into protoporphyrin IX to form protoheme; involved in protoheme biosynthesis; in some organisms this protein is membrane-associated while in others it is cytosolic; ferrochelatase 2596348 hemH 4579888 hemH Paracoccus denitrificans PD1222 ferrochelatase YP_916366.1 2595317 R 318586 CDS YP_916367.1 119385311 4580683 complement(2596345..2597184) 1 NC_008686.1 KEGG: rsp:RSP_1196 SAM-dependent methyltransferase; SAM-dependent methyltransferase 2597184 4580683 Pden_2584 Paracoccus denitrificans PD1222 SAM-dependent methyltransferase YP_916367.1 2596345 R 318586 CDS YP_916368.1 119385312 4580684 2597216..2597953 1 NC_008686.1 KEGG: rsp:RSP_1195 competence protein F; competence protein F 2597953 4580684 Pden_2585 Paracoccus denitrificans PD1222 competence protein F YP_916368.1 2597216 D 318586 CDS YP_916369.1 119385313 4580685 2597986..2598252 1 NC_008686.1 TIGRFAM: glutaredoxin 3; PFAM: glutaredoxin; glutaredoxin 2; KEGG: rsp:RSP_1194 glutaredoxin; glutaredoxin 3 2598252 4580685 Pden_2586 Paracoccus denitrificans PD1222 glutaredoxin 3 YP_916369.1 2597986 D 318586 CDS YP_916370.1 119385314 4580686 2598249..2599100 1 NC_008686.1 PFAM: Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase; KEGG: sil:SPO0069 hydrolase, carbon-nitrogen family; nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase 2599100 4580686 Pden_2587 Paracoccus denitrificans PD1222 nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase YP_916370.1 2598249 D 318586 CDS YP_916371.1 119385315 4580687 2599097..2599606 1 NC_008686.1 PFAM: regulatory protein, MarR; KEGG: rsp:RSP_1191 transcriptional regulator, MarR family; MarR family transcriptional regulator 2599606 4580687 Pden_2588 Paracoccus denitrificans PD1222 MarR family transcriptional regulator YP_916371.1 2599097 D 318586 CDS YP_916372.1 119385316 4580688 complement(2599691..2600479) 1 NC_008686.1 Involved in ubiquinone biosynthesis; 3-demethylubiquinone-9 3-methyltransferase 2600479 4580688 Pden_2589 Paracoccus denitrificans PD1222 3-demethylubiquinone-9 3-methyltransferase YP_916372.1 2599691 R 318586 CDS YP_916373.1 119385317 4580689 2600516..2601502 1 NC_008686.1 KEGG: rsp:RSP_1174 prolyl aminopeptidase; TIGRFAM: proline iminopeptidase; PFAM: alpha/beta hydrolase fold; proline iminopeptidase 2601502 4580689 Pden_2590 Paracoccus denitrificans PD1222 proline iminopeptidase YP_916373.1 2600516 D 318586 CDS YP_916374.1 119385318 4580690 2601698..2602318 1 NC_008686.1 in Streptococcus pneumoniae this gene was found to be essential; structure determination of the Streptococcus protein shows that it is similar to a number of other proteins; hypothetical protein 2602318 4580690 Pden_2591 Paracoccus denitrificans PD1222 hypothetical protein YP_916374.1 2601698 D 318586 CDS YP_916375.1 119385319 4580691 2602322..2604001 1 NC_008686.1 modifies transcription through interactions with RNA polymerase affecting elongation, readthrough, termination, and antitermination; transcription elongation factor NusA 2604001 nusA 4580691 nusA Paracoccus denitrificans PD1222 transcription elongation factor NusA YP_916375.1 2602322 D 318586 CDS YP_916376.1 119385320 4580692 2604017..2604637 1 NC_008686.1 PFAM: protein of unknown function DUF448; KEGG: jan:Jann_0039 protein of unknown function DUF448; hypothetical protein 2604637 4580692 Pden_2593 Paracoccus denitrificans PD1222 hypothetical protein YP_916376.1 2604017 D 318586 CDS YP_916377.1 119385321 4580693 2604645..2607191 1 NC_008686.1 Protects formylmethionyl-tRNA from spontaneous hydrolysis and promotes its binding to the 30S ribosomal subunits during initiation of protein synthesis. Also involved in the hydrolysis of GTP during the formation of the 70S ribosomal complex; translation initiation factor IF-2 2607191 infB 4580693 infB Paracoccus denitrificans PD1222 translation initiation factor IF-2 YP_916377.1 2604645 D 318586 CDS YP_916378.1 119385322 4580694 complement(2607332..2607460) 1 NC_008686.1 hypothetical protein 2607460 4580694 Pden_2595 Paracoccus denitrificans PD1222 hypothetical protein YP_916378.1 2607332 R 318586 CDS YP_916379.1 119385323 4580695 complement(2607579..2607977) 1 NC_008686.1 TIGRFAM: mutator MutT protein; PFAM: NUDIX hydrolase; KEGG: sil:SPO0060 mutator MutT protein; mutator MutT protein 2607977 4580695 Pden_2596 Paracoccus denitrificans PD1222 mutator MutT protein YP_916379.1 2607579 R 318586 CDS YP_916380.1 119385324 4580696 complement(2607974..2609371) 1 NC_008686.1 bifunctional arginine biosynthesis protein ArgJ; functions at the 1st and 5th steps in arginine biosynthesis; involved in synthesis of acetylglutamate from glutamate and acetyl-CoA and ornithine by transacetylation between acetylornithine and glutmate; bifunctional ornithine acetyltransferase/N-acetylglutamate synthase 2609371 argJ 4580696 argJ Paracoccus denitrificans PD1222 bifunctional ornithine acetyltransferase/N-acetylglutamate synthase YP_916380.1 2607974 R 318586 CDS YP_916381.1 119385325 4580697 complement(2609375..2610214) 1 NC_008686.1 PFAM: PpiC-type peptidyl-prolyl cis-trans isomerase; KEGG: jan:Jann_0290 PpiC-type peptidyl-prolyl cis-trans isomerase; PpiC-type peptidyl-prolyl cis-trans isomerase 2610214 4580697 Pden_2598 Paracoccus denitrificans PD1222 PpiC-type peptidyl-prolyl cis-trans isomerase YP_916381.1 2609375 R 318586 CDS YP_916382.2 162139377 4580698 2610423..2613128 1 NC_008686.1 functions in protein export; can interact with acidic membrane phospholipids and the SecYEG protein complex; binds to preproteins; binds to ATP and undergoes a conformational change to promote membrane insertion of SecA/bound preprotein; ATP hydrolysis appears to drive release of the preprotein from SecA and deinsertion of SecA from the membrane; additional proteins SecD/F/YajC aid SecA recycling; exists in an equilibrium between monomers and dimers; may possibly form higher order oligomers; proteins in this cluster correspond SecA1; SecA2 is not essential and seems to play a role in secretion of a subset of proteins; preprotein translocase subunit SecA 2613128 4580698 Pden_2599 Paracoccus denitrificans PD1222 preprotein translocase subunit SecA YP_916382.2 2610423 D 318586 CDS YP_916383.1 119385327 4580699 complement(2613274..2613993) 1 NC_008686.1 PFAM: response regulator receiver; transcriptional regulator domain protein; KEGG: rsp:RSP_1138 two component transcriptional regulator, winged helix family; two component transcriptional regulator 2613993 4580699 Pden_2600 Paracoccus denitrificans PD1222 two component transcriptional regulator YP_916383.1 2613274 R 318586 CDS YP_916384.1 119385328 4580700 complement(2613990..2614508) 1 NC_008686.1 PFAM: regulatory protein, MarR; KEGG: rsp:RSP_1139 transcriptional regulator, MarR family; MarR family transcriptional regulator 2614508 4580700 Pden_2601 Paracoccus denitrificans PD1222 MarR family transcriptional regulator YP_916384.1 2613990 R 318586 CDS YP_916385.1 119385329 4580701 2614661..2615530 1 NC_008686.1 catalyzes the transamination of the branched-chain amino acids to their respective alpha-keto acids; branched-chain amino acid aminotransferase 2615530 4580701 Pden_2602 Paracoccus denitrificans PD1222 branched-chain amino acid aminotransferase YP_916385.1 2614661 D 318586 CDS YP_916386.1 119385330 4580702 complement(2615882..2616346) 1 NC_008686.1 PFAM: phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 2; KEGG: rsp:RSP_1158 PTS IIA-like nitrogen-regulatory protein PtsN; PTS transporter subunit IIA-like nitrogen-regulatory protein PtsN 2616346 4580702 Pden_2603 Paracoccus denitrificans PD1222 PTS transporter subunit IIA-like nitrogen-regulatory protein PtsN YP_916386.1 2615882 R 318586 CDS YP_916387.1 119385331 4580703 complement(2616429..2617007) 1 NC_008686.1 TIGRFAM: ribosomal subunit interface protein; PFAM: sigma 54 modulation protein/ribosomal protein S30EA; KEGG: rsp:RSP_1157 ribosomal subunit interface protein Y; sigma 54 modulation protein/ribosomal protein S30EA 2617007 4580703 Pden_2604 Paracoccus denitrificans PD1222 sigma 54 modulation protein/ribosomal protein S30EA YP_916387.1 2616429 R 318586 CDS YP_916388.1 119385332 4580704 complement(2617172..2617906) 1 NC_008686.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rsp:RSP_1156 ABC transporter, ATPase subunit; ABC transporter 2617906 4580704 Pden_2605 Paracoccus denitrificans PD1222 ABC transporter YP_916388.1 2617172 R 318586 CDS YP_916389.1 119385333 4580705 complement(2617911..2618396) 1 NC_008686.1 PFAM: OstA family protein; KEGG: sil:SPO0080 hypothetical protein; OstA family protein 2618396 4580705 Pden_2606 Paracoccus denitrificans PD1222 OstA family protein YP_916389.1 2617911 R 318586 CDS YP_916390.1 119385334 4580706 complement(2618449..2619030) 1 NC_008686.1 KEGG: rsp:RSP_1154 hypothetical protein; hypothetical protein 2619030 4580706 Pden_2607 Paracoccus denitrificans PD1222 hypothetical protein YP_916390.1 2618449 R 318586 CDS YP_916391.1 119385335 4580707 complement(2619033..2619980) 1 NC_008686.1 KEGG: rsp:RSP_1153 sugar phosphate isomerase; TIGRFAM: KpsF/GutQ family protein; PFAM: CBS domain containing protein; sugar isomerase (SIS); KpsF/GutQ family protein 2619980 4580707 Pden_2608 Paracoccus denitrificans PD1222 KpsF/GutQ family protein YP_916391.1 2619033 R 318586 CDS YP_916392.1 119385336 4580708 complement(2619991..2620605) 1 NC_008686.1 PFAM: 3'-5' exonuclease; KEGG: rsp:RSP_1152 ribonuclease D; 3'-5' exonuclease 2620605 4580708 Pden_2609 Paracoccus denitrificans PD1222 3'-5' exonuclease YP_916392.1 2619991 R 318586 CDS YP_916393.1 119385337 4580709 2620850..2622847 1 NC_008686.1 PFAM: TonB-dependent receptor; TonB-dependent receptor, plug; KEGG: bmb:BruAb2_1126 TonB dependent receptor domain protein; TonB-dependent receptor 2622847 4580709 Pden_2610 Paracoccus denitrificans PD1222 TonB-dependent receptor YP_916393.1 2620850 D 318586 CDS YP_916394.1 119385338 4580710 2622995..2623249 1 NC_008686.1 KEGG: mes:Meso_2258 transcriptional regulator, XRE family; XRE family transcriptional regulator 2623249 4580710 Pden_2611 Paracoccus denitrificans PD1222 XRE family transcriptional regulator YP_916394.1 2622995 D 318586 CDS YP_916395.1 119385339 4580711 2623316..2624983 1 NC_008686.1 PFAM: Sulfate transporter/antisigma-factor antagonist STAS; Xanthine/uracil/vitamin C permease; sulphate transporter; KEGG: mes:Meso_2257 sulphate transporter; sulfate transporter 2624983 4580711 Pden_2612 Paracoccus denitrificans PD1222 sulfate transporter YP_916395.1 2623316 D 318586 CDS YP_916396.1 119385340 4580712 complement(2625098..2625982) 1 NC_008686.1 produces formate from formyl-tetrahydrofolate which is the major source of formate for PurT in de novo purine nucleotide biosynthesis; has a role in one-carbon metabolism; forms a homohexamer; activated by methionine and inhibited by glycine; formyltetrahydrofolate deformylase 2625982 purU 4580712 purU Paracoccus denitrificans PD1222 formyltetrahydrofolate deformylase YP_916396.1 2625098 R 318586 CDS YP_916397.1 119385341 4580713 complement(2626054..2626950) 1 NC_008686.1 catalyzes the formation of 5,10-methenyltetrahydrofolate from 5,10-methylenetetrahydrofolate and subsequent formation of 10-formyltetrahydrofolate from 5,10-methenyltetrahydrofolate; bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase 2626950 4580713 Pden_2614 Paracoccus denitrificans PD1222 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase YP_916397.1 2626054 R 318586 CDS YP_916398.1 119385342 4580714 complement(2627184..2629964) 1 NC_008686.1 PFAM: Patatin; KEGG: sus:Acid_5056 patatin; patatin 2629964 4580714 Pden_2615 Paracoccus denitrificans PD1222 patatin YP_916398.1 2627184 R 318586 CDS YP_916399.1 119385343 4580715 complement(2630065..2631792) 1 NC_008686.1 KEGG: atc:AGR_L_695 hypothetical protein; hypothetical protein 2631792 4580715 Pden_2616 Paracoccus denitrificans PD1222 hypothetical protein YP_916399.1 2630065 R 318586 CDS YP_916400.1 119385344 4580716 complement(2631792..2632925) 1 NC_008686.1 PFAM: iron-containing alcohol dehydrogenase; KEGG: rsp:RSP_2661 iron-containing alcohol dehydrogenase; iron-containing alcohol dehydrogenase 2632925 4580716 Pden_2617 Paracoccus denitrificans PD1222 iron-containing alcohol dehydrogenase YP_916400.1 2631792 R 318586 CDS YP_916401.1 119385345 4580717 complement(2632922..2634409) 1 NC_008686.1 TIGRFAM: glycerol kinase; PFAM: carbohydrate kinase, FGGY; KEGG: rsp:RSP_2662 glycerol kinase; glycerol kinase 2634409 4580717 Pden_2618 Paracoccus denitrificans PD1222 glycerol kinase YP_916401.1 2632922 R 318586 CDS YP_916402.1 119385346 4580718 2634599..2635369 1 NC_008686.1 PFAM: regulatory protein, DeoR; Helix-turn-helix, type 11 domain protein; KEGG: rsp:RSP_0457 probable glycerol-3-phosphate regulon repressor; DeoR family transcriptional regulator 2635369 4580718 Pden_2619 Paracoccus denitrificans PD1222 DeoR family transcriptional regulator YP_916402.1 2634599 D 318586 CDS YP_916403.1 119385347 4580719 complement(2635379..2636623) 1 NC_008686.1 TIGRFAM: kynureninase; PFAM: aminotransferase, class V; KEGG: mlo:mll0621 probable kynureninase (kyurenine hydrolase); kynureninase 2636623 4580719 Pden_2620 Paracoccus denitrificans PD1222 kynureninase YP_916403.1 2635379 R 318586 CDS YP_916404.1 119385348 4580720 complement(2636641..2637669) 1 NC_008686.1 PFAM: regulatory protein, LacI; periplasmic binding protein/LacI transcriptional regulator; KEGG: sme:SMb20324 ThuR, regulatory protein for trehalosemaltose transport system; periplasmic binding protein/LacI transcriptional regulator 2637669 4580720 Pden_2621 Paracoccus denitrificans PD1222 periplasmic binding protein/LacI transcriptional regulator YP_916404.1 2636641 R 318586 CDS YP_916405.1 119385349 4580721 complement(2637985..2638272) 1 NC_008686.1 KEGG: rsp:RSP_6001 hypothetical protein; hypothetical protein 2638272 4580721 Pden_2622 Paracoccus denitrificans PD1222 hypothetical protein YP_916405.1 2637985 R 318586 CDS YP_916406.1 119385350 4580722 complement(2638276..2638668) 1 NC_008686.1 hypothetical protein 2638668 4580722 Pden_2623 Paracoccus denitrificans PD1222 hypothetical protein YP_916406.1 2638276 R 318586 CDS YP_916407.1 119385351 4580723 complement(2638735..2639379) 1 NC_008686.1 PFAM: regulatory protein, TetR; KEGG: rsp:RSP_6137 transcriptional regulator, TetR family; TetR family transcriptional regulator 2639379 4580723 Pden_2624 Paracoccus denitrificans PD1222 TetR family transcriptional regulator YP_916407.1 2638735 R 318586 CDS YP_916408.1 119385352 4580724 complement(2639404..2639751) 1 NC_008686.1 hypothetical protein 2639751 4580724 Pden_2625 Paracoccus denitrificans PD1222 hypothetical protein YP_916408.1 2639404 R 318586 CDS YP_916409.1 119385353 4580725 complement(2640280..2641386) 1 NC_008686.1 membrane protein responsible for substrate specificity switching from rod/hook-type export to filament-type export; flagellar biosynthesis protein FlhB 2641386 flhB 4580725 flhB Paracoccus denitrificans PD1222 flagellar biosynthesis protein FlhB YP_916409.1 2640280 R 318586 CDS YP_916410.1 119385354 4580726 complement(2641383..2642141) 1 NC_008686.1 KEGG: sil:SPO0171 flagellar biosynthetic protein FliR; flagellar biosynthetic protein FliR 2642141 4580726 Pden_2627 Paracoccus denitrificans PD1222 flagellar biosynthetic protein FliR YP_916410.1 2641383 R 318586 CDS YP_916411.1 119385355 4580727 complement(2642138..2644222) 1 NC_008686.1 membrane protein involved in the flagellar export apparatus; flagellar biosynthesis protein FlhA 2644222 flhA 4580727 flhA Paracoccus denitrificans PD1222 flagellar biosynthesis protein FlhA YP_916411.1 2642138 R 318586 CDS YP_916412.1 119385356 4580728 complement(2644219..2644488) 1 NC_008686.1 hypothetical protein 2644488 4580728 Pden_2629 Paracoccus denitrificans PD1222 hypothetical protein YP_916412.1 2644219 R 318586 CDS YP_916413.1 119385357 4580729 complement(2644485..2644985) 1 NC_008686.1 KEGG: rsp:RSP_1316 flagellar motor protein; flagellar motor protein 2644985 4580729 Pden_2630 Paracoccus denitrificans PD1222 flagellar motor protein YP_916413.1 2644485 R 318586 CDS YP_916414.1 119385358 4580730 2645365..2645898 1 NC_008686.1 KEGG: rpa:RPA1896 homologue of rhodobacter capsulatus gene transfer agent (GTA) orfg6 (21% identity); hypothetical protein 2645898 4580730 Pden_2631 Paracoccus denitrificans PD1222 hypothetical protein YP_916414.1 2645365 D 318586 CDS YP_916415.1 119385359 4580731 2645895..2646161 1 NC_008686.1 hypothetical protein 2646161 4580731 Pden_2632 Paracoccus denitrificans PD1222 hypothetical protein YP_916415.1 2645895 D 318586 CDS YP_916416.1 119385360 4580732 2646726..2648360 1 NC_008686.1 PFAM: phage Terminase; KEGG: rsp:RSP_0213 phage terminase-like protein large subunit; phage terminase 2648360 4580732 Pden_2633 Paracoccus denitrificans PD1222 phage terminase YP_916416.1 2646726 D 318586 CDS YP_916417.1 119385361 4580733 2648357..2648689 1 NC_008686.1 PFAM: HNH endonuclease; SMART: HNH nuclease; KEGG: rsp:RSP_0212 HNH nuclease; HNH endonuclease 2648689 4580733 Pden_2634 Paracoccus denitrificans PD1222 HNH endonuclease YP_916417.1 2648357 D 318586 CDS YP_916418.1 119385362 4580734 2648698..2649933 1 NC_008686.1 KEGG: rsp:RSP_0211 hypothetical protein; hypothetical protein 2649933 4580734 Pden_2635 Paracoccus denitrificans PD1222 hypothetical protein YP_916418.1 2648698 D 318586 CDS YP_916419.1 119385363 4580735 2649933..2650484 1 NC_008686.1 TIGRFAM: phage prohead protease, HK97 family; PFAM: peptidase U35, phage prohead HK97; KEGG: rsp:RSP_0209 possible prophage Lp3 protein 18; HK97 family phage prohead protease 2650484 4580735 Pden_2636 Paracoccus denitrificans PD1222 HK97 family phage prohead protease YP_916419.1 2649933 D 318586 CDS YP_916420.1 119385364 4580736 2650486..2651547 1 NC_008686.1 KEGG: rsp:RSP_0208 hypothetical protein; hypothetical protein 2651547 4580736 Pden_2637 Paracoccus denitrificans PD1222 hypothetical protein YP_916420.1 2650486 D 318586 CDS YP_916421.1 119385365 4580737 2651547..2652053 1 NC_008686.1 KEGG: rsp:RSP_0207 hypothetical protein; hypothetical protein 2652053 4580737 Pden_2638 Paracoccus denitrificans PD1222 hypothetical protein YP_916421.1 2651547 D 318586 CDS YP_916422.1 119385366 4580738 2652029..2652595 1 NC_008686.1 KEGG: rsp:RSP_0206 hypothetical protein; hypothetical protein 2652595 4580738 Pden_2639 Paracoccus denitrificans PD1222 hypothetical protein YP_916422.1 2652029 D 318586 CDS YP_916423.1 119385367 4580739 2652588..2652845 1 NC_008686.1 hypothetical protein 2652845 4580739 Pden_2640 Paracoccus denitrificans PD1222 hypothetical protein YP_916423.1 2652588 D 318586 CDS YP_916424.1 119385368 4580740 2652854..2653138 1 NC_008686.1 hypothetical protein 2653138 4580740 Pden_2641 Paracoccus denitrificans PD1222 hypothetical protein YP_916424.1 2652854 D 318586 CDS YP_916425.1 119385369 4580741 2653148..2653450 1 NC_008686.1 hypothetical protein 2653450 4580741 Pden_2642 Paracoccus denitrificans PD1222 hypothetical protein YP_916425.1 2653148 D 318586 CDS YP_916426.1 119385370 4581188 2653740..2653967 1 NC_008686.1 hypothetical protein 2653967 4581188 Pden_2643 Paracoccus denitrificans PD1222 hypothetical protein YP_916426.1 2653740 D 318586 CDS YP_916427.1 119385371 4581189 2654388..2655395 1 NC_008686.1 PFAM: phage integrase family protein; KEGG: rsp:RSP_2080 tyrosine recombinase; phage integrase family protein 2655395 4581189 Pden_2644 Paracoccus denitrificans PD1222 phage integrase family protein YP_916427.1 2654388 D 318586 CDS YP_916428.1 119385372 4581190 complement(2655460..2655906) 1 NC_008686.1 KEGG: sit:TM1040_2951 chemotaxis protein MotA; chemotaxis protein MotA 2655906 4581190 Pden_2645 Paracoccus denitrificans PD1222 chemotaxis protein MotA YP_916428.1 2655460 R 318586 CDS YP_916429.1 119385373 4581191 complement(2655915..2656457) 1 NC_008686.1 KEGG: rsp:RSP_1315 hypothetical protein; hypothetical protein 2656457 4581191 Pden_2646 Paracoccus denitrificans PD1222 hypothetical protein YP_916429.1 2655915 R 318586 CDS YP_916430.1 119385374 4581192 complement(2656450..2656797) 1 NC_008686.1 KEGG: sit:TM1040_2949 conserved hypothetical protein; hypothetical protein 2656797 4581192 Pden_2647 Paracoccus denitrificans PD1222 hypothetical protein YP_916430.1 2656450 R 318586 CDS YP_916431.1 119385375 4581193 complement(2656794..2657276) 1 NC_008686.1 PFAM: flagellar basal body-associated protein FliL; KEGG: rsp:RSP_1313 possible flagellar synthesis protein; flagellar basal body protein FliL 2657276 4581193 Pden_2648 Paracoccus denitrificans PD1222 flagellar basal body protein FliL YP_916431.1 2656794 R 318586 CDS YP_916432.1 119385376 4581194 2657379..2658959 1 NC_008686.1 the MS-ring anchors the flagellum to the cytoplasmic membrane; part of the flagellar basal body which consists of four rings L, P, S, and M mounted on a central rod; flagellar MS-ring protein 2658959 fliF 4581194 fliF Paracoccus denitrificans PD1222 flagellar MS-ring protein YP_916432.1 2657379 D 318586 CDS YP_916433.1 119385377 4581195 2658956..2659516 1 NC_008686.1 hypothetical protein 2659516 4581195 Pden_2650 Paracoccus denitrificans PD1222 hypothetical protein YP_916433.1 2658956 D 318586 CDS YP_916434.1 119385378 4581196 2659519..2659776 1 NC_008686.1 PFAM: surface presentation of antigens (SPOA) protein; KEGG: rsp:RSP_1310 flagellar motor switch protein FliN/FliY; surface presentation of antigens (SPOA) protein 2659776 4581196 Pden_2651 Paracoccus denitrificans PD1222 surface presentation of antigens (SPOA) protein YP_916434.1 2659519 D 318586 CDS YP_916435.1 119385379 4581197 2659773..2660498 1 NC_008686.1 FliP, with proteins FliQ and FliR, forms the core of the central channel in the flagella export apparatus; flagellar biosynthesis protein FliP 2660498 fliP 4581197 fliP Paracoccus denitrificans PD1222 flagellar biosynthesis protein FliP YP_916435.1 2659773 D 318586 CDS YP_916436.1 119385380 4581198 2660610..2661785 1 NC_008686.1 TIGRFAM: efflux transporter, RND family, MFP subunit; PFAM: secretion protein HlyD family protein; KEGG: mlo:mll5520 RND efflux membrane fusion protein; RND family efflux transporter MFP subunit 2661785 4581198 Pden_2653 Paracoccus denitrificans PD1222 RND family efflux transporter MFP subunit YP_916436.1 2660610 D 318586 CDS YP_916437.1 119385381 4581199 2661782..2662882 1 NC_008686.1 TIGRFAM: efflux transporter, RND family, MFP subunit; PFAM: secretion protein HlyD family protein; KEGG: ret:RHE_PF00285 probable protein secretion protein, HlyD family; RND family efflux transporter MFP subunit 2662882 4581199 Pden_2654 Paracoccus denitrificans PD1222 RND family efflux transporter MFP subunit YP_916437.1 2661782 D 318586 CDS YP_916438.1 119385382 4581200 2662879..2665974 1 NC_008686.1 PFAM: acriflavin resistance protein; KEGG: ret:RHE_PF00284 probable efflux transporter protein, acriflavin resistance protein family; acriflavin resistance protein 2665974 4581200 Pden_2655 Paracoccus denitrificans PD1222 acriflavin resistance protein YP_916438.1 2662879 D 318586 CDS YP_916439.1 119385383 4581201 complement(2666082..2668454) 1 NC_008686.1 KEGG: rsp:RSP_1359 DEAD/DEAH box helicase; TIGRFAM: ATP-dependent DNA helicase, RecQ family; ATP-dependent DNA helicase RecQ; PFAM: helicase domain protein; HRDC domain protein; DEAD/DEAH box helicase domain protein; SMART: DEAD-like helicases-like; ATP-dependent DNA helicase RecQ 2668454 4581201 Pden_2656 Paracoccus denitrificans PD1222 ATP-dependent DNA helicase RecQ YP_916439.1 2666082 R 318586 CDS YP_916440.1 119385384 4581202 2668554..2669126 1 NC_008686.1 KEGG: sit:TM1040_2661 conserved hypothetical protein; hypothetical protein 2669126 4581202 Pden_2657 Paracoccus denitrificans PD1222 hypothetical protein YP_916440.1 2668554 D 318586 CDS YP_916441.1 119385385 4581203 2669142..2670551 1 NC_008686.1 PFAM: major facilitator superfamily MFS_1; KEGG: rsp:RSP_1362 major facilitator superfamily (MFS) transporter; major facilitator superfamily transporter 2670551 4581203 Pden_2658 Paracoccus denitrificans PD1222 major facilitator superfamily transporter YP_916441.1 2669142 D 318586 CDS YP_916442.1 119385386 4581204 2670548..2671420 1 NC_008686.1 D-alanyl-D-alanine endopeptidase; functions in hydrolyzing cell wall peptidoglycan; similar to LAS metallopeptidases; forms a dimer in periplasm; penicillin-insensitive murein endopeptidase 2671420 mepA 4581204 mepA Paracoccus denitrificans PD1222 penicillin-insensitive murein endopeptidase YP_916442.1 2670548 D 318586 CDS YP_916443.1 119385387 4581205 2671393..2672361 1 NC_008686.1 KEGG: rsp:RSP_1364 hypothetical protein; hypothetical protein 2672361 4581205 Pden_2660 Paracoccus denitrificans PD1222 hypothetical protein YP_916443.1 2671393 D 318586 CDS YP_916444.1 119385388 4581206 2672358..2673491 1 NC_008686.1 PFAM: beta-lactamase; KEGG: bte:BTH_II1108 beta-lactamase; beta-lactamase 2673491 4581206 Pden_2661 Paracoccus denitrificans PD1222 beta-lactamase YP_916444.1 2672358 D 318586 CDS YP_916445.1 119385389 4581207 2673590..2674204 1 NC_008686.1 TIGRFAM: conserved hypothetical integral membrane protein; PFAM: protein of unknown function DUF165; KEGG: rde:RD1_0365 hypothetical protein; hypothetical protein 2674204 4581207 Pden_2662 Paracoccus denitrificans PD1222 hypothetical protein YP_916445.1 2673590 D 318586 CDS YP_916446.1 119385390 4581208 complement(2674609..2675790) 1 NC_008686.1 catalyzes the formation of beta-ketovaleryl-CoA from acetyl-CoA and propionyl-CoA; beta-ketothiolase 2675790 4581208 Pden_2663 Paracoccus denitrificans PD1222 beta-ketothiolase YP_916446.1 2674609 R 318586 CDS YP_916447.1 119385391 4581209 2675895..2676251 1 NC_008686.1 PFAM: regulatory protein, LysR; KEGG: nha:Nham_2952 transcriptional regulator, ModE family; ModE family transcriptional regulator 2676251 4581209 Pden_2664 Paracoccus denitrificans PD1222 ModE family transcriptional regulator YP_916447.1 2675895 D 318586 CDS YP_916448.1 119385392 4581210 2676318..2677058 1 NC_008686.1 TIGRFAM: molybdenum ABC transporter, periplasmic molybdate-binding protein; PFAM: extracellular solute-binding protein, family 1; KEGG: atc:AGR_C_4642 molybdate-binding periplasmic protein; molybdenum ABC transporter periplasmic molybdate-binding protein 2677058 4581210 Pden_2665 Paracoccus denitrificans PD1222 molybdenum ABC transporter periplasmic molybdate-binding protein YP_916448.1 2676318 D 318586 CDS YP_916449.1 119385393 4581211 2677055..2677759 1 NC_008686.1 TIGRFAM: molybdate ABC transporter, inner membrane subunit; PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: rde:RD1_2914 molybdate ABC transporter, permease protein; molybdate ABC transporter inner membrane subunit 2677759 4581211 Pden_2666 Paracoccus denitrificans PD1222 molybdate ABC transporter inner membrane subunit YP_916449.1 2677055 D 318586 CDS YP_916450.1 119385394 4581212 2677759..2678814 1 NC_008686.1 KEGG: sil:SPO0697 molybdate ABC transporter, ATP-binding protein; TIGRFAM: molybdate ABC transporter, ATPase subunit; PFAM: ABC transporter related; TOBE domain protein; SMART: AAA ATPase; molybdate ABC transporter ATPase 2678814 4581212 Pden_2667 Paracoccus denitrificans PD1222 molybdate ABC transporter ATPase YP_916450.1 2677759 D 318586 CDS YP_916451.1 119385395 4581213 2678889..2679467 1 NC_008686.1 KEGG: rsp:RSP_1496 hypothetical protein; hypothetical protein 2679467 4581213 Pden_2668 Paracoccus denitrificans PD1222 hypothetical protein YP_916451.1 2678889 D 318586 CDS YP_916452.1 119385396 4581214 complement(2679482..2680078) 1 NC_008686.1 PFAM: outer membrane lipoprotein carrier protein LolA; KEGG: rsp:RSP_1497 outer membrane lipoprotein carrier protein; outer membrane lipoprotein carrier protein LolA 2680078 4581214 Pden_2669 Paracoccus denitrificans PD1222 outer membrane lipoprotein carrier protein LolA YP_916452.1 2679482 R 318586 CDS YP_916453.1 119385397 4581215 complement(2680168..2681427) 1 NC_008686.1 TIGRFAM: Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; PFAM: monooxygenase, FAD-binding; KEGG: rsp:RSP_1492 UbiH/COQ6 monooxygenase family; UbiH/UbiF/VisC/COQ6 family ubiquinone biosynthesis hydroxylase 2681427 4581215 Pden_2670 Paracoccus denitrificans PD1222 UbiH/UbiF/VisC/COQ6 family ubiquinone biosynthesis hydroxylase YP_916453.1 2680168 R 318586 CDS YP_916454.1 119385398 4581216 2681521..2682846 1 NC_008686.1 PFAM: Amidase; KEGG: rsp:RSP_1493 amidase; amidase 2682846 4581216 Pden_2671 Paracoccus denitrificans PD1222 amidase YP_916454.1 2681521 D 318586 CDS YP_916455.1 119385399 4581217 2682975..2684168 1 NC_008686.1 PFAM: aminotransferase, class I and II; KEGG: rsp:RSP_1494 aspartate aminotransferase; class I and II aminotransferase 2684168 4581217 Pden_2672 Paracoccus denitrificans PD1222 class I and II aminotransferase YP_916455.1 2682975 D 318586 CDS YP_916456.1 119385400 4581218 2684172..2686856 1 NC_008686.1 PFAM: cell divisionFtsK/SpoIIIE; SMART: AAA ATPase; KEGG: sil:SPO3416 FtsK/SpoIIIE family protein; DNA translocase FtsK 2686856 4581218 Pden_2673 Paracoccus denitrificans PD1222 DNA translocase FtsK YP_916456.1 2684172 D 318586 CDS YP_916457.1 119385401 4581219 complement(2686926..2687822) 1 NC_008686.1 KEGG: ppu:PP_0532 hypothetical protein; hypothetical protein 2687822 4581219 Pden_2674 Paracoccus denitrificans PD1222 hypothetical protein YP_916457.1 2686926 R 318586 CDS YP_916458.1 119385402 4581220 complement(2687928..2689010) 1 NC_008686.1 PFAM: secretion protein HlyD family protein; KEGG: rru:Rru_A3484 secretion protein HlyD; secretion protein HlyD family protein 2689010 4581220 Pden_2675 Paracoccus denitrificans PD1222 secretion protein HlyD family protein YP_916458.1 2687928 R 318586 CDS YP_916459.1 119385403 4581221 complement(2689007..2690668) 1 NC_008686.1 KEGG: sme:SMc00563 transport protein transmembrane; transporter 2690668 4581221 Pden_2676 Paracoccus denitrificans PD1222 transporter YP_916459.1 2689007 R 318586 CDS YP_916460.1 119385404 4581222 complement(2690665..2691126) 1 NC_008686.1 PFAM: regulatory protein, MarR; KEGG: sme:SMc00562 transcription regulator protein; MarR family transcriptional regulator 2691126 4581222 Pden_2677 Paracoccus denitrificans PD1222 MarR family transcriptional regulator YP_916460.1 2690665 R 318586 CDS YP_916461.1 119385405 4581223 complement(2691217..2695722) 1 NC_008686.1 PFAM: protein of unknown function DUF490; KEGG: rsp:RSP_1183 hypothetical protein; hypothetical protein 2695722 4581223 Pden_2678 Paracoccus denitrificans PD1222 hypothetical protein YP_916461.1 2691217 R 318586 CDS YP_916462.1 119385406 4581224 complement(2695722..2697605) 1 NC_008686.1 PFAM: surface antigen (D15); KEGG: rsp:RSP_1182 outer membrane protein; surface antigen (D15) 2697605 4581224 Pden_2679 Paracoccus denitrificans PD1222 surface antigen (D15) YP_916462.1 2695722 R 318586 CDS YP_916463.1 119385407 4581225 complement(2697697..2698620) 1 NC_008686.1 PFAM: Glucokinase; KEGG: sil:SPO0864 glucokinase; glucokinase 2698620 4581225 Pden_2680 Paracoccus denitrificans PD1222 glucokinase YP_916463.1 2697697 R 318586 CDS YP_916464.1 119385408 4581226 2698786..2699229 1 NC_008686.1 hypothetical protein 2699229 4581226 Pden_2681 Paracoccus denitrificans PD1222 hypothetical protein YP_916464.1 2698786 D 318586 CDS YP_916465.1 119385409 4581227 2699299..2700690 1 NC_008686.1 catalyzes the formation of L-homocysteine from S-adenosyl-L-homocysteine; S-adenosyl-L-homocysteine hydrolase 2700690 4581227 Pden_2682 Paracoccus denitrificans PD1222 S-adenosyl-L-homocysteine hydrolase YP_916465.1 2699299 D 318586 CDS YP_916466.1 119385410 4581228 2700753..2701202 1 NC_008686.1 PFAM: histidine triad (HIT) protein; KEGG: bbr:BB0059 histidine triad protein; histidine triad (HIT) protein 2701202 4581228 Pden_2683 Paracoccus denitrificans PD1222 histidine triad (HIT) protein YP_916466.1 2700753 D 318586 CDS YP_916467.1 119385411 4581229 2701280..2701621 1 NC_008686.1 KEGG: sit:TM1040_2834 conserved hypothetical protein; hypothetical protein 2701621 4581229 Pden_2684 Paracoccus denitrificans PD1222 hypothetical protein YP_916467.1 2701280 D 318586 CDS YP_916468.1 119385412 4581230 complement(2701707..2702327) 1 NC_008686.1 PFAM: Enoyl-CoA hydratase/isomerase; KEGG: rsp:RSP_0913 enoyl-CoA hydratase/isomerase; enoyl-CoA hydratase 2702327 4581230 Pden_2685 Paracoccus denitrificans PD1222 enoyl-CoA hydratase YP_916468.1 2701707 R 318586 CDS YP_916469.1 119385413 4581231 2702411..2703961 1 NC_008686.1 KEGG: sil:SPO3441 hypothetical protein; hypothetical protein 2703961 4581231 Pden_2686 Paracoccus denitrificans PD1222 hypothetical protein YP_916469.1 2702411 D 318586 CDS YP_916470.1 119385414 4581232 2704057..2705409 1 NC_008686.1 PFAM: peptidase U62, modulator of DNA gyrase; KEGG: jan:Jann_0403 peptidase U62, modulator of DNA gyrase; C69 family peptidase 2705409 4581232 Pden_2687 Paracoccus denitrificans PD1222 C69 family peptidase YP_916470.1 2704057 D 318586 CDS YP_916471.1 119385415 4581233 2705396..2706217 1 NC_008686.1 PFAM: inositol monophosphatase; KEGG: rsp:RSP_0917 inositol monophosphatase; inositol monophosphatase 2706217 4581233 Pden_2688 Paracoccus denitrificans PD1222 inositol monophosphatase YP_916471.1 2705396 D 318586 CDS YP_916472.1 119385416 4581234 2706278..2706823 1 NC_008686.1 PFAM: flavin reductase domain protein, FMN-binding; KEGG: atc:AGR_L_3083 hypothetical protein; flavin reductase domain-containing protein 2706823 4581234 Pden_2689 Paracoccus denitrificans PD1222 flavin reductase domain-containing protein YP_916472.1 2706278 D 318586 CDS YP_916473.1 119385417 4581235 complement(2706830..2707306) 1 NC_008686.1 KEGG: ppu:PP_4887 hypothetical protein; hypothetical protein 2707306 4581235 Pden_2690 Paracoccus denitrificans PD1222 hypothetical protein YP_916473.1 2706830 R 318586 CDS YP_916474.1 119385418 4581236 complement(2707385..2708035) 1 NC_008686.1 PFAM: protein of unknown function DUF330; KEGG: sit:TM1040_3329 protein of unknown function DUF330; hypothetical protein 2708035 4581236 Pden_2691 Paracoccus denitrificans PD1222 hypothetical protein YP_916474.1 2707385 R 318586 CDS YP_916475.1 119385419 4581237 complement(2708037..2710103) 1 NC_008686.1 PFAM: Mammalian cell entry related domain protein; KEGG: sit:TM1040_3328 mammalian cell entry related; hypothetical protein 2710103 4581237 Pden_2692 Paracoccus denitrificans PD1222 hypothetical protein YP_916475.1 2708037 R 318586 CDS YP_916476.1 119385420 4581238 complement(2710100..2710759) 1 NC_008686.1 PFAM: Paraquat-inducible protein A; KEGG: sit:TM1040_3327 paraquat-inducible protein A; paraquat-inducible protein A 2710759 4581238 Pden_2693 Paracoccus denitrificans PD1222 paraquat-inducible protein A YP_916476.1 2710100 R 318586 CDS YP_916477.1 119385421 4581239 complement(2710756..2711436) 1 NC_008686.1 PFAM: Paraquat-inducible protein A; KEGG: sit:TM1040_3326 paraquat-inducible protein A; paraquat-inducible protein A 2711436 4581239 Pden_2694 Paracoccus denitrificans PD1222 paraquat-inducible protein A YP_916477.1 2710756 R 318586 CDS YP_916478.1 119385422 4581240 2711699..2712499 1 NC_008686.1 KEGG: rsp:RSP_1302 chemotaxis MotB protein; chemotaxis protein MotB 2712499 4581240 Pden_2695 Paracoccus denitrificans PD1222 chemotaxis protein MotB YP_916478.1 2711699 D 318586 CDS YP_916479.1 119385423 4581241 2712587..2713927 1 NC_008686.1 PFAM: flagellar basal body rod protein; protein of unknown function DUF1078 domain protein; KEGG: rsp:RSP_1303 flagellar hook protein; hypothetical protein 2713927 4581241 Pden_2696 Paracoccus denitrificans PD1222 hypothetical protein YP_916479.1 2712587 D 318586 CDS YP_916480.1 119385424 4581242 2713983..2715443 1 NC_008686.1 with FlgL acts as a hook filament junction protein to join the flagellar filament to the hook; flagellar hook-associated protein FlgK 2715443 flgK 4581242 flgK Paracoccus denitrificans PD1222 flagellar hook-associated protein FlgK YP_916480.1 2713983 D 318586 CDS YP_916481.1 119385425 4581243 2715440..2716459 1 NC_008686.1 KEGG: rsp:RSP_1305 flagellar hook-associated protein; flagellar hook-associated protein 2716459 4581243 Pden_2698 Paracoccus denitrificans PD1222 flagellar hook-associated protein YP_916481.1 2715440 D 318586 CDS YP_916482.1 119385426 4581244 2716456..2717556 1 NC_008686.1 part of the basal body which consists of four rings L, P, S, and M mounted on a central rod; Vibrio parahaemolyticus, Yersinia, Bradyrhizobium and other bacteria have two copies of this and other flagellar genes; the V. parahaemolyticus protein is associated with the polar flagella and the Bradyrhizobium protein is associated with the thick flagellum; flagellar basal body P-ring biosynthesis protein FlgA 2717556 flgI 4581244 flgI Paracoccus denitrificans PD1222 flagellar basal body P-ring biosynthesis protein FlgA YP_916482.1 2716456 D 318586 CDS YP_916483.1 119385427 4581245 complement(2719808..2720194) 1 NC_008686.1 PFAM: transposase, IS4 family protein; KEGG: nmu:Nmul_A2650 transposase, IS4; transposase, IS4 family protein 2720194 4581245 Pden_2703 Paracoccus denitrificans PD1222 transposase, IS4 family protein YP_916483.1 2719808 R 318586 CDS YP_916484.1 119385428 4580339 complement(2720191..2720559) 1 NC_008686.1 KEGG: mag:amb0408 transposase and inactivated derivative; transposase and inactivated derivative 2720559 4580339 Pden_2704 Paracoccus denitrificans PD1222 transposase and inactivated derivative YP_916484.1 2720191 R 318586 CDS YP_916485.1 119385429 4580340 complement(2720874..2721524) 1 NC_008686.1 PFAM: carbonic anhydrase; KEGG: rsp:RSP_1377 carbonic anhydrase; carbonate dehydratase 2721524 4580340 Pden_2705 Paracoccus denitrificans PD1222 carbonate dehydratase YP_916485.1 2720874 R 318586 CDS YP_916486.1 119385430 4580341 2721656..2722045 1 NC_008686.1 KEGG: rde:RD1_0313 hypothetical protein; hypothetical protein 2722045 4580341 Pden_2706 Paracoccus denitrificans PD1222 hypothetical protein YP_916486.1 2721656 D 318586 CDS YP_916487.1 119385431 4580342 2722118..2723521 1 NC_008686.1 PFAM: peptidase M17, leucyl aminopeptidase domain protein; KEGG: sit:TM1040_3455 leucyl aminopeptidase; leucyl aminopeptidase 2723521 4580342 Pden_2707 Paracoccus denitrificans PD1222 leucyl aminopeptidase YP_916487.1 2722118 D 318586 CDS YP_916488.1 119385432 4580343 2723518..2724366 1 NC_008686.1 PFAM: NLP/P60 protein; KEGG: rsp:RSP_1380 hypothetical protein; NLP/P60 protein 2724366 4580343 Pden_2708 Paracoccus denitrificans PD1222 NLP/P60 protein YP_916488.1 2723518 D 318586 CDS YP_916489.1 119385433 4580344 2724389..2725444 1 NC_008686.1 PFAM: alanine dehydrogenase/PNT domain protein; KEGG: sil:SPO3307 saccharopine dehydrogenase; NAD(P) transhydrogenase subunit alpha 2725444 4580344 Pden_2709 Paracoccus denitrificans PD1222 NAD(P) transhydrogenase subunit alpha YP_916489.1 2724389 D 318586 CDS YP_916490.1 119385434 4580345 2725508..2726692 1 NC_008686.1 PFAM: glucose sorbosone dehydrogenase; KEGG: neu:NE1997 glucose dehydrogenase B; glucose sorbosone dehydrogenase 2726692 4580345 Pden_2710 Paracoccus denitrificans PD1222 glucose sorbosone dehydrogenase YP_916490.1 2725508 D 318586 CDS YP_916491.1 119385435 4580346 complement(2726876..2727247) 1 NC_008686.1 KEGG: sil:SPO3310 hypothetical protein; hypothetical protein 2727247 4580346 Pden_2711 Paracoccus denitrificans PD1222 hypothetical protein YP_916491.1 2726876 R 318586 CDS YP_916492.1 119385436 4580347 complement(2727297..2727944) 1 NC_008686.1 KEGG: rsp:RSP_3367 hypothetical protein; hypothetical protein 2727944 4580347 Pden_2712 Paracoccus denitrificans PD1222 hypothetical protein YP_916492.1 2727297 R 318586 CDS YP_916493.1 119385437 4580348 complement(2727941..2729761) 1 NC_008686.1 This protein is involved in the repair of mismatches in DNA. It is required for dam-dependent methyl-directed DNA mismatch repair. Promotes the formation of a stable complex between two or more DNA-binding proteins in an ATP-dependent manner without itself being part of a final effector complex; DNA mismatch repair protein 2729761 mutL 4580348 mutL Paracoccus denitrificans PD1222 DNA mismatch repair protein YP_916493.1 2727941 R 318586 CDS YP_916494.1 119385438 4580349 complement(2729805..2731118) 1 NC_008686.1 PFAM: peptidase M16 domain protein; KEGG: rde:RD1_0659 peptidase, M16 family; peptidase M16 domain-containing protein 2731118 4580349 Pden_2714 Paracoccus denitrificans PD1222 peptidase M16 domain-containing protein YP_916494.1 2729805 R 318586 CDS YP_916495.1 119385439 4580350 complement(2731115..2732533) 1 NC_008686.1 PFAM: peptidase M16 domain protein; KEGG: rsp:RSP_1097 zinc protease; peptidase M16 domain-containing protein 2732533 4580350 Pden_2715 Paracoccus denitrificans PD1222 peptidase M16 domain-containing protein YP_916495.1 2731115 R 318586 CDS YP_916496.1 119385440 4580351 complement(2732634..2733206) 1 NC_008686.1 KEGG: rsp:RSP_1098 hypothetical protein; hypothetical protein 2733206 4580351 Pden_2716 Paracoccus denitrificans PD1222 hypothetical protein YP_916496.1 2732634 R 318586 CDS YP_916497.1 119385441 4580352 complement(2733238..2733921) 1 NC_008686.1 TIGRFAM: lipoprotein signal peptidase; PFAM: peptidase A8, signal peptidase II; KEGG: rsp:RSP_1099 signal peptidase II; lipoprotein signal peptidase 2733921 4580352 Pden_2717 Paracoccus denitrificans PD1222 lipoprotein signal peptidase YP_916497.1 2733238 R 318586 CDS YP_916498.1 119385442 4580353 complement(2733921..2735510) 1 NC_008686.1 involved in de novo purine biosynthesis; bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase 2735510 purH 4580353 purH Paracoccus denitrificans PD1222 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase YP_916498.1 2733921 R 318586 CDS YP_916499.1 119385443 4580354 complement(2735550..2737199) 1 NC_008686.1 PFAM: Heparinase II/III family protein; KEGG: sil:SPO3375 hypothetical protein; heparinase II/III family protein 2737199 4580354 Pden_2719 Paracoccus denitrificans PD1222 heparinase II/III family protein YP_916499.1 2735550 R 318586 CDS YP_916500.1 119385444 4580355 complement(2737230..2738837) 1 NC_008686.1 PFAM: Fmu (Sun) domain protein; NusB/RsmB/TIM44; methyltransferase small; KEGG: sil:SPO3376 ribosomal RNA small subunit methyltransferase B; Fmu (Sun) domain-containing protein 2738837 4580355 Pden_2720 Paracoccus denitrificans PD1222 Fmu (Sun) domain-containing protein YP_916500.1 2737230 R 318586 CDS YP_916501.1 119385445 4580356 2738891..2740060 1 NC_008686.1 TIGRFAM: efflux transporter, RND family, MFP subunit; PFAM: secretion protein HlyD family protein; KEGG: atc:AGR_C_4619 hypothetical protein; RND family efflux transporter MFP subunit 2740060 4580356 Pden_2721 Paracoccus denitrificans PD1222 RND family efflux transporter MFP subunit YP_916501.1 2738891 D 318586 CDS YP_916502.1 119385446 4580357 2740064..2743162 1 NC_008686.1 TIGRFAM: transporter, hydrophobe/amphiphile efflux-1 (HAE1) family; PFAM: acriflavin resistance protein; KEGG: ret:RHE_CH03412 probable multidrug efflux transporter protein; hydrophobe/amphiphile efflux-1 (HAE1) family protein 2743162 4580357 Pden_2722 Paracoccus denitrificans PD1222 hydrophobe/amphiphile efflux-1 (HAE1) family protein YP_916502.1 2740064 D 318586 CDS YP_916503.1 119385447 4580358 2743159..2744202 1 NC_008686.1 catalyzes the formation of selenophosphate from selenide and ATP; selenophosphate synthetase 2744202 4580358 Pden_2723 Paracoccus denitrificans PD1222 selenophosphate synthetase YP_916503.1 2743159 D 318586 CDS YP_916504.1 119385448 4580359 2744297..2744662 1 NC_008686.1 KEGG: sme:SMa0026 hypothetical protein; hypothetical protein 2744662 4580359 Pden_2724 Paracoccus denitrificans PD1222 hypothetical protein YP_916504.1 2744297 D 318586 CDS YP_916505.1 119385449 4580360 2744730..2745149 1 NC_008686.1 TIGRFAM: uncharacterized domain 1; PFAM: thioesterase superfamily protein; KEGG: rpe:RPE_2404 uncharacterized domain 1; hypothetical protein 2745149 4580360 Pden_2725 Paracoccus denitrificans PD1222 hypothetical protein YP_916505.1 2744730 D 318586 CDS YP_916506.1 119385450 4580361 2745472..2746125 1 NC_008686.1 PFAM: protein-L-isoaspartate(D-aspartate) O-methyltransferase; Methyltransferase type 11; KEGG: sit:TM1040_1992 protein-L-isoaspartate(D-aspartate) O-methyltransferase; protein-L-isoaspartate(D-aspartate) O-methyltransferase 2746125 4580361 Pden_2726 Paracoccus denitrificans PD1222 protein-L-isoaspartate(D-aspartate) O-methyltransferase YP_916506.1 2745472 D 318586 CDS YP_916507.1 119385451 4580362 2746148..2747542 1 NC_008686.1 TIGRFAM: type I secretion outer membrane protein, TolC family; PFAM: outer membrane efflux protein; KEGG: rsp:RSP_0251 outer membrane efflux protein; TolC family type I secretion outer membrane protein 2747542 4580362 Pden_2727 Paracoccus denitrificans PD1222 TolC family type I secretion outer membrane protein YP_916507.1 2746148 D 318586 CDS YP_916508.1 119385452 4580363 2747569..2748357 1 NC_008686.1 KEGG: rsp:RSP_0250 hypothetical protein; hypothetical protein 2748357 4580363 Pden_2728 Paracoccus denitrificans PD1222 hypothetical protein YP_916508.1 2747569 D 318586 CDS YP_916509.1 119385453 4580364 complement(2748435..2749604) 1 NC_008686.1 PFAM: Peptidoglycan-binding LysM; peptidase M23B; KEGG: rsp:RSP_2543 peptidoglycan-binding LysM (possible peptidase); peptidase M23B 2749604 4580364 Pden_2729 Paracoccus denitrificans PD1222 peptidase M23B YP_916509.1 2748435 R 318586 CDS YP_916510.1 119385454 4580365 complement(2749636..2750286) 1 NC_008686.1 KEGG: rsp:RSP_2544 protein-L-isoaspartate O-methyltransferase; TIGRFAM: protein-L-isoaspartate O-methyltransferase; PFAM: protein-L-isoaspartate(D-aspartate) O-methyltransferase; protein-L-isoaspartate O-methyltransferase 2750286 4580365 Pden_2730 Paracoccus denitrificans PD1222 protein-L-isoaspartate O-methyltransferase YP_916510.1 2749636 R 318586 CDS YP_916511.1 119385455 4580366 complement(2750295..2751089) 1 NC_008686.1 catalyzes the conversion of a phosphate monoester to an alcohol and a phosphate; stationary phase survival protein SurE 2751089 4580366 Pden_2731 Paracoccus denitrificans PD1222 stationary phase survival protein SurE YP_916511.1 2750295 R 318586 CDS YP_916512.1 119385456 4580367 2751281..2752204 1 NC_008686.1 PFAM: protein of unknown function DUF81; KEGG: rsp:RSP_2206 hypothetical protein; hypothetical protein 2752204 4580367 Pden_2732 Paracoccus denitrificans PD1222 hypothetical protein YP_916512.1 2751281 D 318586 CDS YP_916513.1 119385457 4580368 2752201..2752998 1 NC_008686.1 KEGG: rde:RD1_1641 hypothetical protein; hypothetical protein 2752998 4580368 Pden_2733 Paracoccus denitrificans PD1222 hypothetical protein YP_916513.1 2752201 D 318586 CDS YP_916514.1 119385458 4580369 complement(2752985..2754142) 1 NC_008686.1 PFAM: protein of unknown function DUF482; KEGG: sil:SPO3732 hypothetical protein; hypothetical protein 2754142 4580369 Pden_2734 Paracoccus denitrificans PD1222 hypothetical protein YP_916514.1 2752985 R 318586 CDS YP_916515.1 119385459 4580370 complement(2754163..2754918) 1 NC_008686.1 PFAM: glycerophosphoryl diester phosphodiesterase; KEGG: jan:Jann_0436 glycerophosphoryl diester phosphodiesterase; glycerophosphoryl diester phosphodiesterase 2754918 4580370 Pden_2735 Paracoccus denitrificans PD1222 glycerophosphoryl diester phosphodiesterase YP_916515.1 2754163 R 318586 CDS YP_916516.1 119385460 4580371 complement(2754918..2755358) 1 NC_008686.1 PFAM: Endoribonuclease L-PSP; KEGG: rsp:RSP_0894 hypothetical protein; endoribonuclease L-PSP 2755358 4580371 Pden_2736 Paracoccus denitrificans PD1222 endoribonuclease L-PSP YP_916516.1 2754918 R 318586 CDS YP_916517.1 119385461 4580372 complement(2755368..2755820) 1 NC_008686.1 KEGG: sal:Sala_1312 hypothetical protein; hypothetical protein 2755820 4580372 Pden_2737 Paracoccus denitrificans PD1222 hypothetical protein YP_916517.1 2755368 R 318586 CDS YP_916518.1 119385462 4580373 complement(2755866..2759369) 1 NC_008686.1 TIGRFAM: chromosome segregation protein SMC; PFAM: SMC domain protein; SMCs flexible hinge domain protein; KEGG: rsp:RSP_0876 chromosome segregation protein SMC2; chromosome segregation protein SMC 2759369 4580373 Pden_2738 Paracoccus denitrificans PD1222 chromosome segregation protein SMC YP_916518.1 2755866 R 318586 CDS YP_916519.1 119385463 4580374 2759463..2759816 1 NC_008686.1 PFAM: LrgA family protein; KEGG: bcn:Bcen_5769 LrgA; LrgA family protein 2759816 4580374 Pden_2739 Paracoccus denitrificans PD1222 LrgA family protein YP_916519.1 2759463 D 318586 CDS YP_916520.1 119385464 4580375 2759813..2760529 1 NC_008686.1 PFAM: LrgB family protein; KEGG: rsp:RSP_3332 transmembrane protein; LrgB family protein 2760529 4580375 Pden_2740 Paracoccus denitrificans PD1222 LrgB family protein YP_916520.1 2759813 D 318586 CDS YP_916521.1 119385465 4580376 complement(2760542..2761012) 1 NC_008686.1 hypothetical protein 2761012 4580376 Pden_2741 Paracoccus denitrificans PD1222 hypothetical protein YP_916521.1 2760542 R 318586 CDS YP_916522.1 119385466 4580377 complement(2761122..2761448) 1 NC_008686.1 KEGG: rsp:RSP_6107 hypothetical protein; hypothetical protein 2761448 4580377 Pden_2742 Paracoccus denitrificans PD1222 hypothetical protein YP_916522.1 2761122 R 318586 CDS YP_916523.1 119385467 4580378 2761790..2762353 1 NC_008686.1 Involved in peptide bond synthesis; alters the affinity of the ribosome for aminoacyl-tRNA; elongation factor P 2762353 4580378 Pden_2743 Paracoccus denitrificans PD1222 elongation factor P YP_916523.1 2761790 D 318586 CDS YP_916524.1 119385468 4580379 2762441..2763574 1 NC_008686.1 KEGG: jan:Jann_1003 hypothetical protein; acetyltransferase 2763574 4580379 Pden_2744 Paracoccus denitrificans PD1222 acetyltransferase YP_916524.1 2762441 D 318586 CDS YP_916525.1 119385469 4580380 2763832..2764896 1 NC_008686.1 KEGG: mes:Meso_0838 sugar uptake ABC transporter periplasmic solute-binding protein precursor; sugar uptake ABC transporter periplasmic solute-binding protein 2764896 4580380 Pden_2745 Paracoccus denitrificans PD1222 sugar uptake ABC transporter periplasmic solute-binding protein YP_916525.1 2763832 D 318586 CDS YP_916526.1 119385470 4580381 2764956..2766530 1 NC_008686.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: mes:Meso_0839 ABC transporter related; ABC transporter 2766530 4580381 Pden_2746 Paracoccus denitrificans PD1222 ABC transporter YP_916526.1 2764956 D 318586 CDS YP_916527.1 119385471 4580382 2766523..2767707 1 NC_008686.1 PFAM: inner-membrane translocator; KEGG: mes:Meso_0840 inner-membrane translocator; inner-membrane translocator 2767707 4580382 Pden_2747 Paracoccus denitrificans PD1222 inner-membrane translocator YP_916527.1 2766523 D 318586 CDS YP_916528.1 119385472 4580383 2767704..2768606 1 NC_008686.1 PFAM: 2-keto-3-deoxy-galactonokinase; KEGG: rsp:RSP_1371 2-dehydro-3-deoxygalactonokinase; 2-keto-3-deoxy-galactonokinase 2768606 4580383 Pden_2748 Paracoccus denitrificans PD1222 2-keto-3-deoxy-galactonokinase YP_916528.1 2767704 D 318586 CDS YP_916529.1 119385473 4580384 2768603..2769205 1 NC_008686.1 catalyzes the formation of D-glyceraldehyde 3-phosphate and pyruvate from 2-dehydro-3-deoxy-D-galactonate 6-phosphate; functions in galactonate metabolism; 2-dehydro-3-deoxy-6-phosphogalactonate aldolase 2769205 4580384 Pden_2749 Paracoccus denitrificans PD1222 2-dehydro-3-deoxy-6-phosphogalactonate aldolase YP_916529.1 2768603 D 318586 CDS YP_916530.1 119385474 4580385 2769202..2770044 1 NC_008686.1 PFAM: SMP-30/Gluconolaconase/LRE domain protein; KEGG: jan:Jann_3831 senescence marker protein-30 (SMP-30); SMP-30/gluconolaconase/LRE domain-containing protein 2770044 4580385 Pden_2750 Paracoccus denitrificans PD1222 SMP-30/gluconolaconase/LRE domain-containing protein YP_916530.1 2769202 D 318586 CDS YP_916531.1 119385475 4580386 2770041..2771051 1 NC_008686.1 PFAM: Aldose 1-epimerase; KEGG: sme:SMc03798 probable aldose 1-epimerase protein; aldose 1-epimerase 2771051 4580386 Pden_2751 Paracoccus denitrificans PD1222 aldose 1-epimerase YP_916531.1 2770041 D 318586 CDS YP_916532.1 119385476 4580387 2771095..2771817 1 NC_008686.1 PFAM: regulatory protein GntR, HTH; GntR domain protein; KEGG: sil:SPO1722 transcriptional regulator, GntR family; GntR family transcriptional regulator 2771817 4580387 Pden_2752 Paracoccus denitrificans PD1222 GntR family transcriptional regulator YP_916532.1 2771095 D 318586 CDS YP_916533.1 119385477 4580388 complement(2771858..2772703) 1 NC_008686.1 PFAM: fumarylacetoacetate (FAA) hydrolase; KEGG: bcn:Bcen_5340 5-carboxymethyl-2-hydroxymuconate delta-isomerase; 5-carboxymethyl-2-hydroxymuconate delta-isomerase 2772703 4580388 Pden_2753 Paracoccus denitrificans PD1222 5-carboxymethyl-2-hydroxymuconate delta-isomerase YP_916533.1 2771858 R 318586 CDS YP_916534.1 119385478 4580389 complement(2772733..2773470) 1 NC_008686.1 PFAM: NAD-dependent epimerase/dehydratase; short-chain dehydrogenase/reductase SDR; KR; KEGG: sil:SPO2409 oxidoreductase, short chain dehydrogenase/reductase family; short-chain dehydrogenase/reductase SDR 2773470 4580389 Pden_2754 Paracoccus denitrificans PD1222 short-chain dehydrogenase/reductase SDR YP_916534.1 2772733 R 318586 CDS YP_916535.1 119385479 4580390 complement(2773558..2775009) 1 NC_008686.1 PFAM: aldehyde dehydrogenase; KEGG: rsp:RSP_1507 aldehyde dehydrogenase; aldehyde dehydrogenase 2775009 4580390 Pden_2755 Paracoccus denitrificans PD1222 aldehyde dehydrogenase YP_916535.1 2773558 R 318586 CDS YP_916536.1 119385480 4580391 2775171..2775827 1 NC_008686.1 PFAM: alkyl hydroperoxide reductase/ Thiol specific antioxidant/ Mal allergen; Redoxin domain protein; KEGG: sil:SPO3383 thiol-specific antioxidant protein; peroxidase 2775827 4580391 Pden_2756 Paracoccus denitrificans PD1222 peroxidase YP_916536.1 2775171 D 318586 CDS YP_916537.1 119385481 4580392 complement(2775867..2776655) 1 NC_008686.1 PFAM: glycosyl transferase, family 25; KEGG: sfr:Sfri_3927 glycosyl transferase, family 25; glycosyl transferase family protein 2776655 4580392 Pden_2757 Paracoccus denitrificans PD1222 glycosyl transferase family protein YP_916537.1 2775867 R 318586 CDS YP_916538.1 119385482 4580393 complement(2776652..2777455) 1 NC_008686.1 hypothetical protein 2777455 4580393 Pden_2758 Paracoccus denitrificans PD1222 hypothetical protein YP_916538.1 2776652 R 318586 CDS YP_916539.1 119385483 4580394 complement(2777503..2779713) 1 NC_008686.1 PFAM: 3' exoribonuclease; RNA binding S1 domain protein; KH, type 1, domain protein; SMART: KH domain protein; KEGG: rsp:RSP_1112 polyribonucleotide nucleotidyltransferase; polynucleotide phosphorylase 2779713 4580394 Pden_2759 Paracoccus denitrificans PD1222 polynucleotide phosphorylase YP_916539.1 2777503 R 318586 CDS YP_916540.1 119385484 4580395 complement(2780143..2780412) 1 NC_008686.1 primary rRNA binding protein; helps nucleate assembly of 30S; binds directly to the 16S rRNA and an intersubunit bridge to the 23S rRNA; autoregulates translation through interactions with the mRNA leader sequence; 30S ribosomal protein S15 2780412 rpsO 4580395 rpsO Paracoccus denitrificans PD1222 30S ribosomal protein S15 YP_916540.1 2780143 R 318586 CDS YP_916541.1 119385485 4580396 complement(2780558..2781487) 1 NC_008686.1 KEGG: sil:SPO2352 type I secretion target repeat protein; type I secretion target repeat-containing protein 2781487 4580396 Pden_2761 Paracoccus denitrificans PD1222 type I secretion target repeat-containing protein YP_916541.1 2780558 R 318586 CDS YP_916542.1 119385486 4580397 complement(2781594..2782247) 1 NC_008686.1 PFAM: alanine racemase domain protein; KEGG: rsp:RSP_0844 hypothetical protein; alanine racemase 2782247 4580397 Pden_2762 Paracoccus denitrificans PD1222 alanine racemase YP_916542.1 2781594 R 318586 CDS YP_916543.1 119385487 4581342 complement(2782317..2783438) 1 NC_008686.1 KEGG: sil:SPO3430 outer membrane porin; porin 2783438 4581342 Pden_2763 Paracoccus denitrificans PD1222 porin YP_916543.1 2782317 R 318586 CDS YP_916544.1 119385488 4581343 2783615..2784124 1 NC_008686.1 KEGG: sil:SPO3431 hypothetical protein; hypothetical protein 2784124 4581343 Pden_2764 Paracoccus denitrificans PD1222 hypothetical protein YP_916544.1 2783615 D 318586 CDS YP_916545.1 119385489 4581344 2784200..2786734 1 NC_008686.1 leucine--tRNA ligase; LeuRS; class-I aminoacyl-tRNA synthetase; charges leucine by linking carboxyl group to alpha-phosphate of ATP and then transfers aminoacyl-adenylate to its tRNA; due to the large number of codons that tRNA(Leu) recognizes, the leucyl-tRNA synthetase does not recognize the anticodon loop of the tRNA, but instead recognition is dependent on a conserved discriminator base A37 and a long arm; an editing domain hydrolyzes misformed products; in Methanothermobacter thermautotrophicus this enzyme associates with prolyl-tRNA synthetase; leucyl-tRNA synthetase 2786734 leuS 4581344 leuS Paracoccus denitrificans PD1222 leucyl-tRNA synthetase YP_916545.1 2784200 D 318586 CDS YP_916546.1 119385490 4581345 2786721..2787206 1 NC_008686.1 KEGG: rsp:RSP_0839 predicted secreted periplasmic protein; secreted periplasmic protein 2787206 4581345 Pden_2766 Paracoccus denitrificans PD1222 secreted periplasmic protein YP_916546.1 2786721 D 318586 CDS YP_916547.1 119385491 4581346 2787203..2788231 1 NC_008686.1 TIGRFAM: DNA polymerase III, delta subunit; PFAM: DNA polymerase III, delta; KEGG: sil:SPO3434 DNA polymerase III delta subunit; DNA polymerase III subunit delta 2788231 4581346 Pden_2767 Paracoccus denitrificans PD1222 DNA polymerase III subunit delta YP_916547.1 2787203 D 318586 CDS YP_916548.1 119385492 4581347 2788228..2789433 1 NC_008686.1 PFAM: HI0933 family protein; KEGG: rsp:RSP_0836 flavoprotein; hypothetical protein 2789433 4581347 Pden_2768 Paracoccus denitrificans PD1222 hypothetical protein YP_916548.1 2788228 D 318586 CDS YP_916549.1 119385493 4581348 complement(2789409..2789996) 1 NC_008686.1 PFAM: Glutathione S-transferase, N-terminal domain; KEGG: rde:RD1_0053 glutathione S-transferase family protein; glutathione S-transferase domain-containing protein 2789996 4581348 Pden_2769 Paracoccus denitrificans PD1222 glutathione S-transferase domain-containing protein YP_916549.1 2789409 R 318586 CDS YP_916550.1 119385494 4581349 2790118..2791362 1 NC_008686.1 PFAM: major facilitator superfamily MFS_1; KEGG: rsp:RSP_1372 major facilitator superfamily (MFS) transporter; major facilitator superfamily transporter 2791362 4581349 Pden_2770 Paracoccus denitrificans PD1222 major facilitator superfamily transporter YP_916550.1 2790118 D 318586 CDS YP_916551.1 119385495 4581350 2791452..2792228 1 NC_008686.1 TIGRFAM: 5'-nucleotidase, lipoprotein e(P4) family; PFAM: acid phosphatase (Class B); KEGG: hpy:HP1285 conserved hypothetical secreted protein; 5'-nucleotidase 2792228 4581350 Pden_2771 Paracoccus denitrificans PD1222 5'-nucleotidase YP_916551.1 2791452 D 318586 CDS YP_916552.1 119385496 4581351 2792380..2793573 1 NC_008686.1 PFAM: major facilitator superfamily MFS_1; KEGG: rsp:RSP_1373 major facilitator superfamily (MFS) transporter; major facilitator superfamily transporter 2793573 4581351 Pden_2772 Paracoccus denitrificans PD1222 major facilitator superfamily transporter YP_916552.1 2792380 D 318586 CDS YP_916553.1 119385497 4581352 2793566..2794612 1 NC_008686.1 PFAM: glycosyl transferase, group 1; KEGG: rsp:RSP_1374 lipopolysaccharide core biosynthesis mannosyltransferase protein; group 1 glycosyl transferase 2794612 4581352 Pden_2773 Paracoccus denitrificans PD1222 group 1 glycosyl transferase YP_916553.1 2793566 D 318586 CDS YP_916554.1 119385498 4581353 2794609..2795223 1 NC_008686.1 KEGG: rsp:RSP_1375 hypothetical protein; hypothetical protein 2795223 4581353 Pden_2774 Paracoccus denitrificans PD1222 hypothetical protein YP_916554.1 2794609 D 318586 CDS YP_916555.1 119385499 4581354 2795325..2796347 1 NC_008686.1 catalyzes the formation of 4-aspartyl phosphate from aspartate 4-semialdehyde; aspartate-semialdehyde dehydrogenase 2796347 4581354 Pden_2775 Paracoccus denitrificans PD1222 aspartate-semialdehyde dehydrogenase YP_916555.1 2795325 D 318586 CDS YP_916556.1 119385500 4581355 2796442..2798079 1 NC_008686.1 KEGG: sit:TM1040_3460 conserved hypothetical protein; hypothetical protein 2798079 4581355 Pden_2776 Paracoccus denitrificans PD1222 hypothetical protein YP_916556.1 2796442 D 318586 CDS YP_916557.1 119385501 4581356 complement(2798267..2798905) 1 NC_008686.1 Enables the cleavage of the glycosidic bond in both 5'-methylthioadenosine and S-adenosylhomocysteine; 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase 2798905 4581356 Pden_2777 Paracoccus denitrificans PD1222 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase YP_916557.1 2798267 R 318586 CDS YP_916558.1 119385502 4581357 complement(2799011..2800606) 1 NC_008686.1 SMART: PAS domain containing protein; KEGG: rsp:RSP_1521 hypothetical protein; PAS/PAC sensor protein 2800606 4581357 Pden_2778 Paracoccus denitrificans PD1222 PAS/PAC sensor protein YP_916558.1 2799011 R 318586 CDS YP_916559.1 119385503 4581358 complement(2800682..2802070) 1 NC_008686.1 PFAM: ATP-binding region, ATPase domain protein domain protein; histidine kinase A domain protein domain protein; KEGG: rsp:RSP_1520 sensor histidine kinase PrrB (RegB); integral membrane sensor signal transduction histidine kinase 2802070 4581358 Pden_2779 Paracoccus denitrificans PD1222 integral membrane sensor signal transduction histidine kinase YP_916559.1 2800682 R 318586 CDS YP_916560.1 119385504 4581359 2802107..2802757 1 NC_008686.1 PFAM: electron transport protein SCO1/SenC; KEGG: rde:RD1_0460 SenC protein; electron transport protein SCO1/SenC 2802757 4581359 Pden_2780 Paracoccus denitrificans PD1222 electron transport protein SCO1/SenC YP_916560.1 2802107 D 318586 CDS YP_916561.1 119385505 4581360 2802810..2803358 1 NC_008686.1 PFAM: response regulator receiver; KEGG: sit:TM1040_2838 response regulator receiver protein; Fis family transcriptional regulator 2803358 4581360 Pden_2781 Paracoccus denitrificans PD1222 Fis family transcriptional regulator YP_916561.1 2802810 D 318586 CDS YP_916562.1 119385506 4581361 2803442..2803750 1 NC_008686.1 PFAM: histone family protein nucleoid-structuring protein H-NS; KEGG: rsp:RSP_1517 histone-like protein of HNS family; histone family protein nucleoid-structuring protein H-NS 2803750 4581361 Pden_2782 Paracoccus denitrificans PD1222 histone family protein nucleoid-structuring protein H-NS YP_916562.1 2803442 D 318586 CDS YP_916563.1 119385507 4581362 complement(2803796..2804404) 1 NC_008686.1 PFAM: metal-dependent phosphohydrolase, HD sub domain; KEGG: rsp:RSP_1516 S-adenosyl L-homocystein hydrolase; metal dependent phosphohydrolase 2804404 4581362 Pden_2783 Paracoccus denitrificans PD1222 metal dependent phosphohydrolase YP_916563.1 2803796 R 318586 CDS YP_916564.1 119385508 4581363 complement(2804552..2805085) 1 NC_008686.1 molecular chaperone that is required for the normal export of envelope proteins out of the cell cytoplasm; in Escherichia coli this proteins forms a homotetramer in the cytoplasm and delivers proteins to be exported to SecA; preprotein translocase subunit SecB 2805085 4581363 Pden_2784 Paracoccus denitrificans PD1222 preprotein translocase subunit SecB YP_916564.1 2804552 R 318586 CDS YP_916565.1 119385509 4581364 complement(2805135..2805713) 1 NC_008686.1 PFAM: FxsA cytoplasmic membrane protein; KEGG: ppr:PBPRA3390 FxsA protein; FxsA cytoplasmic membrane protein 2805713 4581364 Pden_2785 Paracoccus denitrificans PD1222 FxsA cytoplasmic membrane protein YP_916565.1 2805135 R 318586 CDS YP_916566.1 119385510 4581365 2805825..2806481 1 NC_008686.1 PFAM: import inner membrane translocase, subunit Tim44; KEGG: jan:Jann_0191 import inner membrane translocase, subunit Tim44; import inner membrane translocase subunit Tim44 2806481 4581365 Pden_2786 Paracoccus denitrificans PD1222 import inner membrane translocase subunit Tim44 YP_916566.1 2805825 D 318586 CDS YP_916567.1 119385511 4581366 2806485..2807093 1 NC_008686.1 PFAM: Smr protein/MutS2; KEGG: rsp:RSP_1241 Smr protein/MutS2; Smr protein/MutS2 2807093 4581366 Pden_2787 Paracoccus denitrificans PD1222 Smr protein/MutS2 YP_916567.1 2806485 D 318586 CDS YP_916568.1 119385512 4581367 complement(2807090..2808163) 1 NC_008686.1 PFAM: protein of unknown function DUF900, hydrolase family protein; KEGG: sil:SPO3883 lipoprotein; hypothetical protein 2808163 4581367 Pden_2788 Paracoccus denitrificans PD1222 hypothetical protein YP_916568.1 2807090 R 318586 CDS YP_916569.1 119385513 4581368 complement(2808226..2808402) 1 NC_008686.1 KEGG: rpb:RPB_1461 hypothetical protein; hypothetical protein 2808402 4581368 Pden_2789 Paracoccus denitrificans PD1222 hypothetical protein YP_916569.1 2808226 R 318586 CDS YP_916570.1 119385514 4581369 complement(2808460..2809767) 1 NC_008686.1 heat shock protein involved in degradation of misfolded proteins; ATP-dependent protease ATP-binding subunit HslU 2809767 hslU 4581369 hslU Paracoccus denitrificans PD1222 ATP-dependent protease ATP-binding subunit HslU YP_916570.1 2808460 R 318586 CDS YP_916571.1 119385515 4581370 complement(2809962..2810516) 1 NC_008686.1 heat shock protein involved in degradation of misfolded proteins; ATP-dependent protease peptidase subunit 2810516 4581370 Pden_2791 Paracoccus denitrificans PD1222 ATP-dependent protease peptidase subunit YP_916571.1 2809962 R 318586 CDS YP_916572.1 119385516 4581371 2810620..2811540 1 NC_008686.1 KEGG: rsp:RSP_1530 hypothetical protein; hypothetical protein 2811540 4581371 Pden_2792 Paracoccus denitrificans PD1222 hypothetical protein YP_916572.1 2810620 D 318586 CDS YP_916573.1 119385517 4581372 complement(2811544..2811867) 1 NC_008686.1 TIGRFAM: thioredoxin; PFAM: glutaredoxin; Thioredoxin domain; KEGG: jan:Jann_4067 thioredoxin; thioredoxin 2811867 4581372 Pden_2793 Paracoccus denitrificans PD1222 thioredoxin YP_916573.1 2811544 R 318586 CDS YP_916574.1 119385518 4581373 complement(2811921..2815295) 1 NC_008686.1 TIGRFAM: UvrD-like DNA helicase, C terminal; PFAM: UvrD/REP helicase; KEGG: rsp:RSP_1527 helicase, UvrD/Rep family; UvrD-like DNA helicase domain-containing protein 2815295 4581373 Pden_2794 Paracoccus denitrificans PD1222 UvrD-like DNA helicase domain-containing protein YP_916574.1 2811921 R 318586 CDS YP_916575.1 119385519 4581374 complement(2815285..2818227) 1 NC_008686.1 KEGG: rsp:RSP_1525 helicase/exonuclease; helicase/exonuclease 2818227 4581374 Pden_2795 Paracoccus denitrificans PD1222 helicase/exonuclease YP_916575.1 2815285 R 318586 CDS YP_916576.1 119385520 4581375 complement(2818220..2818891) 1 NC_008686.1 PFAM: Nucleotidyl transferase; KEGG: rsp:RSP_1524 nucleotidyltransferase family protein; nucleotidyl transferase 2818891 4581375 Pden_2796 Paracoccus denitrificans PD1222 nucleotidyl transferase YP_916576.1 2818220 R 318586 CDS YP_916577.1 119385521 4581376 complement(2818888..2820306) 1 NC_008686.1 PFAM: aminoglycoside phosphotransferase; protein of unknown function UPF0079; KEGG: rpb:RPB_0625 hypothetical protein; hypothetical protein 2820306 4581376 Pden_2797 Paracoccus denitrificans PD1222 hypothetical protein YP_916577.1 2818888 R 318586 CDS YP_916578.1 119385522 4581377 complement(2820352..2821158) 1 NC_008686.1 catalyzes the reduction of 2,3-dihydrodipicolinate to 2,3,4,5-tetrahydrodipicolinate in lysine and diaminopimelate biosynthesis; dihydrodipicolinate reductase 2821158 4581377 Pden_2798 Paracoccus denitrificans PD1222 dihydrodipicolinate reductase YP_916578.1 2820352 R 318586 CDS YP_916579.1 119385523 4581378 2821228..2821644 1 NC_008686.1 associates with free 30S ribosomal subunits; essential for efficient processing of 16S rRNA; in Escherichia coli rbfA is induced by cold shock; ribosome-binding factor A 2821644 rbfA 4581378 rbfA Paracoccus denitrificans PD1222 ribosome-binding factor A YP_916579.1 2821228 D 318586 CDS YP_916580.1 119385524 4581379 2821634..2822389 1 NC_008686.1 KEGG: rsp:RSP_1107 hypothetical protein; hypothetical protein 2822389 4581379 Pden_2800 Paracoccus denitrificans PD1222 hypothetical protein YP_916580.1 2821634 D 318586 CDS YP_916581.1 119385525 4581380 2822391..2823287 1 NC_008686.1 catalyzes isomerization of specific uridines in RNA to pseudouridine; responsible for residues in T loops of many tRNAs; tRNA pseudouridine synthase B 2823287 truB 4581380 truB Paracoccus denitrificans PD1222 tRNA pseudouridine synthase B YP_916581.1 2822391 D 318586 CDS YP_916582.1 119385526 4581381 complement(2823284..2824120) 1 NC_008686.1 KEGG: sme:SMc02687 hypothetical protein; hypothetical protein 2824120 4581381 Pden_2802 Paracoccus denitrificans PD1222 hypothetical protein YP_916582.1 2823284 R 318586 CDS YP_916583.1 119385527 4581382 complement(2824229..2825167) 1 NC_008686.1 PFAM: beta-lactamase domain protein; KEGG: rsp:RSP_0799 hypothetical protein; beta-lactamase domain-containing protein 2825167 4581382 Pden_2803 Paracoccus denitrificans PD1222 beta-lactamase domain-containing protein YP_916583.1 2824229 R 318586 CDS YP_916584.1 119385528 4581383 complement(2825242..2825889) 1 NC_008686.1 PFAM: pseudouridine synthase; KEGG: rsp:RSP_1506 pseudouridine synthase, Rlu; pseudouridylate synthase 2825889 4581383 Pden_2804 Paracoccus denitrificans PD1222 pseudouridylate synthase YP_916584.1 2825242 R 318586 CDS YP_916585.1 119385529 4581384 complement(2825886..2826512) 1 NC_008686.1 PFAM: Lysine exporter protein (LYSE/YGGA); KEGG: rru:Rru_A3172 lysine exporter protein (LysE/YggA); lysine exporter protein LysE/YggA 2826512 4581384 Pden_2805 Paracoccus denitrificans PD1222 lysine exporter protein LysE/YggA YP_916585.1 2825886 R 318586 CDS YP_916586.1 119385530 4581385 complement(2826562..2826957) 1 NC_008686.1 PFAM: glutathione-dependent formaldehyde-activating, GFA; KEGG: sit:TM1040_0070 glutathione-dependent formaldehyde-activating, GFA; glutathione-dependent formaldehyde-activating protein 2826957 4581385 Pden_2806 Paracoccus denitrificans PD1222 glutathione-dependent formaldehyde-activating protein YP_916586.1 2826562 R 318586 CDS YP_916587.1 119385531 4581386 complement(2826935..2827387) 1 NC_008686.1 KEGG: rde:RD1_0024 hypothetical protein; hypothetical protein 2827387 4581386 Pden_2807 Paracoccus denitrificans PD1222 hypothetical protein YP_916587.1 2826935 R 318586 CDS YP_916588.1 119385532 4581387 complement(2827435..2827812) 1 NC_008686.1 hypothetical protein 2827812 4581387 Pden_2808 Paracoccus denitrificans PD1222 hypothetical protein YP_916588.1 2827435 R 318586 CDS YP_916589.1 119385533 4581388 complement(2827915..2828736) 1 NC_008686.1 PFAM: NAD-dependent epimerase/dehydratase; 3-beta hydroxysteroid dehydrogenase/isomerase; dTDP-4-dehydrorhamnose reductase; KEGG: rsp:RSP_2567 sulfolipid biosynthesis protein; NAD-dependent epimerase/dehydratase 2828736 4581388 Pden_2809 Paracoccus denitrificans PD1222 NAD-dependent epimerase/dehydratase YP_916589.1 2827915 R 318586 CDS YP_916590.1 119385534 4581389 complement(2828733..2829587) 1 NC_008686.1 PFAM: glycosyl transferase, family 8; KEGG: rsp:RSP_2568 glycosyl transferase (sulfolipid biosynthesis) protein; glycosyl transferase family protein 2829587 4581389 Pden_2810 Paracoccus denitrificans PD1222 glycosyl transferase family protein YP_916590.1 2828733 R 318586 CDS YP_916591.1 119385535 4581390 complement(2829584..2830804) 1 NC_008686.1 PFAM: NAD-dependent epimerase/dehydratase; KEGG: rsp:RSP_2569 sulfolipid (UDP-sulfoquinovose) biosynthesis protein; NAD-dependent epimerase/dehydratase 2830804 4581390 Pden_2811 Paracoccus denitrificans PD1222 NAD-dependent epimerase/dehydratase YP_916591.1 2829584 R 318586 CDS YP_916592.1 119385536 4581391 2830922..2831401 1 NC_008686.1 TIGRFAM: transcriptional regulator, Rrf2 family; PFAM: protein of unknown function UPF0074; KEGG: rru:Rru_A3399 transcriptional regulator, BadM/Rrf2 family; BadM/Rrf2 family transcriptional regulator 2831401 4581391 Pden_2812 Paracoccus denitrificans PD1222 BadM/Rrf2 family transcriptional regulator YP_916592.1 2830922 D 318586 CDS YP_916593.1 119385537 4581392 2831555..2832403 1 NC_008686.1 AroE; catalyzes the conversion of shikimate to 3-dehydroshikimate; shikimate 5-dehydrogenase 2832403 aroE 4581392 aroE Paracoccus denitrificans PD1222 shikimate 5-dehydrogenase YP_916593.1 2831555 D 318586 CDS YP_916594.1 119385538 4581393 2832400..2832996 1 NC_008686.1 KEGG: rsp:RSP_1235 dephospho-CoA kinase; TIGRFAM: dephospho-CoA kinase; PFAM: Dephospho-CoA kinase; dephospho-CoA kinase 2832996 4581393 Pden_2814 Paracoccus denitrificans PD1222 dephospho-CoA kinase YP_916594.1 2832400 D 318586 CDS YP_916595.1 119385539 4581394 2832989..2833708 1 NC_008686.1 KEGG: rde:RD1_0440 DNA polymerase III, epsilon subunit; TIGRFAM: DNA polymerase III, epsilon subunit; PFAM: Exonuclease, RNase T and DNA polymerase III; SMART: Exonuclease; DNA polymerase III subunit epsilon 2833708 4581394 Pden_2815 Paracoccus denitrificans PD1222 DNA polymerase III subunit epsilon YP_916595.1 2832989 D 318586 CDS YP_916596.1 119385540 4581395 2833781..2834662 1 NC_008686.1 TIGRFAM: ribonuclease BN; PFAM: ribonuclease BN; KEGG: rde:RD1_0088 ribonuclease BN; ribonuclease BN 2834662 4581395 Pden_2816 Paracoccus denitrificans PD1222 ribonuclease BN YP_916596.1 2833781 D 318586 CDS YP_916597.1 119385541 4581396 2834698..2835090 1 NC_008686.1 PFAM: glutathione-dependent formaldehyde-activating, GFA; KEGG: pae:PA2722 hypothetical protein; glutathione-dependent formaldehyde-activating protein 2835090 4581396 Pden_2817 Paracoccus denitrificans PD1222 glutathione-dependent formaldehyde-activating protein YP_916597.1 2834698 D 318586 CDS YP_916598.1 119385542 4581397 complement(2835095..2835727) 1 NC_008686.1 PFAM: Lysine exporter protein (LYSE/YGGA); KEGG: pen:PSEEN2025 transporter, LysE family; lysine exporter protein LysE/YggA 2835727 4581397 Pden_2818 Paracoccus denitrificans PD1222 lysine exporter protein LysE/YggA YP_916598.1 2835095 R 318586 CDS YP_916599.1 119385543 4581398 complement(2835831..2837624) 1 NC_008686.1 PFAM: ATP-binding region, ATPase domain protein domain protein; histidine kinase, HAMP region domain protein; histidine kinase, dimerisation/phosphoacceptor; KEGG: rsp:RSP_1271 periplasmic sensor signal transduction histidine kinase; signal transduction histidine kinase 2837624 4581398 Pden_2819 Paracoccus denitrificans PD1222 signal transduction histidine kinase YP_916599.1 2835831 R 318586 CDS YP_916600.1 119385544 4581399 complement(2837634..2838227) 1 NC_008686.1 Bacteria have multiple sigma factors which are active under specific conditions; the sigma factor binds with the catalytic core of RNA polymerase to produce the holoenzyme and directs bacterial core RNA polymerase to specific promoter elements to initiate transcription; RNA polymerase sigma factor 2838227 4581399 Pden_2820 Paracoccus denitrificans PD1222 RNA polymerase sigma factor YP_916600.1 2837634 R 318586 CDS YP_916601.1 119385545 4581152 complement(2838233..2838379) 1 NC_008686.1 KEGG: rsp:RSP_1273 hypothetical protein; hypothetical protein 2838379 4581152 Pden_2821 Paracoccus denitrificans PD1222 hypothetical protein YP_916601.1 2838233 R 318586 CDS YP_916602.1 119385546 4581153 2838473..2839276 1 NC_008686.1 in Caulobacter crescentus, CC3477 is differentially expressed in minimal salts media with glucose as compared to complex media; two-component response regulator 2839276 4581153 Pden_2822 Paracoccus denitrificans PD1222 two-component response regulator YP_916602.1 2838473 D 318586 CDS YP_916603.1 119385547 4581154 complement(2839399..2840286) 1 NC_008686.1 PFAM: 2-nitropropane dioxygenase, NPD; KEGG: jan:Jann_2812 2-nitropropane dioxygenase, NPD; 2-nitropropane dioxygenase 2840286 4581154 Pden_2823 Paracoccus denitrificans PD1222 2-nitropropane dioxygenase YP_916603.1 2839399 R 318586 CDS YP_916604.1 119385548 4581155 complement(2840283..2841512) 1 NC_008686.1 PFAM: aldo/keto reductase; KEGG: sil:SPO1433 oxidoreductase, aldo/keto reductase family; aldo/keto reductase 2841512 4581155 Pden_2824 Paracoccus denitrificans PD1222 aldo/keto reductase YP_916604.1 2840283 R 318586 CDS YP_916605.1 119385549 4581156 complement(2841629..2843560) 1 NC_008686.1 TIGRFAM: selenocysteine-specific translation elongation factor; small GTP-binding protein; PFAM: protein synthesis factor, GTP-binding; elongation factor Tu, domain 2 protein; KEGG: sme:SMa0015 SelB selenocysteine-specific elongation factor; selenocysteine-specific translation elongation factor 2843560 4581156 Pden_2825 Paracoccus denitrificans PD1222 selenocysteine-specific translation elongation factor YP_916605.1 2841629 R 318586 CDS YP_916606.1 119385550 4581157 complement(2843580..2844488) 1 NC_008686.1 TIGRFAM: formate dehydrogenase accessory protein FdhE; PFAM: formate dehydrogenase accessory protein; KEGG: sme:SMa0009 probable FdhE formate formation; formate dehydrogenase accessory protein FdhE 2844488 4581157 Pden_2826 Paracoccus denitrificans PD1222 formate dehydrogenase accessory protein FdhE YP_916606.1 2843580 R 318586 CDS YP_916607.1 119385551 4581158 complement(2844513..2845199) 1 NC_008686.1 TIGRFAM: formate dehydrogenase, gamma subunit; KEGG: sme:SMa0007 probable FdoI formate dehydrogenase-O,gamma subunit; formate dehydrogenase subunit gamma 2845199 4581158 Pden_2827 Paracoccus denitrificans PD1222 formate dehydrogenase subunit gamma YP_916607.1 2844513 R 318586 CDS YP_916608.1 119385552 4581159 complement(2845199..2846197) 1 NC_008686.1 TIGRFAM: formate dehydrogenase, beta subunit; PFAM: 4Fe-4S ferredoxin, iron-sulfur binding domain protein; KEGG: sme:SMa0005 probable FdoH formate dehydrogenase-O, beta subunit; formate dehydrogenase subunit beta 2846197 4581159 Pden_2828 Paracoccus denitrificans PD1222 formate dehydrogenase subunit beta YP_916608.1 2845199 R 318586 CDS YP_916609.1 119385553 4581160 complement(2846194..2848656) 1 NC_008686.1 KEGG: sme:SMa0002 probable FdoG formate dehydrogenase-O alpha subunit; TIGRFAM: formate dehydrogenase, alpha subunit; PFAM: molybdopterin oxidoreductase; molydopterin dinucleotide-binding region; formate dehydrogenase subunit alpha 2848656 4581160 Pden_2829 Paracoccus denitrificans PD1222 formate dehydrogenase subunit alpha YP_916609.1 2846194 R 318586 CDS YP_916610.1 119385554 4581161 complement(2848678..2849277) 1 NC_008686.1 PFAM: molybdopterin oxidoreductase Fe4S4 region; KEGG: sme:SMa0002 probable FdoG formate dehydrogenase-O alpha subunit; molybdopterin oxidoreductase Fe4S4 region 2849277 4581161 Pden_2830 Paracoccus denitrificans PD1222 molybdopterin oxidoreductase Fe4S4 region YP_916610.1 2848678 R 318586 CDS YP_916611.1 119385555 4581162 complement(2849430..2850506) 1 NC_008686.1 PFAM: ferredoxin; oxidoreductase FAD/NAD(P)-binding domain protein; Oxidoreductase FAD-binding domain protein; KEGG: rsp:RSP_3979 ferredoxin; ferredoxin 2850506 4581162 Pden_2831 Paracoccus denitrificans PD1222 ferredoxin YP_916611.1 2849430 R 318586 CDS YP_916612.1 119385556 4581163 complement(2850506..2851744) 1 NC_008686.1 PFAM: Rieske [2Fe-2S] domain protein; KEGG: sit:TM1040_3219 Rieske (2Fe-2S) region; Rieske (2Fe-2S) domain-containing protein 2851744 4581163 Pden_2832 Paracoccus denitrificans PD1222 Rieske (2Fe-2S) domain-containing protein YP_916612.1 2850506 R 318586 CDS YP_916613.1 119385558 4581400 405..1751 1 NC_008687.1 binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication; can also affect transcription of multiple genes including itself.; chromosomal replication initiation protein 1751 dnaA 4581400 dnaA Paracoccus denitrificans PD1222 chromosomal replication initiation protein YP_916613.1 405 D 318586 CDS YP_916614.1 119385559 4581401 1843..2961 1 NC_008687.1 binds the polymerase to DNA and acts as a sliding clamp; DNA polymerase III subunit beta 2961 4581401 Pden_2834 Paracoccus denitrificans PD1222 DNA polymerase III subunit beta YP_916614.1 1843 D 318586 CDS YP_916615.1 119385560 4581402 2958..4034 1 NC_008687.1 Required for DNA replication; binds preferentially to single-stranded, linear DNA; recombination protein F 4034 recF 4581402 recF Paracoccus denitrificans PD1222 recombination protein F YP_916615.1 2958 D 318586 CDS YP_916616.1 119385561 4581403 complement(4068..5861) 1 NC_008687.1 KEGG: sit:TM1040_2799 adenine deaminase; TIGRFAM: adenine deaminase; PFAM: amidohydrolase; adenine deaminase 5861 4581403 Pden_2836 Paracoccus denitrificans PD1222 adenine deaminase YP_916616.1 4068 R 318586 CDS YP_916617.1 119385562 4581404 5907..6635 1 NC_008687.1 involved in DNA repair and RecFOR pathway recombination; RecFOR proteins displace ssDNA-binding protein and facilitate the production of RecA-coated ssDNA; DNA repair protein RecO 6635 recO 4581404 recO Paracoccus denitrificans PD1222 DNA repair protein RecO YP_916617.1 5907 D 318586 CDS YP_916618.1 119385563 4581425 complement(6604..6987) 1 NC_008687.1 PFAM: protein of unknown function DUF306, Meta and HslJ; KEGG: sil:SPO3197 hypothetical protein; hypothetical protein 6987 4581425 Pden_2838 Paracoccus denitrificans PD1222 hypothetical protein YP_916618.1 6604 R 318586 CDS YP_916619.1 119385564 4581426 complement(7020..7439) 1 NC_008687.1 PFAM: protein of unknown function DUF306, Meta and HslJ; hypothetical protein 7439 4581426 Pden_2839 Paracoccus denitrificans PD1222 hypothetical protein YP_916619.1 7020 R 318586 CDS YP_916620.1 119385565 4581427 complement(7517..9172) 1 NC_008687.1 PFAM: acyl-CoA dehydrogenase domain protein; Acyl-CoA dehydrogenase, type 2, C-terminal domain; KEGG: rsp:RSP_1679 acyl-CoA dehydrogenase; acyl-CoA dehydrogenase 9172 4581427 Pden_2840 Paracoccus denitrificans PD1222 acyl-CoA dehydrogenase YP_916620.1 7517 R 318586 CDS YP_916621.1 119385566 4581428 9330..10103 1 NC_008687.1 PFAM: protein of unknown function DUF81; KEGG: sit:TM1040_2445 protein of unknown function DUF81; hypothetical protein 10103 4581428 Pden_2841 Paracoccus denitrificans PD1222 hypothetical protein YP_916621.1 9330 D 318586 CDS YP_916622.1 119385567 4581429 10132..11280 1 NC_008687.1 dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase (DapE), catalyzes the hydrolysis of N-succinyl-L,Ldiaminopimelate L,L-SDAP to L,L-diaminopimelate and succinate. It is a metalloprotease containing dinuclear active sites. Its structure is similar to the carboxypeptidase G2 from Pseudomonas sp. strain RS-16 and the aminopeptidase from Aeromonas proteolytica.; succinyl-diaminopimelate desuccinylase 11280 4581429 Pden_2842 Paracoccus denitrificans PD1222 succinyl-diaminopimelate desuccinylase YP_916622.1 10132 D 318586 CDS YP_916623.1 119385568 4581430 11277..11696 1 NC_008687.1 PFAM: GCN5-related N-acetyltransferase; KEGG: rsp:RSP_1127 acetyltransferase, GNAT family; N-acetyltransferase GCN5 11696 4581430 Pden_2843 Paracoccus denitrificans PD1222 N-acetyltransferase GCN5 YP_916623.1 11277 D 318586 CDS YP_916624.1 119385569 4581431 11693..12208 1 NC_008687.1 KEGG: rsp:RSP_1006 hypothetical protein; hypothetical protein 12208 4581431 Pden_2844 Paracoccus denitrificans PD1222 hypothetical protein YP_916624.1 11693 D 318586 CDS YP_916625.1 119385570 4581432 12258..13637 1 NC_008687.1 TIGRFAM: glutamate--cysteine ligase; PFAM: glutamate--cysteine ligase, GCS2; KEGG: sil:SPO3626 glutamate--cysteine ligase; glutamate--cysteine ligase 13637 4581432 Pden_2845 Paracoccus denitrificans PD1222 glutamate--cysteine ligase YP_916625.1 12258 D 318586 CDS YP_916626.1 119385571 4581433 complement(13690..14103) 1 NC_008687.1 KEGG: jan:Jann_1905 hypothetical protein; hypothetical protein 14103 4581433 Pden_2846 Paracoccus denitrificans PD1222 hypothetical protein YP_916626.1 13690 R 318586 CDS YP_916627.1 119385572 4581434 complement(14216..14827) 1 NC_008687.1 PFAM: regulatory protein, TetR; KEGG: rsp:RSP_0014 transcriptional regulator, TetR family; TetR family transcriptional regulator 14827 4581434 Pden_2847 Paracoccus denitrificans PD1222 TetR family transcriptional regulator YP_916627.1 14216 R 318586 CDS YP_916628.1 119385573 4581435 complement(14837..15127) 1 NC_008687.1 TIGRFAM: phosphocarrier, HPr family; PFAM: phosphocarrier HPr protein; KEGG: rsp:RSP_1686 phosphocarrier HPr protein; phosphotransferase system, phosphocarrier protein HPr 15127 4581435 Pden_2848 Paracoccus denitrificans PD1222 phosphotransferase system, phosphocarrier protein HPr YP_916628.1 14837 R 318586 CDS YP_916629.1 119385574 4581436 complement(15124..15549) 1 NC_008687.1 PFAM: PTS system fructose subfamily IIA component; KEGG: sil:SPO0714 PTS system IIA component, Man family; PTS system fructose subfamily transporter subunit IIA 15549 4581436 Pden_2849 Paracoccus denitrificans PD1222 PTS system fructose subfamily transporter subunit IIA YP_916629.1 15124 R 318586 CDS YP_916630.1 119385575 4581437 complement(15574..16533) 1 NC_008687.1 PFAM: Uncharacterized P-loop ATPase UPF0042; KEGG: rsp:RSP_1684 hypothetical protein; hypothetical protein 16533 4581437 Pden_2850 Paracoccus denitrificans PD1222 hypothetical protein YP_916630.1 15574 R 318586 CDS YP_916631.1 119385576 4581438 complement(16542..16970) 1 NC_008687.1 KEGG: sil:SPO0712 HPr serine kinase/phosphatase domain protein; HPr kinase 16970 4581438 Pden_2851 Paracoccus denitrificans PD1222 HPr kinase YP_916631.1 16542 R 318586 CDS YP_916632.1 119385577 4581439 17197..18795 1 NC_008687.1 PEP carboxykinase; PEP carboxylase; PEPCK; catalyzes the phosphorylation and decarboxylation of oxaloacetate to form phosphoenolpyruvate using ATP; phosphoenolpyruvate carboxykinase 18795 4581439 Pden_2852 Paracoccus denitrificans PD1222 phosphoenolpyruvate carboxykinase YP_916632.1 17197 D 318586 CDS YP_916633.1 119385578 4581440 complement(18955..21219) 1 NC_008687.1 KEGG: rsp:RSP_1126 exoribonuclease R; TIGRFAM: VacB and RNase II family 3'-5' exoribonucleases; ribonuclease R; PFAM: ribonuclease II; RNA binding S1 domain protein; ribonuclease R 21219 4581440 Pden_2853 Paracoccus denitrificans PD1222 ribonuclease R YP_916633.1 18955 R 318586 CDS YP_916634.1 119385579 4581441 complement(21264..21485) 1 NC_008687.1 KEGG: sme:SMc03086 NAD-dependent formate dehydrogenase delta subunit protein; NAD-dependent formate dehydrogenase delta subunit protein 21485 4581441 Pden_2854 Paracoccus denitrificans PD1222 NAD-dependent formate dehydrogenase delta subunit protein YP_916634.1 21264 R 318586 CDS YP_916635.1 119385580 4581442 complement(21492..22313) 1 NC_008687.1 TIGRFAM: formate dehydrogenase family accessory protein FdhD; PFAM: formate dehydrogenase, subunit FdhD; KEGG: rpd:RPD_0622 formate dehydrogenase family accessory protein FdhD; formate dehydrogenase family accessory protein FdhD 22313 4581442 Pden_2855 Paracoccus denitrificans PD1222 formate dehydrogenase family accessory protein FdhD YP_916635.1 21492 R 318586 CDS YP_916636.1 119385581 4581443 complement(22318..25197) 1 NC_008687.1 TIGRFAM: formate dehydrogenase, alpha subunit; PFAM: ferredoxin; 4Fe-4S ferredoxin, iron-sulfur binding domain protein; molybdopterin oxidoreductase; molydopterin dinucleotide-binding region; molybdopterin oxidoreductase Fe4S4 region; KEGG: rsp:RSP_1080 NAD-dependent formate dehydrogenase, alpha subunit; formate dehydrogenase subunit alpha 25197 4581443 Pden_2856 Paracoccus denitrificans PD1222 formate dehydrogenase subunit alpha YP_916636.1 22318 R 318586 CDS YP_916637.1 119385582 4581444 complement(25194..26735) 1 NC_008687.1 PFAM: Respiratory-chain NADH dehydrogenase domain, 51 kDa subunit; KEGG: rsp:RSP_1079 NAD dependent formate dehydrogenase, beta subunit (51 kDa); NADH dehydrogenase (quinone) 26735 4581444 Pden_2857 Paracoccus denitrificans PD1222 NADH dehydrogenase (quinone) YP_916637.1 25194 R 318586 CDS YP_916638.1 119385583 4581445 complement(26732..27211) 1 NC_008687.1 PFAM: NADH dehydrogenase (ubiquinone), 24 kDa subunit; KEGG: gbe:GbCGDNIH1_1932 NAD-dependent formate dehydrogenase gamma subunit (FdsG); NADH dehydrogenase (ubiquinone), 24 kDa subunit 27211 4581445 Pden_2858 Paracoccus denitrificans PD1222 NADH dehydrogenase (ubiquinone), 24 kDa subunit YP_916638.1 26732 R 318586 CDS YP_916639.1 119385584 4581446 complement(27287..28159) 1 NC_008687.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: rsp:RSP_1077 transcriptional regulator, LysR family; LysR family transcriptional regulator 28159 4581446 Pden_2859 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_916639.1 27287 R 318586 CDS YP_916640.1 119385585 4581447 complement(28248..28487) 1 NC_008687.1 TIGRFAM: phosphoribosylformylglycinamidine synthase, purS; PFAM: phosphoribosylformylglycinamidine synthetase PurS; KEGG: rsp:RSP_2127 component of phosphoribosylformylglycinamidine (FGAM) synthetase; phosphoribosylformylglycinamidine synthase PurS 28487 4581447 Pden_2860 Paracoccus denitrificans PD1222 phosphoribosylformylglycinamidine synthase PurS YP_916640.1 28248 R 318586 CDS YP_916641.1 119385586 4581448 complement(28499..29263) 1 NC_008687.1 catalyzes the formation of (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4- carboxamido)succinate from 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate and L-aspartate in purine biosynthesis; SAICAR synthase; phosphoribosylaminoimidazole-succinocarboxamide synthase 29263 4581448 Pden_2861 Paracoccus denitrificans PD1222 phosphoribosylaminoimidazole-succinocarboxamide synthase YP_916641.1 28499 R 318586 CDS YP_916642.1 119385587 4581449 29411..29725 1 NC_008687.1 PFAM: protein of unknown function DUF1476; KEGG: sil:SPO1886 hypothetical protein; hypothetical protein 29725 4581449 Pden_2862 Paracoccus denitrificans PD1222 hypothetical protein YP_916642.1 29411 D 318586 CDS YP_916643.1 119385588 4581450 complement(29772..31109) 1 NC_008687.1 TIGRFAM: MATE efflux family protein; PFAM: multi antimicrobial extrusion protein MatE; KEGG: rsp:RSP_2204 multidrug efflux pump, MATE family; MATE efflux family protein 31109 4581450 Pden_2863 Paracoccus denitrificans PD1222 MATE efflux family protein YP_916643.1 29772 R 318586 CDS YP_916644.1 119385589 4581451 complement(31102..31605) 1 NC_008687.1 PFAM: thioesterase superfamily protein; KEGG: rsp:RSP_2203 hypothetical protein; thioesterase superfamily protein 31605 4581451 Pden_2864 Paracoccus denitrificans PD1222 thioesterase superfamily protein YP_916644.1 31102 R 318586 CDS YP_916645.1 119385590 4581452 complement(31607..32110) 1 NC_008687.1 TIGRFAM: uncharacterized domain 1; PFAM: thioesterase superfamily protein; KEGG: sil:SPO2911 thioesterase family protein; hypothetical protein 32110 4581452 Pden_2865 Paracoccus denitrificans PD1222 hypothetical protein YP_916645.1 31607 R 318586 CDS YP_916646.1 119385591 4581453 32188..32604 1 NC_008687.1 PFAM: regulatory protein, MerR; KEGG: rsp:RSP_2201 transcriptional regulator, MerR family; MerR family transcriptional regulator 32604 4581453 Pden_2866 Paracoccus denitrificans PD1222 MerR family transcriptional regulator YP_916646.1 32188 D 318586 CDS YP_916647.1 119385592 4581454 32576..33085 1 NC_008687.1 PFAM: regulatory protein, MerR; KEGG: sit:TM1040_1556 transcriptional regulator, MerR family; MerR family transcriptional regulator 33085 4581454 Pden_2867 Paracoccus denitrificans PD1222 MerR family transcriptional regulator YP_916647.1 32576 D 318586 CDS YP_916648.1 119385593 4581455 33110..34888 1 NC_008687.1 PFAM: acyl-CoA dehydrogenase domain protein; KEGG: rsp:RSP_2199 acyl-CoA dehydrogenase; acyl-CoA dehydrogenase 34888 4581455 Pden_2868 Paracoccus denitrificans PD1222 acyl-CoA dehydrogenase YP_916648.1 33110 D 318586 CDS YP_916649.1 119385594 4581456 35165..35806 1 NC_008687.1 PFAM: Glutathione S-transferase, N-terminal domain; Glutathione S-transferase, C-terminal domain; KEGG: sit:TM1040_1560 glutathione S-transferase-like; glutathione S-transferase domain-containing protein 35806 4581456 Pden_2869 Paracoccus denitrificans PD1222 glutathione S-transferase domain-containing protein YP_916649.1 35165 D 318586 CDS YP_916650.1 119385595 4581457 35803..37014 1 NC_008687.1 Catalyzes the synthesis of acetoacetyl coenzyme A from two molecules of acetyl coenzyme A. It can also act as a thiolase, catalyzing the reverse reaction and generating two-carbon units from the four-carbon product of fatty acid oxidation; acetyl-CoA acetyltransferase 37014 4581457 Pden_2870 Paracoccus denitrificans PD1222 acetyl-CoA acetyltransferase YP_916650.1 35803 D 318586 CDS YP_916651.1 119385596 4581458 37026..39209 1 NC_008687.1 PFAM: Enoyl-CoA hydratase/isomerase; 3-hydroxyacyl-CoA dehydrogenase domain protein; 3-hydroxyacyl-CoA dehydrogenase, NAD-binding; KEGG: rsp:RSP_2196 enoyl-CoA hydratase / 3-hydroxyacyl-CoA dehydrogenase / 3-hydroxybutyryl-CoA epimerase; 3-hydroxyacyl-CoA dehydrogenase 39209 4581458 Pden_2871 Paracoccus denitrificans PD1222 3-hydroxyacyl-CoA dehydrogenase YP_916651.1 37026 D 318586 CDS YP_916652.1 119385597 4581459 complement(39349..40356) 1 NC_008687.1 PFAM: PfkB domain protein; KEGG: jan:Jann_1671 PfkB; ribokinase-like domain-containing protein 40356 4581459 Pden_2872 Paracoccus denitrificans PD1222 ribokinase-like domain-containing protein YP_916652.1 39349 R 318586 CDS YP_916653.1 119385598 4581460 complement(40353..41021) 1 NC_008687.1 KEGG: rsp:RSP_1031 endonuclease III; TIGRFAM: endonuclease III; PFAM: helix-hairpin-helix motif; HhH-GPD family protein; SMART: iron-sulfur cluster loop; endonuclease III 41021 4581460 Pden_2873 Paracoccus denitrificans PD1222 endonuclease III YP_916653.1 40353 R 318586 CDS YP_916654.1 119385599 4581461 41122..41718 1 NC_008687.1 TIGRFAM: methylated-DNA--protein-cysteine methyltransferase; PFAM: methylated-DNA-[protein]-cysteine S-methyltransferase; KEGG: sit:TM1040_2450 transcriptional regulator, AraC family; methylated-DNA--protein-cysteine methyltransferase 41718 4581461 Pden_2874 Paracoccus denitrificans PD1222 methylated-DNA--protein-cysteine methyltransferase YP_916654.1 41122 D 318586 CDS YP_916655.1 119385600 4581462 41880..42527 1 NC_008687.1 PFAM: OmpA/MotB domain protein; KEGG: rde:RD1_0967 OmpA family domain protein; OmpA/MotB domain-containing protein 42527 4581462 Pden_2875 Paracoccus denitrificans PD1222 OmpA/MotB domain-containing protein YP_916655.1 41880 D 318586 CDS YP_916656.1 119385601 4581463 complement(42697..43251) 1 NC_008687.1 produces ATP from ADP in the presence of a proton gradient across the membrane; subunit B is part of the membrane proton channel.; F0F1 ATP synthase subunit B 43251 4581463 Pden_2876 Paracoccus denitrificans PD1222 F0F1 ATP synthase subunit B YP_916656.1 42697 R 318586 CDS YP_916657.1 119385602 4581405 complement(43248..43895) 1 NC_008687.1 produces ATP from ADP in the presence of a proton gradient across the membrane; subunit B' is part of the membrane proton channel.; F0F1 ATP synthase subunit B' 43895 4581405 Pden_2877 Paracoccus denitrificans PD1222 F0F1 ATP synthase subunit B' YP_916657.1 43248 R 318586 CDS YP_916658.1 119385603 4581406 complement(43975..44208) 1 NC_008687.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit C is part of the membrane proton channel F0; F0F1 ATP synthase subunit C 44208 4581406 Pden_2878 Paracoccus denitrificans PD1222 F0F1 ATP synthase subunit C YP_916658.1 43975 R 318586 CDS YP_916659.1 119385604 4581407 complement(44268..45014) 1 NC_008687.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit A is part of the membrane proton channel F0; F0F1 ATP synthase subunit A 45014 4581407 Pden_2879 Paracoccus denitrificans PD1222 F0F1 ATP synthase subunit A YP_916659.1 44268 R 318586 CDS YP_916660.1 119385605 4581408 complement(45017..45358) 1 NC_008687.1 KEGG: sit:TM1040_2595 ATP synthase F0, subunit I; hypothetical protein 45358 4581408 Pden_2880 Paracoccus denitrificans PD1222 hypothetical protein YP_916660.1 45017 R 318586 CDS YP_916661.1 119385606 4581409 45545..45901 1 NC_008687.1 PFAM: regulatory protein, ArsR; KEGG: sil:SPO3238 transcriptional regulator, ArsR family; regulatory protein ArsR 45901 4581409 Pden_2881 Paracoccus denitrificans PD1222 regulatory protein ArsR YP_916661.1 45545 D 318586 CDS YP_916662.1 119385607 4581410 complement(45967..47568) 1 NC_008687.1 PFAM: metallophosphoesterase; 5'-Nucleotidase domain protein; KEGG: sit:TM1040_1548 5'-nucleotidase-like; 5'-nucleotidase domain-containing protein 47568 4581410 Pden_2882 Paracoccus denitrificans PD1222 5'-nucleotidase domain-containing protein YP_916662.1 45967 R 318586 CDS YP_916663.1 119385608 4581411 47660..48034 1 NC_008687.1 PFAM: protein of unknown function DUF952; KEGG: rsp:RSP_0956 hypothetical protein; hypothetical protein 48034 4581411 Pden_2883 Paracoccus denitrificans PD1222 hypothetical protein YP_916663.1 47660 D 318586 CDS YP_916664.1 119385609 4581412 48031..49089 1 NC_008687.1 catalyzes the conversion of dihydroorotate to orotate in the pyrimidine biosynthesis pathway; uses a flavin nucleotide as an essential cofactor; class 2 enzymes are monomeric and compared to the class 1 class 2 possess an extended N terminus, which plays a role in the membrane association of the enzyme and provides the binding site for the respiratory quinones that serve as physiological electron acceptors; dihydroorotate dehydrogenase 2 49089 4581412 Pden_2884 Paracoccus denitrificans PD1222 dihydroorotate dehydrogenase 2 YP_916664.1 48031 D 318586 CDS YP_916665.1 119385610 4581413 complement(49086..49925) 1 NC_008687.1 KEGG: rsp:RSP_2481 serine acetyltransferase; TIGRFAM: serine O-acetyltransferase; PFAM: transferase hexapeptide repeat containing protein; serine acetyltransferase domain protein; serine O-acetyltransferase 49925 4581413 Pden_2885 Paracoccus denitrificans PD1222 serine O-acetyltransferase YP_916665.1 49086 R 318586 CDS YP_916666.1 119385611 4581414 complement(49990..50712) 1 NC_008687.1 KEGG: jan:Jann_1647 hypothetical protein; hypothetical protein 50712 4581414 Pden_2886 Paracoccus denitrificans PD1222 hypothetical protein YP_916666.1 49990 R 318586 CDS YP_916667.1 119385612 4581415 complement(50705..54595) 1 NC_008687.1 KEGG: rsp:RSP_2479 phage host specificity protein; phage host specificity protein 54595 4581415 Pden_2887 Paracoccus denitrificans PD1222 phage host specificity protein YP_916667.1 50705 R 318586 CDS YP_916668.1 119385613 4581416 complement(54614..55039) 1 NC_008687.1 TIGRFAM: phage cell wall peptidase, NlpC/P60 family; PFAM: NLP/P60 protein; KEGG: rde:RD1_3017 hypothetical protein; NlpC/P60 family phage cell wall peptidase 55039 4581416 Pden_2888 Paracoccus denitrificans PD1222 NlpC/P60 family phage cell wall peptidase YP_916668.1 54614 R 318586 CDS YP_916669.1 119385614 4581417 complement(55036..55854) 1 NC_008687.1 KEGG: sit:TM1040_1070 phage conserved hypothetical protein BR0599; phage protein 55854 4581417 Pden_2889 Paracoccus denitrificans PD1222 phage protein YP_916669.1 55036 R 318586 CDS YP_916670.1 119385615 4581418 complement(55851..56492) 1 NC_008687.1 KEGG: sit:TM1040_1069 conserved hypothetical protein; hypothetical protein 56492 4581418 Pden_2890 Paracoccus denitrificans PD1222 hypothetical protein YP_916670.1 55851 R 318586 CDS YP_916671.1 119385616 4581419 complement(56485..57156) 1 NC_008687.1 KEGG: jan:Jann_1642 phage-related minor tail protein-like; phage-related minor tail protein-like 57156 4581419 Pden_2891 Paracoccus denitrificans PD1222 phage-related minor tail protein-like YP_916671.1 56485 R 318586 CDS YP_916672.1 119385617 4581420 complement(57181..57393) 1 NC_008687.1 KEGG: sit:TM1040_1067 conserved hypothetical protein; hypothetical protein 57393 4581420 Pden_2892 Paracoccus denitrificans PD1222 hypothetical protein YP_916672.1 57181 R 318586 CDS YP_916673.1 119385618 4581421 complement(57390..57707) 1 NC_008687.1 KEGG: sil:SPO2256 hypothetical protein; hypothetical protein 57707 4581421 Pden_2893 Paracoccus denitrificans PD1222 hypothetical protein YP_916673.1 57390 R 318586 CDS YP_916674.1 119385619 4581422 complement(57709..58122) 1 NC_008687.1 TIGRFAM: phage major tail protein, TP901-1 family; KEGG: sit:TM1040_1065 phage major tail protein, TP901-1; TP901-1 family phage major tail protein 58122 4581422 Pden_2894 Paracoccus denitrificans PD1222 TP901-1 family phage major tail protein YP_916674.1 57709 R 318586 CDS YP_916675.1 119385620 4581423 complement(58135..58554) 1 NC_008687.1 KEGG: jan:Jann_1638 hypothetical protein; hypothetical protein 58554 4581423 Pden_2895 Paracoccus denitrificans PD1222 hypothetical protein YP_916675.1 58135 R 318586 CDS YP_916676.1 119385621 4581424 complement(58551..58901) 1 NC_008687.1 KEGG: sil:SPO2259 head-tail adaptor; head-tail adaptor 58901 4581424 Pden_2896 Paracoccus denitrificans PD1222 head-tail adaptor YP_916676.1 58551 R 318586 CDS YP_916677.1 119385622 4581464 complement(58898..59515) 1 NC_008687.1 KEGG: rsp:RSP_2472 hypothetical protein; hypothetical protein 59515 4581464 Pden_2897 Paracoccus denitrificans PD1222 hypothetical protein YP_916677.1 58898 R 318586 CDS YP_916678.1 119385623 4581465 complement(59644..60810) 1 NC_008687.1 TIGRFAM: phage major capsid protein, HK97 family; PFAM: phage major capsid protein, HK97; KEGG: sil:SPO2261 major capsid protein, HK97 family; HK97 family phage major capsid protein 60810 4581465 Pden_2898 Paracoccus denitrificans PD1222 HK97 family phage major capsid protein YP_916678.1 59644 R 318586 CDS YP_916679.1 119385624 4581466 complement(60834..61391) 1 NC_008687.1 TIGRFAM: phage prohead protease, HK97 family; PFAM: peptidase U35, phage prohead HK97; KEGG: rsp:RSP_2470 prohead protease; HK97 family phage prohead protease 61391 4581466 Pden_2899 Paracoccus denitrificans PD1222 HK97 family phage prohead protease YP_916679.1 60834 R 318586 CDS YP_916680.1 119385625 4581467 complement(61372..61605) 1 NC_008687.1 KEGG: rde:RD1_3031 hypothetical protein; hypothetical protein 61605 4581467 Pden_2900 Paracoccus denitrificans PD1222 hypothetical protein YP_916680.1 61372 R 318586 CDS YP_916681.1 119385626 4581468 complement(61607..62809) 1 NC_008687.1 TIGRFAM: phage portal protein, HK97 family; PFAM: phage portal protein; KEGG: rde:RD1_3033 phage portal protein; HK97 family phage portal protein 62809 4581468 Pden_2901 Paracoccus denitrificans PD1222 HK97 family phage portal protein YP_916681.1 61607 R 318586 CDS YP_916682.1 119385627 4581469 complement(62958..64349) 1 NC_008687.1 PFAM: protein of unknown function DUF264; KEGG: rde:RD1_3034 hypothetical protein; hypothetical protein 64349 4581469 Pden_2902 Paracoccus denitrificans PD1222 hypothetical protein YP_916682.1 62958 R 318586 CDS YP_916683.1 119385628 4581470 complement(64871..66049) 1 NC_008687.1 PFAM: aminodeoxychorismate lyase; KEGG: rsp:RSP_2465 hypothetical protein; aminodeoxychorismate lyase 66049 4581470 Pden_2903 Paracoccus denitrificans PD1222 aminodeoxychorismate lyase YP_916683.1 64871 R 318586 CDS YP_916684.1 119385629 4581471 complement(66046..67308) 1 NC_008687.1 FabF; beta-ketoacyl-ACP synthase II, KASII; catalyzes a condensation reaction in fatty acid biosynthesis: addition of an acyl acceptor of two carbons from malonyl-ACP; required for the elongation of short-chain unsaturated acyl-ACP; 3-oxoacyl-ACP synthase 67308 4581471 Pden_2904 Paracoccus denitrificans PD1222 3-oxoacyl-ACP synthase YP_916684.1 66046 R 318586 CDS YP_916685.1 119385630 4581472 complement(67429..68199) 1 NC_008687.1 PFAM: Enoyl-CoA hydratase/isomerase; KEGG: mmc:Mmcs_4156 enoyl-CoA hydratase/isomerase; enoyl-CoA hydratase/isomerase 68199 4581472 Pden_2905 Paracoccus denitrificans PD1222 enoyl-CoA hydratase/isomerase YP_916685.1 67429 R 318586 CDS YP_916686.1 119385631 4581473 complement(68209..69336) 1 NC_008687.1 PFAM: acyl-CoA dehydrogenase domain protein; Acyl-CoA dehydrogenase, type 2, C-terminal domain; KEGG: bms:BRA0447 acyl-CoA dehydrogenase; acyl-CoA dehydrogenase 69336 4581473 Pden_2906 Paracoccus denitrificans PD1222 acyl-CoA dehydrogenase YP_916686.1 68209 R 318586 CDS YP_916687.1 119385632 4581474 complement(69333..70514) 1 NC_008687.1 KEGG: bms:BRA0448 acetyl-CoA acetyltransferase; TIGRFAM: acetyl-CoA acetyltransferases; PFAM: Thiolase; acetyl-CoA acetyltransferase 70514 4581474 Pden_2907 Paracoccus denitrificans PD1222 acetyl-CoA acetyltransferase YP_916687.1 69333 R 318586 CDS YP_916688.1 119385633 4581475 complement(70527..71294) 1 NC_008687.1 PFAM: short-chain dehydrogenase/reductase SDR; KR; KEGG: bms:BRA0449 3-hydroxyacyl-CoA dehydrogenase; short-chain dehydrogenase/reductase SDR 71294 4581475 Pden_2908 Paracoccus denitrificans PD1222 short-chain dehydrogenase/reductase SDR YP_916688.1 70527 R 318586 CDS YP_916689.1 119385634 4581476 complement(71302..72993) 1 NC_008687.1 PFAM: AMP-dependent synthetase and ligase; KEGG: bms:BRA0450 acetyl-CoA synthetase; AMP-dependent synthetase/ligase 72993 4581476 Pden_2909 Paracoccus denitrificans PD1222 AMP-dependent synthetase/ligase YP_916689.1 71302 R 318586 CDS YP_916690.1 119385635 4581477 73096..74118 1 NC_008687.1 PFAM: helix-turn-helix- domain containing protein, AraC type; KEGG: bms:BRA0451 transcriptional regulator, AraC family; helix-turn-helix domain-containing protein 74118 4581477 Pden_2910 Paracoccus denitrificans PD1222 helix-turn-helix domain-containing protein YP_916690.1 73096 D 318586 CDS YP_916691.1 119385636 4581478 complement(74075..75058) 1 NC_008687.1 KEGG: rsp:RSP_1308 hypothetical protein; hypothetical protein 75058 4581478 Pden_2911 Paracoccus denitrificans PD1222 hypothetical protein YP_916691.1 74075 R 318586 CDS YP_916692.1 119385637 4581479 complement(75215..76324) 1 NC_008687.1 KEGG: sil:SPOA0303 replication protein; replication protein 76324 4581479 Pden_2912 Paracoccus denitrificans PD1222 replication protein YP_916692.1 75215 R 318586 CDS YP_916693.1 119385638 4581480 complement(76321..77625) 1 NC_008687.1 PFAM: Cobyrinic acid a,c-diamide synthase; KEGG: sil:SPOA0304 replication protein; cobyrinic acid a,c-diamide synthase 77625 4581480 Pden_2913 Paracoccus denitrificans PD1222 cobyrinic acid a,c-diamide synthase YP_916693.1 76321 R 318586 CDS YP_916694.1 119385639 4581481 78109..78783 1 NC_008687.1 KEGG: sil:SPOA0305 hypothetical protein; hypothetical protein 78783 4581481 Pden_2914 Paracoccus denitrificans PD1222 hypothetical protein YP_916694.1 78109 D 318586 CDS YP_916695.1 119385640 4581482 78876..79133 1 NC_008687.1 KEGG: rsp:RSP_7166 hypothetical protein; hypothetical protein 79133 4581482 Pden_2915 Paracoccus denitrificans PD1222 hypothetical protein YP_916695.1 78876 D 318586 CDS YP_916696.1 119385641 4581483 79269..80231 1 NC_008687.1 KEGG: atc:AGR_L_1708 biotin synthetase; TIGRFAM: biotin synthase; PFAM: Radical SAM domain protein; biotin and thiamin synthesis associated; SMART: Elongator protein 3/MiaB/NifB; biotin synthase 80231 4581483 Pden_2916 Paracoccus denitrificans PD1222 biotin synthase YP_916696.1 79269 D 318586 CDS YP_916697.1 119385642 4581484 80228..81343 1 NC_008687.1 catalyzes the formation of 8-amino-7-oxononanoate from 6-carboxyhexanoyl-CoA and L-alanine; 8-amino-7-oxononanoate synthase 81343 4581484 Pden_2917 Paracoccus denitrificans PD1222 8-amino-7-oxononanoate synthase YP_916697.1 80228 D 318586 CDS YP_916698.1 119385643 4581485 81340..81948 1 NC_008687.1 DTB synthetase; dethiobiotin synthase; involved in production of dethiobiotin from ATP and 7,8-diaminononanoate and carbon dioxide; contains magnesium; dithiobiotin synthetase 81948 bioD 4581485 bioD Paracoccus denitrificans PD1222 dithiobiotin synthetase YP_916698.1 81340 D 318586 CDS YP_916699.1 119385644 4581486 81948..83231 1 NC_008687.1 TIGRFAM: adenosylmethionine-8-amino-7-oxononanoate aminotransferase; PFAM: aminotransferase class-III; KEGG: ngo:NGO0308 adenosylmethionine-8-amino-7-oxononanoate aminotranferase; adenosylmethionine-8-amino-7-oxononanoate aminotransferase 83231 4581486 Pden_2919 Paracoccus denitrificans PD1222 adenosylmethionine-8-amino-7-oxononanoate aminotransferase YP_916699.1 81948 D 318586 CDS YP_916700.1 119385645 4581487 83228..83836 1 NC_008687.1 PFAM: protein of unknown function DUF452; KEGG: nme:NMB0473 hypothetical protein; hypothetical protein 83836 4581487 Pden_2920 Paracoccus denitrificans PD1222 hypothetical protein YP_916700.1 83228 D 318586 CDS YP_916701.1 119385646 4581488 83833..84576 1 NC_008687.1 PFAM: Methyltransferase type 11; Methyltransferase type 12; KEGG: cte:CT0049 biotin synthesis protein; methyltransferase type 11 84576 4581488 Pden_2921 Paracoccus denitrificans PD1222 methyltransferase type 11 YP_916701.1 83833 D 318586 CDS YP_916702.1 119385647 4581489 complement(84573..85238) 1 NC_008687.1 PFAM: regulatory protein GntR, HTH; GntR domain protein; KEGG: mlo:mlr7428 transcription regulator; GntR family transcriptional regulator 85238 4581489 Pden_2922 Paracoccus denitrificans PD1222 GntR family transcriptional regulator YP_916702.1 84573 R 318586 CDS YP_916703.1 119385648 4581490 complement(85282..85866) 1 NC_008687.1 PFAM: 2',5' RNA ligase; KEGG: bxe:Bxe_A1918 ligase; 2'-5' RNA ligase 85866 4581490 Pden_2923 Paracoccus denitrificans PD1222 2'-5' RNA ligase YP_916703.1 85282 R 318586 CDS YP_916704.1 119385649 4581491 complement(85916..86572) 1 NC_008687.1 PFAM: protein of unknown function DUF162; KEGG: rde:RD1_0071 hypothetical protein; hypothetical protein 86572 4581491 Pden_2924 Paracoccus denitrificans PD1222 hypothetical protein YP_916704.1 85916 R 318586 CDS YP_916705.1 119385650 4581492 complement(86569..87984) 1 NC_008687.1 TIGRFAM: iron-sulfur cluster binding protein; PFAM: 4Fe-4S ferredoxin, iron-sulfur binding domain protein; KEGG: rde:RD1_0072 4Fe-4S binding domain protein; iron-sulfur cluster binding protein 87984 4581492 Pden_2925 Paracoccus denitrificans PD1222 iron-sulfur cluster binding protein YP_916705.1 86569 R 318586 CDS YP_916706.1 119385651 4581493 complement(87981..88751) 1 NC_008687.1 PFAM: protein of unknown function DUF224, cysteine-rich region domain protein; KEGG: rde:RD1_0073 hypothetical protein; hypothetical protein 88751 4581493 Pden_2926 Paracoccus denitrificans PD1222 hypothetical protein YP_916706.1 87981 R 318586 CDS YP_916707.1 119385652 4581494 complement(88761..90527) 1 NC_008687.1 TIGRFAM: L-lactate transport; PFAM: L-lactate permease; KEGG: par:Psyc_1653 glycolate/L-lactate:H+ symporter; L-lactate transport 90527 4581494 Pden_2927 Paracoccus denitrificans PD1222 L-lactate transport YP_916707.1 88761 R 318586 CDS YP_916708.1 119385653 4581495 complement(90605..92314) 1 NC_008687.1 component of the membrane-bound D-lactate oxidase, FAD-binding, NADH independent; D-lactate dehydrogenase 92314 4581495 Pden_2928 Paracoccus denitrificans PD1222 D-lactate dehydrogenase YP_916708.1 90605 R 318586 CDS YP_916709.1 119385654 4581496 92529..93302 1 NC_008687.1 PFAM: regulatory protein GntR, HTH; GntR domain protein; Helix-turn-helix, type 11 domain protein; KEGG: mag:amb0238 transcriptional regulator; GntR family transcriptional regulator 93302 4581496 Pden_2929 Paracoccus denitrificans PD1222 GntR family transcriptional regulator YP_916709.1 92529 D 318586 CDS YP_916710.1 119385655 4581497 93367..93633 1 NC_008687.1 KEGG: rsp:RSP_2678 hypothetical protein; hypothetical protein 93633 4581497 Pden_2930 Paracoccus denitrificans PD1222 hypothetical protein YP_916710.1 93367 D 318586 CDS YP_916711.1 119385656 4581498 93763..95139 1 NC_008687.1 TIGRFAM: gluconate transporter; PFAM: Gluconate transporter; Citrate transporter; KEGG: eca:ECA4158 gluconate permease; gluconate transporter 95139 4581498 Pden_2931 Paracoccus denitrificans PD1222 gluconate transporter YP_916711.1 93763 D 318586 CDS YP_916712.1 119385657 4581499 95148..95651 1 NC_008687.1 KEGG: tfu:Tfu_2114 carbohydrate kinase, thermoresistant glucokinase; TIGRFAM: carbohydrate kinase, thermoresistant glucokinase family; PFAM: shikimate kinase; carbohydrate kinase 95651 4581499 Pden_2932 Paracoccus denitrificans PD1222 carbohydrate kinase YP_916712.1 95148 D 318586 CDS YP_916713.1 119385658 4581500 complement(95810..97648) 1 NC_008687.1 catalyzes the dehydration of 2,3-dihydroxy-3-methylbutanoate to 3-methyl-2-oxobutanoate in valine and isoleucine biosynthesis; dihydroxy-acid dehydratase 97648 4581500 Pden_2933 Paracoccus denitrificans PD1222 dihydroxy-acid dehydratase YP_916713.1 95810 R 318586 CDS YP_916714.1 119385659 4581501 complement(97755..98402) 1 NC_008687.1 PFAM: CDP-alcohol phosphatidyltransferase; KEGG: sme:SMc02159 hypothetical protein; CDP-alcohol phosphatidyltransferase 98402 4581501 Pden_2934 Paracoccus denitrificans PD1222 CDP-alcohol phosphatidyltransferase YP_916714.1 97755 R 318586 CDS YP_916715.1 119385660 4581502 complement(98399..99337) 1 NC_008687.1 PFAM: phosphatidate cytidylyltransferase; KEGG: xcv:XCV0555 phosphatidate cytidiltransferase; phosphatidate cytidylyltransferase 99337 4581502 Pden_2935 Paracoccus denitrificans PD1222 phosphatidate cytidylyltransferase YP_916715.1 98399 R 318586 CDS YP_916716.1 119385661 4581503 complement(99341..99973) 1 NC_008687.1 PFAM: phospholipid/glycerol acyltransferase; KEGG: reu:Reut_B4015 phospholipid/glycerol acyltransferase; phospholipid/glycerol acyltransferase 99973 4581503 Pden_2936 Paracoccus denitrificans PD1222 phospholipid/glycerol acyltransferase YP_916716.1 99341 R 318586 CDS YP_916717.1 119385662 4581504 complement(100393..102399) 1 NC_008687.1 PFAM: ABC transporter related; protein of unknown function DUF214; SMART: AAA ATPase; KEGG: rpb:RPB_2235 hypothetical protein; ABC transporter 102399 4581504 Pden_2937 Paracoccus denitrificans PD1222 ABC transporter YP_916717.1 100393 R 318586 CDS YP_916718.1 119385663 4581505 complement(102392..103726) 1 NC_008687.1 TIGRFAM: efflux transporter, RND family, MFP subunit; PFAM: secretion protein HlyD family protein; KEGG: rpc:RPC_1868 secretion protein HlyD; RND family efflux transporter MFP subunit 103726 4581505 Pden_2938 Paracoccus denitrificans PD1222 RND family efflux transporter MFP subunit YP_916718.1 102392 R 318586 CDS YP_916719.1 119385664 4581506 104045..104569 1 NC_008687.1 hypothetical protein 104569 4581506 Pden_2939 Paracoccus denitrificans PD1222 hypothetical protein YP_916719.1 104045 D 318586 CDS YP_916720.1 119385665 4581507 104685..105251 1 NC_008687.1 PFAM: regulatory protein, TetR; KEGG: rru:Rru_A1116 transcriptional regulator, TetR family; TetR family transcriptional regulator 105251 4581507 Pden_2940 Paracoccus denitrificans PD1222 TetR family transcriptional regulator YP_916720.1 104685 D 318586 CDS YP_916721.1 119385666 4581508 105290..106483 1 NC_008687.1 TIGRFAM: efflux transporter, RND family, MFP subunit; PFAM: secretion protein HlyD family protein; KEGG: atc:AGR_L_3215 RND multidrug efflux membrane fusion protein MexC precursor; RND family efflux transporter MFP subunit 106483 4581508 Pden_2941 Paracoccus denitrificans PD1222 RND family efflux transporter MFP subunit YP_916721.1 105290 D 318586 CDS YP_916722.1 119385667 4581509 106488..109613 1 NC_008687.1 TIGRFAM: transporter, hydrophobe/amphiphile efflux-1 (HAE1) family; PFAM: acriflavin resistance protein; KEGG: atc:AGR_L_3217 RND multidrug efflux transporter MexD; hydrophobe/amphiphile efflux-1 (HAE1) family protein 109613 4581509 Pden_2942 Paracoccus denitrificans PD1222 hydrophobe/amphiphile efflux-1 (HAE1) family protein YP_916722.1 106488 D 318586 CDS YP_916723.1 119385668 4581510 109715..111163 1 NC_008687.1 TIGRFAM: RND efflux system, outer membrane lipoprotein, NodT family; PFAM: outer membrane efflux protein; KEGG: atc:AGR_C_4622 hypothetical protein; RND efflux system outer membrane lipoprotein 111163 4581510 Pden_2943 Paracoccus denitrificans PD1222 RND efflux system outer membrane lipoprotein YP_916723.1 109715 D 318586 CDS YP_916724.1 119385669 4581511 111383..113182 1 NC_008687.1 required for the synthesis of the hydromethylpyrimidine moiety of thiamine; thiamine biosynthesis protein ThiC 113182 4581511 Pden_2944 Paracoccus denitrificans PD1222 thiamine biosynthesis protein ThiC YP_916724.1 111383 D 318586 CDS YP_916725.1 119385670 4581512 complement(113238..113993) 1 NC_008687.1 PFAM: Exopolysaccharide synthesis, ExoD; KEGG: mes:Meso_1827 exopolysaccharide synthesis, ExoD; exopolysaccharide synthesis, ExoD 113993 4581512 Pden_2945 Paracoccus denitrificans PD1222 exopolysaccharide synthesis, ExoD YP_916725.1 113238 R 318586 CDS YP_916726.1 119385671 4581513 complement(114101..115021) 1 NC_008687.1 PFAM: PfkB domain protein; KEGG: rsp:RSP_2257 fructokinase; ribokinase-like domain-containing protein 115021 4581513 Pden_2946 Paracoccus denitrificans PD1222 ribokinase-like domain-containing protein YP_916726.1 114101 R 318586 CDS YP_916727.1 119385672 4581514 complement(115042..116349) 1 NC_008687.1 KEGG: rsp:RSP_2260 hypothetical protein; hypothetical protein 116349 4581514 Pden_2947 Paracoccus denitrificans PD1222 hypothetical protein YP_916727.1 115042 R 318586 CDS YP_916728.1 119385673 4581515 complement(116359..117489) 1 NC_008687.1 KEGG: rsp:RSP_2261 antifreeze protein, type I; antifreeze protein, type I 117489 4581515 Pden_2948 Paracoccus denitrificans PD1222 antifreeze protein, type I YP_916728.1 116359 R 318586 CDS YP_916729.1 119385674 4581516 complement(117505..118170) 1 NC_008687.1 hypothetical protein 118170 4581516 Pden_2949 Paracoccus denitrificans PD1222 hypothetical protein YP_916729.1 117505 R 318586 CDS YP_916730.1 119385675 4581517 complement(118177..119208) 1 NC_008687.1 KEGG: rsp:RSP_2263 hypothetical protein; hypothetical protein 119208 4581517 Pden_2950 Paracoccus denitrificans PD1222 hypothetical protein YP_916730.1 118177 R 318586 CDS YP_916731.1 119385676 4581518 complement(119205..120398) 1 NC_008687.1 PFAM: toxic anion resistance family protein; KEGG: sil:SPO2986 tellurite resistance protein; toxic anion resistance family protein 120398 4581518 Pden_2951 Paracoccus denitrificans PD1222 toxic anion resistance family protein YP_916731.1 119205 R 318586 CDS YP_916732.1 119385677 4581519 complement(120579..121031) 1 NC_008687.1 hypothetical protein 121031 4581519 Pden_2952 Paracoccus denitrificans PD1222 hypothetical protein YP_916732.1 120579 R 318586 CDS YP_916733.1 119385678 4581520 complement(121116..122165) 1 NC_008687.1 PFAM: helix-turn-helix- domain containing protein, AraC type; KEGG: mes:Meso_0590 transcriptional regulator, AraC family; helix-turn-helix domain-containing protein 122165 4581520 Pden_2953 Paracoccus denitrificans PD1222 helix-turn-helix domain-containing protein YP_916733.1 121116 R 318586 CDS YP_916734.1 119385679 4581521 complement(122201..123535) 1 NC_008687.1 PFAM: protein of unknown function UPF0118; KEGG: jan:Jann_2214 protein of unknown function UPF0118; hypothetical protein 123535 4581521 Pden_2954 Paracoccus denitrificans PD1222 hypothetical protein YP_916734.1 122201 R 318586 CDS YP_916735.1 119385680 4581522 complement(123627..124850) 1 NC_008687.1 PFAM: Saccharopine dehydrogenase; KEGG: rsp:RSP_1475 saccharopine dehydrogenase family; saccharopine dehydrogenase 124850 4581522 Pden_2955 Paracoccus denitrificans PD1222 saccharopine dehydrogenase YP_916735.1 123627 R 318586 CDS YP_916736.1 119385681 4581523 complement(124897..126003) 1 NC_008687.1 TIGRFAM: carboxynorspermidine decarboxylase; PFAM: Orn/DAP/Arg decarboxylase 2; KEGG: sme:SMb21631 carboxynorspermidine decarboxylase; carboxynorspermidine decarboxylase 126003 4581523 Pden_2956 Paracoccus denitrificans PD1222 carboxynorspermidine decarboxylase YP_916736.1 124897 R 318586 CDS YP_916737.1 119385682 4581524 complement(126127..127152) 1 NC_008687.1 PFAM: oxidoreductase domain protein; homoserine dehydrogenase, NAD-binding; KEGG: mes:Meso_2709 oxidoreductase-like; oxidoreductase domain-containing protein 127152 4581524 Pden_2957 Paracoccus denitrificans PD1222 oxidoreductase domain-containing protein YP_916737.1 126127 R 318586 CDS YP_916738.1 119385683 4581525 complement(127156..127614) 1 NC_008687.1 TIGRFAM: transcriptional regulator, Rrf2 family; PFAM: protein of unknown function UPF0074; KEGG: rsp:RSP_0443 Rrf2 family transcriptional regulator; BadM/Rrf2 family transcriptional regulator 127614 4581525 Pden_2958 Paracoccus denitrificans PD1222 BadM/Rrf2 family transcriptional regulator YP_916738.1 127156 R 318586 CDS YP_916739.1 119385684 4581526 127780..128439 1 NC_008687.1 KEGG: jan:Jann_2367 hypothetical protein; hypothetical protein 128439 4581526 Pden_2959 Paracoccus denitrificans PD1222 hypothetical protein YP_916739.1 127780 D 318586 CDS YP_916740.1 119385685 4581527 128477..129601 1 NC_008687.1 PFAM: metal-dependent phosphohydrolase, HD sub domain; SMART: metal-dependent phosphohydrolase, HD region; KEGG: sil:SPO2028 HD domain protein; metal dependent phosphohydrolase 129601 4581527 Pden_2960 Paracoccus denitrificans PD1222 metal dependent phosphohydrolase YP_916740.1 128477 D 318586 CDS YP_916741.1 119385686 4581528 129721..130935 1 NC_008687.1 Converts isocitrate to alpha ketoglutarate; isocitrate dehydrogenase 130935 4581528 Pden_2961 Paracoccus denitrificans PD1222 isocitrate dehydrogenase YP_916741.1 129721 D 318586 CDS YP_916742.1 119385687 4581529 131180..131848 1 NC_008687.1 TIGRFAM: phosphoribosylformylglycinamidine synthase I; PFAM: CobB/CobQ domain protein glutamine amidotransferase; KEGG: rsp:RSP_2128 phosphoribosylformylglycinamidine synthase I (FGAM) synthase; phosphoribosylformylglycinamidine synthase I 131848 4581529 Pden_2962 Paracoccus denitrificans PD1222 phosphoribosylformylglycinamidine synthase I YP_916742.1 131180 D 318586 CDS YP_916743.1 119385688 4581530 131915..133708 1 NC_008687.1 PFAM: ATP-binding region, ATPase domain protein domain protein; histidine kinase A domain protein domain protein; KEGG: rsp:RSP_2129 sensor histidine kinase; integral membrane sensor signal transduction histidine kinase 133708 4581530 Pden_2963 Paracoccus denitrificans PD1222 integral membrane sensor signal transduction histidine kinase YP_916743.1 131915 D 318586 CDS YP_916744.1 119385689 4581531 133728..135053 1 NC_008687.1 PFAM: response regulator receiver; sigma-54 factor, interaction domain-containing protein; helix-turn-helix, Fis-type; SMART: AAA ATPase; KEGG: sit:TM1040_1461 two component, sigma54 specific, transcriptional regulator, fis family; two component, sigma54 specific, Fis family transcriptional regulator 135053 4581531 Pden_2964 Paracoccus denitrificans PD1222 two component, sigma54 specific, Fis family transcriptional regulator YP_916744.1 133728 D 318586 CDS YP_916745.1 119385690 4581532 135504..138113 1 NC_008687.1 TIGRFAM: ribonuclease, Rne/Rng family; PFAM: RNA binding S1 domain protein; KEGG: sil:SPO1893 ribonuclease, Rne/Rng family; ribonuclease 138113 4581532 Pden_2965 Paracoccus denitrificans PD1222 ribonuclease YP_916745.1 135504 D 318586 CDS YP_916746.1 119385691 4581533 138190..138933 1 NC_008687.1 PFAM: cytochrome c biogenesis protein, transmembrane region; KEGG: rde:RD1_2269 cytochrome c-type biogenesis protein CcdA; cytochrome c biogenesis protein, transmembrane region 138933 4581533 Pden_2966 Paracoccus denitrificans PD1222 cytochrome c biogenesis protein, transmembrane region YP_916746.1 138190 D 318586 CDS YP_916747.1 119385692 4581534 complement(138930..139730) 1 NC_008687.1 PFAM: Enoyl-CoA hydratase/isomerase; KEGG: rsp:RSP_3833 enoyl-CoA hydratase; enoyl-CoA hydratase/isomerase 139730 4581534 Pden_2967 Paracoccus denitrificans PD1222 enoyl-CoA hydratase/isomerase YP_916747.1 138930 R 318586 CDS YP_916748.1 119385693 4581535 139815..140237 1 NC_008687.1 TIGRFAM: uncharacterized domain 1; PFAM: thioesterase superfamily protein; KEGG: sit:TM1040_1390 phenylacetic acid degradation-related protein; hypothetical protein 140237 4581535 Pden_2968 Paracoccus denitrificans PD1222 hypothetical protein YP_916748.1 139815 D 318586 CDS YP_916749.1 119385694 4581536 140388..140852 1 NC_008687.1 in Escherichia coli this protein is one of the earliest assembly proteins in the large subunit; 50S ribosomal protein L13 140852 rplM 4581536 rplM Paracoccus denitrificans PD1222 50S ribosomal protein L13 YP_916749.1 140388 D 318586 CDS YP_916750.1 119385695 4581537 140856..141335 1 NC_008687.1 forms a direct contact with the tRNA during translation; 30S ribosomal protein S9 141335 rpsI 4581537 rpsI Paracoccus denitrificans PD1222 30S ribosomal protein S9 YP_916750.1 140856 D 318586 CDS YP_916751.1 119385696 4581538 141439..141723 1 NC_008687.1 hypothetical protein 141723 4581538 Pden_2971 Paracoccus denitrificans PD1222 hypothetical protein YP_916751.1 141439 D 318586 CDS YP_916752.1 119385697 4581539 complement(147370..148221) 1 NC_008687.1 KEGG: lbl:LBL_1989 transposase, ISLbp9; hypothetical protein 148221 4581539 Pden_2972 Paracoccus denitrificans PD1222 hypothetical protein YP_916752.1 147370 R 318586 CDS YP_916753.1 119385698 4581540 complement(148499..150403) 1 NC_008687.1 PFAM: helicase domain protein; KEGG: rpe:RPE_2164 helicase domain protein; helicase 150403 4581540 Pden_2974 Paracoccus denitrificans PD1222 helicase YP_916753.1 148499 R 318586 CDS YP_916754.1 119385699 4581541 complement(150397..150711) 1 NC_008687.1 KEGG: pat:Patl_4096 DNA-cytosine methyltransferase; hypothetical protein 150711 4581541 Pden_2975 Paracoccus denitrificans PD1222 hypothetical protein YP_916754.1 150397 R 318586 CDS YP_916755.1 119385700 4581542 complement(150708..151268) 1 NC_008687.1 PFAM: transposase, IS4 family protein; KEGG: sil:SPOA0134 ISSpo7, transposase; transposase, IS4 family protein 151268 4581542 Pden_2976 Paracoccus denitrificans PD1222 transposase, IS4 family protein YP_916755.1 150708 R 318586 CDS YP_916756.1 119385701 4581543 complement(151529..153085) 1 NC_008687.1 PFAM: Secretin/TonB, short N-terminal domain; TonB-dependent receptor, plug; KEGG: rso:RSc2920 hydroxamate-type ferrisiderophore receptor signal peptide protein; TonB-dependent receptor, plug 153085 4581543 Pden_2977 Paracoccus denitrificans PD1222 TonB-dependent receptor, plug YP_916756.1 151529 R 318586 CDS YP_916757.1 119385702 4581544 complement(153212..154198) 1 NC_008687.1 PFAM: FecR protein; KEGG: nwi:Nwi_2050 probable FecR, iron siderophore sensor protein; FecR protein 154198 4581544 Pden_2978 Paracoccus denitrificans PD1222 FecR protein YP_916757.1 153212 R 318586 CDS YP_916758.1 119385703 4581545 complement(154267..154779) 1 NC_008687.1 PFAM: sigma-70 region 2 domain protein; sigma-70 region 4 domain protein; Sigma-70, region 4 type 2; KEGG: bbr:BB4120 ECF-family sigma factor; ECF subfamily RNA polymerase sigma-24 factor 154779 4581545 Pden_2979 Paracoccus denitrificans PD1222 ECF subfamily RNA polymerase sigma-24 factor YP_916758.1 154267 R 318586 CDS YP_916759.1 119385704 4581546 155557..156567 1 NC_008687.1 PFAM: periplasmic binding protein; KEGG: ppu:PP_2418 iron ABC transporter, periplasmic iron-binding protein; periplasmic binding protein 156567 4581546 Pden_2980 Paracoccus denitrificans PD1222 periplasmic binding protein YP_916759.1 155557 D 318586 CDS YP_916760.1 119385705 4581547 156564..157625 1 NC_008687.1 PFAM: transport system permease; KEGG: bmb:BruAb2_0477 iron compound ABC transporter, permease; transport system permease 157625 4581547 Pden_2981 Paracoccus denitrificans PD1222 transport system permease YP_916760.1 156564 D 318586 CDS YP_916761.1 119385706 4581548 157622..158386 1 NC_008687.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rsp:RSP_3390 ABC Fe3+-siderophores transporter, ATPase subunit; ABC transporter 158386 4581548 Pden_2982 Paracoccus denitrificans PD1222 ABC transporter YP_916761.1 157622 D 318586 CDS YP_916762.1 119385707 4581549 158387..158818 1 NC_008687.1 TIGRFAM: pseudoazurin; PFAM: blue (type 1) copper domain protein; KEGG: rru:Rru_A1139 blue (type 1) copper subtype; pseudoazurin 158818 4581549 Pden_2983 Paracoccus denitrificans PD1222 pseudoazurin YP_916762.1 158387 D 318586 CDS YP_916763.1 119385708 4581550 158815..159498 1 NC_008687.1 PFAM: UbiE/COQ5 methyltransferase; Methyltransferase type 11; Methyltransferase type 12; KEGG: mba:Mbar_A0646 UbiE/COQ5 methyltransferase; methyltransferase type 11 159498 4581550 Pden_2984 Paracoccus denitrificans PD1222 methyltransferase type 11 YP_916763.1 158815 D 318586 CDS YP_916764.1 119385709 4581551 complement(159505..159954) 1 NC_008687.1 KEGG: hne:HNE_1237 DNA-binding protein; DNA-binding protein 159954 4581551 Pden_2985 Paracoccus denitrificans PD1222 DNA-binding protein YP_916764.1 159505 R 318586 CDS YP_916765.1 119385710 4581552 159971..160462 1 NC_008687.1 KEGG: rpa:RPA2395 carboxyphosphonoenolpyruvate phosphonomutase; PEP phosphonomutase 160462 4581552 Pden_2986 Paracoccus denitrificans PD1222 PEP phosphonomutase YP_916765.1 159971 D 318586 CDS YP_916766.1 119385711 4581553 complement(160576..161202) 1 NC_008687.1 TIGRFAM: anaerobic ribonucleoside-triphosphate reductase activating protein; PFAM: Radical SAM domain protein; KEGG: rpe:RPE_3175 anaerobic ribonucleoside-triphosphate reductase activating protein; anaerobic ribonucleoside-triphosphate reductase activating protein 161202 4581553 Pden_2987 Paracoccus denitrificans PD1222 anaerobic ribonucleoside-triphosphate reductase activating protein YP_916766.1 160576 R 318586 CDS YP_916767.1 119385712 4581554 complement(161195..161377) 1 NC_008687.1 KEGG: rpc:RPC_3516 hypothetical protein; hypothetical protein 161377 4581554 Pden_2988 Paracoccus denitrificans PD1222 hypothetical protein YP_916767.1 161195 R 318586 CDS YP_916768.1 119385713 4581555 complement(161392..163137) 1 NC_008687.1 Catalyzes the reduction of nucleoside 5'-triphosphates to 2'-deoxynucleoside 5'-triphosphates; anaerobic ribonucleoside triphosphate reductase 163137 4581555 Pden_2989 Paracoccus denitrificans PD1222 anaerobic ribonucleoside triphosphate reductase YP_916768.1 161392 R 318586 CDS YP_916769.1 119385714 4581556 complement(163940..164611) 1 NC_008687.1 PFAM: regulatory protein, LuxR; response regulator receiver; KEGG: rpe:RPE_3142 two component transcriptional regulator, LuxR family; two component LuxR family transcriptional regulator 164611 4581556 Pden_2990 Paracoccus denitrificans PD1222 two component LuxR family transcriptional regulator YP_916769.1 163940 R 318586 CDS YP_916770.1 119385715 4581557 complement(164596..166023) 1 NC_008687.1 PFAM: ATP-binding region, ATPase domain protein domain protein; histidine kinase, HAMP region domain protein; histidine kinase, dimerisation and phosphoacceptor region; KEGG: rpe:RPE_3141 signal transduction histidine kinase; integral membrane sensor signal transduction histidine kinase 166023 4581557 Pden_2991 Paracoccus denitrificans PD1222 integral membrane sensor signal transduction histidine kinase YP_916770.1 164596 R 318586 CDS YP_916771.1 119385716 4581558 complement(166020..166484) 1 NC_008687.1 hypothetical protein 166484 4581558 Pden_2992 Paracoccus denitrificans PD1222 hypothetical protein YP_916771.1 166020 R 318586 CDS YP_916772.1 119385717 4581559 166833..168731 1 NC_008687.1 PFAM: Pyrrolo-quinoline quinone; KEGG: rpe:RPE_3139 pyrrolo-quinoline quinone; Pyrrolo-quinoline quinone 168731 4581559 Pden_2993 Paracoccus denitrificans PD1222 Pyrrolo-quinoline quinone YP_916772.1 166833 D 318586 CDS YP_916773.1 119385718 4581560 168805..169635 1 NC_008687.1 SMART: extracellular solute-binding protein, family 3; KEGG: rpc:RPC_1908 extracellular solute-binding protein, family 3; extracellular solute-binding protein 169635 4581560 Pden_2994 Paracoccus denitrificans PD1222 extracellular solute-binding protein YP_916773.1 168805 D 318586 CDS YP_916774.1 119385719 4581561 169646..170179 1 NC_008687.1 PFAM: cytochrome c, class I; KEGG: rpc:RPC_1909 cytochrome c, class I; cytochrome c, class I 170179 4581561 Pden_2995 Paracoccus denitrificans PD1222 cytochrome c, class I YP_916774.1 169646 D 318586 CDS YP_916775.1 119385720 4581562 170234..170545 1 NC_008687.1 PFAM: methanol dehydrogenase, beta subunit; KEGG: rpe:RPE_3136 methanol dehydrogenase, beta subunit; methanol dehydrogenase, beta subunit 170545 4581562 Pden_2996 Paracoccus denitrificans PD1222 methanol dehydrogenase, beta subunit YP_916775.1 170234 D 318586 CDS YP_916776.1 119385721 4581563 170607..171626 1 NC_008687.1 PFAM: ATPase associated with various cellular activities, AAA_3; ATPase associated with various cellular activities, AAA_5; SMART: AAA ATPase; KEGG: rpe:RPE_3135 ATPase associated with various cellular activities, AAA_3; ATPase 171626 4581563 Pden_2997 Paracoccus denitrificans PD1222 ATPase YP_916776.1 170607 D 318586 CDS YP_916777.1 119385722 4581564 171623..172477 1 NC_008687.1 KEGG: rpc:RPC_1912 hypothetical protein; hypothetical protein 172477 4581564 Pden_2998 Paracoccus denitrificans PD1222 hypothetical protein YP_916777.1 171623 D 318586 CDS YP_916778.1 119385723 4581565 172474..173277 1 NC_008687.1 KEGG: rpc:RPC_1913 MxaA protein; MxaA protein 173277 4581565 Pden_2999 Paracoccus denitrificans PD1222 MxaA protein YP_916778.1 172474 D 318586 CDS YP_916779.1 119385724 4581566 173274..174281 1 NC_008687.1 PFAM: von Willebrand factor, type A; KEGG: rpe:RPE_3132 von Willebrand factor, type A; von Willebrand factor A 174281 4581566 Pden_3000 Paracoccus denitrificans PD1222 von Willebrand factor A YP_916779.1 173274 D 318586 CDS YP_916780.1 119385725 4581567 174278..174829 1 NC_008687.1 KEGG: rpe:RPE_3131 hypothetical protein; hypothetical protein 174829 4581567 Pden_3001 Paracoccus denitrificans PD1222 hypothetical protein YP_916780.1 174278 D 318586 CDS YP_916781.1 119385726 4581568 174955..175758 1 NC_008687.1 KEGG: rpe:RPE_3130 von Willebrand factor, type A; von Willebrand factor A 175758 4581568 Pden_3002 Paracoccus denitrificans PD1222 von Willebrand factor A YP_916781.1 174955 D 318586 CDS YP_916782.1 119385727 4581569 175755..176288 1 NC_008687.1 KEGG: rpe:RPE_3129 MxaD protein; MxaD protein 176288 4581569 Pden_3003 Paracoccus denitrificans PD1222 MxaD protein YP_916782.1 175755 D 318586 CDS YP_916783.1 119385728 4581570 complement(176306..177154) 1 NC_008687.1 PFAM: peptidase S15; dienelactone hydrolase; KEGG: tte:TTE1809 hydrolases of the alpha/beta superfamily; peptidase S15 177154 4581570 Pden_3004 Paracoccus denitrificans PD1222 peptidase S15 YP_916783.1 176306 R 318586 CDS YP_916784.1 119385729 4581571 complement(177218..177655) 1 NC_008687.1 hypothetical protein 177655 4581571 Pden_3005 Paracoccus denitrificans PD1222 hypothetical protein YP_916784.1 177218 R 318586 CDS YP_916785.1 119385730 4581572 complement(177706..178218) 1 NC_008687.1 hypothetical protein 178218 4581572 Pden_3006 Paracoccus denitrificans PD1222 hypothetical protein YP_916785.1 177706 R 318586 CDS YP_916786.1 119385731 4581573 complement(178458..180536) 1 NC_008687.1 TIGRFAM: TonB-dependent siderophore receptor; PFAM: TonB-dependent receptor; TonB-dependent receptor, plug; KEGG: rru:Rru_A2312 TonB-dependent receptor; TonB-dependent siderophore receptor 180536 4581573 Pden_3007 Paracoccus denitrificans PD1222 TonB-dependent siderophore receptor YP_916786.1 178458 R 318586 CDS YP_916787.1 119385732 4581574 180896..182563 1 NC_008687.1 PFAM: AMP-dependent synthetase and ligase; KEGG: bur:Bcep18194_B0670 AMP-dependent synthetase and ligase; AMP-dependent synthetase/ligase 182563 4581574 Pden_3008 Paracoccus denitrificans PD1222 AMP-dependent synthetase/ligase YP_916787.1 180896 D 318586 CDS YP_916788.1 119385733 4581575 182560..183015 1 NC_008687.1 TIGRFAM: chorismate mutase related enzymes; PFAM: Chorismate mutase; KEGG: pfl:PFL_3489 isochorismate pyruvate-lyase; chorismate mutase related enzymes 183015 4581575 Pden_3009 Paracoccus denitrificans PD1222 chorismate mutase related enzymes YP_916788.1 182560 D 318586 CDS YP_916789.1 119385734 4581576 complement(182950..183927) 1 NC_008687.1 PFAM: periplasmic binding protein; KEGG: ecs:ECs3913 ferrichrome-binding protein; periplasmic binding protein 183927 4581576 Pden_3010 Paracoccus denitrificans PD1222 periplasmic binding protein YP_916789.1 182950 R 318586 CDS YP_916790.1 119385735 4581577 complement(183941..184975) 1 NC_008687.1 PFAM: transport system permease; KEGG: hch:HCH_03457 ABC-type enterobactin transport system, permease component; transport system permease 184975 4581577 Pden_3011 Paracoccus denitrificans PD1222 transport system permease YP_916790.1 183941 R 318586 CDS YP_916791.1 119385736 4581578 complement(184972..185970) 1 NC_008687.1 PFAM: transport system permease; KEGG: pfl:PFL_3624 ferric vibriobactin ABC transporter, permease VC0777; transport system permease 185970 4581578 Pden_3012 Paracoccus denitrificans PD1222 transport system permease YP_916791.1 184972 R 318586 CDS YP_916792.1 119385737 4581579 complement(185967..186746) 1 NC_008687.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: bur:Bcep18194_A4781 ABC cobalamin/Fe3+-siderophore transporter, ATPase subunit; ABC transporter 186746 4581579 Pden_3013 Paracoccus denitrificans PD1222 ABC transporter YP_916792.1 185967 R 318586 CDS YP_916793.1 119385738 4581580 186830..188014 1 NC_008687.1 KEGG: pfl:PFL_3619 monooxygenase, NtaA/SnaA/SoxA family; NtaA/SnaA/SoxA family monooxygenase 188014 4581580 Pden_3014 Paracoccus denitrificans PD1222 NtaA/SnaA/SoxA family monooxygenase YP_916793.1 186830 D 318586 CDS YP_916794.1 119385739 4581581 complement(187954..193665) 1 NC_008687.1 TIGRFAM: amino acid adenylation domain; PFAM: AMP-dependent synthetase and ligase; condensation domain protein; phosphopantetheine-binding; Non-ribosomal peptide synthetase; KEGG: pen:PSEEN2503 non-ribosomal peptide synthetase BasA/D; amino acid adenylation protein 193665 4581581 Pden_3015 Paracoccus denitrificans PD1222 amino acid adenylation protein YP_916794.1 187954 R 318586 CDS YP_916795.1 119385740 4581582 193771..194019 1 NC_008687.1 PFAM: phosphopantetheine-binding; KEGG: pen:PSEEN2505 2,3-dihydroxybenzoate-AMP ligase; phosphopantetheine-binding protein 194019 4581582 Pden_3016 Paracoccus denitrificans PD1222 phosphopantetheine-binding protein YP_916795.1 193771 D 318586 CDS YP_916796.1 119385741 4581583 194271..196073 1 NC_008687.1 PFAM: ABC transporter, transmembrane region; ABC transporter related; SMART: AAA ATPase; KEGG: eci:UTI89_C2181 inner membrane ABC-transporter; ABC transporter 196073 4581583 Pden_3017 Paracoccus denitrificans PD1222 ABC transporter YP_916796.1 194271 D 318586 CDS YP_916797.1 119385742 4581584 196070..197857 1 NC_008687.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: yps:YPTB1599 inner membrane ABC-transporter YbtQ; ABC transporter 197857 4581584 Pden_3018 Paracoccus denitrificans PD1222 ABC transporter YP_916797.1 196070 D 318586 CDS YP_916798.1 119385743 4581585 complement(198236..198676) 1 NC_008687.1 PFAM: CBS domain containing protein; KEGG: lpf:lpl2035 hypothetical protein; signal-transduction protein 198676 4581585 Pden_3019 Paracoccus denitrificans PD1222 signal-transduction protein YP_916798.1 198236 R 318586 CDS YP_916799.1 119385744 4581586 complement(198689..199072) 1 NC_008687.1 PFAM: succinate dehydrogenase, cytochrome b subunit; KEGG: mca:MCA1549 succinate dehydrogenase, hydrophobic membrane anchor protein; succinate dehydrogenase, cytochrome b subunit 199072 4581586 Pden_3020 Paracoccus denitrificans PD1222 succinate dehydrogenase, cytochrome b subunit YP_916799.1 198689 R 318586 CDS YP_916800.1 119385745 4581587 complement(199069..199446) 1 NC_008687.1 PFAM: succinate dehydrogenase, cytochrome b subunit; KEGG: aeh:Mlg_1332 succinate dehydrogenase, cytochrome b subunit; succinate dehydrogenase, cytochrome b subunit 199446 4581587 Pden_3021 Paracoccus denitrificans PD1222 succinate dehydrogenase, cytochrome b subunit YP_916800.1 199069 R 318586 CDS YP_916801.1 119385746 4581588 complement(199462..199830) 1 NC_008687.1 KEGG: rru:Rru_A1205 succinate dehydrogenase/fumarate reductase iron-sulfur protein; succinate dehydrogenase (ubiquinone) 199830 4581588 Pden_3022 Paracoccus denitrificans PD1222 succinate dehydrogenase (ubiquinone) YP_916801.1 199462 R 318586 CDS YP_916802.1 119385747 4581589 complement(199948..200400) 1 NC_008687.1 KEGG: rde:RD1_1693 hypothetical protein; hypothetical protein 200400 4581589 Pden_3023 Paracoccus denitrificans PD1222 hypothetical protein YP_916802.1 199948 R 318586 CDS YP_916803.1 119385748 4581590 complement(200422..200859) 1 NC_008687.1 TIGRFAM: transcriptional regulator, Rrf2 family; PFAM: protein of unknown function UPF0074; KEGG: hne:HNE_1541 transcriptional regulator; BadM/Rrf2 family transcriptional regulator 200859 4581590 Pden_3024 Paracoccus denitrificans PD1222 BadM/Rrf2 family transcriptional regulator YP_916803.1 200422 R 318586 CDS YP_916804.1 119385749 4581591 201003..201674 1 NC_008687.1 PFAM: protein of unknown function DUF542, ScdA domain protein; Hemerythrin HHE cation binding domain protein; KEGG: rso:RS02289 hypothetical protein; hypothetical protein 201674 4581591 Pden_3025 Paracoccus denitrificans PD1222 hypothetical protein YP_916804.1 201003 D 318586 CDS YP_916805.1 119385750 4581592 201788..202111 1 NC_008687.1 KEGG: sil:SPOA0172 hypothetical protein; hypothetical protein 202111 4581592 Pden_3026 Paracoccus denitrificans PD1222 hypothetical protein YP_916805.1 201788 D 318586 CDS YP_916806.1 119385751 4581593 202131..202469 1 NC_008687.1 TIGRFAM: alkylhydroperoxidase like protein, AhpD family; PFAM: Carboxymuconolactone decarboxylase; KEGG: nha:Nham_4301 alkylhydroperoxidase AhpD core; alkylhydroperoxidase 202469 4581593 Pden_3027 Paracoccus denitrificans PD1222 alkylhydroperoxidase YP_916806.1 202131 D 318586 CDS YP_916807.1 119385752 4581594 202683..204353 1 NC_008687.1 PFAM: cytochrome c oxidase, subunit I; KEGG: rsp:RSP_1877 cytochrome c oxidase, aa3 type, subunit I; cytochrome-c oxidase 204353 4581594 Pden_3028 Paracoccus denitrificans PD1222 cytochrome-c oxidase YP_916807.1 202683 D 318586 CDS YP_916808.1 119385753 4581595 204776..206932 1 NC_008687.1 TIGRFAM: TonB-dependent siderophore receptor; PFAM: TonB-dependent receptor; TonB-dependent receptor, plug; KEGG: ecp:ECP_2036 hypothetical TonB dependent receptor; TonB-dependent siderophore receptor 206932 4581595 Pden_3029 Paracoccus denitrificans PD1222 TonB-dependent siderophore receptor YP_916808.1 204776 D 318586 CDS YP_916809.1 119385754 4581596 206944..207768 1 NC_008687.1 PFAM: Methyltransferase type 12; KEGG: dps:DP0853 hypothetical protein; methyltransferase type 12 207768 4581596 Pden_3030 Paracoccus denitrificans PD1222 methyltransferase type 12 YP_916809.1 206944 D 318586 CDS YP_916810.1 119385755 4581597 207773..208786 1 NC_008687.1 PFAM: transport system permease; KEGG: nha:Nham_0954 transport system permease; transport system permease 208786 4581597 Pden_3031 Paracoccus denitrificans PD1222 transport system permease YP_916810.1 207773 D 318586 CDS YP_916811.1 119385756 4581598 208783..209553 1 NC_008687.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: nwi:Nwi_2074 ABC transporter, ATPase subunit; ABC transporter 209553 4581598 Pden_3032 Paracoccus denitrificans PD1222 ABC transporter YP_916811.1 208783 D 318586 CDS YP_916812.1 119385757 4581599 209564..210601 1 NC_008687.1 PFAM: periplasmic binding protein; KEGG: eca:ECA3564 iron-chelating periplasmic-binding protein; periplasmic binding protein 210601 4581599 Pden_3033 Paracoccus denitrificans PD1222 periplasmic binding protein YP_916812.1 209564 D 318586 CDS YP_916813.1 119385758 4581600 210616..210993 1 NC_008687.1 hypothetical protein 210993 4581600 Pden_3034 Paracoccus denitrificans PD1222 hypothetical protein YP_916813.1 210616 D 318586 CDS YP_916814.1 119385759 4581601 complement(211066..211221) 1 NC_008687.1 KEGG: rru:Rru_A1382 butyrate-acetoacetate CoA-transferase; butyrate-acetoacetate CoA-transferase 211221 4581601 Pden_3035 Paracoccus denitrificans PD1222 butyrate-acetoacetate CoA-transferase YP_916814.1 211066 R 318586 CDS YP_916815.1 119385760 4581602 211416..212906 1 NC_008687.1 PFAM: Sulfate transporter/antisigma-factor antagonist STAS; Xanthine/uracil/vitamin C permease; sulphate transporter; KEGG: rsp:RSP_4197 antisigma-factor antagonist, STAS; sulfate transporter 212906 4581602 Pden_3036 Paracoccus denitrificans PD1222 sulfate transporter YP_916815.1 211416 D 318586 CDS YP_916816.1 119385761 4581603 complement(213391..214716) 1 NC_008687.1 PFAM: Cl- channel, voltage-gated family protein; KEGG: mes:Meso_1046 Cl-channel, voltage gated; Cl- channel, voltage-gated family protein 214716 4581603 Pden_3037 Paracoccus denitrificans PD1222 Cl- channel, voltage-gated family protein YP_916816.1 213391 R 318586 CDS YP_916817.1 119385762 4581604 complement(214845..216509) 1 NC_008687.1 TIGRFAM: choline/carnitine/betaine transporter; PFAM: BCCT transporter; KEGG: rsp:RSP_3080 choline/carnitine/betaine transporter, BCCT family; choline/carnitine/betaine transporter 216509 4581604 Pden_3038 Paracoccus denitrificans PD1222 choline/carnitine/betaine transporter YP_916817.1 214845 R 318586 CDS YP_916818.1 119385763 4581605 216885..218168 1 NC_008687.1 KEGG: pol:Bpro_5072 hypothetical protein; hypothetical protein 218168 4581605 Pden_3039 Paracoccus denitrificans PD1222 hypothetical protein YP_916818.1 216885 D 318586 CDS YP_916819.1 119385764 4581606 complement(218003..218413) 1 NC_008687.1 KEGG: sil:SPOA0122 ISSpo9, transposase; ISSpo9, transposase 218413 4581606 Pden_3040 Paracoccus denitrificans PD1222 ISSpo9, transposase YP_916819.1 218003 R 318586 CDS YP_916820.1 119385765 4581607 complement(218479..218688) 1 NC_008687.1 KEGG: bja:blr1867 hypothetical protein; hypothetical protein 218688 4581607 Pden_3041 Paracoccus denitrificans PD1222 hypothetical protein YP_916820.1 218479 R 318586 CDS YP_916821.1 119385766 4581608 complement(221466..222683) 1 NC_008687.1 PFAM: major facilitator superfamily MFS_1; KEGG: bja:bll3850 multidrug resistance protein; major facilitator transporter 222683 4581608 Pden_3044 Paracoccus denitrificans PD1222 major facilitator transporter YP_916821.1 221466 R 318586 CDS YP_916822.1 119385767 4581609 complement(222708..223940) 1 NC_008687.1 PFAM: major facilitator superfamily MFS_1; KEGG: stm:STM1545 multidrug efflux protein; major facilitator transporter 223940 4581609 Pden_3045 Paracoccus denitrificans PD1222 major facilitator transporter YP_916822.1 222708 R 318586 CDS YP_916823.1 119385768 4581610 224252..225097 1 NC_008687.1 PFAM: Alcohol dehydrogenase, zinc-binding domain protein; KEGG: rpc:RPC_4092 alcohol dehydrogenase, zinc-binding; alcohol dehydrogenase 225097 4581610 Pden_3046 Paracoccus denitrificans PD1222 alcohol dehydrogenase YP_916823.1 224252 D 318586 CDS YP_916824.1 119385769 4581611 complement(225122..225607) 1 NC_008687.1 PFAM: regulatory protein, MarR; KEGG: ret:RHE_CH02035 probable transcriptional regulator protein, MarR family; MarR family transcriptional regulator 225607 4581611 Pden_3047 Paracoccus denitrificans PD1222 MarR family transcriptional regulator YP_916824.1 225122 R 318586 CDS YP_916825.1 119385770 4581612 225654..227174 1 NC_008687.1 PFAM: monooxygenase, FAD-binding; FAD dependent oxidoreductase; KEGG: ret:RHE_CH02034 probable monooxygenase; hypothetical protein 227174 4581612 Pden_3048 Paracoccus denitrificans PD1222 hypothetical protein YP_916825.1 225654 D 318586 CDS YP_916826.1 119385771 4581613 228088..229941 1 NC_008687.1 PFAM: dehydrogenase, E1 component; Transketolase, central region; Transketolase domain protein; KEGG: aeh:Mlg_2596 dehydrogenase, E1 component; transketolase, central region 229941 4581613 Pden_3049 Paracoccus denitrificans PD1222 transketolase, central region YP_916826.1 228088 D 318586 CDS YP_916827.1 119385772 4581614 229941..230696 1 NC_008687.1 PFAM: regulatory proteins, IclR; KEGG: rha:RHA1_ro08622 probable transcriptional regulator, IclR family; regulatory proteins, IclR 230696 4581614 Pden_3050 Paracoccus denitrificans PD1222 regulatory proteins, IclR YP_916827.1 229941 D 318586 CDS YP_916828.1 119385773 4581615 230709..231107 1 NC_008687.1 PFAM: Endoribonuclease L-PSP; KEGG: mlo:mlr1297 hypothetical protein; endoribonuclease L-PSP 231107 4581615 Pden_3051 Paracoccus denitrificans PD1222 endoribonuclease L-PSP YP_916828.1 230709 D 318586 CDS YP_916829.1 119385774 4581616 231104..232495 1 NC_008687.1 PFAM: aminotransferase class-III; KEGG: pol:Bpro_0421 aminotransferase class-III; class III aminotransferase 232495 4581616 Pden_3052 Paracoccus denitrificans PD1222 class III aminotransferase YP_916829.1 231104 D 318586 CDS YP_916830.1 119385775 4581617 232485..233912 1 NC_008687.1 PFAM: Amidase; KEGG: mxa:MXAN_2852 amidase family protein; amidase 233912 4581617 Pden_3053 Paracoccus denitrificans PD1222 amidase YP_916830.1 232485 D 318586 CDS YP_916831.1 119385776 4581618 233971..235251 1 NC_008687.1 KEGG: sil:SPO2534 branched-chain amino acid ABC transporter, periplasmic branched-chain amino acid-binding protein; branched-chain amino acid ABC transporter 235251 4581618 Pden_3054 Paracoccus denitrificans PD1222 branched-chain amino acid ABC transporter YP_916831.1 233971 D 318586 CDS YP_916832.1 119385777 4581619 235254..236066 1 NC_008687.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sil:SPO2533 branched-chain amino acid ABC transporter, ATP-binding protein; ABC transporter 236066 4581619 Pden_3055 Paracoccus denitrificans PD1222 ABC transporter YP_916832.1 235254 D 318586 CDS YP_916833.1 119385778 4581620 236056..236769 1 NC_008687.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sil:SPO2532 branched-chain amino acid ABC transporter, ATP-binding protein; ABC transporter 236769 4581620 Pden_3056 Paracoccus denitrificans PD1222 ABC transporter YP_916833.1 236056 D 318586 CDS YP_916834.1 119385779 4581621 236773..237651 1 NC_008687.1 PFAM: inner-membrane translocator; KEGG: sil:SPO2531 branched-chain amino acid ABC transporter, permease; inner-membrane translocator 237651 4581621 Pden_3057 Paracoccus denitrificans PD1222 inner-membrane translocator YP_916834.1 236773 D 318586 CDS YP_916835.1 119385780 4581622 237648..238664 1 NC_008687.1 PFAM: inner-membrane translocator; KEGG: sil:SPO2530 branched-chain amino acid ABC transporter, permease; inner-membrane translocator 238664 4581622 Pden_3058 Paracoccus denitrificans PD1222 inner-membrane translocator YP_916835.1 237648 D 318586 CDS YP_916836.1 119385781 4581623 238652..240073 1 NC_008687.1 PFAM: Amidase; KEGG: bxe:Bxe_B1011 indole acetamide hydrolase; amidase 240073 4581623 Pden_3059 Paracoccus denitrificans PD1222 amidase YP_916836.1 238652 D 318586 CDS YP_916837.1 119385782 4581624 complement(240368..240727) 1 NC_008687.1 KEGG: gox:GOX2722 truncated transposase; hypothetical protein 240727 4581624 Pden_3060 Paracoccus denitrificans PD1222 hypothetical protein YP_916837.1 240368 R 318586 CDS YP_916838.1 119385783 4581625 240832..242865 1 NC_008687.1 TIGRFAM: outer membrane autotransporter barrel domain; PFAM: Autotransporter beta- domain protein; KEGG: bbr:BB0916 autotransporter; outer membrane autotransporter 242865 4581625 Pden_3061 Paracoccus denitrificans PD1222 outer membrane autotransporter YP_916838.1 240832 D 318586 CDS YP_916839.1 119385784 4581626 242895..243410 1 NC_008687.1 KEGG: mlo:mlr4672 hypothetical protein; hypothetical protein 243410 4581626 Pden_3062 Paracoccus denitrificans PD1222 hypothetical protein YP_916839.1 242895 D 318586 CDS YP_916840.1 119385785 4581627 complement(243469..243720) 1 NC_008687.1 hypothetical protein 243720 4581627 Pden_3063 Paracoccus denitrificans PD1222 hypothetical protein YP_916840.1 243469 R 318586 CDS YP_916841.1 119385786 4581628 243789..245771 1 NC_008687.1 KEGG: zmo:ZMO0213 autotransporter; hypothetical protein 245771 4581628 Pden_3064 Paracoccus denitrificans PD1222 hypothetical protein YP_916841.1 243789 D 318586 CDS YP_916842.1 119385787 4581629 complement(246211..246522) 1 NC_008687.1 PFAM: plasmid stabilization system; KEGG: rsp:RSP_3809 hypothetical protein; plasmid stabilization system protein 246522 4581629 Pden_3065 Paracoccus denitrificans PD1222 plasmid stabilization system protein YP_916842.1 246211 R 318586 CDS YP_916843.1 119385788 4581630 complement(246527..246793) 1 NC_008687.1 KEGG: rsp:RSP_3810 hypothetical protein; hypothetical protein 246793 4581630 Pden_3066 Paracoccus denitrificans PD1222 hypothetical protein YP_916843.1 246527 R 318586 CDS YP_916844.1 119385789 4581631 247092..247268 1 NC_008687.1 KEGG: mes:Meso_0525 hypothetical protein; hypothetical protein 247268 4581631 Pden_3067 Paracoccus denitrificans PD1222 hypothetical protein YP_916844.1 247092 D 318586 CDS YP_916845.1 119385790 4581632 247372..248271 1 NC_008687.1 PFAM: protein of unknown function DUF6, transmembrane; KEGG: sit:TM1040_2078 protein of unknown function DUF6, transmembrane; hypothetical protein 248271 4581632 Pden_3068 Paracoccus denitrificans PD1222 hypothetical protein YP_916845.1 247372 D 318586 CDS YP_916846.1 119385791 4581633 248442..248864 1 NC_008687.1 KEGG: bmb:BruAb1_1812 transcriptional regulator, LysR family; LysR family transcriptional regulator 248864 4581633 Pden_3069 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_916846.1 248442 D 318586 CDS YP_916847.1 119385792 4581634 complement(248809..249432) 1 NC_008687.1 hypothetical protein 249432 4581634 Pden_3070 Paracoccus denitrificans PD1222 hypothetical protein YP_916847.1 248809 R 318586 CDS YP_916848.1 119385793 4581635 complement(249529..252093) 1 NC_008687.1 catalyzes the conversion of citrate to isocitrate; aconitate hydratase 252093 acnA 4581635 acnA Paracoccus denitrificans PD1222 aconitate hydratase YP_916848.1 249529 R 318586 CDS YP_916849.1 119385794 4581636 complement(252149..253021) 1 NC_008687.1 PFAM: regulatory protein GntR, HTH; GntR domain protein; Helix-turn-helix, type 11 domain protein; KEGG: rso:RS05438 probable transcription regulator protein; GntR family transcriptional regulator 253021 4581636 Pden_3072 Paracoccus denitrificans PD1222 GntR family transcriptional regulator YP_916849.1 252149 R 318586 CDS YP_916850.1 119385795 4581637 complement(253108..254607) 1 NC_008687.1 PFAM: protein of unknown function DUF112, transmembrane; KEGG: bja:blr3163 hypothetical protein; hypothetical protein 254607 4581637 Pden_3073 Paracoccus denitrificans PD1222 hypothetical protein YP_916850.1 253108 R 318586 CDS YP_916851.1 119385796 4581638 complement(254618..255088) 1 NC_008687.1 KEGG: bja:blr3162 tricarboxylic transport membrane protein; tricarboxylic transport membrane protein 255088 4581638 Pden_3074 Paracoccus denitrificans PD1222 tricarboxylic transport membrane protein YP_916851.1 254618 R 318586 CDS YP_916852.1 119385797 4581639 complement(255140..256111) 1 NC_008687.1 PFAM: Uncharacterized protein UPF0065; KEGG: bja:blr3161 tricarboxylic transport membrane protein; hypothetical protein 256111 4581639 Pden_3075 Paracoccus denitrificans PD1222 hypothetical protein YP_916852.1 255140 R 318586 CDS YP_916853.1 119385798 4581640 256282..256695 1 NC_008687.1 KEGG: gme:Gmet_0306 CoA-binding protein; hypothetical protein 256695 4581640 Pden_3076 Paracoccus denitrificans PD1222 hypothetical protein YP_916853.1 256282 D 318586 CDS YP_916854.1 119385799 4581641 256692..259682 1 NC_008687.1 KEGG: nwi:Nwi_0792 gene transfer agent (GTA) like protein; gene transfer agent (GTA) like protein 259682 4581641 Pden_3077 Paracoccus denitrificans PD1222 gene transfer agent (GTA) like protein YP_916854.1 256692 D 318586 CDS YP_916855.1 119385800 4581642 259693..260769 1 NC_008687.1 KEGG: rde:RD1_0477 hypothetical protein; hypothetical protein 260769 4581642 Pden_3078 Paracoccus denitrificans PD1222 hypothetical protein YP_916855.1 259693 D 318586 CDS YP_916856.1 119385801 4581643 261211..261627 1 NC_008687.1 PFAM: transposase IS200-family protein; KEGG: dra:DR1927 transposase; transposase IS200-family protein 261627 4581643 Pden_3079 Paracoccus denitrificans PD1222 transposase IS200-family protein YP_916856.1 261211 D 318586 CDS YP_916857.1 119385802 4581644 complement(261632..262105) 1 NC_008687.1 KEGG: sil:SPO2736 hypothetical protein; hypothetical protein 262105 4581644 Pden_3080 Paracoccus denitrificans PD1222 hypothetical protein YP_916857.1 261632 R 318586 CDS YP_916858.1 119385803 4581645 complement(262396..263058) 1 NC_008687.1 hypothetical protein 263058 4581645 Pden_3081 Paracoccus denitrificans PD1222 hypothetical protein YP_916858.1 262396 R 318586 CDS YP_916859.1 119385804 4581646 complement(263530..267024) 1 NC_008687.1 TIGRFAM: outer membrane autotransporter barrel domain; PFAM: Autotransporter beta- domain protein; KEGG: zmo:ZMO0213 autotransporter; outer membrane autotransporter 267024 4581646 Pden_3082 Paracoccus denitrificans PD1222 outer membrane autotransporter YP_916859.1 263530 R 318586 CDS YP_916860.1 119385805 4581647 267354..267965 1 NC_008687.1 KEGG: rsp:RSP_2718 possible outer membrane protein; outer membrane protein 267965 4581647 Pden_3083 Paracoccus denitrificans PD1222 outer membrane protein YP_916860.1 267354 D 318586 CDS YP_916861.1 119385806 4581648 268005..268373 1 NC_008687.1 KEGG: nwi:Nwi_1490 lipoprotein; lipoprotein 268373 4581648 Pden_3084 Paracoccus denitrificans PD1222 lipoprotein YP_916861.1 268005 D 318586 CDS YP_916862.1 119385807 4581649 268564..268971 1 NC_008687.1 PFAM: protein of unknown function DUF1311; KEGG: pfo:Pfl_3894 protein of unknown function DUF1311; hypothetical protein 268971 4581649 Pden_3085 Paracoccus denitrificans PD1222 hypothetical protein YP_916862.1 268564 D 318586 CDS YP_916863.1 119385808 4581650 268991..269851 1 NC_008687.1 KEGG: sme:SMb21025 hypothetical protein; hypothetical protein 269851 4581650 Pden_3086 Paracoccus denitrificans PD1222 hypothetical protein YP_916863.1 268991 D 318586 CDS YP_916864.1 119385809 4581651 270066..271148 1 NC_008687.1 PFAM: extracellular solute-binding protein, family 3; SMART: ionotropic glutamate receptor; KEGG: gbe:GbCGDNIH1_1769 glutamate-gated potassium channel; extracellular solute-binding protein 271148 4581651 Pden_3087 Paracoccus denitrificans PD1222 extracellular solute-binding protein YP_916864.1 270066 D 318586 CDS YP_916865.1 119385810 4581652 complement(271163..271765) 1 NC_008687.1 KEGG: mlo:mll4938 hypothetical protein; hypothetical protein 271765 4581652 Pden_3088 Paracoccus denitrificans PD1222 hypothetical protein YP_916865.1 271163 R 318586 CDS YP_916866.1 119385811 4581653 complement(271811..272704) 1 NC_008687.1 PFAM: helix-turn-helix- domain containing protein, AraC type; KEGG: mes:Meso_3689 transcriptional regulator, AraC family; helix-turn-helix domain-containing protein 272704 4581653 Pden_3089 Paracoccus denitrificans PD1222 helix-turn-helix domain-containing protein YP_916866.1 271811 R 318586 CDS YP_916867.1 119385812 4581654 complement(273007..273519) 1 NC_008687.1 hypothetical protein 273519 4581654 Pden_3090 Paracoccus denitrificans PD1222 hypothetical protein YP_916867.1 273007 R 318586 CDS YP_916868.1 119385813 4581655 complement(273579..274733) 1 NC_008687.1 PFAM: phage integrase family protein; KEGG: sit:TM1040_3585 phage integrase; phage integrase family protein 274733 4581655 Pden_3091 Paracoccus denitrificans PD1222 phage integrase family protein YP_916868.1 273579 R 318586 CDS YP_916869.1 119385814 4581656 274853..276391 1 NC_008687.1 KEGG: rpe:RPE_2955 hypothetical protein; hypothetical protein 276391 4581656 Pden_3092 Paracoccus denitrificans PD1222 hypothetical protein YP_916869.1 274853 D 318586 CDS YP_916870.1 119385815 4581657 276953..278287 1 NC_008687.1 KEGG: rsp:RSP_0491 hydrogen uptake histidine-kinase; TIGRFAM: PAS sensor protein; PFAM: ATP-binding region, ATPase domain protein domain protein; histidine kinase A domain protein domain protein; PAS fold-4 domain protein; PAS fold domain protein; SMART: PAS domain containing protein; PAS/PAC sensor signal transduction histidine kinase 278287 4581657 Pden_3093 Paracoccus denitrificans PD1222 PAS/PAC sensor signal transduction histidine kinase YP_916870.1 276953 D 318586 CDS YP_916871.1 119385816 4581658 278284..279273 1 NC_008687.1 PFAM: NADH ubiquinone oxidoreductase, 20 kDa subunit; KEGG: rsp:RSP_0492 hydrogenase small subunit; NADH ubiquinone oxidoreductase, 20 kDa subunit 279273 4581658 Pden_3094 Paracoccus denitrificans PD1222 NADH ubiquinone oxidoreductase, 20 kDa subunit YP_916871.1 278284 D 318586 CDS YP_916872.1 119385817 4581659 279291..280724 1 NC_008687.1 PFAM: nickel-dependent hydrogenase, large subunit; KEGG: rsp:RSP_0493 hydrogenase large subunit; nickel-dependent hydrogenase, large subunit 280724 4581659 Pden_3095 Paracoccus denitrificans PD1222 nickel-dependent hydrogenase, large subunit YP_916872.1 279291 D 318586 CDS YP_916873.1 119385818 4581660 280745..282994 1 NC_008687.1 TIGRFAM: [NiFe] hydrogenase maturation protein HypF; PFAM: acylphosphatase; SUA5/yciO/yrdC, N-terminal domain; zinc finger, HypF domain protein; KEGG: rsp:RSP_0494 hydrogenase maturation factor F; (NiFe) hydrogenase maturation protein HypF 282994 4581660 Pden_3096 Paracoccus denitrificans PD1222 (NiFe) hydrogenase maturation protein HypF YP_916873.1 280745 D 318586 CDS YP_916874.1 119385819 4581661 283197..284282 1 NC_008687.1 KEGG: rsp:RSP_0495 hydrogenase small subunit; TIGRFAM: hydrogenase (NiFe) small subunit HydA; PFAM: NADH ubiquinone oxidoreductase, 20 kDa subunit; Nickel-iron dehydrogenase small subunit, N-terminal domain protein; hydrogenase (NiFe) small subunit HydA 284282 4581661 Pden_3097 Paracoccus denitrificans PD1222 hydrogenase (NiFe) small subunit HydA YP_916874.1 283197 D 318586 CDS YP_916875.1 119385820 4581662 284286..286079 1 NC_008687.1 PFAM: nickel-dependent hydrogenase, large subunit; KEGG: rsp:RSP_0496 hydrogenase large subunit; nickel-dependent hydrogenase, large subunit 286079 4581662 Pden_3098 Paracoccus denitrificans PD1222 nickel-dependent hydrogenase, large subunit YP_916875.1 284286 D 318586 CDS YP_916876.1 119385821 4581663 286095..286679 1 NC_008687.1 PFAM: HupE/UreJ protein; KEGG: rsp:RSP_0497 HupE/UreJ accessory protein; HupE/UreJ protein 286679 4581663 Pden_3099 Paracoccus denitrificans PD1222 HupE/UreJ protein YP_916876.1 286095 D 318586 CDS YP_916877.1 119385822 4581664 286684..287430 1 NC_008687.1 TIGRFAM: Ni/Fe-hydrogenase, b-type cytochrome subunit; PFAM: cytochrome B561; KEGG: aeh:Mlg_2027 Ni/Fe-hydrogenase, b-type cytochrome subunit; Ni/Fe-hydrogenase, b-type cytochrome subunit 287430 4581664 Pden_3100 Paracoccus denitrificans PD1222 Ni/Fe-hydrogenase, b-type cytochrome subunit YP_916877.1 286684 D 318586 CDS YP_916878.1 119385823 4581665 287636..288304 1 NC_008687.1 TIGRFAM: hydrogenase maturation protease; hydrogenase expression/formation protein; hydrogenase maturation peptidase superfamily; PFAM: peptidase M52, hydrogen uptake protein; KEGG: rsp:RSP_0499 HycI, hydrogenase maturation protease; hydrogenase expression/formation protein 288304 4581665 Pden_3101 Paracoccus denitrificans PD1222 hydrogenase expression/formation protein YP_916878.1 287636 D 318586 CDS YP_916879.1 119385824 4581666 288304..288615 1 NC_008687.1 PFAM: hydrogenase expression/formation protein (HUPF/HYPC); KEGG: rsp:RSP_0500 HupF/HypC hydrogenase; hydrogenase expression/formation protein HupF/HypC 288615 4581666 Pden_3102 Paracoccus denitrificans PD1222 hydrogenase expression/formation protein HupF/HypC YP_916879.1 288304 D 318586 CDS YP_916880.1 119385825 4581667 288619..289038 1 NC_008687.1 PFAM: hydrogenase-1 expression HyaE; KEGG: rsp:RSP_0501 HupG hydrogenase expression/formation protein; hydrogenase-1 expression HyaE 289038 4581667 Pden_3103 Paracoccus denitrificans PD1222 hydrogenase-1 expression HyaE YP_916880.1 288619 D 318586 CDS YP_916881.1 119385826 4581668 289051..289884 1 NC_008687.1 PFAM: HupH hydrogenase expression protein; KEGG: rsp:RSP_0502 HupH hydrogenase expression/formation protein; HupH hydrogenase expression protein 289884 4581668 Pden_3104 Paracoccus denitrificans PD1222 HupH hydrogenase expression protein YP_916881.1 289051 D 318586 CDS YP_916882.1 119385827 4581669 289881..290732 1 NC_008687.1 PFAM: Rubredoxin-type Fe(Cys)4 protein; KEGG: rsp:RSP_0503 HupJ, contains rubredoxin domain; rubredoxin-type Fe(Cys)4 protein 290732 4581669 Pden_3105 Paracoccus denitrificans PD1222 rubredoxin-type Fe(Cys)4 protein YP_916882.1 289881 D 318586 CDS YP_916883.1 119385828 4581670 290729..291631 1 NC_008687.1 KEGG: rsp:RSP_0504 HupK; HupK protein 291631 4581670 Pden_3106 Paracoccus denitrificans PD1222 HupK protein YP_916883.1 290729 D 318586 CDS YP_916884.1 119385829 4581671 291624..291965 1 NC_008687.1 TIGRFAM: hydrogenase nickel insertion protein HypA; PFAM: hydrogenase expression/synthesis, HypA; KEGG: rsp:RSP_0505 hydrogenase expression/synthesis, HypA family; hydrogenase nickel incorporation protein HypA 291965 4581671 Pden_3107 Paracoccus denitrificans PD1222 hydrogenase nickel incorporation protein HypA YP_916884.1 291624 D 318586 CDS YP_916885.1 119385830 4581672 291965..292885 1 NC_008687.1 TIGRFAM: hydrogenase accessory protein HypB; PFAM: cobalamin synthesis protein, P47K; KEGG: rsp:RSP_0506 NI2+-binding GTPase HypB; hydrogenase nickel incorporation protein HypB 292885 4581672 Pden_3108 Paracoccus denitrificans PD1222 hydrogenase nickel incorporation protein HypB YP_916885.1 291965 D 318586 CDS YP_916886.1 119385831 4581673 292889..294370 1 NC_008687.1 PFAM: response regulator receiver; sigma-54 factor, interaction domain-containing protein; helix-turn-helix, Fis-type; KEGG: rsp:RSP_0507 HupR response regulator; two component, sigma54 specific, Fis family transcriptional regulator 294370 4581673 Pden_3109 Paracoccus denitrificans PD1222 two component, sigma54 specific, Fis family transcriptional regulator YP_916886.1 292889 D 318586 CDS YP_916887.1 119385832 4581674 294373..294657 1 NC_008687.1 TIGRFAM: hydrogenase assembly chaperone hypC/hupF; PFAM: hydrogenase expression/formation protein (HUPF/HYPC); KEGG: rsp:RSP_0508 hydrogenase expression/formation protein HypC; hydrogenase assembly chaperone HypC/HupF 294657 4581674 Pden_3110 Paracoccus denitrificans PD1222 hydrogenase assembly chaperone HypC/HupF YP_916887.1 294373 D 318586 CDS YP_916888.1 119385833 4581675 294654..295790 1 NC_008687.1 TIGRFAM: hydrogenase expression/formation protein HypD; PFAM: hydrogenase formation HypD protein; KEGG: rsp:RSP_0509 hydrogenase isoenzyme formation protein HypD; hydrogenase expression/formation protein HypD 295790 4581675 Pden_3111 Paracoccus denitrificans PD1222 hydrogenase expression/formation protein HypD YP_916888.1 294654 D 318586 CDS YP_916889.1 119385834 4581676 295803..296858 1 NC_008687.1 TIGRFAM: hydrogenase expression/formation protein HypE; PFAM: AIR synthase related protein; AIR synthase related protein domain protein; KEGG: rsp:RSP_0510 hydrogenase expression/formation protein HypE; hydrogenase expression/formation protein HypE 296858 4581676 Pden_3112 Paracoccus denitrificans PD1222 hydrogenase expression/formation protein HypE YP_916889.1 295803 D 318586 CDS YP_916890.1 119385835 4581677 297085..297600 1 NC_008687.1 hypothetical protein 297600 4581677 Pden_3113 Paracoccus denitrificans PD1222 hypothetical protein YP_916890.1 297085 D 318586 CDS YP_916891.1 119385836 4581678 complement(297507..298544) 1 NC_008687.1 PFAM: CBS domain containing protein; protein of unknown function DUF21; KEGG: rha:RHA1_ro03326 possible CBS domain-containing protein; hypothetical protein 298544 4581678 Pden_3114 Paracoccus denitrificans PD1222 hypothetical protein YP_916891.1 297507 R 318586 CDS YP_916892.1 119385837 4581679 complement(298541..299911) 1 NC_008687.1 PFAM: CBS domain containing protein; protein of unknown function DUF21; transporter-associated region; KEGG: nfa:nfa28250 hypothetical protein; hypothetical protein 299911 4581679 Pden_3115 Paracoccus denitrificans PD1222 hypothetical protein YP_916892.1 298541 R 318586 CDS YP_916893.1 119385838 4581680 complement(300689..301594) 1 NC_008687.1 PFAM: helix-turn-helix- domain containing protein, AraC type; KEGG: bxe:Bxe_C1385 transcriptional regulator, AraC family; helix-turn-helix domain-containing protein 301594 4581680 Pden_3116 Paracoccus denitrificans PD1222 helix-turn-helix domain-containing protein YP_916893.1 300689 R 318586 CDS YP_916894.1 119385839 4581681 301647..302417 1 NC_008687.1 PFAM: short-chain dehydrogenase/reductase SDR; KEGG: mmc:Mmcs_1038 short-chain dehydrogenase/reductase SDR; short-chain dehydrogenase/reductase SDR 302417 4581681 Pden_3117 Paracoccus denitrificans PD1222 short-chain dehydrogenase/reductase SDR YP_916894.1 301647 D 318586 CDS YP_916895.1 119385840 4581682 complement(302450..303199) 1 NC_008687.1 catalyzes the removal of N-terminal amino acids from peptides and arylamides; generally Co(II) however activity has been shown for some methionine aminopeptidases with Zn, Fe, or Mn; methionine aminopeptidase 303199 4581682 Pden_3118 Paracoccus denitrificans PD1222 methionine aminopeptidase YP_916895.1 302450 R 318586 CDS YP_916896.1 119385841 4581683 303258..303755 1 NC_008687.1 PFAM: protein of unknown function UPF0074; Helix-turn-helix, type 11 domain protein; KEGG: rpb:RPB_3952 transcriptional regulator, BadM/Rrf2 family; BadM/Rrf2 family transcriptional regulator 303755 4581683 Pden_3119 Paracoccus denitrificans PD1222 BadM/Rrf2 family transcriptional regulator YP_916896.1 303258 D 318586 CDS YP_916897.1 119385842 4581684 303759..304643 1 NC_008687.1 PFAM: FAD-dependent pyridine nucleotide-disulphide oxidoreductase; KEGG: rpb:RPB_3951 FAD-dependent pyridine nucleotide-disulphide oxidoreductase; FAD-dependent pyridine nucleotide-disulfide oxidoreductase 304643 4581684 Pden_3120 Paracoccus denitrificans PD1222 FAD-dependent pyridine nucleotide-disulfide oxidoreductase YP_916897.1 303759 D 318586 CDS YP_916898.1 119385843 4581685 304640..305311 1 NC_008687.1 PFAM: Methyltransferase type 11; Methyltransferase type 12; KEGG: rpb:RPB_3655 SAM binding protein; methyltransferase type 12 305311 4581685 Pden_3121 Paracoccus denitrificans PD1222 methyltransferase type 12 YP_916898.1 304640 D 318586 CDS YP_916899.1 119385844 4581686 complement(305322..306503) 1 NC_008687.1 PFAM: phage integrase family protein; KEGG: sit:TM1040_3585 phage integrase; phage integrase family protein 306503 4581686 Pden_3122 Paracoccus denitrificans PD1222 phage integrase family protein YP_916899.1 305322 R 318586 CDS YP_916900.1 119385845 4581687 complement(306693..308351) 1 NC_008687.1 PFAM: Resolvase, N-terminal domain; Recombinase; KEGG: nha:Nham_3864 recombinase; recombinase 308351 4581687 Pden_3123 Paracoccus denitrificans PD1222 recombinase YP_916900.1 306693 R 318586 CDS YP_916901.1 119385846 4581688 complement(308371..308598) 1 NC_008687.1 hypothetical protein 308598 4581688 Pden_3124 Paracoccus denitrificans PD1222 hypothetical protein YP_916901.1 308371 R 318586 CDS YP_916902.1 119385847 4581689 complement(308737..309381) 1 NC_008687.1 KEGG: rde:RD1_1995 hypothetical protein; hypothetical protein 309381 4581689 Pden_3125 Paracoccus denitrificans PD1222 hypothetical protein YP_916902.1 308737 R 318586 CDS YP_916903.1 119385848 4581690 complement(309663..310022) 1 NC_008687.1 hypothetical protein 310022 4581690 Pden_3126 Paracoccus denitrificans PD1222 hypothetical protein YP_916903.1 309663 R 318586 CDS YP_916904.1 119385849 4581691 complement(310237..310989) 1 NC_008687.1 PFAM: Peptidase C24, Calicivirus polyprotein ORF 1; KEGG: rpd:RPD_2286 hypothetical protein; peptidase C24 310989 4581691 Pden_3127 Paracoccus denitrificans PD1222 peptidase C24 YP_916904.1 310237 R 318586 CDS YP_916905.1 119385850 4581692 complement(311064..312305) 1 NC_008687.1 KEGG: nar:Saro_2202 hypothetical protein; hypothetical protein 312305 4581692 Pden_3128 Paracoccus denitrificans PD1222 hypothetical protein YP_916905.1 311064 R 318586 CDS YP_916906.1 119385851 4581693 complement(312313..313308) 1 NC_008687.1 PFAM: SMF family protein; KEGG: nar:Saro_2201 smf protein; SMF family protein 313308 4581693 Pden_3129 Paracoccus denitrificans PD1222 SMF family protein YP_916906.1 312313 R 318586 CDS YP_916907.1 119385852 4581694 313398..313784 1 NC_008687.1 KEGG: nwi:Nwi_0831 phage integrase; phage integrase 313784 4581694 Pden_3130 Paracoccus denitrificans PD1222 phage integrase YP_916907.1 313398 D 318586 CDS YP_916908.1 119385853 4581695 complement(314148..315512) 1 NC_008687.1 TIGRFAM: chromate transporter, chromate ion transporter (CHR) family; PFAM: Chromate transporter; KEGG: sme:SMc00808 chromate transport protein; chromate transporter 315512 4581695 Pden_3131 Paracoccus denitrificans PD1222 chromate transporter YP_916908.1 314148 R 318586 CDS YP_916909.1 119385854 4581696 complement(315509..316354) 1 NC_008687.1 SMART: Rhodanese domain protein; KEGG: mlo:mlr5406 hypothetical protein; rhodanese domain-containing protein 316354 4581696 Pden_3132 Paracoccus denitrificans PD1222 rhodanese domain-containing protein YP_916909.1 315509 R 318586 CDS YP_916910.1 119385855 4581697 complement(316569..317276) 1 NC_008687.1 PFAM: NADPH-dependent FMN reductase; KEGG: rsp:RSP_2731 arsenical resistance protein, ArsH; NADPH-dependent FMN reductase 317276 4581697 Pden_3133 Paracoccus denitrificans PD1222 NADPH-dependent FMN reductase YP_916910.1 316569 R 318586 CDS YP_916911.1 119385856 4581698 complement(317273..318346) 1 NC_008687.1 TIGRFAM: arsenical-resistance protein; PFAM: Bile acid:sodium symporter; KEGG: sal:Sala_2405 arsenical-resistance protein; arsenical-resistance protein 318346 4581698 Pden_3134 Paracoccus denitrificans PD1222 arsenical-resistance protein YP_916911.1 317273 R 318586 CDS YP_916912.1 119385857 4581699 complement(318359..318784) 1 NC_008687.1 TIGRFAM: arsenate reductase; PFAM: arsenate reductase and related; KEGG: sal:Sala_2539 arsenate reductase; arsenate reductase 318784 4581699 Pden_3135 Paracoccus denitrificans PD1222 arsenate reductase YP_916912.1 318359 R 318586 CDS YP_916913.1 119385858 4581700 complement(318787..319146) 1 NC_008687.1 PFAM: regulatory protein, ArsR; KEGG: nwi:Nwi_3123 transcriptional regulatory protein, ArsR family; regulatory protein ArsR 319146 4581700 Pden_3136 Paracoccus denitrificans PD1222 regulatory protein ArsR YP_916913.1 318787 R 318586 CDS YP_916914.1 119385859 4581701 complement(319199..319678) 1 NC_008687.1 hypothetical protein 319678 4581701 Pden_3137 Paracoccus denitrificans PD1222 hypothetical protein YP_916914.1 319199 R 318586 CDS YP_916915.1 119385860 4581702 complement(320014..320844) 1 NC_008687.1 hypothetical protein 320844 4581702 Pden_3138 Paracoccus denitrificans PD1222 hypothetical protein YP_916915.1 320014 R 318586 CDS YP_916916.1 119385861 4581703 320864..321223 1 NC_008687.1 hypothetical protein 321223 4581703 Pden_3139 Paracoccus denitrificans PD1222 hypothetical protein YP_916916.1 320864 D 318586 CDS YP_916917.1 119385862 4581704 321481..321687 1 NC_008687.1 PFAM: Cold-shock protein, DNA-binding; SMART: Cold shock protein; KEGG: rsp:RSP_3621 cold-shock DNA-binding protein; cold-shock DNA-binding domain-containing protein 321687 4581704 Pden_3140 Paracoccus denitrificans PD1222 cold-shock DNA-binding domain-containing protein YP_916917.1 321481 D 318586 CDS YP_916918.1 119385863 4581705 321760..322095 1 NC_008687.1 KEGG: rsp:RSP_3622 hypothetical protein; hypothetical protein 322095 4581705 Pden_3141 Paracoccus denitrificans PD1222 hypothetical protein YP_916918.1 321760 D 318586 CDS YP_916919.1 119385864 4581706 complement(322388..322627) 1 NC_008687.1 hypothetical protein 322627 4581706 Pden_3142 Paracoccus denitrificans PD1222 hypothetical protein YP_916919.1 322388 R 318586 CDS YP_916920.1 119385865 4581707 322642..322848 1 NC_008687.1 PFAM: Cold-shock protein, DNA-binding; SMART: Cold shock protein; KEGG: sil:SPO3625 cold shock protein CspA; cold-shock DNA-binding domain-containing protein 322848 4581707 Pden_3143 Paracoccus denitrificans PD1222 cold-shock DNA-binding domain-containing protein YP_916920.1 322642 D 318586 CDS YP_916921.1 119385866 4581708 322903..323103 1 NC_008687.1 hypothetical protein 323103 4581708 Pden_3144 Paracoccus denitrificans PD1222 hypothetical protein YP_916921.1 322903 D 318586 CDS YP_916922.1 119385867 4581709 323419..323967 1 NC_008687.1 PFAM: heat shock protein Hsp20; KEGG: ret:RHE_CH01244 probable molecular chaperone small heat shock protein, HSP20 family; heat shock protein Hsp20 323967 4581709 Pden_3145 Paracoccus denitrificans PD1222 heat shock protein Hsp20 YP_916922.1 323419 D 318586 CDS YP_916923.1 119385868 4581710 324049..324552 1 NC_008687.1 PFAM: heat shock protein Hsp20; KEGG: ret:RHE_CH01245 probable molecular chaperone small heat shock protein, HSP20 family; heat shock protein Hsp20 324552 4581710 Pden_3146 Paracoccus denitrificans PD1222 heat shock protein Hsp20 YP_916923.1 324049 D 318586 CDS YP_916924.1 119385869 4581711 324652..325017 1 NC_008687.1 KEGG: ret:RHE_CH01246 hypothetical protein; hypothetical protein 325017 4581711 Pden_3147 Paracoccus denitrificans PD1222 hypothetical protein YP_916924.1 324652 D 318586 CDS YP_916925.1 119385870 4581712 325116..326492 1 NC_008687.1 TIGRFAM: protease Do; PFAM: peptidase S1 and S6, chymotrypsin/Hap; PDZ/DHR/GLGF domain protein; KEGG: nmu:Nmul_A0510 peptidase S1C, Do; protease Do 326492 4581712 Pden_3148 Paracoccus denitrificans PD1222 protease Do YP_916925.1 325116 D 318586 CDS YP_916926.1 119385871 4581713 complement(326590..327381) 1 NC_008687.1 PFAM: Phytanoyl-CoA dioxygenase; KEGG: mxa:MXAN_4531 hypothetical protein; phytanoyl-CoA dioxygenase 327381 4581713 Pden_3149 Paracoccus denitrificans PD1222 phytanoyl-CoA dioxygenase YP_916926.1 326590 R 318586 CDS YP_916927.1 119385872 4581714 complement(327688..328374) 1 NC_008687.1 PFAM: protein of unknown function DUF899, thioredoxin family protein; KEGG: pfo:Pfl_1441 protein of unknown function DUF899, thioredoxin-like; hypothetical protein 328374 4581714 Pden_3150 Paracoccus denitrificans PD1222 hypothetical protein YP_916927.1 327688 R 318586 CDS YP_916928.1 119385873 4581715 328642..329901 1 NC_008687.1 PFAM: Tetratricopeptide TPR_4; KEGG: mes:Meso_0992 tetratricopeptide TPR_4; hypothetical protein 329901 4581715 Pden_3151 Paracoccus denitrificans PD1222 hypothetical protein YP_916928.1 328642 D 318586 CDS YP_916929.1 119385874 4581716 329911..330552 1 NC_008687.1 KEGG: mes:Meso_0991 hypothetical protein; hypothetical protein 330552 4581716 Pden_3152 Paracoccus denitrificans PD1222 hypothetical protein YP_916929.1 329911 D 318586 CDS YP_916930.1 119385875 4581717 330661..331068 1 NC_008687.1 PFAM: Cupin 2, conserved barrel domain protein; KEGG: pol:Bpro_3707 cupin 2, conserved barrel; cupin 331068 4581717 Pden_3153 Paracoccus denitrificans PD1222 cupin YP_916930.1 330661 D 318586 CDS YP_916931.1 119385876 4581718 331073..331906 1 NC_008687.1 PFAM: aminoglycoside 3-N-acetyltransferase; KEGG: gvi:gll0484 aminoglycoside N3'-acetyltransferase; aminoglycoside N(3')-acetyltransferase 331906 4581718 Pden_3154 Paracoccus denitrificans PD1222 aminoglycoside N(3')-acetyltransferase YP_916931.1 331073 D 318586 CDS YP_916932.1 119385877 4581719 331919..332353 1 NC_008687.1 PFAM: Methyltransferase type 11; Methyltransferase type 12; KEGG: gvi:glr1626 hypothetical protein; methyltransferase type 12 332353 4581719 Pden_3155 Paracoccus denitrificans PD1222 methyltransferase type 12 YP_916932.1 331919 D 318586 CDS YP_916933.1 119385878 4581720 332449..332766 1 NC_008687.1 PFAM: histone family protein nucleoid-structuring protein H-NS; KEGG: jan:Jann_4229 histone-like nucleoid-structuring protein H-NS; histone family protein nucleoid-structuring protein H-NS 332766 4581720 Pden_3156 Paracoccus denitrificans PD1222 histone family protein nucleoid-structuring protein H-NS YP_916933.1 332449 D 318586 CDS YP_916934.1 119385879 4581721 332782..333399 1 NC_008687.1 PFAM: plasmid pRiA4b ORF-3 family protein; KEGG: sme:SMa0896 hypothetical protein; plasmid pRiA4b ORF-3 family protein 333399 4581721 Pden_3157 Paracoccus denitrificans PD1222 plasmid pRiA4b ORF-3 family protein YP_916934.1 332782 D 318586 CDS YP_916935.1 119385880 4581722 333475..333834 1 NC_008687.1 hypothetical protein 333834 4581722 Pden_3158 Paracoccus denitrificans PD1222 hypothetical protein YP_916935.1 333475 D 318586 CDS YP_916936.1 119385881 4581723 333864..334322 1 NC_008687.1 PFAM: GCN5-related N-acetyltransferase; KEGG: sal:Sala_0626 gentamicin 3'-N-acetyltransferase; gentamicin 3'-N-acetyltransferase 334322 4581723 Pden_3159 Paracoccus denitrificans PD1222 gentamicin 3'-N-acetyltransferase YP_916936.1 333864 D 318586 CDS YP_916937.1 119385882 4581724 complement(334803..335831) 1 NC_008687.1 PFAM: transposase, IS111A/IS1328/IS1533; transposase IS116/IS110/IS902 family protein; KEGG: nha:Nham_3955 transposase IS116/IS110/IS902; transposase IS116/IS110/IS902 family protein 335831 4581724 Pden_3160 Paracoccus denitrificans PD1222 transposase IS116/IS110/IS902 family protein YP_916937.1 334803 R 318586 CDS YP_916938.1 119385883 4581725 335940..336263 1 NC_008687.1 PFAM: transposase IS3/IS911 family protein; KEGG: nwi:Nwi_2119 transposase IS3/IS911; transposase IS3/IS911 family protein 336263 4581725 Pden_3161 Paracoccus denitrificans PD1222 transposase IS3/IS911 family protein YP_916938.1 335940 D 318586 CDS YP_916939.1 119385884 4581726 336263..337168 1 NC_008687.1 PFAM: Integrase, catalytic region; KEGG: nwi:Nwi_2120 integrase, catalytic region; integrase catalytic subunit 337168 4581726 Pden_3162 Paracoccus denitrificans PD1222 integrase catalytic subunit YP_916939.1 336263 D 318586 CDS YP_916940.1 119385885 4581727 337267..337683 1 NC_008687.1 KEGG: mes:Meso_3831 hypothetical protein; hypothetical protein 337683 4581727 Pden_3163 Paracoccus denitrificans PD1222 hypothetical protein YP_916940.1 337267 D 318586 CDS YP_916941.1 119385886 4581728 338133..338810 1 NC_008687.1 PFAM: DNA methylase N-4/N-6 domain protein; KEGG: ret:RHE_CH01977 probable DNA-methyltransferase (hemagglutinin-associated protein); DNA methylase N-4/N-6 domain-containing protein 338810 4581728 Pden_3164 Paracoccus denitrificans PD1222 DNA methylase N-4/N-6 domain-containing protein YP_916941.1 338133 D 318586 CDS YP_916942.1 119385887 4581729 338882..339184 1 NC_008687.1 hypothetical protein 339184 4581729 Pden_3165 Paracoccus denitrificans PD1222 hypothetical protein YP_916942.1 338882 D 318586 CDS YP_916943.1 119385888 4581730 339330..340253 1 NC_008687.1 PFAM: protein of unknown function DUF81; KEGG: rsp:RSP_1646 possible transmembrane protein; hypothetical protein 340253 4581730 Pden_3166 Paracoccus denitrificans PD1222 hypothetical protein YP_916943.1 339330 D 318586 CDS YP_916944.1 119385889 4581731 341031..341438 1 NC_008687.1 TIGRFAM: single-strand binding protein; PFAM: single-strand binding protein/Primosomal replication protein n; KEGG: nha:Nham_4669 single-strand binding protein; single-strand binding protein 341438 4581731 Pden_3167 Paracoccus denitrificans PD1222 single-strand binding protein YP_916944.1 341031 D 318586 CDS YP_916945.1 119385890 4581732 341929..342132 1 NC_008687.1 hypothetical protein 342132 4581732 Pden_3168 Paracoccus denitrificans PD1222 hypothetical protein YP_916945.1 341929 D 318586 CDS YP_916946.1 119385891 4581733 342234..342449 1 NC_008687.1 hypothetical protein 342449 4581733 Pden_3169 Paracoccus denitrificans PD1222 hypothetical protein YP_916946.1 342234 D 318586 CDS YP_916947.1 119385892 4581734 342529..342795 1 NC_008687.1 hypothetical protein 342795 4581734 Pden_3170 Paracoccus denitrificans PD1222 hypothetical protein YP_916947.1 342529 D 318586 CDS YP_916948.1 119385893 4581735 complement(342906..343163) 1 NC_008687.1 PFAM: helix-turn-helix domain protein; KEGG: ret:RHE_PA00165 transcriptional regulator protein; XRE family transcriptional regulator 343163 4581735 Pden_3171 Paracoccus denitrificans PD1222 XRE family transcriptional regulator YP_916948.1 342906 R 318586 CDS YP_916949.1 119385894 4581736 343217..343663 1 NC_008687.1 KEGG: mes:Meso_0527 hypothetical protein; hypothetical protein 343663 4581736 Pden_3172 Paracoccus denitrificans PD1222 hypothetical protein YP_916949.1 343217 D 318586 CDS YP_916950.1 119385895 4581737 343788..344096 1 NC_008687.1 KEGG: mes:Meso_0526 hypothetical protein; hypothetical protein 344096 4581737 Pden_3173 Paracoccus denitrificans PD1222 hypothetical protein YP_916950.1 343788 D 318586 CDS YP_916951.1 119385896 4581738 344116..344568 1 NC_008687.1 KEGG: mes:Meso_0525 hypothetical protein; hypothetical protein 344568 4581738 Pden_3174 Paracoccus denitrificans PD1222 hypothetical protein YP_916951.1 344116 D 318586 CDS YP_916952.1 119385897 4581739 344690..345589 1 NC_008687.1 PFAM: protein of unknown function DUF6, transmembrane; KEGG: sit:TM1040_2078 protein of unknown function DUF6, transmembrane; hypothetical protein 345589 4581739 Pden_3175 Paracoccus denitrificans PD1222 hypothetical protein YP_916952.1 344690 D 318586 CDS YP_916953.1 119385898 4581740 complement(345773..346171) 1 NC_008687.1 KEGG: sme:SMc01177 hypothetical protein; hypothetical protein 346171 4581740 Pden_3176 Paracoccus denitrificans PD1222 hypothetical protein YP_916953.1 345773 R 318586 CDS YP_916954.1 119385899 4581741 complement(346168..346452) 1 NC_008687.1 TIGRFAM: transcriptional regulator, AbrB family; PFAM: SpoVT/AbrB domain protein; KEGG: sme:SMc01176 hypothetical protein; AbrB family transcriptional regulator 346452 4581741 Pden_3177 Paracoccus denitrificans PD1222 AbrB family transcriptional regulator YP_916954.1 346168 R 318586 CDS YP_916955.1 119385900 4581742 346610..346891 1 NC_008687.1 KEGG: mes:Meso_3841 transcriptional regulator; transcriptional regulator 346891 4581742 Pden_3178 Paracoccus denitrificans PD1222 transcriptional regulator YP_916955.1 346610 D 318586 CDS YP_916956.1 119385901 4581743 346902..348014 1 NC_008687.1 KEGG: mes:Meso_3842 replication protein A; replication protein A 348014 4581743 Pden_3179 Paracoccus denitrificans PD1222 replication protein A YP_916956.1 346902 D 318586 CDS YP_916957.1 119385902 4581744 348011..348313 1 NC_008687.1 hypothetical protein 348313 4581744 Pden_3180 Paracoccus denitrificans PD1222 hypothetical protein YP_916957.1 348011 D 318586 CDS YP_916958.1 119385903 4581745 348310..348798 1 NC_008687.1 KEGG: mes:Meso_2334 hypothetical protein; hypothetical protein 348798 4581745 Pden_3181 Paracoccus denitrificans PD1222 hypothetical protein YP_916958.1 348310 D 318586 CDS YP_916959.1 119385904 4581746 348795..350282 1 NC_008687.1 PFAM: C-5 cytosine-specific DNA methylase; KEGG: ngo:NGO1894 5-methylcytosine methyltransferase; C-5 cytosine-specific DNA methylase 350282 4581746 Pden_3182 Paracoccus denitrificans PD1222 C-5 cytosine-specific DNA methylase YP_916959.1 348795 D 318586 CDS YP_916960.1 119385905 4581747 350279..350881 1 NC_008687.1 KEGG: mes:Meso_3845 conjugal transfer protein precursor; conjugal transfer protein precursor 350881 4581747 Pden_3183 Paracoccus denitrificans PD1222 conjugal transfer protein precursor YP_916960.1 350279 D 318586 CDS YP_916961.1 119385906 4581748 350878..351216 1 NC_008687.1 PFAM: protein of unknown function DUF736; KEGG: mes:Meso_2332 protein of unknown function DUF736; hypothetical protein 351216 4581748 Pden_3184 Paracoccus denitrificans PD1222 hypothetical protein YP_916961.1 350878 D 318586 CDS YP_916962.1 119385907 4581749 351220..352026 1 NC_008687.1 PFAM: Lytic transglycosylase, catalytic; KEGG: mes:Meso_0517 lytic transglycosylase, catalytic; lytic transglycosylase, catalytic 352026 4581749 Pden_3185 Paracoccus denitrificans PD1222 lytic transglycosylase, catalytic YP_916962.1 351220 D 318586 CDS YP_916963.1 119385908 4581750 352076..352657 1 NC_008687.1 hypothetical protein 352657 4581750 Pden_3186 Paracoccus denitrificans PD1222 hypothetical protein YP_916963.1 352076 D 318586 CDS YP_916964.1 119385909 4581751 352908..354701 1 NC_008687.1 KEGG: mes:Meso_3848 hypothetical protein; hypothetical protein 354701 4581751 Pden_3187 Paracoccus denitrificans PD1222 hypothetical protein YP_916964.1 352908 D 318586 CDS YP_916965.1 119385910 4581752 354719..356728 1 NC_008687.1 type IV secretion VirD4 coupling protein family; conjugal transfer coupling protein TraG 356728 4581752 Pden_3188 Paracoccus denitrificans PD1222 conjugal transfer coupling protein TraG YP_916965.1 354719 D 318586 CDS YP_916966.1 119385911 4581753 356759..357280 1 NC_008687.1 KEGG: mes:Meso_0514 helix-turn-helix protein, CopG; hypothetical protein 357280 4581753 Pden_3189 Paracoccus denitrificans PD1222 hypothetical protein YP_916966.1 356759 D 318586 CDS YP_916967.1 119385912 4581754 complement(357306..357827) 1 NC_008687.1 KEGG: mxa:MXAN_3433 hypothetical protein; hypothetical protein 357827 4581754 Pden_3190 Paracoccus denitrificans PD1222 hypothetical protein YP_916967.1 357306 R 318586 CDS YP_916968.1 119385913 4581755 complement(357824..358063) 1 NC_008687.1 hypothetical protein 358063 4581755 Pden_3191 Paracoccus denitrificans PD1222 hypothetical protein YP_916968.1 357824 R 318586 CDS YP_916969.1 119385914 4581756 complement(358045..358470) 1 NC_008687.1 PFAM: PilT protein domain protein; KEGG: plu:plu3057 hypothetical protein; twitching motility protein PilT 358470 4581756 Pden_3192 Paracoccus denitrificans PD1222 twitching motility protein PilT YP_916969.1 358045 R 318586 CDS YP_916970.1 119385915 4581757 complement(358467..358730) 1 NC_008687.1 KEGG: ret:RHE_PE00297 plasmid stabilization protein; plasmid stabilization protein 358730 4581757 Pden_3193 Paracoccus denitrificans PD1222 plasmid stabilization protein YP_916970.1 358467 R 318586 CDS YP_916971.1 119385916 4581758 359010..360014 1 NC_008687.1 PFAM: type II secretion system protein E; KEGG: mes:Meso_2324 type II secretion system protein E; type II secretion system protein E 360014 4581758 Pden_3194 Paracoccus denitrificans PD1222 type II secretion system protein E YP_916971.1 359010 D 318586 CDS YP_916972.1 119385917 4581759 360011..360343 1 NC_008687.1 PFAM: Conjugal transfer protein TrbC; KEGG: mes:Meso_0508 conjugal transfer protein TrbC; conjugal transfer protein TrbC 360343 4581759 Pden_3195 Paracoccus denitrificans PD1222 conjugal transfer protein TrbC YP_916972.1 360011 D 318586 CDS YP_916973.1 119385918 4581760 360343..360624 1 NC_008687.1 KEGG: mes:Meso_2322 conjugal transfer protein TrbB; conjugal transfer protein TrbB 360624 4581760 Pden_3196 Paracoccus denitrificans PD1222 conjugal transfer protein TrbB YP_916973.1 360343 D 318586 CDS YP_916974.1 119385919 4581761 360637..363270 1 NC_008687.1 type IV secretion system VirB4 family; conjugal transfer ATPase TrbE 363270 4581761 Pden_3197 Paracoccus denitrificans PD1222 conjugal transfer ATPase TrbE YP_916974.1 360637 D 318586 CDS YP_916975.1 119385920 4581762 363267..364064 1 NC_008687.1 KEGG: mes:Meso_3855 conjugal transfer protein TrbJ; conjugal transfer protein TrbJ 364064 4581762 Pden_3198 Paracoccus denitrificans PD1222 conjugal transfer protein TrbJ YP_916975.1 363267 D 318586 CDS YP_916976.1 119385921 4581763 364085..364372 1 NC_008687.1 KEGG: mes:Meso_2319 hypothetical protein; hypothetical protein 364372 4581763 Pden_3199 Paracoccus denitrificans PD1222 hypothetical protein YP_916976.1 364085 D 318586 CDS YP_916977.1 119385922 4581764 364380..365702 1 NC_008687.1 type IV secretion VirB6 family; conjugal transfer protein TrbL 365702 4581764 Pden_3200 Paracoccus denitrificans PD1222 conjugal transfer protein TrbL YP_916977.1 364380 D 318586 CDS YP_916978.1 119385923 4581765 365699..366388 1 NC_008687.1 PFAM: Conjugal transfer protein; KEGG: mes:Meso_0502 conjugal transfer protein; conjugal transfer protein TrbF 366388 4581765 Pden_3201 Paracoccus denitrificans PD1222 conjugal transfer protein TrbF YP_916978.1 365699 D 318586 CDS YP_916979.1 119385924 4581766 366385..367428 1 NC_008687.1 PFAM: Conjugal transfer protein TrbG/VirB9/CagX; KEGG: mes:Meso_0501 conjugal transfer protein TrbG/VirB9/CagX; conjugal transfer protein TrbG/VirB9/CagX 367428 4581766 Pden_3202 Paracoccus denitrificans PD1222 conjugal transfer protein TrbG/VirB9/CagX YP_916979.1 366385 D 318586 CDS YP_916980.1 119385925 4581767 367428..368594 1 NC_008687.1 PFAM: conjugation TrbI family protein; KEGG: mes:Meso_0500 conjugation TrbI-like protein; conjugation TrbI family protein 368594 4581767 Pden_3203 Paracoccus denitrificans PD1222 conjugation TrbI family protein YP_916980.1 367428 D 318586 CDS YP_916981.1 119385926 4581768 368591..368845 1 NC_008687.1 KEGG: rpc:RPC_3531 hypothetical protein; hypothetical protein 368845 4581768 Pden_3204 Paracoccus denitrificans PD1222 hypothetical protein YP_916981.1 368591 D 318586 CDS YP_916982.1 119385927 4581769 complement(368847..369791) 1 NC_008687.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: mes:Meso_3862 transcriptional regulator, LysR family; LysR family transcriptional regulator 369791 4581769 Pden_3205 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_916982.1 368847 R 318586 CDS YP_916983.1 119385928 4581770 complement(369824..370534) 1 NC_008687.1 PFAM: regulatory protein GntR, HTH; GntR domain protein; Helix-turn-helix, type 11 domain protein; KEGG: bxe:Bxe_C0266 transcriptional regulator, GntR family; regulatory protein GntR 370534 4581770 Pden_3206 Paracoccus denitrificans PD1222 regulatory protein GntR YP_916983.1 369824 R 318586 CDS YP_916984.1 119385929 4581771 complement(370806..372089) 1 NC_008687.1 TIGRFAM: TRAP dicarboxylate transporter, DctM subunit; PFAM: TRAP C4-dicarboxylate transport system permease DctM subunit; KEGG: rpd:RPD_0611 TRAP dicarboxylate transporter-DctM subunit; TRAP dicarboxylate transporter, DctM subunit 372089 4581771 Pden_3207 Paracoccus denitrificans PD1222 TRAP dicarboxylate transporter, DctM subunit YP_916984.1 370806 R 318586 CDS YP_916985.1 119385930 4581772 complement(372102..372653) 1 NC_008687.1 KEGG: rpd:RPD_0610 tripartite ATP-independent periplasmic transporter, DctQ component; hypothetical protein 372653 4581772 Pden_3208 Paracoccus denitrificans PD1222 hypothetical protein YP_916985.1 372102 R 318586 CDS YP_916986.1 119385931 4581773 complement(372650..373663) 1 NC_008687.1 PFAM: TRAP dicarboxylate transporter- DctP subunit; KEGG: bja:bll6794 hypothetical protein; TRAP dicarboxylate transporter- DctP subunit 373663 4581773 Pden_3209 Paracoccus denitrificans PD1222 TRAP dicarboxylate transporter- DctP subunit YP_916986.1 372650 R 318586 CDS YP_916987.1 119385932 4581774 374073..375254 1 NC_008687.1 PFAM: iron-containing alcohol dehydrogenase; KEGG: bbr:BB0636 iron-containing alcohol dehydrogenase; iron-containing alcohol dehydrogenase 375254 4581774 Pden_3210 Paracoccus denitrificans PD1222 iron-containing alcohol dehydrogenase YP_916987.1 374073 D 318586 CDS YP_916988.1 119385933 4581775 375275..376708 1 NC_008687.1 PFAM: aldehyde dehydrogenase; KEGG: rme:Rmet_1577 aldehyde dehydrogenase; aldehyde dehydrogenase 376708 4581775 Pden_3211 Paracoccus denitrificans PD1222 aldehyde dehydrogenase YP_916988.1 375275 D 318586 CDS YP_916989.1 119385934 4581776 376719..377762 1 NC_008687.1 PFAM: Alcohol dehydrogenase, zinc-binding domain protein; Alcohol dehydrogenase GroES domain protein; KEGG: sma:SAV3314 NADP-dependent alcohol dehydrogenase; alcohol dehydrogenase 377762 4581776 Pden_3212 Paracoccus denitrificans PD1222 alcohol dehydrogenase YP_916989.1 376719 D 318586 CDS YP_916990.1 119385935 4581777 377773..378576 1 NC_008687.1 PFAM: Enoyl-CoA hydratase/isomerase; KEGG: bxe:Bxe_C0603 enoyl-CoA hydratase/isomerase; enoyl-CoA hydratase/isomerase 378576 4581777 Pden_3213 Paracoccus denitrificans PD1222 enoyl-CoA hydratase/isomerase YP_916990.1 377773 D 318586 CDS YP_916991.1 119385936 4581778 378583..378828 1 NC_008687.1 hypothetical protein 378828 4581778 Pden_3214 Paracoccus denitrificans PD1222 hypothetical protein YP_916991.1 378583 D 318586 CDS YP_916992.1 119385937 4581779 complement(378959..379333) 1 NC_008687.1 PFAM: Carboxymuconolactone decarboxylase; KEGG: sai:Saci_1814 carboxymuconolactone decarboxylase; carboxymuconolactone decarboxylase 379333 4581779 Pden_3215 Paracoccus denitrificans PD1222 carboxymuconolactone decarboxylase YP_916992.1 378959 R 318586 CDS YP_916993.1 119385938 4581780 complement(379406..380335) 1 NC_008687.1 PFAM: NADP oxidoreductase, coenzyme F420-dependent; 6-phosphogluconate dehydrogenase, NAD-binding; KEGG: dar:Daro_3339 6-phosphogluconate dehydrogenase, NAD-binding; 3-hydroxyisobutyrate dehydrogenase 380335 4581780 Pden_3216 Paracoccus denitrificans PD1222 3-hydroxyisobutyrate dehydrogenase YP_916993.1 379406 R 318586 CDS YP_916994.1 119385939 4581781 complement(380455..380880) 1 NC_008687.1 PFAM: Cupin 2, conserved barrel domain protein; KEGG: sme:SMc01911 hypothetical protein; cupin 380880 4581781 Pden_3217 Paracoccus denitrificans PD1222 cupin YP_916994.1 380455 R 318586 CDS YP_916995.1 119385940 4581782 complement(380901..381794) 1 NC_008687.1 PFAM: beta-lactamase domain protein; KEGG: bja:bll0351 hypothetical protein; beta-lactamase domain-containing protein 381794 4581782 Pden_3218 Paracoccus denitrificans PD1222 beta-lactamase domain-containing protein YP_916995.1 380901 R 318586 CDS YP_916996.1 119385941 4581783 complement(381847..382848) 1 NC_008687.1 PFAM: TRAP dicarboxylate transporter- DctP subunit; KEGG: bja:bll6794 hypothetical protein; TRAP dicarboxylate transporter- DctP subunit 382848 4581783 Pden_3219 Paracoccus denitrificans PD1222 TRAP dicarboxylate transporter- DctP subunit YP_916996.1 381847 R 318586 CDS YP_916997.1 119385942 4581784 complement(382965..383393) 1 NC_008687.1 PFAM: thioesterase superfamily protein; KEGG: rha:RHA1_ro00319 possible thioesterase; thioesterase superfamily protein 383393 4581784 Pden_3220 Paracoccus denitrificans PD1222 thioesterase superfamily protein YP_916997.1 382965 R 318586 CDS YP_916998.1 119385943 4581785 complement(383452..384405) 1 NC_008687.1 PFAM: Uncharacterized protein UPF0065; KEGG: bbr:BB3965 hypothetical protein; hypothetical protein 384405 4581785 Pden_3221 Paracoccus denitrificans PD1222 hypothetical protein YP_916998.1 383452 R 318586 CDS YP_916999.1 119385944 4581786 complement(384445..385959) 1 NC_008687.1 PFAM: protein of unknown function DUF112, transmembrane; KEGG: mes:Meso_2918 protein of unknown function DUF112, transmembrane; hypothetical protein 385959 4581786 Pden_3222 Paracoccus denitrificans PD1222 hypothetical protein YP_916999.1 384445 R 318586 CDS YP_917000.1 119385945 4581787 complement(385965..386414) 1 NC_008687.1 PFAM: protein of unknown function DUF1468; KEGG: bpa:BPP0373 hypothetical protein; hypothetical protein 386414 4581787 Pden_3223 Paracoccus denitrificans PD1222 hypothetical protein YP_917000.1 385965 R 318586 CDS YP_917001.1 119385946 4581788 complement(386490..388244) 1 NC_008687.1 PFAM: acyl-CoA dehydrogenase domain protein; KEGG: abo:ABO_2098 acyl-CoA dehydrogenase; acyl-CoA dehydrogenase 388244 4581788 Pden_3224 Paracoccus denitrificans PD1222 acyl-CoA dehydrogenase YP_917001.1 386490 R 318586 CDS YP_917002.1 119385947 4581789 complement(388262..390559) 1 NC_008687.1 PFAM: Enoyl-CoA hydratase/isomerase; 3-hydroxyacyl-CoA dehydrogenase domain protein; 3-hydroxyacyl-CoA dehydrogenase, NAD-binding; KEGG: rru:Rru_A1309 acetoacetyl-CoA reductase; 3-hydroxyacyl-CoA dehydrogenase, NAD-binding 390559 4581789 Pden_3225 Paracoccus denitrificans PD1222 3-hydroxyacyl-CoA dehydrogenase, NAD-binding YP_917002.1 388262 R 318586 CDS YP_917003.1 119385948 4581790 complement(390556..391677) 1 NC_008687.1 KEGG: rru:Rru_A1310 acetyl-CoA C-acyltransferase; TIGRFAM: acetyl-CoA acetyltransferases; PFAM: Thiolase; acetyl-CoA acetyltransferase 391677 4581790 Pden_3226 Paracoccus denitrificans PD1222 acetyl-CoA acetyltransferase YP_917003.1 390556 R 318586 CDS YP_917004.1 119385949 4581791 complement(391797..393029) 1 NC_008687.1 PFAM: L-carnitine dehydratase/bile acid-inducible protein F; KEGG: rha:RHA1_ro00763 probable formyl-CoA transferase; L-carnitine dehydratase/bile acid-inducible protein F 393029 4581791 Pden_3227 Paracoccus denitrificans PD1222 L-carnitine dehydratase/bile acid-inducible protein F YP_917004.1 391797 R 318586 CDS YP_917005.1 119385950 4581792 complement(393111..394610) 1 NC_008687.1 PFAM: aldehyde dehydrogenase; KEGG: bur:Bcep18194_C7342 aldehyde dehydrogenase; aldehyde dehydrogenase 394610 4581792 Pden_3228 Paracoccus denitrificans PD1222 aldehyde dehydrogenase YP_917005.1 393111 R 318586 CDS YP_917006.1 119385951 4581793 394918..396066 1 NC_008687.1 KEGG: fal:FRAAL2833 hypothetical protein; hypothetical protein 396066 4581793 Pden_3229 Paracoccus denitrificans PD1222 hypothetical protein YP_917006.1 394918 D 318586 CDS YP_917007.1 119385952 4581794 396188..397768 1 NC_008687.1 PFAM: AMP-dependent synthetase and ligase; KEGG: mmc:Mmcs_3946 AMP-dependent synthetase and ligase; AMP-dependent synthetase/ligase 397768 4581794 Pden_3230 Paracoccus denitrificans PD1222 AMP-dependent synthetase/ligase YP_917007.1 396188 D 318586 CDS YP_917008.1 119385953 4581795 397808..398662 1 NC_008687.1 KEGG: rha:RHA1_ro03060 probable transciptional regulator, IclR family; IclR family transciptional regulator 398662 4581795 Pden_3231 Paracoccus denitrificans PD1222 IclR family transciptional regulator YP_917008.1 397808 D 318586 CDS YP_917009.1 119385954 4581796 complement(398991..399803) 1 NC_008687.1 PFAM: ATP-binding region, ATPase domain protein domain protein; histidine kinase A domain protein domain protein; KEGG: mag:amb3346 signal transduction histidine kinase; histidine kinase 399803 4581796 Pden_3232 Paracoccus denitrificans PD1222 histidine kinase YP_917009.1 398991 R 318586 CDS YP_917010.1 119385955 4581797 complement(400008..400685) 1 NC_008687.1 PFAM: transposase IS116/IS110/IS902 family protein; KEGG: nha:Nham_3955 transposase IS116/IS110/IS902; transposase IS116/IS110/IS902 family protein 400685 4581797 Pden_3233 Paracoccus denitrificans PD1222 transposase IS116/IS110/IS902 family protein YP_917010.1 400008 R 318586 CDS YP_917011.1 119385956 4581798 complement(400725..401084) 1 NC_008687.1 KEGG: yps:YPTB1994 hypothetical protein; hypothetical protein 401084 4581798 Pden_3234 Paracoccus denitrificans PD1222 hypothetical protein YP_917011.1 400725 R 318586 CDS YP_917012.1 119385957 4581799 401247..402308 1 NC_008687.1 KEGG: mes:Meso_3912 hypothetical protein; hypothetical protein 402308 4581799 Pden_3235 Paracoccus denitrificans PD1222 hypothetical protein YP_917012.1 401247 D 318586 CDS YP_917013.1 119385958 4581800 402410..403183 1 NC_008687.1 PFAM: NAD-dependent epimerase/dehydratase; dTDP-4-dehydrorhamnose reductase; NmrA family protein; KEGG: mes:Meso_3897 NmrA-like; NmrA family protein 403183 4581800 Pden_3236 Paracoccus denitrificans PD1222 NmrA family protein YP_917013.1 402410 D 318586 CDS YP_917014.1 119385959 4581801 complement(403185..404078) 1 NC_008687.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: mes:Meso_3905 transcriptional regulator, LysR family; LysR family transcriptional regulator 404078 4581801 Pden_3237 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_917014.1 403185 R 318586 CDS YP_917015.1 119385960 4581802 404224..404697 1 NC_008687.1 KEGG: mes:Meso_3908 hypothetical protein; hypothetical protein 404697 4581802 Pden_3238 Paracoccus denitrificans PD1222 hypothetical protein YP_917015.1 404224 D 318586 CDS YP_917016.1 119385961 4581803 404744..405418 1 NC_008687.1 KEGG: mes:Meso_3907 hypothetical protein; hypothetical protein 405418 4581803 Pden_3239 Paracoccus denitrificans PD1222 hypothetical protein YP_917016.1 404744 D 318586 CDS YP_917017.1 119385962 4581804 405618..406619 1 NC_008687.1 KEGG: ade:Adeh_3220 hypothetical protein; hypothetical protein 406619 4581804 Pden_3240 Paracoccus denitrificans PD1222 hypothetical protein YP_917017.1 405618 D 318586 CDS YP_917018.1 119385963 4581805 406649..407218 1 NC_008687.1 KEGG: mes:Meso_3899 twin-arginine translocation pathway signal; twin-arginine translocation pathway signal 407218 4581805 Pden_3241 Paracoccus denitrificans PD1222 twin-arginine translocation pathway signal YP_917018.1 406649 D 318586 CDS YP_917019.1 119385964 4581806 407264..408247 1 NC_008687.1 PFAM: aldo/keto reductase; KEGG: bur:Bcep18194_B2855 aldo/keto reductase; aldo/keto reductase 408247 4581806 Pden_3242 Paracoccus denitrificans PD1222 aldo/keto reductase YP_917019.1 407264 D 318586 CDS YP_917020.1 119385965 4581807 408296..409462 1 NC_008687.1 PFAM: aldo/keto reductase; KEGG: mes:Meso_3904 twin-arginine translocation pathway signal; aldo/keto reductase 409462 4581807 Pden_3243 Paracoccus denitrificans PD1222 aldo/keto reductase YP_917020.1 408296 D 318586 CDS YP_917021.1 119385966 4581808 409473..410462 1 NC_008687.1 PFAM: aldo/keto reductase; KEGG: bxe:Bxe_B1949 aldo/keto reductase; aldo/keto reductase 410462 4581808 Pden_3244 Paracoccus denitrificans PD1222 aldo/keto reductase YP_917021.1 409473 D 318586 CDS YP_917022.1 119385967 4581809 410491..411477 1 NC_008687.1 KEGG: mes:Meso_3911 hypothetical protein; hypothetical protein 411477 4581809 Pden_3245 Paracoccus denitrificans PD1222 hypothetical protein YP_917022.1 410491 D 318586 CDS YP_917023.1 119385968 4581810 411556..411753 1 NC_008687.1 KEGG: nha:Nham_3076 transposase; hypothetical protein 411753 4581810 Pden_3246 Paracoccus denitrificans PD1222 hypothetical protein YP_917023.1 411556 D 318586 CDS YP_917024.1 119385969 4581811 411867..412448 1 NC_008687.1 KEGG: mag:amb0411 transposase; transposase 412448 4581811 Pden_3247 Paracoccus denitrificans PD1222 transposase YP_917024.1 411867 D 318586 CDS YP_917025.1 119385970 4581812 complement(412476..413243) 1 NC_008687.1 PFAM: regulatory proteins, IclR; KEGG: rha:RHA1_ro06686 probable transciptional regulator, IclR family; regulatory proteins, IclR 413243 4581812 Pden_3248 Paracoccus denitrificans PD1222 regulatory proteins, IclR YP_917025.1 412476 R 318586 CDS YP_917026.1 119385971 4581813 complement(414038..414535) 1 NC_008687.1 PFAM: protein of unknown function DUF1468; KEGG: bpa:BPP0373 hypothetical protein; hypothetical protein 414535 4581813 Pden_3250 Paracoccus denitrificans PD1222 hypothetical protein YP_917026.1 414038 R 318586 CDS YP_917027.1 119385972 4581814 414737..415615 1 NC_008687.1 PFAM: alpha/beta hydrolase fold; PGAP1 family protein; KEGG: dar:Daro_3230 alpha/beta hydrolase fold; alpha/beta hydrolase 415615 4581814 Pden_3251 Paracoccus denitrificans PD1222 alpha/beta hydrolase YP_917027.1 414737 D 318586 CDS YP_917028.1 119385973 4581815 415612..415989 1 NC_008687.1 SMART: regulatory protein, MerR; KEGG: rsp:RSP_2201 transcriptional regulator, MerR family; MerR family transcriptional regulator 415989 4581815 Pden_3252 Paracoccus denitrificans PD1222 MerR family transcriptional regulator YP_917028.1 415612 D 318586 CDS YP_917029.1 119385974 4581816 416027..417628 1 NC_008687.1 PFAM: protein of unknown function DUF894, DitE; major facilitator superfamily MFS_1; KEGG: rsp:RSP_0945 major facilitator superfamily (MFS) transporter; hypothetical protein 417628 4581816 Pden_3253 Paracoccus denitrificans PD1222 hypothetical protein YP_917029.1 416027 D 318586 CDS YP_917030.1 119385975 4581817 418832..419227 1 NC_008687.1 PFAM: Cupin 2, conserved barrel domain protein; KEGG: mes:Meso_2098 cupin 2, conserved barrel; cupin 419227 4581817 Pden_3255 Paracoccus denitrificans PD1222 cupin YP_917030.1 418832 D 318586 CDS YP_917031.1 119385976 4581818 419378..420307 1 NC_008687.1 PFAM: 6-phosphogluconate dehydrogenase, NAD-binding; KEGG: sth:STH938 3-hydroxyisobutyrate dehydrogenase; 3-hydroxyisobutyrate dehydrogenase 420307 4581818 Pden_3256 Paracoccus denitrificans PD1222 3-hydroxyisobutyrate dehydrogenase YP_917031.1 419378 D 318586 CDS YP_917032.1 119385977 4581819 420270..420716 1 NC_008687.1 PFAM: Carboxymuconolactone decarboxylase; KEGG: pst:PSPTO_4478 4-carboxymuconolactone decarboxylase; carboxymuconolactone decarboxylase 420716 4581819 Pden_3257 Paracoccus denitrificans PD1222 carboxymuconolactone decarboxylase YP_917032.1 420270 D 318586 CDS YP_917033.1 119385978 4581820 420838..421839 1 NC_008687.1 PFAM: TRAP dicarboxylate transporter- DctP subunit; KEGG: rpd:RPD_0609 TRAP dicarboxylate transporter-DctP subunit; TRAP dicarboxylate transporter- DctP subunit 421839 4581820 Pden_3258 Paracoccus denitrificans PD1222 TRAP dicarboxylate transporter- DctP subunit YP_917033.1 420838 D 318586 CDS YP_917034.1 119385979 4581821 422255..422542 1 NC_008687.1 KEGG: sme:SMa2189 integrase/recombinase; integrase/recombinase 422542 4581821 Pden_3259 Paracoccus denitrificans PD1222 integrase/recombinase YP_917034.1 422255 D 318586 CDS YP_917035.1 119385980 4581822 422920..424332 1 NC_008687.1 PFAM: aldehyde dehydrogenase; KEGG: dra:DRA0126 aldehyde dehydrogenase; aldehyde dehydrogenase 424332 4581822 Pden_3260 Paracoccus denitrificans PD1222 aldehyde dehydrogenase YP_917035.1 422920 D 318586 CDS YP_917036.1 119385981 4581823 425326..426882 1 NC_008687.1 PFAM: transposase, IS204/IS1001/IS1096/IS1165 family protein; KEGG: atu:Atu5094 ISL3 family transposase; transposase, IS204/IS1001/IS1096/IS1165 family protein 426882 4581823 Pden_3262 Paracoccus denitrificans PD1222 transposase, IS204/IS1001/IS1096/IS1165 family protein YP_917036.1 425326 D 318586 CDS YP_917037.1 119385982 4581824 complement(426907..427194) 1 NC_008687.1 hypothetical protein 427194 4581824 Pden_3263 Paracoccus denitrificans PD1222 hypothetical protein YP_917037.1 426907 R 318586 CDS YP_917038.1 119385983 4581825 complement(427531..429057) 1 NC_008687.1 PFAM: aldehyde dehydrogenase; KEGG: sme:SMb20262 semialdehyde dehydrogenase; aldehyde dehydrogenase 429057 4581825 Pden_3264 Paracoccus denitrificans PD1222 aldehyde dehydrogenase YP_917038.1 427531 R 318586 CDS YP_917039.1 119385984 4581826 complement(429142..430152) 1 NC_008687.1 KEGG: mes:Meso_2079 ABC transporter, periplasmic substrate-binding protein; ABC-type nitrate/sulfonate/bicarbonate transport systems periplasmic components-like 430152 4581826 Pden_3265 Paracoccus denitrificans PD1222 ABC-type nitrate/sulfonate/bicarbonate transport systems periplasmic components-like YP_917039.1 429142 R 318586 CDS YP_917040.1 119385985 4581827 430569..431600 1 NC_008687.1 PFAM: Uncharacterized protein UPF0065; KEGG: dsy:DSY0976 hypothetical protein; hypothetical protein 431600 4581827 Pden_3266 Paracoccus denitrificans PD1222 hypothetical protein YP_917040.1 430569 D 318586 CDS YP_917041.1 119385986 4581828 431624..432613 1 NC_008687.1 PFAM: amidohydrolase 2; KEGG: reu:Reut_B5784 amidohydrolase 2; amidohydrolase 432613 4581828 Pden_3267 Paracoccus denitrificans PD1222 amidohydrolase YP_917041.1 431624 D 318586 CDS YP_917042.1 119385987 4581829 432650..434680 1 NC_008687.1 PFAM: protein of unknown function DUF112, transmembrane; KEGG: bcl:ABC0625 hypothetical protein; hypothetical protein 434680 4581829 Pden_3268 Paracoccus denitrificans PD1222 hypothetical protein YP_917042.1 432650 D 318586 CDS YP_917043.1 119385988 4581830 434713..435375 1 NC_008687.1 KEGG: bja:bll1020 hypothetical protein; hypothetical protein 435375 4581830 Pden_3269 Paracoccus denitrificans PD1222 hypothetical protein YP_917043.1 434713 D 318586 CDS YP_917044.1 119385989 4581831 complement(435394..436701) 1 NC_008687.1 PFAM: protein of unknown function DUF894, DitE; major facilitator superfamily MFS_1; KEGG: hne:HNE_1254 major facilitator family protein; major facilitator transporter 436701 4581831 Pden_3270 Paracoccus denitrificans PD1222 major facilitator transporter YP_917044.1 435394 R 318586 CDS YP_917045.1 119385990 4581832 436878..438143 1 NC_008687.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: csa:Csal_0331 transcriptional regulator, LysR family; LysR family transcriptional regulator 438143 4581832 Pden_3271 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_917045.1 436878 D 318586 CDS YP_917046.1 119385991 4581833 complement(438194..439045) 1 NC_008687.1 PFAM: HpcH/HpaI aldolase; KEGG: sus:Acid_0199 HpcH/HpaI aldolase; HpcH/HpaI aldolase 439045 4581833 Pden_3272 Paracoccus denitrificans PD1222 HpcH/HpaI aldolase YP_917046.1 438194 R 318586 CDS YP_917047.1 119385992 4581834 complement(439072..440046) 1 NC_008687.1 KEGG: bja:blr3843 hypothetical protein; hypothetical protein 440046 4581834 Pden_3273 Paracoccus denitrificans PD1222 hypothetical protein YP_917047.1 439072 R 318586 CDS YP_917048.1 119385993 4581835 440299..441330 1 NC_008687.1 PFAM: amidohydrolase 2; KEGG: rme:Rmet_3705 amidohydrolase 2; amidohydrolase 441330 4581835 Pden_3274 Paracoccus denitrificans PD1222 amidohydrolase YP_917048.1 440299 D 318586 CDS YP_917049.1 119385994 4581836 441327..443006 1 NC_008687.1 PFAM: thiamine pyrophosphate enzyme domain protein TPP-binding; thiamine pyrophosphate enzyme, central region; thiamine pyrophosphate enzyme TPP binding domain protein; KEGG: bms:BRA0945 acetolactate synthase large subunit; thiamine pyrophosphate binding domain-containing protein 443006 4581836 Pden_3275 Paracoccus denitrificans PD1222 thiamine pyrophosphate binding domain-containing protein YP_917049.1 441327 D 318586 CDS YP_917050.1 119385995 4581837 443021..443260 1 NC_008687.1 hypothetical protein 443260 4581837 Pden_3276 Paracoccus denitrificans PD1222 hypothetical protein YP_917050.1 443021 D 318586 CDS YP_917051.1 119385996 4581838 443257..444138 1 NC_008687.1 PFAM: amidohydrolase 2; KEGG: reu:Reut_B5784 amidohydrolase 2; amidohydrolase 444138 4581838 Pden_3277 Paracoccus denitrificans PD1222 amidohydrolase YP_917051.1 443257 D 318586 CDS YP_917052.1 119385997 4581839 444135..445052 1 NC_008687.1 KEGG: bja:blr3843 hypothetical protein; hypothetical protein 445052 4581839 Pden_3278 Paracoccus denitrificans PD1222 hypothetical protein YP_917052.1 444135 D 318586 CDS YP_917053.1 119385998 4581840 445296..446237 1 NC_008687.1 KEGG: sil:SPO3430 outer membrane porin; hypothetical protein 446237 4581840 Pden_3279 Paracoccus denitrificans PD1222 hypothetical protein YP_917053.1 445296 D 318586 CDS YP_917054.1 119385999 4581841 complement(446254..447207) 1 NC_008687.1 PFAM: Integrase, catalytic region; KEGG: rsp:RSP_3937 probable transposase, Y4bF; integrase catalytic subunit 447207 4581841 Pden_3280 Paracoccus denitrificans PD1222 integrase catalytic subunit YP_917054.1 446254 R 318586 CDS YP_917055.1 119386000 4581842 447565..449121 1 NC_008687.1 PFAM: transposase, IS204/IS1001/IS1096/IS1165 family protein; KEGG: atu:Atu5094 ISL3 family transposase; transposase, IS204/IS1001/IS1096/IS1165 family protein 449121 4581842 Pden_3281 Paracoccus denitrificans PD1222 transposase, IS204/IS1001/IS1096/IS1165 family protein YP_917055.1 447565 D 318586 CDS YP_917056.1 119386001 4581843 complement(449183..449533) 1 NC_008687.1 hypothetical protein 449533 4581843 Pden_3282 Paracoccus denitrificans PD1222 hypothetical protein YP_917056.1 449183 R 318586 CDS YP_917057.1 119386002 4581844 complement(449813..451183) 1 NC_008687.1 PFAM: ATP-binding region, ATPase domain protein domain protein; histidine kinase A domain protein domain protein; KEGG: rsp:RSP_3975 periplasmic sensor signal transduction histidine kinase; integral membrane sensor signal transduction histidine kinase 451183 4581844 Pden_3283 Paracoccus denitrificans PD1222 integral membrane sensor signal transduction histidine kinase YP_917057.1 449813 R 318586 CDS YP_917058.1 119386003 4581845 complement(451180..451839) 1 NC_008687.1 PFAM: response regulator receiver; transcriptional regulator domain protein; KEGG: bmb:BruAb2_0224 two component response regulator; two component transcriptional regulator 451839 4581845 Pden_3284 Paracoccus denitrificans PD1222 two component transcriptional regulator YP_917058.1 451180 R 318586 CDS YP_917059.1 119386004 4581846 451981..452295 1 NC_008687.1 KEGG: rsp:RSP_7166 hypothetical protein; hypothetical protein 452295 4581846 Pden_3285 Paracoccus denitrificans PD1222 hypothetical protein YP_917059.1 451981 D 318586 CDS YP_917060.1 119386005 4581847 452288..452920 1 NC_008687.1 PFAM: cytochrome B561; KEGG: rsp:RSP_2807 cytochrome b; cytochrome B561 452920 4581847 Pden_3286 Paracoccus denitrificans PD1222 cytochrome B561 YP_917060.1 452288 D 318586 CDS YP_917061.1 119386006 4581848 453110..453412 1 NC_008687.1 KEGG: bmb:BruAb1_1622 hypothetical protein; hypothetical protein 453412 4581848 Pden_3287 Paracoccus denitrificans PD1222 hypothetical protein YP_917061.1 453110 D 318586 CDS YP_917062.1 119386007 4581849 453524..453904 1 NC_008687.1 KEGG: bma:BMAA0783 hypothetical protein; hypothetical protein 453904 4581849 Pden_3288 Paracoccus denitrificans PD1222 hypothetical protein YP_917062.1 453524 D 318586 CDS YP_917063.1 119386008 4581850 453931..454401 1 NC_008687.1 KEGG: bmb:BruAb2_0227 hypothetical protein; hypothetical protein 454401 4581850 Pden_3289 Paracoccus denitrificans PD1222 hypothetical protein YP_917063.1 453931 D 318586 CDS YP_917064.1 119386009 4581851 454411..456618 1 NC_008687.1 PFAM: oxidoreductase FAD/NAD(P)-binding domain protein; PepSY-associated TM helix domain protein; flavodoxin/nitric oxide synthase; Oxidoreductase FAD-binding domain protein; KEGG: bms:BRA0233 oxidoreductase, FAD-binding; oxidoreductase FAD/NAD(P)-binding subunit 456618 4581851 Pden_3290 Paracoccus denitrificans PD1222 oxidoreductase FAD/NAD(P)-binding subunit YP_917064.1 454411 D 318586 CDS YP_917065.1 119386010 4581852 456599..457591 1 NC_008687.1 PFAM: ApbE family lipoprotein; KEGG: bmb:BruAb2_0229 ApbE family protein; ApbE family lipoprotein 457591 4581852 Pden_3291 Paracoccus denitrificans PD1222 ApbE family lipoprotein YP_917065.1 456599 D 318586 CDS YP_917066.1 119386011 4581853 457734..458207 1 NC_008687.1 KEGG: dar:Daro_1035 hypothetical protein; hypothetical protein 458207 4581853 Pden_3292 Paracoccus denitrificans PD1222 hypothetical protein YP_917066.1 457734 D 318586 CDS YP_917067.1 119386012 4581854 complement(458241..459146) 1 NC_008687.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: rsp:RSP_3052 transcriptional regulator, LysR family; LysR family transcriptional regulator 459146 4581854 Pden_3293 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_917067.1 458241 R 318586 CDS YP_917068.1 119386013 4581855 459255..459473 1 NC_008687.1 PFAM: Heavy metal transport/detoxification protein; KEGG: rxy:Rxyl_1802 heavy metal transport/detoxification protein; heavy metal transport/detoxification protein 459473 4581855 Pden_3294 Paracoccus denitrificans PD1222 heavy metal transport/detoxification protein YP_917068.1 459255 D 318586 CDS YP_917069.1 119386014 4581856 459535..461454 1 NC_008687.1 TIGRFAM: ATPase, P-type (transporting), HAD superfamily, subfamily IC; cadmium-translocating P-type ATPase; heavy metal translocating P-type ATPase; PFAM: Haloacid dehalogenase domain protein hydrolase; E1-E2 ATPase-associated domain protein; KEGG: rxy:Rxyl_1801 heavy metal translocating P-type ATPase; heavy metal translocating P-type ATPase 461454 4581856 Pden_3295 Paracoccus denitrificans PD1222 heavy metal translocating P-type ATPase YP_917069.1 459535 D 318586 CDS YP_917070.1 119386015 4581857 461511..462173 1 NC_008687.1 PFAM: protein of unknown function DUF924; KEGG: gvi:glr1115 hypothetical protein; hypothetical protein 462173 4581857 Pden_3296 Paracoccus denitrificans PD1222 hypothetical protein YP_917070.1 461511 D 318586 CDS YP_917071.1 119386016 4581858 complement(462189..464129) 1 NC_008687.1 TIGRFAM: ATPase, P-type (transporting), HAD superfamily, subfamily IC; cadmium-translocating P-type ATPase; heavy metal translocating P-type ATPase; PFAM: Haloacid dehalogenase domain protein hydrolase; E1-E2 ATPase-associated domain protein; KEGG: nwi:Nwi_1949 heavy metal translocating P-type ATPase; heavy metal translocating P-type ATPase 464129 4581858 Pden_3297 Paracoccus denitrificans PD1222 heavy metal translocating P-type ATPase YP_917071.1 462189 R 318586 CDS YP_917072.1 119386017 4581859 complement(464191..464571) 1 NC_008687.1 KEGG: sat:SYN_02345 hypothetical membrane protein; hypothetical protein 464571 4581859 Pden_3298 Paracoccus denitrificans PD1222 hypothetical protein YP_917072.1 464191 R 318586 CDS YP_917073.1 119386018 4581860 complement(464586..465278) 1 NC_008687.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: mag:amb2540 ABC-type antimicrobial peptide transport system, ATPase component; ABC transporter 465278 4581860 Pden_3299 Paracoccus denitrificans PD1222 ABC transporter YP_917073.1 464586 R 318586 CDS YP_917074.1 119386019 4581861 complement(465284..466417) 1 NC_008687.1 PFAM: protein of unknown function DUF214; KEGG: mag:amb2541 ABC-type antimicrobial peptide transport system, permease component; hypothetical protein 466417 4581861 Pden_3300 Paracoccus denitrificans PD1222 hypothetical protein YP_917074.1 465284 R 318586 CDS YP_917075.1 119386020 4581862 complement(466414..467559) 1 NC_008687.1 TIGRFAM: efflux transporter, RND family, MFP subunit; PFAM: secretion protein HlyD family protein; KEGG: mag:amb2542 membrane-fusion protein; RND family efflux transporter MFP subunit 467559 4581862 Pden_3301 Paracoccus denitrificans PD1222 RND family efflux transporter MFP subunit YP_917075.1 466414 R 318586 CDS YP_917076.1 119386021 4581863 complement(467563..468210) 1 NC_008687.1 PFAM: regulatory protein, TetR; KEGG: eba:ebA6247 transcriptional regulator, TetR family; TetR family transcriptional regulator 468210 4581863 Pden_3302 Paracoccus denitrificans PD1222 TetR family transcriptional regulator YP_917076.1 467563 R 318586 CDS YP_917077.1 119386022 4581864 470021..471202 1 NC_008687.1 PFAM: filamentation induced by cAMP protein Fic; KEGG: atc:AGR_pAT_51 hypothetical protein; filamentation induced by cAMP protein fic 471202 4581864 Pden_3305 Paracoccus denitrificans PD1222 filamentation induced by cAMP protein fic YP_917077.1 470021 D 318586 CDS YP_917078.1 119386023 4581865 complement(471348..471779) 1 NC_008687.1 KEGG: bja:blr1867 hypothetical protein; hypothetical protein 471779 4581865 Pden_3306 Paracoccus denitrificans PD1222 hypothetical protein YP_917078.1 471348 R 318586 CDS YP_917079.1 119386024 4581866 complement(471872..472897) 1 NC_008687.1 PFAM: transposase IS66; KEGG: bja:blr1700 transposase; transposase IS66 472897 4581866 Pden_3307 Paracoccus denitrificans PD1222 transposase IS66 YP_917079.1 471872 R 318586 CDS YP_917080.1 119386025 4581867 complement(472952..473305) 1 NC_008687.1 PFAM: IS66 Orf2 family protein; KEGG: bja:bll2160 transposase; IS66 Orf2 family protein 473305 4581867 Pden_3308 Paracoccus denitrificans PD1222 IS66 Orf2 family protein YP_917080.1 472952 R 318586 CDS YP_917081.1 119386026 4581868 complement(473299..473631) 1 NC_008687.1 PFAM: transposase IS3/IS911 family protein; KEGG: atc:AGR_pTi_30 hypothetical protein; transposase IS3/IS911 family protein 473631 4581868 Pden_3309 Paracoccus denitrificans PD1222 transposase IS3/IS911 family protein YP_917081.1 473299 R 318586 CDS YP_917082.1 119386027 4581869 473734..474063 1 NC_008687.1 KEGG: sme:SMb21085 hypothetical protein encoded by ORF3 of ISRm14, IS66 family; hypothetical protein 474063 4581869 Pden_3310 Paracoccus denitrificans PD1222 hypothetical protein YP_917082.1 473734 D 318586 CDS YP_917083.1 119386028 4581870 complement(474208..475173) 1 NC_008687.1 PFAM: regulatory protein, LuxR; response regulator receiver; KEGG: rpd:RPD_3866 response regulator receiver; response regulator receiver protein 475173 4581870 Pden_3311 Paracoccus denitrificans PD1222 response regulator receiver protein YP_917083.1 474208 R 318586 CDS YP_917084.1 119386029 4581871 complement(475170..476507) 1 NC_008687.1 PFAM: ATP-binding region, ATPase domain protein domain protein; histidine kinase A domain protein domain protein; KEGG: ret:RHE_PF00324 probable two-component sensor histidine kinase/response regulator hybrid protein; integral membrane sensor signal transduction histidine kinase 476507 4581871 Pden_3312 Paracoccus denitrificans PD1222 integral membrane sensor signal transduction histidine kinase YP_917084.1 475170 R 318586 CDS YP_917085.1 119386030 4581872 complement(476504..476986) 1 NC_008687.1 KEGG: rde:RD1_3578 hypothetical protein; hypothetical protein 476986 4581872 Pden_3313 Paracoccus denitrificans PD1222 hypothetical protein YP_917085.1 476504 R 318586 CDS YP_917086.1 119386031 4581873 477123..477602 1 NC_008687.1 hypothetical protein 477602 4581873 Pden_3314 Paracoccus denitrificans PD1222 hypothetical protein YP_917086.1 477123 D 318586 CDS YP_917087.1 119386032 4581874 477604..478176 1 NC_008687.1 hypothetical protein 478176 4581874 Pden_3315 Paracoccus denitrificans PD1222 hypothetical protein YP_917087.1 477604 D 318586 CDS YP_917088.1 119386033 4581875 478185..478664 1 NC_008687.1 hypothetical protein 478664 4581875 Pden_3316 Paracoccus denitrificans PD1222 hypothetical protein YP_917088.1 478185 D 318586 CDS YP_917089.1 119386034 4581876 478661..479188 1 NC_008687.1 hypothetical protein 479188 4581876 Pden_3317 Paracoccus denitrificans PD1222 hypothetical protein YP_917089.1 478661 D 318586 CDS YP_917090.1 119386035 4581877 479185..479709 1 NC_008687.1 hypothetical protein 479709 4581877 Pden_3318 Paracoccus denitrificans PD1222 hypothetical protein YP_917090.1 479185 D 318586 CDS YP_917091.1 119386036 4581878 479733..480704 1 NC_008687.1 KEGG: mlo:mlr7467 hypothetical protein; hypothetical protein 480704 4581878 Pden_3319 Paracoccus denitrificans PD1222 hypothetical protein YP_917091.1 479733 D 318586 CDS YP_917092.1 119386037 4581879 480701..483268 1 NC_008687.1 PFAM: von Willebrand factor, type A; KEGG: jan:Jann_1721 von Willebrand factor, type A; von Willebrand factor, type A 483268 4581879 Pden_3320 Paracoccus denitrificans PD1222 von Willebrand factor, type A YP_917092.1 480701 D 318586 CDS YP_917093.1 119386038 4581880 483265..483801 1 NC_008687.1 hypothetical protein 483801 4581880 Pden_3321 Paracoccus denitrificans PD1222 hypothetical protein YP_917093.1 483265 D 318586 CDS YP_917094.1 119386039 4581881 483798..484283 1 NC_008687.1 hypothetical protein 484283 4581881 Pden_3322 Paracoccus denitrificans PD1222 hypothetical protein YP_917094.1 483798 D 318586 CDS YP_917095.1 119386040 4581882 484311..484901 1 NC_008687.1 hypothetical protein 484901 4581882 Pden_3323 Paracoccus denitrificans PD1222 hypothetical protein YP_917095.1 484311 D 318586 CDS YP_917096.1 119386041 4581883 484910..485728 1 NC_008687.1 KEGG: rpe:RPE_0562 type III restriction enzyme, res subunit; type III restriction enzyme, res subunit 485728 4581883 Pden_3324 Paracoccus denitrificans PD1222 type III restriction enzyme, res subunit YP_917096.1 484910 D 318586 CDS YP_917097.1 119386042 4581884 485821..488112 1 NC_008687.1 KEGG: rfr:Rfer_4292 hypothetical protein; hypothetical protein 488112 4581884 Pden_3325 Paracoccus denitrificans PD1222 hypothetical protein YP_917097.1 485821 D 318586 CDS YP_917098.1 119386043 4581885 complement(488297..490102) 1 NC_008687.1 PFAM: Resolvase, N-terminal domain; Recombinase; KEGG: nha:Nham_3864 recombinase; recombinase 490102 4581885 Pden_3326 Paracoccus denitrificans PD1222 recombinase YP_917098.1 488297 R 318586 CDS YP_917099.1 119386044 4581886 490103..490552 1 NC_008687.1 hypothetical protein 490552 4581886 Pden_3327 Paracoccus denitrificans PD1222 hypothetical protein YP_917099.1 490103 D 318586 CDS YP_917100.1 119386045 4581888 492010..492963 1 NC_008687.1 PFAM: helix-turn-helix- domain containing protein, AraC type; AraC-type transcriptional regulator domain protein; KEGG: rsp:RSP_3202 transcriptional regulator, AraC family; AraC family transcriptional regulator 492963 4581888 Pden_3330 Paracoccus denitrificans PD1222 AraC family transcriptional regulator YP_917100.1 492010 D 318586 CDS YP_917101.1 119386046 4581889 493215..493538 1 NC_008687.1 hypothetical protein 493538 4581889 Pden_3331 Paracoccus denitrificans PD1222 hypothetical protein YP_917101.1 493215 D 318586 CDS YP_917102.1 119386047 4581890 493535..494413 1 NC_008687.1 KEGG: bxe:Bxe_A0212 hypothetical protein; XRE family transcriptional regulator 494413 4581890 Pden_3332 Paracoccus denitrificans PD1222 XRE family transcriptional regulator YP_917102.1 493535 D 318586 CDS YP_917103.1 119386048 4581891 complement(494397..494957) 1 NC_008687.1 PFAM: transposase, IS4 family protein; KEGG: sil:SPOA0134 ISSpo7, transposase; transposase, IS4 family protein 494957 4581891 Pden_3333 Paracoccus denitrificans PD1222 transposase, IS4 family protein YP_917103.1 494397 R 318586 CDS YP_917104.1 119386049 4581892 495252..495524 1 NC_008687.1 hypothetical protein 495524 4581892 Pden_3334 Paracoccus denitrificans PD1222 hypothetical protein YP_917104.1 495252 D 318586 CDS YP_917105.1 119386050 4581893 complement(495620..495898) 1 NC_008687.1 PFAM: SH3, type 3 domain protein; KEGG: rsp:RSP_6161 hypothetical protein; SH3 type 3 domain-containing protein 495898 4581893 Pden_3335 Paracoccus denitrificans PD1222 SH3 type 3 domain-containing protein YP_917105.1 495620 R 318586 CDS YP_917106.1 119386051 4581894 495960..496316 1 NC_008687.1 hypothetical protein 496316 4581894 Pden_3336 Paracoccus denitrificans PD1222 hypothetical protein YP_917106.1 495960 D 318586 CDS YP_917107.1 119386052 4581895 complement(496474..497838) 1 NC_008687.1 TIGRFAM: chromate transporter, chromate ion transporter (CHR) family; PFAM: Chromate transporter; KEGG: sme:SMc00808 chromate transport protein; chromate transporter 497838 4581895 Pden_3337 Paracoccus denitrificans PD1222 chromate transporter YP_917107.1 496474 R 318586 CDS YP_917108.1 119386053 4581896 complement(497835..498680) 1 NC_008687.1 SMART: Rhodanese domain protein; KEGG: mlo:mlr5406 hypothetical protein; rhodanese domain-containing protein 498680 4581896 Pden_3338 Paracoccus denitrificans PD1222 rhodanese domain-containing protein YP_917108.1 497835 R 318586 CDS YP_917109.1 119386054 4581897 complement(498895..499602) 1 NC_008687.1 PFAM: NADPH-dependent FMN reductase; KEGG: rsp:RSP_2731 arsenical resistance protein, ArsH; NADPH-dependent FMN reductase 499602 4581897 Pden_3339 Paracoccus denitrificans PD1222 NADPH-dependent FMN reductase YP_917109.1 498895 R 318586 CDS YP_917110.1 119386055 4581898 complement(499599..500675) 1 NC_008687.1 TIGRFAM: arsenical-resistance protein; PFAM: Bile acid:sodium symporter; KEGG: sal:Sala_2405 arsenical-resistance protein; arsenical-resistance protein 500675 4581898 Pden_3340 Paracoccus denitrificans PD1222 arsenical-resistance protein YP_917110.1 499599 R 318586 CDS YP_917111.1 119386056 4581899 complement(500685..501638) 1 NC_008687.1 TIGRFAM: arsenate reductase; PFAM: low molecular weight phosphotyrosine protein phosphatase; arsenate reductase and related; KEGG: nwi:Nwi_3124 low molecular weight phosphotyrosine protein phosphatase; arsenate reductase 501638 4581899 Pden_3341 Paracoccus denitrificans PD1222 arsenate reductase YP_917111.1 500685 R 318586 CDS YP_917112.1 119386057 4581900 complement(501631..501993) 1 NC_008687.1 PFAM: regulatory protein, ArsR; KEGG: nwi:Nwi_3123 transcriptional regulatory protein, ArsR family; regulatory protein ArsR 501993 4581900 Pden_3342 Paracoccus denitrificans PD1222 regulatory protein ArsR YP_917112.1 501631 R 318586 CDS YP_917113.1 119386058 4581901 complement(502687..504177) 1 NC_008687.1 PFAM: Sulfate transporter/antisigma-factor antagonist STAS; Xanthine/uracil/vitamin C permease; sulphate transporter; KEGG: rsp:RSP_4197 antisigma-factor antagonist, STAS; sulfate transporter 504177 4581901 Pden_3344 Paracoccus denitrificans PD1222 sulfate transporter YP_917113.1 502687 R 318586 CDS YP_917114.1 119386059 4581902 504673..504870 1 NC_008687.1 PFAM: protein of unknown function DUF1127; KEGG: rde:RD1_2086 hypothetical protein; hypothetical protein 504870 4581902 Pden_3345 Paracoccus denitrificans PD1222 hypothetical protein YP_917114.1 504673 D 318586 CDS YP_917115.1 119386060 4581903 505006..505248 1 NC_008687.1 hypothetical protein 505248 4581903 Pden_3346 Paracoccus denitrificans PD1222 hypothetical protein YP_917115.1 505006 D 318586 CDS YP_917116.1 119386061 4581904 505270..505680 1 NC_008687.1 PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase; KEGG: mlo:mlr1197 hypothetical protein; glyoxalase/bleomycin resistance protein/dioxygenase 505680 4581904 Pden_3347 Paracoccus denitrificans PD1222 glyoxalase/bleomycin resistance protein/dioxygenase YP_917116.1 505270 D 318586 CDS YP_917117.1 119386062 4581905 505686..506120 1 NC_008687.1 PFAM: Methyltransferase type 11; Methyltransferase type 12; KEGG: gvi:glr1626 hypothetical protein; methyltransferase type 12 506120 4581905 Pden_3348 Paracoccus denitrificans PD1222 methyltransferase type 12 YP_917117.1 505686 D 318586 CDS YP_917118.1 119386063 4581906 506216..506533 1 NC_008687.1 PFAM: histone family protein nucleoid-structuring protein H-NS; KEGG: jan:Jann_4229 histone-like nucleoid-structuring protein H-NS; histone family protein nucleoid-structuring protein H-NS 506533 4581906 Pden_3349 Paracoccus denitrificans PD1222 histone family protein nucleoid-structuring protein H-NS YP_917118.1 506216 D 318586 CDS YP_917119.1 119386064 4581907 506549..507166 1 NC_008687.1 PFAM: plasmid pRiA4b ORF-3 family protein; KEGG: sme:SMa0896 hypothetical protein; plasmid pRiA4b ORF-3 family protein 507166 4581907 Pden_3350 Paracoccus denitrificans PD1222 plasmid pRiA4b ORF-3 family protein YP_917119.1 506549 D 318586 CDS YP_917120.1 119386065 4581908 complement(507323..508096) 1 NC_008687.1 PFAM: Methyltransferase type 11; Methyltransferase type 12; KEGG: bja:blr0060 hypothetical protein; methyltransferase type 11 508096 4581908 Pden_3351 Paracoccus denitrificans PD1222 methyltransferase type 11 YP_917120.1 507323 R 318586 CDS YP_917121.1 119386066 4581909 508181..508453 1 NC_008687.1 PFAM: protein of unknown function DUF156; KEGG: atc:AGR_C_1623 hypothetical protein; hypothetical protein 508453 4581909 Pden_3352 Paracoccus denitrificans PD1222 hypothetical protein YP_917121.1 508181 D 318586 CDS YP_917122.1 119386067 4581910 508469..509425 1 NC_008687.1 TIGRFAM: cation diffusion facilitator family transporter; PFAM: cation efflux protein; KEGG: sme:SMc04167 histidine-rich transporter transmembrane protein; cation diffusion facilitator family transporter 509425 4581910 Pden_3353 Paracoccus denitrificans PD1222 cation diffusion facilitator family transporter YP_917122.1 508469 D 318586 CDS YP_917123.1 119386068 4581911 509433..509882 1 NC_008687.1 hypothetical protein 509882 4581911 Pden_3354 Paracoccus denitrificans PD1222 hypothetical protein YP_917123.1 509433 D 318586 CDS YP_917124.1 119386069 4581912 509912..510370 1 NC_008687.1 PFAM: GCN5-related N-acetyltransferase; KEGG: sal:Sala_0626 gentamicin 3'-N-acetyltransferase; gentamicin 3'-N-acetyltransferase 510370 4581912 Pden_3355 Paracoccus denitrificans PD1222 gentamicin 3'-N-acetyltransferase YP_917124.1 509912 D 318586 CDS YP_917125.1 119386070 4581913 510604..511020 1 NC_008687.1 KEGG: mes:Meso_3831 hypothetical protein; hypothetical protein 511020 4581913 Pden_3356 Paracoccus denitrificans PD1222 hypothetical protein YP_917125.1 510604 D 318586 CDS YP_917126.1 119386071 4581914 511449..512126 1 NC_008687.1 PFAM: DNA methylase N-4/N-6 domain protein; KEGG: nha:Nham_0569 DNA methylase N-4/N-6; DNA methylase N-4/N-6 domain-containing protein 512126 4581914 Pden_3357 Paracoccus denitrificans PD1222 DNA methylase N-4/N-6 domain-containing protein YP_917126.1 511449 D 318586 CDS YP_917127.1 119386072 4581915 512201..512491 1 NC_008687.1 hypothetical protein 512491 4581915 Pden_3358 Paracoccus denitrificans PD1222 hypothetical protein YP_917127.1 512201 D 318586 CDS YP_917128.1 119386073 4581916 512788..513231 1 NC_008687.1 PFAM: GCN5-related N-acetyltransferase; KEGG: atc:AGR_L_1711 acetyltransferase; hypothetical protein 513231 4581916 Pden_3359 Paracoccus denitrificans PD1222 hypothetical protein YP_917128.1 512788 D 318586 CDS YP_917129.1 119386074 4581917 complement(513239..513475) 1 NC_008687.1 hypothetical protein 513475 4581917 Pden_3360 Paracoccus denitrificans PD1222 hypothetical protein YP_917129.1 513239 R 318586 CDS YP_917130.1 119386075 4581918 513986..514396 1 NC_008687.1 TIGRFAM: single-strand binding protein; PFAM: single-strand binding protein/Primosomal replication protein n; KEGG: nha:Nham_4669 single-strand binding protein; single-strand binding protein 514396 4581918 Pden_3361 Paracoccus denitrificans PD1222 single-strand binding protein YP_917130.1 513986 D 318586 CDS YP_917131.1 119386076 4581919 514440..514847 1 NC_008687.1 hypothetical protein 514847 4581919 Pden_3362 Paracoccus denitrificans PD1222 hypothetical protein YP_917131.1 514440 D 318586 CDS YP_917132.1 119386077 4581920 514954..515157 1 NC_008687.1 hypothetical protein 515157 4581920 Pden_3363 Paracoccus denitrificans PD1222 hypothetical protein YP_917132.1 514954 D 318586 CDS YP_917133.1 119386078 4581921 515762..515974 1 NC_008687.1 hypothetical protein 515974 4581921 Pden_3364 Paracoccus denitrificans PD1222 hypothetical protein YP_917133.1 515762 D 318586 CDS YP_917134.1 119386079 4581922 complement(515995..516369) 1 NC_008687.1 KEGG: mes:Meso_3838 hypothetical protein; hypothetical protein 516369 4581922 Pden_3365 Paracoccus denitrificans PD1222 hypothetical protein YP_917134.1 515995 R 318586 CDS YP_917135.1 119386080 4581923 complement(516539..516805) 1 NC_008687.1 hypothetical protein 516805 4581923 Pden_3366 Paracoccus denitrificans PD1222 hypothetical protein YP_917135.1 516539 R 318586 CDS YP_917136.1 119386081 4581924 complement(516952..517215) 1 NC_008687.1 KEGG: nwi:Nwi_0844 hypothetical protein; hypothetical protein 517215 4581924 Pden_3367 Paracoccus denitrificans PD1222 hypothetical protein YP_917136.1 516952 R 318586 CDS YP_917137.1 119386082 4581925 complement(517401..517637) 1 NC_008687.1 PFAM: helix-turn-helix domain protein; KEGG: mlo:msr6108 transcriptional regulator; XRE family transcriptional regulator 517637 4581925 Pden_3368 Paracoccus denitrificans PD1222 XRE family transcriptional regulator YP_917137.1 517401 R 318586 CDS YP_917138.1 119386083 4581926 517829..518098 1 NC_008687.1 KEGG: nwi:Nwi_0845 hypothetical protein; hypothetical protein 518098 4581926 Pden_3369 Paracoccus denitrificans PD1222 hypothetical protein YP_917138.1 517829 D 318586 CDS YP_917139.1 119386084 4581927 518095..518964 1 NC_008687.1 KEGG: nwi:Nwi_0846 possible replication protein A; replication protein A 518964 4581927 Pden_3370 Paracoccus denitrificans PD1222 replication protein A YP_917139.1 518095 D 318586 CDS YP_917140.1 119386085 4581928 519220..519720 1 NC_008687.1 KEGG: mes:Meso_2334 hypothetical protein; hypothetical protein 519720 4581928 Pden_3371 Paracoccus denitrificans PD1222 hypothetical protein YP_917140.1 519220 D 318586 CDS YP_917141.1 119386086 4581929 519717..521225 1 NC_008687.1 PFAM: C-5 cytosine-specific DNA methylase; KEGG: ngo:NGO1894 5-methylcytosine methyltransferase; C-5 cytosine-specific DNA methylase 521225 4581929 Pden_3372 Paracoccus denitrificans PD1222 C-5 cytosine-specific DNA methylase YP_917141.1 519717 D 318586 CDS YP_917142.1 119386087 4581930 521222..521788 1 NC_008687.1 KEGG: mes:Meso_2333 conjugal transfer protein precursor; conjugal transfer protein precursor 521788 4581930 Pden_3373 Paracoccus denitrificans PD1222 conjugal transfer protein precursor YP_917142.1 521222 D 318586 CDS YP_917143.1 119386088 4581931 521824..522159 1 NC_008687.1 PFAM: protein of unknown function DUF736; KEGG: mes:Meso_2332 protein of unknown function DUF736; hypothetical protein 522159 4581931 Pden_3374 Paracoccus denitrificans PD1222 hypothetical protein YP_917143.1 521824 D 318586 CDS YP_917144.1 119386089 4581932 522163..522981 1 NC_008687.1 PFAM: Lytic transglycosylase, catalytic; KEGG: mes:Meso_0517 lytic transglycosylase, catalytic; lytic transglycosylase, catalytic 522981 4581932 Pden_3375 Paracoccus denitrificans PD1222 lytic transglycosylase, catalytic YP_917144.1 522163 D 318586 CDS YP_917145.1 119386090 4581933 523031..523612 1 NC_008687.1 hypothetical protein 523612 4581933 Pden_3376 Paracoccus denitrificans PD1222 hypothetical protein YP_917145.1 523031 D 318586 CDS YP_917146.1 119386091 4581934 523854..525593 1 NC_008687.1 KEGG: bja:bll0044 hypothetical protein; hypothetical protein 525593 4581934 Pden_3377 Paracoccus denitrificans PD1222 hypothetical protein YP_917146.1 523854 D 318586 CDS YP_917147.1 119386092 4581935 525662..525913 1 NC_008687.1 TIGRFAM: prevent-host-death family protein; PFAM: protein of unknown function DUF172; KEGG: rru:Rru_A0090 prevent-host-death protein; prevent-host-death family protein 525913 4581935 Pden_3378 Paracoccus denitrificans PD1222 prevent-host-death family protein YP_917147.1 525662 D 318586 CDS YP_917148.1 119386093 4581936 525917..526351 1 NC_008687.1 PFAM: PilT protein domain protein; KEGG: rru:Rru_A0091 PilT protein-like; twitching motility protein PilT 526351 4581936 Pden_3379 Paracoccus denitrificans PD1222 twitching motility protein PilT YP_917148.1 525917 D 318586 CDS YP_917149.1 119386094 4581937 complement(526562..526813) 1 NC_008687.1 KEGG: nmu:Nmul_A0143 ATP-dependent endonuclease of the OLD family-like; hypothetical protein 526813 4581937 Pden_3380 Paracoccus denitrificans PD1222 hypothetical protein YP_917149.1 526562 R 318586 CDS YP_917150.1 119386095 4581938 526818..527030 1 NC_008687.1 PFAM: helix-turn-helix- domain containing protein, AraC type; KEGG: rsp:RSP_3202 transcriptional regulator, AraC family; helix-turn-helix domain-containing protein 527030 4581938 Pden_3381 Paracoccus denitrificans PD1222 helix-turn-helix domain-containing protein YP_917150.1 526818 D 318586 CDS YP_917151.1 119386096 4581939 complement(527269..527922) 1 NC_008687.1 PFAM: class II aldolase/adducin family protein; KEGG: bja:bll2927 hypothetical protein; class II aldolase/adducin family protein 527922 4581939 Pden_3382 Paracoccus denitrificans PD1222 class II aldolase/adducin family protein YP_917151.1 527269 R 318586 CDS YP_917152.1 119386097 4581940 complement(527919..529178) 1 NC_008687.1 PFAM: type III effector Hrp-dependent outers; KEGG: reu:Reut_A1426 type III effector Hrp-dependent outers; Hrp-dependent type III effector protein 529178 4581940 Pden_3383 Paracoccus denitrificans PD1222 Hrp-dependent type III effector protein YP_917152.1 527919 R 318586 CDS YP_917153.1 119386098 4581941 complement(529196..530473) 1 NC_008687.1 TIGRFAM: TRAP dicarboxylate transporter, DctM subunit; PFAM: TRAP C4-dicarboxylate transport system permease DctM subunit; KEGG: gka:GK1972 transporter; TRAP dicarboxylate transporter, DctM subunit 530473 4581941 Pden_3384 Paracoccus denitrificans PD1222 TRAP dicarboxylate transporter, DctM subunit YP_917153.1 529196 R 318586 CDS YP_917154.1 119386099 4581942 complement(530470..531030) 1 NC_008687.1 PFAM: Tripartite ATP-independent periplasmic transporter, DctQ component; KEGG: msu:MS0052 hypothetical protein; tripartite ATP-independent periplasmic transporter DctQ 531030 4581942 Pden_3385 Paracoccus denitrificans PD1222 tripartite ATP-independent periplasmic transporter DctQ YP_917154.1 530470 R 318586 CDS YP_917155.1 119386100 4581943 complement(531027..531698) 1 NC_008687.1 PFAM: cyclase family protein; KEGG: pmu:PM1641 hypothetical Synechocystis sp.; cyclase family protein 531698 4581943 Pden_3386 Paracoccus denitrificans PD1222 cyclase family protein YP_917155.1 531027 R 318586 CDS YP_917156.1 119386101 4581944 complement(531715..532722) 1 NC_008687.1 TIGRFAM: TRAP dicarboxylate transporter, DctP subunit; PFAM: TRAP dicarboxylate transporter- DctP subunit; KEGG: hso:HS_0762 possible C4-dicarboxylate transport system, periplasmic component; TRAP dicarboxylate transporter, DctP subunit 532722 4581944 Pden_3387 Paracoccus denitrificans PD1222 TRAP dicarboxylate transporter, DctP subunit YP_917156.1 531715 R 318586 CDS YP_917157.1 119386102 4581945 complement(532760..534163) 1 NC_008687.1 PFAM: SAF domain; KEGG: rru:Rru_A3141 homoserine dehydrogenase, NAD-binding; SAF domain-containing protein 534163 4581945 Pden_3388 Paracoccus denitrificans PD1222 SAF domain-containing protein YP_917157.1 532760 R 318586 CDS YP_917158.1 119386103 4581946 534444..535115 1 NC_008687.1 PFAM: regulatory protein GntR, HTH; GntR domain protein; KEGG: sme:SMb20773 transcriptional regulator, GntR family protein; GntR family transcriptional regulator 535115 4581946 Pden_3389 Paracoccus denitrificans PD1222 GntR family transcriptional regulator YP_917158.1 534444 D 318586 CDS YP_917159.1 119386104 4581947 complement(535370..538231) 1 NC_008687.1 KEGG: ade:Adeh_3797 hypothetical protein; hypothetical protein 538231 4581947 Pden_3390 Paracoccus denitrificans PD1222 hypothetical protein YP_917159.1 535370 R 318586 CDS YP_917160.1 119386105 4581948 complement(538268..539467) 1 NC_008687.1 hypothetical protein 539467 4581948 Pden_3391 Paracoccus denitrificans PD1222 hypothetical protein YP_917160.1 538268 R 318586 CDS YP_917161.1 119386106 4581949 complement(539614..539919) 1 NC_008687.1 hypothetical protein 539919 4581949 Pden_3392 Paracoccus denitrificans PD1222 hypothetical protein YP_917161.1 539614 R 318586 CDS YP_917162.1 119386107 4581951 540885..541514 1 NC_008687.1 KEGG: sal:Sala_0067 transposase; transposase 541514 4581951 Pden_3395 Paracoccus denitrificans PD1222 transposase YP_917162.1 540885 D 318586 CDS YP_917163.1 119386108 4581952 complement(541860..542732) 1 NC_008687.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: abo:ABO_1099 transcriptional regulator, LysR family; LysR family transcriptional regulator 542732 4581952 Pden_3396 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_917163.1 541860 R 318586 CDS YP_917164.1 119386109 4581953 542800..543111 1 NC_008687.1 hypothetical protein 543111 4581953 Pden_3397 Paracoccus denitrificans PD1222 hypothetical protein YP_917164.1 542800 D 318586 CDS YP_917165.1 119386110 4581954 543498..543977 1 NC_008687.1 KEGG: rpb:RPB_3880 twin-arginine translocation pathway signal; twin-arginine translocation pathway signal 543977 4581954 Pden_3398 Paracoccus denitrificans PD1222 twin-arginine translocation pathway signal YP_917165.1 543498 D 318586 CDS YP_917166.1 119386111 4581955 543983..544609 1 NC_008687.1 PFAM: Ferric reductase domain protein transmembrane component, N-terminal domain; KEGG: rde:RD1_1724 hypothetical protein; ferric reductase domain-containing protein 544609 4581955 Pden_3399 Paracoccus denitrificans PD1222 ferric reductase domain-containing protein YP_917166.1 543983 D 318586 CDS YP_917167.1 119386112 4581956 complement(544753..545640) 1 NC_008687.1 TIGRFAM: molybdenum cofactor synthesis domain; PFAM: molybdopterin binding domain; MoeA domain protein, domain IV; KEGG: rru:Rru_A2222 molybdopterin biosynthesis protein; molybdenum cofactor synthesis domain-containing protein 545640 4581956 Pden_3400 Paracoccus denitrificans PD1222 molybdenum cofactor synthesis domain-containing protein YP_917167.1 544753 R 318586 CDS YP_917168.1 119386113 4581957 545967..546131 1 NC_008687.1 KEGG: nwi:Nwi_2919 transposase, IS4; transposase, IS4 546131 4581957 Pden_3401 Paracoccus denitrificans PD1222 transposase, IS4 YP_917168.1 545967 D 318586 CDS YP_917169.1 119386114 4581958 complement(546172..547575) 1 NC_008687.1 PFAM: ATP-binding region, ATPase domain protein domain protein; histidine kinase A domain protein domain protein; KEGG: rfr:Rfer_3645 periplasmic sensor signal transduction histidine kinase; integral membrane sensor signal transduction histidine kinase 547575 4581958 Pden_3402 Paracoccus denitrificans PD1222 integral membrane sensor signal transduction histidine kinase YP_917169.1 546172 R 318586 CDS YP_917170.1 119386115 4581959 complement(547568..548272) 1 NC_008687.1 PFAM: response regulator receiver; transcriptional regulator domain protein; KEGG: rfr:Rfer_3646 two component transcriptional regulator, winged helix family; two component transcriptional regulator 548272 4581959 Pden_3403 Paracoccus denitrificans PD1222 two component transcriptional regulator YP_917170.1 547568 R 318586 CDS YP_917171.1 119386116 4581960 548443..549684 1 NC_008687.1 PFAM: extracellular solute-binding protein, family 1; KEGG: pub:SAR11_0769 probable binding protein component of ABC sugar transporter; extracellular solute-binding protein 549684 4581960 Pden_3404 Paracoccus denitrificans PD1222 extracellular solute-binding protein YP_917171.1 548443 D 318586 CDS YP_917172.1 119386117 4581961 549751..550623 1 NC_008687.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: rru:Rru_A0093 binding-protein-dependent transport systems inner membrane component; binding-protein-dependent transport system inner membrane protein 550623 4581961 Pden_3405 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_917172.1 549751 D 318586 CDS YP_917173.1 119386118 4581962 550613..551482 1 NC_008687.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: rru:Rru_A0094 binding-protein-dependent transport systems inner membrane component; binding-protein-dependent transport systems inner membrane component 551482 4581962 Pden_3406 Paracoccus denitrificans PD1222 binding-protein-dependent transport systems inner membrane component YP_917173.1 550613 D 318586 CDS YP_917174.1 119386119 4581963 551486..552592 1 NC_008687.1 PFAM: ABC transporter related; Transport-associated OB domain protein; SMART: AAA ATPase; KEGG: sme:SMc04393 ATP-binding ABC transporter protein; ABC transporter 552592 4581963 Pden_3407 Paracoccus denitrificans PD1222 ABC transporter YP_917174.1 551486 D 318586 CDS YP_917175.1 119386120 4581964 552977..553237 1 NC_008687.1 hypothetical protein 553237 4581964 Pden_3408 Paracoccus denitrificans PD1222 hypothetical protein YP_917175.1 552977 D 318586 CDS YP_917176.1 119386121 4581965 553476..554615 1 NC_008687.1 PFAM: creatinase; peptidase M24; KEGG: ppu:PP_3667 creatinase; creatinase 554615 4581965 Pden_3409 Paracoccus denitrificans PD1222 creatinase YP_917176.1 553476 D 318586 CDS YP_917177.1 119386122 4581966 complement(554677..555207) 1 NC_008687.1 KEGG: rxy:Rxyl_0459 creatininase; hypothetical protein 555207 4581966 Pden_3410 Paracoccus denitrificans PD1222 hypothetical protein YP_917177.1 554677 R 318586 CDS YP_917178.1 119386123 4581967 complement(555233..556117) 1 NC_008687.1 KEGG: ccr:CC1457 flagellin modification protein FlmG; hypothetical protein 556117 4581967 Pden_3411 Paracoccus denitrificans PD1222 hypothetical protein YP_917178.1 555233 R 318586 CDS YP_917179.1 119386124 4581968 complement(556142..557041) 1 NC_008687.1 hypothetical protein 557041 4581968 Pden_3412 Paracoccus denitrificans PD1222 hypothetical protein YP_917179.1 556142 R 318586 CDS YP_917180.1 119386125 4581969 complement(557134..557493) 1 NC_008687.1 hypothetical protein 557493 4581969 Pden_3413 Paracoccus denitrificans PD1222 hypothetical protein YP_917180.1 557134 R 318586 CDS YP_917181.1 119386126 4581970 complement(558039..558896) 1 NC_008687.1 KEGG: rpa:RPA2826 hypothetical protein; hypothetical protein 558896 4581970 Pden_3414 Paracoccus denitrificans PD1222 hypothetical protein YP_917181.1 558039 R 318586 CDS YP_917182.1 119386127 4581971 559011..560171 1 NC_008687.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: atc:AGR_pAT_469 hypothetical protein; LysR family transcriptional regulator 560171 4581971 Pden_3415 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_917182.1 559011 D 318586 CDS YP_917183.1 119386128 4581972 complement(560290..561237) 1 NC_008687.1 PFAM: Acetamidase/Formamidase; KEGG: rsp:RSP_3443 acetamidase/formamidase; acetamidase/formamidase 561237 4581972 Pden_3416 Paracoccus denitrificans PD1222 acetamidase/formamidase YP_917183.1 560290 R 318586 CDS YP_917184.1 119386129 4581973 complement(561264..561575) 1 NC_008687.1 hypothetical protein 561575 4581973 Pden_3417 Paracoccus denitrificans PD1222 hypothetical protein YP_917184.1 561264 R 318586 CDS YP_917185.1 119386130 4581974 complement(561585..562298) 1 NC_008687.1 PFAM: Dimethylmenaquinone methyltransferase; KEGG: rsp:RSP_3441 hypothetical protein; hypothetical protein 562298 4581974 Pden_3418 Paracoccus denitrificans PD1222 hypothetical protein YP_917185.1 561585 R 318586 CDS YP_917186.1 119386131 4581975 complement(562313..563098) 1 NC_008687.1 PFAM: short-chain dehydrogenase/reductase SDR; KEGG: rsp:RSP_3440 short chain dehydrogenase; short-chain dehydrogenase/reductase SDR 563098 4581975 Pden_3419 Paracoccus denitrificans PD1222 short-chain dehydrogenase/reductase SDR YP_917186.1 562313 R 318586 CDS YP_917187.1 119386132 4581976 complement(563140..564366) 1 NC_008687.1 PFAM: aminotransferase, class I and II; KEGG: rsp:RSP_3439 aspartate aminotransferase; class I and II aminotransferase 564366 4581976 Pden_3420 Paracoccus denitrificans PD1222 class I and II aminotransferase YP_917187.1 563140 R 318586 CDS YP_917188.1 119386133 4581977 complement(564392..564814) 1 NC_008687.1 PFAM: Endoribonuclease L-PSP; KEGG: rsp:RSP_3438 translation initiation inhibitor; endoribonuclease L-PSP 564814 4581977 Pden_3421 Paracoccus denitrificans PD1222 endoribonuclease L-PSP YP_917188.1 564392 R 318586 CDS YP_917189.1 119386134 4581978 complement(564811..566043) 1 NC_008687.1 catalyzes the formation of oxalozcetate and L-glutamate from L-aspartate and 2-oxoglutarate; aspartate aminotransferase 566043 4581978 Pden_3422 Paracoccus denitrificans PD1222 aspartate aminotransferase YP_917189.1 564811 R 318586 CDS YP_917190.1 119386135 4581979 566180..567067 1 NC_008687.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: rsp:RSP_3436 transcriptional regulator, LysR-family; LysR family transcriptional regulator 567067 4581979 Pden_3423 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_917190.1 566180 D 318586 CDS YP_917191.1 119386136 4581980 complement(567071..567997) 1 NC_008687.1 PFAM: dihydrodipicolinate synthetase; KEGG: rsp:RSP_3456 dihydrodipicolinate synthase; dihydrodipicolinate synthetase 567997 4581980 Pden_3424 Paracoccus denitrificans PD1222 dihydrodipicolinate synthetase YP_917191.1 567071 R 318586 CDS YP_917192.1 119386137 4581981 complement(568008..568865) 1 NC_008687.1 PFAM: aminotransferase, class IV; KEGG: rsp:RSP_3455 D-alanine aminotransferase; aminotransferase, class IV 568865 4581981 Pden_3425 Paracoccus denitrificans PD1222 aminotransferase, class IV YP_917192.1 568008 R 318586 CDS YP_917193.1 119386138 4581982 complement(568877..569647) 1 NC_008687.1 PFAM: LamB/YcsF family protein; KEGG: rsp:RSP_3454 hypothetical protein; LamB/YcsF family protein 569647 4581982 Pden_3426 Paracoccus denitrificans PD1222 LamB/YcsF family protein YP_917193.1 568877 R 318586 CDS YP_917194.1 119386139 4581983 569820..570806 1 NC_008687.1 PFAM: TRAP dicarboxylate transporter- DctP subunit; KEGG: rsp:RSP_3453 TRAP-T family transporter, periplasmic binding protein; TRAP dicarboxylate transporter- DctP subunit 570806 4581983 Pden_3427 Paracoccus denitrificans PD1222 TRAP dicarboxylate transporter- DctP subunit YP_917194.1 569820 D 318586 CDS YP_917195.1 119386140 4581984 570897..571439 1 NC_008687.1 PFAM: Tripartite ATP-independent periplasmic transporter, DctQ component; KEGG: rsp:RSP_3452 TRAP-T family transporter, small (4TMs) inner membrane subunit; tripartite ATP-independent periplasmic transporter DctQ 571439 4581984 Pden_3428 Paracoccus denitrificans PD1222 tripartite ATP-independent periplasmic transporter DctQ YP_917195.1 570897 D 318586 CDS YP_917196.1 119386141 4581985 571452..572753 1 NC_008687.1 TIGRFAM: TRAP dicarboxylate transporter, DctM subunit; PFAM: TRAP C4-dicarboxylate transport system permease DctM subunit; KEGG: rsp:RSP_3451 TRAP-T family transporter, large (12TMs) inner membrane subunit; TRAP dicarboxylate transporter subunit DctM 572753 4581985 Pden_3429 Paracoccus denitrificans PD1222 TRAP dicarboxylate transporter subunit DctM YP_917196.1 571452 D 318586 CDS YP_917197.1 119386142 4581986 572761..573534 1 NC_008687.1 PFAM: Allophanate hydrolase subunit 1; KEGG: rsp:RSP_3450 hypothetical protein; allophanate hydrolase subunit 1 573534 4581986 Pden_3430 Paracoccus denitrificans PD1222 allophanate hydrolase subunit 1 YP_917197.1 572761 D 318586 CDS YP_917198.1 119386143 4581987 573531..574595 1 NC_008687.1 TIGRFAM: urea amidolyase related protein; PFAM: Allophanate hydrolase subunit 2; KEGG: rsp:RSP_3449 allophanate hydrolase subunit 2; urea amidolyase 574595 4581987 Pden_3431 Paracoccus denitrificans PD1222 urea amidolyase YP_917198.1 573531 D 318586 CDS YP_917199.1 119386144 4581988 574592..575242 1 NC_008687.1 PFAM: regulatory protein GntR, HTH; GntR domain protein; KEGG: rsp:RSP_3448 transcriptional regulator, GntR-family; GntR family transcriptional regulator 575242 4581988 Pden_3432 Paracoccus denitrificans PD1222 GntR family transcriptional regulator YP_917199.1 574592 D 318586 CDS YP_917200.1 119386145 4581989 575239..576189 1 NC_008687.1 PFAM: D-isomer specific 2-hydroxyacid dehydrogenase, catalytic region; D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding; KEGG: rsp:RSP_3447 dehydrogenase; D-isomer specific 2-hydroxyacid dehydrogenase 576189 4581989 Pden_3433 Paracoccus denitrificans PD1222 D-isomer specific 2-hydroxyacid dehydrogenase YP_917200.1 575239 D 318586 CDS YP_917201.1 119386146 4581990 576186..577457 1 NC_008687.1 allantoate amidohydrolase and N-carbamoyl-L-amino acid amidohydrolase are very similar; the allantoate amidohydrolase from Escherichia coli forms a dimer and binds zinc ions for catalytic activity and catalyzes the conversion of allantoate to (S)-ureidoglycolate and ammonia; carbamoyl amidohydrolase from Bacillus sp. converts N-carbamoyl amino acids to amino acids, ammonia, and carbon dioxide; allantoate amidohydrolase 577457 4581990 Pden_3434 Paracoccus denitrificans PD1222 allantoate amidohydrolase YP_917201.1 576186 D 318586 CDS YP_917202.1 119386147 4581991 577454..578089 1 NC_008687.1 PFAM: regulatory protein GntR, HTH; GntR domain protein; KEGG: rsp:RSP_3445 transcriptional regulator, GntR family; GntR family transcriptional regulator 578089 4581991 Pden_3435 Paracoccus denitrificans PD1222 GntR family transcriptional regulator YP_917202.1 577454 D 318586 CDS YP_917203.1 119386148 4581992 578094..579287 1 NC_008687.1 PFAM: peptidase M24; KEGG: rsp:RSP_3444 Xaa-Pro aminopeptidase; peptidase M24 579287 4581992 Pden_3436 Paracoccus denitrificans PD1222 peptidase M24 YP_917203.1 578094 D 318586 CDS YP_917204.1 119386149 4581993 579311..579997 1 NC_008687.1 PFAM: fumarylacetoacetate (FAA) hydrolase; KEGG: jan:Jann_2909 5-carboxymethyl-2-hydroxymuconate delta-isomerase; fumarylacetoacetate (FAA) hydrolase 579997 4581993 Pden_3437 Paracoccus denitrificans PD1222 fumarylacetoacetate (FAA) hydrolase YP_917204.1 579311 D 318586 CDS YP_917205.1 119386150 4581994 complement(580165..581424) 1 NC_008687.1 PFAM: ATP-binding region, ATPase domain protein domain protein; histidine kinase, HAMP region domain protein; histidine kinase A domain protein domain protein; KEGG: rpc:RPC_3026 histidine kinase; integral membrane sensor signal transduction histidine kinase 581424 4581994 Pden_3438 Paracoccus denitrificans PD1222 integral membrane sensor signal transduction histidine kinase YP_917205.1 580165 R 318586 CDS YP_917206.1 119386151 4581995 complement(581421..582140) 1 NC_008687.1 PFAM: response regulator receiver; transcriptional regulator domain protein; KEGG: rpc:RPC_3029 two component transcriptional regulator, winged helix family; two component transcriptional regulator 582140 4581995 Pden_3439 Paracoccus denitrificans PD1222 two component transcriptional regulator YP_917206.1 581421 R 318586 CDS YP_917207.1 119386152 4581996 582349..582957 1 NC_008687.1 hypothetical protein 582957 4581996 Pden_3440 Paracoccus denitrificans PD1222 hypothetical protein YP_917207.1 582349 D 318586 CDS YP_917208.1 119386153 4581997 583029..583505 1 NC_008687.1 hypothetical protein 583505 4581997 Pden_3441 Paracoccus denitrificans PD1222 hypothetical protein YP_917208.1 583029 D 318586 CDS YP_917209.1 119386154 4581998 583517..583921 1 NC_008687.1 hypothetical protein 583921 4581998 Pden_3442 Paracoccus denitrificans PD1222 hypothetical protein YP_917209.1 583517 D 318586 CDS YP_917210.1 119386155 4581999 complement(583981..584262) 1 NC_008687.1 hypothetical protein 584262 4581999 Pden_3443 Paracoccus denitrificans PD1222 hypothetical protein YP_917210.1 583981 R 318586 CDS YP_917211.1 119386156 4582000 complement(584310..586316) 1 NC_008687.1 PFAM: ABC transporter related; protein of unknown function DUF214; SMART: AAA ATPase; KEGG: rpb:RPB_2235 hypothetical protein; ABC transporter 586316 4582000 Pden_3444 Paracoccus denitrificans PD1222 ABC transporter YP_917211.1 584310 R 318586 CDS YP_917212.1 119386157 4582001 complement(586309..587514) 1 NC_008687.1 TIGRFAM: efflux transporter, RND family, MFP subunit; PFAM: secretion protein HlyD family protein; KEGG: rpc:RPC_1868 secretion protein HlyD; RND family efflux transporter MFP subunit 587514 4582001 Pden_3445 Paracoccus denitrificans PD1222 RND family efflux transporter MFP subunit YP_917212.1 586309 R 318586 CDS YP_917213.1 119386158 4582002 587614..588063 1 NC_008687.1 hypothetical protein 588063 4582002 Pden_3446 Paracoccus denitrificans PD1222 hypothetical protein YP_917213.1 587614 D 318586 CDS YP_917214.1 119386159 4582003 588344..589516 1 NC_008687.1 TIGRFAM: efflux transporter, RND family, MFP subunit; PFAM: secretion protein HlyD family protein; KEGG: ret:RHE_CH03411 probable protein secretion protein, HlyD family; RND family efflux transporter MFP subunit 589516 4582003 Pden_3447 Paracoccus denitrificans PD1222 RND family efflux transporter MFP subunit YP_917214.1 588344 D 318586 CDS YP_917215.1 119386160 4582004 589521..592625 1 NC_008687.1 TIGRFAM: transporter, hydrophobe/amphiphile efflux-1 (HAE1) family; PFAM: acriflavin resistance protein; KEGG: ret:RHE_CH03412 probable multidrug efflux transporter protein; hydrophobe/amphiphile efflux-1 (HAE1) family protein 592625 4582004 Pden_3448 Paracoccus denitrificans PD1222 hydrophobe/amphiphile efflux-1 (HAE1) family protein YP_917215.1 589521 D 318586 CDS YP_917216.1 119386161 4582005 592622..593998 1 NC_008687.1 TIGRFAM: RND efflux system, outer membrane lipoprotein, NodT family; PFAM: outer membrane efflux protein; KEGG: ret:RHE_CH03413 nodulation protein (outer membrane efflux protein); RND efflux system outer membrane lipoprotein 593998 4582005 Pden_3449 Paracoccus denitrificans PD1222 RND efflux system outer membrane lipoprotein YP_917216.1 592622 D 318586 CDS YP_917217.1 119386162 4582006 complement(594069..595274) 1 NC_008687.1 PFAM: beta-lactamase; KEGG: rsp:RSP_3749 beta-lactamase precursor; beta-lactamase 595274 ampC 4582006 ampC Paracoccus denitrificans PD1222 beta-lactamase YP_917217.1 594069 R 318586 CDS YP_917218.1 119386163 4582007 595356..596231 1 NC_008687.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: sme:SMa2293 probable beta lactamase transcriptional activator; LysR family transcriptional regulator 596231 4582007 Pden_3451 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_917218.1 595356 D 318586 CDS YP_917219.1 119386164 4582008 596329..596745 1 NC_008687.1 hypothetical protein 596745 4582008 Pden_3452 Paracoccus denitrificans PD1222 hypothetical protein YP_917219.1 596329 D 318586 CDS YP_917220.1 119386165 4582009 596845..597135 1 NC_008687.1 hypothetical protein 597135 4582009 Pden_3453 Paracoccus denitrificans PD1222 hypothetical protein YP_917220.1 596845 D 318586 CDS YP_917221.1 119386166 4582010 complement(597192..598448) 1 NC_008687.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: rde:RD1_4140 transcriptional regulator, LysR family; LysR family transcriptional regulator 598448 4582010 Pden_3454 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_917221.1 597192 R 318586 CDS YP_917222.1 119386167 4582011 complement(598445..599119) 1 NC_008687.1 PFAM: protein of unknown function DUF1028; KEGG: rde:RD1_4139 hypothetical protein; hypothetical protein 599119 4582011 Pden_3455 Paracoccus denitrificans PD1222 hypothetical protein YP_917222.1 598445 R 318586 CDS YP_917223.1 119386168 4582012 complement(599124..599540) 1 NC_008687.1 PFAM: Endoribonuclease L-PSP; KEGG: rde:RD1_4138 endoribonuclease L-PSP family protein; endoribonuclease L-PSP 599540 4582012 Pden_3456 Paracoccus denitrificans PD1222 endoribonuclease L-PSP YP_917223.1 599124 R 318586 CDS YP_917224.1 119386169 4582013 complement(599599..600870) 1 NC_008687.1 PFAM: FAD dependent oxidoreductase; KEGG: pau:PA14_71210 monooxygenase; FAD dependent oxidoreductase 600870 4582013 Pden_3457 Paracoccus denitrificans PD1222 FAD dependent oxidoreductase YP_917224.1 599599 R 318586 CDS YP_917225.1 119386170 4582014 601117..602274 1 NC_008687.1 catalyzes the formation of L-ornithine from N(2)-acetyl-L-ornithine; acetylornithine deacetylase 602274 4582014 Pden_3458 Paracoccus denitrificans PD1222 acetylornithine deacetylase YP_917225.1 601117 D 318586 CDS YP_917226.1 119386171 4582015 602523..603659 1 NC_008687.1 KEGG: rsp:RSP_1882 ABC polyamine/opine transporter, ATPase subunit; TIGRFAM: spermidine/putrescine ABC transporter ATPase subunit; PFAM: ABC transporter related; Transport-associated OB domain protein; SMART: AAA ATPase; spermidine/putrescine ABC transporter ATPase 603659 4582015 Pden_3459 Paracoccus denitrificans PD1222 spermidine/putrescine ABC transporter ATPase YP_917226.1 602523 D 318586 CDS YP_917227.1 119386172 4582016 603742..604812 1 NC_008687.1 KEGG: rsp:RSP_1883 ABC polyamine/opine transporter, periplasmic substrate-binding protein; ABC polyamine/opine transporter, periplasmic substrate-binding protein 604812 4582016 Pden_3460 Paracoccus denitrificans PD1222 ABC polyamine/opine transporter, periplasmic substrate-binding protein YP_917227.1 603742 D 318586 CDS YP_917228.1 119386173 4582017 604937..606229 1 NC_008687.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: rsp:RSP_1884 ABC polyamine/opine transporter, inner membrane subunit; binding-protein-dependent transport system inner membrane protein 606229 4582017 Pden_3461 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_917228.1 604937 D 318586 CDS YP_917229.1 119386174 4582018 606235..607188 1 NC_008687.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: rsp:RSP_1886 ABC polyamine/opine transporter, inner membrane subunit; binding-protein-dependent transport system inner membrane protein 607188 4582018 Pden_3462 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_917229.1 606235 D 318586 CDS YP_917230.1 119386175 4582019 607236..608441 1 NC_008687.1 PFAM: FAD-dependent pyridine nucleotide-disulphide oxidoreductase; KEGG: sil:SPO3737 pyridine nucleotide-disulphide oxidoreductase family protein; FAD-dependent pyridine nucleotide-disulfide oxidoreductase 608441 4582019 Pden_3463 Paracoccus denitrificans PD1222 FAD-dependent pyridine nucleotide-disulfide oxidoreductase YP_917230.1 607236 D 318586 CDS YP_917231.1 119386176 4582020 complement(608674..609030) 1 NC_008687.1 PFAM: ferredoxin; KEGG: sil:SPO0766 iron-sulfur cluster-binding protein; ferredoxin 609030 4582020 Pden_3464 Paracoccus denitrificans PD1222 ferredoxin YP_917231.1 608674 R 318586 CDS YP_917232.1 119386177 4582021 complement(609104..610258) 1 NC_008687.1 PFAM: Rieske [2Fe-2S] domain protein; KEGG: bxe:Bxe_A3468 iron-sulphur rieske protein; Rieske (2Fe-2S) domain-containing protein 610258 4582021 Pden_3465 Paracoccus denitrificans PD1222 Rieske (2Fe-2S) domain-containing protein YP_917232.1 609104 R 318586 CDS YP_917233.1 119386178 4582022 610387..611307 1 NC_008687.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: csa:Csal_2385 transcriptional regulator, LysR family; LysR family transcriptional regulator 611307 4582022 Pden_3466 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_917233.1 610387 D 318586 CDS YP_917234.1 119386179 4582023 complement(611548..612549) 1 NC_008687.1 PFAM: proline racemase; KEGG: atc:AGR_L_1800 hypothetical protein; hydroxyproline-2-epimerase 612549 4582023 Pden_3467 Paracoccus denitrificans PD1222 hydroxyproline-2-epimerase YP_917234.1 611548 R 318586 CDS YP_917235.1 119386180 4582024 complement(612943..613653) 1 NC_008687.1 PFAM: cyclic nucleotide-binding; regulatory protein, Crp; KEGG: sil:SPOA0206 transcriptional regulator, Crp/Fnr family; CRP/FNR family transcriptional regulator 613653 4582024 Pden_3468 Paracoccus denitrificans PD1222 CRP/FNR family transcriptional regulator YP_917235.1 612943 R 318586 CDS YP_917236.1 119386181 4582025 613765..614847 1 NC_008687.1 KEGG: ade:Adeh_2705 response regulator receiver; hypothetical protein 614847 4582025 Pden_3469 Paracoccus denitrificans PD1222 hypothetical protein YP_917236.1 613765 D 318586 CDS YP_917237.1 119386182 4582026 complement(615004..615549) 1 NC_008687.1 KEGG: ret:RHE_PC00193 hypothetical protein; hypothetical protein 615549 4582026 Pden_3470 Paracoccus denitrificans PD1222 hypothetical protein YP_917237.1 615004 R 318586 CDS YP_917238.1 119386183 4582027 complement(615599..616954) 1 NC_008687.1 PFAM: TfuA domain protein, core; KEGG: mxa:MXAN_2398 hypothetical protein; TfuA domain-containing protein 616954 4582027 Pden_3471 Paracoccus denitrificans PD1222 TfuA domain-containing protein YP_917238.1 615599 R 318586 CDS YP_917239.1 119386184 4582028 complement(616951..618120) 1 NC_008687.1 TIGRFAM: uncharacterized domain; PFAM: protein of unknown function DUF181; KEGG: ret:RHE_PE00437 hypothetical protein; hypothetical protein 618120 4582028 Pden_3472 Paracoccus denitrificans PD1222 hypothetical protein YP_917239.1 616951 R 318586 CDS YP_917240.1 119386185 4582029 618747..620537 1 NC_008687.1 PFAM: adenylyl cyclase class-3/4/guanylyl cyclase; TPR repeat-containing protein; Tetratricopeptide TPR_2 repeat protein; SMART: Tetratricopeptide domain protein; KEGG: mlo:mll3276 adenylate cyclase cya3 [Sinorhizobium meliloti]; adenylyl cyclase 620537 4582029 Pden_3473 Paracoccus denitrificans PD1222 adenylyl cyclase YP_917240.1 618747 D 318586 CDS YP_917241.1 119386186 4582030 620705..622696 1 NC_008687.1 PFAM: protein of unknown function DUF839; KEGG: rsp:RSP_3051 phosphatase; hypothetical protein 622696 4582030 Pden_3474 Paracoccus denitrificans PD1222 hypothetical protein YP_917241.1 620705 D 318586 CDS YP_917242.1 119386187 4582031 complement(622786..623484) 1 NC_008687.1 PFAM: ThiJ/PfpI domain protein; KEGG: bms:BRA0227 ThiJ/PfpI family protein; ThiJ/PfpI domain-containing protein 623484 4582031 Pden_3475 Paracoccus denitrificans PD1222 ThiJ/PfpI domain-containing protein YP_917242.1 622786 R 318586 CDS YP_917243.1 119386188 4582032 complement(623489..624766) 1 NC_008687.1 PFAM: NADH:flavin oxidoreductase/NADH oxidase; KEGG: ccr:CC3083 FMN oxidoreductase; NADH:flavin oxidoreductase 624766 4582032 Pden_3476 Paracoccus denitrificans PD1222 NADH:flavin oxidoreductase YP_917243.1 623489 R 318586 CDS YP_917244.1 119386189 4582033 624840..625202 1 NC_008687.1 PFAM: regulatory protein, MerR; KEGG: ccr:CC3082 transcriptional regulator, MerR family; MerR family transcriptional regulator 625202 4582033 Pden_3477 Paracoccus denitrificans PD1222 MerR family transcriptional regulator YP_917244.1 624840 D 318586 CDS YP_917245.1 119386190 4582034 complement(625891..626646) 1 NC_008687.1 PFAM: regulatory proteins, IclR; KEGG: rpc:RPC_0118 transcriptional regulator, IclR family; regulatory proteins, IclR 626646 4582034 Pden_3479 Paracoccus denitrificans PD1222 regulatory proteins, IclR YP_917245.1 625891 R 318586 CDS YP_917246.1 119386191 4582035 626754..627746 1 NC_008687.1 TIGRFAM: TRAP dicarboxylate transporter, DctP subunit; PFAM: TRAP dicarboxylate transporter- DctP subunit; KEGG: gka:GK1971 C4-dicarboxylate transport system (C4-dicarboxylate-binding protein); TRAP dicarboxylate transporter, DctP subunit 627746 4582035 Pden_3480 Paracoccus denitrificans PD1222 TRAP dicarboxylate transporter, DctP subunit YP_917246.1 626754 D 318586 CDS YP_917247.1 119386192 4582036 627805..628311 1 NC_008687.1 PFAM: Tripartite ATP-independent periplasmic transporter, DctQ component; KEGG: dvu:DVU0010 TRAP transporter, DctQ subunit; tripartite ATP-independent periplasmic transporter DctQ 628311 4582036 Pden_3481 Paracoccus denitrificans PD1222 tripartite ATP-independent periplasmic transporter DctQ YP_917247.1 627805 D 318586 CDS YP_917248.1 119386193 4582037 628308..629591 1 NC_008687.1 TIGRFAM: TRAP dicarboxylate transporter, DctM subunit; PFAM: TRAP C4-dicarboxylate transport system permease DctM subunit; KEGG: csa:Csal_2978 TRAP dicarboxylate transporter-DctM subunit; TRAP dicarboxylate transporter, DctM subunit 629591 4582037 Pden_3482 Paracoccus denitrificans PD1222 TRAP dicarboxylate transporter, DctM subunit YP_917248.1 628308 D 318586 CDS YP_917249.1 119386194 4582038 629588..630667 1 NC_008687.1 PFAM: dihydroorotate dehydrogenase; KEGG: tac:Ta0404 dihydroorotate oxidase; dihydroorotate dehydrogenase 630667 4582038 Pden_3483 Paracoccus denitrificans PD1222 dihydroorotate dehydrogenase YP_917249.1 629588 D 318586 CDS YP_917250.1 119386195 4582039 630664..631563 1 NC_008687.1 KEGG: pol:Bpro_3857 hypothetical protein; hypothetical protein 631563 4582039 Pden_3484 Paracoccus denitrificans PD1222 hypothetical protein YP_917250.1 630664 D 318586 CDS YP_917251.1 119386196 4582040 631560..632309 1 NC_008687.1 PFAM: HpcH/HpaI aldolase; KEGG: bxe:Bxe_C0507 HpcH/HpaI aldolase; HpcH/HpaI aldolase 632309 4582040 Pden_3485 Paracoccus denitrificans PD1222 HpcH/HpaI aldolase YP_917251.1 631560 D 318586 CDS YP_917252.1 119386197 4582041 632340..633242 1 NC_008687.1 KEGG: rpc:RPC_0116 hypothetical protein; hypothetical protein 633242 4582041 Pden_3486 Paracoccus denitrificans PD1222 hypothetical protein YP_917252.1 632340 D 318586 CDS YP_917253.1 119386198 4582042 complement(633436..634008) 1 NC_008687.1 PFAM: regulatory protein, MarR; KEGG: bja:bll4221 transcriptional regulatory protein; MarR family transcriptional regulator 634008 4582042 Pden_3487 Paracoccus denitrificans PD1222 MarR family transcriptional regulator YP_917253.1 633436 R 318586 CDS YP_917254.1 119386199 4582043 634065..635972 1 NC_008687.1 catalyzes the formation of catechol from phenol; phenol 2-monooxygenase 635972 4582043 Pden_3488 Paracoccus denitrificans PD1222 phenol 2-monooxygenase YP_917254.1 634065 D 318586 CDS YP_917255.1 119386200 4582044 complement(635969..636961) 1 NC_008687.1 TIGRFAM: pca operon transcription factor PcaQ; PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: sil:SPOA0047 pca operon transcriptional activator PcaQ; LysR family transcriptional regulator 636961 4582044 Pden_3489 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_917255.1 635969 R 318586 CDS YP_917256.1 119386201 4582045 637053..638222 1 NC_008687.1 catalyzes the formation of protocatechuate from 4-hydroxybenzoate; 4-hydroxybenzoate 3-monooxygenase 638222 4582045 Pden_3490 Paracoccus denitrificans PD1222 4-hydroxybenzoate 3-monooxygenase YP_917256.1 637053 D 318586 CDS YP_917257.1 119386202 4582046 638222..639010 1 NC_008687.1 TIGRFAM: 3-oxoadipate enol-lactonase; PFAM: alpha/beta hydrolase fold; KEGG: jan:Jann_1663 3-oxoadipate enol-lactonase; 3-oxoadipate enol-lactonase 639010 4582046 Pden_3491 Paracoccus denitrificans PD1222 3-oxoadipate enol-lactonase YP_917257.1 638222 D 318586 CDS YP_917258.1 119386203 4582047 639003..639434 1 NC_008687.1 TIGRFAM: 4-carboxymuconolactone decarboxylase; PFAM: Carboxymuconolactone decarboxylase; KEGG: sit:TM1040_0559 4-carboxymuconolactone decarboxylase; 4-carboxymuconolactone decarboxylase 639434 4582047 Pden_3492 Paracoccus denitrificans PD1222 4-carboxymuconolactone decarboxylase YP_917258.1 639003 D 318586 CDS YP_917259.1 119386204 4582048 639431..640153 1 NC_008687.1 TIGRFAM: protocatechuate 3,4-dioxygenase, beta subunit; PFAM: intradiol ring-cleavage dioxygenase; KEGG: sil:SPOA0044 protocatechuate 3,4-dioxygenase beta subunit; protocatechuate 3,4-dioxygenase subunit beta 640153 4582048 Pden_3493 Paracoccus denitrificans PD1222 protocatechuate 3,4-dioxygenase subunit beta YP_917259.1 639431 D 318586 CDS YP_917260.1 119386205 4582049 640153..640863 1 NC_008687.1 KEGG: sil:SPOA0043 protocatechuate 3,4-dioxygenase alpha subunit; TIGRFAM: protocatechuate 3,4-dioxygenase, alpha subunit; PFAM: intradiol ring-cleavage dioxygenase; protocatechuate 3,4-dioxygenase subunit alpha 640863 4582049 Pden_3494 Paracoccus denitrificans PD1222 protocatechuate 3,4-dioxygenase subunit alpha YP_917260.1 640153 D 318586 CDS YP_917261.1 119386206 4582050 640856..641701 1 NC_008687.1 PFAM: protein of unknown function DUF849; KEGG: sil:SPOA0042 hypothetical protein; hypothetical protein 641701 4582050 Pden_3495 Paracoccus denitrificans PD1222 hypothetical protein YP_917261.1 640856 D 318586 CDS YP_917262.1 119386207 4582051 641701..643002 1 NC_008687.1 PFAM: fumarate lyase; KEGG: sil:SPOA0432 3-carboxy-cis,cis-muconate cycloisomerase; fumarate lyase 643002 4582051 Pden_3496 Paracoccus denitrificans PD1222 fumarate lyase YP_917262.1 641701 D 318586 CDS YP_917263.1 119386208 4582052 643024..644049 1 NC_008687.1 PFAM: TRAP dicarboxylate transporter- DctP subunit; KEGG: eba:ebA5362 predicted TRAP dicarboxylate transporter, DctP subunit; TRAP dicarboxylate transporter- DctP subunit 644049 4582052 Pden_3497 Paracoccus denitrificans PD1222 TRAP dicarboxylate transporter- DctP subunit YP_917263.1 643024 D 318586 CDS YP_917264.1 119386209 4582053 644067..644588 1 NC_008687.1 KEGG: eba:ebB188 hypothetical protein; hypothetical protein 644588 4582053 Pden_3498 Paracoccus denitrificans PD1222 hypothetical protein YP_917264.1 644067 D 318586 CDS YP_917265.1 119386210 4582054 644585..645904 1 NC_008687.1 TIGRFAM: TRAP dicarboxylate transporter, DctM subunit; PFAM: TRAP C4-dicarboxylate transport system permease DctM subunit; KEGG: eba:ebA5367 conserved hypothetical protein, predicted TRAP C4-dicarboxylate transport system permease DctM subunit,DedA falily; TRAP dicarboxylate transporter, DctM subunit 645904 4582054 Pden_3499 Paracoccus denitrificans PD1222 TRAP dicarboxylate transporter, DctM subunit YP_917265.1 644585 D 318586 CDS YP_917266.1 119386211 4582055 complement(645946..646842) 1 NC_008687.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: atc:AGR_L_1754 hypothetical protein; LysR family transcriptional regulator 646842 4582055 Pden_3500 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_917266.1 645946 R 318586 CDS YP_917267.1 119386212 4582056 646964..647896 1 NC_008687.1 PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase; KEGG: atc:AGR_L_1752 hypothetical protein; glyoxalase/bleomycin resistance protein/dioxygenase 647896 4582056 Pden_3501 Paracoccus denitrificans PD1222 glyoxalase/bleomycin resistance protein/dioxygenase YP_917267.1 646964 D 318586 CDS YP_917268.1 119386213 4582057 647954..648583 1 NC_008687.1 KEGG: rde:RD1_A0097 RC150; hypothetical protein 648583 4582057 Pden_3502 Paracoccus denitrificans PD1222 hypothetical protein YP_917268.1 647954 D 318586 CDS YP_917269.1 119386214 4582058 648580..648828 1 NC_008687.1 PFAM: protein of unknown function DUF1427; KEGG: rde:RD1_A0096 hypothetical protein; hypothetical protein 648828 4582058 Pden_3503 Paracoccus denitrificans PD1222 hypothetical protein YP_917269.1 648580 D 318586 CDS YP_917270.1 119386215 4582059 648874..649563 1 NC_008687.1 PFAM: isochorismatase hydrolase; KEGG: rde:RD1_A0094 hydrolase; isochorismatase hydrolase 649563 4582059 Pden_3504 Paracoccus denitrificans PD1222 isochorismatase hydrolase YP_917270.1 648874 D 318586 CDS YP_917271.1 119386216 4582060 649884..650186 1 NC_008687.1 KEGG: rde:RD1_A0090 hypothetical protein; hypothetical protein 650186 4582060 Pden_3505 Paracoccus denitrificans PD1222 hypothetical protein YP_917271.1 649884 D 318586 CDS YP_917272.1 119386217 4582061 650236..650454 1 NC_008687.1 KEGG: reu:Reut_B4847 DoxX; DoxX 650454 4582061 Pden_3506 Paracoccus denitrificans PD1222 DoxX YP_917272.1 650236 D 318586 CDS YP_917273.1 119386218 4582062 650698..652557 1 NC_008687.1 PFAM: Amidohydrolase 3; KEGG: reu:Reut_B4849 conserved hypothetical protein PA2699; amidohydrolase 652557 4582062 Pden_3507 Paracoccus denitrificans PD1222 amidohydrolase YP_917273.1 650698 D 318586 CDS YP_917274.1 119386219 4582063 652649..654229 1 NC_008687.1 PFAM: protein of unknown function DUF894, DitE; major facilitator superfamily MFS_1; KEGG: tbd:Tbd_1578 probable MFS transporter; hypothetical protein 654229 4582063 Pden_3508 Paracoccus denitrificans PD1222 hypothetical protein YP_917274.1 652649 D 318586 CDS YP_917275.1 119386220 4582064 654270..654662 1 NC_008687.1 PFAM: DoxX family protein; KEGG: mes:Meso_0934 DoxX; DoxX family protein 654662 4582064 Pden_3509 Paracoccus denitrificans PD1222 DoxX family protein YP_917275.1 654270 D 318586 CDS YP_917276.1 119386221 4582065 654707..655651 1 NC_008687.1 PFAM: Pirin domain protein domain protein; Pirin domain protein; KEGG: sit:TM1040_1889 pirin-like; pirin 655651 4582065 Pden_3510 Paracoccus denitrificans PD1222 pirin YP_917276.1 654707 D 318586 CDS YP_917277.1 119386222 4582066 complement(655815..656942) 1 NC_008687.1 KEGG: bbr:BB2355 hypothetical protein; hypothetical protein 656942 4582066 Pden_3511 Paracoccus denitrificans PD1222 hypothetical protein YP_917277.1 655815 R 318586 CDS YP_917278.1 119386223 4582067 complement(656939..657409) 1 NC_008687.1 PFAM: regulatory protein, MarR; KEGG: gme:Gmet_0359 transcriptional regulator, MarR family; MarR family transcriptional regulator 657409 4582067 Pden_3512 Paracoccus denitrificans PD1222 MarR family transcriptional regulator YP_917278.1 656939 R 318586 CDS YP_917279.1 119386224 4582068 657528..658811 1 NC_008687.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: mes:Meso_2630 transcriptional regulator, LysR family; LysR family transcriptional regulator 658811 4582068 Pden_3513 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_917279.1 657528 D 318586 CDS YP_917280.1 119386225 4582069 658965..660347 1 NC_008687.1 PFAM: amidohydrolase; KEGG: mes:Meso_2641 amidohydrolase; allantoinase 660347 4582069 Pden_3514 Paracoccus denitrificans PD1222 allantoinase YP_917280.1 658965 D 318586 CDS YP_917281.1 119386226 4582070 660347..661585 1 NC_008687.1 allantoate amidohydrolase and N-carbamoyl-L-amino acid amidohydrolase are very similar; the allantoate amidohydrolase from Escherichia coli forms a dimer and binds zinc ions for catalytic activity and catalyzes the conversion of allantoate to (S)-ureidoglycolate and ammonia; carbamoyl amidohydrolase from Bacillus sp. converts N-carbamoyl amino acids to amino acids, ammonia, and carbon dioxide; allantoate amidohydrolase 661585 4582070 Pden_3515 Paracoccus denitrificans PD1222 allantoate amidohydrolase YP_917281.1 660347 D 318586 CDS YP_917282.1 119386227 4582071 661587..662678 1 NC_008687.1 PFAM: protein of unknown function DUF917; KEGG: mes:Meso_2639 protein of unknown function DUF917; hypothetical protein 662678 4582071 Pden_3516 Paracoccus denitrificans PD1222 hypothetical protein YP_917282.1 661587 D 318586 CDS YP_917283.1 119386228 4582072 662681..664339 1 NC_008687.1 catalyzes the formation of 4-imidazolone-5-propanoate from urocanate during histidine metabolism; urocanate hydratase 664339 4582072 Pden_3517 Paracoccus denitrificans PD1222 urocanate hydratase YP_917283.1 662681 D 318586 CDS YP_917284.1 119386229 4582073 664452..665795 1 NC_008687.1 PFAM: General substrate transporter; major facilitator superfamily MFS_1; KEGG: bur:Bcep18194_B3017 major facilitator superfamily (MFS_1) transporter; major facilitator transporter 665795 4582073 Pden_3518 Paracoccus denitrificans PD1222 major facilitator transporter YP_917284.1 664452 D 318586 CDS YP_917285.1 119386230 4582074 665822..667486 1 NC_008687.1 PFAM: phenylalanine/histidine ammonia-lyase; KEGG: son:SO3057 Pal/histidase family protein; phenylalanine/histidine ammonia-lyase 667486 4582074 Pden_3519 Paracoccus denitrificans PD1222 phenylalanine/histidine ammonia-lyase YP_917285.1 665822 D 318586 CDS YP_917286.1 119386231 4582075 667754..668722 1 NC_008687.1 PFAM: helix-turn-helix- domain containing protein, AraC type; KEGG: sme:SMa1749 transcriptional regulator; helix-turn-helix domain-containing protein 668722 4582075 Pden_3520 Paracoccus denitrificans PD1222 helix-turn-helix domain-containing protein YP_917286.1 667754 D 318586 CDS YP_917287.1 119386232 4582076 complement(668767..670866) 1 NC_008687.1 TIGRFAM: TonB-dependent siderophore receptor; PFAM: TonB-dependent receptor; TonB-dependent receptor, plug; KEGG: sme:SMa1747 ferrichrome-iron receptor; TonB-dependent siderophore receptor 670866 4582076 Pden_3521 Paracoccus denitrificans PD1222 TonB-dependent siderophore receptor YP_917287.1 668767 R 318586 CDS YP_917288.1 119386233 4582077 671140..672141 1 NC_008687.1 PFAM: periplasmic binding protein; KEGG: rsp:RSP_3416 ABC Fe+3-siderophore transporter, periplasmic binding protein; periplasmic binding protein 672141 4582077 Pden_3522 Paracoccus denitrificans PD1222 periplasmic binding protein YP_917288.1 671140 D 318586 CDS YP_917289.1 119386234 4582078 672138..673163 1 NC_008687.1 PFAM: transport system permease; KEGG: sme:SMa1745 iron uptake protein; transport system permease 673163 4582078 Pden_3523 Paracoccus denitrificans PD1222 transport system permease YP_917289.1 672138 D 318586 CDS YP_917290.1 119386235 4582079 673166..674206 1 NC_008687.1 PFAM: transport system permease; KEGG: sme:SMa1742 iron uptake protein; transport system permease 674206 4582079 Pden_3524 Paracoccus denitrificans PD1222 transport system permease YP_917290.1 673166 D 318586 CDS YP_917291.1 119386236 4582080 674203..675066 1 NC_008687.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rsp:RSP_3413 ABC Fe+3-siderophore transporter, ATPase subunit; ABC transporter 675066 4582080 Pden_3525 Paracoccus denitrificans PD1222 ABC transporter YP_917291.1 674203 D 318586 CDS YP_917292.1 119386237 4582081 complement(675279..676580) 1 NC_008687.1 KEGG: pae:PA4155 hypothetical protein; hypothetical protein 676580 4582081 Pden_3526 Paracoccus denitrificans PD1222 hypothetical protein YP_917292.1 675279 R 318586 CDS YP_917293.1 119386238 4582082 complement(676659..678743) 1 NC_008687.1 PFAM: TonB-dependent receptor; TonB-dependent receptor, plug; KEGG: rpb:RPB_2695 TonB-dependent receptor; TonB-dependent receptor 678743 4582082 Pden_3527 Paracoccus denitrificans PD1222 TonB-dependent receptor YP_917293.1 676659 R 318586 CDS YP_917294.1 119386239 4582083 678951..679748 1 NC_008687.1 PFAM: regulatory proteins, IclR; KEGG: pfl:PFL_3621 transcriptional regulator, IclR family; regulatory proteins, IclR 679748 4582083 Pden_3528 Paracoccus denitrificans PD1222 regulatory proteins, IclR YP_917294.1 678951 D 318586 CDS YP_917295.1 119386240 4582084 complement(679749..680531) 1 NC_008687.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: pau:PA14_10180 ferric enterobactin transport protein FepC; ABC transporter 680531 4582084 Pden_3529 Paracoccus denitrificans PD1222 ABC transporter YP_917295.1 679749 R 318586 CDS YP_917296.1 119386241 4582085 680760..681563 1 NC_008687.1 PFAM: Siderophore-interacting protein; FAD-binding 9, siderophore-interacting domain protein; KEGG: cgb:cg0054 iron-chelator utilization protein; siderophore-interacting protein 681563 4582085 Pden_3530 Paracoccus denitrificans PD1222 siderophore-interacting protein YP_917296.1 680760 D 318586 CDS YP_917297.1 119386242 4582086 681573..682511 1 NC_008687.1 with FepCDG is involved in the transport of ferric enterobactin; iron-enterobactin transporter periplasmic binding protein 682511 4582086 Pden_3531 Paracoccus denitrificans PD1222 iron-enterobactin transporter periplasmic binding protein YP_917297.1 681573 D 318586 CDS YP_917298.1 119386243 4582087 682508..683215 1 NC_008687.1 PFAM: transport system permease; KEGG: pfl:PFL_3624 ferric vibriobactin ABC transporter, permease VC0777; transport system permease 683215 4582087 Pden_3532 Paracoccus denitrificans PD1222 transport system permease YP_917298.1 682508 D 318586 CDS YP_917299.1 119386244 4582088 683199..683549 1 NC_008687.1 PFAM: transport system permease; KEGG: pfl:PFL_3624 ferric vibriobactin ABC transporter, permease VC0777; transport system permease 683549 4582088 Pden_3533 Paracoccus denitrificans PD1222 transport system permease YP_917299.1 683199 D 318586 CDS YP_917300.1 119386245 4582089 683546..684598 1 NC_008687.1 PFAM: transport system permease; KEGG: pfl:PFL_3625 ferric vibriobactin ABC transporter, permease VC0778; transport system permease 684598 4582089 Pden_3534 Paracoccus denitrificans PD1222 transport system permease YP_917300.1 683546 D 318586 CDS YP_917301.1 119386246 4582090 complement(684676..685290) 1 NC_008687.1 PFAM: Glutathione S-transferase, N-terminal domain; KEGG: sil:SPO0270 glutathione S-transferase family protein; glutathione S-transferase domain-containing protein 685290 4582090 Pden_3535 Paracoccus denitrificans PD1222 glutathione S-transferase domain-containing protein YP_917301.1 684676 R 318586 CDS YP_917302.1 119386247 4582091 complement(685290..686033) 1 NC_008687.1 PFAM: regulatory protein GntR, HTH; GntR domain protein; KEGG: pau:PA14_64820 transcriptional regulator; GntR family transcriptional regulator 686033 4582091 Pden_3536 Paracoccus denitrificans PD1222 GntR family transcriptional regulator YP_917302.1 685290 R 318586 CDS YP_917303.1 119386248 4582092 686155..686913 1 NC_008687.1 PFAM: NAD-dependent epimerase/dehydratase; short-chain dehydrogenase/reductase SDR; KR; KEGG: mes:Meso_3712 short-chain dehydrogenase/reductase SDR; short-chain dehydrogenase/reductase SDR 686913 4582092 Pden_3537 Paracoccus denitrificans PD1222 short-chain dehydrogenase/reductase SDR YP_917303.1 686155 D 318586 CDS YP_917304.1 119386249 4582093 686930..687436 1 NC_008687.1 KEGG: rsp:RSP_0635 TRAP-T family transporter, DctQ (4 TMs) subunit; TRAP dicarboxylate family transporter subunit DctQ 687436 4582093 Pden_3538 Paracoccus denitrificans PD1222 TRAP dicarboxylate family transporter subunit DctQ YP_917304.1 686930 D 318586 CDS YP_917305.1 119386250 4582094 687446..688756 1 NC_008687.1 TIGRFAM: TRAP dicarboxylate transporter, DctM subunit; PFAM: TRAP C4-dicarboxylate transport system permease DctM subunit; KEGG: rsp:RSP_0634 TRAP-T family transporter, DctM (12 TMs) subunit; TRAP dicarboxylate transporter subunit DctM 688756 4582094 Pden_3539 Paracoccus denitrificans PD1222 TRAP dicarboxylate transporter subunit DctM YP_917305.1 687446 D 318586 CDS YP_917306.1 119386251 4582095 688822..689940 1 NC_008687.1 PFAM: TRAP dicarboxylate transporter- DctP subunit; KEGG: rsp:RSP_0636 TRAP-T family transporter, DctP (periplasmic binding) subunit; TRAP dicarboxylate transporter- DctP subunit 689940 4582095 Pden_3540 Paracoccus denitrificans PD1222 TRAP dicarboxylate transporter- DctP subunit YP_917306.1 688822 D 318586 CDS YP_917307.1 119386252 4582096 690013..690750 1 NC_008687.1 PFAM: short-chain dehydrogenase/reductase SDR; KR; KEGG: bxe:Bxe_A1074 3-oxoacyl-(acyl-carrier-protein) reductase; short-chain dehydrogenase/reductase SDR 690750 4582096 Pden_3541 Paracoccus denitrificans PD1222 short-chain dehydrogenase/reductase SDR YP_917307.1 690013 D 318586 CDS YP_917308.1 119386253 4582097 690766..691551 1 NC_008687.1 PFAM: short-chain dehydrogenase/reductase SDR; Male sterility C-terminal domain; KEGG: bur:Bcep18194_C7123 short-chain dehydrogenase/reductase SDR; short-chain dehydrogenase/reductase SDR 691551 4582097 Pden_3542 Paracoccus denitrificans PD1222 short-chain dehydrogenase/reductase SDR YP_917308.1 690766 D 318586 CDS YP_917309.1 119386254 4582098 691538..693247 1 NC_008687.1 PFAM: fumarate reductase/succinate dehydrogenase flavoprotein domain protein; FAD dependent oxidoreductase; KEGG: bja:blr6805 dehydrogenase; fumarate reductase/succinate dehydrogenase flavoprotein domain-containing protein 693247 4582098 Pden_3543 Paracoccus denitrificans PD1222 fumarate reductase/succinate dehydrogenase flavoprotein domain-containing protein YP_917309.1 691538 D 318586 CDS YP_917310.1 119386255 4582099 693244..693693 1 NC_008687.1 hypothetical protein 693693 4582099 Pden_3544 Paracoccus denitrificans PD1222 hypothetical protein YP_917310.1 693244 D 318586 CDS YP_917311.1 119386256 4582100 693902..694393 1 NC_008687.1 PFAM: regulatory protein, MarR; KEGG: mlo:mll8302 transcriptional regulator; MarR family transcriptional regulator 694393 4582100 Pden_3545 Paracoccus denitrificans PD1222 MarR family transcriptional regulator YP_917311.1 693902 D 318586 CDS YP_917312.1 119386257 4582101 complement(694390..694821) 1 NC_008687.1 PFAM: regulatory protein, MarR; KEGG: rde:RD1_3650 transcriptional regulator MarR/EmrR family; MarR family transcriptional regulator 694821 4582101 Pden_3546 Paracoccus denitrificans PD1222 MarR family transcriptional regulator YP_917312.1 694390 R 318586 CDS YP_917313.1 119386258 4582102 694964..696325 1 NC_008687.1 An oxygenase that acts to open the ring of homogentisate formingmaleylacetoacetate as part of the catabolism of L-tyrosine and L-phenylalanine; homogentisate 1,2-dioxygenase 696325 4582102 Pden_3547 Paracoccus denitrificans PD1222 homogentisate 1,2-dioxygenase YP_917313.1 694964 D 318586 CDS YP_917314.1 119386259 4582103 696400..697605 1 NC_008687.1 KEGG: sit:TM1040_2622 fumarylacetoacetase; TIGRFAM: fumarylacetoacetase; PFAM: fumarylacetoacetate (FAA) hydrolase; fumarylacetoacetase 697605 4582103 Pden_3548 Paracoccus denitrificans PD1222 fumarylacetoacetase YP_917314.1 696400 D 318586 CDS YP_917315.1 119386260 4582104 697602..698237 1 NC_008687.1 TIGRFAM: maleylacetoacetate isomerase; PFAM: Glutathione S-transferase, N-terminal domain; KEGG: sme:SMc03206 maleylacetoacetate isomerase (glutathione transferase ZETA 1) protein; maleylacetoacetate isomerase 698237 4582104 Pden_3549 Paracoccus denitrificans PD1222 maleylacetoacetate isomerase YP_917315.1 697602 D 318586 CDS YP_917316.1 119386261 4582105 698668..699378 1 NC_008687.1 PFAM: acylneuraminate cytidylyltransferase; KEGG: aeh:Mlg_2324 acylneuraminate cytidylyltransferase; acylneuraminate cytidylyltransferase 699378 4582105 Pden_3550 Paracoccus denitrificans PD1222 acylneuraminate cytidylyltransferase YP_917316.1 698668 D 318586 CDS YP_917317.1 119386262 4582106 699375..700421 1 NC_008687.1 KEGG: ccr:CC2854 flagellin modification protein FlmD; flagellin modification protein FlmD 700421 4582106 Pden_3551 Paracoccus denitrificans PD1222 flagellin modification protein FlmD YP_917317.1 699375 D 318586 CDS YP_917318.1 119386263 4582107 700418..701539 1 NC_008687.1 PFAM: phosphoribosylglycinamide synthetase; ATP-dependent carboxylate-amine ligase domain protein, ATP-grasp; protein of unknown function DUF201; KEGG: bce:BC5272 carbamoyl-phosphate synthase small chain; ATP-dependent carboxylate-amine ligase domain-containing protein 701539 4582107 Pden_3552 Paracoccus denitrificans PD1222 ATP-dependent carboxylate-amine ligase domain-containing protein YP_917318.1 700418 D 318586 CDS YP_917319.1 119386264 4582108 701536..702444 1 NC_008687.1 PFAM: NAD-dependent epimerase/dehydratase; 3-beta hydroxysteroid dehydrogenase/isomerase; dTDP-4-dehydrorhamnose reductase; Male sterility C-terminal domain; KEGG: sth:STH781 UDP-glucose 4-epimerase; NAD-dependent epimerase/dehydratase 702444 4582108 Pden_3553 Paracoccus denitrificans PD1222 NAD-dependent epimerase/dehydratase YP_917319.1 701536 D 318586 CDS YP_917320.1 119386265 4582109 complement(702466..704322) 1 NC_008687.1 hypothetical protein 704322 4582109 Pden_3554 Paracoccus denitrificans PD1222 hypothetical protein YP_917320.1 702466 R 318586 CDS YP_917321.1 119386266 4582110 complement(704351..707368) 1 NC_008687.1 hypothetical protein 707368 4582110 Pden_3555 Paracoccus denitrificans PD1222 hypothetical protein YP_917321.1 704351 R 318586 CDS YP_917322.1 119386267 4582111 complement(707372..708448) 1 NC_008687.1 PFAM: N-acetylneuraminic acid synthase, N-terminal domain; SAF domain; KEGG: mhu:Mhun_3098 N-acylneuraminate-9-phosphate synthase; N-acylneuraminate-9-phosphate synthase 708448 4582111 Pden_3556 Paracoccus denitrificans PD1222 N-acylneuraminate-9-phosphate synthase YP_917322.1 707372 R 318586 CDS YP_917323.1 119386268 4582112 complement(708579..709733) 1 NC_008687.1 PFAM: DegT/DnrJ/EryC1/StrS aminotransferase; KEGG: aeh:Mlg_2323 DegT/DnrJ/EryC1/StrS aminotransferase; DegT/DnrJ/EryC1/StrS aminotransferase 709733 4582112 Pden_3557 Paracoccus denitrificans PD1222 DegT/DnrJ/EryC1/StrS aminotransferase YP_917323.1 708579 R 318586 CDS YP_917324.1 119386269 4582113 complement(709730..710731) 1 NC_008687.1 PFAM: NAD-dependent epimerase/dehydratase; short-chain dehydrogenase/reductase SDR; 3-beta hydroxysteroid dehydrogenase/isomerase; polysaccharide biosynthesis protein CapD; dTDP-4-dehydrorhamnose reductase; Male sterility C-terminal domain; KEGG: son:SO3271 polysaccharide biosynthesis protein; polysaccharide biosynthesis protein CapD 710731 4582113 Pden_3558 Paracoccus denitrificans PD1222 polysaccharide biosynthesis protein CapD YP_917324.1 709730 R 318586 CDS YP_917325.1 119386270 4582114 711428..711823 1 NC_008687.1 KEGG: rso:RS01910 probable transport transmembrane protein; transport transmembrane protein 711823 4582114 Pden_3560 Paracoccus denitrificans PD1222 transport transmembrane protein YP_917325.1 711428 D 318586 CDS YP_917326.1 119386271 4582115 complement(712270..713298) 1 NC_008687.1 PFAM: transposase, IS111A/IS1328/IS1533; transposase IS116/IS110/IS902 family protein; KEGG: nha:Nham_3955 transposase IS116/IS110/IS902; transposase IS116/IS110/IS902 family protein 713298 4582115 Pden_3561 Paracoccus denitrificans PD1222 transposase IS116/IS110/IS902 family protein YP_917326.1 712270 R 318586 CDS YP_917327.1 119386272 4582116 713407..713730 1 NC_008687.1 PFAM: transposase IS3/IS911 family protein; KEGG: nwi:Nwi_2119 transposase IS3/IS911; transposase IS3/IS911 family protein 713730 4582116 Pden_3562 Paracoccus denitrificans PD1222 transposase IS3/IS911 family protein YP_917327.1 713407 D 318586 CDS YP_917328.1 119386273 4582117 714938..715459 1 NC_008687.1 hypothetical protein 715459 4582117 Pden_3564 Paracoccus denitrificans PD1222 hypothetical protein YP_917328.1 714938 D 318586 CDS YP_917329.1 119386274 4582118 715570..715953 1 NC_008687.1 KEGG: rsp:RSP_0396 hypothetical protein; hypothetical protein 715953 4582118 Pden_3565 Paracoccus denitrificans PD1222 hypothetical protein YP_917329.1 715570 D 318586 CDS YP_917330.1 119386275 4582119 716125..716892 1 NC_008687.1 PFAM: response regulator receiver; transcriptional regulator domain protein; KEGG: bja:blr6651 two-component response regulator; two component transcriptional regulator 716892 4582119 Pden_3566 Paracoccus denitrificans PD1222 two component transcriptional regulator YP_917330.1 716125 D 318586 CDS YP_917331.1 119386276 4582120 complement(716868..717983) 1 NC_008687.1 PFAM: response regulator receiver; ATP-binding region, ATPase domain protein domain protein; histidine kinase A domain protein domain protein; KEGG: mxa:MXAN_4244 sensor histidine kinase / response regulator; response regulator receiver sensor signal transduction histidine kinase 717983 4582120 Pden_3567 Paracoccus denitrificans PD1222 response regulator receiver sensor signal transduction histidine kinase YP_917331.1 716868 R 318586 CDS YP_917332.1 119386277 4582121 complement(717980..720604) 1 NC_008687.1 PFAM: ATP-binding region, ATPase domain protein domain protein; histidine kinase A domain protein domain protein; KEGG: pst:PSPTO_4079 sensor histidine kinase/response regulator; integral membrane sensor signal transduction histidine kinase 720604 4582121 Pden_3568 Paracoccus denitrificans PD1222 integral membrane sensor signal transduction histidine kinase YP_917332.1 717980 R 318586 CDS YP_917333.1 119386278 4582122 720832..722058 1 NC_008687.1 PFAM: Acetamidase/Formamidase; KEGG: bbr:BB1405 formamidase; formamidase 722058 4582122 Pden_3569 Paracoccus denitrificans PD1222 formamidase YP_917333.1 720832 D 318586 CDS YP_917334.1 119386279 4582123 722119..722631 1 NC_008687.1 PFAM: AmiS/UreI transporter; KEGG: bpa:BPP1188 transporter protein; AmiS/UreI transporter 722631 4582123 Pden_3570 Paracoccus denitrificans PD1222 AmiS/UreI transporter YP_917334.1 722119 D 318586 CDS YP_917335.1 119386280 4582124 722641..722937 1 NC_008687.1 KEGG: abo:ABO_1977 hypothetical protein; hypothetical protein 722937 4582124 Pden_3571 Paracoccus denitrificans PD1222 hypothetical protein YP_917335.1 722641 D 318586 CDS YP_917336.1 119386281 4582125 complement(723093..723860) 1 NC_008687.1 PFAM: short-chain dehydrogenase/reductase SDR; KR; KEGG: bcn:Bcen_4032 short-chain dehydrogenase/reductase SDR; short-chain dehydrogenase/reductase SDR 723860 4582125 Pden_3572 Paracoccus denitrificans PD1222 short-chain dehydrogenase/reductase SDR YP_917336.1 723093 R 318586 CDS YP_917337.1 119386282 4582126 complement(723857..724570) 1 NC_008687.1 PFAM: regulatory protein GntR, HTH; GntR domain protein; KEGG: reu:Reut_C6220 regulatory protein GntR, HTH:GntR, C-terminal; GntR family transcriptional regulator 724570 4582126 Pden_3573 Paracoccus denitrificans PD1222 GntR family transcriptional regulator YP_917337.1 723857 R 318586 CDS YP_917338.1 119386283 4582127 724667..725908 1 NC_008687.1 KEGG: rso:RS05343 hypothetical protein; hypothetical protein 725908 4582127 Pden_3574 Paracoccus denitrificans PD1222 hypothetical protein YP_917338.1 724667 D 318586 CDS YP_917339.1 119386284 4582128 725984..726859 1 NC_008687.1 PFAM: inner-membrane translocator; KEGG: bja:bll3662 ABC transporter permease; inner-membrane translocator 726859 4582128 Pden_3575 Paracoccus denitrificans PD1222 inner-membrane translocator YP_917339.1 725984 D 318586 CDS YP_917340.1 119386285 4582129 726867..729383 1 NC_008687.1 PFAM: inner-membrane translocator; ABC transporter related; SMART: AAA ATPase; KEGG: bja:bll3661 ABC transporter ATP-binding/permease; ABC transporter related 729383 4582129 Pden_3576 Paracoccus denitrificans PD1222 ABC transporter related YP_917340.1 726867 D 318586 CDS YP_917341.1 119386286 4582130 729392..730327 1 NC_008687.1 PFAM: 3-hydroxyacyl-CoA dehydrogenase domain protein; 3-hydroxyacyl-CoA dehydrogenase, NAD-binding; NAD-dependent glycerol-3-phosphate dehydrogenase domain protein; KEGG: rsp:RSP_3970 3-hydroxybutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase 730327 4582130 Pden_3577 Paracoccus denitrificans PD1222 3-hydroxyacyl-CoA dehydrogenase YP_917341.1 729392 D 318586 CDS YP_917342.1 119386287 4582131 730346..731278 1 NC_008687.1 PFAM: protein of unknown function DUF849; KEGG: rde:RD1_4158 hypothetical protein; hypothetical protein 731278 4582131 Pden_3578 Paracoccus denitrificans PD1222 hypothetical protein YP_917342.1 730346 D 318586 CDS YP_917343.1 119386288 4582132 731289..732599 1 NC_008687.1 catalyzes the oxidation of L-histidinol to L-histidinaldehyde and then to L-histidine in histidine biosynthesis; functions as a dimer; histidinol dehydrogenase 732599 4582132 Pden_3579 Paracoccus denitrificans PD1222 histidinol dehydrogenase YP_917343.1 731289 D 318586 CDS YP_917344.1 119386289 4582133 732596..733354 1 NC_008687.1 PFAM: short-chain dehydrogenase/reductase SDR; KR; KEGG: bxe:Bxe_C0308 short-chain dehydrogenase/reductase; short-chain dehydrogenase/reductase SDR 733354 4582133 Pden_3580 Paracoccus denitrificans PD1222 short-chain dehydrogenase/reductase SDR YP_917344.1 732596 D 318586 CDS YP_917345.1 119386290 4582134 complement(733447..733827) 1 NC_008687.1 hypothetical protein 733827 4582134 Pden_3581 Paracoccus denitrificans PD1222 hypothetical protein YP_917345.1 733447 R 318586 CDS YP_917346.1 119386291 4582135 complement(733985..734776) 1 NC_008687.1 PFAM: regulatory protein, LuxR; Sigma-70, region 4 type 2; KEGG: sme:SMc01630 transcription regulator protein; response regulator receiver protein 734776 4582135 Pden_3582 Paracoccus denitrificans PD1222 response regulator receiver protein YP_917346.1 733985 R 318586 CDS YP_917347.1 119386292 4582136 734835..735674 1 NC_008687.1 PFAM: short-chain dehydrogenase/reductase SDR; KR; KEGG: sme:SMc00778 oxidoreductase; short-chain dehydrogenase/reductase SDR 735674 4582136 Pden_3583 Paracoccus denitrificans PD1222 short-chain dehydrogenase/reductase SDR YP_917347.1 734835 D 318586 CDS YP_917348.1 119386293 4582137 735702..736973 1 NC_008687.1 TIGRFAM: FAD-linked oxidoreductase; PFAM: FAD linked oxidase domain protein; KEGG: sme:SMc00779 FAD-dependent oxidoreductase; FAD-linked oxidoreductase 736973 4582137 Pden_3584 Paracoccus denitrificans PD1222 FAD-linked oxidoreductase YP_917348.1 735702 D 318586 CDS YP_917349.1 119386294 4582138 737038..738234 1 NC_008687.1 PFAM: Ethanolamine utilisation protein, EutH; KEGG: pfl:PFL_5470 ethanolamine utilization protein EutH; ethanolamine utilisation protein, EutH 738234 4582138 Pden_3585 Paracoccus denitrificans PD1222 ethanolamine utilisation protein, EutH YP_917349.1 737038 D 318586 CDS YP_917350.1 119386295 4582139 complement(738420..739511) 1 NC_008687.1 PFAM: transglutaminase domain protein; KEGG: eba:ebA3478 predicted transglutaminase-like enzyme, cysteine protease; transglutaminase domain-containing protein 739511 4582139 Pden_3586 Paracoccus denitrificans PD1222 transglutaminase domain-containing protein YP_917350.1 738420 R 318586 CDS YP_917351.1 119386296 4582140 complement(739698..740423) 1 NC_008687.1 KEGG: atc:AGR_L_572 hypothetical protein; hypothetical protein 740423 4582140 Pden_3587 Paracoccus denitrificans PD1222 hypothetical protein YP_917351.1 739698 R 318586 CDS YP_917352.1 119386297 4582141 complement(740435..741883) 1 NC_008687.1 PFAM: amidohydrolase; KEGG: sus:Acid_5787 amidohydrolase; amidohydrolase 741883 4582141 Pden_3588 Paracoccus denitrificans PD1222 amidohydrolase YP_917352.1 740435 R 318586 CDS YP_917353.1 119386298 4582142 complement(741907..742203) 1 NC_008687.1 hypothetical protein 742203 4582142 Pden_3589 Paracoccus denitrificans PD1222 hypothetical protein YP_917353.1 741907 R 318586 CDS YP_917354.1 119386299 4582143 complement(742380..742631) 1 NC_008687.1 hypothetical protein 742631 4582143 Pden_3590 Paracoccus denitrificans PD1222 hypothetical protein YP_917354.1 742380 R 318586 CDS YP_917355.1 119386300 4582144 742686..742979 1 NC_008687.1 TIGRFAM: addiction module antitoxin, RelB/DinJ family; PFAM: RelB antitoxin; KEGG: sme:SMa0471 DNA-damage-inducibile protein; addiction module antitoxin 742979 4582144 Pden_3591 Paracoccus denitrificans PD1222 addiction module antitoxin YP_917355.1 742686 D 318586 CDS YP_917356.1 119386301 4582145 742972..743247 1 NC_008687.1 TIGRFAM: addiction module toxin, RelE/StbE family; PFAM: plasmid stabilization system; KEGG: plu:plu2210 hypothetical protein; addiction module antitoxin 743247 4582145 Pden_3592 Paracoccus denitrificans PD1222 addiction module antitoxin YP_917356.1 742972 D 318586 CDS YP_917357.1 119386302 4582146 complement(743455..744669) 1 NC_008687.1 PFAM: transposase IS66; KEGG: mag:amb3320 transposase and inactivated derivative; transposase IS66 744669 4582146 Pden_3593 Paracoccus denitrificans PD1222 transposase IS66 YP_917357.1 743455 R 318586 CDS YP_917358.1 119386303 4582147 complement(745050..745397) 1 NC_008687.1 PFAM: IS66 Orf2 family protein; KEGG: pol:Bpro_5536 IS66 Orf2 like; IS66 Orf2 family protein 745397 4582147 Pden_3595 Paracoccus denitrificans PD1222 IS66 Orf2 family protein YP_917358.1 745050 R 318586 CDS YP_917359.1 119386304 4582148 745691..747589 1 NC_008687.1 TIGRFAM: phage tape measure protein; KEGG: nwi:Nwi_1471 hypothetical protein; phage tape measure protein 747589 4582148 Pden_3596 Paracoccus denitrificans PD1222 phage tape measure protein YP_917359.1 745691 D 318586 CDS YP_917360.1 119386305 4582149 747589..748251 1 NC_008687.1 hypothetical protein 748251 4582149 Pden_3597 Paracoccus denitrificans PD1222 hypothetical protein YP_917360.1 747589 D 318586 CDS YP_917361.1 119386306 4582150 748251..748835 1 NC_008687.1 hypothetical protein 748835 4582150 Pden_3598 Paracoccus denitrificans PD1222 hypothetical protein YP_917361.1 748251 D 318586 CDS YP_917362.1 119386307 4582151 complement(748845..749105) 1 NC_008687.1 hypothetical protein 749105 4582151 Pden_3599 Paracoccus denitrificans PD1222 hypothetical protein YP_917362.1 748845 R 318586 CDS YP_917363.1 119386308 4582152 749213..749608 1 NC_008687.1 hypothetical protein 749608 4582152 Pden_3600 Paracoccus denitrificans PD1222 hypothetical protein YP_917363.1 749213 D 318586 CDS YP_917364.1 119386309 4582153 749608..751692 1 NC_008687.1 PFAM: Fibronectin, type III domain protein; KEGG: mlo:mlr8544 hypothetical protein; fibronectin, type III domain-containing protein 751692 4582153 Pden_3601 Paracoccus denitrificans PD1222 fibronectin, type III domain-containing protein YP_917364.1 749608 D 318586 CDS YP_917365.1 119386310 4582154 751752..753809 1 NC_008687.1 KEGG: mlo:mlr8029 hypothetical protein; hypothetical protein 753809 4582154 Pden_3602 Paracoccus denitrificans PD1222 hypothetical protein YP_917365.1 751752 D 318586 CDS YP_917366.1 119386311 4582155 753875..754198 1 NC_008687.1 hypothetical protein 754198 4582155 Pden_3603 Paracoccus denitrificans PD1222 hypothetical protein YP_917366.1 753875 D 318586 CDS YP_917367.1 119386312 4582156 754198..757080 1 NC_008687.1 hypothetical protein 757080 4582156 Pden_3604 Paracoccus denitrificans PD1222 hypothetical protein YP_917367.1 754198 D 318586 CDS YP_917368.1 119386313 4582157 757105..757386 1 NC_008687.1 hypothetical protein 757386 4582157 Pden_3605 Paracoccus denitrificans PD1222 hypothetical protein YP_917368.1 757105 D 318586 CDS YP_917369.1 119386314 4582158 757589..758383 1 NC_008687.1 PFAM: glycoside hydrolase, family 19; Peptidoglycan-binding domain 1 protein; KEGG: sme:SMb20518 hypothetical protein; peptidoglycan binding domain-containing protein 758383 4582158 Pden_3606 Paracoccus denitrificans PD1222 peptidoglycan binding domain-containing protein YP_917369.1 757589 D 318586 CDS YP_917370.1 119386315 4582159 complement(759034..759303) 1 NC_008687.1 hypothetical protein 759303 4582159 Pden_3607 Paracoccus denitrificans PD1222 hypothetical protein YP_917370.1 759034 R 318586 CDS YP_917371.1 119386316 4582160 complement(759414..759689) 1 NC_008687.1 hypothetical protein 759689 4582160 Pden_3608 Paracoccus denitrificans PD1222 hypothetical protein YP_917371.1 759414 R 318586 CDS YP_917372.1 119386317 4582161 complement(760497..762914) 1 NC_008687.1 KEGG: rsp:RSP_2806 probable ATP-dependent protease La protein; TIGRFAM: ATP-dependent protease La; PFAM: peptidase S16, lon domain protein; AAA ATPase, central domain protein; ATPase associated with various cellular activities, AAA_5; SMART: AAA ATPase; ATP-dependent protease La 762914 4582161 Pden_3609 Paracoccus denitrificans PD1222 ATP-dependent protease La YP_917372.1 760497 R 318586 CDS YP_917373.1 119386318 4582162 complement(763116..763316) 1 NC_008687.1 PFAM: CsbD family protein; KEGG: rpb:RPB_1394 CsbD-like; CsbD family protein 763316 4582162 Pden_3610 Paracoccus denitrificans PD1222 CsbD family protein YP_917373.1 763116 R 318586 CDS YP_917374.1 119386319 4582163 764201..765376 1 NC_008687.1 KEGG: sit:TM1040_0586 conserved hypothetical protein; hypothetical protein 765376 4582163 Pden_3611 Paracoccus denitrificans PD1222 hypothetical protein YP_917374.1 764201 D 318586 CDS YP_917375.1 119386320 4582164 complement(765426..768389) 1 NC_008687.1 IleRS; catalyzes the formation of isoleucyl-tRNA(Ile) from isoleucine and tRNA(Ile); since isoleucine and other amino acids such as valine are similar, there are additional editing function in this enzyme; one is involved in hydrolysis of activated valine-AMP and the other is involved in deacylation of mischarged Val-tRNA(Ile); there are two active sites, one for aminoacylation and one for editing; class-I aminoacyl-tRNA synthetase family type 1 subfamily; some organisms carry two different copies of this enzyme; isoleucyl-tRNA synthetase 768389 ileS 4582164 ileS Paracoccus denitrificans PD1222 isoleucyl-tRNA synthetase YP_917375.1 765426 R 318586 CDS YP_917376.1 119386321 4582165 768541..769713 1 NC_008687.1 PFAM: monooxygenase, FAD-binding; FAD dependent oxidoreductase; KEGG: jan:Jann_3466 monooxygenase, FAD-binding; monooxygenase, FAD-binding 769713 4582165 Pden_3613 Paracoccus denitrificans PD1222 monooxygenase, FAD-binding YP_917376.1 768541 D 318586 CDS YP_917377.1 119386322 4582166 769733..770155 1 NC_008687.1 KEGG: sil:SPO3139 hypothetical protein; hypothetical protein 770155 4582166 Pden_3614 Paracoccus denitrificans PD1222 hypothetical protein YP_917377.1 769733 D 318586 CDS YP_917378.1 119386323 4582167 770204..770527 1 NC_008687.1 PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase; KEGG: jan:Jann_0570 glyoxalase/bleomycin resistance protein/dioxygenase; glyoxalase/bleomycin resistance protein/dioxygenase 770527 4582167 Pden_3615 Paracoccus denitrificans PD1222 glyoxalase/bleomycin resistance protein/dioxygenase YP_917378.1 770204 D 318586 CDS YP_917379.1 119386324 4582168 complement(770524..771156) 1 NC_008687.1 PFAM: protein of unknown function UPF0126; KEGG: sil:SPO3213 hypothetical protein; hypothetical protein 771156 4582168 Pden_3616 Paracoccus denitrificans PD1222 hypothetical protein YP_917379.1 770524 R 318586 CDS YP_917380.1 119386325 4582169 complement(771153..771620) 1 NC_008687.1 An endonuclease that specifically degrades the RNA strand of RNA-DNA hybrids; ribonuclease H 771620 rnhA 4582169 rnhA Paracoccus denitrificans PD1222 ribonuclease H YP_917380.1 771153 R 318586 CDS YP_917381.1 119386326 4582170 complement(771617..772222) 1 NC_008687.1 PFAM: Glutathione S-transferase, N-terminal domain; Glutathione S-transferase, C-terminal domain; KEGG: bmb:BruAb1_1487 glutathione S-transferase family protein; glutathione S-transferase domain-containing protein 772222 4582170 Pden_3618 Paracoccus denitrificans PD1222 glutathione S-transferase domain-containing protein YP_917381.1 771617 R 318586 CDS YP_917382.1 119386327 4582171 complement(772316..773266) 1 NC_008687.1 catalyzes the conversion of 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate into isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP); functions in the nonmevalonate isoprenoid biosynthesis pathway; 4-hydroxy-3-methylbut-2-enyl diphosphate reductase 773266 ispH 4582171 ispH Paracoccus denitrificans PD1222 4-hydroxy-3-methylbut-2-enyl diphosphate reductase YP_917382.1 772316 R 318586 CDS YP_917383.1 119386328 4582172 complement(773306..773869) 1 NC_008687.1 catalyzes a salvage reaction resulting in the formation of AMP which is metabolically less costly than a de novo synthesis; adenine phosphoribosyltransferase 773869 4582172 Pden_3620 Paracoccus denitrificans PD1222 adenine phosphoribosyltransferase YP_917383.1 773306 R 318586 CDS YP_917384.1 119386329 4582173 complement(773869..774531) 1 NC_008687.1 KEGG: sit:TM1040_2319 conserved hypothetical protein; hypothetical protein 774531 4582173 Pden_3621 Paracoccus denitrificans PD1222 hypothetical protein YP_917384.1 773869 R 318586 CDS YP_917385.1 119386330 4582174 774687..775247 1 NC_008687.1 PFAM: GCN5-related N-acetyltransferase; KEGG: sil:SPO3055 acetyltransferase, GNAT family; N-acetyltransferase GCN5 775247 4582174 Pden_3622 Paracoccus denitrificans PD1222 N-acetyltransferase GCN5 YP_917385.1 774687 D 318586 CDS YP_917386.1 119386331 4582175 complement(775235..775804) 1 NC_008687.1 inactivates vertebrate C-type lysozyme; C-lysozyme inhibitor 775804 4582175 Pden_3623 Paracoccus denitrificans PD1222 C-lysozyme inhibitor YP_917386.1 775235 R 318586 CDS YP_917387.1 119386332 4582176 775896..776762 1 NC_008687.1 KEGG: rde:RD1_2154 hypothetical protein; hypothetical protein 776762 4582176 Pden_3624 Paracoccus denitrificans PD1222 hypothetical protein YP_917387.1 775896 D 318586 CDS YP_917388.1 119386333 4582177 complement(776774..778309) 1 NC_008687.1 SMART: AAA ATPase; KEGG: jan:Jann_0847 ATPase; ATPase AAA 778309 4582177 Pden_3625 Paracoccus denitrificans PD1222 ATPase AAA YP_917388.1 776774 R 318586 CDS YP_917389.1 119386334 4582178 complement(778453..778971) 1 NC_008687.1 PFAM: regulatory protein, AsnC/Lrp family; KEGG: rde:RD1_1000 transcriptional regulator, AsnC family; AsnC family transcriptional regulator 778971 4582178 Pden_3626 Paracoccus denitrificans PD1222 AsnC family transcriptional regulator YP_917389.1 778453 R 318586 CDS YP_917390.1 119386335 4582179 778997..779587 1 NC_008687.1 PFAM: Lysine exporter protein (LYSE/YGGA); KEGG: sal:Sala_1362 lysine exporter protein (LysE/YggA); lysine exporter protein LysE/YggA 779587 4582179 Pden_3627 Paracoccus denitrificans PD1222 lysine exporter protein LysE/YggA YP_917390.1 778997 D 318586 CDS YP_917391.1 119386336 4582180 complement(779574..780452) 1 NC_008687.1 PFAM: protein of unknown function DUF6, transmembrane; KEGG: rpe:RPE_0156 protein of unknown function DUF6, transmembrane; hypothetical protein 780452 4582180 Pden_3628 Paracoccus denitrificans PD1222 hypothetical protein YP_917391.1 779574 R 318586 CDS YP_917392.1 119386337 4582181 complement(780469..781497) 1 NC_008687.1 catalyzes the formation of coproporphyrinogen from uroporphyrinogen III; uroporphyrinogen decarboxylase 781497 hemE 4582181 hemE Paracoccus denitrificans PD1222 uroporphyrinogen decarboxylase YP_917392.1 780469 R 318586 CDS YP_917393.1 119386338 4582182 781573..782514 1 NC_008687.1 transformation of porphobilinogen to hydroxymethylbilane in porphyrin biosynthesis; porphobilinogen deaminase 782514 hemC 4582182 hemC Paracoccus denitrificans PD1222 porphobilinogen deaminase YP_917393.1 781573 D 318586 CDS YP_917394.1 119386339 4582183 complement(782511..783443) 1 NC_008687.1 TIGRFAM: cobalamin biosynthesis protein CobD; PFAM: cobalamin biosynthesis protein CbiB; KEGG: rsp:RSP_0430 cobalamin biosynthesis protein CobD; cobalamin biosynthesis protein CobD 783443 4582183 Pden_3631 Paracoccus denitrificans PD1222 cobalamin biosynthesis protein CobD YP_917394.1 782511 R 318586 CDS YP_917395.1 119386340 4582184 complement(783440..784039) 1 NC_008687.1 PFAM: Phosphoglycerate mutase; KEGG: rpa:RPA0993 possible alpha-ribazole-5'-phosphate phosphatase CobC (vit B12 synthesis); phosphoglycerate mutase 784039 4582184 Pden_3632 Paracoccus denitrificans PD1222 phosphoglycerate mutase YP_917395.1 783440 R 318586 CDS YP_917396.1 119386341 4582185 784178..785338 1 NC_008687.1 PFAM: acyl-CoA dehydrogenase domain protein; Acyl-CoA dehydrogenase, type 2, C-terminal domain; KEGG: sil:SPO2793 isovaleryl-CoA dehydrogenase; acyl-CoA dehydrogenase 785338 4582185 Pden_3633 Paracoccus denitrificans PD1222 acyl-CoA dehydrogenase YP_917396.1 784178 D 318586 CDS YP_917397.1 119386342 4582186 785338..785877 1 NC_008687.1 PFAM: protein of unknown function DUF1311; KEGG: mmr:Mmar10_1738 protein of unknown function DUF1311; hypothetical protein 785877 4582186 Pden_3634 Paracoccus denitrificans PD1222 hypothetical protein YP_917397.1 785338 D 318586 CDS YP_917398.1 119386343 4582187 785895..786359 1 NC_008687.1 PFAM: protein of unknown function DUF1311; hypothetical protein 786359 4582187 Pden_3635 Paracoccus denitrificans PD1222 hypothetical protein YP_917398.1 785895 D 318586 CDS YP_917399.1 119386344 4582188 complement(786419..787054) 1 NC_008687.1 PFAM: OmpW family protein; KEGG: xcb:XC_0970 outer membrane protein; OmpW family protein 787054 4582188 Pden_3636 Paracoccus denitrificans PD1222 OmpW family protein YP_917399.1 786419 R 318586 CDS YP_917400.1 119386345 4582189 787177..788781 1 NC_008687.1 PFAM: carboxyl transferase; KEGG: sit:TM1040_0737 propionyl-CoA carboxylase; propionyl-CoA carboxylase 788781 4582189 Pden_3637 Paracoccus denitrificans PD1222 propionyl-CoA carboxylase YP_917400.1 787177 D 318586 CDS YP_917401.1 119386346 4582190 788787..789287 1 NC_008687.1 PFAM: Appr-1-p processing domain protein; KEGG: cvi:CV3563 hypothetical protein; appr-1-p processing domain-containing protein 789287 4582190 Pden_3638 Paracoccus denitrificans PD1222 appr-1-p processing domain-containing protein YP_917401.1 788787 D 318586 CDS YP_917402.1 119386347 4582191 789367..791295 1 NC_008687.1 PFAM: biotin/lipoyl attachment domain-containing protein; Carbamoyl-phosphate synthase L chain, ATP-binding; Carbamoyl-phosphate synthetase large chain domain protein; biotin carboxylase domain protein; KEGG: jan:Jann_1147 carbamoyl-phosphate synthase L chain, ATP-binding; carbamoyl-phosphate synthase subunit L 791295 4582191 Pden_3639 Paracoccus denitrificans PD1222 carbamoyl-phosphate synthase subunit L YP_917402.1 789367 D 318586 CDS YP_917403.1 119386348 4582192 791292..791945 1 NC_008687.1 PFAM: Glutathione S-transferase, N-terminal domain; KEGG: jan:Jann_1148 glutathione S-transferase-like; glutathione S-transferase domain-containing protein 791945 4582192 Pden_3640 Paracoccus denitrificans PD1222 glutathione S-transferase domain-containing protein YP_917403.1 791292 D 318586 CDS YP_917404.1 119386349 4582193 791932..792801 1 NC_008687.1 catalyzes the formation of acetoacetate and acetyl-CoA from 3-hydroxy-3-methylglutaryl-CoA; hydroxymethylglutaryl-CoA lyase 792801 4582193 Pden_3641 Paracoccus denitrificans PD1222 hydroxymethylglutaryl-CoA lyase YP_917404.1 791932 D 318586 CDS YP_917405.1 119386350 4582194 792801..793583 1 NC_008687.1 Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA; enoyl-CoA hydratase 793583 4582194 Pden_3642 Paracoccus denitrificans PD1222 enoyl-CoA hydratase YP_917405.1 792801 D 318586 CDS YP_917406.1 119386351 4582195 793859..795055 1 NC_008687.1 PFAM: major facilitator superfamily MFS_1; KEGG: bja:blr4870 MFS permease; major facilitator transporter 795055 4582195 Pden_3643 Paracoccus denitrificans PD1222 major facilitator transporter YP_917406.1 793859 D 318586 CDS YP_917407.1 119386352 4582196 complement(794966..795748) 1 NC_008687.1 KEGG: rde:RD1_0624 hypothetical protein; hypothetical protein 795748 4582196 Pden_3644 Paracoccus denitrificans PD1222 hypothetical protein YP_917407.1 794966 R 318586 CDS YP_917408.1 119386353 4582197 795841..796083 1 NC_008687.1 PFAM: protein of unknown function DUF465; KEGG: bms:BRA0175 hypothetical protein; hypothetical protein 796083 4582197 Pden_3645 Paracoccus denitrificans PD1222 hypothetical protein YP_917408.1 795841 D 318586 CDS YP_917409.1 119386354 4582198 796319..796765 1 NC_008687.1 PFAM: heat shock protein Hsp20; KEGG: sil:SPO3484 heat shock protein, Hsp20 family; heat shock protein Hsp20 796765 4582198 Pden_3646 Paracoccus denitrificans PD1222 heat shock protein Hsp20 YP_917409.1 796319 D 318586 CDS YP_917410.1 119386355 4582199 complement(796871..797470) 1 NC_008687.1 involved in a recombinational process of DNA repair, independent of the recBC complex; recombination protein RecR 797470 recR 4582199 recR Paracoccus denitrificans PD1222 recombination protein RecR YP_917410.1 796871 R 318586 CDS YP_917411.1 119386356 4582200 complement(797471..797812) 1 NC_008687.1 PFAM: conserved hypothetical protein 103; KEGG: jan:Jann_3877 conserved hypothetical protein 103; hypothetical protein 797812 4582200 Pden_3648 Paracoccus denitrificans PD1222 hypothetical protein YP_917411.1 797471 R 318586 CDS YP_917412.1 119386357 4582201 complement(797816..799594) 1 NC_008687.1 catalyzes the DNA-template-directed extension of the 3'-end of a DNA strand; the tau chain serves as a scaffold to help in the dimerizaton of the alpha,epsilon and theta core complex; the gamma chain seems to interact with the delta and delta' subunits to transfer the beta subunit on the DNA; DNA polymerase III subunits gamma and tau 799594 4582201 Pden_3649 Paracoccus denitrificans PD1222 DNA polymerase III subunits gamma and tau YP_917412.1 797816 R 318586 CDS YP_917413.1 119386358 4582202 complement(799654..799950) 1 NC_008687.1 KEGG: bmb:BruAb1_1279 hypothetical protein; hypothetical protein 799950 4582202 Pden_3650 Paracoccus denitrificans PD1222 hypothetical protein YP_917413.1 799654 R 318586 CDS YP_917414.1 119386359 4582203 complement(800145..800831) 1 NC_008687.1 porin involved in osmoregulation allowing water to move into and out of the cell in response to osmotic pressure; aquaporin Z 800831 4582203 Pden_3651 Paracoccus denitrificans PD1222 aquaporin Z YP_917414.1 800145 R 318586 CDS YP_917415.1 119386360 4582204 800979..802793 1 NC_008687.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rsp:RSP_2717 UUP ATPase; ABC transporter 802793 4582204 Pden_3652 Paracoccus denitrificans PD1222 ABC transporter YP_917415.1 800979 D 318586 CDS YP_917416.1 119386361 4582205 802948..803190 1 NC_008687.1 PFAM: Cold-shock protein, DNA-binding; SMART: Cold shock protein; KEGG: rsp:RSP_1952 cold-shock DNA-binding domain protein; cold-shock DNA-binding domain-containing protein 803190 4582205 Pden_3653 Paracoccus denitrificans PD1222 cold-shock DNA-binding domain-containing protein YP_917416.1 802948 D 318586 CDS YP_917417.1 119386362 4582206 complement(804012..805649) 1 NC_008687.1 60 kDa chaperone family; promotes refolding of misfolded polypeptides especially under stressful conditions; forms two stacked rings of heptamers to form a barrel-shaped 14mer; ends can be capped by GroES; misfolded proteins enter the barrel where they are refolded when GroES binds; many bacteria have multiple copies of the groEL gene which are active under different environmental conditions; the B.japonicum protein in this cluster is expressed constitutively; in Rhodobacter, Corynebacterium and Rhizobium this protein is not essential for growth; molecular chaperone GroEL 805649 groEL 4582206 groEL Paracoccus denitrificans PD1222 molecular chaperone GroEL YP_917417.1 804012 R 318586 CDS YP_917418.1 119386363 4582207 806209..807537 1 NC_008687.1 PFAM: glycosyl transferase, group 1; KEGG: jan:Jann_4272 glycosyl transferase, group 1; group 1 glycosyl transferase 807537 4582207 Pden_3655 Paracoccus denitrificans PD1222 group 1 glycosyl transferase YP_917418.1 806209 D 318586 CDS YP_917419.1 119386364 4582208 807534..808592 1 NC_008687.1 PFAM: GumN family protein; KEGG: rsp:RSP_2309 hypothetical protein; GumN family protein 808592 4582208 Pden_3656 Paracoccus denitrificans PD1222 GumN family protein YP_917419.1 807534 D 318586 CDS YP_917420.1 119386365 4582209 808582..808917 1 NC_008687.1 KEGG: sme:SMc01433 hypothetical protein; hypothetical protein 808917 4582209 Pden_3657 Paracoccus denitrificans PD1222 hypothetical protein YP_917420.1 808582 D 318586 CDS YP_917421.1 119386366 4582210 808917..809558 1 NC_008687.1 PFAM: protein of unknown function DUF1345; KEGG: sme:SMc01272 hypothetical protein; hypothetical protein 809558 4582210 Pden_3658 Paracoccus denitrificans PD1222 hypothetical protein YP_917421.1 808917 D 318586 CDS YP_917422.1 119386367 4582211 809625..810545 1 NC_008687.1 catalyzes the hydrolysis of pyrophosphate to phosphate; manganese-dependent inorganic pyrophosphatase 810545 4582211 Pden_3659 Paracoccus denitrificans PD1222 manganese-dependent inorganic pyrophosphatase YP_917422.1 809625 D 318586 CDS YP_917423.1 119386368 4582212 810561..811430 1 NC_008687.1 TIGRFAM: HAD-superfamily subfamily IIA hydrolase like protein; HAD-superfamily hydrolase, subfamily IIA; PFAM: Haloacid dehalogenase domain protein hydrolase; KEGG: rsp:RSP_2306 HAD superfamily protein; HAD family hydrolase 811430 4582212 Pden_3660 Paracoccus denitrificans PD1222 HAD family hydrolase YP_917423.1 810561 D 318586 CDS YP_917424.1 119386369 4582213 811536..811982 1 NC_008687.1 PFAM: MaoC domain protein dehydratase; KEGG: rsp:RSP_2305 MaoC family protein; dehydratase 811982 4582213 Pden_3661 Paracoccus denitrificans PD1222 dehydratase YP_917424.1 811536 D 318586 CDS YP_917425.1 119386370 4582214 812015..812944 1 NC_008687.1 TIGRFAM: riboflavin biosynthesis protein RibF; PFAM: Riboflavin kinase / FAD synthetase; KEGG: rsp:RSP_2304 riboflavin kinase / FAD synthetase = FMN adenylyltransferase, RibF; riboflavin biosynthesis protein RibF 812944 4582214 Pden_3662 Paracoccus denitrificans PD1222 riboflavin biosynthesis protein RibF YP_917425.1 812015 D 318586 CDS YP_917426.1 119386371 4582215 812944..813384 1 NC_008687.1 PFAM: protein of unknown function UPF0153; KEGG: sil:SPO3155 hypothetical protein; hypothetical protein 813384 4582215 Pden_3663 Paracoccus denitrificans PD1222 hypothetical protein YP_917426.1 812944 D 318586 CDS YP_917427.1 119386372 4582216 813381..814424 1 NC_008687.1 PFAM: aromatic amino acid beta-eliminating lyase/threonine aldolase; KEGG: rsp:RSP_2302 low specificity L-threonine aldolase; threonine aldolase 814424 4582216 Pden_3664 Paracoccus denitrificans PD1222 threonine aldolase YP_917427.1 813381 D 318586 CDS YP_917428.1 119386373 4582217 complement(814421..814840) 1 NC_008687.1 PFAM: CinA domain protein; KEGG: rde:RD1_2769 competence/damage-inducible protein CinA; CinA domain-containing protein 814840 4582217 Pden_3665 Paracoccus denitrificans PD1222 CinA domain-containing protein YP_917428.1 814421 R 318586 CDS YP_917429.1 119386374 4582218 complement(814885..815385) 1 NC_008687.1 PFAM: phosphatidylglycerophosphatase A; KEGG: rde:RD1_2768 phosphatidylglycerophosphatase A; phosphatidylglycerophosphatase A 815385 4582218 Pden_3666 Paracoccus denitrificans PD1222 phosphatidylglycerophosphatase A YP_917429.1 814885 R 318586 CDS YP_917430.1 119386375 4582219 complement(815398..816633) 1 NC_008687.1 TIGRFAM: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase; 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; PFAM: 4-diphosphocytidyl-2C-methyl-D-erythritol synthase; MECDP-synthase; KEGG: sil:SPO2090 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase/2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase 816633 4582219 Pden_3667 Paracoccus denitrificans PD1222 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase YP_917430.1 815398 R 318586 CDS YP_917431.1 119386376 4582220 816691..817416 1 NC_008687.1 KEGG: rsp:RSP_0359 ribose-5-phosphate isomerase; TIGRFAM: ribose 5-phosphate isomerase; PFAM: Ribose 5-phosphate isomerase; ribose 5-phosphate isomerase 817416 4582220 Pden_3668 Paracoccus denitrificans PD1222 ribose 5-phosphate isomerase YP_917431.1 816691 D 318586 CDS YP_917432.1 119386377 4582221 817413..818813 1 NC_008687.1 PFAM: FAD-dependent pyridine nucleotide-disulphide oxidoreductase; pyridine nucleotide-disulphide oxidoreductase dimerisation region; KEGG: rsp:RSP_0358 probable glutathione reductase; pyridine nucleotide-disulfide oxidoreductase dimerisation subunit 818813 4582221 Pden_3669 Paracoccus denitrificans PD1222 pyridine nucleotide-disulfide oxidoreductase dimerisation subunit YP_917432.1 817413 D 318586 CDS YP_917433.1 119386378 4582222 818872..820071 1 NC_008687.1 TIGRFAM: HflK protein; PFAM: band 7 protein; KEGG: rsp:RSP_0357 probable HflK protein; HflK protein 820071 4582222 Pden_3670 Paracoccus denitrificans PD1222 HflK protein YP_917433.1 818872 D 318586 CDS YP_917434.1 119386379 4582223 820071..821180 1 NC_008687.1 TIGRFAM: HflC protein; PFAM: band 7 protein; KEGG: rsp:RSP_0356 probable HflC protein; HflC protein 821180 4582223 Pden_3671 Paracoccus denitrificans PD1222 HflC protein YP_917434.1 820071 D 318586 CDS YP_917435.1 119386380 4582224 complement(821309..822499) 1 NC_008687.1 PFAM: protein of unknown function UPF0118; KEGG: rsp:RSP_1564 transmembrane transport protein; hypothetical protein 822499 4582224 Pden_3672 Paracoccus denitrificans PD1222 hypothetical protein YP_917435.1 821309 R 318586 CDS YP_917436.1 119386381 4582225 822864..823505 1 NC_008687.1 PFAM: TENA/THI-4 domain protein; KEGG: ppu:PP_3185 pet18 protein; TenA family transcription regulator 823505 4582225 Pden_3673 Paracoccus denitrificans PD1222 TenA family transcription regulator YP_917436.1 822864 D 318586 CDS YP_917437.1 119386382 4582226 complement(823509..823982) 1 NC_008687.1 PFAM: NUDIX hydrolase; KEGG: sco:SCO5600 hypothetical protein; NUDIX hydrolase 823982 4582226 Pden_3674 Paracoccus denitrificans PD1222 NUDIX hydrolase YP_917437.1 823509 R 318586 CDS YP_917438.1 119386383 4582227 complement(824056..824379) 1 NC_008687.1 KEGG: sit:TM1040_0507 conserved hypothetical protein; hypothetical protein 824379 4582227 Pden_3675 Paracoccus denitrificans PD1222 hypothetical protein YP_917438.1 824056 R 318586 CDS YP_917439.1 119386384 4582228 824528..825211 1 NC_008687.1 PFAM: protein of unknown function DUF45; KEGG: rsp:RSP_0982 zinc metallopeptidase-like protein; hypothetical protein 825211 4582228 Pden_3676 Paracoccus denitrificans PD1222 hypothetical protein YP_917439.1 824528 D 318586 CDS YP_917440.1 119386385 4582229 825257..825901 1 NC_008687.1 PFAM: regulatory protein GntR, HTH; GntR domain protein; KEGG: rsp:RSP_0981 transcriptional regulator, GntR family; GntR family transcriptional regulator 825901 4582229 Pden_3677 Paracoccus denitrificans PD1222 GntR family transcriptional regulator YP_917440.1 825257 D 318586 CDS YP_917441.1 119386386 4582230 complement(825984..827300) 1 NC_008687.1 catalyzes the formation of L-aspartate 4-semialdehyde from L-homoserine; homoserine dehydrogenase 827300 4582230 Pden_3678 Paracoccus denitrificans PD1222 homoserine dehydrogenase YP_917441.1 825984 R 318586 CDS YP_917442.1 119386387 4582231 complement(827368..827901) 1 NC_008687.1 KEGG: syf:Synpcc7942_1655 hypothetical protein; hypothetical protein 827901 4582231 Pden_3679 Paracoccus denitrificans PD1222 hypothetical protein YP_917442.1 827368 R 318586 CDS YP_917443.1 119386388 4582232 complement(828021..828509) 1 NC_008687.1 PFAM: GCN5-related N-acetyltransferase; KEGG: rsp:RSP_0784 acetyltransferase, GNAT family; N-acetyltransferase GCN5 828509 4582232 Pden_3680 Paracoccus denitrificans PD1222 N-acetyltransferase GCN5 YP_917443.1 828021 R 318586 CDS YP_917444.1 119386389 4582233 complement(828616..830760) 1 NC_008687.1 MDM; functions in conversion of succinate to propionate; methylmalonyl-CoA mutase 830760 4582233 Pden_3681 Paracoccus denitrificans PD1222 methylmalonyl-CoA mutase YP_917444.1 828616 R 318586 CDS YP_917445.1 119386390 4582234 830818..831345 1 NC_008687.1 KEGG: sil:SPO1103 hypothetical protein; hypothetical protein 831345 4582234 Pden_3682 Paracoccus denitrificans PD1222 hypothetical protein YP_917445.1 830818 D 318586 CDS YP_917446.1 119386391 4582235 complement(831593..832252) 1 NC_008687.1 hypothetical protein 832252 4582235 Pden_3683 Paracoccus denitrificans PD1222 hypothetical protein YP_917446.1 831593 R 318586 CDS YP_917447.1 119386392 4582236 complement(832302..834359) 1 NC_008687.1 PFAM: biotin/lipoyl attachment domain-containing protein; ATP-dependent carboxylate-amine ligase domain protein, ATP-grasp; Carbamoyl-phosphate synthase L chain, ATP-binding; Carbamoyl-phosphate synthetase large chain domain protein; biotin carboxylase domain protein; RimK domain protein ATP-grasp; KEGG: sil:SPO1101 propionyl-CoA carboxylase, alpha subunit; carbamoyl-phosphate synthase subunit L 834359 4582236 Pden_3684 Paracoccus denitrificans PD1222 carbamoyl-phosphate synthase subunit L YP_917447.1 832302 R 318586 CDS YP_917448.1 119386393 4582237 complement(834756..835001) 1 NC_008687.1 hypothetical protein 835001 4582237 Pden_3685 Paracoccus denitrificans PD1222 hypothetical protein YP_917448.1 834756 R 318586 CDS YP_917449.1 119386394 4582238 complement(835147..835560) 1 NC_008687.1 KEGG: rsp:RSP_2190 hypothetical protein; hypothetical protein 835560 4582238 Pden_3686 Paracoccus denitrificans PD1222 hypothetical protein YP_917449.1 835147 R 318586 CDS YP_917450.1 119386395 4582239 complement(835970..836623) 1 NC_008687.1 KEGG: rsp:RSP_6040 hypothetical protein; hypothetical protein 836623 4582239 Pden_3687 Paracoccus denitrificans PD1222 hypothetical protein YP_917450.1 835970 R 318586 CDS YP_917451.1 119386396 4582240 complement(836649..838181) 1 NC_008687.1 PFAM: carboxyl transferase; KEGG: rsp:RSP_2189 propionyl-CoA carboxylase beta chain; carboxyl transferase 838181 4582240 Pden_3688 Paracoccus denitrificans PD1222 carboxyl transferase YP_917451.1 836649 R 318586 CDS YP_917452.1 119386397 4582241 838262..839359 1 NC_008687.1 KEGG: sil:SPO2670 alanine racemase; TIGRFAM: alanine racemase; PFAM: alanine racemase domain protein; alanine racemase 839359 4582241 Pden_3689 Paracoccus denitrificans PD1222 alanine racemase YP_917452.1 838262 D 318586 CDS YP_917453.1 119386398 4582242 839356..840114 1 NC_008687.1 PFAM: protein of unknown function DUF140; KEGG: rsp:RSP_2459 ABC transporter, inner membrane subunit; hypothetical protein 840114 4582242 Pden_3690 Paracoccus denitrificans PD1222 hypothetical protein YP_917453.1 839356 D 318586 CDS YP_917454.1 119386399 4582243 840114..840851 1 NC_008687.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rsp:RSP_2458 ABC transporter, ATPase subunit; ABC transporter 840851 4582243 Pden_3691 Paracoccus denitrificans PD1222 ABC transporter YP_917454.1 840114 D 318586 CDS YP_917455.1 119386400 4582244 840967..842094 1 NC_008687.1 PFAM: PhoH family protein; KEGG: rsp:RSP_3599 hypothetical protein; PhoH family protein 842094 4582244 Pden_3692 Paracoccus denitrificans PD1222 PhoH family protein YP_917455.1 840967 D 318586 CDS YP_917456.1 119386401 4582245 842087..842611 1 NC_008687.1 PFAM: protein of unknown function UPF0054; KEGG: rsp:RSP_3598 hypothetical protein; hypothetical protein 842611 4582245 Pden_3693 Paracoccus denitrificans PD1222 hypothetical protein YP_917456.1 842087 D 318586 CDS YP_917457.1 119386402 4582246 842608..843540 1 NC_008687.1 PFAM: CBS domain containing protein; transporter-associated region; KEGG: rsp:RSP_3597 CorC/HlyC family protein with CBS domains; hypothetical protein 843540 4582246 Pden_3694 Paracoccus denitrificans PD1222 hypothetical protein YP_917457.1 842608 D 318586 CDS YP_917458.1 119386403 4582247 complement(843547..844356) 1 NC_008687.1 PFAM: GCN5-related N-acetyltransferase; Antibiotic biosynthesis monooxygenase; KEGG: aba:Acid345_3954 GCN5-related N-acetyltransferase; N-acetyltransferase GCN5 844356 4582247 Pden_3695 Paracoccus denitrificans PD1222 N-acetyltransferase GCN5 YP_917458.1 843547 R 318586 CDS YP_917459.1 119386404 4582248 complement(844552..846111) 1 NC_008687.1 contains glutamine-hydrolyzing domain and glutamine amidotransferase; GMP-binding domain; functions to produce GMP from XMP in the IMP pathway; GMP synthase 846111 guaA 4582248 guaA Paracoccus denitrificans PD1222 GMP synthase YP_917459.1 844552 R 318586 CDS YP_917460.1 119386405 4582249 complement(846293..846904) 1 NC_008687.1 PFAM: thiamine monophosphate synthase; KEGG: rsp:RSP_3828 thiamine-phosphate pyrophosphorylase; thiamine monophosphate synthase 846904 4582249 Pden_3697 Paracoccus denitrificans PD1222 thiamine monophosphate synthase YP_917460.1 846293 R 318586 CDS YP_917461.1 119386406 4582250 846979..847719 1 NC_008687.1 TIGRFAM: RNA methyltransferase, TrmH family, group 1; PFAM: tRNA/rRNA methyltransferase (SpoU); KEGG: rsp:RSP_3829 tRNA/rRNA methyltransferase (SpoU); RNA methyltransferase 847719 4582250 Pden_3698 Paracoccus denitrificans PD1222 RNA methyltransferase YP_917461.1 846979 D 318586 CDS YP_917462.1 119386407 4582251 847745..848920 1 NC_008687.1 PFAM: cytochrome oxidase assembly; KEGG: sit:TM1040_1335 cytochrome oxidase assembly; cytochrome oxidase assembly 848920 4582251 Pden_3699 Paracoccus denitrificans PD1222 cytochrome oxidase assembly YP_917462.1 847745 D 318586 CDS YP_917463.1 119386408 4582252 848917..850389 1 NC_008687.1 PFAM: peptidase M32, carboxypeptidase Taq metallopeptidase; KEGG: rsp:RSP_3832 thermostable carboxypeptidase 1; carboxypeptidase Taq 850389 4582252 Pden_3700 Paracoccus denitrificans PD1222 carboxypeptidase Taq YP_917463.1 848917 D 318586 CDS YP_917464.1 119386409 4582253 850505..851842 1 NC_008687.1 catalyzes the formation of 2-methylthio-N6-(dimethylallyl)adenosine (ms(2)i(6)A) at position 37 in tRNAs that read codons beginning with uridine from N6-(dimethylallyl)adenosine (i(6)A); (dimethylallyl)adenosine tRNA methylthiotransferase 851842 4582253 Pden_3701 Paracoccus denitrificans PD1222 (dimethylallyl)adenosine tRNA methylthiotransferase YP_917464.1 850505 D 318586 CDS YP_917465.1 119386410 4582254 complement(851875..853206) 1 NC_008687.1 PFAM: glutamine synthetase, catalytic region; KEGG: rsp:RSP_0375 probable glutamine synthetase; glutamate--ammonia ligase 853206 4582254 Pden_3702 Paracoccus denitrificans PD1222 glutamate--ammonia ligase YP_917465.1 851875 R 318586 CDS YP_917466.1 119386411 4582255 complement(853210..854037) 1 NC_008687.1 TIGRFAM: polar amino acid ABC transporter, inner membrane subunit; PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: rsp:RSP_0374 ABC basic amino acid transporter, inner membrane subunit; polar amino acid ABC transporter inner membrane subunit 854037 4582255 Pden_3703 Paracoccus denitrificans PD1222 polar amino acid ABC transporter inner membrane subunit YP_917466.1 853210 R 318586 CDS YP_917467.1 119386412 4582256 complement(854034..854915) 1 NC_008687.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: sit:TM1040_1713 binding-protein-dependent transport systems inner membrane component; binding-protein-dependent transport system inner membrane protein 854915 4582256 Pden_3704 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_917467.1 854034 R 318586 CDS YP_917468.1 119386413 4582257 complement(854964..855686) 1 NC_008687.1 PFAM: extracellular solute-binding protein, family 3; KEGG: sil:SPO1306 His/Glu/Gln/Arg/opine family ABC transporter, periplasmic His/Glu/Gln/Arg/opine family-binding protein; extracellular solute-binding protein 855686 4582257 Pden_3705 Paracoccus denitrificans PD1222 extracellular solute-binding protein YP_917468.1 854964 R 318586 CDS YP_917469.1 119386414 4582258 complement(855711..856532) 1 NC_008687.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rsp:RSP_0371 ABC basic amino acid transporter, ATPase subunit; ABC transporter 856532 4582258 Pden_3706 Paracoccus denitrificans PD1222 ABC transporter YP_917469.1 855711 R 318586 CDS YP_917470.1 119386415 4582259 complement(856657..857118) 1 NC_008687.1 PFAM: protein of unknown function DUF1332; KEGG: sil:SPO1309 hypothetical protein; hypothetical protein 857118 4582259 Pden_3707 Paracoccus denitrificans PD1222 hypothetical protein YP_917470.1 856657 R 318586 CDS YP_917471.1 119386416 4582260 complement(857171..857467) 1 NC_008687.1 PFAM: protein of unknown function DUF1330; KEGG: sit:TM1040_1707 protein of unknown function DUF1330; hypothetical protein 857467 4582260 Pden_3708 Paracoccus denitrificans PD1222 hypothetical protein YP_917471.1 857171 R 318586 CDS YP_917472.1 119386417 4582261 complement(857539..858447) 1 NC_008687.1 PFAM: protein of unknown function DUF344; KEGG: sme:SMa0172 hypothetical protein; hypothetical protein 858447 4582261 Pden_3709 Paracoccus denitrificans PD1222 hypothetical protein YP_917472.1 857539 R 318586 CDS YP_917473.1 119386418 4582262 complement(858511..858966) 1 NC_008687.1 hypothetical protein 858966 4582262 Pden_3710 Paracoccus denitrificans PD1222 hypothetical protein YP_917473.1 858511 R 318586 CDS YP_917474.1 119386419 4582263 complement(859014..860657) 1 NC_008687.1 CTP synthase; cytidine triphosphate synthetase; catalyzes the ATP-dependent amination of UTP to CTP with either L-glutamine or ammonia as the source of nitrogen; in Escherichia coli this enzyme forms a homotetramer; CTP synthetase 860657 pyrG 4582263 pyrG Paracoccus denitrificans PD1222 CTP synthetase YP_917474.1 859014 R 318586 CDS YP_917475.1 119386420 4582264 complement(860806..861336) 1 NC_008687.1 TIGRFAM: preprotein translocase, SecG subunit; PFAM: Preprotein translocase SecG subunit; KEGG: rsp:RSP_0367 preprotein translocase SecG subunit; preprotein translocase subunit SecG 861336 secG 4582264 secG Paracoccus denitrificans PD1222 preprotein translocase subunit SecG YP_917475.1 860806 R 318586 CDS YP_917476.1 119386421 4582265 861405..862838 1 NC_008687.1 TIGRFAM: cobyric acid synthase CobQ; PFAM: Cobyrinic acid a,c-diamide synthase; CobB/CobQ domain protein glutamine amidotransferase; KEGG: rsp:RSP_0796 cobyric acid synthase; cobyric acid synthase CobQ 862838 4582265 Pden_3713 Paracoccus denitrificans PD1222 cobyric acid synthase CobQ YP_917476.1 861405 D 318586 CDS YP_917477.1 119386422 4582266 complement(862835..863545) 1 NC_008687.1 PFAM: short-chain dehydrogenase/reductase SDR; KEGG: rsp:RSP_2453 oxidoreductase (NAD/NADP dependent); short-chain dehydrogenase/reductase SDR 863545 4582266 Pden_3714 Paracoccus denitrificans PD1222 short-chain dehydrogenase/reductase SDR YP_917477.1 862835 R 318586 CDS YP_917478.1 119386423 4582267 complement(863640..864020) 1 NC_008687.1 PFAM: protein of unknown function DUF1284; KEGG: wol:WD1205 hypothetical protein; hypothetical protein 864020 4582267 Pden_3715 Paracoccus denitrificans PD1222 hypothetical protein YP_917478.1 863640 R 318586 CDS YP_917479.1 119386424 4582268 complement(864089..865381) 1 NC_008687.1 KEGG: sit:TM1040_1132 citrate synthase I; TIGRFAM: citrate synthase I; PFAM: Citrate synthase; citrate synthase I 865381 4582268 Pden_3716 Paracoccus denitrificans PD1222 citrate synthase I YP_917479.1 864089 R 318586 CDS YP_917480.1 119386425 4582269 complement(865436..866842) 1 NC_008687.1 Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation; glutamyl-tRNA synthetase 866842 gltX 4582269 gltX Paracoccus denitrificans PD1222 glutamyl-tRNA synthetase YP_917480.1 865436 R 318586 CDS YP_917481.1 119386426 4582270 866992..869145 1 NC_008687.1 PFAM: ComEC/Rec2-related protein; KEGG: sil:SPO2155 competence protein; ComEC/Rec2-like protein 869145 4582270 Pden_3718 Paracoccus denitrificans PD1222 ComEC/Rec2-like protein YP_917481.1 866992 D 318586 CDS YP_917482.1 119386427 4582271 869183..869752 1 NC_008687.1 PFAM: Heme NO binding domain protein; KEGG: rsp:RSP_6114 hypothetical protein; heme NO binding domain-containing protein 869752 4582271 Pden_3719 Paracoccus denitrificans PD1222 heme NO binding domain-containing protein YP_917482.1 869183 D 318586 CDS YP_917483.1 119386428 4582272 869749..870711 1 NC_008687.1 TIGRFAM: diguanylate cyclase; PFAM: GGDEF domain containing protein; KEGG: rsp:RSP_0410 sensor diguanylate cyclase (GGDEF); diguanylate cyclase 870711 4582272 Pden_3720 Paracoccus denitrificans PD1222 diguanylate cyclase YP_917483.1 869749 D 318586 CDS YP_917484.1 119386429 4582273 870984..871859 1 NC_008687.1 KEGG: sit:TM1040_0587 conserved hypothetical protein; hypothetical protein 871859 4582273 Pden_3721 Paracoccus denitrificans PD1222 hypothetical protein YP_917484.1 870984 D 318586 CDS YP_917485.1 119386430 4582274 871922..872185 1 NC_008687.1 hypothetical protein 872185 4582274 Pden_3722 Paracoccus denitrificans PD1222 hypothetical protein YP_917485.1 871922 D 318586 CDS YP_917486.1 119386431 4582275 872182..872424 1 NC_008687.1 hypothetical protein 872424 4582275 Pden_3723 Paracoccus denitrificans PD1222 hypothetical protein YP_917486.1 872182 D 318586 CDS YP_917487.1 119386432 4582276 872490..873362 1 NC_008687.1 PFAM: regulatory protein, LuxR; Bacterio-opsin activator, HTH domain protein; Sigma-70, region 4 type 2; KEGG: sit:TM1040_1212 transcriptional regulator, LuxR family; response regulator receiver protein 873362 4582276 Pden_3724 Paracoccus denitrificans PD1222 response regulator receiver protein YP_917487.1 872490 D 318586 CDS YP_917488.1 119386433 4582277 complement(873445..874335) 1 NC_008687.1 EF-Ts; functions during elongation stage of protein translation; forms a dimer; associates with EF-Tu-GDP complex and promotes exchange of GDP to GTP resulting in regeneration of the active form of EF-Tu; elongation factor Ts 874335 tsf 4582277 tsf Paracoccus denitrificans PD1222 elongation factor Ts YP_917488.1 873445 R 318586 CDS YP_917489.1 119386434 4582278 complement(874433..875218) 1 NC_008687.1 one of the last subunits in the assembly of the 30S subunit; absence of S2 does not inhibit assembly but results in an inactive subunit; 30S ribosomal protein S2 875218 rpsB 4582278 rpsB Paracoccus denitrificans PD1222 30S ribosomal protein S2 YP_917489.1 874433 R 318586 CDS YP_917490.1 119386435 4582279 875753..875902 1 NC_008687.1 hypothetical protein 875902 4582279 Pden_3727 Paracoccus denitrificans PD1222 hypothetical protein YP_917490.1 875753 D 318586 CDS YP_917491.1 119386436 4582280 complement(876103..877131) 1 NC_008687.1 PFAM: phage integrase family protein; KEGG: sit:TM1040_1692 phage integrase; phage integrase family protein 877131 4582280 Pden_3728 Paracoccus denitrificans PD1222 phage integrase family protein YP_917491.1 876103 R 318586 CDS YP_917492.1 119386437 4582281 complement(877128..877334) 1 NC_008687.1 hypothetical protein 877334 4582281 Pden_3729 Paracoccus denitrificans PD1222 hypothetical protein YP_917492.1 877128 R 318586 CDS YP_917493.1 119386438 4582282 complement(877335..877580) 1 NC_008687.1 hypothetical protein 877580 4582282 Pden_3730 Paracoccus denitrificans PD1222 hypothetical protein YP_917493.1 877335 R 318586 CDS YP_917494.1 119386439 4582283 complement(877561..878016) 1 NC_008687.1 PFAM: HNH endonuclease; SMART: HNH nuclease; KEGG: sty:HCM1.27c hypothetical protein; HNH endonuclease 878016 4582283 Pden_3731 Paracoccus denitrificans PD1222 HNH endonuclease YP_917494.1 877561 R 318586 CDS YP_917495.1 119386440 4582284 complement(878016..878258) 1 NC_008687.1 hypothetical protein 878258 4582284 Pden_3732 Paracoccus denitrificans PD1222 hypothetical protein YP_917495.1 878016 R 318586 CDS YP_917496.1 119386441 4582285 complement(878356..878757) 1 NC_008687.1 hypothetical protein 878757 4582285 Pden_3733 Paracoccus denitrificans PD1222 hypothetical protein YP_917496.1 878356 R 318586 CDS YP_917497.1 119386442 4582286 complement(878995..879273) 1 NC_008687.1 hypothetical protein 879273 4582286 Pden_3734 Paracoccus denitrificans PD1222 hypothetical protein YP_917497.1 878995 R 318586 CDS YP_917498.1 119386443 4582287 complement(879266..879910) 1 NC_008687.1 hypothetical protein 879910 4582287 Pden_3735 Paracoccus denitrificans PD1222 hypothetical protein YP_917498.1 879266 R 318586 CDS YP_917499.1 119386444 4582288 complement(879900..880430) 1 NC_008687.1 hypothetical protein 880430 4582288 Pden_3736 Paracoccus denitrificans PD1222 hypothetical protein YP_917499.1 879900 R 318586 CDS YP_917500.1 119386445 4582289 complement(880555..880806) 1 NC_008687.1 KEGG: rde:RD1_2835 hypothetical protein; hypothetical protein 880806 4582289 Pden_3737 Paracoccus denitrificans PD1222 hypothetical protein YP_917500.1 880555 R 318586 CDS YP_917501.1 119386446 4582290 complement(880905..881876) 1 NC_008687.1 KEGG: gox:GOX2477 hypothetical protein; Fis family transcriptional regulator 881876 4582290 Pden_3738 Paracoccus denitrificans PD1222 Fis family transcriptional regulator YP_917501.1 880905 R 318586 CDS YP_917502.1 119386447 4582291 complement(881888..882856) 1 NC_008687.1 KEGG: par:Psyc_0982 probable phage-related protein; hypothetical protein 882856 4582291 Pden_3739 Paracoccus denitrificans PD1222 hypothetical protein YP_917502.1 881888 R 318586 CDS YP_917503.1 119386448 4582292 complement(882959..883261) 1 NC_008687.1 hypothetical protein 883261 4582292 Pden_3740 Paracoccus denitrificans PD1222 hypothetical protein YP_917503.1 882959 R 318586 CDS YP_917504.1 119386449 4582293 complement(883261..883566) 1 NC_008687.1 hypothetical protein 883566 4582293 Pden_3741 Paracoccus denitrificans PD1222 hypothetical protein YP_917504.1 883261 R 318586 CDS YP_917505.1 119386450 4582294 complement(883566..883850) 1 NC_008687.1 hypothetical protein 883850 4582294 Pden_3742 Paracoccus denitrificans PD1222 hypothetical protein YP_917505.1 883566 R 318586 CDS YP_917506.1 119386451 4582295 complement(883987..884574) 1 NC_008687.1 hypothetical protein 884574 4582295 Pden_3743 Paracoccus denitrificans PD1222 hypothetical protein YP_917506.1 883987 R 318586 CDS YP_917507.1 119386452 4582296 complement(884562..884804) 1 NC_008687.1 hypothetical protein 884804 4582296 Pden_3744 Paracoccus denitrificans PD1222 hypothetical protein YP_917507.1 884562 R 318586 CDS YP_917508.1 119386453 4582297 complement(884798..885220) 1 NC_008687.1 hypothetical protein 885220 4582297 Pden_3745 Paracoccus denitrificans PD1222 hypothetical protein YP_917508.1 884798 R 318586 CDS YP_917509.1 119386454 4582298 complement(885407..885880) 1 NC_008687.1 XRE family transcriptional regulator 885880 4582298 Pden_3746 Paracoccus denitrificans PD1222 XRE family transcriptional regulator YP_917509.1 885407 R 318586 CDS YP_917510.1 119386455 4582299 886094..886435 1 NC_008687.1 hypothetical protein 886435 4582299 Pden_3747 Paracoccus denitrificans PD1222 hypothetical protein YP_917510.1 886094 D 318586 CDS YP_917511.1 119386456 4582300 886553..886882 1 NC_008687.1 hypothetical protein 886882 4582300 Pden_3748 Paracoccus denitrificans PD1222 hypothetical protein YP_917511.1 886553 D 318586 CDS YP_917512.1 119386457 4582301 886882..887592 1 NC_008687.1 KEGG: rsp:RSP_3792 hypothetical protein; hypothetical protein 887592 4582301 Pden_3749 Paracoccus denitrificans PD1222 hypothetical protein YP_917512.1 886882 D 318586 CDS YP_917513.1 119386458 4582302 887626..888087 1 NC_008687.1 hypothetical protein 888087 4582302 Pden_3750 Paracoccus denitrificans PD1222 hypothetical protein YP_917513.1 887626 D 318586 CDS YP_917514.1 119386459 4582303 888087..888629 1 NC_008687.1 KEGG: sit:TM1040_0792 hypothetical protein; hypothetical protein 888629 4582303 Pden_3751 Paracoccus denitrificans PD1222 hypothetical protein YP_917514.1 888087 D 318586 CDS YP_917515.1 119386460 4582304 888626..888994 1 NC_008687.1 KEGG: xfa:XF1666 hypothetical protein; hypothetical protein 888994 4582304 Pden_3752 Paracoccus denitrificans PD1222 hypothetical protein YP_917515.1 888626 D 318586 CDS YP_917516.1 119386461 4582305 890380..890703 1 NC_008687.1 hypothetical protein 890703 4582305 Pden_3754 Paracoccus denitrificans PD1222 hypothetical protein YP_917516.1 890380 D 318586 CDS YP_917517.1 119386462 4582306 890706..891107 1 NC_008687.1 KEGG: ngo:NGO0494 hypothetical protein, phage associated protein; hypothetical protein 891107 4582306 Pden_3755 Paracoccus denitrificans PD1222 hypothetical protein YP_917517.1 890706 D 318586 CDS YP_917518.1 119386463 4582307 891208..892533 1 NC_008687.1 TIGRFAM: phage terminase, large subunit, PBSX family; KEGG: zmo:ZMO0379 terminase; PBSX family phage terminase large subunit 892533 4582307 Pden_3756 Paracoccus denitrificans PD1222 PBSX family phage terminase large subunit YP_917518.1 891208 D 318586 CDS YP_917519.1 119386464 4582308 892594..892848 1 NC_008687.1 hypothetical protein 892848 4582308 Pden_3757 Paracoccus denitrificans PD1222 hypothetical protein YP_917519.1 892594 D 318586 CDS YP_917520.1 119386465 4582309 892848..896072 1 NC_008687.1 KEGG: ppu:PP_1573 major tail protein; hypothetical protein 896072 4582309 Pden_3758 Paracoccus denitrificans PD1222 hypothetical protein YP_917520.1 892848 D 318586 CDS YP_917521.1 119386466 4582310 896330..898006 1 NC_008687.1 KEGG: ppr:PBPRB0567 head-tail connector protein; head-tail connector protein 898006 4582310 Pden_3759 Paracoccus denitrificans PD1222 head-tail connector protein YP_917521.1 896330 D 318586 CDS YP_917522.1 119386467 4582311 898003..898332 1 NC_008687.1 hypothetical protein 898332 4582311 Pden_3760 Paracoccus denitrificans PD1222 hypothetical protein YP_917522.1 898003 D 318586 CDS YP_917523.1 119386468 4582312 898325..898981 1 NC_008687.1 KEGG: ppr:PBPRB0569 endoprotease; hypothetical protein 898981 4582312 Pden_3761 Paracoccus denitrificans PD1222 hypothetical protein YP_917523.1 898325 D 318586 CDS YP_917524.1 119386469 4582313 898985..900016 1 NC_008687.1 KEGG: ppr:PBPRB0570 hypothetical protein; hypothetical protein 900016 4582313 Pden_3762 Paracoccus denitrificans PD1222 hypothetical protein YP_917524.1 898985 D 318586 CDS YP_917525.1 119386470 4582314 900074..900502 1 NC_008687.1 KEGG: ppr:PBPRB0571 hypothetical protein; hypothetical protein 900502 4582314 Pden_3763 Paracoccus denitrificans PD1222 hypothetical protein YP_917525.1 900074 D 318586 CDS YP_917526.1 119386471 4582315 900495..900818 1 NC_008687.1 hypothetical protein 900818 4582315 Pden_3764 Paracoccus denitrificans PD1222 hypothetical protein YP_917526.1 900495 D 318586 CDS YP_917527.1 119386472 4582316 900876..901178 1 NC_008687.1 KEGG: pol:Bpro_3742 hypothetical protein; hypothetical protein 901178 4582316 Pden_3765 Paracoccus denitrificans PD1222 hypothetical protein YP_917527.1 900876 D 318586 CDS YP_917528.1 119386473 4582317 901229..901837 1 NC_008687.1 KEGG: dde:Dde_2546 hypothetical protein; hypothetical protein 901837 4582317 Pden_3766 Paracoccus denitrificans PD1222 hypothetical protein YP_917528.1 901229 D 318586 CDS YP_917529.1 119386474 4582318 901837..903876 1 NC_008687.1 KEGG: dvu:DVU1714 hypothetical protein; hypothetical protein 903876 4582318 Pden_3767 Paracoccus denitrificans PD1222 hypothetical protein YP_917529.1 901837 D 318586 CDS YP_917530.1 119386475 4582319 903878..904345 1 NC_008687.1 KEGG: ppr:PBPRB_2036 hypothetical protein; hypothetical protein 904345 4582319 Pden_3768 Paracoccus denitrificans PD1222 hypothetical protein YP_917530.1 903878 D 318586 CDS YP_917531.1 119386476 4582320 904345..904896 1 NC_008687.1 KEGG: sgl:SG1192 hypothetical protein; hypothetical protein 904896 4582320 Pden_3769 Paracoccus denitrificans PD1222 hypothetical protein YP_917531.1 904345 D 318586 CDS YP_917532.1 119386477 4582321 904896..907511 1 NC_008687.1 KEGG: mlo:mlr2365 hypothetical protein; hypothetical protein 907511 4582321 Pden_3770 Paracoccus denitrificans PD1222 hypothetical protein YP_917532.1 904896 D 318586 CDS YP_917533.1 119386478 4582322 907529..910828 1 NC_008687.1 KEGG: mag:amb3639 hypothetical protein; hypothetical protein 910828 4582322 Pden_3771 Paracoccus denitrificans PD1222 hypothetical protein YP_917533.1 907529 D 318586 CDS YP_917534.1 119386479 4582323 complement(910818..911285) 1 NC_008687.1 hypothetical protein 911285 4582323 Pden_3772 Paracoccus denitrificans PD1222 hypothetical protein YP_917534.1 910818 R 318586 CDS YP_917535.1 119386480 4582324 complement(911496..911693) 1 NC_008687.1 KEGG: jan:Jann_1865 hypothetical protein; hypothetical protein 911693 4582324 Pden_3773 Paracoccus denitrificans PD1222 hypothetical protein YP_917535.1 911496 R 318586 CDS YP_917536.1 119386481 4582325 complement(911697..911996) 1 NC_008687.1 PFAM: Arc domain protein DNA binding domain protein; KEGG: ypn:YPN_1596 phage regulatory protein; Arc domain-containing protein 911996 4582325 Pden_3774 Paracoccus denitrificans PD1222 Arc domain-containing protein YP_917536.1 911697 R 318586 CDS YP_917537.1 119386482 4582326 912308..913123 1 NC_008687.1 KEGG: nha:Nham_2408 uncharacterized phage-encoded protein-like; hypothetical protein 913123 4582326 Pden_3775 Paracoccus denitrificans PD1222 hypothetical protein YP_917537.1 912308 D 318586 CDS YP_917538.1 119386483 4582327 913120..913377 1 NC_008687.1 hypothetical protein 913377 4582327 Pden_3776 Paracoccus denitrificans PD1222 hypothetical protein YP_917538.1 913120 D 318586 CDS YP_917539.1 119386484 4582328 913374..913730 1 NC_008687.1 hypothetical protein 913730 4582328 Pden_3777 Paracoccus denitrificans PD1222 hypothetical protein YP_917539.1 913374 D 318586 CDS YP_917540.1 119386485 4582329 914005..916314 1 NC_008687.1 PFAM: metallophosphoesterase; metallophosphoesterase 916314 4582329 Pden_3778 Paracoccus denitrificans PD1222 metallophosphoesterase YP_917540.1 914005 D 318586 CDS YP_917541.1 119386486 4582330 916324..916611 1 NC_008687.1 hypothetical protein 916611 4582330 Pden_3779 Paracoccus denitrificans PD1222 hypothetical protein YP_917541.1 916324 D 318586 CDS YP_917542.1 119386487 4582331 916814..917608 1 NC_008687.1 PFAM: Peptidoglycan-binding domain 1 protein; KEGG: sme:SMb20518 hypothetical protein; peptidoglycan binding domain-containing protein 917608 4582331 Pden_3780 Paracoccus denitrificans PD1222 peptidoglycan binding domain-containing protein YP_917542.1 916814 D 318586 CDS YP_917543.1 119386488 4582332 917805..918059 1 NC_008687.1 hypothetical protein 918059 4582332 Pden_3781 Paracoccus denitrificans PD1222 hypothetical protein YP_917543.1 917805 D 318586 CDS YP_917544.1 119386489 4582333 complement(918515..918847) 1 NC_008687.1 hypothetical protein 918847 4582333 Pden_3782 Paracoccus denitrificans PD1222 hypothetical protein YP_917544.1 918515 R 318586 CDS YP_917545.1 119386490 4582334 complement(919205..919489) 1 NC_008687.1 hypothetical protein 919489 4582334 Pden_3783 Paracoccus denitrificans PD1222 hypothetical protein YP_917545.1 919205 R 318586 CDS YP_917546.1 119386491 4582335 920022..920606 1 NC_008687.1 Catalyzes the formation of (d)CDP from ATP and (d)CMP; cytidylate kinase 920606 cmk 4582335 cmk Paracoccus denitrificans PD1222 cytidylate kinase YP_917546.1 920022 D 318586 CDS YP_917547.1 119386492 4582336 920603..921682 1 NC_008687.1 PFAM: dihydroorotate dehydrogenase; 2-nitropropane dioxygenase, NPD; KEGG: reu:Reut_B5128 2-nitropropane dioxygenase, NPD; 2-nitropropane dioxygenase 921682 4582336 Pden_3785 Paracoccus denitrificans PD1222 2-nitropropane dioxygenase YP_917547.1 920603 D 318586 CDS YP_917548.1 119386493 4582337 921809..923524 1 NC_008687.1 in Escherichia coli this protein is involved in binding to the leader sequence of mRNAs and is itself bound to the 30S subunit; autoregulates expression via a C-terminal domain; in most gram negative organisms this protein is composed of 6 repeats of the S1 domain while in gram positive there are 4 repeats; the S1 nucleic acid-binding domain is found associated with other proteins; 30S ribosomal protein S1 923524 rpsA 4582337 rpsA Paracoccus denitrificans PD1222 30S ribosomal protein S1 YP_917548.1 921809 D 318586 CDS YP_917549.1 119386494 4582338 923722..924009 1 NC_008687.1 This protein is one of the two subunits of integration host factor, a specific DNA-binding protein that functions in genetic recombination as well as in transcriptional and translational control; integration host factor subunit beta 924009 ihfB 4582338 ihfB Paracoccus denitrificans PD1222 integration host factor subunit beta YP_917549.1 923722 D 318586 CDS YP_917550.1 119386495 4582339 924048..924449 1 NC_008687.1 KEGG: sil:SPO0805 hypothetical protein; hypothetical protein 924449 4582339 Pden_3788 Paracoccus denitrificans PD1222 hypothetical protein YP_917550.1 924048 D 318586 CDS YP_917551.1 119386496 4582340 924454..925101 1 NC_008687.1 PFAM: N-(5'phosphoribosyl)anthranilate isomerase (PRAI); KEGG: sil:SPO0806 N-(5'-phosphoribosyl)anthranilate isomerase; phosphoribosylanthranilate isomerase 925101 4582340 Pden_3789 Paracoccus denitrificans PD1222 phosphoribosylanthranilate isomerase YP_917551.1 924454 D 318586 CDS YP_917552.1 119386497 4582341 925113..925565 1 NC_008687.1 PFAM: GCN5-related N-acetyltransferase; KEGG: rsp:RSP_3586 aromatic pathway regulator; N-acetyltransferase GCN5 925565 4582341 Pden_3790 Paracoccus denitrificans PD1222 N-acetyltransferase GCN5 YP_917552.1 925113 D 318586 CDS YP_917553.1 119386498 4582342 925618..926850 1 NC_008687.1 catalyzes the formation of L-tryptophan from L-serine and 1-(indol-3-yl)glycerol 3-phosphate; tryptophan synthase subunit beta 926850 4582342 Pden_3791 Paracoccus denitrificans PD1222 tryptophan synthase subunit beta YP_917553.1 925618 D 318586 CDS YP_917554.1 119386499 4582343 complement(926867..927484) 1 NC_008687.1 PFAM: DSBA oxidoreductase; KEGG: sil:SPOA0362 27kDa outer membrane protein; DSBA oxidoreductase 927484 4582343 Pden_3792 Paracoccus denitrificans PD1222 DSBA oxidoreductase YP_917554.1 926867 R 318586 CDS YP_917555.1 119386500 4582344 927552..928208 1 NC_008687.1 PFAM: 2OG-Fe(II) oxygenase; KEGG: bmb:BruAb2_0689 AlkB, alkylated DNA repair protein; 2OG-Fe(II) oxygenase 928208 4582344 Pden_3793 Paracoccus denitrificans PD1222 2OG-Fe(II) oxygenase YP_917555.1 927552 D 318586 CDS YP_917556.1 119386501 4582345 complement(928302..929129) 1 NC_008687.1 PFAM: protein of unknown function DUF861, cupin_3; Cupin 2, conserved barrel domain protein; KEGG: aor:AO090026000040 uncharacterized protein, possibly involved in glyoxylate utilization Pfam: Cupin_3 Cupin_2 AraC_binding Cupin_1; hypothetical protein 929129 4582345 Pden_3794 Paracoccus denitrificans PD1222 hypothetical protein YP_917556.1 928302 R 318586 CDS YP_917557.1 119386502 4582346 complement(929216..930628) 1 NC_008687.1 PFAM: polysaccharide deacetylase; KEGG: sil:SPO0872 polysaccharide deacetylase family protein; polysaccharide deacetylase 930628 4582346 Pden_3795 Paracoccus denitrificans PD1222 polysaccharide deacetylase YP_917557.1 929216 R 318586 CDS YP_917558.1 119386503 4582347 930848..932212 1 NC_008687.1 PFAM: Xanthine/uracil/vitamin C permease; KEGG: bms:BRA0661 uracil-xanthine permease; xanthine/uracil/vitamin C permease 932212 4582347 Pden_3796 Paracoccus denitrificans PD1222 xanthine/uracil/vitamin C permease YP_917558.1 930848 D 318586 CDS YP_917559.1 119386504 4582348 complement(932343..933260) 1 NC_008687.1 PFAM: helix-turn-helix protein RpiR; sugar isomerase (SIS); KEGG: sme:SMb20276 transcriptional regulator protein; RpiR family transcriptional regulator 933260 4582348 Pden_3797 Paracoccus denitrificans PD1222 RpiR family transcriptional regulator YP_917559.1 932343 R 318586 CDS YP_917560.1 119386505 4582349 933412..934737 1 NC_008687.1 PFAM: aminotransferase class-III; KEGG: sme:SMb20277 hypothetical protein; hypothetical protein 934737 4582349 Pden_3798 Paracoccus denitrificans PD1222 hypothetical protein YP_917560.1 933412 D 318586 CDS YP_917561.1 119386506 4582350 934745..936244 1 NC_008687.1 PFAM: MlrC domain protein; KEGG: rpd:RPD_1322 MlrC-like; MlrC domain-containing protein 936244 4582350 Pden_3799 Paracoccus denitrificans PD1222 MlrC domain-containing protein YP_917561.1 934745 D 318586 CDS YP_917562.1 119386507 4582351 936241..937833 1 NC_008687.1 PFAM: extracellular solute-binding protein, family 5; KEGG: rpc:RPC_1200 extracellular solute-binding protein, family 5; extracellular solute-binding protein 937833 4582351 Pden_3800 Paracoccus denitrificans PD1222 extracellular solute-binding protein YP_917562.1 936241 D 318586 CDS YP_917563.1 119386508 4582352 937889..938833 1 NC_008687.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: rpd:RPD_4024 binding-protein-dependent transport systems inner membrane component; binding-protein-dependent transport system inner membrane protein 938833 4582352 Pden_3801 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_917563.1 937889 D 318586 CDS YP_917564.1 119386509 4582353 938830..939693 1 NC_008687.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: rpc:RPC_1196 binding-protein-dependent transport systems inner membrane component; binding-protein-dependent transport systems inner membrane component 939693 4582353 Pden_3802 Paracoccus denitrificans PD1222 binding-protein-dependent transport systems inner membrane component YP_917564.1 938830 D 318586 CDS YP_917565.1 119386510 4582354 939693..941363 1 NC_008687.1 PFAM: ABC transporter related; Oligopeptide/dipeptide ABC transporter, C-terminal domain protein; SMART: AAA ATPase; KEGG: bja:blr5600 ABC transporter ATP-binding protein; ABC transporter 941363 4582354 Pden_3803 Paracoccus denitrificans PD1222 ABC transporter YP_917565.1 939693 D 318586 CDS YP_917566.1 119386511 4582355 941360..942220 1 NC_008687.1 PFAM: Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase; KEGG: bxe:Bxe_C1311 carbon-nitrogen hydrolase; nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase 942220 4582355 Pden_3804 Paracoccus denitrificans PD1222 nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase YP_917566.1 941360 D 318586 CDS YP_917567.1 119386512 4582356 942233..942772 1 NC_008687.1 PFAM: Carboxymuconolactone decarboxylase; KEGG: jan:Jann_2958 carboxymuconolactone decarboxylase; carboxymuconolactone decarboxylase 942772 4582356 Pden_3805 Paracoccus denitrificans PD1222 carboxymuconolactone decarboxylase YP_917567.1 942233 D 318586 CDS YP_917568.1 119386513 4582357 complement(942769..943281) 1 NC_008687.1 TIGRFAM: single-strand binding protein; PFAM: single-strand binding protein/Primosomal replication protein n; KEGG: sil:SPO1637 single-strand binding protein; single-strand binding protein 943281 4582357 Pden_3806 Paracoccus denitrificans PD1222 single-strand binding protein YP_917568.1 942769 R 318586 CDS YP_917569.1 119386514 4582358 943514..944161 1 NC_008687.1 PFAM: Lytic transglycosylase, catalytic; KEGG: rsp:RSP_1794 lytic transglycosylase; lytic transglycosylase, catalytic 944161 4582358 Pden_3807 Paracoccus denitrificans PD1222 lytic transglycosylase, catalytic YP_917569.1 943514 D 318586 CDS YP_917570.1 119386515 4582359 complement(944224..944796) 1 NC_008687.1 KEGG: rsp:RSP_2847 hypothetical protein; hypothetical protein 944796 4582359 Pden_3808 Paracoccus denitrificans PD1222 hypothetical protein YP_917570.1 944224 R 318586 CDS YP_917571.1 119386516 4582360 complement(944867..945787) 1 NC_008687.1 catalyzes the formation of porphobilinogen from 5-aminolevulinate; delta-aminolevulinic acid dehydratase 945787 4582360 Pden_3809 Paracoccus denitrificans PD1222 delta-aminolevulinic acid dehydratase YP_917571.1 944867 R 318586 CDS YP_917572.1 119386517 4582361 945864..946583 1 NC_008687.1 KEGG: rde:RD1_2747 hypothetical protein; hypothetical protein 946583 4582361 Pden_3810 Paracoccus denitrificans PD1222 hypothetical protein YP_917572.1 945864 D 318586 CDS YP_917573.1 119386518 4582362 946626..950090 1 NC_008687.1 KEGG: rsp:RSP_2850 transcription-repair coupling factor (helicase); TIGRFAM: transcription-repair coupling factor; PFAM: helicase domain protein; transcription factor CarD; TRCF domain protein; type III restriction enzyme, res subunit; DEAD/DEAH box helicase domain protein; SMART: DEAD-like helicases-like; transcription-repair coupling factor 950090 4582362 Pden_3811 Paracoccus denitrificans PD1222 transcription-repair coupling factor YP_917573.1 946626 D 318586 CDS YP_917574.1 119386519 4582363 complement(950384..952702) 1 NC_008687.1 KEGG: rsp:RSP_2293 chaperonin ClpA/B; TIGRFAM: ATP-dependent Clp protease, ATP-binding subunit clpA; PFAM: AAA ATPase, central domain protein; Clp N terminal domain protein; ATPase associated with various cellular activities, AAA_5; ATPase AAA-2 domain protein; SMART: AAA ATPase; ATP-dependent Clp protease ATP-binding protein ClpA 952702 4582363 Pden_3812 Paracoccus denitrificans PD1222 ATP-dependent Clp protease ATP-binding protein ClpA YP_917574.1 950384 R 318586 CDS YP_917575.1 119386520 4582364 complement(952964..953710) 1 NC_008687.1 PFAM: beta-lactamase domain protein; KEGG: sil:SPO3168 hydroxyacylglutathione hydrolase; hydroxyacylglutathione hydrolase 953710 4582364 Pden_3813 Paracoccus denitrificans PD1222 hydroxyacylglutathione hydrolase YP_917575.1 952964 R 318586 CDS YP_917576.1 119386521 4582365 953762..954544 1 NC_008687.1 PFAM: Methyltransferase type 11; KEGG: rsp:RSP_2295 hypothetical protein; methyltransferase type 11 954544 4582365 Pden_3814 Paracoccus denitrificans PD1222 methyltransferase type 11 YP_917576.1 953762 D 318586 CDS YP_917577.1 119386522 4582366 954784..955419 1 NC_008687.1 TIGRFAM: ATP synthase F1, delta subunit; PFAM: H+-transporting two-sector ATPase, delta (OSCP) subunit; KEGG: rde:RD1_3536 ATP synthase F1, delta subunit; ATP synthase F1 subunit delta 955419 4582366 Pden_3815 Paracoccus denitrificans PD1222 ATP synthase F1 subunit delta YP_917577.1 954784 D 318586 CDS YP_917578.1 119386523 4582367 955419..956954 1 NC_008687.1 produces ATP from ADP in the presence of a proton gradient across the membrane; the alpha chain is a catalytic subunit; F0F1 ATP synthase subunit alpha 956954 4582367 Pden_3816 Paracoccus denitrificans PD1222 F0F1 ATP synthase subunit alpha YP_917578.1 955419 D 318586 CDS YP_917579.1 119386524 4582368 956967..957839 1 NC_008687.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is a regulatory subunit; F0F1 ATP synthase subunit gamma 957839 4582368 Pden_3817 Paracoccus denitrificans PD1222 F0F1 ATP synthase subunit gamma YP_917579.1 956967 D 318586 CDS YP_917580.1 119386525 4582369 957857..959281 1 NC_008687.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. The beta chain is a regulatory subunit; F0F1 ATP synthase subunit beta 959281 4582369 Pden_3818 Paracoccus denitrificans PD1222 F0F1 ATP synthase subunit beta YP_917580.1 957857 D 318586 CDS YP_917581.1 119386526 4582370 959291..959737 1 NC_008687.1 TIGRFAM: ATP synthase F1, epsilon subunit; PFAM: H+-transporting two-sector ATPase, delta/epsilon subunit; KEGG: sit:TM1040_2085 ATP synthase F1, epsilon subunit; ATP synthase F1 subunit epsilon 959737 4582370 Pden_3819 Paracoccus denitrificans PD1222 ATP synthase F1 subunit epsilon YP_917581.1 959291 D 318586 CDS YP_917582.1 119386527 4582371 959832..960182 1 NC_008687.1 KEGG: sil:SPO3160 hypothetical protein; hypothetical protein 960182 4582371 Pden_3820 Paracoccus denitrificans PD1222 hypothetical protein YP_917582.1 959832 D 318586 CDS YP_917583.1 119386528 4582372 complement(960188..960958) 1 NC_008687.1 PFAM: alpha/beta hydrolase fold; KEGG: sil:SPO3157 hydrolase, alpha/beta fold family; alpha/beta hydrolase 960958 4582372 Pden_3821 Paracoccus denitrificans PD1222 alpha/beta hydrolase YP_917583.1 960188 R 318586 CDS YP_917584.1 119386529 4582373 complement(960955..961554) 1 NC_008687.1 PFAM: DSBA oxidoreductase; KEGG: sil:SPO3158 2-hydroxychromene-2-carboxylate isomerase; DSBA oxidoreductase 961554 4582373 Pden_3822 Paracoccus denitrificans PD1222 DSBA oxidoreductase YP_917584.1 960955 R 318586 CDS YP_917585.1 119386530 4582374 961636..962655 1 NC_008687.1 KEGG: rsp:RSP_2301 phosphoribosyl pyrophosphate synthetase; TIGRFAM: ribose-phosphate pyrophosphokinase; PFAM: phosphoribosyltransferase; ribose-phosphate pyrophosphokinase 962655 4582374 Pden_3823 Paracoccus denitrificans PD1222 ribose-phosphate pyrophosphokinase YP_917585.1 961636 D 318586 CDS YP_917586.1 119386531 4582375 complement(962723..963175) 1 NC_008687.1 PFAM: CoA-binding domain protein; KEGG: rsp:RSP_2240 hypothetical protein; CoA-binding domain-containing protein 963175 4582375 Pden_3824 Paracoccus denitrificans PD1222 CoA-binding domain-containing protein YP_917586.1 962723 R 318586 CDS YP_917587.1 119386532 4582376 complement(963359..963772) 1 NC_008687.1 KEGG: sit:TM1040_2051 hypothetical protein; hypothetical protein 963772 4582376 Pden_3825 Paracoccus denitrificans PD1222 hypothetical protein YP_917587.1 963359 R 318586 CDS YP_917588.1 119386533 4582377 complement(963873..964670) 1 NC_008687.1 TIGRFAM: RNA methyltransferase, TrmH family, group 3; PFAM: tRNA/rRNA methyltransferase (SpoU); RNA 2-O ribose methyltransferase, substrate binding; KEGG: rsp:RSP_2239 tRNA/rRNA metyltransferase; RNA methyltransferase 964670 4582377 Pden_3826 Paracoccus denitrificans PD1222 RNA methyltransferase YP_917588.1 963873 R 318586 CDS YP_917589.1 119386534 4582378 complement(964815..965072) 1 NC_008687.1 hypothetical protein 965072 4582378 Pden_3827 Paracoccus denitrificans PD1222 hypothetical protein YP_917589.1 964815 R 318586 CDS YP_917590.1 119386535 4582379 965152..966009 1 NC_008687.1 hypothetical protein 966009 4582379 Pden_3828 Paracoccus denitrificans PD1222 hypothetical protein YP_917590.1 965152 D 318586 CDS YP_917591.1 119386536 4582380 966002..967363 1 NC_008687.1 hypothetical protein 967363 4582380 Pden_3829 Paracoccus denitrificans PD1222 hypothetical protein YP_917591.1 966002 D 318586 CDS YP_917592.1 119386537 4582381 967468..967713 1 NC_008687.1 TIGRFAM: addiction module antidote protein, CC2985 family; PFAM: protein of unknown function UPF0156; KEGG: xfa:XF2071 conserved hypothetical protein; CopG/Arc/MetJ family transcriptional regulator 967713 4582381 Pden_3830 Paracoccus denitrificans PD1222 CopG/Arc/MetJ family transcriptional regulator YP_917592.1 967468 D 318586 CDS YP_917593.1 119386538 4582382 967710..967997 1 NC_008687.1 PFAM: plasmid stabilization system; KEGG: sme:SMb20063 hypothetical protein; plasmid stabilization system protein 967997 4582382 Pden_3831 Paracoccus denitrificans PD1222 plasmid stabilization system protein YP_917593.1 967710 D 318586 CDS YP_917594.1 119386539 4582383 968083..968589 1 NC_008687.1 hypothetical protein 968589 4582383 Pden_3832 Paracoccus denitrificans PD1222 hypothetical protein YP_917594.1 968083 D 318586 CDS YP_917595.1 119386540 4582384 complement(968814..969986) 1 NC_008687.1 KEGG: mlo:mlr9349 hypothetical protein; hypothetical protein 969986 4582384 Pden_3833 Paracoccus denitrificans PD1222 hypothetical protein YP_917595.1 968814 R 318586 CDS YP_917596.1 119386541 4582385 970254..970937 1 NC_008687.1 hypothetical protein 970937 4582385 Pden_3834 Paracoccus denitrificans PD1222 hypothetical protein YP_917596.1 970254 D 318586 CDS YP_917597.1 119386542 4582386 complement(970940..971449) 1 NC_008687.1 hypothetical protein 971449 4582386 Pden_3835 Paracoccus denitrificans PD1222 hypothetical protein YP_917597.1 970940 R 318586 CDS YP_917598.1 119386543 4582387 complement(971625..971948) 1 NC_008687.1 hypothetical protein 971948 4582387 Pden_3836 Paracoccus denitrificans PD1222 hypothetical protein YP_917598.1 971625 R 318586 CDS YP_917599.1 119386544 4582388 972058..972303 1 NC_008687.1 PFAM: helix-turn-helix domain protein; KEGG: nha:Nham_0800 transcriptional regulator, XRE family; helix-turn-helix domain-containing protein 972303 4582388 Pden_3837 Paracoccus denitrificans PD1222 helix-turn-helix domain-containing protein YP_917599.1 972058 D 318586 CDS YP_917600.1 119386545 4582389 972636..973571 1 NC_008687.1 PFAM: DNA methylase N-4/N-6 domain protein; KEGG: sal:Sala_2300 DNA methylase N-4/N-6; DNA methylase N-4/N-6 domain-containing protein 973571 4582389 Pden_3838 Paracoccus denitrificans PD1222 DNA methylase N-4/N-6 domain-containing protein YP_917600.1 972636 D 318586 CDS YP_917601.1 119386546 4582390 973574..974044 1 NC_008687.1 hypothetical protein 974044 4582390 Pden_3839 Paracoccus denitrificans PD1222 hypothetical protein YP_917601.1 973574 D 318586 CDS YP_917602.1 119386547 4582391 974059..975390 1 NC_008687.1 hypothetical protein 975390 4582391 Pden_3840 Paracoccus denitrificans PD1222 hypothetical protein YP_917602.1 974059 D 318586 CDS YP_917603.1 119386548 4582392 975397..977307 1 NC_008687.1 PFAM: helicase domain protein; SMART: DEAD-like helicases-like; KEGG: ppe:PEPE_0535 superfamily II DNA/RNA helicase, SNF2 family; helicase 977307 4582392 Pden_3841 Paracoccus denitrificans PD1222 helicase YP_917603.1 975397 D 318586 CDS YP_917604.1 119386549 4582393 977304..978140 1 NC_008687.1 hypothetical protein 978140 4582393 Pden_3842 Paracoccus denitrificans PD1222 hypothetical protein YP_917604.1 977304 D 318586 CDS YP_917605.1 119386550 4582394 978209..978457 1 NC_008687.1 hypothetical protein 978457 4582394 Pden_3843 Paracoccus denitrificans PD1222 hypothetical protein YP_917605.1 978209 D 318586 CDS YP_917606.1 119386551 4582395 complement(978675..979703) 1 NC_008687.1 PFAM: transposase, IS111A/IS1328/IS1533; transposase IS116/IS110/IS902 family protein; KEGG: nha:Nham_3955 transposase IS116/IS110/IS902; transposase IS116/IS110/IS902 family protein 979703 4582395 Pden_3844 Paracoccus denitrificans PD1222 transposase IS116/IS110/IS902 family protein YP_917606.1 978675 R 318586 CDS YP_917607.1 119386552 4582396 979812..980135 1 NC_008687.1 PFAM: transposase IS3/IS911 family protein; KEGG: nwi:Nwi_2119 transposase IS3/IS911; transposase IS3/IS911 family protein 980135 4582396 Pden_3845 Paracoccus denitrificans PD1222 transposase IS3/IS911 family protein YP_917607.1 979812 D 318586 CDS YP_917608.1 119386553 4582397 980135..981040 1 NC_008687.1 PFAM: Integrase, catalytic region; KEGG: nwi:Nwi_2120 integrase, catalytic region; integrase catalytic subunit 981040 4582397 Pden_3846 Paracoccus denitrificans PD1222 integrase catalytic subunit YP_917608.1 980135 D 318586 CDS YP_917609.1 119386554 4582398 complement(981103..981894) 1 NC_008687.1 PFAM: helix-turn-helix domain protein; XRE family transcriptional regulator 981894 4582398 Pden_3847 Paracoccus denitrificans PD1222 XRE family transcriptional regulator YP_917609.1 981103 R 318586 CDS YP_917610.1 119386555 4582399 981969..982262 1 NC_008687.1 hypothetical protein 982262 4582399 Pden_3848 Paracoccus denitrificans PD1222 hypothetical protein YP_917610.1 981969 D 318586 CDS YP_917611.1 119386556 4582400 982462..983535 1 NC_008687.1 PFAM: phage integrase family protein; KEGG: rsp:RSP_1968 possible integrase/recombinase; phage integrase family protein 983535 4582400 Pden_3849 Paracoccus denitrificans PD1222 phage integrase family protein YP_917611.1 982462 D 318586 CDS YP_917612.1 119386557 4582401 983791..984180 1 NC_008687.1 hypothetical protein 984180 4582401 Pden_3850 Paracoccus denitrificans PD1222 hypothetical protein YP_917612.1 983791 D 318586 CDS YP_917613.1 119386558 4582402 complement(984185..986230) 1 NC_008687.1 hypothetical protein 986230 4582402 Pden_3851 Paracoccus denitrificans PD1222 hypothetical protein YP_917613.1 984185 R 318586 CDS YP_917614.1 119386559 4582403 complement(986350..987189) 1 NC_008687.1 hypothetical protein 987189 4582403 Pden_3852 Paracoccus denitrificans PD1222 hypothetical protein YP_917614.1 986350 R 318586 CDS YP_917615.1 119386560 4582404 complement(987193..987768) 1 NC_008687.1 hypothetical protein 987768 4582404 Pden_3853 Paracoccus denitrificans PD1222 hypothetical protein YP_917615.1 987193 R 318586 CDS YP_917616.1 119386561 4582405 988104..988364 1 NC_008687.1 hypothetical protein 988364 4582405 Pden_3854 Paracoccus denitrificans PD1222 hypothetical protein YP_917616.1 988104 D 318586 CDS YP_917617.1 119386562 4582406 complement(988330..988797) 1 NC_008687.1 hypothetical protein 988797 4582406 Pden_3855 Paracoccus denitrificans PD1222 hypothetical protein YP_917617.1 988330 R 318586 CDS YP_917618.1 119386563 4582407 988892..989887 1 NC_008687.1 PFAM: Substrate-binding region of ABC-type glycine betaine transport system; KEGG: rsp:RSP_3059 ABC proline/glycine betaine transporter, periplasmic substrate-binding protein; substrate-binding region of ABC-type glycine betaine transport system 989887 4582407 Pden_3856 Paracoccus denitrificans PD1222 substrate-binding region of ABC-type glycine betaine transport system YP_917618.1 988892 D 318586 CDS YP_917619.1 119386564 4582408 989964..990845 1 NC_008687.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: sme:SMc02379 permease; binding-protein-dependent transport system inner membrane protein 990845 4582408 Pden_3857 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_917619.1 989964 D 318586 CDS YP_917620.1 119386565 4582409 990842..991888 1 NC_008687.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rsp:RSP_3057 ABC proline/glycine betaine transporter, ATPase subunit; ABC transporter 991888 4582409 Pden_3858 Paracoccus denitrificans PD1222 ABC transporter YP_917620.1 990842 D 318586 CDS YP_917621.1 119386566 4582410 991961..992359 1 NC_008687.1 hypothetical protein 992359 4582410 Pden_3859 Paracoccus denitrificans PD1222 hypothetical protein YP_917621.1 991961 D 318586 CDS YP_917622.1 119386567 4582411 992416..993522 1 NC_008687.1 PFAM: NUDIX hydrolase; KEGG: rsp:RSP_2146 tellurite resistance protein; NUDIX hydrolase 993522 4582411 Pden_3860 Paracoccus denitrificans PD1222 NUDIX hydrolase YP_917622.1 992416 D 318586 CDS YP_917623.1 119386568 4582412 993557..994588 1 NC_008687.1 CysK; forms a complex with serine acetyltransferase CysE; functions in cysteine biosynthesis; cysteine synthase A 994588 4582412 Pden_3861 Paracoccus denitrificans PD1222 cysteine synthase A YP_917623.1 993557 D 318586 CDS YP_917624.1 119386569 4582413 994597..997089 1 NC_008687.1 PFAM: MscS Mechanosensitive ion channel; KEGG: rsp:RSP_2148 small conductance mechanosensitive ion channel; MscS mechanosensitive ion channel 997089 4582413 Pden_3862 Paracoccus denitrificans PD1222 MscS mechanosensitive ion channel YP_917624.1 994597 D 318586 CDS YP_917625.1 119386570 4582414 997086..997472 1 NC_008687.1 KEGG: atc:AGR_C_4132 hypothetical protein; hypothetical protein 997472 4582414 Pden_3863 Paracoccus denitrificans PD1222 hypothetical protein YP_917625.1 997086 D 318586 CDS YP_917626.1 119386571 4582415 complement(997469..998539) 1 NC_008687.1 PFAM: protein of unknown function UPF0118; KEGG: rsp:RSP_3345 hypothetical protein; hypothetical protein 998539 4582415 Pden_3864 Paracoccus denitrificans PD1222 hypothetical protein YP_917626.1 997469 R 318586 CDS YP_917627.1 119386572 4582416 complement(998605..1001346) 1 NC_008687.1 negatively supercoils closed circular double-stranded DNA; DNA gyrase subunit A 1001346 4582416 Pden_3865 Paracoccus denitrificans PD1222 DNA gyrase subunit A YP_917627.1 998605 R 318586 CDS YP_917628.1 119386573 4582417 complement(1001441..1001935) 1 NC_008687.1 PFAM: Disulphide bond formation protein DsbB; KEGG: sil:SPO2117 disulfide bond formation protein, DsbB family; disulfide bond formation protein DsbB 1001935 4582417 Pden_3866 Paracoccus denitrificans PD1222 disulfide bond formation protein DsbB YP_917628.1 1001441 R 318586 CDS YP_917629.1 119386574 4582418 complement(1001988..1002584) 1 NC_008687.1 KEGG: rpd:RPD_2135 DedA family protein; DedA family protein 1002584 4582418 Pden_3867 Paracoccus denitrificans PD1222 DedA family protein YP_917629.1 1001988 R 318586 CDS YP_917630.1 119386575 4582419 1002716..1003567 1 NC_008687.1 PFAM: protein of unknown function, zinc metallopeptidase KEGG: sil:SPO3546 zinc metallopeptidase; zinc metallopeptidase 1003567 4582419 Pden_3868 Paracoccus denitrificans PD1222 zinc metallopeptidase YP_917630.1 1002716 D 318586 CDS YP_917631.1 119386576 4582420 complement(1003738..1003926) 1 NC_008687.1 hypothetical protein 1003926 4582420 Pden_3869 Paracoccus denitrificans PD1222 hypothetical protein YP_917631.1 1003738 R 318586 CDS YP_917632.1 119386577 4582421 1003986..1004438 1 NC_008687.1 PFAM: cyclase/dehydrase; KEGG: rsp:RSP_2787 hypothetical protein; cyclase/dehydrase 1004438 4582421 Pden_3870 Paracoccus denitrificans PD1222 cyclase/dehydrase YP_917632.1 1003986 D 318586 CDS YP_917633.1 119386578 4582422 complement(1004426..1005031) 1 NC_008687.1 KEGG: jan:Jann_1985 hypothetical protein; hypothetical protein 1005031 4582422 Pden_3871 Paracoccus denitrificans PD1222 hypothetical protein YP_917633.1 1004426 R 318586 CDS YP_917634.1 119386579 4582423 complement(1005125..1006486) 1 NC_008687.1 converts 2-oxoglutarate to glutamate; in Escherichia coli this enzyme plays a role in glutamate synthesis when the cell is under energy restriction; uses NADPH; forms a homohexamer; glutamate dehydrogenase 1006486 4582423 Pden_3872 Paracoccus denitrificans PD1222 glutamate dehydrogenase YP_917634.1 1005125 R 318586 CDS YP_917635.1 119386580 4582424 complement(1006744..1008033) 1 NC_008687.1 TIGRFAM: crotonyl-CoA reductase; PFAM: Alcohol dehydrogenase, zinc-binding domain protein; Alcohol dehydrogenase GroES domain protein; KEGG: rsp:RSP_0960 alcohol dehydrogenase; crotonyl-CoA reductase 1008033 4582424 Pden_3873 Paracoccus denitrificans PD1222 crotonyl-CoA reductase YP_917635.1 1006744 R 318586 CDS YP_917636.1 119386581 4582425 complement(1008225..1009139) 1 NC_008687.1 KEGG: fal:FRAAL4242 hypothetical protein; hypothetical protein 1009139 4582425 Pden_3874 Paracoccus denitrificans PD1222 hypothetical protein YP_917636.1 1008225 R 318586 CDS YP_917637.1 119386582 4582426 1009234..1011300 1 NC_008687.1 KEGG: sil:SPO0368 methylmalonyl-CoA mutase; TIGRFAM: methylmalonyl-CoA mutase, large subunit; PFAM: methylmalonyl-CoA mutase; cobalamin B12-binding domain protein; methylmalonyl-CoA mutase large subunit 1011300 4582426 Pden_3875 Paracoccus denitrificans PD1222 methylmalonyl-CoA mutase large subunit YP_917637.1 1009234 D 318586 CDS YP_917638.1 119386583 4582427 complement(1011399..1012304) 1 NC_008687.1 PFAM: protein of unknown function DUF6, transmembrane; KEGG: sil:SPO3239 integral membrane protein; hypothetical protein 1012304 4582427 Pden_3876 Paracoccus denitrificans PD1222 hypothetical protein YP_917638.1 1011399 R 318586 CDS YP_917639.1 119386584 4582428 complement(1012304..1012906) 1 NC_008687.1 TIGRFAM: alkylhydroperoxidase like protein, AhpD family; uncharacterized peroxidase-related enzyme; PFAM: Carboxymuconolactone decarboxylase; KEGG: rpe:RPE_2026 uncharacterized peroxidase-related enzyme; peroxidase-like protein 1012906 4582428 Pden_3877 Paracoccus denitrificans PD1222 peroxidase-like protein YP_917639.1 1012304 R 318586 CDS YP_917640.1 119386585 4582429 1013103..1014599 1 NC_008687.1 KEGG: rsp:RSP_1053 signal recognition particle protein ffh; TIGRFAM: signal recognition particle protein; PFAM: GTP-binding signal recognition particle SRP54, G- domain; Signal peptide binding (SRP54) M- domain protein; GTP-binding signal recognition particle SRP54, helical bundle; SMART: AAA ATPase; signal recognition particle protein 1014599 4582429 Pden_3878 Paracoccus denitrificans PD1222 signal recognition particle protein YP_917640.1 1013103 D 318586 CDS YP_917641.1 119386586 4582430 1014604..1015134 1 NC_008687.1 PFAM: GCN5-related N-acetyltransferase; KEGG: rsp:RSP_1051 hypothetical protein; N-acetyltransferase GCN5 1015134 4582430 Pden_3879 Paracoccus denitrificans PD1222 N-acetyltransferase GCN5 YP_917641.1 1014604 D 318586 CDS YP_917642.1 119386587 4582431 1015131..1015481 1 NC_008687.1 catalyzes the interconversion of chorismate to prephenate; chorismate mutase 1015481 4582431 Pden_3880 Paracoccus denitrificans PD1222 chorismate mutase YP_917642.1 1015131 D 318586 CDS YP_917643.1 119386588 4582432 1015531..1015905 1 NC_008687.1 binds to lower part of 30S body where it stabilizes two domains; required for efficient assembly of 30S; in Escherichia coli this protein has nuclease activity; 30S ribosomal protein S16 1015905 rpsP 4582432 rpsP Paracoccus denitrificans PD1222 30S ribosomal protein S16 YP_917643.1 1015531 D 318586 CDS YP_917644.1 119386589 4582433 1015905..1016408 1 NC_008687.1 Essential for efficient processing of 16S rRNA; 16S rRNA-processing protein RimM 1016408 rimM 4582433 rimM Paracoccus denitrificans PD1222 16S rRNA-processing protein RimM YP_917644.1 1015905 D 318586 CDS YP_917645.1 119386590 4582434 1016405..1017274 1 NC_008687.1 KEGG: rsp:RSP_1045 tRNA (guanine-N1-)-methyltransferase; TIGRFAM: tRNA (guanine-N1)-methyltransferase; PFAM: tRNA (guanine-N1-)-methyltransferase; tRNA (guanine-N1)-methyltransferase 1017274 4582434 Pden_3883 Paracoccus denitrificans PD1222 tRNA (guanine-N1)-methyltransferase YP_917645.1 1016405 D 318586 CDS YP_917646.1 119386591 4582435 1017271..1017651 1 NC_008687.1 this protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site; 50S ribosomal protein L19 1017651 rplS 4582435 rplS Paracoccus denitrificans PD1222 50S ribosomal protein L19 YP_917646.1 1017271 D 318586 CDS YP_917647.1 119386592 4582436 1017663..1017884 1 NC_008687.1 PFAM: ribosomal protein L31; KEGG: rde:RD1_1304 ribosomal protein L31; 50S ribosomal protein L31 1017884 4582436 Pden_3885 Paracoccus denitrificans PD1222 50S ribosomal protein L31 YP_917647.1 1017663 D 318586 CDS YP_917648.1 119386593 4582437 complement(1018209..1018454) 1 NC_008687.1 hypothetical protein 1018454 4582437 Pden_3886 Paracoccus denitrificans PD1222 hypothetical protein YP_917648.1 1018209 R 318586 CDS YP_917649.1 119386594 4582438 1018726..1019508 1 NC_008687.1 KEGG: rsp:RSP_1042 chromosome partitioning protein; chromosome partitioning protein 1019508 4582438 Pden_3887 Paracoccus denitrificans PD1222 chromosome partitioning protein YP_917649.1 1018726 D 318586 CDS YP_917650.1 119386595 4582439 1019578..1020747 1 NC_008687.1 TIGRFAM: efflux transporter, RND family, MFP subunit; PFAM: secretion protein HlyD family protein; KEGG: rsp:RSP_2854 cation/multidrug efflux pump, membrane fusion protein (MFP) family; Fis family transcriptional regulator 1020747 4582439 Pden_3888 Paracoccus denitrificans PD1222 Fis family transcriptional regulator YP_917650.1 1019578 D 318586 CDS YP_917651.1 119386596 4582440 1020744..1023800 1 NC_008687.1 PFAM: acriflavin resistance protein; KEGG: rpa:RPA4680 efflux transporter; acriflavin resistance protein 1023800 4582440 Pden_3889 Paracoccus denitrificans PD1222 acriflavin resistance protein YP_917651.1 1020744 D 318586 CDS YP_917652.1 119386597 4582441 complement(1023906..1025210) 1 NC_008687.1 KEGG: rde:RD1_3014 pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase; TIGRFAM: pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase; PFAM: biotin/lipoyl attachment domain-containing protein; catalytic domain of components of various dehydrogenase complexes; E3 binding domain protein; branched-chain alpha-keto acid dehydrogenase subunit E2 1025210 4582441 Pden_3890 Paracoccus denitrificans PD1222 branched-chain alpha-keto acid dehydrogenase subunit E2 YP_917652.1 1023906 R 318586 CDS YP_917653.1 119386598 4582442 complement(1025223..1026593) 1 NC_008687.1 catalyzes the oxidative decarboxylation of pyruvate with concomitant acetylation of a lipoic acid-containing dihydrolipoamide acetyltransferase within the complex. The E1 component of the pyruvate dehydrogenase complex catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2). It contains multiple copies of three enzymatic components: pyruvate dehydrogenase (E1), dihydrolipoamide acetyltransferase(E2) and lipoamide dehydrogenase; pyruvate dehydrogenase subunit beta 1026593 4582442 Pden_3891 Paracoccus denitrificans PD1222 pyruvate dehydrogenase subunit beta YP_917653.1 1025223 R 318586 CDS YP_917654.1 119386599 4582443 complement(1026606..1027637) 1 NC_008687.1 PFAM: dehydrogenase, E1 component; KEGG: sit:TM1040_1079 pyruvate dehydrogenase (lipoamide); pyruvate dehydrogenase (acetyl-transferring) 1027637 4582443 Pden_3892 Paracoccus denitrificans PD1222 pyruvate dehydrogenase (acetyl-transferring) YP_917654.1 1026606 R 318586 CDS YP_917655.1 119386600 4582444 complement(1027872..1028165) 1 NC_008687.1 PFAM: Septum formation initiator; KEGG: sit:TM1040_1081 septum formation initiator; septum formation initiator 1028165 4582444 Pden_3893 Paracoccus denitrificans PD1222 septum formation initiator YP_917655.1 1027872 R 318586 CDS YP_917656.1 119386601 4582445 complement(1028190..1029491) 1 NC_008687.1 dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase (DapE), catalyzes the hydrolysis of N-succinyl-L,Ldiaminopimelate L,L-SDAP to L,L-diaminopimelate and succinate. It is a metalloprotease containing dinuclear active sites. Its structure is similar to the carboxypeptidase G2 from Pseudomonas sp. strain RS-16 and the aminopeptidase from Aeromonas proteolytica.; succinyl-diaminopimelate desuccinylase 1029491 4582445 Pden_3894 Paracoccus denitrificans PD1222 succinyl-diaminopimelate desuccinylase YP_917656.1 1028190 R 318586 CDS YP_917657.1 119386602 4582446 1029595..1029876 1 NC_008687.1 KEGG: rde:RD1_0930 hypothetical protein; hypothetical protein 1029876 4582446 Pden_3895 Paracoccus denitrificans PD1222 hypothetical protein YP_917657.1 1029595 D 318586 CDS YP_917658.1 119386603 4582447 1029887..1030546 1 NC_008687.1 PFAM: protein of unknown function DUF1523; KEGG: rsp:RSP_1760 hypothetical protein; hypothetical protein 1030546 4582447 Pden_3896 Paracoccus denitrificans PD1222 hypothetical protein YP_917658.1 1029887 D 318586 CDS YP_917659.1 119386604 4582448 1030550..1031494 1 NC_008687.1 KEGG: rsp:RSP_3739 deoxyribose phosphate aldolase; TIGRFAM: deoxyribose-phosphate aldolase; PFAM: deoxyribose-phosphate aldolase/phospho-2-dehydro-3-deoxyheptonate aldolase; deoxyribose-phosphate aldolase 1031494 4582448 Pden_3897 Paracoccus denitrificans PD1222 deoxyribose-phosphate aldolase YP_917659.1 1030550 D 318586 CDS YP_917660.1 119386605 4582449 1031497..1033827 1 NC_008687.1 PFAM: aldehyde dehydrogenase; KEGG: mes:Meso_0313 aldehyde dehydrogenase; aldehyde dehydrogenase 1033827 4582449 Pden_3898 Paracoccus denitrificans PD1222 aldehyde dehydrogenase YP_917660.1 1031497 D 318586 CDS YP_917661.1 119386606 4582450 complement(1033911..1034666) 1 NC_008687.1 PFAM: Xylose isomerase domain protein TIM barrel; KEGG: sit:TM1040_2765 hydroxypyruvate isomerase; hydroxypyruvate isomerase 1034666 4582450 Pden_3899 Paracoccus denitrificans PD1222 hydroxypyruvate isomerase YP_917661.1 1033911 R 318586 CDS YP_917662.1 119386607 4582451 complement(1034669..1035214) 1 NC_008687.1 PFAM: protein of unknown function DUF1285; KEGG: jan:Jann_0682 protein of unknown function DUF1285; hypothetical protein 1035214 4582451 Pden_3900 Paracoccus denitrificans PD1222 hypothetical protein YP_917662.1 1034669 R 318586 CDS YP_917663.1 119386608 4582452 1035276..1036277 1 NC_008687.1 PFAM: ATPase associated with various cellular activities, AAA_3; ATPase associated with various cellular activities, AAA_5; SMART: AAA ATPase; KEGG: rsp:RSP_1024 MoxR family protein; ATPase 1036277 4582452 Pden_3901 Paracoccus denitrificans PD1222 ATPase YP_917663.1 1035276 D 318586 CDS YP_917664.1 119386609 4582453 1036274..1037143 1 NC_008687.1 KEGG: jan:Jann_0684 hypothetical protein; hypothetical protein 1037143 4582453 Pden_3902 Paracoccus denitrificans PD1222 hypothetical protein YP_917664.1 1036274 D 318586 CDS YP_917665.1 119386610 4582454 1037143..1039062 1 NC_008687.1 TIGRFAM: conserved hypothetical membrane protein; KEGG: rsp:RSP_1022 conserved hypothetical protein (possibly transmembrane); hypothetical protein 1039062 4582454 Pden_3903 Paracoccus denitrificans PD1222 hypothetical protein YP_917665.1 1037143 D 318586 CDS YP_917666.1 119386611 4582455 1039059..1039898 1 NC_008687.1 KEGG: rde:RD1_0355 N-terminal double-transmembrane domain protein; hypothetical protein 1039898 4582455 Pden_3904 Paracoccus denitrificans PD1222 hypothetical protein YP_917666.1 1039059 D 318586 CDS YP_917667.1 119386612 4582456 1039895..1041997 1 NC_008687.1 KEGG: rde:RD1_0356 hypothetical protein; hypothetical protein 1041997 4582456 Pden_3905 Paracoccus denitrificans PD1222 hypothetical protein YP_917667.1 1039895 D 318586 CDS YP_917668.1 119386613 4582457 1042009..1042554 1 NC_008687.1 TIGRFAM: beta-hydroxyacyl-(acyl-carrier-protein) dehydratase FabZ; PFAM: Beta-hydroxyacyl-(acyl-carrier-protein) dehydratase, FabA/FabZ; KEGG: rsp:RSP_2712 probable 3-hydroxymyristoyl/3-hydroxydecanoyl-(acyl carrier protein) dehydratase; beta-hydroxyacyl-(acyl-carrier-protein) dehydratase FabZ 1042554 4582457 Pden_3906 Paracoccus denitrificans PD1222 beta-hydroxyacyl-(acyl-carrier-protein) dehydratase FabZ YP_917668.1 1042009 D 318586 CDS YP_917669.1 119386614 4582458 1042547..1043332 1 NC_008687.1 catalyzes the addition of (R)-3-hydroxytetradecanoyl to the glucosamine disaccharide in lipid A biosynthesis; UDP-N-acetylglucosamine acyltransferase 1043332 4582458 Pden_3907 Paracoccus denitrificans PD1222 UDP-N-acetylglucosamine acyltransferase YP_917669.1 1042547 D 318586 CDS YP_917670.1 119386615 4582459 1043329..1044126 1 NC_008687.1 PFAM: protein of unknown function DUF1009; KEGG: rsp:RSP_2715 hypothetical protein; hypothetical protein 1044126 4582459 Pden_3908 Paracoccus denitrificans PD1222 hypothetical protein YP_917670.1 1043329 D 318586 CDS YP_917671.1 119386616 4582460 1044291..1045454 1 NC_008687.1 KEGG: rsp:RSP_2716 lipid-A-disaccharide synthase; TIGRFAM: lipid-A-disaccharide synthase; PFAM: glycosyl transferase, family 19; lipid-A-disaccharide synthase 1045454 4582460 Pden_3909 Paracoccus denitrificans PD1222 lipid-A-disaccharide synthase YP_917671.1 1044291 D 318586 CDS YP_917672.1 119386617 4582461 complement(1045429..1045779) 1 NC_008687.1 PFAM: Endoribonuclease L-PSP; KEGG: bms:BRA1019 hypothetical protein; endoribonuclease L-PSP 1045779 4582461 Pden_3910 Paracoccus denitrificans PD1222 endoribonuclease L-PSP YP_917672.1 1045429 R 318586 CDS YP_917673.1 119386618 4582462 complement(1045807..1046553) 1 NC_008687.1 PFAM: protein of unknown function DUF81; KEGG: ade:Adeh_2178 protein of unknown function DUF81; hypothetical protein 1046553 4582462 Pden_3911 Paracoccus denitrificans PD1222 hypothetical protein YP_917673.1 1045807 R 318586 CDS YP_917674.1 119386619 4582463 1046946..1047236 1 NC_008687.1 hypothetical protein 1047236 4582463 Pden_3912 Paracoccus denitrificans PD1222 hypothetical protein YP_917674.1 1046946 D 318586 CDS YP_917675.1 119386620 4582464 complement(1047397..1048095) 1 NC_008687.1 PFAM: NodS family protein; Methyltransferase type 11; Methyltransferase type 12; KEGG: bja:bll5506 hypothetical protein; methyltransferase type 11 1048095 4582464 Pden_3913 Paracoccus denitrificans PD1222 methyltransferase type 11 YP_917675.1 1047397 R 318586 CDS YP_917676.1 119386621 4582465 complement(1048159..1049406) 1 NC_008687.1 PFAM: protein of unknown function DUF989; KEGG: sil:SPO0869 hypothetical protein; hypothetical protein 1049406 4582465 Pden_3914 Paracoccus denitrificans PD1222 hypothetical protein YP_917676.1 1048159 R 318586 CDS YP_917677.1 119386622 4582466 complement(1049608..1049958) 1 NC_008687.1 PFAM: Transthyretin; KEGG: rde:RD1_4150 hypothetical protein; transthyretin 1049958 4582466 Pden_3915 Paracoccus denitrificans PD1222 transthyretin YP_917677.1 1049608 R 318586 CDS YP_917678.1 119386623 4582467 complement(1049975..1051318) 1 NC_008687.1 catalyzes the transformation of hydroxyatrazine to N-isopropylammelide and ethylamine in the atrazine degradation pathway.; hydroxydechloroatrazine ethylaminohydrolase 1051318 4582467 Pden_3916 Paracoccus denitrificans PD1222 hydroxydechloroatrazine ethylaminohydrolase YP_917678.1 1049975 R 318586 CDS YP_917679.1 119386624 4582468 complement(1051318..1052799) 1 NC_008687.1 TIGRFAM: uracil-xanthine permease; PFAM: Xanthine/uracil/vitamin C permease; KEGG: sme:SMc02512 permease transmembrane protein; uracil-xanthine permease 1052799 4582468 Pden_3917 Paracoccus denitrificans PD1222 uracil-xanthine permease YP_917679.1 1051318 R 318586 CDS YP_917680.1 119386625 4582469 complement(1052841..1053803) 1 NC_008687.1 PFAM: ornithine cyclodeaminase/mu-crystallin; Shikimate/quinate 5-dehydrogenase; KEGG: mes:Meso_4368 ornithine cyclodeaminase/mu-crystallin; ornithine cyclodeaminase 1053803 4582469 Pden_3918 Paracoccus denitrificans PD1222 ornithine cyclodeaminase YP_917680.1 1052841 R 318586 CDS YP_917681.1 119386626 4582470 complement(1053803..1054966) 1 NC_008687.1 PFAM: alanine racemase domain protein; KEGG: mes:Meso_4367 alanine racemase-like; alanine racemase 1054966 4582470 Pden_3919 Paracoccus denitrificans PD1222 alanine racemase YP_917681.1 1053803 R 318586 CDS YP_917682.1 119386627 4582471 complement(1054988..1055935) 1 NC_008687.1 PFAM: Pyridoxal-5'-phosphate-dependent enzyme, beta subunit; KEGG: sil:SPOA0145 pyridoxal-phosphate dependent enzyme; pyridoxal-5'-phosphate-dependent protein subunit beta 1055935 4582471 Pden_3920 Paracoccus denitrificans PD1222 pyridoxal-5'-phosphate-dependent protein subunit beta YP_917682.1 1054988 R 318586 CDS YP_917683.1 119386628 4582472 complement(1055950..1057140) 1 NC_008687.1 PFAM: aminotransferase, class V; KEGG: mes:Meso_3308 aminotransferase, class V; serine--glyoxylate transaminase 1057140 4582472 Pden_3921 Paracoccus denitrificans PD1222 serine--glyoxylate transaminase YP_917683.1 1055950 R 318586 CDS YP_917684.1 119386629 4582473 1057325..1058164 1 NC_008687.1 PFAM: regulatory protein, DeoR; regulatory proteins, IclR; KEGG: sil:SPOA0143 transcriptional regulator, IclR family; regulatory proteins, IclR 1058164 4582473 Pden_3922 Paracoccus denitrificans PD1222 regulatory proteins, IclR YP_917684.1 1057325 D 318586 CDS YP_917685.1 119386630 4582474 1058292..1060046 1 NC_008687.1 hypothetical protein 1060046 4582474 Pden_3923 Paracoccus denitrificans PD1222 hypothetical protein YP_917685.1 1058292 D 318586 CDS YP_917686.1 119386631 4582475 1060135..1060851 1 NC_008687.1 PFAM: pentapeptide repeat protein; KEGG: cyb:CYB_1243 pentapeptide repeat family protein; pentapeptide repeat-containing protein 1060851 4582475 Pden_3924 Paracoccus denitrificans PD1222 pentapeptide repeat-containing protein YP_917686.1 1060135 D 318586 CDS YP_917687.1 119386632 4582476 complement(1060864..1062450) 1 NC_008687.1 KEGG: jan:Jann_1578 transcriptional regulator, SARP family; SARP family transcriptional regulator 1062450 4582476 Pden_3925 Paracoccus denitrificans PD1222 SARP family transcriptional regulator YP_917687.1 1060864 R 318586 CDS YP_917688.1 119386633 4582477 1062638..1063684 1 NC_008687.1 catalyzes the formation of 1-(5-phosphoribosyl)-5-aminoimidazole from 2-(formamido)-N1-(5-phosphoribosyl)acetamidine and ATP in purine biosynthesis; phosphoribosylaminoimidazole synthetase 1063684 4582477 Pden_3926 Paracoccus denitrificans PD1222 phosphoribosylaminoimidazole synthetase YP_917688.1 1062638 D 318586 CDS YP_917689.1 119386634 4582478 1063681..1064277 1 NC_008687.1 TIGRFAM: phosphoribosylglycinamide formyltransferase; PFAM: formyl transferase domain protein; KEGG: rsp:RSP_1970 phosphoribosylglycinamide formyltransferase; phosphoribosylglycinamide formyltransferase 1064277 4582478 Pden_3927 Paracoccus denitrificans PD1222 phosphoribosylglycinamide formyltransferase YP_917689.1 1063681 D 318586 CDS YP_917690.1 119386635 4582479 complement(1064359..1065699) 1 NC_008687.1 PFAM: inner-membrane translocator; KEGG: sil:SPO1935 branched-chain amino acid ABC transporter, permease; inner-membrane translocator 1065699 4582479 Pden_3928 Paracoccus denitrificans PD1222 inner-membrane translocator YP_917690.1 1064359 R 318586 CDS YP_917691.1 119386636 4582480 complement(1065715..1066716) 1 NC_008687.1 PFAM: inner-membrane translocator; KEGG: rsp:RSP_2926 ABC branched-chain amino acid transporter family, inner membrane subunit; inner-membrane translocator 1066716 4582480 Pden_3929 Paracoccus denitrificans PD1222 inner-membrane translocator YP_917691.1 1065715 R 318586 CDS YP_917692.1 119386637 4582481 complement(1066719..1067429) 1 NC_008687.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rsp:RSP_2925 ABC branched-chain amino acid transporter family, ATPase subunit; ABC transporter 1067429 4582481 Pden_3930 Paracoccus denitrificans PD1222 ABC transporter YP_917692.1 1066719 R 318586 CDS YP_917693.1 119386638 4582482 complement(1067429..1068334) 1 NC_008687.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rde:RD1_2630 branched-chain amino acid ABC transporter, ATP-binding protein; ABC transporter 1068334 4582482 Pden_3931 Paracoccus denitrificans PD1222 ABC transporter YP_917693.1 1067429 R 318586 CDS YP_917694.1 119386639 4582483 complement(1068413..1069597) 1 NC_008687.1 PFAM: Extracellular ligand-binding receptor; KEGG: rsp:RSP_2923 ABC branched amino acid transporter family, periplasmic substrate-binding protein; extracellular ligand-binding receptor 1069597 4582483 Pden_3932 Paracoccus denitrificans PD1222 extracellular ligand-binding receptor YP_917694.1 1068413 R 318586 CDS YP_917695.1 119386640 4582484 complement(1069721..1070734) 1 NC_008687.1 PFAM: helix-turn-helix- domain containing protein, AraC type; ThiJ/PfpI domain protein; KEGG: rsp:RSP_2922 transcriptional regulator, AraC family; AraC family transcriptional regulator 1070734 4582484 Pden_3933 Paracoccus denitrificans PD1222 AraC family transcriptional regulator YP_917695.1 1069721 R 318586 CDS YP_917696.1 119386641 4582485 1070820..1072262 1 NC_008687.1 KEGG: rsp:RSP_2921 phospho-2-dehydro-3-deoxyheptonate; TIGRFAM: phospho-2-dehydro-3-deoxyheptonate aldolase; PFAM: DAHP synthetase, class II; phospho-2-dehydro-3-deoxyheptonate aldolase 1072262 4582485 Pden_3934 Paracoccus denitrificans PD1222 phospho-2-dehydro-3-deoxyheptonate aldolase YP_917696.1 1070820 D 318586 CDS YP_917697.1 119386642 4582486 complement(1072372..1073130) 1 NC_008687.1 KEGG: rde:RD1_2636 hypothetical protein; hypothetical protein 1073130 4582486 Pden_3935 Paracoccus denitrificans PD1222 hypothetical protein YP_917697.1 1072372 R 318586 CDS YP_917698.1 119386643 4582487 1073313..1073951 1 NC_008687.1 Essential for recycling GMP and indirectly, cGMP; guanylate kinase 1073951 gmk 4582487 gmk Paracoccus denitrificans PD1222 guanylate kinase YP_917698.1 1073313 D 318586 CDS YP_917699.1 119386644 4582488 1073948..1074475 1 NC_008687.1 KEGG: jan:Jann_2439 transferase hexapeptide protein; transferase 1074475 4582488 Pden_3937 Paracoccus denitrificans PD1222 transferase YP_917699.1 1073948 D 318586 CDS YP_917700.1 119386645 4582489 1074472..1075524 1 NC_008687.1 PFAM: ATP-binding region, ATPase domain protein domain protein; histidine kinase A domain protein domain protein; PAS fold-4 domain protein; PAS fold domain protein; SMART: PAS domain containing protein; KEGG: sil:SPO1947 phosphate regulon sensor histidine kinase; PAS/PAC sensor signal transduction histidine kinase 1075524 4582489 Pden_3938 Paracoccus denitrificans PD1222 PAS/PAC sensor signal transduction histidine kinase YP_917700.1 1074472 D 318586 CDS YP_917701.1 119386646 4582490 complement(1075615..1077114) 1 NC_008687.1 Catalyzes first step of the de novo purine nucleotide biosynthetic pathway; amidophosphoribosyltransferase 1077114 4582490 Pden_3939 Paracoccus denitrificans PD1222 amidophosphoribosyltransferase YP_917701.1 1075615 R 318586 CDS YP_917702.1 119386647 4582491 complement(1077245..1077856) 1 NC_008687.1 PFAM: Colicin V production protein; KEGG: rsp:RSP_2455 colicin V production protein, DedE; colicin V production protein 1077856 4582491 Pden_3940 Paracoccus denitrificans PD1222 colicin V production protein YP_917702.1 1077245 R 318586 CDS YP_917703.1 119386648 4582492 complement(1077900..1079264) 1 NC_008687.1 Sms; stabilizes the strand-invasion intermediate during the DNA repair; involved in recombination of donor DNA and plays an important role in DNA damage repair after exposure to mutagenic agents; DNA repair protein RadA 1079264 4582492 Pden_3941 Paracoccus denitrificans PD1222 DNA repair protein RadA YP_917703.1 1077900 R 318586 CDS YP_917704.1 119386649 4582493 complement(1079413..1080603) 1 NC_008687.1 TIGRFAM: Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; PFAM: monooxygenase, FAD-binding; KEGG: rsp:RSP_1869 2-octaprenyl-6-methoxyphenyl hydroxylase; 2-octaprenyl-6-methoxyphenyl hydroxylase 1080603 4582493 Pden_3942 Paracoccus denitrificans PD1222 2-octaprenyl-6-methoxyphenyl hydroxylase YP_917704.1 1079413 R 318586 CDS YP_917705.1 119386650 4582494 complement(1080857..1081543) 1 NC_008687.1 TIGRFAM: HAD-superfamily hydrolase, subfamily IA, variant 3; pyrimidine 5'-nucleotidase; PFAM: Haloacid dehalogenase domain protein hydrolase; KEGG: sil:SPO1374 pyrimidine 5'-nucleotidase; pyrimidine 5'-nucleotidase 1081543 4582494 Pden_3943 Paracoccus denitrificans PD1222 pyrimidine 5'-nucleotidase YP_917705.1 1080857 R 318586 CDS YP_917706.1 119386651 4582495 1081609..1082244 1 NC_008687.1 PFAM: regulatory protein GntR, HTH; GntR domain protein; KEGG: rsp:RSP_1871 transcriptional regulator, GntR family; GntR family transcriptional regulator 1082244 4582495 Pden_3944 Paracoccus denitrificans PD1222 GntR family transcriptional regulator YP_917706.1 1081609 D 318586 CDS YP_917707.1 119386652 4582496 1082244..1082867 1 NC_008687.1 PFAM: HhH-GPD family protein; KEGG: sil:SPO2127 DNA-3-methyladenine glycosylase II; HhH-GPD family protein 1082867 4582496 Pden_3945 Paracoccus denitrificans PD1222 HhH-GPD family protein YP_917707.1 1082244 D 318586 CDS YP_917708.1 119386653 4582497 1082878..1083537 1 NC_008687.1 PFAM: dienelactone hydrolase; phospholipase/Carboxylesterase; KEGG: rsp:RSP_2728 phospholipase/carboxylesterase; phospholipase/carboxylesterase 1083537 4582497 Pden_3946 Paracoccus denitrificans PD1222 phospholipase/carboxylesterase YP_917708.1 1082878 D 318586 CDS YP_917709.1 119386654 4582498 complement(1083740..1084216) 1 NC_008687.1 PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase; KEGG: mlo:mlr4624 lactoylglutathione lyase; glyoxalase/bleomycin resistance protein/dioxygenase 1084216 4582498 Pden_3947 Paracoccus denitrificans PD1222 glyoxalase/bleomycin resistance protein/dioxygenase YP_917709.1 1083740 R 318586 CDS YP_917710.1 119386655 4582499 1084256..1084576 1 NC_008687.1 PFAM: small multidrug resistance protein; KEGG: pau:PA14_40170 transporter; small multidrug resistance protein 1084576 4582499 Pden_3948 Paracoccus denitrificans PD1222 small multidrug resistance protein YP_917710.1 1084256 D 318586 CDS YP_917711.1 119386656 4582500 1084712..1085308 1 NC_008687.1 PFAM: HNH endonuclease; SMART: HNH nuclease; KEGG: sil:SPO2123 HNH endonuclease family protein; HNH endonuclease 1085308 4582500 Pden_3949 Paracoccus denitrificans PD1222 HNH endonuclease YP_917711.1 1084712 D 318586 CDS YP_917712.1 119386657 4582501 1085439..1085807 1 NC_008687.1 hypothetical protein 1085807 4582501 Pden_3950 Paracoccus denitrificans PD1222 hypothetical protein YP_917712.1 1085439 D 318586 CDS YP_917713.1 119386658 4582502 1086199..1087281 1 NC_008687.1 PFAM: Radical SAM domain protein; SMART: Elongator protein 3/MiaB/NifB; KEGG: sil:SPO2159 radical SAM domain protein; radical SAM domain-containing protein 1087281 4582502 Pden_3951 Paracoccus denitrificans PD1222 radical SAM domain-containing protein YP_917713.1 1086199 D 318586 CDS YP_917714.1 119386659 4582503 complement(1087282..1088241) 1 NC_008687.1 catalyzes the formation of methionine from L-homocysteine and S-adenosyl-L-methionine; methionine synthase I 1088241 4582503 Pden_3952 Paracoccus denitrificans PD1222 methionine synthase I YP_917714.1 1087282 R 318586 CDS YP_917715.1 119386660 4582504 complement(1088330..1089349) 1 NC_008687.1 catalyzes a two-step reaction, first charging a tryptophan molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; tryptophanyl-tRNA synthetase 1089349 4582504 Pden_3953 Paracoccus denitrificans PD1222 tryptophanyl-tRNA synthetase YP_917715.1 1088330 R 318586 CDS YP_917716.1 119386661 4582505 1089460..1090173 1 NC_008687.1 PFAM: Rhomboid family protein; KEGG: sit:TM1040_0444 rhomboid-like protein; rhomboid family protein 1090173 4582505 Pden_3954 Paracoccus denitrificans PD1222 rhomboid family protein YP_917716.1 1089460 D 318586 CDS YP_917717.1 119386662 4582506 complement(1090164..1091708) 1 NC_008687.1 TIGRFAM: integral membrane protein MviN; PFAM: polysaccharide biosynthesis protein; virulence factor MVIN family protein; KEGG: rsp:RSP_1810 virulence factor, MviN; integral membrane protein MviN 1091708 4582506 Pden_3955 Paracoccus denitrificans PD1222 integral membrane protein MviN YP_917717.1 1090164 R 318586 CDS YP_917718.1 119386663 4582507 complement(1091719..1094529) 1 NC_008687.1 catalyzes the uridylylation or deuridylylation of the PII nitrogen regulatory protein; PII uridylyl-transferase 1094529 4582507 Pden_3956 Paracoccus denitrificans PD1222 PII uridylyl-transferase YP_917718.1 1091719 R 318586 CDS YP_917719.1 119386664 4582508 complement(1094532..1095734) 1 NC_008687.1 KEGG: rsp:RSP_1812 hypothetical protein; hypothetical protein 1095734 4582508 Pden_3957 Paracoccus denitrificans PD1222 hypothetical protein YP_917719.1 1094532 R 318586 CDS YP_917720.1 119386665 4582509 1095839..1096747 1 NC_008687.1 PFAM: Uroporphyrin-III C/tetrapyrrole (Corrin/Porphyrin) methyltransferase; KEGG: rsp:RSP_1813 hypothetical protein; uroporphyrin-III C/tetrapyrrole methyltransferase 1096747 4582509 Pden_3958 Paracoccus denitrificans PD1222 uroporphyrin-III C/tetrapyrrole methyltransferase YP_917720.1 1095839 D 318586 CDS YP_917721.1 119386666 4582510 1096744..1097157 1 NC_008687.1 PFAM: protein of unknown function UPF0102; KEGG: sil:SPO0400 endonuclease; hypothetical protein 1097157 4582510 Pden_3959 Paracoccus denitrificans PD1222 hypothetical protein YP_917721.1 1096744 D 318586 CDS YP_917722.1 119386667 4582511 1097346..1098296 1 NC_008687.1 catalyzes the second step in the glutathione biosynthesis pathway, where it synthesizes ATP + gamma-L-glutamyl-L-cysteine + glycine = ADP + phosphate + glutathione; glutathione synthetase 1098296 4582511 Pden_3960 Paracoccus denitrificans PD1222 glutathione synthetase YP_917722.1 1097346 D 318586 CDS YP_917723.1 119386668 4582512 complement(1098421..1099953) 1 NC_008687.1 KEGG: sil:SPO0402 competence protein ComM; TIGRFAM: Mg chelatase, subunit ChlI; PFAM: magnesium chelatase, ChlI subunit; SMART: AAA ATPase; Mg chelatase subunit ChlI 1099953 4582512 Pden_3961 Paracoccus denitrificans PD1222 Mg chelatase subunit ChlI YP_917723.1 1098421 R 318586 CDS YP_917724.1 119386669 4582513 1100033..1101343 1 NC_008687.1 catalyzes the conjugation of cysteine to 4'-phosphopantothenate to form 4-phosphopantothenoylcysteine, which is then decarboxylated to form 4'-phosphopantotheine; bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase 1101343 4582513 Pden_3962 Paracoccus denitrificans PD1222 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase YP_917724.1 1100033 D 318586 CDS YP_917725.1 119386670 4582514 1101340..1102407 1 NC_008687.1 PFAM: aminotransferase, class V; KEGG: rsp:RSP_0442 aminotransferase; cysteine desulfurase 1102407 4582514 Pden_3963 Paracoccus denitrificans PD1222 cysteine desulfurase YP_917725.1 1101340 D 318586 CDS YP_917726.1 119386671 4582515 1102409..1103935 1 NC_008687.1 with SufCD activates cysteine desulfurase SufS; cysteine desulfurase activator complex subunit SufB 1103935 4582515 Pden_3964 Paracoccus denitrificans PD1222 cysteine desulfurase activator complex subunit SufB YP_917726.1 1102409 D 318586 CDS YP_917727.1 119386672 4582516 1103932..1104243 1 NC_008687.1 PFAM: protein of unknown function DUF74; KEGG: rsp:RSP_0439 hypothetical protein; hypothetical protein 1104243 4582516 Pden_3965 Paracoccus denitrificans PD1222 hypothetical protein YP_917727.1 1103932 D 318586 CDS YP_917728.1 119386673 4582517 1104253..1105008 1 NC_008687.1 KEGG: sil:SPO2018 FeS assembly ATPase SufC; TIGRFAM: FeS assembly ATPase SufC; PFAM: ABC transporter related; SMART: AAA ATPase; FeS assembly ATPase SufC 1105008 4582517 Pden_3966 Paracoccus denitrificans PD1222 FeS assembly ATPase SufC YP_917728.1 1104253 D 318586 CDS YP_917729.1 119386674 4582518 1105008..1106354 1 NC_008687.1 PFAM: SufBD protein; KEGG: rde:RD1_2692 FeS assembly protein SufD; SufBD protein 1106354 4582518 Pden_3967 Paracoccus denitrificans PD1222 SufBD protein YP_917729.1 1105008 D 318586 CDS YP_917730.1 119386675 4582519 1106351..1106839 1 NC_008687.1 KEGG: rsp:RSP_0433 hypothetical protein; hypothetical protein 1106839 4582519 Pden_3968 Paracoccus denitrificans PD1222 hypothetical protein YP_917730.1 1106351 D 318586 CDS YP_917731.1 119386676 4582520 1106836..1107423 1 NC_008687.1 KEGG: rsp:RSP_0432 hypothetical protein; hypothetical protein 1107423 4582520 Pden_3969 Paracoccus denitrificans PD1222 hypothetical protein YP_917731.1 1106836 D 318586 CDS YP_917732.1 119386677 4582521 1107420..1108631 1 NC_008687.1 TIGRFAM: cysteine desulfurases, SufS subfamily; PFAM: aminotransferase, class V; aromatic amino acid beta-eliminating lyase/threonine aldolase; KEGG: sil:SPO2014 cysteine desulfurase SufS; SufS subfamily cysteine desulfurase 1108631 4582521 Pden_3970 Paracoccus denitrificans PD1222 SufS subfamily cysteine desulfurase YP_917732.1 1107420 D 318586 CDS YP_917733.1 119386678 4582522 complement(1109057..1111228) 1 NC_008687.1 catalyzes the formation of 2-(formamido)-N1-(5-phospho-D-ribosyl)acetamidine from N2-formyl-N1-(5-phospho-D-ribosyl)glycinamide and L-glutamine in purine biosynthesis; phosphoribosylformylglycinamidine synthase II 1111228 4582522 Pden_3971 Paracoccus denitrificans PD1222 phosphoribosylformylglycinamidine synthase II YP_917733.1 1109057 R 318586 CDS YP_917734.1 119386679 4582523 complement(1111534..1112475) 1 NC_008687.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: rsp:RSP_2950 transcriptional regulator, LysR family; LysR family transcriptional regulator 1112475 4582523 Pden_3972 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_917734.1 1111534 R 318586 CDS YP_917735.1 119386680 4582524 1112959..1113771 1 NC_008687.1 KEGG: rsp:RSP_2947 glutamate racemase; TIGRFAM: glutamate racemase; PFAM: Asp/Glu racemase; glutamate racemase 1113771 4582524 Pden_3973 Paracoccus denitrificans PD1222 glutamate racemase YP_917735.1 1112959 D 318586 CDS YP_917736.1 119386681 4582525 1113790..1114233 1 NC_008687.1 CycJ; periplasmic heme chaperone that binds heme transiently via a histidine residue and delivers it to newly synthesized and exported c-type cytochromes; requires the ATP hydrolysis activity of the CcmA protein in order to transfer the heme to the apocytochrome; part of the cytochrome c maturation system; periplasmic protein anchored to the inner membrane; cytochrome c-type biogenesis protein CcmE 1114233 4582525 Pden_3974 Paracoccus denitrificans PD1222 cytochrome c-type biogenesis protein CcmE YP_917736.1 1113790 D 318586 CDS YP_917737.1 119386682 4582526 1114309..1114920 1 NC_008687.1 PFAM: protein of unknown function DUF847; KEGG: rsp:RSP_2944 hypothetical protein; hypothetical protein 1114920 4582526 Pden_3975 Paracoccus denitrificans PD1222 hypothetical protein YP_917737.1 1114309 D 318586 CDS YP_917738.1 119386683 4582527 1114911..1115441 1 NC_008687.1 KEGG: rsp:RSP_6081 hypothetical protein; hypothetical protein 1115441 4582527 Pden_3976 Paracoccus denitrificans PD1222 hypothetical protein YP_917738.1 1114911 D 318586 CDS YP_917739.1 119386684 4582528 1115530..1117491 1 NC_008687.1 TIGRFAM: cytochrome c-type biogenesis protein CcmF; PFAM: cytochrome c assembly protein; KEGG: rsp:RSP_2633 cytochrome c maturation protein, CcmF; cytochrome c-type biogenesis protein CcmF 1117491 4582528 Pden_3977 Paracoccus denitrificans PD1222 cytochrome c-type biogenesis protein CcmF YP_917739.1 1115530 D 318586 CDS YP_917740.1 119386685 4582529 1117495..1117947 1 NC_008687.1 PFAM: cytochrome C biogenesis protein; KEGG: sil:SPO1881 cytochrome c biogenesis family protein; cytochrome C biogenesis protein 1117947 4582529 Pden_3978 Paracoccus denitrificans PD1222 cytochrome C biogenesis protein YP_917740.1 1117495 D 318586 CDS YP_917741.1 119386686 4582530 1118017..1118787 1 NC_008687.1 PFAM: Enoyl-CoA hydratase/isomerase; KEGG: jan:Jann_2154 enoyl-CoA hydratase/isomerase; enoyl-CoA hydratase/isomerase 1118787 4582530 Pden_3979 Paracoccus denitrificans PD1222 enoyl-CoA hydratase/isomerase YP_917741.1 1118017 D 318586 CDS YP_917742.1 119386687 4582531 complement(1118822..1119541) 1 NC_008687.1 PFAM: NUDIX hydrolase; KEGG: rsp:RSP_0419 hypothetical protein; NUDIX hydrolase 1119541 4582531 Pden_3980 Paracoccus denitrificans PD1222 NUDIX hydrolase YP_917742.1 1118822 R 318586 CDS YP_917743.1 119386688 4582532 complement(1119544..1119963) 1 NC_008687.1 PFAM: protein of unknown function DUF983; KEGG: rsp:RSP_0418 hypothetical protein; hypothetical protein 1119963 4582532 Pden_3981 Paracoccus denitrificans PD1222 hypothetical protein YP_917743.1 1119544 R 318586 CDS YP_917744.1 119386689 4582533 complement(1120068..1121462) 1 NC_008687.1 TIGRFAM: diguanylate cyclase; PFAM: GGDEF domain containing protein; response regulator receiver; KEGG: jan:Jann_3131 diguanylate cyclase; response regulator receiver modulated diguanylate cyclase 1121462 4582533 Pden_3982 Paracoccus denitrificans PD1222 response regulator receiver modulated diguanylate cyclase YP_917744.1 1120068 R 318586 CDS YP_917745.1 119386690 4582534 1121571..1121840 1 NC_008687.1 KEGG: rru:Rru_A1259 hypothetical protein; hypothetical protein 1121840 4582534 Pden_3983 Paracoccus denitrificans PD1222 hypothetical protein YP_917745.1 1121571 D 318586 CDS YP_917746.1 119386691 4582535 complement(1121859..1123220) 1 NC_008687.1 PFAM: aminotransferase class-III; KEGG: rsp:RSP_0379 aminotransferase; class III aminotransferase 1123220 4582535 Pden_3984 Paracoccus denitrificans PD1222 class III aminotransferase YP_917746.1 1121859 R 318586 CDS YP_917747.1 119386692 4582536 complement(1123458..1124807) 1 NC_008687.1 PFAM: cytochrome P450; KEGG: sil:SPO1898 cytochrome P450 family protein; cytochrome P450 1124807 4582536 Pden_3985 Paracoccus denitrificans PD1222 cytochrome P450 YP_917747.1 1123458 R 318586 CDS YP_917748.1 119386693 4582537 complement(1124804..1126003) 1 NC_008687.1 KEGG: sil:SPO1897 hypothetical protein; hypothetical protein 1126003 4582537 Pden_3986 Paracoccus denitrificans PD1222 hypothetical protein YP_917748.1 1124804 R 318586 CDS YP_917749.1 119386694 4582538 complement(1126057..1126743) 1 NC_008687.1 PFAM: peptidase M48, Ste24p; KEGG: jan:Jann_2687 peptidase M48, Ste24p; peptidase M48, Ste24p 1126743 4582538 Pden_3987 Paracoccus denitrificans PD1222 peptidase M48, Ste24p YP_917749.1 1126057 R 318586 CDS YP_917750.1 119386695 4582539 complement(1126771..1127952) 1 NC_008687.1 PFAM: VWA containing CoxE family protein; KEGG: rsp:RSP_2650 hypothetical protein; von Willebrand factor A 1127952 4582539 Pden_3988 Paracoccus denitrificans PD1222 von Willebrand factor A YP_917750.1 1126771 R 318586 CDS YP_917751.1 119386696 4582540 1128237..1129361 1 NC_008687.1 PFAM: Ppx/GppA phosphatase; KEGG: rsp:RSP_2771 exopolyphosphatase; Ppx/GppA phosphatase 1129361 4582540 Pden_3989 Paracoccus denitrificans PD1222 Ppx/GppA phosphatase YP_917751.1 1128237 D 318586 CDS YP_917752.1 119386697 4582541 1129363..1130133 1 NC_008687.1 PFAM: ribosomal RNA methyltransferase RrmJ/FtsJ; KEGG: rsp:RSP_2772 23S rRNA methylase; ribosomal RNA methyltransferase RrmJ/FtsJ 1130133 4582541 Pden_3990 Paracoccus denitrificans PD1222 ribosomal RNA methyltransferase RrmJ/FtsJ YP_917752.1 1129363 D 318586 CDS YP_917753.1 119386698 4582542 complement(1130270..1131376) 1 NC_008687.1 PFAM: helix-turn-helix- domain containing protein, AraC type; KEGG: jan:Jann_2462 transcriptional regulator, AraC family; helix-turn-helix domain-containing protein 1131376 4582542 Pden_3991 Paracoccus denitrificans PD1222 helix-turn-helix domain-containing protein YP_917753.1 1130270 R 318586 CDS YP_917754.1 119386699 4582543 complement(1131504..1132412) 1 NC_008687.1 IPP transferase; isopentenyltransferase; involved in tRNA modification; in Escherichia coli this enzyme catalyzes the addition of a delta2-isopentenyl group from dimethylallyl diphosphate to the N6-nitrogen of adenosine adjacent to the anticodon of tRNA species that read codons starting with uracil; further tRNA modifications may occur; mutations in miaA result in defects in translation efficiency and fidelity; tRNA delta(2)-isopentenylpyrophosphate transferase 1132412 miaA 4582543 miaA Paracoccus denitrificans PD1222 tRNA delta(2)-isopentenylpyrophosphate transferase YP_917754.1 1131504 R 318586 CDS YP_917755.1 119386700 4582544 1132498..1133232 1 NC_008687.1 Catalyzes the phosphorylation of UMP to UDP; uridylate kinase 1133232 pyrH 4582544 pyrH Paracoccus denitrificans PD1222 uridylate kinase YP_917755.1 1132498 D 318586 CDS YP_917756.1 119386701 4582545 1133313..1133876 1 NC_008687.1 Rrf; Frr; ribosome-recycling factor; release factor 4; RF4; recycles ribosomes upon translation termination along with release factor RF-3 and elongation factor EF-G; A GTPase-dependent process results in release of 50S from 70S; inhibited by release factor RF-1; essential for viability; structurally similar to tRNAs; ribosome recycling factor 1133876 frr 4582545 frr Paracoccus denitrificans PD1222 ribosome recycling factor YP_917756.1 1133313 D 318586 CDS YP_917757.1 119386702 4582546 1133880..1134614 1 NC_008687.1 KEGG: rsp:RSP_2707 UDP pyrophosphate synthase; TIGRFAM: UDP diphosphate synthase; PFAM: Di-trans-poly-cis-decaprenylcistransferase; UDP diphosphate synthase 1134614 4582546 Pden_3995 Paracoccus denitrificans PD1222 UDP diphosphate synthase YP_917757.1 1133880 D 318586 CDS YP_917758.1 119386703 4582547 1134611..1135465 1 NC_008687.1 PFAM: phosphatidate cytidylyltransferase; KEGG: rsp:RSP_2708 phosphatidate cytidylyltransferase; phosphatidate cytidylyltransferase 1135465 4582547 Pden_3996 Paracoccus denitrificans PD1222 phosphatidate cytidylyltransferase YP_917758.1 1134611 D 318586 CDS YP_917759.1 119386704 4582548 1135470..1136642 1 NC_008687.1 catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate; 1-deoxy-D-xylulose 5-phosphate reductoisomerase 1136642 4582548 Pden_3997 Paracoccus denitrificans PD1222 1-deoxy-D-xylulose 5-phosphate reductoisomerase YP_917759.1 1135470 D 318586 CDS YP_917760.1 119386705 4582549 1136639..1137964 1 NC_008687.1 TIGRFAM: membrane-associated zinc metalloprotease; PFAM: PDZ/DHR/GLGF domain protein; peptidase M50; KEGG: sil:SPO1668 membrane-associated zinc metalloprotease; membrane-associated zinc metalloprotease 1137964 4582549 Pden_3998 Paracoccus denitrificans PD1222 membrane-associated zinc metalloprotease YP_917760.1 1136639 D 318586 CDS YP_917761.1 119386706 4582550 1138068..1140416 1 NC_008687.1 PFAM: surface antigen (D15); surface antigen variable number repeat protein; KEGG: rsp:RSP_2711 outer membrane protein; surface antigen (D15) 1140416 4582550 Pden_3999 Paracoccus denitrificans PD1222 surface antigen (D15) YP_917761.1 1138068 D 318586 CDS YP_917762.1 119386707 4582551 1140416..1141195 1 NC_008687.1 PFAM: outer membrane chaperone Skp (OmpH); KEGG: rde:RD1_2594 hypothetical protein; outer membrane chaperone Skp (OmpH) 1141195 4582551 Pden_4000 Paracoccus denitrificans PD1222 outer membrane chaperone Skp (OmpH) YP_917762.1 1140416 D 318586 CDS YP_917763.1 119386708 4582552 complement(1141217..1142164) 1 NC_008687.1 PFAM: Inosine/uridine-preferring nucleoside hydrolase; KEGG: rsp:RSP_2914 nucleoside hydrolase; purine nucleosidase 1142164 4582552 Pden_4001 Paracoccus denitrificans PD1222 purine nucleosidase YP_917763.1 1141217 R 318586 CDS YP_917764.1 119386709 4582553 complement(1142225..1144681) 1 NC_008687.1 PFAM: peptidase S45, penicillin amidase; KEGG: rsp:RSP_2845 penicillin acylase (penicillin amidase); penicillin amidase 1144681 4582553 Pden_4002 Paracoccus denitrificans PD1222 penicillin amidase YP_917764.1 1142225 R 318586 CDS YP_917765.1 119386710 4582554 1144811..1145677 1 NC_008687.1 PFAM: NADP oxidoreductase, coenzyme F420-dependent; 6-phosphogluconate dehydrogenase, NAD-binding; KEGG: rsp:RSP_2846 3-hydroxyisobutyrate dehydrogenase; 3-hydroxyisobutyrate dehydrogenase 1145677 4582554 Pden_4003 Paracoccus denitrificans PD1222 3-hydroxyisobutyrate dehydrogenase YP_917765.1 1144811 D 318586 CDS YP_917766.1 119386711 4582555 complement(1145983..1146531) 1 NC_008687.1 PFAM: protein of unknown function DUF1130; KEGG: bbr:BB2477 hypothetical protein; hypothetical protein 1146531 4582555 Pden_4004 Paracoccus denitrificans PD1222 hypothetical protein YP_917766.1 1145983 R 318586 CDS YP_917767.1 119386712 4582556 complement(1146544..1146753) 1 NC_008687.1 KEGG: nha:Nham_2097 hypothetical protein; hypothetical protein 1146753 4582556 Pden_4005 Paracoccus denitrificans PD1222 hypothetical protein YP_917767.1 1146544 R 318586 CDS YP_917768.1 119386713 4582557 1147245..1148897 1 NC_008687.1 PFAM: major facilitator superfamily MFS_1; KEGG: atc:AGR_L_343 hypothetical protein; major facilitator transporter 1148897 4582557 Pden_4006 Paracoccus denitrificans PD1222 major facilitator transporter YP_917768.1 1147245 D 318586 CDS YP_917769.1 119386714 4582558 complement(1148956..1150926) 1 NC_008687.1 PFAM: ATP-binding region, ATPase domain protein domain protein; histidine kinase, HAMP region domain protein; histidine kinase A domain protein domain protein; KEGG: sit:TM1040_0406 periplasmic sensor signal transduction histidine kinase; integral membrane sensor signal transduction histidine kinase 1150926 4582558 Pden_4007 Paracoccus denitrificans PD1222 integral membrane sensor signal transduction histidine kinase YP_917769.1 1148956 R 318586 CDS YP_917770.1 119386715 4582559 complement(1150919..1152289) 1 NC_008687.1 PFAM: response regulator receiver; sigma-54 factor, interaction domain-containing protein; helix-turn-helix, Fis-type; ATPase associated with various cellular activities, AAA_5; SMART: AAA ATPase; KEGG: sit:TM1040_0405 two component, sigma54 specific, transcriptional regulator, fis family; two component, sigma54 specific, Fis family transcriptional regulator 1152289 4582559 Pden_4008 Paracoccus denitrificans PD1222 two component, sigma54 specific, Fis family transcriptional regulator YP_917770.1 1150919 R 318586 CDS YP_917771.1 119386716 4582560 1152491..1154755 1 NC_008687.1 KEGG: sal:Sala_0186 oxidoreductase alpha (molybdopterin) subunit; TIGRFAM: oxidoreductase alpha (molybdopterin) subunit; PFAM: molybdopterin oxidoreductase; molydopterin dinucleotide-binding region; oxidoreductase alpha (molybdopterin) subunit 1154755 4582560 Pden_4009 Paracoccus denitrificans PD1222 oxidoreductase alpha (molybdopterin) subunit YP_917771.1 1152491 D 318586 CDS YP_917772.1 119386717 4582561 1154774..1156177 1 NC_008687.1 PFAM: cytochrome bd ubiquinol oxidase, subunit I; KEGG: nar:Saro_1025 cytochrome bd ubiquinol oxidase, subunit I; cytochrome bd ubiquinol oxidase, subunit I 1156177 4582561 Pden_4010 Paracoccus denitrificans PD1222 cytochrome bd ubiquinol oxidase, subunit I YP_917772.1 1154774 D 318586 CDS YP_917773.1 119386718 4582562 1156179..1157183 1 NC_008687.1 TIGRFAM: cytochrome d ubiquinol oxidase, subunit II; PFAM: cytochrome bd ubiquinol oxidase, subunit II; KEGG: nar:Saro_1026 cytochrome d ubiquinol oxidase, subunit II; cytochrome d ubiquinol oxidase, subunit II 1157183 4582562 Pden_4011 Paracoccus denitrificans PD1222 cytochrome d ubiquinol oxidase, subunit II YP_917773.1 1156179 D 318586 CDS YP_917774.1 119386719 4582563 1157362..1160223 1 NC_008687.1 PFAM: AAA ATPase, central domain protein; Clp N terminal domain protein; ATPase associated with various cellular activities, AAA_5; ATPase AAA-2 domain protein; SMART: AAA ATPase; KEGG: bam:Bamb_5668 ATPase AAA-2 domain protein; ATPase 1160223 4582563 Pden_4012 Paracoccus denitrificans PD1222 ATPase YP_917774.1 1157362 D 318586 CDS YP_917775.1 119386720 4582564 1160292..1160924 1 NC_008687.1 PFAM: multiple antibiotic resistance (MarC)-related proteins; KEGG: bur:Bcep18194_C7011 multiple antibiotic resistance (MarC)-related proteins; multiple antibiotic resistance (MarC)-like proteins 1160924 4582564 Pden_4013 Paracoccus denitrificans PD1222 multiple antibiotic resistance (MarC)-like proteins YP_917775.1 1160292 D 318586 CDS YP_917776.1 119386721 4582565 1160987..1162009 1 NC_008687.1 TIGRFAM: Dyp-type peroxidase family; PFAM: Dyp-type peroxidase; KEGG: bam:Bamb_5665 Dyp-type peroxidase family; Dyp-type peroxidase family protein 1162009 4582565 Pden_4014 Paracoccus denitrificans PD1222 Dyp-type peroxidase family protein YP_917776.1 1160987 D 318586 CDS YP_917777.1 119386722 4582566 1162011..1162808 1 NC_008687.1 PFAM: Linocin_M18 bacteriocin protein; KEGG: bbr:BB2479 bacteriocin; Linocin_M18 bacteriocin protein 1162808 4582566 Pden_4015 Paracoccus denitrificans PD1222 Linocin_M18 bacteriocin protein YP_917777.1 1162011 D 318586 CDS YP_917778.1 119386723 4582567 1162815..1163705 1 NC_008687.1 PFAM: protein of unknown function UPF0187; KEGG: pen:PSEEN4044 hypothetical protein; hypothetical protein 1163705 4582567 Pden_4016 Paracoccus denitrificans PD1222 hypothetical protein YP_917778.1 1162815 D 318586 CDS YP_917779.1 119386724 4582568 1164011..1165297 1 NC_008687.1 KEGG: rsp:RSP_0301 ABC branched chain amino acid transporter, substrate binding protein; ABC branched chain amino acid transporter, substrate binding protein 1165297 4582568 Pden_4017 Paracoccus denitrificans PD1222 ABC branched chain amino acid transporter, substrate binding protein YP_917779.1 1164011 D 318586 CDS YP_917780.1 119386725 4582569 1165346..1167265 1 NC_008687.1 PFAM: inner-membrane translocator; KEGG: rsp:RSP_0300 ABC branched chain amino acid transporter, inner membrane subunit; inner-membrane translocator 1167265 4582569 Pden_4018 Paracoccus denitrificans PD1222 inner-membrane translocator YP_917780.1 1165346 D 318586 CDS YP_917781.1 119386726 4582570 1167267..1168502 1 NC_008687.1 PFAM: inner-membrane translocator; KEGG: rsp:RSP_0299 ABC branched chain amino acid transporter, inner membrane subunit; inner-membrane translocator 1168502 4582570 Pden_4019 Paracoccus denitrificans PD1222 inner-membrane translocator YP_917781.1 1167267 D 318586 CDS YP_917782.1 119386727 4582571 1168499..1169239 1 NC_008687.1 PFAM: ABC transporter related; KEGG: rsp:RSP_0298 ABC branched chain amino acid transporter, ATPase subunit; ABC transporter 1169239 4582571 Pden_4020 Paracoccus denitrificans PD1222 ABC transporter YP_917782.1 1168499 D 318586 CDS YP_917783.1 119386728 4582572 1169243..1169950 1 NC_008687.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rsp:RSP_0297 ABC branched chain amino acid transporter, ATPase subunit; ABC transporter 1169950 4582572 Pden_4021 Paracoccus denitrificans PD1222 ABC transporter YP_917783.1 1169243 D 318586 CDS YP_917784.1 119386729 4582573 1170462..1171013 1 NC_008687.1 PFAM: Redoxin domain protein; KEGG: dar:Daro_3587 hypothetical protein; redoxin domain-containing protein 1171013 4582573 Pden_4022 Paracoccus denitrificans PD1222 redoxin domain-containing protein YP_917784.1 1170462 D 318586 CDS YP_917785.1 119386730 4582574 1171014..1171697 1 NC_008687.1 catalyzes the dephosphorylation of 2-phosphoglycolate to form glycolate and phosphate; phosphoglycolate phosphatase 1171697 4582574 Pden_4023 Paracoccus denitrificans PD1222 phosphoglycolate phosphatase YP_917785.1 1171014 D 318586 CDS YP_917786.1 119386731 4582575 1171756..1172226 1 NC_008687.1 PFAM: protein of unknown function DUF442; KEGG: rsp:RSP_0167 hypothetical protein; hypothetical protein 1172226 4582575 Pden_4024 Paracoccus denitrificans PD1222 hypothetical protein YP_917786.1 1171756 D 318586 CDS YP_917787.1 119386732 4582576 1172479..1174299 1 NC_008687.1 TIGRFAM: small GTP-binding protein; GTP-binding protein TypA; PFAM: elongation factor G domain protein; protein synthesis factor, GTP-binding; elongation factor Tu, domain 2 protein; KEGG: rsp:RSP_0448 EF-Tu; elongation factor Tu; GTP-binding protein TypA 1174299 4582576 Pden_4025 Paracoccus denitrificans PD1222 GTP-binding protein TypA YP_917787.1 1172479 D 318586 CDS YP_917788.1 119386733 4582577 1174385..1175020 1 NC_008687.1 hypothetical protein 1175020 4582577 Pden_4026 Paracoccus denitrificans PD1222 hypothetical protein YP_917788.1 1174385 D 318586 CDS YP_917789.1 119386734 4582578 complement(1175033..1175356) 1 NC_008687.1 PFAM: ferredoxin; KEGG: sit:TM1040_1949 ferredoxin; ferredoxin 1175356 4582578 Pden_4027 Paracoccus denitrificans PD1222 ferredoxin YP_917789.1 1175033 R 318586 CDS YP_917790.1 119386735 4582579 complement(1175481..1177040) 1 NC_008687.1 bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides; exodeoxyribonuclease VII large subunit 1177040 xseA 4582579 xseA Paracoccus denitrificans PD1222 exodeoxyribonuclease VII large subunit YP_917790.1 1175481 R 318586 CDS YP_917791.1 119386736 4582580 1177155..1178417 1 NC_008687.1 catalyzes the formation of N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-D-ribosylamine and glycine in purine biosynthesis; phosphoribosylamine--glycine ligase 1178417 4582580 Pden_4029 Paracoccus denitrificans PD1222 phosphoribosylamine--glycine ligase YP_917791.1 1177155 D 318586 CDS YP_917792.1 119386737 4582581 1178755..1180317 1 NC_008687.1 catalyzes the formation of 2-isopropylmalate from acetyl-CoA and 2-oxoisovalerate in leucine biosynthesis; 2-isopropylmalate synthase 1180317 4582581 Pden_4030 Paracoccus denitrificans PD1222 2-isopropylmalate synthase YP_917792.1 1178755 D 318586 CDS YP_917793.1 119386738 4582582 complement(1180350..1181189) 1 NC_008687.1 KEGG: jan:Jann_0572 hypothetical protein; hypothetical protein 1181189 4582582 Pden_4031 Paracoccus denitrificans PD1222 hypothetical protein YP_917793.1 1180350 R 318586 CDS YP_917794.1 119386739 4582583 1181383..1182483 1 NC_008687.1 functions in MreBCD complex in some organisms; rod shape-determining protein MreB 1182483 4582583 Pden_4032 Paracoccus denitrificans PD1222 rod shape-determining protein MreB YP_917794.1 1181383 D 318586 CDS YP_917795.1 119386740 4582584 1182497..1183429 1 NC_008687.1 in some organisms this protein is a transmembrane protein while in others it is periplasmic; involved in some organisms with other components of the MreBCD complex and with penicillin binding proteins in the periplasm or cell wall; rod shape-determining protein MreC 1183429 4582584 Pden_4033 Paracoccus denitrificans PD1222 rod shape-determining protein MreC YP_917795.1 1182497 D 318586 CDS YP_917796.1 119386741 4582585 1183422..1183952 1 NC_008687.1 KEGG: rsp:RSP_2327 rod shape-determining protein MreD; rod shape-determining protein MreD 1183952 4582585 Pden_4034 Paracoccus denitrificans PD1222 rod shape-determining protein MreD YP_917796.1 1183422 D 318586 CDS YP_917797.1 119386742 4582586 1183956..1185899 1 NC_008687.1 PFAM: penicillin-binding protein, transpeptidase; Penicillin-binding protein, dimerisation domain; KEGG: rsp:RSP_2326 cell division protein FtsI; peptidoglycan glycosyltransferase 1185899 4582586 Pden_4035 Paracoccus denitrificans PD1222 peptidoglycan glycosyltransferase YP_917797.1 1183956 D 318586 CDS YP_917798.1 119386743 4582587 1185903..1187045 1 NC_008687.1 TIGRFAM: rod shape-determining protein RodA; PFAM: cell cycle protein; KEGG: rsp:RSP_2325 RodA, rod cell shape determining protein; rod shape-determining protein RodA 1187045 4582587 Pden_4036 Paracoccus denitrificans PD1222 rod shape-determining protein RodA YP_917798.1 1185903 D 318586 CDS YP_917799.1 119386744 4582588 1187055..1187975 1 NC_008687.1 PFAM: D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding; KEGG: jan:Jann_3650 D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding; D-isomer specific 2-hydroxyacid dehydrogenase 1187975 4582588 Pden_4037 Paracoccus denitrificans PD1222 D-isomer specific 2-hydroxyacid dehydrogenase YP_917799.1 1187055 D 318586 CDS YP_917800.1 119386745 4582589 1188106..1189533 1 NC_008687.1 KEGG: sit:TM1040_3778 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; TIGRFAM: mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; PFAM: mannose-6-phosphate isomerase, type II; Nucleotidyl transferase; Cupin 2, conserved barrel domain protein; mannose-1-phosphate guanylyltransferase 1189533 4582589 Pden_4038 Paracoccus denitrificans PD1222 mannose-1-phosphate guanylyltransferase YP_917800.1 1188106 D 318586 CDS YP_917801.1 119386746 4582590 1189606..1190637 1 NC_008687.1 KEGG: rsp:RSP_0179 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components TauA; ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components TauA 1190637 4582590 Pden_4039 Paracoccus denitrificans PD1222 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components TauA YP_917801.1 1189606 D 318586 CDS YP_917802.1 119386747 4582591 1190693..1191298 1 NC_008687.1 PFAM: protein of unknown function DUF161; KEGG: rsp:RSP_0447 hypothetical protein; hypothetical protein 1191298 4582591 Pden_4040 Paracoccus denitrificans PD1222 hypothetical protein YP_917802.1 1190693 D 318586 CDS YP_917803.1 119386748 4582592 complement(1191308..1191634) 1 NC_008687.1 PFAM: arsenate reductase and related; KEGG: rsp:RSP_0387 hypothetical protein; arsenate reductase 1191634 4582592 Pden_4041 Paracoccus denitrificans PD1222 arsenate reductase YP_917803.1 1191308 R 318586 CDS YP_917804.1 119386749 4582593 complement(1191781..1193100) 1 NC_008687.1 KEGG: rsp:RSP_0238 hypothetical protein; hypothetical protein 1193100 4582593 Pden_4042 Paracoccus denitrificans PD1222 hypothetical protein YP_917804.1 1191781 R 318586 CDS YP_917805.1 119386750 4582594 1193259..1193768 1 NC_008687.1 PFAM: ErfK/YbiS/YcfS/YnhG family protein; KEGG: rsp:RSP_1201 hypothetical protein; ErfK/YbiS/YcfS/YnhG family protein 1193768 4582594 Pden_4043 Paracoccus denitrificans PD1222 ErfK/YbiS/YcfS/YnhG family protein YP_917805.1 1193259 D 318586 CDS YP_917806.1 119386751 4582595 1193832..1195346 1 NC_008687.1 PFAM: NnrS family protein; KEGG: sme:SMa1194 hypothetical protein; NnrS family protein 1195346 4582595 Pden_4044 Paracoccus denitrificans PD1222 NnrS family protein YP_917806.1 1193832 D 318586 CDS YP_917807.1 119386752 4582596 1195503..1196720 1 NC_008687.1 TIGRFAM: chromate transporter, chromate ion transporter (CHR) family; PFAM: Chromate transporter; KEGG: atc:AGR_L_3461 probable transporter PA4289; chromate transporter 1196720 4582596 Pden_4045 Paracoccus denitrificans PD1222 chromate transporter YP_917807.1 1195503 D 318586 CDS YP_917808.1 119386753 4582597 1196881..1197174 1 NC_008687.1 hypothetical protein 1197174 4582597 Pden_4046 Paracoccus denitrificans PD1222 hypothetical protein YP_917808.1 1196881 D 318586 CDS YP_917809.1 119386754 4582598 complement(1197245..1198684) 1 NC_008687.1 PFAM: NAD(P) transhydrogenase, beta subunit; KEGG: sil:SPO2819 NAD(P)+ transhydrogenase, beta subunit; NAD(P) transhydrogenase subunit beta 1198684 4582598 Pden_4047 Paracoccus denitrificans PD1222 NAD(P) transhydrogenase subunit beta YP_917809.1 1197245 R 318586 CDS YP_917810.1 119386755 4582599 complement(1198698..1200272) 1 NC_008687.1 forms a tetramer composed of 2 alpha subunits and 2 beta subunits in the inner membrane; involved in catalyzing transfer of hydride ion equivalents between NAD and NADP; stereospecific (AB-specific); functions as a proton pump by translocating protons from cytoplasm to periplasm; NAD(P) transhydrogenase subunit alpha 1200272 pntA 4582599 pntA Paracoccus denitrificans PD1222 NAD(P) transhydrogenase subunit alpha YP_917810.1 1198698 R 318586 CDS YP_917811.1 119386756 4582600 complement(1200368..1201048) 1 NC_008687.1 KEGG: jan:Jann_3303 protein of unknown function DUF1498; hypothetical protein 1201048 4582600 Pden_4049 Paracoccus denitrificans PD1222 hypothetical protein YP_917811.1 1200368 R 318586 CDS YP_917812.1 119386757 4582601 complement(1201059..1201466) 1 NC_008687.1 PFAM: Isoprenylcysteine carboxyl methyltransferase; KEGG: rsp:RSP_0241 protein-S-isoprenylcysteine methyltransferase; isoprenylcysteine carboxyl methyltransferase 1201466 4582601 Pden_4050 Paracoccus denitrificans PD1222 isoprenylcysteine carboxyl methyltransferase YP_917812.1 1201059 R 318586 CDS YP_917813.1 119386758 4582602 complement(1201502..1203649) 1 NC_008687.1 catalyzes the formation of malate from glyoxylate and acetyl-CoA; malate synthase G 1203649 4582602 Pden_4051 Paracoccus denitrificans PD1222 malate synthase G YP_917813.1 1201502 R 318586 CDS YP_917814.1 119386759 4582603 complement(1203819..1204523) 1 NC_008687.1 KEGG: jan:Jann_1769 mucin-associated surface protein; mucin-associated surface protein 1204523 4582603 Pden_4052 Paracoccus denitrificans PD1222 mucin-associated surface protein YP_917814.1 1203819 R 318586 CDS YP_917815.1 119386760 4582604 1204691..1207234 1 NC_008687.1 TIGRFAM: aminopeptidase N; PFAM: peptidase M1, membrane alanine aminopeptidase; KEGG: rsp:RSP_1982 aminopeptidase N; aminopeptidase 1207234 pepN 4582604 pepN Paracoccus denitrificans PD1222 aminopeptidase YP_917815.1 1204691 D 318586 CDS YP_917816.1 119386761 4582605 1207252..1208193 1 NC_008687.1 PFAM: phospholipid/glycerol acyltransferase; KEGG: rsp:RSP_1983 phospholipid/glycerol acyltransferase; phospholipid/glycerol acyltransferase 1208193 4582605 Pden_4054 Paracoccus denitrificans PD1222 phospholipid/glycerol acyltransferase YP_917816.1 1207252 D 318586 CDS YP_917817.1 119386762 4582606 complement(1208346..1209458) 1 NC_008687.1 catalyzes the formation of glutamate 5-phosphate from glutamate in proline biosynthesis; gamma-glutamyl kinase 1209458 4582606 Pden_4055 Paracoccus denitrificans PD1222 gamma-glutamyl kinase YP_917817.1 1208346 R 318586 CDS YP_917818.1 119386763 4582607 complement(1209446..1210477) 1 NC_008687.1 essential GTPase; exhibits high exchange rate for GTP/GDP; associates with 50S ribosomal subunit; involved in regulation of chromosomal replication; GTPase ObgE 1210477 obgE 4582607 obgE Paracoccus denitrificans PD1222 GTPase ObgE YP_917818.1 1209446 R 318586 CDS YP_917819.1 119386764 4582608 1210622..1210960 1 NC_008687.1 PFAM: small multidrug resistance protein; KEGG: hch:HCH_07085 membrane transporters of cations and cationic drugs; small multidrug resistance protein 1210960 4582608 Pden_4057 Paracoccus denitrificans PD1222 small multidrug resistance protein YP_917819.1 1210622 D 318586 CDS YP_917820.1 119386765 4582609 1211023..1212438 1 NC_008687.1 PFAM: protein of unknown function UPF0061; KEGG: sil:SPO2480 hypothetical protein; hypothetical protein 1212438 4582609 Pden_4058 Paracoccus denitrificans PD1222 hypothetical protein YP_917820.1 1211023 D 318586 CDS YP_917821.1 119386766 4582610 1212457..1213239 1 NC_008687.1 PFAM: Endonuclease/exonuclease/phosphatase; KEGG: bme:BMEII0240 dioxygenase; endonuclease/exonuclease/phosphatase 1213239 4582610 Pden_4059 Paracoccus denitrificans PD1222 endonuclease/exonuclease/phosphatase YP_917821.1 1212457 D 318586 CDS YP_917822.1 119386767 4582611 1213306..1214583 1 NC_008687.1 enolase; catalyzes the formation of phosphoenolpyruvate from 2-phospho-D-glycerate in glycolysis; phosphopyruvate hydratase 1214583 eno 4582611 eno Paracoccus denitrificans PD1222 phosphopyruvate hydratase YP_917822.1 1213306 D 318586 CDS YP_917823.1 119386768 4582612 complement(1214632..1215447) 1 NC_008687.1 KEGG: sil:SPO2129 hypothetical protein; hypothetical protein 1215447 4582612 Pden_4061 Paracoccus denitrificans PD1222 hypothetical protein YP_917823.1 1214632 R 318586 CDS YP_917824.1 119386769 4582613 complement(1215444..1217066) 1 NC_008687.1 TIGRFAM: 2-isopropylmalate synthase/homocitrate synthase family protein; PFAM: pyruvate carboxyltransferase; LeuA allosteric (dimerisation) domain; KEGG: jan:Jann_1959 2-isopropylmalate synthase/homocitrate synthase; alpha-isopropylmalate synthase 1217066 4582613 Pden_4062 Paracoccus denitrificans PD1222 alpha-isopropylmalate synthase YP_917824.1 1215444 R 318586 CDS YP_917825.1 119386770 4582614 complement(1217099..1218487) 1 NC_008687.1 KEGG: sit:TM1040_1153 cysteinyl-tRNA synthetase; TIGRFAM: cysteinyl-tRNA synthetase; PFAM: cysteinyl-tRNA synthetase, class Ia; cysteinyl-tRNA synthetase 1218487 4582614 Pden_4063 Paracoccus denitrificans PD1222 cysteinyl-tRNA synthetase YP_917825.1 1217099 R 318586 CDS YP_917826.1 119386771 4582615 1218643..1218984 1 NC_008687.1 KEGG: rsp:RSP_2721 hypothetical protein; hypothetical protein 1218984 4582615 Pden_4064 Paracoccus denitrificans PD1222 hypothetical protein YP_917826.1 1218643 D 318586 CDS YP_917827.1 119386772 4582616 complement(1219068..1219508) 1 NC_008687.1 KEGG: gbe:GbCGDNIH1_2282 hypothetical secreted protein; hypothetical protein 1219508 4582616 Pden_4065 Paracoccus denitrificans PD1222 hypothetical protein YP_917827.1 1219068 R 318586 CDS YP_917828.1 119386773 4582617 complement(1219607..1220746) 1 NC_008687.1 PFAM: ABC transporter related; Transport-associated OB domain protein; SMART: AAA ATPase; KEGG: rsp:RSP_0015 ABC spermidine/putrescine transporter, ATPase subunit; ABC transporter 1220746 4582617 Pden_4066 Paracoccus denitrificans PD1222 ABC transporter YP_917828.1 1219607 R 318586 CDS YP_917829.1 119386774 4582618 complement(1220743..1221549) 1 NC_008687.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: rsp:RSP_0016 ABC spermidine/putrescine transporter, inner membrane subunit; binding-protein-dependent transport system inner membrane protein 1221549 4582618 Pden_4067 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_917829.1 1220743 R 318586 CDS YP_917830.1 119386775 4582619 complement(1221546..1222415) 1 NC_008687.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: rsp:RSP_0017 ABC spermidine/putrescine transporter, inner membrane subunit; binding-protein-dependent transport systems inner membrane component 1222415 4582619 Pden_4068 Paracoccus denitrificans PD1222 binding-protein-dependent transport systems inner membrane component YP_917830.1 1221546 R 318586 CDS YP_917831.1 119386776 4582620 complement(1222509..1222934) 1 NC_008687.1 PFAM: protein of unknown function UPF0047; KEGG: rde:RD1_1797 hypothetical protein; hypothetical protein 1222934 4582620 Pden_4069 Paracoccus denitrificans PD1222 hypothetical protein YP_917831.1 1222509 R 318586 CDS YP_917832.1 119386777 4582621 complement(1222931..1224445) 1 NC_008687.1 PFAM: protein of unknown function DUF195; KEGG: mmr:Mmar10_0441 protein of unknown function DUF195; hypothetical protein 1224445 4582621 Pden_4070 Paracoccus denitrificans PD1222 hypothetical protein YP_917832.1 1222931 R 318586 CDS YP_917833.1 119386778 4582622 1224537..1225085 1 NC_008687.1 PFAM: NADPH-dependent FMN reductase; KEGG: bte:BTH_II2367 NADPH-dependent FMN reductase domain protein; NADPH-dependent FMN reductase 1225085 4582622 Pden_4071 Paracoccus denitrificans PD1222 NADPH-dependent FMN reductase YP_917833.1 1224537 D 318586 CDS YP_917834.1 119386779 4582623 complement(1225149..1227143) 1 NC_008687.1 sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released; this is the primary sigma factor of bacteria; RNA polymerase sigma factor RpoD 1227143 4582623 Pden_4072 Paracoccus denitrificans PD1222 RNA polymerase sigma factor RpoD YP_917834.1 1225149 R 318586 CDS YP_917835.1 119386780 4582624 complement(1227285..1229225) 1 NC_008687.1 synthesizes RNA primers at the replication forks; DNA primase 1229225 dnaG 4582624 dnaG Paracoccus denitrificans PD1222 DNA primase YP_917835.1 1227285 R 318586 CDS YP_917836.1 119386781 4582625 complement(1229265..1229849) 1 NC_008687.1 PFAM: regulatory protein, TetR; KEGG: sil:SPO1736 transcriptional regulator, TetR family; TetR family transcriptional regulator 1229849 4582625 Pden_4074 Paracoccus denitrificans PD1222 TetR family transcriptional regulator YP_917836.1 1229265 R 318586 CDS YP_917837.1 119386782 4582626 1230311..1231474 1 NC_008687.1 PFAM: FMN-dependent alpha-hydroxy acid dehydrogenase; KEGG: rsp:RSP_0829 lactate dehydrogenase; L-lactate dehydrogenase (cytochrome) 1231474 4582626 Pden_4075 Paracoccus denitrificans PD1222 L-lactate dehydrogenase (cytochrome) YP_917837.1 1230311 D 318586 CDS YP_917838.1 119386783 4582627 complement(1231504..1232571) 1 NC_008687.1 KEGG: pfl:PFL_4227 acyltransferase family protein; acyltransferase 1232571 4582627 Pden_4076 Paracoccus denitrificans PD1222 acyltransferase YP_917838.1 1231504 R 318586 CDS YP_917839.1 119386784 4582628 1232663..1233289 1 NC_008687.1 the Ctc family of proteins consists of two types, one that contains the N-terminal ribosomal protein L25 domain only which in Escherichia coli binds the 5S rRNA while a subset of proteins contain a C-terminal extension that is involved in the stress response; 50S ribosomal protein L25 1233289 4582628 Pden_4077 Paracoccus denitrificans PD1222 50S ribosomal protein L25 YP_917839.1 1232663 D 318586 CDS YP_917840.1 119386785 4582629 1233405..1234745 1 NC_008687.1 TrmFO; Gid; glucose-inhibited division protein; similar to GidA; the gene from Bacillus subtilis encodes a tRNA-methyltransferase that utilizes folate as the carbon donor and bound flavin as reductant; modifies tRNA at position 54 (uridine) of the T-psi loop to form a C5-methyluridine; tRNA (uracil-5-)-methyltransferase Gid 1234745 4582629 Pden_4078 Paracoccus denitrificans PD1222 tRNA (uracil-5-)-methyltransferase Gid YP_917840.1 1233405 D 318586 CDS YP_917841.1 119386786 4582630 1234742..1235587 1 NC_008687.1 PFAM: glutamyl-tRNA synthetase, class Ic; KEGG: rsp:RSP_2628 glutamyl-/glutaminyl-tRNA synthetase; glutamyl-tRNA synthetase, class Ic 1235587 4582630 Pden_4079 Paracoccus denitrificans PD1222 glutamyl-tRNA synthetase, class Ic YP_917841.1 1234742 D 318586 CDS YP_917842.1 119386787 4582631 complement(1235569..1235934) 1 NC_008687.1 PFAM: phosphoribosyl-AMP cyclohydrolase; KEGG: rsp:RSP_2627 phosphoribosyl-AMP cyclohydrolase; phosphoribosyl-AMP cyclohydrolase 1235934 4582631 Pden_4080 Paracoccus denitrificans PD1222 phosphoribosyl-AMP cyclohydrolase YP_917842.1 1235569 R 318586 CDS YP_917843.1 119386788 4582632 1235995..1236432 1 NC_008687.1 KEGG: rsp:RSP_2625 NifU-related protein involved in Fe-S cluster formation; NifU-related protein involved in Fe-S cluster formation 1236432 4582632 Pden_4081 Paracoccus denitrificans PD1222 NifU-related protein involved in Fe-S cluster formation YP_917843.1 1235995 D 318586 CDS YP_917844.1 119386789 4582633 complement(1236788..1238881) 1 NC_008687.1 catalyzes branch migration in Holliday junction intermediates; ATP-dependent DNA helicase RecG 1238881 4582633 Pden_4082 Paracoccus denitrificans PD1222 ATP-dependent DNA helicase RecG YP_917844.1 1236788 R 318586 CDS YP_917845.1 119386790 4582634 complement(1238878..1241175) 1 NC_008687.1 KEGG: sil:SPO1680 DNA ligase, NAD-dependent; TIGRFAM: DNA ligase, NAD-dependent; PFAM: BRCT domain protein; zinc-finger, NAD-dependent DNA ligase C4-type; NAD-dependent DNA ligase, OB-fold; NAD-dependent DNA ligase, adenylation; SMART: NAD-dependent DNA ligase-like; NAD-dependent DNA ligase 1241175 4582634 Pden_4083 Paracoccus denitrificans PD1222 NAD-dependent DNA ligase YP_917845.1 1238878 R 318586 CDS YP_917846.1 119386791 4582635 complement(1241333..1241506) 1 NC_008687.1 KEGG: mmr:Mmar10_0669 two component transcriptional regulator, winged helix family; response regulator receiver protein 1241506 4582635 Pden_4084 Paracoccus denitrificans PD1222 response regulator receiver protein YP_917846.1 1241333 R 318586 CDS YP_917847.1 119386792 4582636 complement(1241524..1241892) 1 NC_008687.1 hypothetical protein 1241892 4582636 Pden_4085 Paracoccus denitrificans PD1222 hypothetical protein YP_917847.1 1241524 R 318586 CDS YP_917848.1 119386793 4582637 1241928..1242326 1 NC_008687.1 hypothetical protein 1242326 4582637 Pden_4086 Paracoccus denitrificans PD1222 hypothetical protein YP_917848.1 1241928 D 318586 CDS YP_917849.1 119386794 4582638 complement(1242832..1243461) 1 NC_008687.1 PFAM: protein of unknown function DUF847; KEGG: bmb:BruAb1_0990 secretion activator protein, hypothetical; hypothetical protein 1243461 4582638 Pden_4087 Paracoccus denitrificans PD1222 hypothetical protein YP_917849.1 1242832 R 318586 CDS YP_917850.1 119386795 4582639 complement(1243464..1243733) 1 NC_008687.1 hypothetical protein 1243733 4582639 Pden_4088 Paracoccus denitrificans PD1222 hypothetical protein YP_917850.1 1243464 R 318586 CDS YP_917851.1 119386796 4582640 complement(1243733..1245883) 1 NC_008687.1 PFAM: metallophosphoesterase; KEGG: nha:Nham_3850 complement C1q protein; metallophosphoesterase 1245883 4582640 Pden_4089 Paracoccus denitrificans PD1222 metallophosphoesterase YP_917851.1 1243733 R 318586 CDS YP_917852.1 119386797 4582641 complement(1245880..1246230) 1 NC_008687.1 hypothetical protein 1246230 4582641 Pden_4090 Paracoccus denitrificans PD1222 hypothetical protein YP_917852.1 1245880 R 318586 CDS YP_917853.1 119386798 4582642 complement(1246230..1247267) 1 NC_008687.1 KEGG: sat:SYN_02283 hypothetical cytosolic protein; hypothetical protein 1247267 4582642 Pden_4091 Paracoccus denitrificans PD1222 hypothetical protein YP_917853.1 1246230 R 318586 CDS YP_917854.1 119386799 4582643 1247347..1247706 1 NC_008687.1 KEGG: mlo:mll5675 hypothetical protein; hypothetical protein 1247706 4582643 Pden_4092 Paracoccus denitrificans PD1222 hypothetical protein YP_917854.1 1247347 D 318586 CDS YP_917855.1 119386800 4582644 complement(1247883..1249376) 1 NC_008687.1 KEGG: jan:Jann_0236 hypothetical protein; hypothetical protein 1249376 4582644 Pden_4093 Paracoccus denitrificans PD1222 hypothetical protein YP_917855.1 1247883 R 318586 CDS YP_917856.1 119386801 4582645 complement(1249366..1250628) 1 NC_008687.1 hypothetical protein 1250628 4582645 Pden_4094 Paracoccus denitrificans PD1222 hypothetical protein YP_917856.1 1249366 R 318586 CDS YP_917857.1 119386802 4582646 1250937..1251944 1 NC_008687.1 PFAM: phage integrase family protein; KEGG: mag:amb2709 integrase; phage integrase family protein 1251944 4582646 Pden_4095 Paracoccus denitrificans PD1222 phage integrase family protein YP_917857.1 1250937 D 318586 CDS YP_917858.1 119386803 4582647 complement(1251970..1252524) 1 NC_008687.1 PFAM: response regulator receiver; KEGG: sil:SPO1679 DNA-binding response regulator CtrA; two component transcriptional regulator 1252524 4582647 Pden_4096 Paracoccus denitrificans PD1222 two component transcriptional regulator YP_917858.1 1251970 R 318586 CDS YP_917859.1 119386804 4582648 complement(1252581..1252892) 1 NC_008687.1 PFAM: protein of unknown function DUF1153; KEGG: rsp:RSP_2620 hypothetical protein; hypothetical protein 1252892 4582648 Pden_4097 Paracoccus denitrificans PD1222 hypothetical protein YP_917859.1 1252581 R 318586 CDS YP_917860.1 119386805 4582649 1253056..1254225 1 NC_008687.1 catalyzes a sulfuration reaction to synthesize 2-thiouridine at the U34 position of tRNAs; tRNA-specific 2-thiouridylase MnmA 1254225 mnmA 4582649 mnmA Paracoccus denitrificans PD1222 tRNA-specific 2-thiouridylase MnmA YP_917860.1 1253056 D 318586 CDS YP_917861.1 119386806 4582650 complement(1254239..1254646) 1 NC_008687.1 PFAM: Fe-S metabolism associated SufE; KEGG: jan:Jann_1840 Fe-S metabolism associated SufE; Fe-S metabolism associated SufE 1254646 4582650 Pden_4099 Paracoccus denitrificans PD1222 Fe-S metabolism associated SufE YP_917861.1 1254239 R 318586 CDS YP_917862.1 119386807 4582651 1254775..1255284 1 NC_008687.1 KEGG: rsp:RSP_1972 hypothetical protein; hypothetical protein 1255284 4582651 Pden_4100 Paracoccus denitrificans PD1222 hypothetical protein YP_917862.1 1254775 D 318586 CDS YP_917863.1 119386808 4582652 complement(1255587..1256132) 1 NC_008687.1 PFAM: GCN5-related N-acetyltransferase; KEGG: rsp:RSP_3821 acetyltransferase; N-acetyltransferase GCN5 1256132 4582652 Pden_4101 Paracoccus denitrificans PD1222 N-acetyltransferase GCN5 YP_917863.1 1255587 R 318586 CDS YP_917864.1 119386809 4582653 complement(1256245..1256517) 1 NC_008687.1 involved in the peptidyltransferase reaction during translation; 50S ribosomal protein L27 1256517 rpmA 4582653 rpmA Paracoccus denitrificans PD1222 50S ribosomal protein L27 YP_917864.1 1256245 R 318586 CDS YP_917865.1 119386810 4582654 complement(1256537..1256959) 1 NC_008687.1 PFAM: ribosomal protein L21; KEGG: sil:SPO1990 ribosomal protein L21; 50S ribosomal protein L21 1256959 rplU 4582654 rplU Paracoccus denitrificans PD1222 50S ribosomal protein L21 YP_917865.1 1256537 R 318586 CDS YP_917866.1 119386811 4582655 complement(1257151..1258212) 1 NC_008687.1 PFAM: L-carnitine dehydratase/bile acid-inducible protein F; KEGG: sco:SCO6730 racemase; L-carnitine dehydratase/bile acid-inducible protein F 1258212 4582655 Pden_4104 Paracoccus denitrificans PD1222 L-carnitine dehydratase/bile acid-inducible protein F YP_917866.1 1257151 R 318586 CDS YP_917867.1 119386812 4582656 complement(1258639..1258827) 1 NC_008687.1 KEGG: sil:SPO2944 hypothetical protein; hypothetical protein 1258827 4582656 Pden_4105 Paracoccus denitrificans PD1222 hypothetical protein YP_917867.1 1258639 R 318586 CDS YP_917868.1 119386813 4582657 complement(1258997..1260334) 1 NC_008687.1 KEGG: rha:RHA1_ro05532 nitrilotriacetate monooxygenase; nitrilotriacetate monooxygenase 1260334 4582657 Pden_4106 Paracoccus denitrificans PD1222 nitrilotriacetate monooxygenase YP_917868.1 1258997 R 318586 CDS YP_917869.1 119386814 4582658 complement(1260347..1261075) 1 NC_008687.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: mlo:mll9179 ABC transporter ATP-binding subunit; ABC transporter 1261075 4582658 Pden_4107 Paracoccus denitrificans PD1222 ABC transporter YP_917869.1 1260347 R 318586 CDS YP_917870.1 119386815 4582659 complement(1261072..1261923) 1 NC_008687.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: nfa:nfa18270 transporter; binding-protein-dependent transport system inner membrane protein 1261923 4582659 Pden_4108 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_917870.1 1261072 R 318586 CDS YP_917871.1 119386816 4582660 complement(1261944..1263161) 1 NC_008687.1 KEGG: nfa:nfa18260 sulfonate/nitrate transport system substrate-binding protein; sulfonate/nitrate transport system substrate-binding protein 1263161 4582660 Pden_4109 Paracoccus denitrificans PD1222 sulfonate/nitrate transport system substrate-binding protein YP_917871.1 1261944 R 318586 CDS YP_917872.1 119386817 4582661 complement(1263193..1263993) 1 NC_008687.1 PFAM: HpcH/HpaI aldolase; KEGG: bmb:BruAb2_0163 hypothetical citrate lyase, beta subunit; HpcH/HpaI aldolase 1263993 4582661 Pden_4110 Paracoccus denitrificans PD1222 HpcH/HpaI aldolase YP_917872.1 1263193 R 318586 CDS YP_917873.1 119386818 4582662 complement(1263987..1264820) 1 NC_008687.1 KEGG: bmb:BruAb2_0162 hypothetical protein; hypothetical protein 1264820 4582662 Pden_4111 Paracoccus denitrificans PD1222 hypothetical protein YP_917873.1 1263987 R 318586 CDS YP_917874.1 119386819 4582663 complement(1264817..1265923) 1 NC_008687.1 PFAM: L-carnitine dehydratase/bile acid-inducible protein F; KEGG: rpa:RPA1611 dehydratase; L-carnitine dehydratase/bile acid-inducible protein F 1265923 4582663 Pden_4112 Paracoccus denitrificans PD1222 L-carnitine dehydratase/bile acid-inducible protein F YP_917874.1 1264817 R 318586 CDS YP_917875.1 119386820 4582665 complement(1267193..1267576) 1 NC_008687.1 PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase; KEGG: pfl:PFL_3598 glyoxalase family protein; glyoxalase/bleomycin resistance protein/dioxygenase 1267576 4582665 Pden_4115 Paracoccus denitrificans PD1222 glyoxalase/bleomycin resistance protein/dioxygenase YP_917875.1 1267193 R 318586 CDS YP_917876.1 119386821 4582666 complement(1267591..1269003) 1 NC_008687.1 KEGG: rru:Rru_A2561 hypothetical protein; hypothetical protein 1269003 4582666 Pden_4116 Paracoccus denitrificans PD1222 hypothetical protein YP_917876.1 1267591 R 318586 CDS YP_917877.1 119386822 4582667 1269315..1270067 1 NC_008687.1 PFAM: Methyltransferase type 11; Methyltransferase type 12; KEGG: mag:amb2135 2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase; methyltransferase type 11 1270067 4582667 Pden_4117 Paracoccus denitrificans PD1222 methyltransferase type 11 YP_917877.1 1269315 D 318586 CDS YP_917878.1 119386823 4582668 1270064..1271038 1 NC_008687.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: mag:amb3232 transcriptional regulator; LysR family transcriptional regulator 1271038 4582668 Pden_4118 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_917878.1 1270064 D 318586 CDS YP_917879.1 119386824 4582669 1271048..1272553 1 NC_008687.1 TIGRFAM: hydro-lyases, Fe-S type, tartrate/fumarate subfamily, alpha subunit; hydro-lyases, Fe-S type, tartrate/fumarate subfamily, beta subunit; PFAM: Fe-S type hydro-lyases tartrate/fumarate alpha region; Fe-S type hydro-lyases tartrate/fumarate beta region; KEGG: bbr:BB4081 fumarate hydratase; tartrate/fumarate subfamily Fe-S type hydro-lyase subunit alpha 1272553 4582669 Pden_4119 Paracoccus denitrificans PD1222 tartrate/fumarate subfamily Fe-S type hydro-lyase subunit alpha YP_917879.1 1271048 D 318586 CDS YP_917880.1 119386825 4582670 complement(1272599..1273921) 1 NC_008687.1 TIGRFAM: TRAP dicarboxylate transporter, DctM subunit; PFAM: TRAP C4-dicarboxylate transport system permease DctM subunit; KEGG: rsp:RSP_0912 TRAP-T family C4-dicarboxylate transporter, DctM (12TMs) subunit; TRAP dicarboxylate transporter, DctM subunit 1273921 4582670 Pden_4120 Paracoccus denitrificans PD1222 TRAP dicarboxylate transporter, DctM subunit YP_917880.1 1272599 R 318586 CDS YP_917881.1 119386826 4582671 complement(1273918..1274550) 1 NC_008687.1 PFAM: Tripartite ATP-independent periplasmic transporter, DctQ component; KEGG: rsp:RSP_0911 TRAP-T family C4-dicarboxylate transporter, DctQ (4TMs) subunit; tripartite ATP-independent periplasmic transporter DctQ 1274550 4582671 Pden_4121 Paracoccus denitrificans PD1222 tripartite ATP-independent periplasmic transporter DctQ YP_917881.1 1273918 R 318586 CDS YP_917882.1 119386827 4582672 complement(1274606..1275613) 1 NC_008687.1 TIGRFAM: TRAP dicarboxylate transporter, DctP subunit; PFAM: TRAP dicarboxylate transporter- DctP subunit; KEGG: rsp:RSP_0910 TRAP-T family transporter, C4-dicarboxylate-binding protein DctP; TRAP dicarboxylate transporter, DctP subunit 1275613 4582672 Pden_4122 Paracoccus denitrificans PD1222 TRAP dicarboxylate transporter, DctP subunit YP_917882.1 1274606 R 318586 CDS YP_917883.1 119386828 4582673 complement(1276073..1277380) 1 NC_008687.1 TIGRFAM: small GTP-binding protein; PFAM: GTP-binding protein, HSR1-related; KEGG: rsp:RSP_2844 GTP-binding protein; small GTP-binding protein 1277380 4582673 Pden_4123 Paracoccus denitrificans PD1222 small GTP-binding protein YP_917883.1 1276073 R 318586 CDS YP_917884.1 119386829 4582674 complement(1277381..1277614) 1 NC_008687.1 Stimulates the elongation of poly(A) tails; RNA-binding protein Hfq 1277614 hfq 4582674 hfq Paracoccus denitrificans PD1222 RNA-binding protein Hfq YP_917884.1 1277381 R 318586 CDS YP_917885.1 119386830 4582675 complement(1277695..1279317) 1 NC_008687.1 PFAM: cation transporter; KEGG: rsp:RSP_2842 potassium uptake transporter, transmembrane subunit, TrkH; cation transporter 1279317 4582675 Pden_4125 Paracoccus denitrificans PD1222 cation transporter YP_917885.1 1277695 R 318586 CDS YP_917886.1 119386831 4582676 complement(1279326..1280702) 1 NC_008687.1 involved in potassium uptake; found to be peripherally associated with the inner membrane in Escherichia coli; contains an NAD-binding domain; potassium transporter peripheral membrane protein 1280702 trkA 4582676 trkA Paracoccus denitrificans PD1222 potassium transporter peripheral membrane protein YP_917886.1 1279326 R 318586 CDS YP_917887.1 119386832 4582677 complement(1281036..1282424) 1 NC_008687.1 PFAM: response regulator receiver; sigma-54 factor, interaction domain-containing protein; helix-turn-helix, Fis-type; SMART: AAA ATPase; KEGG: rsp:RSP_2840 nitrogen assimilation transcriptional regulator, NtrX; two component, sigma54 specific, Fis family transcriptional regulator 1282424 4582677 Pden_4127 Paracoccus denitrificans PD1222 two component, sigma54 specific, Fis family transcriptional regulator YP_917887.1 1281036 R 318586 CDS YP_917888.1 119386833 4582678 complement(1282421..1284679) 1 NC_008687.1 KEGG: rsp:RSP_2839 nitrogen regulation protein, NtrY, signal transduction histidine kinase; TIGRFAM: PAS sensor protein; PFAM: ATP-binding region, ATPase domain protein domain protein; histidine kinase, HAMP region domain protein; histidine kinase A domain protein domain protein; PAS fold-4 domain protein; PAS fold domain protein; SMART: PAS domain containing protein; multi-sensor signal transduction histidine kinase 1284679 4582678 Pden_4128 Paracoccus denitrificans PD1222 multi-sensor signal transduction histidine kinase YP_917888.1 1282421 R 318586 CDS YP_917889.1 119386834 4582679 complement(1284765..1286222) 1 NC_008687.1 PFAM: response regulator receiver; sigma-54 factor, interaction domain-containing protein; helix-turn-helix, Fis-type; SMART: AAA ATPase; KEGG: rde:RD1_2763 nitrogen regulation protein; two component, sigma54 specific, Fis family transcriptional regulator 1286222 4582679 Pden_4129 Paracoccus denitrificans PD1222 two component, sigma54 specific, Fis family transcriptional regulator YP_917889.1 1284765 R 318586 CDS YP_917890.1 119386835 4582680 complement(1286231..1287388) 1 NC_008687.1 PFAM: ATP-binding region, ATPase domain protein domain protein; histidine kinase A domain protein domain protein; KEGG: rsp:RSP_2837 nitrogen regulation protein, NtrB signal transduction histidine kinase; signal transduction histidine kinase, nitrogen specific, NtrB 1287388 4582680 Pden_4130 Paracoccus denitrificans PD1222 signal transduction histidine kinase, nitrogen specific, NtrB YP_917890.1 1286231 R 318586 CDS YP_917891.1 119386836 4582681 complement(1287385..1288434) 1 NC_008687.1 TIGRFAM: TIM-barrel protein, nifR3 family; PFAM: dihydrouridine synthase, DuS; KEGG: jan:Jann_2236 dihydrouridine synthase TIM-barrel protein nifR3; nifR3 family TIM-barrel protein 1288434 4582681 Pden_4131 Paracoccus denitrificans PD1222 nifR3 family TIM-barrel protein YP_917891.1 1287385 R 318586 CDS YP_917892.1 119386837 4582682 1288663..1290045 1 NC_008687.1 KEGG: rsp:RSP_0361 probable L-serine dehydratase; TIGRFAM: L-serine dehydratase 1; PFAM: serine dehydratase alpha chain; serine dehydratase beta chain; L-serine dehydratase 1 1290045 4582682 Pden_4132 Paracoccus denitrificans PD1222 L-serine dehydratase 1 YP_917892.1 1288663 D 318586 CDS YP_917893.1 119386838 4582683 1290172..1291083 1 NC_008687.1 KEGG: cal:orf19.4334 hypothetical protein; FHA domain-containing protein 1291083 4582683 Pden_4133 Paracoccus denitrificans PD1222 FHA domain-containing protein YP_917893.1 1290172 D 318586 CDS YP_917894.1 119386839 4582684 1291171..1293366 1 NC_008687.1 PFAM: protein of unknown function DUF940, membrane lipoprotein KEGG: rsp:RSP_1187 hypothetical protein; membrane lipoprotein 1293366 4582684 Pden_4134 Paracoccus denitrificans PD1222 membrane lipoprotein YP_917894.1 1291171 D 318586 CDS YP_917895.1 119386840 4582685 1293363..1294031 1 NC_008687.1 KEGG: rsp:RSP_1186 hypothetical protein; hypothetical protein 1294031 4582685 Pden_4135 Paracoccus denitrificans PD1222 hypothetical protein YP_917895.1 1293363 D 318586 CDS YP_917896.1 119386841 4582686 complement(1294204..1294596) 1 NC_008687.1 hypothetical protein 1294596 4582686 Pden_4136 Paracoccus denitrificans PD1222 hypothetical protein YP_917896.1 1294204 R 318586 CDS YP_917897.1 119386842 4582687 complement(1294622..1295404) 1 NC_008687.1 PFAM: ABC-3 protein; KEGG: rsp:RSP_3567 ABC zinc tranporter, inner membrane subunit ZnuB; ABC-3 protein 1295404 4582687 Pden_4137 Paracoccus denitrificans PD1222 ABC-3 protein YP_917897.1 1294622 R 318586 CDS YP_917898.1 119386843 4582688 complement(1295411..1296175) 1 NC_008687.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rsp:RSP_3568 ABC zinc transporter, ATPase subunit ZnuC; ABC transporter 1296175 4582688 Pden_4138 Paracoccus denitrificans PD1222 ABC transporter YP_917898.1 1295411 R 318586 CDS YP_917899.1 119386844 4582689 complement(1296172..1296666) 1 NC_008687.1 KEGG: rsp:RSP_3569 zinc-uptake regulator, Zur; ferric uptake regulator family protein 1296666 4582689 Pden_4139 Paracoccus denitrificans PD1222 ferric uptake regulator family protein YP_917899.1 1296172 R 318586 CDS YP_917900.1 119386845 4582690 1296748..1297728 1 NC_008687.1 PFAM: periplasmic solute binding protein; KEGG: rsp:RSP_3571 ABC zinc transporter, periplasmic binding protein ZnuA; periplasmic solute binding protein 1297728 4582690 Pden_4140 Paracoccus denitrificans PD1222 periplasmic solute binding protein YP_917900.1 1296748 D 318586 CDS YP_917901.1 119386846 4582691 1297911..1298087 1 NC_008687.1 KEGG: sil:SPO0789 hypothetical protein; hypothetical protein 1298087 4582691 Pden_4141 Paracoccus denitrificans PD1222 hypothetical protein YP_917901.1 1297911 D 318586 CDS YP_917902.1 119386847 4582692 complement(1298113..1299486) 1 NC_008687.1 PFAM: RNA-binding S4 domain protein; pseudouridine synthase; KEGG: rsp:RSP_2266 pseudouridine synthase, (predicted); RNA-binding S4 domain-containing protein 1299486 4582692 Pden_4142 Paracoccus denitrificans PD1222 RNA-binding S4 domain-containing protein YP_917902.1 1298113 R 318586 CDS YP_917903.1 119386848 4582693 1299595..1300044 1 NC_008687.1 PFAM: CMP/dCMP deaminase, zinc-binding; KEGG: rde:RD1_1993 cytidine and deoxycytidylate deaminase family protein; zinc-binding CMP/dCMP deaminase 1300044 4582693 Pden_4143 Paracoccus denitrificans PD1222 zinc-binding CMP/dCMP deaminase YP_917903.1 1299595 D 318586 CDS YP_917904.1 119386849 4582694 1300140..1303574 1 NC_008687.1 biotin-containing enzyme that catalyzes a two step carboxylation of pyruvate to oxaloacetate; pyruvate carboxylase 1303574 4582694 Pden_4144 Paracoccus denitrificans PD1222 pyruvate carboxylase YP_917904.1 1300140 D 318586 CDS YP_917905.1 119386850 4582695 complement(1303951..1305000) 1 NC_008687.1 PFAM: protein of unknown function DUF395, YeeE/YedE; KEGG: sil:SPO0988 YeeE/YedE family protein; hypothetical protein 1305000 4582695 Pden_4145 Paracoccus denitrificans PD1222 hypothetical protein YP_917905.1 1303951 R 318586 CDS YP_917906.1 119386851 4582696 complement(1305071..1305412) 1 NC_008687.1 PFAM: regulatory protein, ArsR; KEGG: rsp:RSP_2606 ArsR family arsenical resistance operon repressor; regulatory protein ArsR 1305412 4582696 Pden_4146 Paracoccus denitrificans PD1222 regulatory protein ArsR YP_917906.1 1305071 R 318586 CDS YP_917907.1 119386852 4582697 complement(1305520..1305903) 1 NC_008687.1 KEGG: rde:RD1_1508 SoxS; SoxS 1305903 4582697 Pden_4147 Paracoccus denitrificans PD1222 SoxS YP_917907.1 1305520 R 318586 CDS YP_917908.1 119386853 4582698 1305975..1306712 1 NC_008687.1 PFAM: cytochrome c biogenesis protein, transmembrane region; KEGG: sil:SPO0991 sulfur oxidation V protein; cytochrome c biogenesis protein, transmembrane region 1306712 4582698 Pden_4148 Paracoccus denitrificans PD1222 cytochrome c biogenesis protein, transmembrane region YP_917908.1 1305975 D 318586 CDS YP_917909.1 119386854 4582699 1306726..1307286 1 NC_008687.1 KEGG: sil:SPO0992 thioredoxin SoxW; thioredoxin SoxW 1307286 4582699 Pden_4149 Paracoccus denitrificans PD1222 thioredoxin SoxW YP_917909.1 1306726 D 318586 CDS YP_917910.1 119386855 4582700 1307402..1307875 1 NC_008687.1 PFAM: cytochrome c, class I; KEGG: sil:SPO0993 monoheme cytochrome c SoxX; cytochrome c, class I 1307875 4582700 Pden_4150 Paracoccus denitrificans PD1222 cytochrome c, class I YP_917910.1 1307402 D 318586 CDS YP_917911.1 119386856 4582701 1307915..1308337 1 NC_008687.1 with SoxZ catalyzes the oxidation of sulfur compounds; sulfur oxidation protein SoxY 1308337 4582701 Pden_4151 Paracoccus denitrificans PD1222 sulfur oxidation protein SoxY YP_917911.1 1307915 D 318586 CDS YP_917912.1 119386857 4582702 1308359..1308688 1 NC_008687.1 KEGG: rde:RD1_1513 sulfur oxidation Z protein; sulfur oxidation Z protein 1308688 4582702 Pden_4152 Paracoccus denitrificans PD1222 sulfur oxidation Z protein YP_917912.1 1308359 D 318586 CDS YP_917913.1 119386858 4582703 1308725..1309597 1 NC_008687.1 KEGG: sil:SPO0996 diheme cytochrome c SoxA; diheme cytochrome c SoxA 1309597 4582703 Pden_4153 Paracoccus denitrificans PD1222 diheme cytochrome c SoxA YP_917913.1 1308725 D 318586 CDS YP_917914.1 119386859 4582704 1309716..1311410 1 NC_008687.1 PFAM: metallophosphoesterase; 5'-Nucleotidase domain protein; KEGG: sil:SPO0997 sulfur oxidation B protein; 5'-nucleotidase domain-containing protein 1311410 4582704 Pden_4154 Paracoccus denitrificans PD1222 5'-nucleotidase domain-containing protein YP_917914.1 1309716 D 318586 CDS YP_917915.1 119386860 4582705 1311433..1312725 1 NC_008687.1 PFAM: oxidoreductase, molybdopterin binding; Mo-co oxidoreductase dimerisation domain; KEGG: rde:RD1_1516 sulfite dehydrogenase SoxC protein; oxidoreductase, molybdopterin binding 1312725 4582705 Pden_4155 Paracoccus denitrificans PD1222 oxidoreductase, molybdopterin binding YP_917915.1 1311433 D 318586 CDS YP_917916.1 119386861 4582706 1312709..1313857 1 NC_008687.1 PFAM: cytochrome c, class I; KEGG: sil:SPO0999 diheme cytochrome c SoxD; cytochrome c, class I 1313857 4582706 Pden_4156 Paracoccus denitrificans PD1222 cytochrome c, class I YP_917916.1 1312709 D 318586 CDS YP_917917.1 119386862 4582707 1313861..1314571 1 NC_008687.1 PFAM: cytochrome c, class I; KEGG: rde:RD1_1518 cytochrome c2; cytochrome c, class I 1314571 4582707 Pden_4157 Paracoccus denitrificans PD1222 cytochrome c, class I YP_917917.1 1313861 D 318586 CDS YP_917918.1 119386863 4582708 1314627..1315889 1 NC_008687.1 PFAM: FAD-dependent pyridine nucleotide-disulphide oxidoreductase; KEGG: sil:SPO1001 sulfur oxidation F protein; FAD-dependent pyridine nucleotide-disulfide oxidoreductase 1315889 4582708 Pden_4158 Paracoccus denitrificans PD1222 FAD-dependent pyridine nucleotide-disulfide oxidoreductase YP_917918.1 1314627 D 318586 CDS YP_917919.1 119386864 4582709 1315907..1316818 1 NC_008687.1 PFAM: beta-lactamase domain protein; KEGG: sil:SPO0788 metallo-beta-lactamase family protein; beta-lactamase domain-containing protein 1316818 4582709 Pden_4159 Paracoccus denitrificans PD1222 beta-lactamase domain-containing protein YP_917919.1 1315907 D 318586 CDS YP_917920.1 119386865 4582710 1316818..1317756 1 NC_008687.1 KEGG: sil:SPO2822 SoxH protein, homolog; SoxH protein-like 1317756 4582710 Pden_4160 Paracoccus denitrificans PD1222 SoxH protein-like YP_917920.1 1316818 D 318586 CDS YP_917921.1 119386866 4582711 complement(1317760..1318842) 1 NC_008687.1 PFAM: protein of unknown function DUF395, YeeE/YedE; KEGG: sil:SPO3123 YeeE/YedE family protein; hypothetical protein 1318842 4582711 Pden_4161 Paracoccus denitrificans PD1222 hypothetical protein YP_917921.1 1317760 R 318586 CDS YP_917922.1 119386867 4582712 1319216..1320298 1 NC_008687.1 KEGG: ana:all1980 unknown protein; hypothetical protein 1320298 4582712 Pden_4162 Paracoccus denitrificans PD1222 hypothetical protein YP_917922.1 1319216 D 318586 CDS YP_917923.1 119386868 4582713 1320373..1321368 1 NC_008687.1 KEGG: sit:TM1040_2280 hypothetical protein; hypothetical protein 1321368 4582713 Pden_4163 Paracoccus denitrificans PD1222 hypothetical protein YP_917923.1 1320373 D 318586 CDS YP_917924.1 119386869 4582714 complement(1321384..1321752) 1 NC_008687.1 PFAM: helix-turn-helix, HxlR type; KEGG: bja:bll5105 transcriptional regulatory protein; HxlR family transcriptional regulator 1321752 4582714 Pden_4164 Paracoccus denitrificans PD1222 HxlR family transcriptional regulator YP_917924.1 1321384 R 318586 CDS YP_917925.1 119386870 4582715 1321888..1322436 1 NC_008687.1 PFAM: NAD(P)H dehydrogenase (quinone); NADPH-dependent FMN reductase; KEGG: bja:blr5106 acyl-carrier-protein phosphodiesterase; ACP phosphodiesterase 1322436 4582715 Pden_4165 Paracoccus denitrificans PD1222 ACP phosphodiesterase YP_917925.1 1321888 D 318586 CDS YP_917926.1 119386871 4582716 complement(1322456..1323625) 1 NC_008687.1 PFAM: NnrS family protein; KEGG: atc:AGR_L_924 hypothetical protein; NnrS family protein 1323625 4582716 Pden_4166 Paracoccus denitrificans PD1222 NnrS family protein YP_917926.1 1322456 R 318586 CDS YP_917927.1 119386872 4582717 complement(1323622..1324371) 1 NC_008687.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: atc:AGR_L_926 probable ATP-binding component of ABC taurine transporter; ABC transporter 1324371 4582717 Pden_4167 Paracoccus denitrificans PD1222 ABC transporter YP_917927.1 1323622 R 318586 CDS YP_917928.1 119386873 4582718 complement(1324368..1325186) 1 NC_008687.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: atc:AGR_L_927 ABC transporter, permease, cysTW family; binding-protein-dependent transport system inner membrane protein 1325186 4582718 Pden_4168 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_917928.1 1324368 R 318586 CDS YP_917929.1 119386874 4582719 complement(1325183..1326178) 1 NC_008687.1 KEGG: atc:AGR_L_928 sulfonate/nitrate transport system substrate-binding protein; sulfonate/nitrate transport system substrate-binding protein 1326178 4582719 Pden_4169 Paracoccus denitrificans PD1222 sulfonate/nitrate transport system substrate-binding protein YP_917929.1 1325183 R 318586 CDS YP_917930.1 119386875 4582720 complement(1326284..1326589) 1 NC_008687.1 KEGG: nha:Nham_2539 hypothetical protein; hypothetical protein 1326589 4582720 Pden_4170 Paracoccus denitrificans PD1222 hypothetical protein YP_917930.1 1326284 R 318586 CDS YP_917931.1 119386876 4582721 complement(1326586..1327206) 1 NC_008687.1 KEGG: net:Neut_2232 conserved hypothetical protein; hypothetical protein 1327206 4582721 Pden_4171 Paracoccus denitrificans PD1222 hypothetical protein YP_917931.1 1326586 R 318586 CDS YP_917932.1 119386877 4582722 complement(1327210..1327758) 1 NC_008687.1 TIGRFAM: transcriptional regulator, Rrf2 family; PFAM: protein of unknown function UPF0074; KEGG: nha:Nham_3286 transcriptional regulator, BadM/Rrf2 family; BadM/Rrf2 family transcriptional regulator 1327758 4582722 Pden_4172 Paracoccus denitrificans PD1222 BadM/Rrf2 family transcriptional regulator YP_917932.1 1327210 R 318586 CDS YP_917933.1 119386878 4582723 complement(1327758..1329977) 1 NC_008687.1 PFAM: TonB-dependent receptor; TonB-dependent receptor, plug; KEGG: rpd:RPD_3065 TonB-dependent receptor; TonB-dependent receptor 1329977 4582723 Pden_4173 Paracoccus denitrificans PD1222 TonB-dependent receptor YP_917933.1 1327758 R 318586 CDS YP_917934.1 119386879 4582724 1330301..1331233 1 NC_008687.1 PFAM: sugar-binding domain protein; KEGG: mes:Meso_3776 transcriptional regulator, DeoR family; DeoR family transcriptional regulator 1331233 4582724 Pden_4174 Paracoccus denitrificans PD1222 DeoR family transcriptional regulator YP_917934.1 1330301 D 318586 CDS YP_917935.1 119386880 4582725 complement(1331237..1332679) 1 NC_008687.1 PFAM: carbohydrate kinase, FGGY; KEGG: mes:Meso_3784 FGGY-family pentulose kinase; carbohydrate kinase 1332679 4582725 Pden_4175 Paracoccus denitrificans PD1222 carbohydrate kinase YP_917935.1 1331237 R 318586 CDS YP_917936.1 119386881 4582726 complement(1332694..1333350) 1 NC_008687.1 TIGRFAM: HAD-superfamily hydrolase, subfamily IA, variant 3; PFAM: Haloacid dehalogenase domain protein hydrolase; KEGG: atc:AGR_L_828 hypothetical protein; HAD family hydrolase 1333350 4582726 Pden_4176 Paracoccus denitrificans PD1222 HAD family hydrolase YP_917936.1 1332694 R 318586 CDS YP_917937.1 119386882 4582727 complement(1333354..1334817) 1 NC_008687.1 PFAM: Mannitol dehydrogenase, C-terminal domain; Mannitol dehydrogenase rossman, N-terminal domain; KEGG: mlo:mll4920 mannitol dehydrogenase; mannitol dehydrogenase 1334817 4582727 Pden_4177 Paracoccus denitrificans PD1222 mannitol dehydrogenase YP_917937.1 1333354 R 318586 CDS YP_917938.1 119386883 4582728 complement(1334887..1335885) 1 NC_008687.1 PFAM: ABC transporter related; TOBE domain protein; Transport-associated OB domain protein; SMART: AAA ATPase; KEGG: sit:TM1040_0428 ABC transporter related; ABC transporter 1335885 4582728 Pden_4178 Paracoccus denitrificans PD1222 ABC transporter YP_917938.1 1334887 R 318586 CDS YP_917939.1 119386884 4582729 complement(1335897..1336727) 1 NC_008687.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: sme:SMc01498 probable sorbitol/mannitol transport inner membrane protein; binding-protein-dependent transport systems inner membrane component 1336727 4582729 Pden_4179 Paracoccus denitrificans PD1222 binding-protein-dependent transport systems inner membrane component YP_917939.1 1335897 R 318586 CDS YP_917940.1 119386885 4582730 complement(1336733..1337602) 1 NC_008687.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: sme:SMc01497 probable sorbitol/mannitol transport inner membrane transmembrane protein; binding-protein-dependent transport systems inner membrane component 1337602 4582730 Pden_4180 Paracoccus denitrificans PD1222 binding-protein-dependent transport systems inner membrane component YP_917940.1 1336733 R 318586 CDS YP_917941.1 119386886 4582731 complement(1337701..1339008) 1 NC_008687.1 PFAM: extracellular solute-binding protein, family 1; KEGG: sme:SMc01496 probable sorbitol-binding periplasmic protein; extracellular solute-binding protein 1339008 4582731 Pden_4181 Paracoccus denitrificans PD1222 extracellular solute-binding protein YP_917941.1 1337701 R 318586 CDS YP_917942.1 119386887 4582732 complement(1339157..1339621) 1 NC_008687.1 NADPH-dependent; catalyzes the reduction of 7-cyano-7-deazaguanine to 7-aminomethyl-7-deazaguanine in queuosine biosynthesis; 7-cyano-7-deazaguanine reductase 1339621 4582732 Pden_4182 Paracoccus denitrificans PD1222 7-cyano-7-deazaguanine reductase YP_917942.1 1339157 R 318586 CDS YP_917943.1 119386888 4582733 complement(1339637..1340344) 1 NC_008687.1 PFAM: Radical SAM domain protein; KEGG: sit:TM1040_2045 radical SAM; radical SAM domain-containing protein 1340344 4582733 Pden_4183 Paracoccus denitrificans PD1222 radical SAM domain-containing protein YP_917943.1 1339637 R 318586 CDS YP_917944.1 119386889 4582734 complement(1340341..1340694) 1 NC_008687.1 PFAM: 6-pyruvoyl tetrahydropterin synthase and hypothetical protein; KEGG: sit:TM1040_2046 6-pyruvoyl tetrahydropterin synthase and hypothetical protein; 6-pyruvoyl tetrahydrobiopterin synthase 1340694 4582734 Pden_4184 Paracoccus denitrificans PD1222 6-pyruvoyl tetrahydrobiopterin synthase YP_917944.1 1340341 R 318586 CDS YP_917945.1 119386890 4582735 complement(1340694..1341395) 1 NC_008687.1 TIGRFAM: exsB protein; PFAM: ExsB family protein; KEGG: sit:TM1040_2047 ExsB; exsB protein 1341395 4582735 Pden_4185 Paracoccus denitrificans PD1222 exsB protein YP_917945.1 1340694 R 318586 CDS YP_917946.1 119386891 4582736 1341593..1342585 1 NC_008687.1 KEGG: mes:Meso_1301 hypothetical protein; hypothetical protein 1342585 4582736 Pden_4186 Paracoccus denitrificans PD1222 hypothetical protein YP_917946.1 1341593 D 318586 CDS YP_917947.1 119386892 4582737 complement(1342595..1343656) 1 NC_008687.1 part of the UgpABCE glycerol-3-phosphate uptake system; glycerol-3-phosphate transporter ATP-binding subunit 1343656 ugpC 4582737 ugpC Paracoccus denitrificans PD1222 glycerol-3-phosphate transporter ATP-binding subunit YP_917947.1 1342595 R 318586 CDS YP_917948.1 119386893 4582738 complement(1343657..1344520) 1 NC_008687.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: rsp:RSP_3288 ABC glycerol-3-phosphate transporter, inner membrane subunit UgpE; binding-protein-dependent transport system inner membrane protein 1344520 4582738 Pden_4188 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_917948.1 1343657 R 318586 CDS YP_917949.1 119386894 4582739 complement(1344513..1345394) 1 NC_008687.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: rsp:RSP_3289 ABC glycerol-3-phosphate transporter, inner membrane subunit UgpA; binding-protein-dependent transport systems inner membrane component 1345394 4582739 Pden_4189 Paracoccus denitrificans PD1222 binding-protein-dependent transport systems inner membrane component YP_917949.1 1344513 R 318586 CDS YP_917950.1 119386895 4582740 complement(1345444..1346739) 1 NC_008687.1 PFAM: extracellular solute-binding protein, family 1; KEGG: rsp:RSP_3290 ABC glycerol-3-phosphate transporter, periplasmic binding protein, UgpB; extracellular solute-binding protein 1346739 4582740 Pden_4190 Paracoccus denitrificans PD1222 extracellular solute-binding protein YP_917950.1 1345444 R 318586 CDS YP_917951.1 119386896 4582741 1346993..1348057 1 NC_008687.1 hypothetical protein 1348057 4582741 Pden_4191 Paracoccus denitrificans PD1222 hypothetical protein YP_917951.1 1346993 D 318586 CDS YP_917952.1 119386897 4582742 1348066..1349481 1 NC_008687.1 KEGG: gvi:glr3599 hypothetical protein; hypothetical protein 1349481 4582742 Pden_4192 Paracoccus denitrificans PD1222 hypothetical protein YP_917952.1 1348066 D 318586 CDS YP_917953.1 119386898 4582743 1349495..1350223 1 NC_008687.1 hypothetical protein 1350223 4582743 Pden_4193 Paracoccus denitrificans PD1222 hypothetical protein YP_917953.1 1349495 D 318586 CDS YP_917954.1 119386899 4582744 complement(1350220..1352109) 1 NC_008687.1 PFAM: transcriptional activator domain; Tetratricopeptide TPR_2 repeat protein; KEGG: mlo:mlr7075 similar to trifolitoxin synthesis, TfuA; SARP family transcriptional regulator 1352109 4582744 Pden_4194 Paracoccus denitrificans PD1222 SARP family transcriptional regulator YP_917954.1 1350220 R 318586 CDS YP_917955.1 119386900 4582745 complement(1352237..1353016) 1 NC_008687.1 PFAM: nitroreductase; KEGG: tko:TK0839 NAD(P)H-flavin oxidoreductase; nitroreductase 1353016 4582745 Pden_4195 Paracoccus denitrificans PD1222 nitroreductase YP_917955.1 1352237 R 318586 CDS YP_917956.1 119386901 4582746 complement(1353021..1354331) 1 NC_008687.1 TIGRFAM: uncharacterized domain; PFAM: protein of unknown function DUF181; KEGG: bcn:Bcen_5136 protein of unknown function DUF181; hypothetical protein 1354331 4582746 Pden_4196 Paracoccus denitrificans PD1222 hypothetical protein YP_917956.1 1353021 R 318586 CDS YP_917957.1 119386902 4582747 complement(1354328..1355443) 1 NC_008687.1 PFAM: UBA/THIF-type NAD/FAD binding protein; KEGG: ccr:CC3726 molybdopterin biosynthesis protein MoeB; UBA/THIF-type NAD/FAD binding protein 1355443 4582747 Pden_4197 Paracoccus denitrificans PD1222 UBA/THIF-type NAD/FAD binding protein YP_917957.1 1354328 R 318586 CDS YP_917958.1 119386903 4582748 complement(1355415..1357277) 1 NC_008687.1 PFAM: Radical SAM domain protein; SMART: Elongator protein 3/MiaB/NifB; KEGG: sus:Acid_0877 radical SAM domain protein; radical SAM domain-containing protein 1357277 4582748 Pden_4198 Paracoccus denitrificans PD1222 radical SAM domain-containing protein YP_917958.1 1355415 R 318586 CDS YP_917959.1 119386904 4582749 complement(1357309..1357701) 1 NC_008687.1 hypothetical protein 1357701 4582749 Pden_4199 Paracoccus denitrificans PD1222 hypothetical protein YP_917959.1 1357309 R 318586 CDS YP_917960.1 119386905 4582750 1358307..1360007 1 NC_008687.1 PFAM: ABC transporter, transmembrane region; ABC transporter related; SMART: AAA ATPase; KEGG: rsp:RSP_3081 ABC multidrug efflux transporter, fused ATPase and inner membrane subunits; ABC transporter 1360007 4582750 Pden_4200 Paracoccus denitrificans PD1222 ABC transporter YP_917960.1 1358307 D 318586 CDS YP_917961.1 119386906 4582751 complement(1360113..1362173) 1 NC_008687.1 TIGRFAM: TonB-dependent heme/hemoglobin receptor family protein; PFAM: TonB-dependent receptor; TonB-dependent receptor, plug; KEGG: jan:Jann_2132 TonB-dependent haem/haemoglobin receptor; TonB-dependent heme/hemoglobin receptor family protein 1362173 4582751 Pden_4201 Paracoccus denitrificans PD1222 TonB-dependent heme/hemoglobin receptor family protein YP_917961.1 1360113 R 318586 CDS YP_917962.1 119386907 4582752 1362333..1363373 1 NC_008687.1 PFAM: Haemin-degrading family protein; KEGG: jan:Jann_2133 haemin-degrading; hemin-degrading family protein 1363373 4582752 Pden_4202 Paracoccus denitrificans PD1222 hemin-degrading family protein YP_917962.1 1362333 D 318586 CDS YP_917963.1 119386908 4582753 1363370..1364245 1 NC_008687.1 PFAM: periplasmic binding protein; KEGG: rde:RD1_4189 hemin ABC transporter, periplasmic hemin-binding protein; periplasmic binding protein 1364245 4582753 Pden_4203 Paracoccus denitrificans PD1222 periplasmic binding protein YP_917963.1 1363370 D 318586 CDS YP_917964.1 119386909 4582754 1364245..1365321 1 NC_008687.1 PFAM: transport system permease; KEGG: jan:Jann_2135 transport system permease; transport system permease 1365321 4582754 Pden_4204 Paracoccus denitrificans PD1222 transport system permease YP_917964.1 1364245 D 318586 CDS YP_917965.1 119386910 4582755 1365318..1366091 1 NC_008687.1 with HmuTU is involved in the transport of hemin; hemin importer ATP-binding subunit 1366091 hmuV 4582755 hmuV Paracoccus denitrificans PD1222 hemin importer ATP-binding subunit YP_917965.1 1365318 D 318586 CDS YP_917966.1 119386911 4582756 1366192..1367175 1 NC_008687.1 PFAM: Alcohol dehydrogenase GroES domain protein; KEGG: bja:blr6070 alcohol dehydrogenase; alcohol dehydrogenase 1367175 4582756 Pden_4206 Paracoccus denitrificans PD1222 alcohol dehydrogenase YP_917966.1 1366192 D 318586 CDS YP_917967.1 119386912 4582757 1367233..1369002 1 NC_008687.1 PFAM: alpha/beta hydrolase fold; Poly-beta-hydroxybutyrate polymerase domain protein; KEGG: bxe:Bxe_B0358 poly-beta-hydroxyalkanoate synthasePhbC; poly-beta-hydroxybutyrate polymerase domain-containing protein 1369002 4582757 Pden_4207 Paracoccus denitrificans PD1222 poly-beta-hydroxybutyrate polymerase domain-containing protein YP_917967.1 1367233 D 318586 CDS YP_917968.1 119386913 4582758 complement(1368999..1370102) 1 NC_008687.1 TIGRFAM: acetate kinase; PFAM: acetate and butyrate kinase; KEGG: lpn:lpg2262 acetate kinase; acetate kinase 1370102 4582758 Pden_4208 Paracoccus denitrificans PD1222 acetate kinase YP_917968.1 1368999 R 318586 CDS YP_917969.1 119386914 4582759 complement(1370099..1371025) 1 NC_008687.1 PFAM: phosphate acetyl/butaryl transferase; KEGG: lpp:lpp2215 phosphate acetyltransferase; phosphate butyryltransferase 1371025 4582759 Pden_4209 Paracoccus denitrificans PD1222 phosphate butyryltransferase YP_917969.1 1370099 R 318586 CDS YP_917970.1 119386915 4582760 complement(1371199..1371570) 1 NC_008687.1 PFAM: response regulator receiver; KEGG: rsp:RSP_0573 response regulator receiver protein; response regulator receiver protein 1371570 4582760 Pden_4210 Paracoccus denitrificans PD1222 response regulator receiver protein YP_917970.1 1371199 R 318586 CDS YP_917971.1 119386916 4582761 complement(1371664..1373379) 1 NC_008687.1 member of the sodium:solute symporter family; cotranscribed with the acs gene which encodes acetyl coenzyme A synthase; mutations affect acetate uptake; acetate permease 1373379 actP 4582761 actP Paracoccus denitrificans PD1222 acetate permease YP_917971.1 1371664 R 318586 CDS YP_917972.1 119386917 4582762 complement(1373376..1373684) 1 NC_008687.1 PFAM: protein of unknown function DUF485; KEGG: rsp:RSP_3141 hypothetical protein; hypothetical protein 1373684 4582762 Pden_4212 Paracoccus denitrificans PD1222 hypothetical protein YP_917972.1 1373376 R 318586 CDS YP_917973.1 119386918 4582763 complement(1373891..1375846) 1 NC_008687.1 TIGRFAM: acetate--CoA ligase; PFAM: AMP-dependent synthetase and ligase; KEGG: rsp:RSP_0579 acetyl-coenzyme A synthetase; acetate--CoA ligase 1375846 4582763 Pden_4213 Paracoccus denitrificans PD1222 acetate--CoA ligase YP_917973.1 1373891 R 318586 CDS YP_917974.1 119386919 4582764 complement(1376134..1377048) 1 NC_008687.1 PFAM: ApbE family lipoprotein; KEGG: rpc:RPC_0433 twin-arginine translocation pathway signal; ApbE family lipoprotein 1377048 4582764 Pden_4214 Paracoccus denitrificans PD1222 ApbE family lipoprotein YP_917974.1 1376134 R 318586 CDS YP_917975.1 119386920 4582765 complement(1377045..1377620) 1 NC_008687.1 PFAM: NosL family protein; KEGG: sil:SPOA0054 nitrous oxide reductase accessory protein; NosL family protein 1377620 4582765 Pden_4215 Paracoccus denitrificans PD1222 NosL family protein YP_917975.1 1377045 R 318586 CDS YP_917976.1 119386921 4582766 complement(1377617..1378441) 1 NC_008687.1 KEGG: sil:SPOA0053 nitrous oxide maturation protein NosY; nitrous oxide maturation protein NosY 1378441 4582766 Pden_4216 Paracoccus denitrificans PD1222 nitrous oxide maturation protein NosY YP_917976.1 1377617 R 318586 CDS YP_917977.1 119386922 4582767 complement(1378438..1379337) 1 NC_008687.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sil:SPOA0052 ABC transporter, ATP-binding protein NosF; ABC transporter 1379337 4582767 Pden_4217 Paracoccus denitrificans PD1222 ABC transporter YP_917977.1 1378438 R 318586 CDS YP_917978.1 119386923 4582768 complement(1379303..1380634) 1 NC_008687.1 PFAM: periplasmic copper-binding; SMART: Parallel beta-helix repeat; Carbohydrate-binding and sugar hydrolysis; KEGG: sil:SPOA0051 nitrous oxide maturation protein NosD; periplasmic copper-binding 1380634 4582768 Pden_4218 Paracoccus denitrificans PD1222 periplasmic copper-binding YP_917978.1 1379303 R 318586 CDS YP_917979.1 119386924 4582769 complement(1380640..1382598) 1 NC_008687.1 reduces nitrous oxide to nitrogen; nitrous-oxide reductase 1382598 4582769 Pden_4219 Paracoccus denitrificans PD1222 nitrous-oxide reductase YP_917979.1 1380640 R 318586 CDS YP_917980.1 119386925 4582770 complement(1382616..1384796) 1 NC_008687.1 PFAM: FMN-binding domain protein; KEGG: sil:SPOA0049 nitrous-oxide reductase transcriptional activator NosR; FMN-binding domain-containing protein 1384796 4582770 Pden_4220 Paracoccus denitrificans PD1222 FMN-binding domain-containing protein YP_917980.1 1382616 R 318586 CDS YP_917981.1 119386926 4582771 complement(1384793..1385203) 1 NC_008687.1 hypothetical protein 1385203 4582771 Pden_4221 Paracoccus denitrificans PD1222 hypothetical protein YP_917981.1 1384793 R 318586 CDS YP_917982.1 119386927 4582772 1385540..1385983 1 NC_008687.1 TIGRFAM: pseudoazurin; PFAM: blue (type 1) copper domain protein; KEGG: sme:SMa1243 Azu1 pseudoazurin (blue copper protein); pseudoazurin 1385983 4582772 Pden_4222 Paracoccus denitrificans PD1222 pseudoazurin YP_917982.1 1385540 D 318586 CDS YP_917983.1 119386928 4582773 1386142..1386414 1 NC_008687.1 KEGG: rde:RD1_1693 hypothetical protein; hypothetical protein 1386414 4582773 Pden_4223 Paracoccus denitrificans PD1222 hypothetical protein YP_917983.1 1386142 D 318586 CDS YP_917984.1 119386929 4582774 complement(1386481..1387161) 1 NC_008687.1 PFAM: protein of unknown function DUF542, ScdA domain protein; Hemerythrin HHE cation binding domain protein; KEGG: sme:SMa1195 hypothetical protein; hypothetical protein 1387161 4582774 Pden_4224 Paracoccus denitrificans PD1222 hypothetical protein YP_917984.1 1386481 R 318586 CDS YP_917985.1 119386930 4582775 complement(1387139..1387732) 1 NC_008687.1 TIGRFAM: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; PFAM: flavoprotein; KEGG: rsp:RSP_0468 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; 3-octaprenyl-4-hydroxybenzoate carboxy-lyase 1387732 4582775 Pden_4225 Paracoccus denitrificans PD1222 3-octaprenyl-4-hydroxybenzoate carboxy-lyase YP_917985.1 1387139 R 318586 CDS YP_917986.1 119386931 4582776 complement(1387729..1389198) 1 NC_008687.1 TIGRFAM: UbiD family decarboxylases; PFAM: Carboxylyase-related protein; KEGG: rsp:RSP_0467 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; UbiD family decarboxylase 1389198 4582776 Pden_4226 Paracoccus denitrificans PD1222 UbiD family decarboxylase YP_917986.1 1387729 R 318586 CDS YP_917987.1 119386932 4582777 1389319..1389852 1 NC_008687.1 KEGG: rsp:RSP_0466 hypothetical protein; hypothetical protein 1389852 4582777 Pden_4227 Paracoccus denitrificans PD1222 hypothetical protein YP_917987.1 1389319 D 318586 CDS YP_917988.1 119386933 4582778 1389849..1390844 1 NC_008687.1 PFAM: peptidase U32; KEGG: rsp:RSP_0465 protease; peptidase U32 1390844 4582778 Pden_4228 Paracoccus denitrificans PD1222 peptidase U32 YP_917988.1 1389849 D 318586 CDS YP_917989.1 119386934 4582779 1390847..1391737 1 NC_008687.1 PFAM: peptidase U32; KEGG: rsp:RSP_0464 protease; peptidase U32 1391737 4582779 Pden_4229 Paracoccus denitrificans PD1222 peptidase U32 YP_917989.1 1390847 D 318586 CDS YP_917990.1 119386935 4582780 1391761..1392975 1 NC_008687.1 PFAM: NnrS family protein; KEGG: rde:RD1_1694 NnrS protein; NnrS family protein 1392975 4582780 Pden_4230 Paracoccus denitrificans PD1222 NnrS family protein YP_917990.1 1391761 D 318586 CDS YP_917991.1 119386936 4582781 complement(1393035..1393547) 1 NC_008687.1 KEGG: sil:SPO1135 hypothetical protein; hypothetical protein 1393547 4582781 Pden_4231 Paracoccus denitrificans PD1222 hypothetical protein YP_917991.1 1393035 R 318586 CDS YP_917992.1 119386937 4582782 complement(1393547..1394350) 1 NC_008687.1 PFAM: PpiC-type peptidyl-prolyl cis-trans isomerase; KEGG: rde:RD1_2446 peptidyl-prolyl cis-trans isomerase; PpiC-type peptidyl-prolyl cis-trans isomerase 1394350 4582782 Pden_4232 Paracoccus denitrificans PD1222 PpiC-type peptidyl-prolyl cis-trans isomerase YP_917992.1 1393547 R 318586 CDS YP_917993.1 119386938 4582783 complement(1394356..1395057) 1 NC_008687.1 TIGRFAM: respiratory nitrate reductase, gamma subunit; PFAM: Nitrate reductase, gamma subunit; KEGG: mmr:Mmar10_2703 respiratory nitrate reductase, gamma subunit; respiratory nitrate reductase subunit gamma 1395057 4582783 Pden_4233 Paracoccus denitrificans PD1222 respiratory nitrate reductase subunit gamma YP_917993.1 1394356 R 318586 CDS YP_917994.1 119386939 4582784 complement(1395072..1395761) 1 NC_008687.1 TIGRFAM: nitrate reductase molybdenum cofactor assembly chaperone; PFAM: Nitrate reductase, delta subunit; KEGG: rde:RD1_2444 nitrate reductase, delta subunit; nitrate reductase molybdenum cofactor assembly chaperone 1395761 4582784 Pden_4234 Paracoccus denitrificans PD1222 nitrate reductase molybdenum cofactor assembly chaperone YP_917994.1 1395072 R 318586 CDS YP_917995.1 119386940 4582785 complement(1395758..1397275) 1 NC_008687.1 TIGRFAM: nitrate reductase, beta subunit; PFAM: 4Fe-4S ferredoxin, iron-sulfur binding domain protein; KEGG: rde:RD1_2443 nitrate reductase, beta subunit; nitrate reductase subunit beta 1397275 4582785 Pden_4235 Paracoccus denitrificans PD1222 nitrate reductase subunit beta YP_917995.1 1395758 R 318586 CDS YP_917996.1 119386941 4582786 complement(1397272..1401036) 1 NC_008687.1 TIGRFAM: nitrate reductase, alpha subunit; PFAM: molybdopterin oxidoreductase; molydopterin dinucleotide-binding region; KEGG: rde:RD1_2442 nitrate reductase, alpha subunit; nitrate reductase subunit alpha 1401036 4582786 Pden_4236 Paracoccus denitrificans PD1222 nitrate reductase subunit alpha YP_917996.1 1397272 R 318586 CDS YP_917997.1 119386942 4582787 complement(1401051..1403768) 1 NC_008687.1 TIGRFAM: nitrite transporter; PFAM: major facilitator superfamily MFS_1; KEGG: bms:BRA0300 nitrite extrusion protein; nitrite transporter 1403768 4582787 Pden_4237 Paracoccus denitrificans PD1222 nitrite transporter YP_917997.1 1401051 R 318586 CDS YP_917998.1 119386943 4582788 1404042..1404746 1 NC_008687.1 upregulated by FixLJ/FixK under oxygen limitation; involved in regulation of genes involved in carbon and amino acid metabolism; transcriptional activator FtrB 1404746 ftrB 4582788 ftrB Paracoccus denitrificans PD1222 transcriptional activator FtrB YP_917998.1 1404042 D 318586 CDS YP_917999.1 119386944 4582789 1404840..1405901 1 NC_008687.1 TIGRFAM: methylated-DNA--protein-cysteine methyltransferase; PFAM: helix-turn-helix- domain containing protein, AraC type; methylated-DNA-[protein]-cysteine S-methyltransferase; Ada, metal-binding domain protein; KEGG: rso:RSc2570 probable ADA regulatory of adaptative response contains: methylated-DNA--protein-cysteine methyltransferaseO-6-methylguanine-DNA transcription regulator; methylated-DNA--protein-cysteine methyltransferase 1405901 4582789 Pden_4239 Paracoccus denitrificans PD1222 methylated-DNA--protein-cysteine methyltransferase YP_917999.1 1404840 D 318586 CDS YP_918000.1 119386945 4582790 1405972..1406949 1 NC_008687.1 PFAM: Siderophore-interacting protein; FAD-binding 9, siderophore-interacting domain protein; KEGG: mes:Meso_0336 siderophore-interacting protein; FAD-binding 9, siderophore-interacting domain-containing protein 1406949 4582790 Pden_4240 Paracoccus denitrificans PD1222 FAD-binding 9, siderophore-interacting domain-containing protein YP_918000.1 1405972 D 318586 CDS YP_918001.1 119386946 4582791 complement(1406954..1408144) 1 NC_008687.1 TIGRFAM: drug resistance transporter, Bcr/CflA subfamily; PFAM: major facilitator superfamily MFS_1; KEGG: rpc:RPC_4760 drug resistance transporter Bcr/CflA subfamily; Bcr/CflA subfamily drug resistance transporter 1408144 4582791 Pden_4241 Paracoccus denitrificans PD1222 Bcr/CflA subfamily drug resistance transporter YP_918001.1 1406954 R 318586 CDS YP_918002.1 119386947 4582792 1408491..1408673 1 NC_008687.1 KEGG: atc:AGR_L_2076 hypothetical protein; hypothetical protein 1408673 4582792 Pden_4242 Paracoccus denitrificans PD1222 hypothetical protein YP_918002.1 1408491 D 318586 CDS YP_918003.1 119386948 4582793 1408704..1409231 1 NC_008687.1 PFAM: GntR domain protein; KEGG: atc:AGR_L_2076 hypothetical protein; GntR family transcriptional regulator 1409231 4582793 Pden_4243 Paracoccus denitrificans PD1222 GntR family transcriptional regulator YP_918003.1 1408704 D 318586 CDS YP_918004.1 119386949 4582794 1409413..1410396 1 NC_008687.1 PFAM: Asparaginase/glutaminase; KEGG: atc:AGR_L_2084 L-asparaginase; asparaginase/glutaminase 1410396 4582794 Pden_4244 Paracoccus denitrificans PD1222 asparaginase/glutaminase YP_918004.1 1409413 D 318586 CDS YP_918005.1 119386950 4582795 complement(1410436..1411347) 1 NC_008687.1 PFAM: oxidoreductase domain protein; KEGG: mes:Meso_0843 oxidoreductase-like; galactose 1-dehydrogenase 1411347 4582795 Pden_4245 Paracoccus denitrificans PD1222 galactose 1-dehydrogenase YP_918005.1 1410436 R 318586 CDS YP_918006.1 119386951 4582796 complement(1411347..1413095) 1 NC_008687.1 catalyzes the formation of 3-methyl-2-oxobutanoate from 2,3,-dihydroxy-3-methylbutanoate; dihydroxy-acid dehydratase 1413095 4582796 Pden_4246 Paracoccus denitrificans PD1222 dihydroxy-acid dehydratase YP_918006.1 1411347 R 318586 CDS YP_918007.1 119386952 4582797 complement(1413095..1414078) 1 NC_008687.1 PFAM: protein of unknown function DUF1238; KEGG: mlo:mll5655 hypothetical protein; hypothetical protein 1414078 4582797 Pden_4247 Paracoccus denitrificans PD1222 hypothetical protein YP_918007.1 1413095 R 318586 CDS YP_918008.1 119386953 4582798 1414230..1415183 1 NC_008687.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: mes:Meso_0837 transcriptional regulator, LysR family; LysR family transcriptional regulator 1415183 4582798 Pden_4248 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_918008.1 1414230 D 318586 CDS YP_918009.1 119386954 4582799 complement(1415269..1416657) 1 NC_008687.1 PFAM: sodium:dicarboxylate symporter; KEGG: yps:YPTB2365 DAACS family Na/dicarboxylate symporter; sodium:dicarboxylate symporter 1416657 4582799 Pden_4249 Paracoccus denitrificans PD1222 sodium:dicarboxylate symporter YP_918009.1 1415269 R 318586 CDS YP_918010.1 119386955 4582800 1416909..1417622 1 NC_008687.1 PFAM: Ankyrin; KEGG: bur:Bcep18194_B0071 ankyrin repeat protein; ankyrin 1417622 4582800 Pden_4250 Paracoccus denitrificans PD1222 ankyrin YP_918010.1 1416909 D 318586 CDS YP_918011.1 119386956 4582801 1417634..1418107 1 NC_008687.1 PFAM: CMP/dCMP deaminase, zinc-binding; KEGG: rme:Rmet_3722 CMP/dCMP deaminase, zinc-binding; zinc-binding CMP/dCMP deaminase 1418107 4582801 Pden_4251 Paracoccus denitrificans PD1222 zinc-binding CMP/dCMP deaminase YP_918011.1 1417634 D 318586 CDS YP_918012.1 119386957 4582802 1418104..1419321 1 NC_008687.1 PFAM: major facilitator superfamily MFS_1; KEGG: reu:Reut_B5382 major facilitator superfamily MFS_1; major facilitator transporter 1419321 4582802 Pden_4252 Paracoccus denitrificans PD1222 major facilitator transporter YP_918012.1 1418104 D 318586 CDS YP_918013.1 119386958 4582803 1419350..1419775 1 NC_008687.1 PFAM: protein of unknown function DUF336; KEGG: cps:CPS_4893 GlcG protein; hypothetical protein 1419775 4582803 Pden_4253 Paracoccus denitrificans PD1222 hypothetical protein YP_918013.1 1419350 D 318586 CDS YP_918014.1 119386959 4582804 1419940..1420677 1 NC_008687.1 PFAM: protein of unknown function DUF81; KEGG: rpa:RPA0111 DUF81; hypothetical protein 1420677 4582804 Pden_4254 Paracoccus denitrificans PD1222 hypothetical protein YP_918014.1 1419940 D 318586 CDS YP_918015.1 119386960 4582805 1420741..1421979 1 NC_008687.1 KEGG: rsp:RSP_3200 molecular chaperone, DnaK; molecular chaperone DnaK 1421979 4582805 Pden_4255 Paracoccus denitrificans PD1222 molecular chaperone DnaK YP_918015.1 1420741 D 318586 CDS YP_918016.1 119386961 4582806 complement(1422043..1422939) 1 NC_008687.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: sit:TM1040_2703 transcriptional regulator, LysR family; LysR family transcriptional regulator 1422939 4582806 Pden_4256 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_918016.1 1422043 R 318586 CDS YP_918017.1 119386962 4582807 1423057..1424502 1 NC_008687.1 PFAM: ferredoxin; molybdopterin dehydrogenase, FAD-binding; [2Fe-2S]-binding domain protein; CO dehydrogenase flavoprotein domain protein; KEGG: sit:TM1040_2704 molybdopterin dehydrogenase, FAD-binding; molybdopterin dehydrogenase 1424502 4582807 Pden_4257 Paracoccus denitrificans PD1222 molybdopterin dehydrogenase YP_918017.1 1423057 D 318586 CDS YP_918018.1 119386963 4582808 1424499..1426811 1 NC_008687.1 PFAM: aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead; aldehyde oxidase and xanthine dehydrogenase, molybdopterin binding; KEGG: sit:TM1040_2705 xanthine dehydrogenase; aldehyde oxidase 1426811 4582808 Pden_4258 Paracoccus denitrificans PD1222 aldehyde oxidase YP_918018.1 1424499 D 318586 CDS YP_918019.1 119386964 4582809 1426808..1427551 1 NC_008687.1 PFAM: protein of unknown function DUF182; KEGG: mlo:mlr5136 xanthine dehydrogenase accessory factor; hypothetical protein 1427551 4582809 Pden_4259 Paracoccus denitrificans PD1222 hypothetical protein YP_918019.1 1426808 D 318586 CDS YP_918020.1 119386965 4582810 1427539..1428816 1 NC_008687.1 Catalyzes the deamination of guanine; guanine deaminase 1428816 4582810 Pden_4260 Paracoccus denitrificans PD1222 guanine deaminase YP_918020.1 1427539 D 318586 CDS YP_918021.1 119386966 4582811 complement(1429004..1429504) 1 NC_008687.1 KEGG: rpc:RPC_3603 acetone carboxylase gamma subunit; acetone carboxylase subunit gamma 1429504 4582811 Pden_4261 Paracoccus denitrificans PD1222 acetone carboxylase subunit gamma YP_918021.1 1429004 R 318586 CDS YP_918022.1 119386967 4582812 complement(1429569..1431884) 1 NC_008687.1 PFAM: Hydantoinase B/oxoprolinase; KEGG: rpc:RPC_3604 hydantoinase B/oxoprolinase; hydantoinase B/oxoprolinase 1431884 4582812 Pden_4262 Paracoccus denitrificans PD1222 hydantoinase B/oxoprolinase YP_918022.1 1429569 R 318586 CDS YP_918023.1 119386968 4582813 complement(1431909..1434080) 1 NC_008687.1 PFAM: Hydantoinase/oxoprolinase; Hydantoinaseoxoprolinase domain protein; KEGG: rpc:RPC_3605 hydantoinase/oxoprolinase; hydantoinase/oxoprolinase 1434080 4582813 Pden_4263 Paracoccus denitrificans PD1222 hydantoinase/oxoprolinase YP_918023.1 1431909 R 318586 CDS YP_918024.1 119386969 4582814 complement(1434201..1436009) 1 NC_008687.1 PFAM: sigma-54 factor, interaction domain-containing protein; helix-turn-helix, Fis-type; GAF domain protein; SMART: AAA ATPase; KEGG: rpc:RPC_3606 sigma54 specific transcriptional regulator with GAF sensor, fis family; Fis family GAF modulated sigma54 specific transcriptional regulator 1436009 4582814 Pden_4264 Paracoccus denitrificans PD1222 Fis family GAF modulated sigma54 specific transcriptional regulator YP_918024.1 1434201 R 318586 CDS YP_918025.1 119386970 4582815 complement(1436146..1436916) 1 NC_008687.1 PFAM: regulatory protein GntR, HTH; GntR domain protein; KEGG: pfl:PFL_3673 transcriptional regulator, GntR family; GntR family transcriptional regulator 1436916 4582815 Pden_4265 Paracoccus denitrificans PD1222 GntR family transcriptional regulator YP_918025.1 1436146 R 318586 CDS YP_918026.1 119386971 4582816 complement(1436925..1438409) 1 NC_008687.1 PFAM: Uncharacterized conserved protein UCP012702; MlrC domain protein; KEGG: bam:Bamb_6097 MlrC domain protein; MlrC domain-containing protein 1438409 4582816 Pden_4266 Paracoccus denitrificans PD1222 MlrC domain-containing protein YP_918026.1 1436925 R 318586 CDS YP_918027.1 119386972 4582817 complement(1438406..1439680) 1 NC_008687.1 KEGG: sil:SPO1781 amidase, hydantoinase/carbamoylase family; TIGRFAM: amidase, hydantoinase/carbamoylase family; PFAM: peptidase M20; peptidase dimerisation domain protein; amidase 1439680 4582817 Pden_4267 Paracoccus denitrificans PD1222 amidase YP_918027.1 1438406 R 318586 CDS YP_918028.1 119386973 4582818 complement(1439677..1440381) 1 NC_008687.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rme:Rmet_4479 ABC transporter related; ABC transporter 1440381 4582818 Pden_4268 Paracoccus denitrificans PD1222 ABC transporter YP_918028.1 1439677 R 318586 CDS YP_918029.1 119386974 4582819 complement(1440378..1441145) 1 NC_008687.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rme:Rmet_4478 ABC transporter related; ABC transporter 1441145 4582819 Pden_4269 Paracoccus denitrificans PD1222 ABC transporter YP_918029.1 1440378 R 318586 CDS YP_918030.1 119386975 4582820 complement(1441147..1442124) 1 NC_008687.1 PFAM: inner-membrane translocator; KEGG: bxe:Bxe_B2564 ABC branched chain amino acid family transporter, inner membrane subunit; inner-membrane translocator 1442124 4582820 Pden_4270 Paracoccus denitrificans PD1222 inner-membrane translocator YP_918030.1 1441147 R 318586 CDS YP_918031.1 119386976 4582821 complement(1442121..1443065) 1 NC_008687.1 PFAM: inner-membrane translocator; KEGG: rme:Rmet_4476 inner-membrane translocator; inner-membrane translocator 1443065 4582821 Pden_4271 Paracoccus denitrificans PD1222 inner-membrane translocator YP_918031.1 1442121 R 318586 CDS YP_918032.1 119386977 4582822 complement(1443040..1444251) 1 NC_008687.1 KEGG: rme:Rmet_4475 branched-chain amino acid ABC transporter, periplasmic amino acid-binding protein; branched-chain amino acid ABC transporter, periplasmic amino acid-binding protein 1444251 4582822 Pden_4272 Paracoccus denitrificans PD1222 branched-chain amino acid ABC transporter, periplasmic amino acid-binding protein YP_918032.1 1443040 R 318586 CDS YP_918033.1 119386978 4582823 1444586..1445965 1 NC_008687.1 PFAM: aminotransferase class-III; KEGG: rsp:RSP_0943 probable adenosylmethionine-8-amino-7-oxononanoate aminotransferase; class III aminotransferase 1445965 4582823 Pden_4273 Paracoccus denitrificans PD1222 class III aminotransferase YP_918033.1 1444586 D 318586 CDS YP_918034.1 119386979 4582824 1446028..1447527 1 NC_008687.1 PFAM: regulatory protein GntR, HTH; aminotransferase, class I and II; KEGG: rde:RD1_0978 transcriptional regulator, GntR family; GntR family transcriptional regulator 1447527 4582824 Pden_4274 Paracoccus denitrificans PD1222 GntR family transcriptional regulator YP_918034.1 1446028 D 318586 CDS YP_918035.1 119386980 4582825 complement(1447511..1448467) 1 NC_008687.1 KEGG: rsp:RSP_4009 phosphate acetyl/butaryl transferase; TIGRFAM: phosphate acetyltransferase; PFAM: phosphate acetyl/butaryl transferase; phosphate acetyltransferase 1448467 4582825 Pden_4275 Paracoccus denitrificans PD1222 phosphate acetyltransferase YP_918035.1 1447511 R 318586 CDS YP_918036.1 119386981 4582826 complement(1448480..1449496) 1 NC_008687.1 PFAM: conserved hypothetical protein 698; KEGG: rsp:RSP_4010 conserved hypothetical protein 698; hypothetical protein 1449496 4582826 Pden_4276 Paracoccus denitrificans PD1222 hypothetical protein YP_918036.1 1448480 R 318586 CDS YP_918037.1 119386982 4582827 complement(1449770..1451551) 1 NC_008687.1 catalyzes the formation of acetyl phosphate and sulfite from 2-sulfoacetaldehyde; is active when grown on taurine as a sole carbon source; sulfoacetaldehyde acetyltransferase 1451551 4582827 Pden_4277 Paracoccus denitrificans PD1222 sulfoacetaldehyde acetyltransferase YP_918037.1 1449770 R 318586 CDS YP_918038.1 119386983 4582828 complement(1451564..1453204) 1 NC_008687.1 PFAM: glucose-methanol-choline oxidoreductase; FAD dependent oxidoreductase; GMC oxidoreductase; KEGG: sil:SPO2359 oxidoreductase, GMC family; glucose-methanol-choline oxidoreductase 1453204 4582828 Pden_4278 Paracoccus denitrificans PD1222 glucose-methanol-choline oxidoreductase YP_918038.1 1451564 R 318586 CDS YP_918039.1 119386984 4582829 complement(1453293..1454600) 1 NC_008687.1 PFAM: General substrate transporter; major facilitator superfamily MFS_1; KEGG: bxe:Bxe_B0699 major facilitator superfamily (MFS)metabolite/H+ symporter; major facilitator transporter 1454600 4582829 Pden_4279 Paracoccus denitrificans PD1222 major facilitator transporter YP_918039.1 1453293 R 318586 CDS YP_918040.1 119386985 4582830 1454824..1455588 1 NC_008687.1 PFAM: regulatory proteins, IclR; KEGG: sil:SPO2355 transcriptional regulator, IclR family; regulatory proteins, IclR 1455588 4582830 Pden_4280 Paracoccus denitrificans PD1222 regulatory proteins, IclR YP_918040.1 1454824 D 318586 CDS YP_918041.1 119386986 4582831 complement(1455734..1456684) 1 NC_008687.1 KEGG: sil:SPO0664 peptide ABC transporter, ATP-binding protein; TIGRFAM: oligopeptide/dipeptide ABC transporter, ATPase subunit; PFAM: ABC transporter related; Oligopeptide/dipeptide ABC transporter, C-terminal domain protein; SMART: AAA ATPase; oligopeptide/dipeptide ABC transporter ATPase 1456684 4582831 Pden_4281 Paracoccus denitrificans PD1222 oligopeptide/dipeptide ABC transporter ATPase YP_918041.1 1455734 R 318586 CDS YP_918042.1 119386987 4582832 complement(1456681..1457673) 1 NC_008687.1 KEGG: sth:STH2824 oligopeptide ABC transporter ATP-binding protein; TIGRFAM: oligopeptide/dipeptide ABC transporter, ATPase subunit; PFAM: ABC transporter related; Oligopeptide/dipeptide ABC transporter, C-terminal domain protein; SMART: AAA ATPase; oligopeptide/dipeptide ABC transporter ATPase 1457673 4582832 Pden_4282 Paracoccus denitrificans PD1222 oligopeptide/dipeptide ABC transporter ATPase YP_918042.1 1456681 R 318586 CDS YP_918043.1 119386988 4582833 complement(1457677..1458555) 1 NC_008687.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: rpa:RPA0100 ABC transporter permease; binding-protein-dependent transport system inner membrane protein 1458555 4582833 Pden_4283 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_918043.1 1457677 R 318586 CDS YP_918044.1 119386989 4582834 complement(1458559..1459530) 1 NC_008687.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: sil:SPO0661 peptide ABC transporter, permease; binding-protein-dependent transport systems inner membrane component 1459530 4582834 Pden_4284 Paracoccus denitrificans PD1222 binding-protein-dependent transport systems inner membrane component YP_918044.1 1458559 R 318586 CDS YP_918045.1 119386990 4582835 complement(1459549..1461141) 1 NC_008687.1 PFAM: extracellular solute-binding protein, family 5; KEGG: rpa:RPA0102 ABC transporter oligopeptide-binding protein; extracellular solute-binding protein 1461141 4582835 Pden_4285 Paracoccus denitrificans PD1222 extracellular solute-binding protein YP_918045.1 1459549 R 318586 CDS YP_918046.1 119386991 4582836 complement(1461247..1462191) 1 NC_008687.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: sil:SPO0659 transcriptional regulator, LysR family; LysR family transcriptional regulator 1462191 4582836 Pden_4286 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_918046.1 1461247 R 318586 CDS YP_918047.1 119386992 4582837 1462297..1463931 1 NC_008687.1 PFAM: amidohydrolase; Amidohydrolase 3; KEGG: jan:Jann_3250 amidohydrolase 3; amidohydrolase 1463931 4582837 Pden_4287 Paracoccus denitrificans PD1222 amidohydrolase YP_918047.1 1462297 D 318586 CDS YP_918048.1 119386993 4582838 1463935..1464846 1 NC_008687.1 PFAM: cobalamin synthesis protein, P47K; cobalamin synthesis CobW domain protein; KEGG: jan:Jann_3251 cobalamin synthesis protein, P47K; cobalamin synthesis protein, P47K 1464846 4582838 Pden_4288 Paracoccus denitrificans PD1222 cobalamin synthesis protein, P47K YP_918048.1 1463935 D 318586 CDS YP_918049.1 119386994 4582839 1465112..1465765 1 NC_008687.1 KEGG: jan:Jann_1560 hypothetical protein; hypothetical protein 1465765 4582839 Pden_4289 Paracoccus denitrificans PD1222 hypothetical protein YP_918049.1 1465112 D 318586 CDS YP_918050.1 119386995 4582840 1465671..1467191 1 NC_008687.1 KEGG: jan:Jann_1559 hypothetical protein; hypothetical protein 1467191 4582840 Pden_4290 Paracoccus denitrificans PD1222 hypothetical protein YP_918050.1 1465671 D 318586 CDS YP_918051.1 119386996 4582841 1467191..1470424 1 NC_008687.1 KEGG: jan:Jann_1558 DNA polymerase III, alpha subunit; TIGRFAM: DNA polymerase III, alpha subunit; PFAM: PHP C-terminal domain protein; nucleic acid binding, OB-fold, tRNA/helicase-type; SMART: phosphoesterase PHP domain protein; DNA polymerase III subunit alpha 1470424 4582841 Pden_4291 Paracoccus denitrificans PD1222 DNA polymerase III subunit alpha YP_918051.1 1467191 D 318586 CDS YP_918052.1 119386997 4582842 complement(1470491..1470658) 1 NC_008687.1 in Escherichia coli BM108, a mutation that results in lack of L33 synthesis had no effect on ribosome synthesis or function; there are paralogous genes in several bacterial genomes, and a CXXC motif for zinc binding and an upstream regulation region of the paralog lacking this motif that are regulated by zinc similar to other ribosomal proteins like L31; the proteins in this group lack the CXXC motif; 50S ribosomal protein L33 1470658 rpmG 4582842 rpmG Paracoccus denitrificans PD1222 50S ribosomal protein L33 YP_918052.1 1470491 R 318586 CDS YP_918053.1 119386998 4582843 complement(1471303..1471668) 1 NC_008687.1 PFAM: helix-turn-helix, HxlR type; KEGG: ccr:CC3368 hypothetical protein; HxlR family transcriptional regulator 1471668 4582843 Pden_4293 Paracoccus denitrificans PD1222 HxlR family transcriptional regulator YP_918053.1 1471303 R 318586 CDS YP_918054.1 119386999 4582844 1471754..1472596 1 NC_008687.1 PFAM: 3-beta hydroxysteroid dehydrogenase/isomerase; NmrA family protein; KEGG: stm:STM4401 reductase; NmrA family protein 1472596 4582844 Pden_4294 Paracoccus denitrificans PD1222 NmrA family protein YP_918054.1 1471754 D 318586 CDS YP_918055.1 119387000 4582845 complement(1472593..1474992) 1 NC_008687.1 PFAM: UvrD/REP helicase; KEGG: rsp:RSP_2092 UvrD/DNA helicase II; UvrD/REP helicase 1474992 4582845 Pden_4295 Paracoccus denitrificans PD1222 UvrD/REP helicase YP_918055.1 1472593 R 318586 CDS YP_918056.1 119387001 4582846 complement(1475039..1475350) 1 NC_008687.1 hypothetical protein 1475350 4582846 Pden_4296 Paracoccus denitrificans PD1222 hypothetical protein YP_918056.1 1475039 R 318586 CDS YP_918057.1 119387002 4582847 complement(1475351..1476316) 1 NC_008687.1 similar protein in Methanocaldococcus converts GTP to 7,8-dihydro-D-neopterin 2',3'-cyclic phosphate as the first step in methanopterin biosynthesis; GTP cyclohydrolase 1476316 4582847 Pden_4297 Paracoccus denitrificans PD1222 GTP cyclohydrolase YP_918057.1 1475351 R 318586 CDS YP_918058.1 119387003 4582848 complement(1476404..1477600) 1 NC_008687.1 TIGRFAM: O-succinylhomoserine sulfhydrylase; PFAM: aminotransferase, class V; Cys/Met metabolism pyridoxal-phosphate-dependent enzymes; aromatic amino acid beta-eliminating lyase/threonine aldolase; aminotransferase, class I and II; KEGG: rsp:RSP_1851 O-succinylhomoserine sulfhydrylase; O-succinylhomoserine sulfhydrylase 1477600 4582848 Pden_4298 Paracoccus denitrificans PD1222 O-succinylhomoserine sulfhydrylase YP_918058.1 1476404 R 318586 CDS YP_918059.1 119387004 4582849 complement(1477671..1478360) 1 NC_008687.1 PFAM: Intracellular septation protein A; KEGG: rsp:RSP_1841 probable intracellular septation protein; intracellular septation protein A 1478360 4582849 Pden_4299 Paracoccus denitrificans PD1222 intracellular septation protein A YP_918059.1 1477671 R 318586 CDS YP_918060.1 119387005 4582850 complement(1478374..1479465) 1 NC_008687.1 PFAM: protein of unknown function DUF1223; KEGG: sil:SPO2311 hypothetical protein; hypothetical protein 1479465 4582850 Pden_4300 Paracoccus denitrificans PD1222 hypothetical protein YP_918060.1 1478374 R 318586 CDS YP_918061.1 119387006 4582851 1479732..1482491 1 NC_008687.1 Catalyzes the conversion of citrate to isocitrate; aconitate hydratase 1482491 4582851 Pden_4301 Paracoccus denitrificans PD1222 aconitate hydratase YP_918061.1 1479732 D 318586 CDS YP_918062.1 119387007 4582852 complement(1482658..1483326) 1 NC_008687.1 KEGG: rsp:RSP_0681 hypothetical protein; hypothetical protein 1483326 4582852 Pden_4302 Paracoccus denitrificans PD1222 hypothetical protein YP_918062.1 1482658 R 318586 CDS YP_918063.1 119387008 4582853 complement(1483465..1484085) 1 NC_008687.1 primary rRNA binding protein; nucleates 30S assembly; involved in translational accuracy with proteins S5 and S12; interacts with protein S5; involved in autogeneously regulating ribosomal proteins by binding to pseudoknot structures in the polycistronic mRNA; interacts with transcription complex and functions similar to protein NusA in antitermination; 30S ribosomal protein S4 1484085 rpsD 4582853 rpsD Paracoccus denitrificans PD1222 30S ribosomal protein S4 YP_918063.1 1483465 R 318586 CDS YP_918064.1 119387009 4582854 1484284..1484655 1 NC_008687.1 TIGRFAM: iron-sulfur cluster assembly accessory protein; PFAM: HesB/YadR/YfhF-family protein; KEGG: rde:RD1_2960 HesB-like iron-sulfur cluster assembly protein; iron-sulfur cluster assembly accessory protein 1484655 4582854 Pden_4304 Paracoccus denitrificans PD1222 iron-sulfur cluster assembly accessory protein YP_918064.1 1484284 D 318586 CDS YP_918065.1 119387010 4582855 1484756..1485499 1 NC_008687.1 PFAM: triosephosphate isomerase; KEGG: rsp:RSP_1947 triosephosphate isomerase; Triose-phosphate isomerase 1485499 4582855 Pden_4305 Paracoccus denitrificans PD1222 Triose-phosphate isomerase YP_918065.1 1484756 D 318586 CDS YP_918066.1 119387011 4582856 1485545..1486678 1 NC_008687.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rsp:RSP_0129 ABC D-methionine uptake transporter, ATPase subunit; ABC transporter 1486678 4582856 Pden_4306 Paracoccus denitrificans PD1222 ABC transporter YP_918066.1 1485545 D 318586 CDS YP_918067.1 119387012 4582857 1486668..1487342 1 NC_008687.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: rsp:RSP_0130 ABC D-methionine uptake transporter, inner membrane subunit; binding-protein-dependent transport system inner membrane protein 1487342 4582857 Pden_4307 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_918067.1 1486668 D 318586 CDS YP_918068.1 119387013 4582858 1487359..1488153 1 NC_008687.1 TIGRFAM: lipoprotein, YaeC family; PFAM: NLPA lipoprotein; KEGG: rsp:RSP_0132 ABC D-methionine uptake transporter, substrate-binding protein; YaeC family lipoprotein 1488153 4582858 Pden_4308 Paracoccus denitrificans PD1222 YaeC family lipoprotein YP_918068.1 1487359 D 318586 CDS YP_918069.1 119387014 4582859 complement(1488263..1489765) 1 NC_008687.1 PFAM: acetyl-CoA hydrolase/transferase; KEGG: rsp:RSP_0029 acetyl-CoA hydrolase/transferase family protein; Acetyl-CoA hydrolase 1489765 4582859 Pden_4309 Paracoccus denitrificans PD1222 Acetyl-CoA hydrolase YP_918069.1 1488263 R 318586 CDS YP_918070.1 119387015 4582860 complement(1489904..1490347) 1 NC_008687.1 PFAM: DoxX family protein; KEGG: bja:bll6552 hypothetical protein; DoxX family protein 1490347 4582860 Pden_4310 Paracoccus denitrificans PD1222 DoxX family protein YP_918070.1 1489904 R 318586 CDS YP_918071.1 119387016 4582861 1490452..1491363 1 NC_008687.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: rru:Rru_A1041 transcriptional regulator, LysR family; LysR family transcriptional regulator 1491363 4582861 Pden_4311 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_918071.1 1490452 D 318586 CDS YP_918072.1 119387017 4582862 complement(1491326..1492726) 1 NC_008687.1 PFAM: FAD linked oxidase domain protein; KEGG: rsp:RSP_1835 FAD dependent oxidoreductase; FAD linked oxidase domain-containing protein 1492726 4582862 Pden_4312 Paracoccus denitrificans PD1222 FAD linked oxidase domain-containing protein YP_918072.1 1491326 R 318586 CDS YP_918073.1 119387018 4582863 complement(1492726..1493307) 1 NC_008687.1 PFAM: GCN5-related N-acetyltransferase; KEGG: jan:Jann_3147 GCN5-related N-acetyltransferase; N-acetyltransferase GCN5 1493307 4582863 Pden_4313 Paracoccus denitrificans PD1222 N-acetyltransferase GCN5 YP_918073.1 1492726 R 318586 CDS YP_918074.1 119387019 4582864 complement(1493307..1494572) 1 NC_008687.1 PFAM: peptidase M16 domain protein; KEGG: rsp:RSP_1832 peptidase, M16 family; peptidase M16 domain-containing protein 1494572 4582864 Pden_4314 Paracoccus denitrificans PD1222 peptidase M16 domain-containing protein YP_918074.1 1493307 R 318586 CDS YP_918075.1 119387020 4582865 complement(1494569..1495957) 1 NC_008687.1 catalyzes the formation of L-threonine from O-phospho-L-homoserine; threonine synthase 1495957 4582865 Pden_4315 Paracoccus denitrificans PD1222 threonine synthase YP_918075.1 1494569 R 318586 CDS YP_918076.1 119387021 4582866 complement(1495967..1496638) 1 NC_008687.1 KEGG: rsp:RSP_1830 SURF1 protein; SURF1 protein 1496638 4582866 Pden_4316 Paracoccus denitrificans PD1222 SURF1 protein YP_918076.1 1495967 R 318586 CDS YP_918077.1 119387022 4582867 complement(1496704..1497528) 1 NC_008687.1 PFAM: cytochrome c oxidase, subunit III; KEGG: rsp:RSP_1829 cytochrome c oxidase, aa3-type, subunit III; cytochrome c oxidase subunit III 1497528 4582867 Pden_4317 Paracoccus denitrificans PD1222 cytochrome c oxidase subunit III YP_918077.1 1496704 R 318586 CDS YP_918078.1 119387023 4582868 complement(1497563..1498150) 1 NC_008687.1 involved in the insertion of copper into subunit I of cytochrome C oxidase; cytochrome C oxidase assembly protein 1498150 4582868 Pden_4318 Paracoccus denitrificans PD1222 cytochrome C oxidase assembly protein YP_918078.1 1497563 R 318586 CDS YP_918079.1 119387024 4582869 complement(1498147..1498422) 1 NC_008687.1 KEGG: jan:Jann_3153 hypothetical protein; hypothetical protein 1498422 4582869 Pden_4319 Paracoccus denitrificans PD1222 hypothetical protein YP_918079.1 1498147 R 318586 CDS YP_918080.1 119387025 4582870 complement(1498416..1499333) 1 NC_008687.1 converts protoheme IX and farnesyl diphosphate to heme O; protoheme IX farnesyltransferase 1499333 4582870 Pden_4320 Paracoccus denitrificans PD1222 protoheme IX farnesyltransferase YP_918080.1 1498416 R 318586 CDS YP_918081.1 119387026 4582871 complement(1499343..1500239) 1 NC_008687.1 PFAM: cytochrome c oxidase, subunit II; cytochrome C oxidase subunit II, transmembrane region; KEGG: sil:SPO3076 cytochrome c oxidase, subunit II; cytochrome-c oxidase 1500239 4582871 Pden_4321 Paracoccus denitrificans PD1222 cytochrome-c oxidase YP_918081.1 1499343 R 318586 CDS YP_918082.1 119387027 4582872 1500382..1501821 1 NC_008687.1 PFAM: peptidase U62, modulator of DNA gyrase; KEGG: rsp:RSP_1825 probable modulator of DNA gyrase; C69 family peptidase 1501821 4582872 Pden_4322 Paracoccus denitrificans PD1222 C69 family peptidase YP_918082.1 1500382 D 318586 CDS YP_918083.1 119387028 4582873 1501919..1503175 1 NC_008687.1 TIGRFAM: DNA protecting protein DprA; PFAM: SMF family protein; KEGG: jan:Jann_3158 DNA processing protein DprA; DNA protecting protein DprA 1503175 4582873 Pden_4323 Paracoccus denitrificans PD1222 DNA protecting protein DprA YP_918083.1 1501919 D 318586 CDS YP_918084.1 119387029 4582874 1503467..1505602 1 NC_008687.1 PFAM: OmpA/MotB domain protein; KEGG: rsp:RSP_1933 outer membrane protein, OmpA/MotB family; OmpA/MotB domain-containing protein 1505602 4582874 Pden_4324 Paracoccus denitrificans PD1222 OmpA/MotB domain-containing protein YP_918084.1 1503467 D 318586 CDS YP_918085.1 119387030 4582875 complement(1505694..1506383) 1 NC_008687.1 TIGRFAM: phosphate regulon transcriptional regulatory protein PhoB; PFAM: response regulator receiver; transcriptional regulator domain protein; KEGG: sil:SPO1953 phosphate regulon transcriptional regulatory protein PhoB; two component transcriptional regulator 1506383 4582875 Pden_4325 Paracoccus denitrificans PD1222 two component transcriptional regulator YP_918085.1 1505694 R 318586 CDS YP_918086.1 119387031 4582876 complement(1506387..1507097) 1 NC_008687.1 TIGRFAM: phosphate transport system regulatory protein PhoU; PFAM: PhoU family protein; KEGG: rsp:RSP_2600 phosphate transport system regulatory protein; phosphate uptake regulator PhoU 1507097 4582876 Pden_4326 Paracoccus denitrificans PD1222 phosphate uptake regulator PhoU YP_918086.1 1506387 R 318586 CDS YP_918087.1 119387032 4582877 complement(1507115..1507912) 1 NC_008687.1 ATP-binding protein; PstABCS is an ATP dependent phosphate uptake system which is responsible for inorganic phosphate uptake during phosphate starvation; phosphate transporter ATP-binding protein 1507912 4582877 Pden_4327 Paracoccus denitrificans PD1222 phosphate transporter ATP-binding protein YP_918087.1 1507115 R 318586 CDS YP_918088.1 119387033 4582878 complement(1507933..1509276) 1 NC_008687.1 TIGRFAM: phosphate ABC transporter, inner membrane subunit PstA; PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: rsp:RSP_2602 ABC phosphate transporter, inner membrane subunit PstA; phosphate ABC transporter permease 1509276 4582878 Pden_4328 Paracoccus denitrificans PD1222 phosphate ABC transporter permease YP_918088.1 1507933 R 318586 CDS YP_918089.1 119387034 4582879 complement(1509273..1510463) 1 NC_008687.1 TIGRFAM: phosphate ABC transporter, inner membrane subunit PstC; PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: jan:Jann_2290 phosphate ABC transporter, permease PstC; phosphate ABC transporter, inner membrane subunit PstC 1510463 4582879 Pden_4329 Paracoccus denitrificans PD1222 phosphate ABC transporter, inner membrane subunit PstC YP_918089.1 1509273 R 318586 CDS YP_918090.1 119387035 4582880 complement(1510524..1511552) 1 NC_008687.1 KEGG: sit:TM1040_1262 phosphate ABC transporter, periplasmic phosphate-binding protein; phosphate ABC transporter, periplasmic phosphate-binding protein 1511552 4582880 Pden_4330 Paracoccus denitrificans PD1222 phosphate ABC transporter, periplasmic phosphate-binding protein YP_918090.1 1510524 R 318586 CDS YP_918091.1 119387036 4582881 complement(1511549..1511791) 1 NC_008687.1 hypothetical protein 1511791 4582881 Pden_4331 Paracoccus denitrificans PD1222 hypothetical protein YP_918091.1 1511549 R 318586 CDS YP_918092.1 119387037 4582882 complement(1511803..1512903) 1 NC_008687.1 catalyzes the formation of chorismate from 5-O-(1-carboxyvinyl)-3-phosphoshikimate in aromatic amino acid biosynthesis; chorismate synthase 1512903 4582882 Pden_4332 Paracoccus denitrificans PD1222 chorismate synthase YP_918092.1 1511803 R 318586 CDS YP_918093.1 119387038 4582883 complement(1513319..1513648) 1 NC_008687.1 hypothetical protein 1513648 4582883 Pden_4333 Paracoccus denitrificans PD1222 hypothetical protein YP_918093.1 1513319 R 318586 CDS YP_918094.1 119387039 4582884 1513676..1515139 1 NC_008687.1 PFAM: amino acid permease-associated region; KEGG: rha:RHA1_ro06596 cationic amino acid transporter, APC family; amino acid permease 1515139 4582884 Pden_4334 Paracoccus denitrificans PD1222 amino acid permease YP_918094.1 1513676 D 318586 CDS YP_918095.1 119387040 4582885 complement(1515167..1516498) 1 NC_008687.1 TIGRFAM: type I secretion membrane fusion protein, HlyD family; PFAM: secretion protein HlyD family protein; KEGG: mes:Meso_2600 type I secretion membrane fusion protein, HlyD family; HlyD family type I secretion membrane fusion protein 1516498 4582885 Pden_4335 Paracoccus denitrificans PD1222 HlyD family type I secretion membrane fusion protein YP_918095.1 1515167 R 318586 CDS YP_918096.1 119387041 4582886 complement(1516482..1518473) 1 NC_008687.1 KEGG: mes:Meso_2599 type I secretion system ATPase; TIGRFAM: type I secretion system ATPase; PFAM: ABC transporter related; SMART: AAA ATPase; type I secretion system ATPase 1518473 4582886 Pden_4336 Paracoccus denitrificans PD1222 type I secretion system ATPase YP_918096.1 1516482 R 318586 CDS YP_918097.1 119387042 4582887 complement(1518470..1520503) 1 NC_008687.1 KEGG: mes:Meso_2598 hypothetical protein; hypothetical protein 1520503 4582887 Pden_4337 Paracoccus denitrificans PD1222 hypothetical protein YP_918097.1 1518470 R 318586 CDS YP_918098.1 119387043 4582888 complement(1520613..1522424) 1 NC_008687.1 KEGG: mes:Meso_2597 PE-PGRS family protein; PE-PGRS family protein 1522424 4582888 Pden_4338 Paracoccus denitrificans PD1222 PE-PGRS family protein YP_918098.1 1520613 R 318586 CDS YP_918099.1 119387044 4582889 1523038..1523739 1 NC_008687.1 PFAM: regulatory protein, LuxR; KEGG: dra:DRB0081 DNA-binding response regulator; response regulator receiver protein 1523739 4582889 Pden_4339 Paracoccus denitrificans PD1222 response regulator receiver protein YP_918099.1 1523038 D 318586 CDS YP_918100.1 119387045 4582890 1523736..1524257 1 NC_008687.1 KEGG: mes:Meso_2596 hypothetical protein; hypothetical protein 1524257 4582890 Pden_4340 Paracoccus denitrificans PD1222 hypothetical protein YP_918100.1 1523736 D 318586 CDS YP_918101.1 119387046 4582891 complement(1524344..1525063) 1 NC_008687.1 KEGG: rru:Rru_A3403 sulphate transport system permease 1; TIGRFAM: sulfate ABC transporter, ATPase subunit; PFAM: ABC transporter related; SMART: AAA ATPase; sulfate ABC transporter ATPase 1525063 4582891 Pden_4341 Paracoccus denitrificans PD1222 sulfate ABC transporter ATPase YP_918101.1 1524344 R 318586 CDS YP_918102.1 119387047 4582892 complement(1525080..1525973) 1 NC_008687.1 TIGRFAM: sulfate ABC transporter, inner membrane subunit; sulfate ABC transporter, inner membrane subunit CysW; PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: sme:SMb21131 sulfate uptake ABC transporter permease; sulfate ABC transporter, inner membrane subunit CysW 1525973 4582892 Pden_4342 Paracoccus denitrificans PD1222 sulfate ABC transporter, inner membrane subunit CysW YP_918102.1 1525080 R 318586 CDS YP_918103.1 119387048 4582893 complement(1525966..1526805) 1 NC_008687.1 TIGRFAM: sulfate ABC transporter, inner membrane subunit; sulfate ABC transporter, inner membrane subunit CysT; PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: rru:Rru_A3401 sulfate ABC transporter, permease CysT; sulfate ABC transporter, inner membrane subunit CysT 1526805 4582893 Pden_4343 Paracoccus denitrificans PD1222 sulfate ABC transporter, inner membrane subunit CysT YP_918103.1 1525966 R 318586 CDS YP_918104.1 119387049 4582894 complement(1526809..1527795) 1 NC_008687.1 TIGRFAM: sulfate ABC transporter, periplasmic sulfate-binding protein; PFAM: extracellular solute-binding protein, family 1; KEGG: sme:SMb21133 sulfate uptake ABC transporter periplasmic solute-binding protein precursor, similar to Y11244; sulfate ABC transporter, periplasmic sulfate-binding protein 1527795 4582894 Pden_4344 Paracoccus denitrificans PD1222 sulfate ABC transporter, periplasmic sulfate-binding protein YP_918104.1 1526809 R 318586 CDS YP_918105.1 119387050 4582895 1528285..1529583 1 NC_008687.1 PFAM: secretion protein HlyD family protein; KEGG: pae:PA4142 probable secretion protein; secretion protein HlyD family protein 1529583 4582895 Pden_4345 Paracoccus denitrificans PD1222 secretion protein HlyD family protein YP_918105.1 1528285 D 318586 CDS YP_918106.1 119387051 4582896 1529573..1531753 1 NC_008687.1 PFAM: ABC transporter, transmembrane region; ABC transporter related; peptidase C39, bacteriocin processing; SMART: AAA ATPase; KEGG: bpm:BURPS1710b_3626 colicin V processing peptidase; ABC transporter 1531753 4582896 Pden_4346 Paracoccus denitrificans PD1222 ABC transporter YP_918106.1 1529573 D 318586 CDS YP_918107.1 119387052 4582897 1532148..1533389 1 NC_008687.1 PFAM: Radical SAM domain protein; KEGG: sma:SAV5715 hypothetical protein; radical SAM domain-containing protein 1533389 4582897 Pden_4347 Paracoccus denitrificans PD1222 radical SAM domain-containing protein YP_918107.1 1532148 D 318586 CDS YP_918108.1 119387053 4582898 1533474..1535159 1 NC_008687.1 PFAM: response regulator receiver; ATP-binding region, ATPase domain protein domain protein; histidine kinase A domain protein domain protein; KEGG: pau:PA14_46370 two-component sensor; integral membrane sensor hybrid histidine kinase 1535159 4582898 Pden_4348 Paracoccus denitrificans PD1222 integral membrane sensor hybrid histidine kinase YP_918108.1 1533474 D 318586 CDS YP_918109.1 119387054 4582899 complement(1535156..1535776) 1 NC_008687.1 PFAM: regulatory protein, LuxR; response regulator receiver; Bacterio-opsin activator, HTH domain protein; Sigma-70, region 4 type 2; KEGG: pfo:Pfl_3254 two component transcriptional regulator, LuxR family; two component LuxR family transcriptional regulator 1535776 4582899 Pden_4349 Paracoccus denitrificans PD1222 two component LuxR family transcriptional regulator YP_918109.1 1535156 R 318586 CDS YP_918110.1 119387055 4582900 complement(1535955..1537556) 1 NC_008687.1 involved in the control of the structural glucose backbone of osmoregulated periplasmic glucans; glucan biosynthesis protein D 1537556 mdoD 4582900 mdoD Paracoccus denitrificans PD1222 glucan biosynthesis protein D YP_918110.1 1535955 R 318586 CDS YP_918111.1 119387056 4582901 complement(1537755..1539227) 1 NC_008687.1 PFAM: permease for cytosine/purines, uracil, thiamine, allantoin; KEGG: rsp:RSP_3174 nucleoside transporter, NCS1 family; cytosine/purines uracil thiamine allantoin permease 1539227 4582901 Pden_4351 Paracoccus denitrificans PD1222 cytosine/purines uracil thiamine allantoin permease YP_918111.1 1537755 R 318586 CDS YP_918112.1 119387057 4582902 complement(1539330..1541114) 1 NC_008687.1 PFAM: Hydantoinase B/oxoprolinase; KEGG: hwa:HQ2241A N-methylhydantoinase B (ATP-hydrolyzing); 5-oxoprolinase 1541114 4582902 Pden_4352 Paracoccus denitrificans PD1222 5-oxoprolinase YP_918112.1 1539330 R 318586 CDS YP_918113.1 119387058 4582903 complement(1541127..1543205) 1 NC_008687.1 PFAM: Hydantoinase/oxoprolinase; Hydantoinaseoxoprolinase domain protein; KEGG: hwa:HQ2242A N-methylhydantoinase A (ATP-hydrolyzing); 5-oxoprolinase 1543205 4582903 Pden_4353 Paracoccus denitrificans PD1222 5-oxoprolinase YP_918113.1 1541127 R 318586 CDS YP_918114.1 119387059 4582904 complement(1543296..1544039) 1 NC_008687.1 PFAM: isochorismatase hydrolase; KEGG: rha:RHA1_ro10206 phthalate ester hydrolase (isochorismatase hydrolase); N-carbamoylsarcosine amidase 1544039 4582904 Pden_4354 Paracoccus denitrificans PD1222 N-carbamoylsarcosine amidase YP_918114.1 1543296 R 318586 CDS YP_918115.1 119387060 4582905 1544204..1545109 1 NC_008687.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: jan:Jann_3249 transcriptional regulator, LysR family; LysR family transcriptional regulator 1545109 4582905 Pden_4355 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_918115.1 1544204 D 318586 CDS YP_918116.1 119387061 4582906 complement(1545213..1545761) 1 NC_008687.1 PFAM: cytochrome B561; KEGG: jan:Jann_0302 cytochrome b561; cytochrome B561 1545761 4582906 Pden_4356 Paracoccus denitrificans PD1222 cytochrome B561 YP_918116.1 1545213 R 318586 CDS YP_918117.1 119387062 4582907 1545866..1546603 1 NC_008687.1 KEGG: jan:Jann_0303 CDP-alcohol phosphatidyltransferase; CDP-alcohol phosphatidyltransferase 1546603 4582907 Pden_4357 Paracoccus denitrificans PD1222 CDP-alcohol phosphatidyltransferase YP_918117.1 1545866 D 318586 CDS YP_918118.1 119387063 4582908 1546600..1548177 1 NC_008687.1 PFAM: sulfatase; KEGG: jan:Jann_0304 hypothetical protein; sulfatase 1548177 4582908 Pden_4358 Paracoccus denitrificans PD1222 sulfatase YP_918118.1 1546600 D 318586 CDS YP_918119.1 119387064 4582909 1548197..1549192 1 NC_008687.1 KEGG: jan:Jann_0306 twin-arginine translocation pathway signal; twin-arginine translocation pathway signal 1549192 4582909 Pden_4359 Paracoccus denitrificans PD1222 twin-arginine translocation pathway signal YP_918119.1 1548197 D 318586 CDS YP_918120.1 119387065 4582910 1549185..1549958 1 NC_008687.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: jan:Jann_0307 ABC transporter related; ABC transporter 1549958 4582910 Pden_4360 Paracoccus denitrificans PD1222 ABC transporter YP_918120.1 1549185 D 318586 CDS YP_918121.1 119387066 4582911 1549955..1551499 1 NC_008687.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: jan:Jann_0308 binding-protein-dependent transport systems inner membrane component; binding-protein-dependent transport systems inner membrane component 1551499 4582911 Pden_4361 Paracoccus denitrificans PD1222 binding-protein-dependent transport systems inner membrane component YP_918121.1 1549955 D 318586 CDS YP_918122.1 119387067 4582912 1551496..1552545 1 NC_008687.1 PFAM: glycosyl transferase, group 1; KEGG: jan:Jann_0309 glycosyl transferase, group 1; group 1 glycosyl transferase 1552545 4582912 Pden_4362 Paracoccus denitrificans PD1222 group 1 glycosyl transferase YP_918122.1 1551496 D 318586 CDS YP_918123.1 119387068 4582913 complement(1552589..1553200) 1 NC_008687.1 PFAM: bifunctional deaminase-reductase domain protein; KEGG: sme:SMc04173 hypothetical protein; deaminase-reductase domain-containing protein 1553200 4582913 Pden_4363 Paracoccus denitrificans PD1222 deaminase-reductase domain-containing protein YP_918123.1 1552589 R 318586 CDS YP_918124.1 119387069 4582914 complement(1553381..1554592) 1 NC_008687.1 PFAM: ThiJ/PfpI domain protein; KEGG: bbr:BB2338 probable transcriptional regulator; ThiJ/PfpI domain-containing protein 1554592 4582914 Pden_4364 Paracoccus denitrificans PD1222 ThiJ/PfpI domain-containing protein YP_918124.1 1553381 R 318586 CDS YP_918125.1 119387070 4582915 1554607..1555581 1 NC_008687.1 PFAM: helix-turn-helix- domain containing protein, AraC type; ThiJ/PfpI domain protein; KEGG: mmr:Mmar10_1581 transcriptional regulator, AraC family; AraC family transcriptional regulator 1555581 4582915 Pden_4365 Paracoccus denitrificans PD1222 AraC family transcriptional regulator YP_918125.1 1554607 D 318586 CDS YP_918126.1 119387071 4582916 complement(1555817..1557880) 1 NC_008687.1 PFAM: helicase domain protein; DbpA, RNA-binding domain protein; DEAD/DEAH box helicase domain protein; SMART: DEAD-like helicases-like; KEGG: rsp:RSP_1485 ATP-dependent RNA helicase; DEAD/DEAH box helicase 1557880 4582916 Pden_4366 Paracoccus denitrificans PD1222 DEAD/DEAH box helicase YP_918126.1 1555817 R 318586 CDS YP_918127.1 119387072 4582917 complement(1558036..1558938) 1 NC_008687.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: sme:SMb20683 transcriptional regulator, LysR family protein; LysR family transcriptional regulator 1558938 4582917 Pden_4367 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_918127.1 1558036 R 318586 CDS YP_918128.1 119387073 4582918 1559113..1560438 1 NC_008687.1 involved in the transport of C4-dicarboxylates across the membrane; C4-dicarboxylate transporter DctA 1560438 4582918 Pden_4368 Paracoccus denitrificans PD1222 C4-dicarboxylate transporter DctA YP_918128.1 1559113 D 318586 CDS YP_918129.1 119387074 4582919 complement(1560541..1561515) 1 NC_008687.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: rpe:RPE_1784 transcriptional regulator, LysR family; LysR family transcriptional regulator 1561515 4582919 Pden_4369 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_918129.1 1560541 R 318586 CDS YP_918130.1 119387075 4582920 1561546..1562565 1 NC_008687.1 PFAM: conserved hypothetical protein 698; KEGG: rpe:RPE_1785 conserved hypothetical protein 698; hypothetical protein 1562565 4582920 Pden_4370 Paracoccus denitrificans PD1222 hypothetical protein YP_918130.1 1561546 D 318586 CDS YP_918131.1 119387076 4582921 1562633..1563463 1 NC_008687.1 KEGG: rsp:RSP_0408 hypothetical protein; hypothetical protein 1563463 4582921 Pden_4371 Paracoccus denitrificans PD1222 hypothetical protein YP_918131.1 1562633 D 318586 CDS YP_918132.1 119387077 4582922 complement(1563453..1563677) 1 NC_008687.1 KEGG: mlo:mll4732 glycolate oxidase, (S)-2-hydroxy-acid oxidase, peroxisomal; hypothetical protein 1563677 4582922 Pden_4372 Paracoccus denitrificans PD1222 hypothetical protein YP_918132.1 1563453 R 318586 CDS YP_918133.1 119387078 4582923 complement(1563763..1566018) 1 NC_008687.1 TIGRFAM: TonB-dependent siderophore receptor; PFAM: TonB-dependent receptor; TonB-dependent receptor, plug; KEGG: shm:Shewmr7_0697 TonB-dependent siderophore receptor; TonB-dependent siderophore receptor 1566018 4582923 Pden_4373 Paracoccus denitrificans PD1222 TonB-dependent siderophore receptor YP_918133.1 1563763 R 318586 CDS YP_918134.1 119387079 4582924 complement(1566089..1566385) 1 NC_008687.1 hypothetical protein 1566385 4582924 Pden_4374 Paracoccus denitrificans PD1222 hypothetical protein YP_918134.1 1566089 R 318586 CDS YP_918135.1 119387080 4582925 1566679..1566900 1 NC_008687.1 TIGRFAM: Glutaredoxin-like protein NrdH; PFAM: glutaredoxin; KEGG: sit:TM1040_0521 glutaredoxin-like protein NrdH; glutaredoxin-like protein NrdH 1566900 4582925 Pden_4375 Paracoccus denitrificans PD1222 glutaredoxin-like protein NrdH YP_918135.1 1566679 D 318586 CDS YP_918136.1 119387081 4582926 1566910..1567326 1 NC_008687.1 in Salmonella NrdI has a stimulatory effect on the ribonucleotide reductase activity of NrdH with NrdEF; ribonucleotide reductase stimulatory protein 1567326 nrdI 4582926 nrdI Paracoccus denitrificans PD1222 ribonucleotide reductase stimulatory protein YP_918136.1 1566910 D 318586 CDS YP_918137.1 119387082 4582927 1567308..1569434 1 NC_008687.1 Catalyzes the rate-limiting step in dNTP synthesis; ribonucleotide-diphosphate reductase subunit alpha 1569434 4582927 Pden_4377 Paracoccus denitrificans PD1222 ribonucleotide-diphosphate reductase subunit alpha YP_918137.1 1567308 D 318586 CDS YP_918138.1 119387083 4582928 1569481..1570470 1 NC_008687.1 B2 or R2 protein; type 1b enzyme; catalyzes the rate-limiting step in dNTP synthesis; converts nucleotides to deoxynucleotides; forms a homodimer and then a multimeric complex with NrdE; ribonucleotide-diphosphate reductase subunit beta 1570470 nrdF 4582928 nrdF Paracoccus denitrificans PD1222 ribonucleotide-diphosphate reductase subunit beta YP_918138.1 1569481 D 318586 CDS YP_918139.1 119387084 4582929 complement(1570467..1571435) 1 NC_008687.1 PFAM: Bile acid:sodium symporter; KEGG: mes:Meso_2484 bile acid:sodium symporter; bile acid:sodium symporter 1571435 4582929 Pden_4379 Paracoccus denitrificans PD1222 bile acid:sodium symporter YP_918139.1 1570467 R 318586 CDS YP_918140.1 119387085 4582930 1571526..1572773 1 NC_008687.1 PFAM: aminotransferase, class I and II; KEGG: xcv:XCV1904 aminotransferase; GntR family transcriptional regulator 1572773 4582930 Pden_4380 Paracoccus denitrificans PD1222 GntR family transcriptional regulator YP_918140.1 1571526 D 318586 CDS YP_918141.1 119387086 4582931 complement(1572796..1574571) 1 NC_008687.1 PFAM: Citrate transporter; TrkA-C domain protein; KEGG: sme:SMa1916 hypothetical protein; TrkA domain-containing protein 1574571 4582931 Pden_4381 Paracoccus denitrificans PD1222 TrkA domain-containing protein YP_918141.1 1572796 R 318586 CDS YP_918142.1 119387087 4582932 1575068..1576975 1 NC_008687.1 PFAM: TonB-dependent receptor; TonB-dependent receptor, plug; KEGG: rru:Rru_A0488 TonB-dependent receptor; TonB-dependent receptor 1576975 4582932 Pden_4382 Paracoccus denitrificans PD1222 TonB-dependent receptor YP_918142.1 1575068 D 318586 CDS YP_918143.1 119387088 4582933 1576969..1577805 1 NC_008687.1 PFAM: periplasmic binding protein; KEGG: rsp:RSP_2403 ABC cobalamin/Fe3+-siderophore transporter, periplasmic substrate-binding subunit; periplasmic binding protein 1577805 4582933 Pden_4383 Paracoccus denitrificans PD1222 periplasmic binding protein YP_918143.1 1576969 D 318586 CDS YP_918144.1 119387089 4582934 1577802..1578797 1 NC_008687.1 PFAM: transport system permease; KEGG: rsp:RSP_2404 ABC cobalamin/Fe3+-siderophore transporter, inner membrane subunit; transport system permease 1578797 4582934 Pden_4384 Paracoccus denitrificans PD1222 transport system permease YP_918144.1 1577802 D 318586 CDS YP_918145.1 119387090 4582935 1578800..1579555 1 NC_008687.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rsp:RSP_2405 ABC cobalamin/Fe3+-siderophore transporter, ATPase subunit; ABC transporter 1579555 4582935 Pden_4385 Paracoccus denitrificans PD1222 ABC transporter YP_918145.1 1578800 D 318586 CDS YP_918146.1 119387091 4582936 complement(1579716..1581206) 1 NC_008687.1 TIGRFAM: glycerol kinase; PFAM: carbohydrate kinase, FGGY; KEGG: rsp:RSP_2662 glycerol kinase; glycerol kinase 1581206 4582936 Pden_4386 Paracoccus denitrificans PD1222 glycerol kinase YP_918146.1 1579716 R 318586 CDS YP_918147.1 119387092 4582937 complement(1581285..1583006) 1 NC_008687.1 KEGG: rsp:RSP_2663 ABC sugar (glycerol) transporter, periplasmic binding protein; ABC sugar (glycerol) transporter, periplasmic binding protein 1583006 4582937 Pden_4387 Paracoccus denitrificans PD1222 ABC sugar (glycerol) transporter, periplasmic binding protein YP_918147.1 1581285 R 318586 CDS YP_918148.1 119387093 4582938 complement(1583090..1583371) 1 NC_008687.1 KEGG: rsp:RSP_2664 hypothetical protein; hypothetical protein 1583371 4582938 Pden_4388 Paracoccus denitrificans PD1222 hypothetical protein YP_918148.1 1583090 R 318586 CDS YP_918149.1 119387094 4582939 complement(1583515..1584318) 1 NC_008687.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: rsp:RSP_2665 ABC sugar (glycerol) transporter, inner membrane subunit; binding-protein-dependent transport systems inner membrane component 1584318 4582939 Pden_4389 Paracoccus denitrificans PD1222 binding-protein-dependent transport systems inner membrane component YP_918149.1 1583515 R 318586 CDS YP_918150.1 119387095 4582940 complement(1584318..1585205) 1 NC_008687.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: rsp:RSP_2666 ABC sugar (glycerol) transporter, inner membrane subunit; binding-protein-dependent transport systems inner membrane component 1585205 4582940 Pden_4390 Paracoccus denitrificans PD1222 binding-protein-dependent transport systems inner membrane component YP_918150.1 1584318 R 318586 CDS YP_918151.1 119387096 4582941 complement(1585205..1586308) 1 NC_008687.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rsp:RSP_2667 ABC sugar (glycerol) transporter, ATPase subunit; ABC transporter 1586308 4582941 Pden_4391 Paracoccus denitrificans PD1222 ABC transporter YP_918151.1 1585205 R 318586 CDS YP_918152.1 119387097 4582942 complement(1586292..1587371) 1 NC_008687.1 PFAM: ABC transporter related; Transport-associated OB domain protein; SMART: AAA ATPase; KEGG: rsp:RSP_2669 ABC sugar (glycerol) transporter, ATPase subunit; ABC transporter 1587371 4582942 Pden_4392 Paracoccus denitrificans PD1222 ABC transporter YP_918152.1 1586292 R 318586 CDS YP_918153.1 119387098 4582943 complement(1587386..1588969) 1 NC_008687.1 in Escherichia coli this homodimeric enzyme is expressed under aerobic conditions; anaerobic expression is repressed by the arcAB system; converts sn-glycerol-3-phosphate and ubiquinone-8 to dihydroxy acetone phosphate and ubiquinol-8; associates with the cytoplasmic membrane; glycerol-3-phosphate dehydrogenase 1588969 glpD 4582943 glpD Paracoccus denitrificans PD1222 glycerol-3-phosphate dehydrogenase YP_918153.1 1587386 R 318586 CDS YP_918154.1 119387099 4582944 1589081..1589401 1 NC_008687.1 hypothetical protein 1589401 4582944 Pden_4394 Paracoccus denitrificans PD1222 hypothetical protein YP_918154.1 1589081 D 318586 CDS YP_918155.1 119387100 4582945 1589413..1590348 1 NC_008687.1 with CysN catalyzes the formation of adenylylsulfate from sulfate and ATP; sulfate adenylyltransferase subunit 2 1590348 4582945 Pden_4395 Paracoccus denitrificans PD1222 sulfate adenylyltransferase subunit 2 YP_918155.1 1589413 D 318586 CDS YP_918156.1 119387101 4582946 1590350..1592272 1 NC_008687.1 in Rhizobium meliloti this protein is involved in the synthesis of nodulation factors that are active on the roots of alfalfa; catalyzes formation of activated sulfate intermediate; converts ATP and sulfate to diphosphate and adenylylsulfate and then ATP and adenylyl sulfate to ADP and 3'-phosphoadenylyl sulfate; the activated intermediate is transferred to the nodulation factors by NodH; may interact with NodP and NodQ; similar to the CysD and CysN proteins from EScherichia coli involved in cysteine biosynthesis; bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase 1592272 4582946 Pden_4396 Paracoccus denitrificans PD1222 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase YP_918156.1 1590350 D 318586 CDS YP_918157.1 119387102 4582947 complement(1592380..1593675) 1 NC_008687.1 PFAM: 4Fe-4S ferredoxin, iron-sulfur binding domain protein; protein of unknown function DUF224, cysteine-rich region domain protein; KEGG: sil:SPO3480 glycolate oxidase, iron-sulfur subunit; hypothetical protein 1593675 4582947 Pden_4397 Paracoccus denitrificans PD1222 hypothetical protein YP_918157.1 1592380 R 318586 CDS YP_918158.1 119387103 4582948 complement(1593677..1594810) 1 NC_008687.1 PFAM: FAD linked oxidase domain protein; KEGG: sit:TM1040_2501 FAD linked oxidase-like; FAD linked oxidase domain-containing protein 1594810 4582948 Pden_4398 Paracoccus denitrificans PD1222 FAD linked oxidase domain-containing protein YP_918158.1 1593677 R 318586 CDS YP_918159.1 119387104 4582949 complement(1594807..1596261) 1 NC_008687.1 PFAM: FAD linked oxidase domain protein; KEGG: rsp:RSP_1020 glycolate oxidase subunit protein; FAD linked oxidase domain-containing protein 1596261 4582949 Pden_4399 Paracoccus denitrificans PD1222 FAD linked oxidase domain-containing protein YP_918159.1 1594807 R 318586 CDS YP_918160.1 119387105 4582950 1596412..1597221 1 NC_008687.1 PFAM: regulatory protein GntR, HTH; GntR domain protein; Helix-turn-helix, type 11 domain protein; KEGG: rru:Rru_A1414 regulatory protein GntR; GntR family transcriptional regulator 1597221 4582950 Pden_4400 Paracoccus denitrificans PD1222 GntR family transcriptional regulator YP_918160.1 1596412 D 318586 CDS YP_918161.1 119387106 4582951 complement(1597278..1598243) 1 NC_008687.1 PFAM: Uncharacterized protein UPF0065; KEGG: sme:SMa1927 hypothetical protein; hypothetical protein 1598243 4582951 Pden_4401 Paracoccus denitrificans PD1222 hypothetical protein YP_918161.1 1597278 R 318586 CDS YP_918162.1 119387107 4582952 complement(1598266..1599774) 1 NC_008687.1 PFAM: protein of unknown function DUF112, transmembrane; KEGG: atc:AGR_C_184 hypothetical protein; hypothetical protein 1599774 4582952 Pden_4402 Paracoccus denitrificans PD1222 hypothetical protein YP_918162.1 1598266 R 318586 CDS YP_918163.1 119387108 4582953 complement(1599787..1600251) 1 NC_008687.1 PFAM: protein of unknown function DUF1468; KEGG: sme:SMb20026 hypothetical protein; hypothetical protein 1600251 4582953 Pden_4403 Paracoccus denitrificans PD1222 hypothetical protein YP_918163.1 1599787 R 318586 CDS YP_918164.1 119387109 4582954 complement(1600310..1601284) 1 NC_008687.1 PFAM: Uncharacterized protein UPF0065; KEGG: sme:SMb20025 hypothetical protein; hypothetical protein 1601284 4582954 Pden_4404 Paracoccus denitrificans PD1222 hypothetical protein YP_918164.1 1600310 R 318586 CDS YP_918165.1 119387110 4582955 complement(1601479..1602825) 1 NC_008687.1 PFAM: response regulator receiver; sigma-54 factor, interaction domain-containing protein; helix-turn-helix, Fis-type; SMART: AAA ATPase; KEGG: ret:RHE_CH03433 probable two-component response regulator protein; two component, sigma54 specific, Fis family transcriptional regulator 1602825 4582955 Pden_4405 Paracoccus denitrificans PD1222 two component, sigma54 specific, Fis family transcriptional regulator YP_918165.1 1601479 R 318586 CDS YP_918166.1 119387111 4582956 complement(1602822..1604690) 1 NC_008687.1 PFAM: ATP-binding region, ATPase domain protein domain protein; histidine kinase A domain protein domain protein; KEGG: ret:RHE_CH03434 probable two-component sensor histidine kinase; histidine kinase 1604690 4582956 Pden_4406 Paracoccus denitrificans PD1222 histidine kinase YP_918166.1 1602822 R 318586 CDS YP_918167.1 119387112 4582957 complement(1604791..1606113) 1 NC_008687.1 KEGG: bur:Bcep18194_A6285 permease for cytosine/purines, uracil, thiamine, allantoin tranporter; cytosine/purines, uracil, thiamine, allantoin permease 1606113 4582957 Pden_4407 Paracoccus denitrificans PD1222 cytosine/purines, uracil, thiamine, allantoin permease YP_918167.1 1604791 R 318586 CDS YP_918168.1 119387113 4582958 complement(1606211..1608346) 1 NC_008687.1 PFAM: Hydantoinase/oxoprolinase; Hydantoinaseoxoprolinase domain protein; KEGG: ppu:PP_3515 hydantoin utilization protein A; 5-oxoprolinase 1608346 4582958 Pden_4408 Paracoccus denitrificans PD1222 5-oxoprolinase YP_918168.1 1606211 R 318586 CDS YP_918169.1 119387114 4582959 complement(1608429..1610177) 1 NC_008687.1 PFAM: Hydantoinase B/oxoprolinase; KEGG: pfl:PFL_2733 hydantoin utilization protein B; 5-oxoprolinase 1610177 4582959 Pden_4409 Paracoccus denitrificans PD1222 5-oxoprolinase YP_918169.1 1608429 R 318586 CDS YP_918170.1 119387115 4582960 1610483..1611439 1 NC_008687.1 PFAM: helix-turn-helix- domain containing protein, AraC type; KEGG: ppu:PP_3516 transcriptional regulator, AraC family; helix-turn-helix domain-containing protein 1611439 4582960 Pden_4410 Paracoccus denitrificans PD1222 helix-turn-helix domain-containing protein YP_918170.1 1610483 D 318586 CDS YP_918171.1 119387116 4582961 complement(1611443..1612588) 1 NC_008687.1 PFAM: L-carnitine dehydratase/bile acid-inducible protein F; KEGG: sil:SPO0820 CaiB/BaiF family protein; L-carnitine dehydratase/bile acid-inducible protein F 1612588 4582961 Pden_4411 Paracoccus denitrificans PD1222 L-carnitine dehydratase/bile acid-inducible protein F YP_918171.1 1611443 R 318586 CDS YP_918172.1 119387117 4582962 complement(1612588..1613799) 1 NC_008687.1 PFAM: acyl-CoA dehydrogenase domain protein; Acyl-CoA dehydrogenase, type 2, C-terminal domain; KEGG: mlo:mll2878 glutaryl Co-A dehydrogenase; acyl-CoA dehydrogenase 1613799 4582962 Pden_4412 Paracoccus denitrificans PD1222 acyl-CoA dehydrogenase YP_918172.1 1612588 R 318586 CDS YP_918173.1 119387118 4582963 1613891..1614793 1 NC_008687.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: mes:Meso_2482 transcriptional regulator, LysR family; LysR family transcriptional regulator 1614793 4582963 Pden_4413 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_918173.1 1613891 D 318586 CDS YP_918174.1 119387119 4582964 complement(1614817..1616097) 1 NC_008687.1 TIGRFAM: 4-aminobutyrate aminotransferase; PFAM: aminotransferase class-III; KEGG: jan:Jann_3070 4-aminobutyrate aminotransferase; 4-aminobutyrate aminotransferase 1616097 4582964 Pden_4414 Paracoccus denitrificans PD1222 4-aminobutyrate aminotransferase YP_918174.1 1614817 R 318586 CDS YP_918175.1 119387120 4582965 1616178..1616819 1 NC_008687.1 PFAM: helix-turn-helix domain protein; Cupin 2, conserved barrel domain protein; KEGG: rde:RD1_0838 transcription regulator; XRE family transcriptional regulator 1616819 4582965 Pden_4415 Paracoccus denitrificans PD1222 XRE family transcriptional regulator YP_918175.1 1616178 D 318586 CDS YP_918176.1 119387121 4582966 complement(1616830..1618263) 1 NC_008687.1 PFAM: aldehyde dehydrogenase; KEGG: atc:AGR_L_2660 hypothetical protein; aldehyde dehydrogenase 1618263 4582966 Pden_4416 Paracoccus denitrificans PD1222 aldehyde dehydrogenase YP_918176.1 1616830 R 318586 CDS YP_918177.1 119387122 4582967 complement(1618631..1620475) 1 NC_008687.1 binds to the ribosome on the universally-conserved alpha-sarcin loop; GTP-binding protein LepA 1620475 4582967 Pden_4417 Paracoccus denitrificans PD1222 GTP-binding protein LepA YP_918177.1 1618631 R 318586 CDS YP_918178.1 119387123 4582968 complement(1620472..1621392) 1 NC_008687.1 PFAM: protein of unknown function DUF6, transmembrane; KEGG: rde:RD1_3141 integral membrane protein; hypothetical protein 1621392 4582968 Pden_4418 Paracoccus denitrificans PD1222 hypothetical protein YP_918178.1 1620472 R 318586 CDS YP_918179.1 119387124 4582969 1621789..1622154 1 NC_008687.1 KEGG: rsp:RSP_2018 hypothetical protein; hypothetical protein 1622154 4582969 Pden_4419 Paracoccus denitrificans PD1222 hypothetical protein YP_918179.1 1621789 D 318586 CDS YP_918180.1 119387125 4582970 1622162..1622842 1 NC_008687.1 PFAM: Silent information regulator protein Sir2; KEGG: rde:RD1_1683 NAD-dependent deacetylase; silent information regulator protein Sir2 1622842 4582970 Pden_4420 Paracoccus denitrificans PD1222 silent information regulator protein Sir2 YP_918180.1 1622162 D 318586 CDS YP_918181.1 119387126 4582971 1623017..1624159 1 NC_008687.1 TIGRFAM: phosphonate metabolism protein PhnM; PFAM: amidohydrolase; Amidohydrolase 3; KEGG: sil:SPO0476 alkylphosphonate utilization protein PhnM; phosphonate metabolism protein PhnM 1624159 4582971 Pden_4421 Paracoccus denitrificans PD1222 phosphonate metabolism protein PhnM YP_918181.1 1623017 D 318586 CDS YP_918182.1 119387127 4582972 1624263..1624601 1 NC_008687.1 TIGRFAM: alkylhydroperoxidase like protein, AhpD family; PFAM: Carboxymuconolactone decarboxylase; KEGG: sil:SPO0640 4-carboxymuconolactone decarboxylase domain/alkylhydroperoxidase AhpD family core domain protein; alkylhydroperoxidase 1624601 4582972 Pden_4422 Paracoccus denitrificans PD1222 alkylhydroperoxidase YP_918182.1 1624263 D 318586 CDS YP_918183.1 119387128 4582973 complement(1624638..1626269) 1 NC_008687.1 catalyzes the interconversion of alpha-D-glucose 1-phosphate to alpha-D-glucose 6-phosphate; phosphoglucomutase 1626269 4582973 Pden_4423 Paracoccus denitrificans PD1222 phosphoglucomutase YP_918183.1 1624638 R 318586 CDS YP_918184.1 119387129 4582974 complement(1626280..1628115) 1 NC_008687.1 KEGG: rde:RD1_2871 4-alpha-glucanotransferase; TIGRFAM: 4-alpha-glucanotransferase; PFAM: glycoside hydrolase, family 77; 4-alpha-glucanotransferase 1628115 4582974 Pden_4424 Paracoccus denitrificans PD1222 4-alpha-glucanotransferase YP_918184.1 1626280 R 318586 CDS YP_918185.1 119387130 4582975 complement(1628108..1630201) 1 NC_008687.1 KEGG: jan:Jann_3116 glycogen debranching enzyme GlgX; TIGRFAM: glycogen debranching enzyme GlgX; PFAM: glycoside hydrolase, family 13 domain protein; alpha amylase, catalytic region; SMART: alpha amylase, catalytic sub domain; glycogen debranching protein GlgX 1630201 4582975 Pden_4425 Paracoccus denitrificans PD1222 glycogen debranching protein GlgX YP_918185.1 1628108 R 318586 CDS YP_918186.1 119387131 4582976 complement(1630201..1631604) 1 NC_008687.1 catalyzes the formation of alpha-1,4-glucan chains from ADP-glucose; glycogen synthase 1631604 glgA 4582976 glgA Paracoccus denitrificans PD1222 glycogen synthase YP_918186.1 1630201 R 318586 CDS YP_918187.1 119387132 4582977 complement(1631601..1632863) 1 NC_008687.1 catalyzes the formation of ADP-glucose and diphosphate from ATP and alpha-D-glucose 1-phosphate; glucose-1-phosphate adenylyltransferase 1632863 glgC 4582977 glgC Paracoccus denitrificans PD1222 glucose-1-phosphate adenylyltransferase YP_918187.1 1631601 R 318586 CDS YP_918188.1 119387133 4582978 complement(1632907..1635102) 1 NC_008687.1 catalyzes the transfer of a segment of a 1,4-alpha-D-glucan chain to a primary hydroxy group in a similar glucan chain; glycogen branching protein 1635102 4582978 Pden_4428 Paracoccus denitrificans PD1222 glycogen branching protein YP_918188.1 1632907 R 318586 CDS YP_918189.1 119387134 4582979 complement(1635124..1637520) 1 NC_008687.1 KEGG: rsp:RSP_2887 glycogen phosphorylase; TIGRFAM: glycogen/starch/alpha-glucan phosphorylases; PFAM: glycosyl transferase, family 35; glycogen/starch/alpha-glucan phosphorylase 1637520 4582979 Pden_4429 Paracoccus denitrificans PD1222 glycogen/starch/alpha-glucan phosphorylase YP_918189.1 1635124 R 318586 CDS YP_918190.1 119387135 4582980 complement(1637767..1638618) 1 NC_008687.1 KEGG: sil:SPO3245 nicotinate-nucleotide pyrophosphorylase; TIGRFAM: nicotinate-nucleotide pyrophosphorylase; PFAM: Quinolinate phosphoribosyl transferase; nicotinate-nucleotide pyrophosphorylase 1638618 4582980 Pden_4430 Paracoccus denitrificans PD1222 nicotinate-nucleotide pyrophosphorylase YP_918190.1 1637767 R 318586 CDS YP_918191.1 119387136 4582981 complement(1638615..1640180) 1 NC_008687.1 catalyzes the formation of oxaloacetate from L-aspartate; L-aspartate oxidase 1640180 4582981 Pden_4431 Paracoccus denitrificans PD1222 L-aspartate oxidase YP_918191.1 1638615 R 318586 CDS YP_918192.1 119387137 4582982 complement(1640184..1641236) 1 NC_008687.1 3 different subfamilies; catalyzes the formation of quinolinate from iminoaspartate and dihydroxyacetone phosphate; quinolinate synthetase 1641236 4582982 Pden_4432 Paracoccus denitrificans PD1222 quinolinate synthetase YP_918192.1 1640184 R 318586 CDS YP_918193.1 119387138 4582983 1641493..1642257 1 NC_008687.1 PFAM: regulatory proteins, IclR; KEGG: sil:SPO2355 transcriptional regulator, IclR family; regulatory proteins, IclR 1642257 4582983 Pden_4433 Paracoccus denitrificans PD1222 regulatory proteins, IclR YP_918193.1 1641493 D 318586 CDS YP_918194.1 119387139 4582984 complement(1642263..1642841) 1 NC_008687.1 KEGG: rsp:RSP_0816 aminotransferase, class IV; hypothetical protein 1642841 4582984 Pden_4434 Paracoccus denitrificans PD1222 hypothetical protein YP_918194.1 1642263 R 318586 CDS YP_918195.1 119387140 4582985 complement(1642850..1644016) 1 NC_008687.1 catalyzes the formation of 4-amino-4-deoxychorismate from chorismate and glutamine; aminodeoxychorismate synthase 1644016 4582985 Pden_4435 Paracoccus denitrificans PD1222 aminodeoxychorismate synthase YP_918195.1 1642850 R 318586 CDS YP_918196.1 119387141 4582986 complement(1644105..1645277) 1 NC_008687.1 PFAM: oxidoreductase domain protein; Oxidoreductase, C-terminal domain; KEGG: rsp:RSP_1245 predicted oxidoreductase, Gfo/Idh/MocA family; oxidoreductase domain-containing protein 1645277 4582986 Pden_4436 Paracoccus denitrificans PD1222 oxidoreductase domain-containing protein YP_918196.1 1644105 R 318586 CDS YP_918197.1 119387142 4582987 complement(1645344..1646393) 1 NC_008687.1 PFAM: oxidoreductase domain protein; Oxidoreductase, C-terminal domain; KEGG: sme:SMb20330 probable trehalosemaltose utilization protein, function; oxidoreductase domain-containing protein 1646393 4582987 Pden_4437 Paracoccus denitrificans PD1222 oxidoreductase domain-containing protein YP_918197.1 1645344 R 318586 CDS YP_918198.1 119387143 4582988 complement(1646393..1647178) 1 NC_008687.1 PFAM: protein of unknown function DUF1037; KEGG: atc:AGR_L_2958 probable ThuA protein, function; hypothetical protein 1647178 4582988 Pden_4438 Paracoccus denitrificans PD1222 hypothetical protein YP_918198.1 1646393 R 318586 CDS YP_918199.1 119387144 4582989 complement(1647221..1648222) 1 NC_008687.1 PFAM: ABC transporter related; TOBE domain protein; Transport-associated OB domain protein; SMART: AAA ATPase; KEGG: ret:RHE_PF00207 trehalosemaltose ABC transporter, ATP-binding protein; ABC transporter 1648222 4582989 Pden_4439 Paracoccus denitrificans PD1222 ABC transporter YP_918199.1 1647221 R 318586 CDS YP_918200.1 119387145 4582990 complement(1648226..1649059) 1 NC_008687.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: bms:BRA0306 sugar ABC transporter, permease; binding-protein-dependent transport systems inner membrane component 1649059 4582990 Pden_4440 Paracoccus denitrificans PD1222 binding-protein-dependent transport systems inner membrane component YP_918200.1 1648226 R 318586 CDS YP_918201.1 119387146 4582991 complement(1649056..1650018) 1 NC_008687.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: sme:SMb20326 probable trehalosemaltose transporter permease; binding-protein-dependent transport systems inner membrane component 1650018 4582991 Pden_4441 Paracoccus denitrificans PD1222 binding-protein-dependent transport systems inner membrane component YP_918201.1 1649056 R 318586 CDS YP_918202.1 119387147 4582992 complement(1650089..1651366) 1 NC_008687.1 PFAM: extracellular solute-binding protein, family 1; KEGG: sme:SMb20325 probable trehalosemaltose-binding protein; extracellular solute-binding protein 1651366 4582992 Pden_4442 Paracoccus denitrificans PD1222 extracellular solute-binding protein YP_918202.1 1650089 R 318586 CDS YP_918203.1 119387148 4582993 complement(1651797..1652429) 1 NC_008687.1 PFAM: electron transport protein SCO1/SenC; KEGG: mes:Meso_1992 electron transport protein SCO1/SenC; electron transport protein SCO1/SenC 1652429 4582993 Pden_4443 Paracoccus denitrificans PD1222 electron transport protein SCO1/SenC YP_918203.1 1651797 R 318586 CDS YP_918204.1 119387149 4582994 complement(1652416..1653402) 1 NC_008687.1 PFAM: protein of unknown function DUF461; nuclear export factor GLE1; KEGG: sme:SMc01242 signal peptide protein; hypothetical protein 1653402 4582994 Pden_4444 Paracoccus denitrificans PD1222 hypothetical protein YP_918204.1 1652416 R 318586 CDS YP_918205.1 119387150 4582995 complement(1653460..1653879) 1 NC_008687.1 hypothetical protein 1653879 4582995 Pden_4445 Paracoccus denitrificans PD1222 hypothetical protein YP_918205.1 1653460 R 318586 CDS YP_918206.1 119387151 4582996 complement(1653933..1655585) 1 NC_008687.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: atc:AGR_C_717 hypothetical protein; binding-protein-dependent transport system inner membrane protein 1655585 4582996 Pden_4446 Paracoccus denitrificans PD1222 binding-protein-dependent transport system inner membrane protein YP_918206.1 1653933 R 318586 CDS YP_918207.1 119387152 4582997 complement(1655608..1656621) 1 NC_008687.1 PFAM: extracellular solute-binding protein, family 1; KEGG: atc:AGR_C_715 iron binding protein; extracellular solute-binding protein 1656621 4582997 Pden_4447 Paracoccus denitrificans PD1222 extracellular solute-binding protein YP_918207.1 1655608 R 318586 CDS YP_918208.1 119387153 4582998 1656714..1657835 1 NC_008687.1 PFAM: ABC transporter related; Transport-associated OB domain protein; SMART: AAA ATPase; KEGG: rsp:RSP_2539 ABC transporter, ATPase subunit; ABC transporter 1657835 4582998 Pden_4448 Paracoccus denitrificans PD1222 ABC transporter YP_918208.1 1656714 D 318586 CDS YP_918209.1 119387154 4582999 complement(1657849..1660461) 1 NC_008687.1 PFAM: molybdopterin oxidoreductase; molydopterin dinucleotide-binding region; molybdopterin oxidoreductase Fe4S4 region; BFD domain protein [2Fe-2S]-binding domain protein; KEGG: jan:Jann_3045 molybdopterin oxidoreductase; molybdopterin oxidoreductase 1660461 4582999 Pden_4449 Paracoccus denitrificans PD1222 molybdopterin oxidoreductase YP_918209.1 1657849 R 318586 CDS YP_918210.1 119387155 4583000 complement(1660470..1661327) 1 NC_008687.1 PFAM: formate/nitrite transporter; KEGG: bcn:Bcen_5755 formate/nitrite transporter; formate/nitrite transporter 1661327 4583000 Pden_4450 Paracoccus denitrificans PD1222 formate/nitrite transporter YP_918210.1 1660470 R 318586 CDS YP_918211.1 119387156 4583001 complement(1661340..1661675) 1 NC_008687.1 TIGRFAM: nitrite reductase [NAD(P)H], small subunit; PFAM: Rieske [2Fe-2S] domain protein; KEGG: rde:RD1_4167 assimilatory nitrite reductase, small subunit; nitrite reductase (NAD(P)H) small subunit 1661675 4583001 Pden_4451 Paracoccus denitrificans PD1222 nitrite reductase (NAD(P)H) small subunit YP_918211.1 1661340 R 318586 CDS YP_918212.1 119387157 4583002 complement(1661672..1664104) 1 NC_008687.1 TIGRFAM: nitrite reductase [NAD(P)H], large subunit; PFAM: FAD-dependent pyridine nucleotide-disulphide oxidoreductase; glucose-inhibited division protein A; nitrite/sulfite reductase, hemoprotein beta-component, ferrodoxin domain protein; nitrite and sulphite reductase 4Fe-4S region; BFD domain protein [2Fe-2S]-binding domain protein; KEGG: rde:RD1_4168 assimilatory nitrite reductase, large subunit; nitrite reductase (NAD(P)H) large subunit 1664104 4583002 Pden_4452 Paracoccus denitrificans PD1222 nitrite reductase (NAD(P)H) large subunit YP_918212.1 1661672 R 318586 CDS YP_918213.1 119387158 4583003 complement(1664120..1665328) 1 NC_008687.1 PFAM: major facilitator superfamily MFS_1; KEGG: sme:SMb20436 nitrate transporter protein; major facilitator transporter 1665328 4583003 Pden_4453 Paracoccus denitrificans PD1222 major facilitator transporter YP_918213.1 1664120 R 318586 CDS YP_918214.1 119387159 4583004 complement(1665613..1666785) 1 NC_008687.1 KEGG: jan:Jann_3039 nitrate transport protein; nitrate transport protein 1666785 4583004 Pden_4454 Paracoccus denitrificans PD1222 nitrate transport protein YP_918214.1 1665613 R 318586 CDS YP_918215.1 119387160 4583005 complement(1666776..1667366) 1 NC_008687.1 PFAM: ANTAR domain protein; KEGG: jan:Jann_3038 response regulator receiver (CheY-like) and ANTAR domain protein; response regulator receiver/ANTAR domain-containing protein 1667366 4583005 Pden_4455 Paracoccus denitrificans PD1222 response regulator receiver/ANTAR domain-containing protein YP_918215.1 1666776 R 318586 CDS YP_918216.1 119387161 4583006 1667596..1668348 1 NC_008687.1 PFAM: 3-alpha; MOSC domain containing protein; KEGG: rsp:RSP_1921 MOSC domain protein; MOSC domain-containing protein 1668348 4583006 Pden_4456 Paracoccus denitrificans PD1222 MOSC domain-containing protein YP_918216.1 1667596 D 318586 CDS YP_918217.1 119387162 4583007 1668345..1669181 1 NC_008687.1 TIGRFAM: pyridoxal kinase; PFAM: Phosphomethylpyrimidine kinase type-1; KEGG: rsp:RSP_1920 pyridoxal/pyridoxine/pyridoxamine kinase; pyridoxal kinase 1669181 4583007 Pden_4457 Paracoccus denitrificans PD1222 pyridoxal kinase YP_918217.1 1668345 D 318586 CDS YP_918218.1 119387163 4583008 complement(1669248..1671560) 1 NC_008687.1 PFAM: RNA binding S1 domain protein; SMART: Resolvase, RNase H domain protein fold; KEGG: sil:SPOA0306 S1 RNA binding domain protein; RNA-binding S1 domain-containing protein 1671560 4583008 Pden_4458 Paracoccus denitrificans PD1222 RNA-binding S1 domain-containing protein YP_918218.1 1669248 R 318586 CDS YP_918219.1 119387164 4583009 complement(1671634..1672110) 1 NC_008687.1 hypothetical protein 1672110 4583009 Pden_4459 Paracoccus denitrificans PD1222 hypothetical protein YP_918219.1 1671634 R 318586 CDS YP_918220.1 119387165 4583010 complement(1672770..1674299) 1 NC_008687.1 TIGRFAM: carbohydrate kinase, YjeF related protein; PFAM: protein of unknown function UPF0031; YjeF-family N-terminal domain protein; KEGG: sit:TM1040_1024 YjeF-related protein-like; carbohydrate kinase 1674299 4583010 Pden_4460 Paracoccus denitrificans PD1222 carbohydrate kinase YP_918220.1 1672770 R 318586 CDS YP_918221.1 119387166 4583011 1674441..1674779 1 NC_008687.1 PFAM: nitrogen regulatory protein P-II; KEGG: rsp:RSP_0146 nitrogen regulatory protein P-II; nitrogen regulatory protein P-II 1674779 4583011 Pden_4461 Paracoccus denitrificans PD1222 nitrogen regulatory protein P-II YP_918221.1 1674441 D 318586 CDS YP_918222.1 119387167 4583012 1674857..1676263 1 NC_008687.1 KEGG: rsp:RSP_0147 glutamine synthetase class-I; TIGRFAM: glutamine synthetase, type I; PFAM: glutamine synthetase, catalytic region; glutamine synthetase, beta-Grasp; glutamine synthetase, type I 1676263 4583012 Pden_4462 Paracoccus denitrificans PD1222 glutamine synthetase, type I YP_918222.1 1674857 D 318586 CDS YP_918223.1 119387168 4583013 1676470..1677786 1 NC_008687.1 Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide; adenylosuccinate lyase 1677786 4583013 Pden_4463 Paracoccus denitrificans PD1222 adenylosuccinate lyase YP_918223.1 1676470 D 318586 CDS YP_918224.1 119387169 4583014 1677847..1678902 1 NC_008687.1 PFAM: flagellar motor switch protein FliG; KEGG: rsp:RSP_2220 possible flagellar motor switch protein (FliG); flagellar motor switch protein FliG 1678902 4583014 Pden_4464 Paracoccus denitrificans PD1222 flagellar motor switch protein FliG YP_918224.1 1677847 D 318586 CDS YP_918225.1 119387170 4583015 1679499..1680500 1 NC_008687.1 KEGG: rsp:RSP_2959 glyceraldehyde-3-phosphate dehydrogenase; TIGRFAM: glyceraldehyde-3-phosphate dehydrogenase, type I; PFAM: glyceraldehyde 3-phosphate dehydrogenase; glyceraldehyde-3-phosphate dehydrogenase, type I 1680500 4583015 Pden_4465 Paracoccus denitrificans PD1222 glyceraldehyde-3-phosphate dehydrogenase, type I YP_918225.1 1679499 D 318586 CDS YP_918226.1 119387171 4583016 complement(1680590..1680904) 1 NC_008687.1 KEGG: rsp:RSP_0307 antifreeze protein, type I; antifreeze protein, type I 1680904 4583016 Pden_4466 Paracoccus denitrificans PD1222 antifreeze protein, type I YP_918226.1 1680590 R 318586 CDS YP_918227.1 119387172 4583017 1681035..1682078 1 NC_008687.1 catalyzes the formation of N-carbamoyl-L-aspartate from (S)-dihydroorotate in pyrimidine biosynthesis; dihydroorotase 1682078 4583017 Pden_4467 Paracoccus denitrificans PD1222 dihydroorotase YP_918227.1 1681035 D 318586 CDS YP_918228.1 119387173 4583018 1682075..1682746 1 NC_008687.1 involved in fifth step of pyrimidine biosynthesis; converts orotidine 5'-phosphate and diphosphate to orotate and 5-phospho-alpha-D-ribose 1-diphosphate; orotate phosphoribosyltransferase 1682746 pyrE 4583018 pyrE Paracoccus denitrificans PD1222 orotate phosphoribosyltransferase YP_918228.1 1682075 D 318586 CDS YP_918229.1 119387174 4583019 1682979..1684478 1 NC_008687.1 unwinds double stranded DNA; replicative DNA helicase 1684478 4583019 Pden_4469 Paracoccus denitrificans PD1222 replicative DNA helicase YP_918229.1 1682979 D 318586 CDS YP_918230.1 119387175 4583020 1684475..1684837 1 NC_008687.1 PFAM: protein of unknown function DUF486; KEGG: rsp:RSP_2188 hypothetical protein; hypothetical protein 1684837 4583020 Pden_4470 Paracoccus denitrificans PD1222 hypothetical protein YP_918230.1 1684475 D 318586 CDS YP_918231.1 119387176 4583021 1684901..1686109 1 NC_008687.1 TIGRFAM: drug resistance transporter, Bcr/CflA subfamily; PFAM: major facilitator superfamily MFS_1; KEGG: rsp:RSP_2187 multidrug efflux pump, major facilitator superfamily (MFS); Bcr/CflA subfamily drug resistance transporter 1686109 4583021 Pden_4471 Paracoccus denitrificans PD1222 Bcr/CflA subfamily drug resistance transporter YP_918231.1 1684901 D 318586 CDS YP_918232.1 119387177 4583022 1686171..1687565 1 NC_008687.1 PFAM: helix-turn-helix domain protein; protein of unknown function DUF955; KEGG: rsp:RSP_2186 transcriptional regulator, MerR family; hypothetical protein 1687565 4583022 Pden_4472 Paracoccus denitrificans PD1222 hypothetical protein YP_918232.1 1686171 D 318586 CDS YP_918233.1 119387178 4583023 1687807..1689282 1 NC_008687.1 PFAM: peptidase M23B; KEGG: rde:RD1_3002 peptidase, M23/M37 family; peptidase M23B 1689282 4583023 Pden_4473 Paracoccus denitrificans PD1222 peptidase M23B YP_918233.1 1687807 D 318586 CDS YP_918234.1 119387179 4583024 1689272..1689769 1 NC_008687.1 PFAM: protein of unknown function DUF583; KEGG: rsp:RSP_2975 hypothetical protein; hypothetical protein 1689769 4583024 Pden_4474 Paracoccus denitrificans PD1222 hypothetical protein YP_918234.1 1689272 D 318586 CDS YP_918235.1 119387180 4583025 complement(1689816..1690679) 1 NC_008687.1 KEGG: rsp:RSP_2976 hypothetical protein; hypothetical protein 1690679 4583025 Pden_4475 Paracoccus denitrificans PD1222 hypothetical protein YP_918235.1 1689816 R 318586 CDS YP_918236.1 119387181 4583026 complement(1690734..1691228) 1 NC_008687.1 Catalyzes the conversion of ATP and pantetheine 4'-phosphate to diphosphate and 3'-dephospho-coA; phosphopantetheine adenylyltransferase 1691228 coaD 4583026 coaD Paracoccus denitrificans PD1222 phosphopantetheine adenylyltransferase YP_918236.1 1690734 R 318586 CDS YP_918237.1 119387182 4583027 complement(1691338..1691775) 1 NC_008687.1 PFAM: CBS domain containing protein; KEGG: rsp:RSP_2961 protein containing a CBS domain; signal-transduction protein 1691775 4583027 Pden_4477 Paracoccus denitrificans PD1222 signal-transduction protein YP_918237.1 1691338 R 318586 CDS YP_918238.1 119387183 4583028 complement(1691868..1692761) 1 NC_008687.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: rsp:RSP_2965 transcriptional regulator, LysR family; LysR family transcriptional regulator 1692761 4583028 Pden_4478 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_918238.1 1691868 R 318586 CDS YP_918239.1 119387184 4583029 1692871..1694370 1 NC_008687.1 TIGRFAM: methylmalonate-semialdehyde dehydrogenase; PFAM: aldehyde dehydrogenase; KEGG: sit:TM1040_1106 methylmalonate-semialdehyde dehydrogenase; methylmalonate-semialdehyde dehydrogenase 1694370 4583029 Pden_4479 Paracoccus denitrificans PD1222 methylmalonate-semialdehyde dehydrogenase YP_918239.1 1692871 D 318586 CDS YP_918240.1 119387185 4583030 1694494..1695639 1 NC_008687.1 PFAM: acyl-CoA dehydrogenase domain protein; Acyl-CoA dehydrogenase, type 2, C-terminal domain; KEGG: rsp:RSP_0156 acyl-CoA dehydrogenase; acyl-CoA dehydrogenase 1695639 4583030 Pden_4480 Paracoccus denitrificans PD1222 acyl-CoA dehydrogenase YP_918240.1 1694494 D 318586 CDS YP_918241.1 119387186 4583031 1695640..1696647 1 NC_008687.1 PFAM: Enoyl-CoA hydratase/isomerase; KEGG: sil:SPO2212 enoyl-CoA hydratase/isomerase family protein; enoyl-CoA hydratase/isomerase 1696647 4583031 Pden_4481 Paracoccus denitrificans PD1222 enoyl-CoA hydratase/isomerase YP_918241.1 1695640 D 318586 CDS YP_918242.1 119387187 4583032 1696644..1697519 1 NC_008687.1 TIGRFAM: 3-hydroxyisobutyrate dehydrogenase; PFAM: NADP oxidoreductase, coenzyme F420-dependent; 6-phosphogluconate dehydrogenase, NAD-binding; KEGG: rsp:RSP_0154 3-hydroxyisobutyrate dehydrogenase; 3-hydroxyisobutyrate dehydrogenase 1697519 4583032 Pden_4482 Paracoccus denitrificans PD1222 3-hydroxyisobutyrate dehydrogenase YP_918242.1 1696644 D 318586 CDS YP_918243.1 119387188 4583033 1697600..1697908 1 NC_008687.1 hypothetical protein 1697908 4583033 Pden_4483 Paracoccus denitrificans PD1222 hypothetical protein YP_918243.1 1697600 D 318586 CDS YP_918244.1 119387189 4583034 complement(1697905..1699548) 1 NC_008687.1 TIGRFAM: DNA repair protein RecN; PFAM: SMC domain protein; KEGG: rsp:RSP_2118 DNA repair protein RecN; DNA repair protein RecN 1699548 4583034 Pden_4484 Paracoccus denitrificans PD1222 DNA repair protein RecN YP_918244.1 1697905 R 318586 CDS YP_918245.1 119387190 4583035 complement(1699556..1700398) 1 NC_008687.1 KEGG: rsp:RSP_2117 ComL lipoprotein; ComL lipoprotein 1700398 4583035 Pden_4485 Paracoccus denitrificans PD1222 ComL lipoprotein YP_918245.1 1699556 R 318586 CDS YP_918246.1 119387191 4583036 complement(1700528..1701466) 1 NC_008687.1 zinc-dependent; catalyzes the deacetylation of UDP-(3-O-acyl)-N-acetylglucosamine to UDP-3-O-(3-hydroxytetradecanoyl)-glucosamine in the second step of lipid A biosynthesis; UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase 1701466 lpxC 4583036 lpxC Paracoccus denitrificans PD1222 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase YP_918246.1 1700528 R 318586 CDS YP_918247.1 119387192 4583037 complement(1701702..1703336) 1 NC_008687.1 GTPase; similar structure to tubulin; forms ring-shaped polymers at the site of cell division; other proteins such as FtsA, ZipA, and ZapA, interact with and regulate FtsZ function; cell division protein FtsZ 1703336 4583037 Pden_4487 Paracoccus denitrificans PD1222 cell division protein FtsZ YP_918247.1 1701702 R 318586 CDS YP_918248.1 119387193 4583038 complement(1703557..1704891) 1 NC_008687.1 PFAM: cell division protein FtsA; KEGG: rsp:RSP_2113 cell division protein FtsA; cell division protein FtsA 1704891 4583038 Pden_4488 Paracoccus denitrificans PD1222 cell division protein FtsA YP_918248.1 1703557 R 318586 CDS YP_918249.1 119387194 4583039 complement(1704913..1705935) 1 NC_008687.1 PFAM: cell division protein FtsQ; KEGG: rsp:RSP_2112 cell division septal protein FtsQ; cell division protein FtsQ 1705935 4583039 Pden_4489 Paracoccus denitrificans PD1222 cell division protein FtsQ YP_918249.1 1704913 R 318586 CDS YP_918250.1 119387195 4583040 complement(1705923..1706858) 1 NC_008687.1 D-alanine--D-alanine ligase; DdlA; DdlB; cytoplasmic; catalyzes the formation of D-alanyl-D-alanine from two D-alanines in peptidoglycan synthesis; there are two forms of this enzyme in Escherichia coli; D-alanine--D-alanine ligase 1706858 ddl 4583040 ddl Paracoccus denitrificans PD1222 D-alanine--D-alanine ligase YP_918250.1 1705923 R 318586 CDS YP_918251.1 119387196 4583041 complement(1706977..1707897) 1 NC_008687.1 catalyzes the reduction of UDP-N-acetylglucosamine enolpyruvate to form UDP-N-acetylmuramate in peptidoglycan biosynthesis; UDP-N-acetylenolpyruvoylglucosamine reductase 1707897 murB 4583041 murB Paracoccus denitrificans PD1222 UDP-N-acetylenolpyruvoylglucosamine reductase YP_918251.1 1706977 R 318586 CDS YP_918252.1 119387197 4583042 complement(1708076..1708444) 1 NC_008687.1 hypothetical protein 1708444 4583042 Pden_4492 Paracoccus denitrificans PD1222 hypothetical protein YP_918252.1 1708076 R 318586 CDS YP_918253.1 119387198 4583043 complement(1708449..1708712) 1 NC_008687.1 KEGG: jan:Jann_2756 hypothetical protein; hypothetical protein 1708712 4583043 Pden_4493 Paracoccus denitrificans PD1222 hypothetical protein YP_918253.1 1708449 R 318586 CDS YP_918254.1 119387199 4583044 complement(1708709..1710136) 1 NC_008687.1 Catalyzes the formation of UDP-N-acetylmuramoyl-L-alanine from UDP-N-acetylmuramate and L-alanine in peptidoglycan synthesis; UDP-N-acetylmuramate--L-alanine ligase 1710136 murC 4583044 murC Paracoccus denitrificans PD1222 UDP-N-acetylmuramate--L-alanine ligase YP_918254.1 1708709 R 318586 CDS YP_918255.1 119387200 4583045 complement(1710133..1711221) 1 NC_008687.1 UDP-N-acetylglucosamine--N-acetylmuramyl- (pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase; involved in cell wall formation; inner membrane-associated; last step of peptidoglycan synthesis; UDPdiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase 1711221 murG 4583045 murG Paracoccus denitrificans PD1222 UDPdiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase YP_918255.1 1710133 R 318586 CDS YP_918256.1 119387201 4583046 complement(1711218..1712387) 1 NC_008687.1 TIGRFAM: cell division protein FtsW; PFAM: cell cycle protein; KEGG: rsp:RSP_2106 cell division protein FtsW; cell division protein FtsW 1712387 4583046 Pden_4496 Paracoccus denitrificans PD1222 cell division protein FtsW YP_918256.1 1711218 R 318586 CDS YP_918257.1 119387202 4583047 complement(1712522..1712911) 1 NC_008687.1 PFAM: DoxX family protein; KEGG: ret:RHE_CH00824 hypothetical conserved membrane protein; DoxX family protein 1712911 4583047 Pden_4497 Paracoccus denitrificans PD1222 DoxX family protein YP_918257.1 1712522 R 318586 CDS YP_918258.1 119387203 4583048 1713154..1714056 1 NC_008687.1 KEGG: rsp:RSP_0009 hypothetical protein; hypothetical protein 1714056 4583048 Pden_4498 Paracoccus denitrificans PD1222 hypothetical protein YP_918258.1 1713154 D 318586 CDS YP_918259.1 119387204 4583049 1714056..1714982 1 NC_008687.1 catalyzes the formation of O-succinyl-L-homoserine from succinyl-CoA and L-homoserine in methionine biosynthesis; homoserine O-succinyltransferase 1714982 4583049 Pden_4499 Paracoccus denitrificans PD1222 homoserine O-succinyltransferase YP_918259.1 1714056 D 318586 CDS YP_918260.1 119387205 4583050 1714985..1715908 1 NC_008687.1 PFAM: protein of unknown function DUF344; KEGG: rsp:RSP_0013 hypothetical protein; hypothetical protein 1715908 4583050 Pden_4500 Paracoccus denitrificans PD1222 hypothetical protein YP_918260.1 1714985 D 318586 CDS YP_918261.1 119387206 4583051 1715930..1716865 1 NC_008687.1 PFAM: protein of unknown function DUF477; KEGG: sil:SPO2950 hypothetical protein; hypothetical protein 1716865 4583051 Pden_4501 Paracoccus denitrificans PD1222 hypothetical protein YP_918261.1 1715930 D 318586 CDS YP_918262.1 119387207 4583052 1716908..1717990 1 NC_008687.1 KEGG: rsp:RSP_2141 ABC polyamine transporter, periplasmic substrate-binding protein; ABC polyamine transporter, periplasmic substrate-binding protein 1717990 4583052 Pden_4502 Paracoccus denitrificans PD1222 ABC polyamine transporter, periplasmic substrate-binding protein YP_918262.1 1716908 D 318586 CDS YP_918263.1 119387208 4583053 1718596..1719867 1 NC_008687.1 Catalyzes the phosphorylation of L-glutamate during the proline biosynthesis pathway; gamma-glutamyl phosphate reductase 1719867 proA 4583053 proA Paracoccus denitrificans PD1222 gamma-glutamyl phosphate reductase YP_918263.1 1718596 D 318586 CDS YP_918264.1 119387209 4583054 complement(1719911..1720567) 1 NC_008687.1 KEGG: rsp:RSP_3825 hypothetical protein; hypothetical protein 1720567 4583054 Pden_4504 Paracoccus denitrificans PD1222 hypothetical protein YP_918264.1 1719911 R 318586 CDS YP_918265.1 119387210 4583055 1720608..1720787 1 NC_008687.1 KEGG: rsp:RSP_6239 hypothetical protein; hypothetical protein 1720787 4583055 Pden_4505 Paracoccus denitrificans PD1222 hypothetical protein YP_918265.1 1720608 D 318586 CDS YP_918266.1 119387211 4583056 1720925..1721704 1 NC_008687.1 KEGG: rsp:RSP_3826 hypothetical protein; hypothetical protein 1721704 4583056 Pden_4506 Paracoccus denitrificans PD1222 hypothetical protein YP_918266.1 1720925 D 318586 CDS YP_918267.1 119387212 4583057 1721701..1722534 1 NC_008687.1 PFAM: phospholipid/glycerol acyltransferase; KEGG: rde:RD1_2655 acyltransferase; phospholipid/glycerol acyltransferase 1722534 4583057 Pden_4507 Paracoccus denitrificans PD1222 phospholipid/glycerol acyltransferase YP_918267.1 1721701 D 318586 CDS YP_918268.1 119387213 4583058 complement(1722683..1724461) 1 NC_008687.1 PFAM: Citrate transporter; TrkA-C domain protein; TRAP C4-dicarboxylate transport system permease DctM subunit; KEGG: jan:Jann_3383 TrkA-like; TrkA domain-containing protein 1724461 4583058 Pden_4508 Paracoccus denitrificans PD1222 TrkA domain-containing protein YP_918268.1 1722683 R 318586 CDS YP_918269.1 119387214 4583059 complement(1724563..1725381) 1 NC_008687.1 KEGG: rde:RD1_2012 hypothetical protein; hypothetical protein 1725381 4583059 Pden_4509 Paracoccus denitrificans PD1222 hypothetical protein YP_918269.1 1724563 R 318586 CDS YP_918270.1 119387215 4583060 complement(1725447..1726982) 1 NC_008687.1 TIGRFAM: 2-polyprenylphenol 6-hydroxylase; PFAM: ABC-1 domain protein; KEGG: jan:Jann_4208 2-polyprenylphenol 6-hydroxylase; 2-polyprenylphenol 6-hydroxylase 1726982 4583060 Pden_4510 Paracoccus denitrificans PD1222 2-polyprenylphenol 6-hydroxylase YP_918270.1 1725447 R 318586 CDS YP_918271.1 119387216 4583061 complement(1726984..1727736) 1 NC_008687.1 TIGRFAM: ubiquinone/menaquinone biosynthesis methyltransferases; PFAM: UbiE/COQ5 methyltransferase; Methyltransferase type 11; Methyltransferase type 12; KEGG: rsp:RSP_1338 methyltransferase; UDP-3-O-(3-hydroxymyristoyl) glucosamine N-acyltransferase LpxD 1727736 4583061 Pden_4511 Paracoccus denitrificans PD1222 UDP-3-O-(3-hydroxymyristoyl) glucosamine N-acyltransferase LpxD YP_918271.1 1726984 R 318586 CDS YP_918272.1 119387217 4583062 1727837..1728682 1 NC_008687.1 KEGG: rsp:RSP_1339 formamidopyrimidine-DNA glycolase; TIGRFAM: formamidopyrimidine-DNA glycosylase; PFAM: Formamidopyrimidine-DNA glycolase; formamidopyrimidine-DNA glycosylase 1728682 4583062 Pden_4512 Paracoccus denitrificans PD1222 formamidopyrimidine-DNA glycosylase YP_918272.1 1727837 D 318586 CDS YP_918273.1 119387218 4583063 1728790..1729566 1 NC_008687.1 PFAM: Enoyl-CoA hydratase/isomerase; KEGG: rsp:RSP_1340 enoyl-CoA hydratase/isomerase; enoyl-CoA hydratase/isomerase 1729566 4583063 Pden_4513 Paracoccus denitrificans PD1222 enoyl-CoA hydratase/isomerase YP_918273.1 1728790 D 318586 CDS YP_918274.1 119387219 4583064 1729720..1729989 1 NC_008687.1 binds directly to the 16S rRNA and is involved in post-translational inhibition of arginine and ornithine decarboxylase; 30S ribosomal protein S20 1729989 rpsT 4583064 rpsT Paracoccus denitrificans PD1222 30S ribosomal protein S20 YP_918274.1 1729720 D 318586 CDS YP_918275.1 119387241 4583099 complement(65..511) 1 NC_008688.1 PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase; 3-demethylubiquinone-9 3-methyltransferase; KEGG: nha:Nham_3665 3-demethylubiquinone-9 3-methyltransferase; 3-demethylubiquinone-9 3-methyltransferase 511 4583099 Pden_4515 Paracoccus denitrificans PD1222 3-demethylubiquinone-9 3-methyltransferase YP_918275.1 65 R 318586 CDS YP_918276.1 119387242 4583100 complement(536..931) 1 NC_008688.1 PFAM: 3-demethylubiquinone-9 3-methyltransferase; KEGG: pau:PA14_46720 hypothetical protein; 3-demethylubiquinone-9 3-methyltransferase 931 4583100 Pden_4516 Paracoccus denitrificans PD1222 3-demethylubiquinone-9 3-methyltransferase YP_918276.1 536 R 318586 CDS YP_918277.1 119387243 4583101 988..1506 1 NC_008688.1 PFAM: regulatory protein, MarR; KEGG: nha:Nham_3666 transcriptional regulator, MarR family; MarR family transcriptional regulator 1506 4583101 Pden_4517 Paracoccus denitrificans PD1222 MarR family transcriptional regulator YP_918277.1 988 D 318586 CDS YP_918278.1 119387244 4583102 complement(1528..1887) 1 NC_008688.1 PFAM: regulatory protein, ArsR; KEGG: sme:SMc02639 transcription regulator protein; regulatory protein, ArsR 1887 4583102 Pden_4518 Paracoccus denitrificans PD1222 regulatory protein, ArsR YP_918278.1 1528 R 318586 CDS YP_918279.1 119387245 4583103 1936..2382 1 NC_008688.1 PFAM: Activator of Hsp90 ATPase 1 family protein; KEGG: sal:Sala_0458 hypothetical protein; activator of Hsp90 ATPase 1 family protein 2382 4583103 Pden_4519 Paracoccus denitrificans PD1222 activator of Hsp90 ATPase 1 family protein YP_918279.1 1936 D 318586 CDS YP_918280.1 119387246 4583104 2524..2937 1 NC_008688.1 PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase; KEGG: mlo:mlr1197 hypothetical protein; glyoxalase/bleomycin resistance protein/dioxygenase 2937 4583104 Pden_4520 Paracoccus denitrificans PD1222 glyoxalase/bleomycin resistance protein/dioxygenase YP_918280.1 2524 D 318586 CDS YP_918281.1 119387247 4583105 3076..4578 1 NC_008688.1 KEGG: mlo:mll0865 hypothetical protein; hypothetical protein 4578 4583105 Pden_4521 Paracoccus denitrificans PD1222 hypothetical protein YP_918281.1 3076 D 318586 CDS YP_918282.1 119387248 4583080 complement(4693..5118) 1 NC_008688.1 PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase; KEGG: bur:Bcep18194_A5393 glyoxalase/bleomycin resistance protein/dioxygenase; glyoxalase/bleomycin resistance protein/dioxygenase 5118 4583080 Pden_4522 Paracoccus denitrificans PD1222 glyoxalase/bleomycin resistance protein/dioxygenase YP_918282.1 4693 R 318586 CDS YP_918283.1 119387249 4583081 complement(5412..5861) 1 NC_008688.1 PFAM: regulatory protein, MerR; KEGG: mes:Meso_2848 transcriptional regulator, MerR family; MerR family transcriptional regulator 5861 4583081 Pden_4523 Paracoccus denitrificans PD1222 MerR family transcriptional regulator YP_918283.1 5412 R 318586 CDS YP_918284.1 119387250 4583082 5936..6553 1 NC_008688.1 hypothetical protein 6553 4583082 Pden_4524 Paracoccus denitrificans PD1222 hypothetical protein YP_918284.1 5936 D 318586 CDS YP_918285.1 119387251 4583083 6621..7568 1 NC_008688.1 PFAM: GCN5-related N-acetyltransferase; regulatory protein, MarR; KEGG: pfo:Pfl_2408 transcriptional regulator, MarR family; MarR family transcriptional regulator 7568 4583083 Pden_4525 Paracoccus denitrificans PD1222 MarR family transcriptional regulator YP_918285.1 6621 D 318586 CDS YP_918286.1 119387252 4583084 complement(7718..8479) 1 NC_008688.1 PFAM: Methyltransferase type 11; Methyltransferase type 12; KEGG: pae:PA2679 hypothetical protein; methyltransferase type 11 8479 4583084 Pden_4526 Paracoccus denitrificans PD1222 methyltransferase type 11 YP_918286.1 7718 R 318586 CDS YP_918287.1 119387253 4583085 complement(8469..8966) 1 NC_008688.1 PFAM: regulatory protein, MarR; KEGG: xcb:XC_0601 transcriptional regulator MarR family; MarR family transcriptional regulator 8966 4583085 Pden_4527 Paracoccus denitrificans PD1222 MarR family transcriptional regulator YP_918287.1 8469 R 318586 CDS YP_918288.1 119387254 4583086 complement(9105..10142) 1 NC_008688.1 PFAM: helix-turn-helix- domain containing protein, AraC type; KEGG: bam:Bamb_5783 transcriptional regulator, AraC family; helix-turn-helix domain-containing protein 10142 4583086 Pden_4528 Paracoccus denitrificans PD1222 helix-turn-helix domain-containing protein YP_918288.1 9105 R 318586 CDS YP_918289.1 119387255 4583087 10534..12111 1 NC_008688.1 PFAM: Na+/solute symporter; KEGG: btk:BT9727_3311 sodium/pantothenate symporter; Na+/solute symporter 12111 4583087 Pden_4529 Paracoccus denitrificans PD1222 Na+/solute symporter YP_918289.1 10534 D 318586 CDS YP_918290.1 119387256 4583088 12108..13175 1 NC_008688.1 KEGG: dsy:DSY4724 hypothetical protein; TIGRFAM: 2-dehydropantoate 2-reductase; PFAM: Ketopantoate reductase ApbA/PanE, N-terminal domain protein; Ketopantoate reductase ApbA/PanE, C-terminal domain protein; 2-dehydropantoate 2-reductase 13175 4583088 Pden_4530 Paracoccus denitrificans PD1222 2-dehydropantoate 2-reductase YP_918290.1 12108 D 318586 CDS YP_918291.1 119387257 4583089 13168..14097 1 NC_008688.1 PFAM: protein of unknown function DUF849; KEGG: rpc:RPC_0103 protein of unknown function DUF849; hypothetical protein 14097 4583089 Pden_4531 Paracoccus denitrificans PD1222 hypothetical protein YP_918291.1 13168 D 318586 CDS YP_918292.1 119387258 4583090 14111..14359 1 NC_008688.1 hypothetical protein 14359 4583090 Pden_4532 Paracoccus denitrificans PD1222 hypothetical protein YP_918292.1 14111 D 318586 CDS YP_918293.1 119387259 4583091 14488..15000 1 NC_008688.1 PFAM: sigma-70 region 2 domain protein; sigma-70 region 4 domain protein; Sigma-70, region 4 type 2; KEGG: pfl:PFL_5380 RNA polymerase sigma-70 factor, ECF subfamily; ECF subfamily RNA polymerase sigma-24 factor 15000 4583091 Pden_4533 Paracoccus denitrificans PD1222 ECF subfamily RNA polymerase sigma-24 factor YP_918293.1 14488 D 318586 CDS YP_918294.1 119387260 4583092 15000..15950 1 NC_008688.1 PFAM: FecR protein; KEGG: pae:PA3409 probable transmembrane sensor; FecR 15950 4583092 Pden_4534 Paracoccus denitrificans PD1222 FecR YP_918294.1 15000 D 318586 CDS YP_918295.1 119387261 4583093 16049..18385 1 NC_008688.1 TIGRFAM: TonB-dependent siderophore receptor; PFAM: TonB-dependent receptor; Secretin/TonB, short N-terminal domain; TonB-dependent receptor, plug; KEGG: rru:Rru_A1440 TonB-dependent siderophore receptor; TonB-dependent siderophore receptor 18385 4583093 Pden_4535 Paracoccus denitrificans PD1222 TonB-dependent siderophore receptor YP_918295.1 16049 D 318586 CDS YP_918296.1 119387262 4583094 18797..19075 1 NC_008688.1 KEGG: bxe:Bxe_A3169 IS66 transposase, TnpC; hypothetical protein 19075 4583094 Pden_4537 Paracoccus denitrificans PD1222 hypothetical protein YP_918296.1 18797 D 318586 CDS YP_918297.1 119387263 4583095 complement(19142..19492) 1 NC_008688.1 hypothetical protein 19492 4583095 Pden_4538 Paracoccus denitrificans PD1222 hypothetical protein YP_918297.1 19142 R 318586 CDS YP_918298.1 119387264 4583096 19602..20843 1 NC_008688.1 PFAM: RNA-directed DNA polymerase (Reverse transcriptase); Group II intron, maturase-specific domain protein; KEGG: plu:plu1111 hypothetical protein; RNA-directed DNA polymerase (Reverse transcriptase) 20843 4583096 Pden_4539 Paracoccus denitrificans PD1222 RNA-directed DNA polymerase (Reverse transcriptase) YP_918298.1 19602 D 318586 CDS YP_918299.1 119387265 4583097 20858..21871 1 NC_008688.1 PFAM: transposase IS66; KEGG: mag:amb3320 transposase and inactivated derivative; transposase IS66 21871 4583097 Pden_4540 Paracoccus denitrificans PD1222 transposase IS66 YP_918299.1 20858 D 318586 CDS YP_918300.1 119387266 4583098 complement(21921..22283) 1 NC_008688.1 hypothetical protein 22283 4583098 Pden_4541 Paracoccus denitrificans PD1222 hypothetical protein YP_918300.1 21921 R 318586 CDS YP_918301.1 119387267 4583281 complement(22329..23213) 1 NC_008688.1 PFAM: helix-turn-helix protein RpiR; sugar isomerase (SIS); KEGG: rsp:RSP_2324 transcriptional regulator, RpiR family; RpiR family transcriptional regulator 23213 4583281 Pden_4542 Paracoccus denitrificans PD1222 RpiR family transcriptional regulator YP_918301.1 22329 R 318586 CDS YP_918302.1 119387268 4583282 23335..24075 1 NC_008688.1 PFAM: N-formylglutamate amidohydrolase; KEGG: rsp:RSP_2323 hypothetical protein; N-formylglutamate amidohydrolase 24075 4583282 Pden_4543 Paracoccus denitrificans PD1222 N-formylglutamate amidohydrolase YP_918302.1 23335 D 318586 CDS YP_918303.1 119387269 4583283 24075..24611 1 NC_008688.1 PFAM: Tripartite ATP-independent periplasmic transporter, DctQ component; KEGG: rsp:RSP_2322 TRAP-T family transporter, DctQ (4TMs) subunit; tripartite ATP-independent periplasmic transporter DctQ 24611 4583283 Pden_4544 Paracoccus denitrificans PD1222 tripartite ATP-independent periplasmic transporter DctQ YP_918303.1 24075 D 318586 CDS YP_918304.1 119387270 4583284 24608..25933 1 NC_008688.1 PFAM: TRAP C4-dicarboxylate transport system permease DctM subunit; KEGG: rsp:RSP_2321 TRAP-T family transporter, DctM (12TMs) subunit; TRAP C4-dicarboxylate transport system permease DctM subunit 25933 4583284 Pden_4545 Paracoccus denitrificans PD1222 TRAP C4-dicarboxylate transport system permease DctM subunit YP_918304.1 24608 D 318586 CDS YP_918305.1 119387271 4583285 25957..26997 1 NC_008688.1 PFAM: TRAP dicarboxylate transporter- DctP subunit; KEGG: rsp:RSP_2320 TRAP-T family transporter, periplasmic binding protein; TRAP dicarboxylate transporter- DctP subunit 26997 4583285 Pden_4546 Paracoccus denitrificans PD1222 TRAP dicarboxylate transporter- DctP subunit YP_918305.1 25957 D 318586 CDS YP_918306.1 119387272 4583286 27051..28412 1 NC_008688.1 PFAM: glutamine synthetase, catalytic region; KEGG: rsp:RSP_2319 glutamine synthetase class-I; glutamate--ammonia ligase 28412 4583286 Pden_4547 Paracoccus denitrificans PD1222 glutamate--ammonia ligase YP_918306.1 27051 D 318586 CDS YP_918307.1 119387273 4583287 28450..29838 1 NC_008688.1 PFAM: aldehyde dehydrogenase; KEGG: rsp:RSP_2318 aldehyde dehydrogenase; aldehyde dehydrogenase 29838 4583287 Pden_4548 Paracoccus denitrificans PD1222 aldehyde dehydrogenase YP_918307.1 28450 D 318586 CDS YP_918308.1 119387274 4583288 29835..30980 1 NC_008688.1 PFAM: iron-containing alcohol dehydrogenase; KEGG: rsp:RSP_2317 iron-containing alcohol dehydrogenase; iron-containing alcohol dehydrogenase 30980 4583288 Pden_4549 Paracoccus denitrificans PD1222 iron-containing alcohol dehydrogenase YP_918308.1 29835 D 318586 CDS YP_918309.1 119387275 4583289 31432..33387 1 NC_008688.1 TIGRFAM: acetate--CoA ligase; PFAM: AMP-dependent synthetase and ligase; KEGG: rsp:RSP_0579 acetyl-coenzyme A synthetase; acetate--CoA ligase 33387 4583289 Pden_4550 Paracoccus denitrificans PD1222 acetate--CoA ligase YP_918309.1 31432 D 318586 CDS YP_918310.1 119387276 4583290 33496..33753 1 NC_008688.1 KEGG: sit:TM1040_3665 conserved hypothetical protein; hypothetical protein 33753 4583290 Pden_4551 Paracoccus denitrificans PD1222 hypothetical protein YP_918310.1 33496 D 318586 CDS YP_918311.1 119387277 4583291 33764..35575 1 NC_008688.1 PFAM: Na+/solute symporter; KEGG: rsp:RSP_0576 Na+/solute symporter; Na+/solute symporter 35575 4583291 Pden_4552 Paracoccus denitrificans PD1222 Na+/solute symporter YP_918311.1 33764 D 318586 CDS YP_918312.1 119387278 4583292 35633..37444 1 NC_008688.1 PFAM: cyclic nucleotide-binding; CBS domain containing protein; protein of unknown function DUF294, nucleotidyltransferase KEGG: rsp:RSP_0575 predicted signal transduction protein containing cyclic nucleotide-binding and CBS domains; cyclic nucleotide-binding protein 37444 4583292 Pden_4553 Paracoccus denitrificans PD1222 cyclic nucleotide-binding protein YP_918312.1 35633 D 318586 CDS YP_918313.1 119387279 4583293 37452..37949 1 NC_008688.1 KEGG: rsp:RSP_0574 hypothetical protein; hypothetical protein 37949 4583293 Pden_4554 Paracoccus denitrificans PD1222 hypothetical protein YP_918313.1 37452 D 318586 CDS YP_918314.1 119387280 4583294 37949..38320 1 NC_008688.1 PFAM: response regulator receiver; KEGG: rsp:RSP_0573 response regulator receiver protein; response regulator receiver protein 38320 4583294 Pden_4555 Paracoccus denitrificans PD1222 response regulator receiver protein YP_918314.1 37949 D 318586 CDS YP_918315.1 119387281 4583295 38314..40293 1 NC_008688.1 KEGG: rsp:RSP_0572 exonuclease; TIGRFAM: DNA polymerase III, epsilon subunit; PFAM: Exonuclease, RNase T and DNA polymerase III; SMART: Exonuclease; DNA polymerase III, epsilon subunit 40293 4583295 Pden_4556 Paracoccus denitrificans PD1222 DNA polymerase III, epsilon subunit YP_918315.1 38314 D 318586 CDS YP_918316.1 119387282 4583296 complement(40436..41701) 1 NC_008688.1 PFAM: peptidase S8 and S53, subtilisin, kexin, sedolisin; KEGG: sme:SMa0142 possible protease; peptidase S8/S53 subtilisin kexin sedolisin 41701 4583296 Pden_4557 Paracoccus denitrificans PD1222 peptidase S8/S53 subtilisin kexin sedolisin YP_918316.1 40436 R 318586 CDS YP_918317.1 119387283 4583297 41802..42293 1 NC_008688.1 PFAM: sigma-70 region 2 domain protein; sigma-70 region 4 domain protein; Sigma-70, region 4 type 2; KEGG: sme:SMa0143 RpoE6 RNA polymerase sigma factor; ECF subfamily RNA polymerase sigma-24 factor 42293 4583297 Pden_4558 Paracoccus denitrificans PD1222 ECF subfamily RNA polymerase sigma-24 factor YP_918317.1 41802 D 318586 CDS YP_918318.1 119387284 4583298 42290..43018 1 NC_008688.1 KEGG: sme:SMa0144 hypothetical protein; hypothetical protein 43018 4583298 Pden_4559 Paracoccus denitrificans PD1222 hypothetical protein YP_918318.1 42290 D 318586 CDS YP_918319.1 119387285 4583299 43068..44735 1 NC_008688.1 PFAM: sodium/sulphate symporter; KEGG: sco:SCO2144 integral membrane transporter; sodium/sulphate symporter 44735 4583299 Pden_4560 Paracoccus denitrificans PD1222 sodium/sulphate symporter YP_918319.1 43068 D 318586 CDS YP_918320.1 119387286 4583300 44868..46031 1 NC_008688.1 PFAM: glycerate kinase; KEGG: bat:BAS2054 glycerate kinase; glycerate kinase 46031 4583300 Pden_4561 Paracoccus denitrificans PD1222 glycerate kinase YP_918320.1 44868 D 318586 CDS YP_918321.1 119387287 4583301 46125..46862 1 NC_008688.1 PFAM: Hemolysin-type calcium-binding region; KEGG: rpb:RPB_0805 glycerophosphoryl diester phosphodiesterase; hemolysin-type calcium-binding region 46862 4583301 Pden_4562 Paracoccus denitrificans PD1222 hemolysin-type calcium-binding region YP_918321.1 46125 D 318586 CDS YP_918322.1 119387288 4583302 complement(47053..47964) 1 NC_008688.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: bbr:BB1277 LysR-family transcriptional regulator; LysR family transcriptional regulator 47964 4583302 Pden_4563 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_918322.1 47053 R 318586 CDS YP_918323.1 119387289 4583303 48060..48686 1 NC_008688.1 stationary phase that binds TrpR repressor; TrpR binding protein WrbA 48686 4583303 Pden_4564 Paracoccus denitrificans PD1222 TrpR binding protein WrbA YP_918323.1 48060 D 318586 CDS YP_918324.1 119387290 4583304 48686..49864 1 NC_008688.1 PFAM: major facilitator superfamily MFS_1; KEGG: mag:amb2984 permease of the major facilitator superfamily; major facilitator transporter 49864 4583304 Pden_4565 Paracoccus denitrificans PD1222 major facilitator transporter YP_918324.1 48686 D 318586 CDS YP_918325.1 119387291 4583305 complement(49852..51039) 1 NC_008688.1 PFAM: protein of unknown function DUF6, transmembrane; KEGG: sme:SMc00381 hypothetical protein; hypothetical protein 51039 4583305 Pden_4566 Paracoccus denitrificans PD1222 hypothetical protein YP_918325.1 49852 R 318586 CDS YP_918326.1 119387292 4583306 complement(51125..53917) 1 NC_008688.1 catalyzes the conversion of citrate to isocitrate and the conversion of 2-methylaconitate to 2-methylisocitrate; bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase 53917 4583306 Pden_4567 Paracoccus denitrificans PD1222 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase YP_918326.1 51125 R 318586 CDS YP_918327.1 119387293 4583307 54000..54425 1 NC_008688.1 hypothetical protein 54425 4583307 Pden_4568 Paracoccus denitrificans PD1222 hypothetical protein YP_918327.1 54000 D 318586 CDS YP_918328.1 119387294 4583308 54428..54691 1 NC_008688.1 hypothetical protein 54691 4583308 Pden_4569 Paracoccus denitrificans PD1222 hypothetical protein YP_918328.1 54428 D 318586 CDS YP_918329.1 119387295 4583309 complement(54785..55594) 1 NC_008688.1 KEGG: bur:Bcep18194_A6516 hypothetical protein; hypothetical protein 55594 4583309 Pden_4570 Paracoccus denitrificans PD1222 hypothetical protein YP_918329.1 54785 R 318586 CDS YP_918330.1 119387296 4583310 complement(55723..56352) 1 NC_008688.1 PFAM: NAD-dependent epimerase/dehydratase; KEGG: mlo:mlr0241 hypothetical protein; NAD-dependent epimerase/dehydratase 56352 4583310 Pden_4571 Paracoccus denitrificans PD1222 NAD-dependent epimerase/dehydratase YP_918330.1 55723 R 318586 CDS YP_918331.1 119387297 4583311 complement(56439..57800) 1 NC_008688.1 PFAM: major facilitator superfamily MFS_1; KEGG: neu:NE2492 general substrate transporters; major facilitator transporter 57800 4583311 Pden_4572 Paracoccus denitrificans PD1222 major facilitator transporter YP_918331.1 56439 R 318586 CDS YP_918332.1 119387298 4583312 57816..58733 1 NC_008688.1 PFAM: protein of unknown function DUF6, transmembrane; KEGG: sil:SPO0261 hypothetical protein; hypothetical protein 58733 4583312 Pden_4573 Paracoccus denitrificans PD1222 hypothetical protein YP_918332.1 57816 D 318586 CDS YP_918333.1 119387299 4583313 58879..59838 1 NC_008688.1 PFAM: aldo/keto reductase; KEGG: jan:Jann_0800 aldo/keto reductase; aldo/keto reductase 59838 4583313 Pden_4574 Paracoccus denitrificans PD1222 aldo/keto reductase YP_918333.1 58879 D 318586 CDS YP_918334.1 119387300 4583314 complement(59908..60876) 1 NC_008688.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: sme:SMa1632 LysR-family transcriptional regulator; LysR family transcriptional regulator 60876 4583314 Pden_4575 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_918334.1 59908 R 318586 CDS YP_918335.1 119387301 4583315 60909..61229 1 NC_008688.1 KEGG: rsp:RSP_2028 hypothetical protein; hypothetical protein 61229 4583315 Pden_4576 Paracoccus denitrificans PD1222 hypothetical protein YP_918335.1 60909 D 318586 CDS YP_918336.1 119387302 4583316 61229..62008 1 NC_008688.1 PFAM: NAD-dependent epimerase/dehydratase; short-chain dehydrogenase/reductase SDR; KEGG: rsp:RSP_2029 short chain dehydrogenase; short chain dehydrogenase 62008 4583316 Pden_4577 Paracoccus denitrificans PD1222 short chain dehydrogenase YP_918336.1 61229 D 318586 CDS YP_918337.1 119387303 4583317 complement(62405..62806) 1 NC_008688.1 PFAM: Cupin 2, conserved barrel domain protein; KEGG: jan:Jann_0773 cupin 2 protein; cupin 2 domain-containing protein 62806 4583317 Pden_4578 Paracoccus denitrificans PD1222 cupin 2 domain-containing protein YP_918337.1 62405 R 318586 CDS YP_918338.1 119387304 4583318 complement(62781..63167) 1 NC_008688.1 PFAM: helix-turn-helix, HxlR type; KEGG: ret:RHE_CH02586 transcriptional regulator protein; HxlR family transcriptional regulator 63167 4583318 Pden_4579 Paracoccus denitrificans PD1222 HxlR family transcriptional regulator YP_918338.1 62781 R 318586 CDS YP_918339.1 119387305 4583319 63261..64172 1 NC_008688.1 PFAM: NADPH-dependent FMN reductase; Antibiotic biosynthesis monooxygenase; KEGG: mlo:mll2599 probable reductase; NADPH-dependent FMN reductase 64172 4583319 Pden_4580 Paracoccus denitrificans PD1222 NADPH-dependent FMN reductase YP_918339.1 63261 D 318586 CDS YP_918340.1 119387306 4583320 complement(64195..65091) 1 NC_008688.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: rme:Rmet_5666 transcriptional regulator, LysR family; LysR family transcriptional regulator 65091 4583320 Pden_4581 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_918340.1 64195 R 318586 CDS YP_918341.1 119387307 4583321 65190..65714 1 NC_008688.1 KEGG: cvi:CV1605 hypothetical protein; hypothetical protein 65714 4583321 Pden_4582 Paracoccus denitrificans PD1222 hypothetical protein YP_918341.1 65190 D 318586 CDS YP_918342.1 119387308 4583322 66007..66354 1 NC_008688.1 PFAM: protein of unknown function DUF1330; KEGG: mlo:mll3541 hypothetical protein; hypothetical protein 66354 4583322 Pden_4583 Paracoccus denitrificans PD1222 hypothetical protein YP_918342.1 66007 D 318586 CDS YP_918343.1 119387309 4583323 66478..67236 1 NC_008688.1 PFAM: short-chain dehydrogenase/reductase SDR; KR; KEGG: sil:SPO3609 short chain dehydrogenase; short chain dehydrogenase 67236 4583323 Pden_4584 Paracoccus denitrificans PD1222 short chain dehydrogenase YP_918343.1 66478 D 318586 CDS YP_918344.1 119387310 4583324 complement(67559..69196) 1 NC_008688.1 60 kDa chaperone family; promotes refolding of misfolded polypeptides especially under stressful conditions; forms two stacked rings of heptamers to form a barrel-shaped 14mer; ends can be capped by GroES; misfolded proteins enter the barrel where they are refolded when GroES binds; many bacteria have multiple copies of the groEL gene which are active under different environmental conditions; the B.japonicum protein in this cluster is expressed constitutively; in Rhodobacter, Corynebacterium and Rhizobium this protein is not essential for growth; molecular chaperone GroEL 69196 groEL 4583324 groEL Paracoccus denitrificans PD1222 molecular chaperone GroEL YP_918344.1 67559 R 318586 CDS YP_918345.1 119387311 4583325 complement(69237..69524) 1 NC_008688.1 10 kDa chaperonin; Cpn10; GroES; forms homoheptameric ring; binds to one or both ends of the GroEL double barrel in the presence of adenine nucleotides capping it; folding of unfolded substrates initiates in a GroEL-substrate bound and capped by GroES; release of the folded substrate is dependent on ATP binding and hydrolysis in the trans ring; co-chaperonin GroES 69524 groES 4583325 groES Paracoccus denitrificans PD1222 co-chaperonin GroES YP_918345.1 69237 R 318586 CDS YP_918346.1 119387312 4583326 69832..70299 1 NC_008688.1 hypothetical protein 70299 4583326 Pden_4587 Paracoccus denitrificans PD1222 hypothetical protein YP_918346.1 69832 D 318586 CDS YP_918347.1 119387313 4583327 70413..70760 1 NC_008688.1 KEGG: ret:RHE_CH01244 probable molecular chaperone small heat shock protein, HSP20 family; Hsp20 family heat-shock protein 70760 4583327 Pden_4588 Paracoccus denitrificans PD1222 Hsp20 family heat-shock protein YP_918347.1 70413 D 318586 CDS YP_918348.1 119387314 4583328 70744..70947 1 NC_008688.1 KEGG: ret:RHE_CH01245 probable molecular chaperone small heat shock protein, HSP20 family; hypothetical protein 70947 4583328 Pden_4589 Paracoccus denitrificans PD1222 hypothetical protein YP_918348.1 70744 D 318586 CDS YP_918349.1 119387315 4583329 complement(71280..72935) 1 NC_008688.1 activates fatty acids by binding to coenzyme A; acyl-CoA synthetase 72935 4583329 Pden_4590 Paracoccus denitrificans PD1222 acyl-CoA synthetase YP_918349.1 71280 R 318586 CDS YP_918350.1 119387316 4583330 complement(72975..73367) 1 NC_008688.1 PFAM: Rhodanese domain protein; KEGG: mes:Meso_2537 rhodanese-like; rhodanese domain-containing protein 73367 4583330 Pden_4591 Paracoccus denitrificans PD1222 rhodanese domain-containing protein YP_918350.1 72975 R 318586 CDS YP_918351.1 119387317 4583331 complement(73370..73948) 1 NC_008688.1 TIGRFAM: alkylhydroperoxidase like protein, AhpD family; uncharacterized peroxidase-related enzyme; PFAM: Carboxymuconolactone decarboxylase; KEGG: rsp:RSP_3419 hypothetical protein; uncharacterized peroxidase-related enzyme 73948 4583331 Pden_4592 Paracoccus denitrificans PD1222 uncharacterized peroxidase-related enzyme YP_918351.1 73370 R 318586 CDS YP_918352.1 119387318 4583332 complement(73945..76260) 1 NC_008688.1 TIGRFAM: molybdopterin guanine dinucleotide-containing S/N-oxide reductases; PFAM: molybdopterin oxidoreductase; molydopterin dinucleotide-binding region; KEGG: rpa:RPA4653 biotin sulfoxide reductase; molybdopterin guanine dinucleotide-containing S/N-oxide reductases 76260 4583332 Pden_4593 Paracoccus denitrificans PD1222 molybdopterin guanine dinucleotide-containing S/N-oxide reductases YP_918352.1 73945 R 318586 CDS YP_918353.1 119387319 4583333 complement(76273..77817) 1 NC_008688.1 thiamine-pyrophosphate requiring enzyme; hypothetical protein 77817 4583333 Pden_4594 Paracoccus denitrificans PD1222 hypothetical protein YP_918353.1 76273 R 318586 CDS YP_918354.1 119387320 4583334 complement(77814..79304) 1 NC_008688.1 PFAM: carbohydrate kinase, FGGY; KEGG: sme:SMc01623 erythritol kinase; carbohydrate kinase, FGGY 79304 4583334 Pden_4595 Paracoccus denitrificans PD1222 carbohydrate kinase, FGGY YP_918354.1 77814 R 318586 CDS YP_918355.1 119387321 4583335 complement(79304..79981) 1 NC_008688.1 PFAM: class II aldolase/adducin family protein; KEGG: bja:bll6170 L-fuculose phosphate aldolase; Fis family transcriptional regulator 79981 4583335 Pden_4596 Paracoccus denitrificans PD1222 Fis family transcriptional regulator YP_918355.1 79304 R 318586 CDS YP_918356.1 119387322 4583336 complement(79990..81036) 1 NC_008688.1 PFAM: D-isomer specific 2-hydroxyacid dehydrogenase, catalytic region; D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding; KEGG: mlo:mlr7269 phosphoglycerate dehydrogenase; D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding 81036 4583336 Pden_4597 Paracoccus denitrificans PD1222 D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding YP_918356.1 79990 R 318586 CDS YP_918357.1 119387323 4583337 complement(81033..82232) 1 NC_008688.1 PFAM: L-carnitine dehydratase/bile acid-inducible protein F; KEGG: pae:PA3592 hypothetical protein; L-carnitine dehydratase/bile acid-inducible protein F 82232 4583337 Pden_4598 Paracoccus denitrificans PD1222 L-carnitine dehydratase/bile acid-inducible protein F YP_918357.1 81033 R 318586 CDS YP_918358.1 119387324 4583338 complement(82229..82996) 1 NC_008688.1 KEGG: rpa:RPA4652 possible CoA transferase, subunit B; CoA transferase, subunit B 82996 4583338 Pden_4599 Paracoccus denitrificans PD1222 CoA transferase, subunit B YP_918358.1 82229 R 318586 CDS YP_918359.1 119387325 4583339 complement(82993..83802) 1 NC_008688.1 KEGG: rpa:RPA4651 possible glutaconate CoA-transferase, subunit A; glutaconate CoA-transferase, subunit A 83802 4583339 Pden_4600 Paracoccus denitrificans PD1222 glutaconate CoA-transferase, subunit A YP_918359.1 82993 R 318586 CDS YP_918360.1 119387326 4583106 84009..85157 1 NC_008688.1 PFAM: ABC transporter related; TOBE domain protein; Transport-associated OB domain protein; SMART: AAA ATPase; KEGG: rpa:RPA4650 spermidine/putrescine transport system ATP-binding protein; ABC transporter related 85157 4583106 Pden_4601 Paracoccus denitrificans PD1222 ABC transporter related YP_918360.1 84009 D 318586 CDS YP_918361.1 119387327 4583107 85154..86929 1 NC_008688.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: rpa:RPA4649 probable ABC transporter permease; binding-protein-dependent transport systems inner membrane component 86929 4583107 Pden_4602 Paracoccus denitrificans PD1222 binding-protein-dependent transport systems inner membrane component YP_918361.1 85154 D 318586 CDS YP_918362.1 119387328 4583108 86961..88037 1 NC_008688.1 KEGG: rpa:RPA4648 possible ABC transporter binding protein component; ABC transporter binding protein component 88037 4583108 Pden_4603 Paracoccus denitrificans PD1222 ABC transporter binding protein component YP_918362.1 86961 D 318586 CDS YP_918363.1 119387329 4583109 88135..88890 1 NC_008688.1 PFAM: regulatory protein, ArsR; regulatory proteins, IclR; KEGG: rpa:RPA4647 probable transcriptional regulator KdgR, IclR family; regulatory proteins, IclR 88890 4583109 Pden_4604 Paracoccus denitrificans PD1222 regulatory proteins, IclR YP_918363.1 88135 D 318586 CDS YP_918364.1 119387330 4583110 89102..89422 1 NC_008688.1 KEGG: atc:AGR_L_2660 hypothetical protein; hypothetical protein 89422 4583110 Pden_4605 Paracoccus denitrificans PD1222 hypothetical protein YP_918364.1 89102 D 318586 CDS YP_918365.1 119387331 4583111 89556..90788 1 NC_008688.1 PFAM: Radical SAM domain protein; SMART: Elongator protein 3/MiaB/NifB; KEGG: gbe:GbCGDNIH1_1531 biotin synthase related domain containing protein; radical SAM domain-containing protein 90788 4583111 Pden_4606 Paracoccus denitrificans PD1222 radical SAM domain-containing protein YP_918365.1 89556 D 318586 CDS YP_918366.1 119387332 4583112 90785..92224 1 NC_008688.1 PFAM: Uracil-DNA glycosylase superfamily; KEGG: gbe:GbCGDNIH1_1530 uracil DNA glycosylase superfamily protein; uracil-DNA glycosylase 92224 4583112 Pden_4607 Paracoccus denitrificans PD1222 uracil-DNA glycosylase YP_918366.1 90785 D 318586 CDS YP_918367.1 119387333 4583113 92297..92779 1 NC_008688.1 KEGG: jan:Jann_0955 general stress protein 26; general stress protein 26 92779 4583113 Pden_4608 Paracoccus denitrificans PD1222 general stress protein 26 YP_918367.1 92297 D 318586 CDS YP_918368.1 119387334 4583114 93059..94534 1 NC_008688.1 PFAM: phospholipase D/Transphosphatidylase; KEGG: rsp:RSP_0113 phospholipase D/transphosphatidylase; phospholipase D/transphosphatidylase 94534 4583114 Pden_4609 Paracoccus denitrificans PD1222 phospholipase D/transphosphatidylase YP_918368.1 93059 D 318586 CDS YP_918369.1 119387335 4583115 complement(94555..95784) 1 NC_008688.1 PFAM: FAD dependent oxidoreductase; KEGG: hne:HNE_2468 oxidoreductase; FAD dependent oxidoreductase 95784 4583115 Pden_4610 Paracoccus denitrificans PD1222 FAD dependent oxidoreductase YP_918369.1 94555 R 318586 CDS YP_918370.1 119387336 4583116 complement(95816..97948) 1 NC_008688.1 PFAM: Catalase domain protein; KEGG: hne:HNE_2467 catalase HPII; catalase 97948 4583116 Pden_4611 Paracoccus denitrificans PD1222 catalase YP_918370.1 95816 R 318586 CDS YP_918371.1 119387337 4583117 98287..99021 1 NC_008688.1 PFAM: Peptidoglycan-binding domain 1 protein; KEGG: jan:Jann_3999 peptidoglycan-binding domain 1; peptidoglycan binding domain-containing protein 99021 4583117 Pden_4612 Paracoccus denitrificans PD1222 peptidoglycan binding domain-containing protein YP_918371.1 98287 D 318586 CDS YP_918372.1 119387338 4583118 99235..99792 1 NC_008688.1 KEGG: bja:bll8025 hypothetical protein; hypothetical protein 99792 4583118 Pden_4613 Paracoccus denitrificans PD1222 hypothetical protein YP_918372.1 99235 D 318586 CDS YP_918373.1 119387339 4583119 99830..100234 1 NC_008688.1 KEGG: rsp:RSP_0683 hypothetical protein; hypothetical protein 100234 4583119 Pden_4614 Paracoccus denitrificans PD1222 hypothetical protein YP_918373.1 99830 D 318586 CDS YP_918374.1 119387340 4583120 100218..101297 1 NC_008688.1 TIGRFAM: esterase, PHB depolymerase family; PFAM: esterase; phospholipase/Carboxylesterase; KEGG: rru:Rru_A1969 esterase, PHB depolymerase; PHB depolymerase family esterase 101297 4583120 Pden_4615 Paracoccus denitrificans PD1222 PHB depolymerase family esterase YP_918374.1 100218 D 318586 CDS YP_918375.1 119387341 4583121 complement(101404..102804) 1 NC_008688.1 catalyzes the hydrolytic cleavage of hydantoin with aromatic side chains at the 5'position; phenylhydantoinase 102804 4583121 Pden_4616 Paracoccus denitrificans PD1222 phenylhydantoinase YP_918375.1 101404 R 318586 CDS YP_918376.1 119387342 4583122 complement(102801..103520) 1 NC_008688.1 PFAM: regulatory protein GntR, HTH; GntR domain protein; KEGG: bja:blr6040 transcriptional regulatory protein; GntR family transcriptional regulator 103520 4583122 Pden_4617 Paracoccus denitrificans PD1222 GntR family transcriptional regulator YP_918376.1 102801 R 318586 CDS YP_918377.1 119387343 4583123 complement(103562..104329) 1 NC_008688.1 PFAM: Asp/Glu racemase; KEGG: pol:Bpro_0550 Asp/Glu racemase; Asp/Glu racemase 104329 4583123 Pden_4618 Paracoccus denitrificans PD1222 Asp/Glu racemase YP_918377.1 103562 R 318586 CDS YP_918378.1 119387344 4583124 104611..105654 1 NC_008688.1 PFAM: TRAP dicarboxylate transporter- DctP subunit; KEGG: pol:Bpro_0556 TRAP dicarboxylate transporter-DctP subunit; TRAP dicarboxylate transporter- DctP subunit 105654 4583124 Pden_4619 Paracoccus denitrificans PD1222 TRAP dicarboxylate transporter- DctP subunit YP_918378.1 104611 D 318586 CDS YP_918379.1 119387345 4583125 105705..106304 1 NC_008688.1 KEGG: pol:Bpro_0557 hypothetical protein; hypothetical protein 106304 4583125 Pden_4620 Paracoccus denitrificans PD1222 hypothetical protein YP_918379.1 105705 D 318586 CDS YP_918380.1 119387346 4583126 106301..107602 1 NC_008688.1 TIGRFAM: TRAP dicarboxylate transporter, DctM subunit; PFAM: TRAP C4-dicarboxylate transport system permease DctM subunit; KEGG: pol:Bpro_0558 TRAP dicarboxylate transporter-DctM subunit; TRAP dicarboxylate transporter, DctM subunit 107602 4583126 Pden_4621 Paracoccus denitrificans PD1222 TRAP dicarboxylate transporter, DctM subunit YP_918380.1 106301 D 318586 CDS YP_918381.1 119387347 4583127 107603..109075 1 NC_008688.1 PFAM: amidohydrolase; KEGG: rde:RD1_2424 amidohydrolase family protein; amidohydrolase 109075 4583127 Pden_4622 Paracoccus denitrificans PD1222 amidohydrolase YP_918381.1 107603 D 318586 CDS YP_918382.1 119387348 4583128 109319..109621 1 NC_008688.1 KEGG: hne:HNE_1970 dipeptidase family protein; dipeptidase family protein 109621 4583128 Pden_4623 Paracoccus denitrificans PD1222 dipeptidase family protein YP_918382.1 109319 D 318586 CDS YP_918383.1 119387349 4583129 complement(109691..110152) 1 NC_008688.1 PFAM: regulatory protein, AsnC/Lrp family; KEGG: sit:TM1040_2780 transcriptional regulator, AsnC family; AsnC family transcriptional regulator 110152 4583129 Pden_4624 Paracoccus denitrificans PD1222 AsnC family transcriptional regulator YP_918383.1 109691 R 318586 CDS YP_918384.1 119387350 4583130 110273..111340 1 NC_008688.1 PFAM: Glu/Leu/Phe/Val dehydrogenase, C terminal; Glu/Leu/Phe/Val dehydrogenase, dimerisation region; KEGG: sit:TM1040_2779 Glu/Leu/Phe/Val dehydrogenase, dimerisation region; Glu/Leu/Phe/Val dehydrogenase, dimerisation region 111340 4583130 Pden_4625 Paracoccus denitrificans PD1222 Glu/Leu/Phe/Val dehydrogenase, dimerisation region YP_918384.1 110273 D 318586 CDS YP_918385.1 119387351 4583131 111423..112142 1 NC_008688.1 PFAM: protein of unknown function DUF161; KEGG: sme:SMc02240 hypothetical protein; hypothetical protein 112142 4583131 Pden_4626 Paracoccus denitrificans PD1222 hypothetical protein YP_918385.1 111423 D 318586 CDS YP_918386.1 119387352 4583132 complement(112278..112646) 1 NC_008688.1 hypothetical protein 112646 4583132 Pden_4627 Paracoccus denitrificans PD1222 hypothetical protein YP_918386.1 112278 R 318586 CDS YP_918387.1 119387353 4583133 complement(112710..113948) 1 NC_008688.1 PFAM: FAD dependent oxidoreductase; KEGG: bja:bll4301 oxidoreductase; D-amino-acid dehydrogenase 113948 4583133 Pden_4628 Paracoccus denitrificans PD1222 D-amino-acid dehydrogenase YP_918387.1 112710 R 318586 CDS YP_918388.1 119387354 4583134 complement(113965..116208) 1 NC_008688.1 PFAM: peptidase S9, prolyl oligopeptidase active site domain protein; peptidase S9B, dipeptidylpeptidase IV domain protein; KEGG: sus:Acid_0469 peptidase S9B, dipeptidylpeptidase IV domain protein; peptidase S9 prolyl oligopeptidase 116208 4583134 Pden_4629 Paracoccus denitrificans PD1222 peptidase S9 prolyl oligopeptidase YP_918388.1 113965 R 318586 CDS YP_918389.1 119387355 4583135 complement(116301..116921) 1 NC_008688.1 PFAM: regulatory protein, TetR; KEGG: mpa:MAP1349c hypothetical protein; TetR family transcriptional regulator 116921 4583135 Pden_4630 Paracoccus denitrificans PD1222 TetR family transcriptional regulator YP_918389.1 116301 R 318586 CDS YP_918390.1 119387356 4583136 117112..118494 1 NC_008688.1 PFAM: major facilitator superfamily MFS_1; KEGG: bam:Bamb_5358 major facilitator superfamily MFS_1; major facilitator transporter 118494 4583136 Pden_4631 Paracoccus denitrificans PD1222 major facilitator transporter YP_918390.1 117112 D 318586 CDS YP_918391.1 119387357 4583137 118543..119655 1 NC_008688.1 PFAM: beta-lactamase; KEGG: bce:BC3013 D-alanyl-D-alanine carboxypeptidase; beta-lactamase 119655 4583137 Pden_4632 Paracoccus denitrificans PD1222 beta-lactamase YP_918391.1 118543 D 318586 CDS YP_918392.1 119387358 4583138 119665..121167 1 NC_008688.1 PFAM: Uncharacterized conserved protein UCP012702; MlrC domain protein; KEGG: bur:Bcep18194_A4349 hypothetical protein; hypothetical protein 121167 4583138 Pden_4633 Paracoccus denitrificans PD1222 hypothetical protein YP_918392.1 119665 D 318586 CDS YP_918393.1 119387359 4583139 121265..122743 1 NC_008688.1 PFAM: peptidase M17, leucyl aminopeptidase domain protein; KEGG: ret:RHE_CH01456 leucine aminopeptidase; leucyl aminopeptidase 122743 4583139 Pden_4634 Paracoccus denitrificans PD1222 leucyl aminopeptidase YP_918393.1 121265 D 318586 CDS YP_918394.1 119387360 4583140 122749..123795 1 NC_008688.1 PFAM: peptidase M42 family protein; KEGG: ava:Ava_3182 peptidases M20 and M42; peptidase M42 family protein 123795 4583140 Pden_4635 Paracoccus denitrificans PD1222 peptidase M42 family protein YP_918394.1 122749 D 318586 CDS YP_918395.1 119387361 4583141 124022..125368 1 NC_008688.1 PFAM: Carbohydrate-selective porin OprB; KEGG: plu:plu0581 porin; carbohydrate-selective porin OprB 125368 4583141 Pden_4636 Paracoccus denitrificans PD1222 carbohydrate-selective porin OprB YP_918395.1 124022 D 318586 CDS YP_918396.1 119387362 4583142 125503..126549 1 NC_008688.1 catalyzes the formation of L-proline from L-ornithine; ornithine cyclodeaminase 126549 4583142 Pden_4637 Paracoccus denitrificans PD1222 ornithine cyclodeaminase YP_918396.1 125503 D 318586 CDS YP_918397.1 119387363 4583143 126559..126942 1 NC_008688.1 hypothetical protein 126942 4583143 Pden_4638 Paracoccus denitrificans PD1222 hypothetical protein YP_918397.1 126559 D 318586 CDS YP_918398.1 119387364 4583144 complement(128042..129550) 1 NC_008688.1 KEGG: sdn:Sden_2083 hypothetical protein; hypothetical protein 129550 4583144 Pden_4641 Paracoccus denitrificans PD1222 hypothetical protein YP_918398.1 128042 R 318586 CDS YP_918399.1 119387365 4583145 complement(129609..131342) 1 NC_008688.1 KEGG: mxa:MXAN_2365 hypothetical protein; hypothetical protein 131342 4583145 Pden_4642 Paracoccus denitrificans PD1222 hypothetical protein YP_918399.1 129609 R 318586 CDS YP_918400.1 119387366 4583146 complement(131369..133168) 1 NC_008688.1 PFAM: tyrosinase; KEGG: hsa:7299 tyrosinase (oculocutaneous albinism IA); tyrosinase 133168 4583146 Pden_4643 Paracoccus denitrificans PD1222 tyrosinase YP_918400.1 131369 R 318586 CDS YP_918401.1 119387367 4583147 133291..133749 1 NC_008688.1 SMART: regulatory protein, AsnC/Lrp family; KEGG: eca:ECA1157 AsnC-family transcriptional regulator; AsnC family transcriptional regulator 133749 4583147 Pden_4644 Paracoccus denitrificans PD1222 AsnC family transcriptional regulator YP_918401.1 133291 D 318586 CDS YP_918402.1 119387368 4583148 complement(133967..134641) 1 NC_008688.1 PFAM: regulatory protein, TetR; KEGG: reu:Reut_A1792 regulatory protein, TetR; TetR family transcriptional regulator 134641 4583148 Pden_4645 Paracoccus denitrificans PD1222 TetR family transcriptional regulator YP_918402.1 133967 R 318586 CDS YP_918403.1 119387369 4583149 134870..135652 1 NC_008688.1 PFAM: cyclase family protein; KEGG: jan:Jann_2038 cyclase; cyclase family protein 135652 4583149 Pden_4646 Paracoccus denitrificans PD1222 cyclase family protein YP_918403.1 134870 D 318586 CDS YP_918404.1 119387370 4583150 135709..136926 1 NC_008688.1 PFAM: major facilitator superfamily MFS_1; KEGG: pol:Bpro_2062 major facilitator superfamily MFS_1; major facilitator transporter 136926 4583150 Pden_4647 Paracoccus denitrificans PD1222 major facilitator transporter YP_918404.1 135709 D 318586 CDS YP_918405.1 119387371 4583151 136951..137886 1 NC_008688.1 PFAM: protein of unknown function DUF849; KEGG: rpc:RPC_0103 protein of unknown function DUF849; hypothetical protein 137886 4583151 Pden_4648 Paracoccus denitrificans PD1222 hypothetical protein YP_918405.1 136951 D 318586 CDS YP_918406.1 119387372 4583152 138208..139215 1 NC_008688.1 PFAM: extracellular solute-binding protein, family 1; KEGG: sth:STH3219 iron ABC transporter substrate-binding protein; extracellular solute-binding protein 139215 4583152 Pden_4649 Paracoccus denitrificans PD1222 extracellular solute-binding protein YP_918406.1 138208 D 318586 CDS YP_918407.1 119387373 4583153 139237..140928 1 NC_008688.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: sth:STH3218 ABC transporter permease; binding-protein-dependent transport systems inner membrane component 140928 4583153 Pden_4650 Paracoccus denitrificans PD1222 binding-protein-dependent transport systems inner membrane component YP_918407.1 139237 D 318586 CDS YP_918408.1 119387374 4583154 140935..142038 1 NC_008688.1 PFAM: ABC transporter related; Transport-associated OB domain protein; SMART: AAA ATPase; KEGG: sth:STH3217 ABC transporter ATP-binding protein; ABC transporter related 142038 4583154 Pden_4651 Paracoccus denitrificans PD1222 ABC transporter related YP_918408.1 140935 D 318586 CDS YP_918409.1 119387375 4583155 142041..142892 1 NC_008688.1 PFAM: inositol monophosphatase; KEGG: sme:SMb20159 inositol monophosphatase; inositol-phosphate phosphatase 142892 4583155 Pden_4652 Paracoccus denitrificans PD1222 inositol-phosphate phosphatase YP_918409.1 142041 D 318586 CDS YP_918410.1 119387376 4583156 142879..143721 1 NC_008688.1 PFAM: helix-turn-helix protein RpiR; sugar isomerase (SIS); KEGG: cvi:CV0148 probable transcriptional regulator; RpiR family transcriptional regulator 143721 4583156 Pden_4653 Paracoccus denitrificans PD1222 RpiR family transcriptional regulator YP_918410.1 142879 D 318586 CDS YP_918411.1 119387377 4583157 143841..144527 1 NC_008688.1 Class B; non-specific; catalyzes the dephosphorylation of organic phosphomonoesters; also has phosphotransferase activity; acid phosphatase/phosphotransferase 144527 aphA 4583157 aphA Paracoccus denitrificans PD1222 acid phosphatase/phosphotransferase YP_918411.1 143841 D 318586 CDS YP_918412.1 119387378 4583158 144688..145875 1 NC_008688.1 KEGG: bbr:BB1453 regulatory lipoprotein; regulatory lipoprotein 145875 4583158 Pden_4655 Paracoccus denitrificans PD1222 regulatory lipoprotein YP_918412.1 144688 D 318586 CDS YP_918413.1 119387379 4583159 145872..147824 1 NC_008688.1 PFAM: ATP-binding region, ATPase domain protein domain protein; histidine kinase, HAMP region domain protein; histidine kinase A domain protein domain protein; KEGG: jan:Jann_1731 periplasmic sensor signal transduction histidine kinase; integral membrane sensor signal transduction histidine kinase 147824 4583159 Pden_4656 Paracoccus denitrificans PD1222 integral membrane sensor signal transduction histidine kinase YP_918413.1 145872 D 318586 CDS YP_918414.1 119387380 4583160 147826..149097 1 NC_008688.1 PFAM: response regulator receiver; sigma-54 factor, interaction domain-containing protein; helix-turn-helix, Fis-type; SMART: AAA ATPase; KEGG: ret:RHE_CH02973 two-component response regulator protein regulating C4-dicarboxylate transport system; two component, sigma54 specific, Fis family transcriptional regulator 149097 4583160 Pden_4657 Paracoccus denitrificans PD1222 two component, sigma54 specific, Fis family transcriptional regulator YP_918414.1 147826 D 318586 CDS YP_918415.1 119387381 4583161 149263..150585 1 NC_008688.1 PFAM: extracellular solute-binding protein, family 1; KEGG: bpe:BP2271 regulatory lipoprotein; extracellular solute-binding protein 150585 4583161 Pden_4658 Paracoccus denitrificans PD1222 extracellular solute-binding protein YP_918415.1 149263 D 318586 CDS YP_918416.1 119387382 4583162 150662..152392 1 NC_008688.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: bbr:BB1452 probable permease component of ABC transporter; binding-protein-dependent transport systems inner membrane component 152392 4583162 Pden_4659 Paracoccus denitrificans PD1222 binding-protein-dependent transport systems inner membrane component YP_918416.1 150662 D 318586 CDS YP_918417.1 119387383 4583163 152405..153448 1 NC_008688.1 PFAM: ABC transporter related; Transport-associated OB domain protein; SMART: AAA ATPase; KEGG: bbr:BB1451 probable ATP-binding component of ABC transporter; ABC transporter related 153448 4583163 Pden_4660 Paracoccus denitrificans PD1222 ABC transporter related YP_918417.1 152405 D 318586 CDS YP_918418.1 119387384 4583164 153452..154009 1 NC_008688.1 PFAM: Phosphoglycerate mutase; KEGG: sus:Acid_7225 phosphoglycerate mutase; phosphoglycerate mutase 154009 4583164 Pden_4661 Paracoccus denitrificans PD1222 phosphoglycerate mutase YP_918418.1 153452 D 318586 CDS YP_918419.1 119387385 4583165 154010..154678 1 NC_008688.1 PFAM: pyridoxamine 5'-phosphate oxidase-related, FMN-binding; KEGG: aor:AO090023000033 pyridoxamine-phosphate oxidase Pfam: Pyridox_oxidase; pyridoxamine-phosphate oxidase 154678 4583165 Pden_4662 Paracoccus denitrificans PD1222 pyridoxamine-phosphate oxidase YP_918419.1 154010 D 318586 CDS YP_918420.1 119387386 4583166 complement(154917..156053) 1 NC_008688.1 KEGG: ret:RHE_PB00156 hypothetical protein; hypothetical protein 156053 4583166 Pden_4663 Paracoccus denitrificans PD1222 hypothetical protein YP_918420.1 154917 R 318586 CDS YP_918421.1 119387387 4583167 complement(156075..156881) 1 NC_008688.1 PFAM: Shikimate/quinate 5-dehydrogenase; Shikimate dehydrogenase substrate binding, N-terminal domain protein; KEGG: mes:Meso_3972 shikimate dehydrogenase substrate binding-like; shikimate dehydrogenase 156881 4583167 Pden_4664 Paracoccus denitrificans PD1222 shikimate dehydrogenase YP_918421.1 156075 R 318586 CDS YP_918422.1 119387388 4583168 complement(156878..158452) 1 NC_008688.1 PFAM: aldehyde dehydrogenase; KEGG: ccr:CC2791 fatty aldehyde dehydrogenase; aldehyde dehydrogenase 158452 4583168 Pden_4665 Paracoccus denitrificans PD1222 aldehyde dehydrogenase YP_918422.1 156878 R 318586 CDS YP_918423.1 119387389 4583169 complement(158454..159386) 1 NC_008688.1 PFAM: dihydrodipicolinate synthetase; KEGG: mes:Meso_3971 dihydrodipicolinate synthetase; dihydrodipicolinate synthetase 159386 4583169 Pden_4666 Paracoccus denitrificans PD1222 dihydrodipicolinate synthetase YP_918423.1 158454 R 318586 CDS YP_918424.1 119387390 4583170 complement(159459..160268) 1 NC_008688.1 PFAM: extracellular solute-binding protein, family 3; KEGG: rfr:Rfer_1029 extracellular solute-binding protein, family 3; extracellular solute-binding protein 160268 4583170 Pden_4667 Paracoccus denitrificans PD1222 extracellular solute-binding protein YP_918424.1 159459 R 318586 CDS YP_918425.1 119387391 4583171 complement(160296..161084) 1 NC_008688.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: mes:Meso_3975 ABC transporter related; ABC transporter related 161084 4583171 Pden_4668 Paracoccus denitrificans PD1222 ABC transporter related YP_918425.1 160296 R 318586 CDS YP_918426.1 119387392 4583172 complement(161088..161732) 1 NC_008688.1 TIGRFAM: polar amino acid ABC transporter, inner membrane subunit; PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: atc:AGR_L_980GM ABC transporter permease; polar amino acid ABC transporter, inner membrane subunit 161732 4583172 Pden_4669 Paracoccus denitrificans PD1222 polar amino acid ABC transporter, inner membrane subunit YP_918426.1 161088 R 318586 CDS YP_918427.1 119387393 4583173 complement(161744..162424) 1 NC_008688.1 TIGRFAM: polar amino acid ABC transporter, inner membrane subunit; PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: mes:Meso_3976 polar amino acid ABC transporter, inner membrane subunit; polar amino acid ABC transporter, inner membrane subunit 162424 4583173 Pden_4670 Paracoccus denitrificans PD1222 polar amino acid ABC transporter, inner membrane subunit YP_918427.1 161744 R 318586 CDS YP_918428.1 119387394 4583174 162586..164157 1 NC_008688.1 PFAM: D-galactarate dehydratase/Altronate hydrolase domain protein; SAF domain; KEGG: bms:BRA0806 hydrolase, UxaA family; altronate dehydratase 164157 4583174 Pden_4671 Paracoccus denitrificans PD1222 altronate dehydratase YP_918428.1 162586 D 318586 CDS YP_918429.1 119387395 4583175 164133..165164 1 NC_008688.1 PFAM: regulatory protein GntR, HTH; GntR domain protein; KEGG: mes:Meso_3969 transcriptional regulator, GntR family; GntR family transcriptional regulator 165164 4583175 Pden_4672 Paracoccus denitrificans PD1222 GntR family transcriptional regulator YP_918429.1 164133 D 318586 CDS YP_918430.1 119387396 4583176 complement(165193..166875) 1 NC_008688.1 PFAM: band 7 protein; KEGG: sit:TM1040_2195 band 7 protein; band 7 protein 166875 4583176 Pden_4673 Paracoccus denitrificans PD1222 band 7 protein YP_918430.1 165193 R 318586 CDS YP_918431.1 119387397 4583177 complement(166911..167633) 1 NC_008688.1 PFAM: protein of unknown function DUF1449; KEGG: jan:Jann_1795 hypothetical protein; hypothetical protein 167633 4583177 Pden_4674 Paracoccus denitrificans PD1222 hypothetical protein YP_918431.1 166911 R 318586 CDS YP_918432.1 119387398 4583178 167769..168779 1 NC_008688.1 PFAM: helix-turn-helix protein RpiR; sugar isomerase (SIS); KEGG: ecp:ECP_3116 hypothetical phosphosugar isomerases; RpiR family transcriptional regulator 168779 4583178 Pden_4675 Paracoccus denitrificans PD1222 RpiR family transcriptional regulator YP_918432.1 167769 D 318586 CDS YP_918433.1 119387399 4583179 complement(168892..169983) 1 NC_008688.1 PFAM: FMN-dependent alpha-hydroxy acid dehydrogenase; dihydroorotate dehydrogenase; KEGG: rme:Rmet_0839 FMN-dependent alpha-hydroxy acid dehydrogenase; FMN-dependent alpha-hydroxy acid dehydrogenase 169983 4583179 Pden_4676 Paracoccus denitrificans PD1222 FMN-dependent alpha-hydroxy acid dehydrogenase YP_918433.1 168892 R 318586 CDS YP_918434.1 119387400 4583180 complement(169987..170670) 1 NC_008688.1 PFAM: 2OG-Fe(II) oxygenase; SMART: Prolyl 4-hydroxylase, alpha subunit; KEGG: rme:Rmet_0838 2OG-Fe(II) oxygenase; hydroxylase 170670 4583180 Pden_4677 Paracoccus denitrificans PD1222 hydroxylase YP_918434.1 169987 R 318586 CDS YP_918435.1 119387401 4583181 complement(170821..171414) 1 NC_008688.1 KEGG: mfa:Mfla_2318 TonB-dependent siderophore receptor; hypothetical protein 171414 4583181 Pden_4678 Paracoccus denitrificans PD1222 hypothetical protein YP_918435.1 170821 R 318586 CDS YP_918436.1 119387402 4583182 171868..172305 1 NC_008688.1 RibE; 6,7-diimethyl-8-ribityllumazine synthase; DMRL synthase; lumazine synthase; beta subunit of riboflavin synthase; condenses 5-amino-6-(1'-D)-ribityl-amino-2,4(1H,3H)-pyrimidinedione with L-3,4-dihydrohy-2-butanone-4-phosphate to generate 6,6-dimethyl-8-lumazine (DMRL); riboflavin synthase then uses 2 molecules of DMRL to produce riboflavin (vitamin B12); involved in the last steps of riboflavin biosynthesis; forms a 60mer (icosahedral shell) in both Bacillus subtilis and Escherichia coli; in Bacillus subtilis this 60mer is associated with the riboflavin synthase subunit (alpha) while in Escherichia coli it is not; riboflavin synthase subunit beta 172305 4583182 Pden_4679 Paracoccus denitrificans PD1222 riboflavin synthase subunit beta YP_918436.1 171868 D 318586 CDS YP_918437.1 119387403 4583183 172602..173063 1 NC_008688.1 PFAM: MaoC domain protein dehydratase; KEGG: rru:Rru_A2194 MaoC-like dehydratase; dehydratase 173063 4583183 Pden_4680 Paracoccus denitrificans PD1222 dehydratase YP_918437.1 172602 D 318586 CDS YP_918438.1 119387404 4583184 173066..173680 1 NC_008688.1 PFAM: regulatory protein, TetR; KEGG: reu:Reut_B4322 regulatory protein, TetR; TetR family transcriptional regulator 173680 4583184 Pden_4681 Paracoccus denitrificans PD1222 TetR family transcriptional regulator YP_918438.1 173066 D 318586 CDS YP_918439.1 119387405 4583185 complement(174512..175090) 1 NC_008688.1 TIGRFAM: PAS sensor protein; PFAM: regulatory protein, LuxR; PAS fold domain protein; KEGG: pen:PSEEN2542 PAS domain containing response regulator, LuxR family; PAS/PAC sensor protein 175090 4583185 Pden_4682 Paracoccus denitrificans PD1222 PAS/PAC sensor protein YP_918439.1 174512 R 318586 CDS YP_918440.1 119387406 4583186 175210..175947 1 NC_008688.1 KEGG: rsp:RSP_1914 3-ketoacid CoA transferase alpha subunit; TIGRFAM: 3-oxoacid CoA-transferase, A subunit; PFAM: coenzyme A transferase; 3-oxoacid CoA-transferase subunit A 175947 4583186 Pden_4683 Paracoccus denitrificans PD1222 3-oxoacid CoA-transferase subunit A YP_918440.1 175210 D 318586 CDS YP_918441.1 119387407 4583187 175947..176591 1 NC_008688.1 KEGG: rsp:RSP_1913 3-oxoadipate CoA-transferase, beta subunit; TIGRFAM: 3-oxoacid CoA-transferase, B subunit; PFAM: coenzyme A transferase; 3-oxoacid CoA-transferase subunit B 176591 4583187 Pden_4684 Paracoccus denitrificans PD1222 3-oxoacid CoA-transferase subunit B YP_918441.1 175947 D 318586 CDS YP_918442.1 119387408 4583188 177048..178337 1 NC_008688.1 PFAM: secretion protein HlyD family protein; KEGG: rpc:RPC_4665 secretion protein HlyD; secretion protein HlyD family protein 178337 4583188 Pden_4685 Paracoccus denitrificans PD1222 secretion protein HlyD family protein YP_918442.1 177048 D 318586 CDS YP_918443.1 119387409 4583189 178334..181072 1 NC_008688.1 PFAM: ABC transporter related; ABC-2 type transporter; SMART: AAA ATPase; KEGG: rpb:RPB_0170 ABC-2 type transport system; ABC transporter related 181072 4583189 Pden_4686 Paracoccus denitrificans PD1222 ABC transporter related YP_918443.1 178334 D 318586 CDS YP_918444.1 119387410 4583190 181069..182181 1 NC_008688.1 PFAM: ABC-2 type transporter; KEGG: bmb:BruAb1_1347 hypothetical ABC transporter, permease; ABC-2 type transporter 182181 4583190 Pden_4687 Paracoccus denitrificans PD1222 ABC-2 type transporter YP_918444.1 181069 D 318586 CDS YP_918445.1 119387411 4583191 complement(182270..182818) 1 NC_008688.1 PFAM: YbaK/prolyl-tRNA synthetase associated region; KEGG: sme:SMc00385 hypothetical protein; prolyl-tRNA synthetase 182818 4583191 Pden_4688 Paracoccus denitrificans PD1222 prolyl-tRNA synthetase YP_918445.1 182270 R 318586 CDS YP_918446.1 119387412 4583192 complement(182815..183270) 1 NC_008688.1 KEGG: zmo:ZMO1010 hypothetical protein; hypothetical protein 183270 4583192 Pden_4689 Paracoccus denitrificans PD1222 hypothetical protein YP_918446.1 182815 R 318586 CDS YP_918447.1 119387413 4583193 complement(183281..183901) 1 NC_008688.1 PFAM: UbiE/COQ5 methyltransferase; Methyltransferase type 11; Methyltransferase type 12; KEGG: sit:TM1040_3086 phosphatidylethanolamine N-methyltransferase; phosphatidylethanolamine N-methyltransferase 183901 4583193 Pden_4690 Paracoccus denitrificans PD1222 phosphatidylethanolamine N-methyltransferase YP_918447.1 183281 R 318586 CDS YP_918448.1 119387414 4583194 complement(183911..184654) 1 NC_008688.1 KEGG: sit:TM1040_3085 CDP-diacylglycerol--serine O-phosphatidyltransferase; TIGRFAM: CDP-diacylglycerol--serine O-phosphatidyltransferase; PFAM: CDP-alcohol phosphatidyltransferase; CDP-diacylglycerol--serine O-phosphatidyltransferase 184654 4583194 Pden_4691 Paracoccus denitrificans PD1222 CDP-diacylglycerol--serine O-phosphatidyltransferase YP_918448.1 183911 R 318586 CDS YP_918449.1 119387415 4583195 complement(184654..185334) 1 NC_008688.1 catalyzes the decarboxylaton of phospatidyl-L-sering to phosphatidylethanolamine; phosphatidylserine decarboxylase 185334 4583195 Pden_4692 Paracoccus denitrificans PD1222 phosphatidylserine decarboxylase YP_918449.1 184654 R 318586 CDS YP_918450.1 119387416 4583196 complement(185444..186895) 1 NC_008688.1 TIGRFAM: uracil-xanthine permease; PFAM: Xanthine/uracil/vitamin C permease; KEGG: bme:BMEII0825 uracil permease; uracil-xanthine permease 186895 4583196 Pden_4693 Paracoccus denitrificans PD1222 uracil-xanthine permease YP_918450.1 185444 R 318586 CDS YP_918451.1 119387417 4583197 187089..188438 1 NC_008688.1 PFAM: FAD-dependent pyridine nucleotide-disulphide oxidoreductase; KEGG: rpe:RPE_3985 FAD-dependent pyridine nucleotide-disulphide oxidoreductase; FAD-dependent pyridine nucleotide-disulphide oxidoreductase 188438 4583197 Pden_4694 Paracoccus denitrificans PD1222 FAD-dependent pyridine nucleotide-disulphide oxidoreductase YP_918451.1 187089 D 318586 CDS YP_918452.1 119387418 4583198 188452..188814 1 NC_008688.1 KEGG: rpb:RPB_0927 hypothetical protein; hypothetical protein 188814 4583198 Pden_4695 Paracoccus denitrificans PD1222 hypothetical protein YP_918452.1 188452 D 318586 CDS YP_918453.1 119387419 4583199 complement(188951..192142) 1 NC_008688.1 PFAM: acriflavin resistance protein; KEGG: rsp:RSP_0460 AcrB/AcrD/AcrF family cation/multidrug efflux pump; acriflavin resistance protein 192142 4583199 Pden_4696 Paracoccus denitrificans PD1222 acriflavin resistance protein YP_918453.1 188951 R 318586 CDS YP_918454.1 119387420 4583200 complement(192139..193098) 1 NC_008688.1 TIGRFAM: efflux transporter, RND family, MFP subunit; KEGG: rsp:RSP_0461 multidrug/cation efflux pump, membrane fusion protein (MFP) family; RND family efflux transporter MFP subunit 193098 4583200 Pden_4697 Paracoccus denitrificans PD1222 RND family efflux transporter MFP subunit YP_918454.1 192139 R 318586 CDS YP_918455.1 119387421 4583201 complement(193110..193310) 1 NC_008688.1 KEGG: rsp:RSP_0589 hypothetical protein; hypothetical protein 193310 4583201 Pden_4698 Paracoccus denitrificans PD1222 hypothetical protein YP_918455.1 193110 R 318586 CDS YP_918456.1 119387422 4583202 complement(193418..194020) 1 NC_008688.1 PFAM: cytochrome B561; KEGG: rsp:RSP_0475 cytochrome b; cytochrome B561 194020 4583202 Pden_4699 Paracoccus denitrificans PD1222 cytochrome B561 YP_918456.1 193418 R 318586 CDS YP_918457.1 119387423 4583203 complement(194022..194477) 1 NC_008688.1 PFAM: cytochrome c, class II; KEGG: rsp:RSP_0474 cytochrome c'; cytochrome c, class II 194477 4583203 Pden_4700 Paracoccus denitrificans PD1222 cytochrome c, class II YP_918457.1 194022 R 318586 CDS YP_918458.1 119387424 4583204 194673..194993 1 NC_008688.1 PFAM: regulatory protein, ArsR; KEGG: bja:bll5773 transcriptional regulatory protein; regulatory protein, ArsR 194993 4583204 Pden_4701 Paracoccus denitrificans PD1222 regulatory protein, ArsR YP_918458.1 194673 D 318586 CDS YP_918459.1 119387425 4583205 complement(195037..195411) 1 NC_008688.1 PFAM: protein of unknown function DUF442; KEGG: bms:BRA0697 hypothetical protein; hypothetical protein 195411 4583205 Pden_4702 Paracoccus denitrificans PD1222 hypothetical protein YP_918459.1 195037 R 318586 CDS YP_918460.1 119387426 4583206 complement(195412..195867) 1 NC_008688.1 PFAM: protein of unknown function DUF395, YeeE/YedE; KEGG: sit:TM1040_3646 protein of unknown function DUF395, YeeE/YedE; hypothetical protein 195867 4583206 Pden_4703 Paracoccus denitrificans PD1222 hypothetical protein YP_918460.1 195412 R 318586 CDS YP_918461.1 119387427 4583207 complement(195869..196294) 1 NC_008688.1 PFAM: protein of unknown function DUF395, YeeE/YedE; KEGG: bur:Bcep18194_B1883 YeeE/YedE family membrane protein; hypothetical protein 196294 4583207 Pden_4704 Paracoccus denitrificans PD1222 hypothetical protein YP_918461.1 195869 R 318586 CDS YP_918462.1 119387428 4583208 complement(196291..196494) 1 NC_008688.1 KEGG: rso:RSc1506 probable transmembrane protein; transmembrane protein 196494 4583208 Pden_4705 Paracoccus denitrificans PD1222 transmembrane protein YP_918462.1 196291 R 318586 CDS YP_918463.1 119387429 4583209 complement(196513..197445) 1 NC_008688.1 PFAM: beta-lactamase domain protein; KEGG: mlo:mll3743 hypothetical protein; beta-lactamase domain-containing protein 197445 4583209 Pden_4706 Paracoccus denitrificans PD1222 beta-lactamase domain-containing protein YP_918463.1 196513 R 318586 CDS YP_918464.1 119387430 4583210 197669..197983 1 NC_008688.1 KEGG: rde:RD1_2193 hypothetical protein; hypothetical protein 197983 4583210 Pden_4707 Paracoccus denitrificans PD1222 hypothetical protein YP_918464.1 197669 D 318586 CDS YP_918465.1 119387431 4583211 198083..198478 1 NC_008688.1 PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase; KEGG: rsp:RSP_3237 lactoylglutathione lyase; glyoxalase/bleomycin resistance protein/dioxygenase 198478 4583211 Pden_4708 Paracoccus denitrificans PD1222 glyoxalase/bleomycin resistance protein/dioxygenase YP_918465.1 198083 D 318586 CDS YP_918466.1 119387432 4583212 198528..199070 1 NC_008688.1 KEGG: rde:RD1_2191 hypothetical protein; hypothetical protein 199070 4583212 Pden_4709 Paracoccus denitrificans PD1222 hypothetical protein YP_918466.1 198528 D 318586 CDS YP_918467.1 119387433 4583213 199082..200662 1 NC_008688.1 PFAM: glucose-methanol-choline oxidoreductase; KEGG: rde:RD1_2190 oxidoreductase; glucose-methanol-choline oxidoreductase 200662 4583213 Pden_4710 Paracoccus denitrificans PD1222 glucose-methanol-choline oxidoreductase YP_918467.1 199082 D 318586 CDS YP_918468.1 119387434 4583214 complement(200737..201006) 1 NC_008688.1 TIGRFAM: cell division topological specificity factor MinE; PFAM: Septum formation topological specificity factor MinE; KEGG: dps:DP0668 probable cell division topological specificity factor (MinE); cell division topological specificity factor MinE 201006 4583214 Pden_4711 Paracoccus denitrificans PD1222 cell division topological specificity factor MinE YP_918468.1 200737 R 318586 CDS YP_918469.1 119387435 4583215 complement(201008..201745) 1 NC_008688.1 TIGRFAM: septum site-determining protein MinD; KEGG: pfl:PFL_4380 septum site-determining protein MinD; septum site-determining protein MinD 201745 4583215 Pden_4712 Paracoccus denitrificans PD1222 septum site-determining protein MinD YP_918469.1 201008 R 318586 CDS YP_918470.1 119387436 4583216 complement(201853..202599) 1 NC_008688.1 TIGRFAM: septum site-determining protein MinC; PFAM: Septum formation inhibitor MinC; KEGG: aeh:Mlg_1998 septum site-determining protein MinC; septum site-determining protein MinC 202599 4583216 Pden_4713 Paracoccus denitrificans PD1222 septum site-determining protein MinC YP_918470.1 201853 R 318586 CDS YP_918471.1 119387437 4583217 202820..203488 1 NC_008688.1 PFAM: phosphoribosyltransferase; KEGG: mes:Meso_3530 phosphoribosyltransferase; phosphoribosyltransferase 203488 4583217 Pden_4714 Paracoccus denitrificans PD1222 phosphoribosyltransferase YP_918471.1 202820 D 318586 CDS YP_918472.1 119387438 4583218 203601..204569 1 NC_008688.1 TIGRFAM: TRAP dicarboxylate transporter, DctP subunit; PFAM: TRAP dicarboxylate transporter- DctP subunit; KEGG: sit:TM1040_3319 TRAP dicarboxylate transporter, DctP subunit; TRAP dicarboxylate transporter, DctP subunit 204569 4583218 Pden_4715 Paracoccus denitrificans PD1222 TRAP dicarboxylate transporter, DctP subunit YP_918472.1 203601 D 318586 CDS YP_918473.1 119387439 4583219 204576..205070 1 NC_008688.1 PFAM: Tripartite ATP-independent periplasmic transporter, DctQ component; KEGG: sit:TM1040_3318 tripartite ATP-independent periplasmic transporter, DctQ component; tripartite ATP-independent periplasmic transporter DctQ 205070 4583219 Pden_4716 Paracoccus denitrificans PD1222 tripartite ATP-independent periplasmic transporter DctQ YP_918473.1 204576 D 318586 CDS YP_918474.1 119387440 4583220 205063..206352 1 NC_008688.1 TIGRFAM: TRAP dicarboxylate transporter, DctM subunit; PFAM: TRAP C4-dicarboxylate transport system permease DctM subunit; KEGG: sit:TM1040_3317 TRAP dicarboxylate transporter-DctM subunit; TRAP dicarboxylate transporter, DctM subunit 206352 4583220 Pden_4717 Paracoccus denitrificans PD1222 TRAP dicarboxylate transporter, DctM subunit YP_918474.1 205063 D 318586 CDS YP_918475.1 119387441 4583221 206504..206752 1 NC_008688.1 hypothetical protein 206752 4583221 Pden_4718 Paracoccus denitrificans PD1222 hypothetical protein YP_918475.1 206504 D 318586 CDS YP_918476.1 119387442 4583222 206786..206965 1 NC_008688.1 PFAM: periplasmic nitrate reductase NapE; KEGG: sme:SMa1241 NapE component of periplasmic nitrate reductase; periplasmic nitrate reductase NapE 206965 4583222 Pden_4719 Paracoccus denitrificans PD1222 periplasmic nitrate reductase NapE YP_918476.1 206786 D 318586 CDS YP_918477.1 119387443 4583223 206975..207313 1 NC_008688.1 PFAM: NapD family protein; KEGG: sme:SMa1239 NapD component of periplasmic nitrate reductase; NapD family protein 207313 4583223 Pden_4720 Paracoccus denitrificans PD1222 NapD family protein YP_918477.1 206975 D 318586 CDS YP_918478.1 119387444 4583224 207310..209805 1 NC_008688.1 periplasmic; catalytic subunit; with NapBC catalyzes the reduction of nitrate to nitrite; NapAB receives electrons from NapC; nitrate reductase catalytic subunit 209805 4583224 Pden_4721 Paracoccus denitrificans PD1222 nitrate reductase catalytic subunit YP_918478.1 207310 D 318586 CDS YP_918479.1 119387445 4583225 209778..210263 1 NC_008688.1 PFAM: Nitrate reductase cytochrome c-type subunit (NapB); KEGG: sme:SMa1233 NapB periplasmic nitrate reductase; nitrate reductase cytochrome c-type subunit (NapB) 210263 4583225 Pden_4722 Paracoccus denitrificans PD1222 nitrate reductase cytochrome c-type subunit (NapB) YP_918479.1 209778 D 318586 CDS YP_918480.1 119387446 4583226 210265..210978 1 NC_008688.1 TIGRFAM: periplasmic nitrate (or nitrite) reductase c-type cytochrome, NapC/NirT family; PFAM: NapC/NirT cytochrome c domain protein; KEGG: sme:SMa1232 NapC membrane protein, e-donor to periplasmic nitrate reductase; NapC/NirT family periplasmic nitrate (or nitrite) reductase c-type cytochrome 210978 4583226 Pden_4723 Paracoccus denitrificans PD1222 NapC/NirT family periplasmic nitrate (or nitrite) reductase c-type cytochrome YP_918480.1 210265 D 318586 CDS YP_918481.1 119387447 4583227 211265..211678 1 NC_008688.1 Regulates the synthesis of nucleoside triphosphates for nucleic acid synthesis, CTP for lipid synthesis, and GTP for protein elongation; nucleoside diphosphate kinase regulator 211678 4583227 Pden_4724 Paracoccus denitrificans PD1222 nucleoside diphosphate kinase regulator YP_918481.1 211265 D 318586 CDS YP_918482.1 119387448 4583228 211902..212627 1 NC_008688.1 KEGG: rpd:RPD_2427 hypothetical protein; hypothetical protein 212627 4583228 Pden_4725 Paracoccus denitrificans PD1222 hypothetical protein YP_918482.1 211902 D 318586 CDS YP_918483.1 119387449 4583229 complement(212549..213526) 1 NC_008688.1 PFAM: MscS Mechanosensitive ion channel; KEGG: eba:ebA6709 mechanosensitive channel protein; MscS mechanosensitive ion channel 213526 4583229 Pden_4726 Paracoccus denitrificans PD1222 MscS mechanosensitive ion channel YP_918483.1 212549 R 318586 CDS YP_918484.1 119387450 4583230 complement(213959..215170) 1 NC_008688.1 PFAM: glucose sorbosone dehydrogenase; KEGG: neu:NE1997 glucose dehydrogenase B; glucose sorbosone dehydrogenase 215170 4583230 Pden_4727 Paracoccus denitrificans PD1222 glucose sorbosone dehydrogenase YP_918484.1 213959 R 318586 CDS YP_918485.1 119387451 4583231 complement(215703..216554) 1 NC_008688.1 PFAM: regulatory protein, LysR; helix-turn-helix, Fis-type; LysR, substrate-binding; KEGG: bja:bll5630 transcriptional regulatory protein; LysR family transcriptional regulator 216554 4583231 Pden_4728 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_918485.1 215703 R 318586 CDS YP_918486.1 119387452 4583232 216737..217570 1 NC_008688.1 KEGG: mfa:Mfla_0547 hypothetical protein; hypothetical protein 217570 4583232 Pden_4729 Paracoccus denitrificans PD1222 hypothetical protein YP_918486.1 216737 D 318586 CDS YP_918487.1 119387453 4583233 217650..218903 1 NC_008688.1 KEGG: mfa:Mfla_0548 amine dehydrogenase; TIGRFAM: methylamine dehydrogenase heavy chain; PFAM: methylamine dehydrogenase heavy subunit; methylamine dehydrogenase heavy chain 218903 4583233 Pden_4730 Paracoccus denitrificans PD1222 methylamine dehydrogenase heavy chain YP_918487.1 217650 D 318586 CDS YP_918488.1 119387454 4583234 218908..219468 1 NC_008688.1 PFAM: methylamine utilisation MauE; KEGG: mfa:Mfla_0549 methylamine utilisation MauE; methylamine utilisation MauE 219468 4583234 Pden_4731 Paracoccus denitrificans PD1222 methylamine utilisation MauE YP_918488.1 218908 D 318586 CDS YP_918489.1 119387455 4583235 219470..220072 1 NC_008688.1 TIGRFAM: methylamine dehydrogenase accessory protein MauD; PFAM: Redoxin domain protein; KEGG: mfa:Mfla_0550 hypothetical protein; methylamine dehydrogenase accessory protein MauD 220072 4583235 Pden_4732 Paracoccus denitrificans PD1222 methylamine dehydrogenase accessory protein MauD YP_918489.1 219470 D 318586 CDS YP_918490.1 119387456 4583236 220115..220681 1 NC_008688.1 KEGG: mfa:Mfla_0551 amine dehydrogenase; TIGRFAM: methylamine dehydrogenase light chain; PFAM: Methylamine dehydrogenase light chain, C terminal domain protein; methylamine dehydrogenase light chain 220681 4583236 Pden_4733 Paracoccus denitrificans PD1222 methylamine dehydrogenase light chain YP_918490.1 220115 D 318586 CDS YP_918491.1 119387457 4583237 220736..221131 1 NC_008688.1 TIGRFAM: amicyanin; PFAM: blue (type 1) copper domain protein; KEGG: mpa:MAP4219 hypothetical protein; amicyanin 221131 4583237 Pden_4734 Paracoccus denitrificans PD1222 amicyanin YP_918491.1 220736 D 318586 CDS YP_918492.1 119387458 4583238 221149..222012 1 NC_008688.1 hypothetical protein 222012 4583238 Pden_4735 Paracoccus denitrificans PD1222 hypothetical protein YP_918492.1 221149 D 318586 CDS YP_918493.1 119387459 4583239 222012..223175 1 NC_008688.1 PFAM: Di-haem cytochrome c peroxidase; KEGG: atc:AGR_C_5068 hypothetical protein; di-haem cytochrome c peroxidase 223175 4583239 Pden_4736 Paracoccus denitrificans PD1222 di-haem cytochrome c peroxidase YP_918493.1 222012 D 318586 CDS YP_918494.1 119387460 4583240 223205..223879 1 NC_008688.1 TIGRFAM: MauM/NapG family ferredoxin-type protein; PFAM: 4Fe-4S ferredoxin, iron-sulfur binding domain protein; KEGG: mfa:Mfla_0554 MauM/NapG family ferredoxin-type protein; MauM/NapG family ferredoxin-type protein 223879 4583240 Pden_4737 Paracoccus denitrificans PD1222 MauM/NapG family ferredoxin-type protein YP_918494.1 223205 D 318586 CDS YP_918495.1 119387461 4583241 223876..224727 1 NC_008688.1 TIGRFAM: ferredoxin-type protein, NapH/MauN family; PFAM: 4Fe-4S ferredoxin, iron-sulfur binding domain protein; KEGG: dar:Daro_3838 ferredoxin-type protein, NapH/MauN family; NapH/MauN family ferredoxin-type protein 224727 4583241 Pden_4738 Paracoccus denitrificans PD1222 NapH/MauN family ferredoxin-type protein YP_918495.1 223876 D 318586 CDS YP_918496.1 119387462 4583242 complement(224785..225129) 1 NC_008688.1 TIGRFAM: alkylphosphonate utilization operon protein PhnA; PFAM: PhnA protein-like; KEGG: rsp:RSP_3090 alkylphosphonate uptake protein, PhnA; alkylphosphonate utilization protein PhnA 225129 4583242 Pden_4739 Paracoccus denitrificans PD1222 alkylphosphonate utilization protein PhnA YP_918496.1 224785 R 318586 CDS YP_918497.1 119387463 4583243 complement(225218..225700) 1 NC_008688.1 PFAM: regulatory protein, LuxR; KEGG: rme:Rmet_5323 two component transcriptional regulator, LuxR family; two component LuxR family transcriptional regulator 225700 4583243 Pden_4740 Paracoccus denitrificans PD1222 two component LuxR family transcriptional regulator YP_918497.1 225218 R 318586 CDS YP_918498.1 119387464 4583244 complement(225816..227240) 1 NC_008688.1 PFAM: ATP-binding region, ATPase domain protein domain protein; histidine kinase A domain protein domain protein; KEGG: ret:RHE_PF00324 probable two-component sensor histidine kinase/response regulator hybrid protein; integral membrane sensor signal transduction histidine kinase 227240 4583244 Pden_4741 Paracoccus denitrificans PD1222 integral membrane sensor signal transduction histidine kinase YP_918498.1 225816 R 318586 CDS YP_918499.1 119387465 4583245 complement(227240..227755) 1 NC_008688.1 KEGG: cvi:CV2214 hypothetical protein; hypothetical protein 227755 4583245 Pden_4742 Paracoccus denitrificans PD1222 hypothetical protein YP_918499.1 227240 R 318586 CDS YP_918500.1 119387466 4583246 228171..229892 1 NC_008688.1 PFAM: Peptidoglycan-binding domain 1 protein; KEGG: jan:Jann_3999 peptidoglycan-binding domain 1; peptidoglycan binding domain-containing protein 229892 4583246 Pden_4743 Paracoccus denitrificans PD1222 peptidoglycan binding domain-containing protein YP_918500.1 228171 D 318586 CDS YP_918501.1 119387467 4583247 complement(229896..231137) 1 NC_008688.1 KEGG: mlo:mlr2623 hypothetical protein; hypothetical protein 231137 4583247 Pden_4744 Paracoccus denitrificans PD1222 hypothetical protein YP_918501.1 229896 R 318586 CDS YP_918502.1 119387468 4583248 complement(231134..232693) 1 NC_008688.1 PFAM: Sel1 domain protein repeat-containing protein; Sel1 domain-containing protein 232693 4583248 Pden_4745 Paracoccus denitrificans PD1222 Sel1 domain-containing protein YP_918502.1 231134 R 318586 CDS YP_918503.1 119387469 4583249 complement(232852..233691) 1 NC_008688.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: ret:RHE_PF00392 probable glycine betaine/L-proline ABC transporter, permease; binding-protein-dependent transport systems inner membrane component 233691 4583249 Pden_4746 Paracoccus denitrificans PD1222 binding-protein-dependent transport systems inner membrane component YP_918503.1 232852 R 318586 CDS YP_918504.1 119387470 4583250 complement(233688..234515) 1 NC_008688.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: ret:RHE_PF00393 probable glycine betaine/L-proline ABC transporter, permease; binding-protein-dependent transport systems inner membrane component 234515 4583250 Pden_4747 Paracoccus denitrificans PD1222 binding-protein-dependent transport systems inner membrane component YP_918504.1 233688 R 318586 CDS YP_918505.1 119387471 4583251 complement(234525..235589) 1 NC_008688.1 KEGG: ret:RHE_PF00394 probable glycine betaine/L-proline ABC transporter, ATP-binding protein; TIGRFAM: glycine betaine/L-proline ABC transporter, ATPase subunit; PFAM: ABC transporter related; SMART: AAA ATPase; glycine betaine/L-proline ABC transporter, ATPase subunit 235589 4583251 Pden_4748 Paracoccus denitrificans PD1222 glycine betaine/L-proline ABC transporter, ATPase subunit YP_918505.1 234525 R 318586 CDS YP_918506.1 119387472 4583252 complement(235660..236511) 1 NC_008688.1 PFAM: Substrate-binding region of ABC-type glycine betaine transport system; KEGG: ret:RHE_PF00395 probable glycine betaine/L-proline ABC transporter, substrate-binding protein; substrate-binding region of ABC-type glycine betaine transport system 236511 4583252 Pden_4749 Paracoccus denitrificans PD1222 substrate-binding region of ABC-type glycine betaine transport system YP_918506.1 235660 R 318586 CDS YP_918507.1 119387473 4583253 complement(236793..237773) 1 NC_008688.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: bur:Bcep18194_C7696 transcriptional regulator, LysR family; LysR family transcriptional regulator 237773 4583253 Pden_4750 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_918507.1 236793 R 318586 CDS YP_918508.1 119387474 4583254 complement(237770..239113) 1 NC_008688.1 PFAM: FAD dependent oxidoreductase; KEGG: rsp:RSP_4005 oxidoreductase, NAD-binding site; FAD dependent oxidoreductase 239113 4583254 Pden_4751 Paracoccus denitrificans PD1222 FAD dependent oxidoreductase YP_918508.1 237770 R 318586 CDS YP_918509.1 119387475 4583255 complement(239115..240620) 1 NC_008688.1 PFAM: aldehyde dehydrogenase; KEGG: rsp:RSP_4003 aldehyde dehydrogenase; aldehyde dehydrogenase 240620 4583255 Pden_4752 Paracoccus denitrificans PD1222 aldehyde dehydrogenase YP_918509.1 239115 R 318586 CDS YP_918510.1 119387476 4583256 complement(240622..241539) 1 NC_008688.1 PFAM: dihydrodipicolinate synthetase; KEGG: rsp:RSP_4002 dihydrodipicolinate synthetase; dihydrodipicolinate synthetase 241539 4583256 Pden_4753 Paracoccus denitrificans PD1222 dihydrodipicolinate synthetase YP_918510.1 240622 R 318586 CDS YP_918511.1 119387477 4583257 complement(241670..243025) 1 NC_008688.1 KEGG: reu:Reut_B3732 hypothetical protein; hypothetical protein 243025 4583257 Pden_4754 Paracoccus denitrificans PD1222 hypothetical protein YP_918511.1 241670 R 318586 CDS YP_918512.1 119387478 4583258 243208..251547 1 NC_008688.1 PFAM: carbohydrate binding; glycosyltransferase 36; glycosyltransferase 36 associated; KEGG: sme:SMc04382 beta-(1,2)-glucan production associated transmembrane protein; carbohydrate binding 251547 4583258 Pden_4755 Paracoccus denitrificans PD1222 carbohydrate binding YP_918512.1 243208 D 318586 CDS YP_918513.1 119387479 4583259 complement(251599..252096) 1 NC_008688.1 PFAM: regulatory protein, AsnC/Lrp family; KEGG: atu:Atu4818 transcriptional regulator, AsnC family; AsnC family transcriptional regulator 252096 4583259 Pden_4756 Paracoccus denitrificans PD1222 AsnC family transcriptional regulator YP_918513.1 251599 R 318586 CDS YP_918514.1 119387480 4583260 252278..253531 1 NC_008688.1 PFAM: dehydrogenase, E1 component; KEGG: bme:BMEII0748 2-oxoisovalerate dehydrogenase alpha subunit; 3-methyl-2-oxobutanoate dehydrogenase 253531 4583260 Pden_4757 Paracoccus denitrificans PD1222 3-methyl-2-oxobutanoate dehydrogenase YP_918514.1 252278 D 318586 CDS YP_918515.1 119387481 4583261 253533..254549 1 NC_008688.1 PFAM: Transketolase, central region; Transketolase domain protein; KEGG: mlo:mll4472 2-oxoisovalerate dehydrogenase (beta subunit); transketolase, central region 254549 4583261 Pden_4758 Paracoccus denitrificans PD1222 transketolase, central region YP_918515.1 253533 D 318586 CDS YP_918516.1 119387482 4583262 254551..255840 1 NC_008688.1 PFAM: biotin/lipoyl attachment domain-containing protein; catalytic domain of components of various dehydrogenase complexes; E3 binding domain protein; KEGG: bms:BRA0526 2-oxoisovalerate dehydrogenase E2 component, dihydrolipoamide acetyltransferase; dehydrogenase catalytic domain-containing protein 255840 4583262 Pden_4759 Paracoccus denitrificans PD1222 dehydrogenase catalytic domain-containing protein YP_918516.1 254551 D 318586 CDS YP_918517.1 119387483 4583263 255845..257233 1 NC_008688.1 TIGRFAM: dihydrolipoamide dehydrogenase; PFAM: FAD-dependent pyridine nucleotide-disulphide oxidoreductase; pyridine nucleotide-disulphide oxidoreductase dimerisation region; KEGG: mlo:mll4470 dihydrolipoamide dehydrogenase; dihydrolipoamide dehydrogenase 257233 4583263 Pden_4760 Paracoccus denitrificans PD1222 dihydrolipoamide dehydrogenase YP_918517.1 255845 D 318586 CDS YP_918518.1 119387484 4583264 257267..257992 1 NC_008688.1 PFAM: protein of unknown function DUF105; KEGG: rsp:RSP_2406 hypothetical protein; hypothetical protein 257992 4583264 Pden_4761 Paracoccus denitrificans PD1222 hypothetical protein YP_918518.1 257267 D 318586 CDS YP_918519.1 119387485 4583265 258120..259136 1 NC_008688.1 KEGG: sit:TM1040_3771 conserved hypothetical protein; hypothetical protein 259136 4583265 Pden_4762 Paracoccus denitrificans PD1222 hypothetical protein YP_918519.1 258120 D 318586 CDS YP_918520.1 119387486 4583266 complement(259133..260473) 1 NC_008688.1 PFAM: response regulator receiver; sigma-54 factor, interaction domain-containing protein; helix-turn-helix, Fis-type; ATPase associated with various cellular activities, AAA_5; SMART: AAA ATPase; KEGG: sme:SMb20613 C4-dicarboxylate transport transcriptional regulatory protein; two component, sigma54 specific, Fis family transcriptional regulator 260473 4583266 Pden_4763 Paracoccus denitrificans PD1222 two component, sigma54 specific, Fis family transcriptional regulator YP_918520.1 259133 R 318586 CDS YP_918521.1 119387487 4583267 complement(260470..262152) 1 NC_008688.1 PFAM: ATP-binding region, ATPase domain protein domain protein; histidine kinase A domain protein domain protein; KEGG: mlo:mlr5841 dicarboxylate sensor protein; integral membrane sensor signal transduction histidine kinase 262152 4583267 Pden_4764 Paracoccus denitrificans PD1222 integral membrane sensor signal transduction histidine kinase YP_918521.1 260470 R 318586 CDS YP_918522.1 119387488 4583268 262357..263724 1 NC_008688.1 PFAM: sodium:dicarboxylate symporter; KEGG: atc:AGR_L_3041 C4-dicarboxylate transport protein; sodium:dicarboxylate symporter 263724 4583268 Pden_4765 Paracoccus denitrificans PD1222 sodium:dicarboxylate symporter YP_918522.1 262357 D 318586 CDS YP_918523.1 119387489 4583269 complement(263791..264801) 1 NC_008688.1 PFAM: regulatory protein, LacI; periplasmic binding protein/LacI transcriptional regulator; KEGG: rsp:RSP_1243 transcriptional regulator, LacI family; periplasmic binding protein/LacI transcriptional regulator 264801 4583269 Pden_4766 Paracoccus denitrificans PD1222 periplasmic binding protein/LacI transcriptional regulator YP_918523.1 263791 R 318586 CDS YP_918524.1 119387490 4583270 264898..265950 1 NC_008688.1 PFAM: AP endonuclease 2 domain protein; Xylose isomerase domain protein TIM barrel; KEGG: bms:BR0545 hypothetical protein; xylose isomerase domain-containing protein 265950 4583270 Pden_4767 Paracoccus denitrificans PD1222 xylose isomerase domain-containing protein YP_918524.1 264898 D 318586 CDS YP_918525.1 119387491 4583271 265947..267041 1 NC_008688.1 PFAM: oxidoreductase domain protein; Oxidoreductase, C-terminal domain; KEGG: atc:AGR_L_984 hypothetical protein; oxidoreductase domain-containing protein 267041 4583271 Pden_4768 Paracoccus denitrificans PD1222 oxidoreductase domain-containing protein YP_918525.1 265947 D 318586 CDS YP_918526.1 119387492 4583272 267038..268522 1 NC_008688.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rsp:RSP_1247 ABC sugar transporter, ATPase subunit; ABC transporter related 268522 4583272 Pden_4769 Paracoccus denitrificans PD1222 ABC transporter related YP_918526.1 267038 D 318586 CDS YP_918527.1 119387493 4583273 268519..269487 1 NC_008688.1 PFAM: inner-membrane translocator; KEGG: rsp:RSP_6150 ABC sugar (ribose) transporter, inner membrane subunit; inner-membrane translocator 269487 4583273 Pden_4770 Paracoccus denitrificans PD1222 inner-membrane translocator YP_918527.1 268519 D 318586 CDS YP_918528.1 119387494 4583274 269506..270465 1 NC_008688.1 KEGG: rsp:RSP_1249 ABC ribose transporter, periplasmic solute-binding protein; ABC ribose transporter, periplasmic solute-binding protein 270465 4583274 Pden_4771 Paracoccus denitrificans PD1222 ABC ribose transporter, periplasmic solute-binding protein YP_918528.1 269506 D 318586 CDS YP_918529.1 119387495 4583275 complement(270444..271328) 1 NC_008688.1 Member of the extracytoplasmic function sigma factors which are active under specific conditions; binds with the catalytic core of RNA polymerase to produce the holoenzyme and directs bacterial core RNA polymerase to specific promoter elements to initiate transcription; RNA polymerase sigma factor SigJ 271328 4583275 Pden_4772 Paracoccus denitrificans PD1222 RNA polymerase sigma factor SigJ YP_918529.1 270444 R 318586 CDS YP_918530.1 119387496 4583276 complement(271318..271791) 1 NC_008688.1 TIGRFAM: alkylhydroperoxidase like protein, AhpD family; PFAM: Carboxymuconolactone decarboxylase; KEGG: rsp:RSP_0606 redox protein; alkylhydroperoxidase 271791 4583276 Pden_4773 Paracoccus denitrificans PD1222 alkylhydroperoxidase YP_918530.1 271318 R 318586 CDS YP_918531.1 119387497 4583277 complement(271895..273037) 1 NC_008688.1 TIGRFAM: phosphonate metabolism protein PhnM; PFAM: Amidohydrolase 3; KEGG: sil:SPO0476 alkylphosphonate utilization protein PhnM; phosphonate metabolism protein PhnM 273037 4583277 Pden_4774 Paracoccus denitrificans PD1222 phosphonate metabolism protein PhnM YP_918531.1 271895 R 318586 CDS YP_918532.1 119387498 4583278 273133..273813 1 NC_008688.1 PFAM: protein of unknown function DUF1045; KEGG: rsp:RSP_2937 hypothetical protein; hypothetical protein 273813 4583278 Pden_4775 Paracoccus denitrificans PD1222 hypothetical protein YP_918532.1 273133 D 318586 CDS YP_918533.1 119387499 4583279 complement(273795..274328) 1 NC_008688.1 TIGRFAM: phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN; SMART: guanylate kinase/L-type calcium channel region; KEGG: jan:Jann_2855 phosphonate metabolism, 1,5-bisphosphokinase (PRPP-forming) PhnN; phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN 274328 4583279 Pden_4776 Paracoccus denitrificans PD1222 phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN YP_918533.1 273795 R 318586 CDS YP_918534.1 119387500 4583280 complement(274325..275008) 1 NC_008688.1 KEGG: sit:TM1040_3698 phosphonate C-P lyase system, PhnL; TIGRFAM: phosphonate C-P lyase system protein PhnL; PFAM: ABC transporter related; SMART: AAA ATPase; phosphonate C-P lyase system protein PhnL 275008 4583280 Pden_4777 Paracoccus denitrificans PD1222 phosphonate C-P lyase system protein PhnL YP_918534.1 274325 R 318586 CDS YP_918535.1 119387501 4583340 complement(275013..275795) 1 NC_008688.1 KEGG: rde:RD1_2390 phosphonate C-P lyase system protein PhnK; TIGRFAM: phosphonate C-P lyase system protein PhnK; PFAM: ABC transporter related; SMART: AAA ATPase; phosphonate C-P lyase system protein PhnK 275795 phnK 4583340 phnK Paracoccus denitrificans PD1222 phosphonate C-P lyase system protein PhnK YP_918535.1 275013 R 318586 CDS YP_918536.1 119387502 4583341 complement(275792..276664) 1 NC_008688.1 PFAM: phosphonate metabolism PhnJ; KEGG: rde:RD1_2391 phosphonate metabolism protein PhnJ; phosphonate metabolism PhnJ 276664 4583341 Pden_4779 Paracoccus denitrificans PD1222 phosphonate metabolism PhnJ YP_918536.1 275792 R 318586 CDS YP_918537.1 119387503 4583342 complement(276661..277743) 1 NC_008688.1 PFAM: phosphonate metabolism; KEGG: rde:RD1_2392 phosphonate metabolism protein; phosphonate metabolism 277743 4583342 Pden_4780 Paracoccus denitrificans PD1222 phosphonate metabolism YP_918537.1 276661 R 318586 CDS YP_918538.1 119387504 4583343 complement(277743..278309) 1 NC_008688.1 PFAM: phosphonate metabolism; KEGG: rde:RD1_2393 phosphonate metabolism protein; carbon-phosphorus lyase complex subunit 278309 phnH 4583343 phnH Paracoccus denitrificans PD1222 carbon-phosphorus lyase complex subunit YP_918538.1 277743 R 318586 CDS YP_918539.1 119387505 4583344 complement(278306..278758) 1 NC_008688.1 PFAM: phosphonate metabolism PhnG; KEGG: sit:TM1040_3703 phosphonate metabolism PhnG; phosphonate metabolism PhnG 278758 4583344 Pden_4782 Paracoccus denitrificans PD1222 phosphonate metabolism PhnG YP_918539.1 278306 R 318586 CDS YP_918540.1 119387506 4583345 278877..279608 1 NC_008688.1 TIGRFAM: phosphonates metabolism transcriptional regulator PhnF; PFAM: regulatory protein GntR, HTH; UbiC transcription regulator-associated domain protein; KEGG: sil:SPO0467 transcriptional regulator, GntR family; phosphonates metabolism transcriptional regulator PhnF 279608 4583345 Pden_4783 Paracoccus denitrificans PD1222 phosphonates metabolism transcriptional regulator PhnF YP_918540.1 278877 D 318586 CDS YP_918541.1 119387507 4583346 complement(279605..280930) 1 NC_008688.1 TIGRFAM: phosphonate ABC transporter, inner membrane subunit; PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: sil:SPO0783 phosphonate ABC transporter, permease; phosphonate ABC transporter, inner membrane subunit 280930 4583346 Pden_4784 Paracoccus denitrificans PD1222 phosphonate ABC transporter, inner membrane subunit YP_918541.1 279605 R 318586 CDS YP_918542.1 119387508 4583347 complement(280934..281776) 1 NC_008688.1 TIGRFAM: phosphonate ABC transporter, inner membrane subunit; PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: sil:SPO0782 phosphonate ABC transporter, permease; phosphonate ABC transporter, inner membrane subunit 281776 4583347 Pden_4785 Paracoccus denitrificans PD1222 phosphonate ABC transporter, inner membrane subunit YP_918542.1 280934 R 318586 CDS YP_918543.1 119387509 4583348 complement(281840..282751) 1 NC_008688.1 TIGRFAM: phosphonate ABC transporter, periplasmic phosphonate-binding protein; KEGG: sit:TM1040_3708 phosphonate-binding periplasmic protein; phosphonate ABC transporter, periplasmic phosphonate-binding protein 282751 4583348 Pden_4786 Paracoccus denitrificans PD1222 phosphonate ABC transporter, periplasmic phosphonate-binding protein YP_918543.1 281840 R 318586 CDS YP_918544.1 119387510 4583349 complement(282787..283605) 1 NC_008688.1 KEGG: sit:TM1040_3709 phosphonate ABC transporter PhnC, ATP-binding; TIGRFAM: phosphonate ABC transporter, ATPase subunit; PFAM: ABC transporter related; SMART: AAA ATPase; phosphonate ABC transporter, ATPase subunit 283605 4583349 Pden_4787 Paracoccus denitrificans PD1222 phosphonate ABC transporter, ATPase subunit YP_918544.1 282787 R 318586 CDS YP_918545.1 119387511 4583350 283918..284115 1 NC_008688.1 hypothetical protein 284115 4583350 Pden_4788 Paracoccus denitrificans PD1222 hypothetical protein YP_918545.1 283918 D 318586 CDS YP_918546.1 119387512 4583351 complement(284182..284724) 1 NC_008688.1 PFAM: NADPH-dependent FMN reductase; KEGG: rsp:RSP_3069 NADPH-dependent FMN reductase; NADPH-dependent FMN reductase 284724 4583351 Pden_4789 Paracoccus denitrificans PD1222 NADPH-dependent FMN reductase YP_918546.1 284182 R 318586 CDS YP_918547.1 119387513 4583352 complement(284832..285551) 1 NC_008688.1 PFAM: 5-formyltetrahydrofolate cyclo-ligase; KEGG: mlo:mll0364 hypothetical protein; 5-formyltetrahydrofolate cyclo-ligase 285551 4583352 Pden_4790 Paracoccus denitrificans PD1222 5-formyltetrahydrofolate cyclo-ligase YP_918547.1 284832 R 318586 CDS YP_918548.1 119387514 4583353 285774..286877 1 NC_008688.1 catalyzes the formation of 3-deoxy-D-arabino-hept-2-ulosonate 7 phosphate from phosphoenolpyruvate and D-erythrose 4-phosphate, phenylalanine sensitive; phospho-2-dehydro-3-deoxyheptonate aldolase 286877 4583353 Pden_4791 Paracoccus denitrificans PD1222 phospho-2-dehydro-3-deoxyheptonate aldolase YP_918548.1 285774 D 318586 CDS YP_918549.1 119387515 4583354 complement(286921..288861) 1 NC_008688.1 PFAM: Enoyl-CoA hydratase/isomerase; 3-hydroxyacyl-CoA dehydrogenase domain protein; 3-hydroxyacyl-CoA dehydrogenase, NAD-binding; KEGG: rsp:RSP_3535 enoyl-CoA hydratase/3-hydroxyacyl-CoA dehydrogenase bifunctional enzyme; 3-hydroxyacyl-CoA dehydrogenase 288861 4583354 Pden_4792 Paracoccus denitrificans PD1222 3-hydroxyacyl-CoA dehydrogenase YP_918549.1 286921 R 318586 CDS YP_918550.1 119387516 4583355 complement(288866..289567) 1 NC_008688.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: bbr:BB3153 high-affinity branched-chain amino acid transport, ATP-binding protein; ABC transporter related 289567 4583355 Pden_4793 Paracoccus denitrificans PD1222 ABC transporter related YP_918550.1 288866 R 318586 CDS YP_918551.1 119387517 4583356 complement(289554..290333) 1 NC_008688.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: bpe:BP1649 high-affinity branched-chain amino acid transport, ATP-binding protein; ABC transporter related 290333 4583356 Pden_4794 Paracoccus denitrificans PD1222 ABC transporter related YP_918551.1 289554 R 318586 CDS YP_918552.1 119387518 4583357 complement(290330..291289) 1 NC_008688.1 PFAM: inner-membrane translocator; KEGG: bbr:BB3151 ABC-transporter permease component; inner-membrane translocator 291289 4583357 Pden_4795 Paracoccus denitrificans PD1222 inner-membrane translocator YP_918552.1 290330 R 318586 CDS YP_918553.1 119387519 4583358 complement(291289..292161) 1 NC_008688.1 PFAM: inner-membrane translocator; KEGG: bbr:BB3150 ABC-transporter permease component; inner-membrane translocator 292161 4583358 Pden_4796 Paracoccus denitrificans PD1222 inner-membrane translocator YP_918553.1 291289 R 318586 CDS YP_918554.1 119387520 4583359 complement(292229..293374) 1 NC_008688.1 PFAM: Extracellular ligand-binding receptor; KEGG: bpa:BPP2828 ABC-transporter substrate-binding protein; extracellular ligand-binding receptor 293374 4583359 Pden_4797 Paracoccus denitrificans PD1222 extracellular ligand-binding receptor YP_918554.1 292229 R 318586 CDS YP_918555.1 119387521 4583360 complement(293415..295094) 1 NC_008688.1 TIGRFAM: phenylacetic acid degradation protein paaN; PFAM: aldehyde dehydrogenase; KEGG: bbr:BB3430 oxidoreductase; phenylacetic acid degradation protein paaN 295094 4583360 Pden_4798 Paracoccus denitrificans PD1222 phenylacetic acid degradation protein paaN YP_918555.1 293415 R 318586 CDS YP_918556.1 119387522 4583361 295167..295955 1 NC_008688.1 Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA; enoyl-CoA hydratase 295955 4583361 Pden_4799 Paracoccus denitrificans PD1222 enoyl-CoA hydratase YP_918556.1 295167 D 318586 CDS YP_918557.1 119387523 4583362 295952..296416 1 NC_008688.1 TIGRFAM: uncharacterized domain 1; phenylacetic acid degradation protein PaaD; PFAM: thioesterase superfamily protein; KEGG: nha:Nham_0937 phenylacetic acid degradation protein PaaD; phenylacetic acid degradation protein PaaD 296416 4583362 Pden_4800 Paracoccus denitrificans PD1222 phenylacetic acid degradation protein PaaD YP_918557.1 295952 D 318586 CDS YP_918558.1 119387524 4583363 296445..297755 1 NC_008688.1 TIGRFAM: phenylacetate-CoA ligase; KEGG: jan:Jann_0656 phenylacetate-CoA ligase; phenylacetate-CoA ligase 297755 4583363 Pden_4801 Paracoccus denitrificans PD1222 phenylacetate-CoA ligase YP_918558.1 296445 D 318586 CDS YP_918559.1 119387525 4583364 297880..298479 1 NC_008688.1 PFAM: regulatory protein, TetR; KEGG: nha:Nham_0935 transcriptional regulator, TetR family; TetR family transcriptional regulator 298479 4583364 Pden_4802 Paracoccus denitrificans PD1222 TetR family transcriptional regulator YP_918559.1 297880 D 318586 CDS YP_918560.1 119387526 4583365 298650..299360 1 NC_008688.1 KEGG: sme:SMa2315 aminoglycoside adenylyltransferase; adenylyltransferase 299360 4583365 Pden_4803 Paracoccus denitrificans PD1222 adenylyltransferase YP_918560.1 298650 D 318586 CDS YP_918561.1 119387527 4583366 complement(299460..301520) 1 NC_008688.1 catalyzes the ring cleavage reaction in phenylacetate degradation and the formation of 3-hydroxyacyl-CoA from crotonyl-CoA; bifunctional aldehyde dehydrogenase/enoyl-CoA hydratase 301520 4583366 Pden_4804 Paracoccus denitrificans PD1222 bifunctional aldehyde dehydrogenase/enoyl-CoA hydratase YP_918561.1 299460 R 318586 CDS YP_918562.1 119387528 4583367 complement(301596..302348) 1 NC_008688.1 PFAM: phenylacetic acid catabolic family protein; KEGG: nha:Nham_0933 phenylacetic acid catabolic; phenylacetic acid catabolic family protein 302348 4583367 Pden_4805 Paracoccus denitrificans PD1222 phenylacetic acid catabolic family protein YP_918562.1 301596 R 318586 CDS YP_918563.1 119387529 4583368 complement(302371..303447) 1 NC_008688.1 TIGRFAM: phenylacetate-CoA oxygenase/reductase, PaaK subunit; PFAM: ferredoxin; oxidoreductase FAD/NAD(P)-binding domain protein; Oxidoreductase FAD-binding domain protein; KEGG: nha:Nham_0932 ferredoxin; phenylacetate-CoA oxygenase/reductase, PaaK subunit 303447 4583368 Pden_4806 Paracoccus denitrificans PD1222 phenylacetate-CoA oxygenase/reductase, PaaK subunit YP_918563.1 302371 R 318586 CDS YP_918564.1 119387530 4583369 complement(303479..304000) 1 NC_008688.1 TIGRFAM: phenylacetate-CoA oxygenase, PaaJ subunit; PFAM: protein of unknown function DUF59; KEGG: nha:Nham_0931 phenylacetate-CoA oxygenase, PaaJ subunit; phenylacetate-CoA oxygenase, PaaJ subunit 304000 4583369 Pden_4807 Paracoccus denitrificans PD1222 phenylacetate-CoA oxygenase, PaaJ subunit YP_918564.1 303479 R 318586 CDS YP_918565.1 119387531 4583370 complement(304007..304819) 1 NC_008688.1 TIGRFAM: phenylacetate-CoA oxygenase, PaaI subunit; PFAM: phenylacetic acid catabolic family protein; KEGG: nha:Nham_0930 phenylacetate-CoA oxygenase, PaaI subunit; phenylacetate-CoA oxygenase, PaaI subunit 304819 4583370 Pden_4808 Paracoccus denitrificans PD1222 phenylacetate-CoA oxygenase, PaaI subunit YP_918565.1 304007 R 318586 CDS YP_918566.1 119387532 4583371 complement(304819..305103) 1 NC_008688.1 with PaaBCDE catalyzes the hydroxylation of phenylacetyl-CoA; involved in phenylacetate degradation; phenylacetate-CoA oxygenase subunit PaaB 305103 paaB 4583371 paaB Paracoccus denitrificans PD1222 phenylacetate-CoA oxygenase subunit PaaB YP_918566.1 304819 R 318586 CDS YP_918567.1 119387533 4583372 complement(305175..306164) 1 NC_008688.1 with PaaBCDE catalyzes the hydroxylation of phenylacetyl-CoA; phenylacetate-CoA oxygenase subunit PaaA 306164 paaA 4583372 paaA Paracoccus denitrificans PD1222 phenylacetate-CoA oxygenase subunit PaaA YP_918567.1 305175 R 318586 CDS YP_918568.1 119387534 4583373 complement(306183..307388) 1 NC_008688.1 KEGG: dar:Daro_0375 thiolase; TIGRFAM: acetyl-CoA acetyltransferases; beta-ketoadipyl CoA thiolase; PFAM: Thiolase; beta-ketoadipyl CoA thiolase 307388 4583373 Pden_4811 Paracoccus denitrificans PD1222 beta-ketoadipyl CoA thiolase YP_918568.1 306183 R 318586 CDS YP_918569.1 119387535 4583374 complement(307534..308388) 1 NC_008688.1 PFAM: PaaX domain protein; PaaX domain protein, C-terminal domain; KEGG: sme:SMb21641 regulator of phenylacetic acid degradation, ArsR family protein; PaaX domain-containing protein 308388 4583374 Pden_4812 Paracoccus denitrificans PD1222 PaaX domain-containing protein YP_918569.1 307534 R 318586 CDS YP_918570.1 119387536 4583375 complement(308495..310867) 1 NC_008688.1 PFAM: peptidase S45, penicillin amidase; KEGG: sbo:SBO_4393 penicillin G acylase; penicillin amidase 310867 4583375 Pden_4813 Paracoccus denitrificans PD1222 penicillin amidase YP_918570.1 308495 R 318586 CDS YP_918571.1 119387537 4583376 311088..311471 1 NC_008688.1 KEGG: hne:HNE_3363 hypothetical protein; hypothetical protein 311471 4583376 Pden_4814 Paracoccus denitrificans PD1222 hypothetical protein YP_918571.1 311088 D 318586 CDS YP_918572.1 119387538 4583377 311475..311948 1 NC_008688.1 KEGG: hne:HNE_3362 hypothetical protein; hypothetical protein 311948 4583377 Pden_4815 Paracoccus denitrificans PD1222 hypothetical protein YP_918572.1 311475 D 318586 CDS YP_918573.1 119387539 4583378 312233..314110 1 NC_008688.1 PFAM: Tripartite ATP-independent periplasmic transporter, DctQ component; TRAP C4-dicarboxylate transport system permease DctM subunit; KEGG: atc:AGR_L_113 hypothetical protein; TRAP C4-dicarboxylate transport system permease DctM subunit 314110 4583378 Pden_4816 Paracoccus denitrificans PD1222 TRAP C4-dicarboxylate transport system permease DctM subunit YP_918573.1 312233 D 318586 CDS YP_918574.1 119387540 4583379 314140..315156 1 NC_008688.1 TIGRFAM: TRAP dicarboxylate transporter, DctP subunit; PFAM: TRAP dicarboxylate transporter- DctP subunit; KEGG: bja:blr4511 probable ABC transporter substrate-binding protein; TRAP dicarboxylate transporter, DctP subunit 315156 4583379 Pden_4817 Paracoccus denitrificans PD1222 TRAP dicarboxylate transporter, DctP subunit YP_918574.1 314140 D 318586 CDS YP_918575.1 119387541 4583380 315156..315995 1 NC_008688.1 PFAM: regulatory proteins, IclR; KEGG: sme:SMc00263 transcription regulator protein; regulatory proteins, IclR 315995 4583380 Pden_4818 Paracoccus denitrificans PD1222 regulatory proteins, IclR YP_918575.1 315156 D 318586 CDS YP_918576.1 119387542 4583381 315992..317161 1 NC_008688.1 Catalyzes the synthesis of acetoacetyl coenzyme A from two molecules of acetyl coenzyme A. It can also act as a thiolase, catalyzing the reverse reaction and generating two-carbon units from the four-carbon product of fatty acid oxidation; acetyl-CoA acetyltransferase 317161 4583381 Pden_4819 Paracoccus denitrificans PD1222 acetyl-CoA acetyltransferase YP_918576.1 315992 D 318586 CDS YP_918577.1 119387543 4583382 317158..318759 1 NC_008688.1 activates fatty acids by binding to coenzyme A; acyl-CoA synthetase 318759 4583382 Pden_4820 Paracoccus denitrificans PD1222 acyl-CoA synthetase YP_918577.1 317158 D 318586 CDS YP_918578.1 119387544 4583383 318756..319583 1 NC_008688.1 KEGG: atc:AGR_L_127 hypothetical protein; hypothetical protein 319583 4583383 Pden_4821 Paracoccus denitrificans PD1222 hypothetical protein YP_918578.1 318756 D 318586 CDS YP_918579.1 119387545 4583384 319580..320341 1 NC_008688.1 PFAM: NAD-dependent epimerase/dehydratase; short-chain dehydrogenase/reductase SDR; KR; KEGG: pol:Bpro_0097 short-chain dehydrogenase/reductase SDR; short-chain dehydrogenase/reductase SDR 320341 4583384 Pden_4822 Paracoccus denitrificans PD1222 short-chain dehydrogenase/reductase SDR YP_918579.1 319580 D 318586 CDS YP_918580.1 119387546 4583385 complement(320376..321647) 1 NC_008688.1 KEGG: nha:Nham_1901 membrane protein; membrane protein 321647 4583385 Pden_4823 Paracoccus denitrificans PD1222 membrane protein YP_918580.1 320376 R 318586 CDS YP_918581.1 119387547 4583386 321817..323316 1 NC_008688.1 PFAM: phosphoglucomutase/phosphomannomutase C terminal; phosphoglucomutase/phosphomannomutase alpha/beta/alpha domain I; phosphoglucomutase/phosphomannomutase alpha/beta/alpha domain II; phosphoglucomutase/phosphomannomutase alpha/beta/alpha domain III; KEGG: ftf:FTF1447c phosphomannomutase; phosphoglucomutase/phosphomannomutase alpha/beta/subunit 323316 4583386 Pden_4824 Paracoccus denitrificans PD1222 phosphoglucomutase/phosphomannomutase alpha/beta/subunit YP_918581.1 321817 D 318586 CDS YP_918582.1 119387548 4583387 complement(323332..325164) 1 NC_008688.1 KEGG: mfa:Mfla_1168 ATP-dependent metalloprotease FtsH; TIGRFAM: ATP-dependent metalloprotease FtsH; PFAM: peptidase M41; AAA ATPase, central domain protein; peptidase M41, FtsH extracellular; SMART: AAA ATPase; ATP-dependent metalloprotease FtsH 325164 4583387 Pden_4825 Paracoccus denitrificans PD1222 ATP-dependent metalloprotease FtsH YP_918582.1 323332 R 318586 CDS YP_918583.1 119387549 4583388 complement(325307..325822) 1 NC_008688.1 KEGG: sit:TM1040_2140 hypothetical protein; hypothetical protein 325822 4583388 Pden_4826 Paracoccus denitrificans PD1222 hypothetical protein YP_918583.1 325307 R 318586 CDS YP_918584.1 119387550 4583389 326381..328453 1 NC_008688.1 TIGRFAM: TonB-dependent siderophore receptor; PFAM: TonB-dependent receptor; TonB-dependent receptor, plug; KEGG: rpb:RPB_0102 TonB-dependent siderophore receptor; TonB-dependent siderophore receptor 328453 4583389 Pden_4827 Paracoccus denitrificans PD1222 TonB-dependent siderophore receptor YP_918584.1 326381 D 318586 CDS YP_918585.1 119387551 4583390 328455..329231 1 NC_008688.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sco:SCO0998 Fe uptake system permease; ABC transporter related 329231 4583390 Pden_4828 Paracoccus denitrificans PD1222 ABC transporter related YP_918585.1 328455 D 318586 CDS YP_918586.1 119387552 4583391 329242..330195 1 NC_008688.1 PFAM: periplasmic binding protein; KEGG: rde:RD1_3480 iron ABC transporter, periplasmic binding protein; periplasmic binding protein 330195 4583391 Pden_4829 Paracoccus denitrificans PD1222 periplasmic binding protein YP_918586.1 329242 D 318586 CDS YP_918587.1 119387553 4583392 330205..331230 1 NC_008688.1 PFAM: transport system permease; KEGG: rde:RD1_3479 hemin ABC transport protein, permease component; transport system permease 331230 4583392 Pden_4830 Paracoccus denitrificans PD1222 transport system permease YP_918587.1 330205 D 318586 CDS YP_918588.1 119387554 4583393 complement(331703..332341) 1 NC_008688.1 PFAM: Negative transcriptional regulator; KEGG: rme:Rmet_4524 negative transcriptional regulator; FMN-binding negative transcriptional regulator 332341 4583393 Pden_4832 Paracoccus denitrificans PD1222 FMN-binding negative transcriptional regulator YP_918588.1 331703 R 318586 CDS YP_918589.1 119387555 4583394 332445..333902 1 NC_008688.1 PFAM: regulatory protein GntR, HTH; aminotransferase, class I and II; KEGG: mlo:mlr6174 transcriptional regulator; GntR family transcriptional regulator 333902 4583394 Pden_4833 Paracoccus denitrificans PD1222 GntR family transcriptional regulator YP_918589.1 332445 D 318586 CDS YP_918590.1 119387556 4583395 complement(333973..334761) 1 NC_008688.1 PFAM: AraC protein, arabinose-binding/dimerisation; SMART: helix-turn-helix- domain containing protein, AraC type; KEGG: pae:PA0791 probable transcriptional regulator; AraC family transcriptional regulator 334761 4583395 Pden_4834 Paracoccus denitrificans PD1222 AraC family transcriptional regulator YP_918590.1 333973 R 318586 CDS YP_918591.1 119387557 4583396 334892..336103 1 NC_008688.1 PFAM: major facilitator superfamily MFS_1; KEGG: sus:Acid_6582 major facilitator superfamily MFS_1; major facilitator transporter 336103 4583396 Pden_4835 Paracoccus denitrificans PD1222 major facilitator transporter YP_918591.1 334892 D 318586 CDS YP_918592.1 119387558 4583397 complement(336108..337487) 1 NC_008688.1 PFAM: regulatory protein GntR, HTH; aromatic amino acid beta-eliminating lyase/threonine aldolase; aminotransferase, class I and II; KEGG: bja:blr0404 transcriptional regulatory protein; GntR family transcriptional regulator 337487 4583397 Pden_4836 Paracoccus denitrificans PD1222 GntR family transcriptional regulator YP_918592.1 336108 R 318586 CDS YP_918593.1 119387559 4583398 337651..338505 1 NC_008688.1 PFAM: protein of unknown function DUF6, transmembrane; KEGG: bja:bll0403 hypothetical protein; hypothetical protein 338505 4583398 Pden_4837 Paracoccus denitrificans PD1222 hypothetical protein YP_918593.1 337651 D 318586 CDS YP_918594.1 119387560 4583399 338602..338784 1 NC_008688.1 KEGG: xfa:XF1750 hypothetical protein; hypothetical protein 338784 4583399 Pden_4838 Paracoccus denitrificans PD1222 hypothetical protein YP_918594.1 338602 D 318586 CDS YP_918595.1 119387561 4583400 complement(338830..339504) 1 NC_008688.1 TIGRFAM: HAD-superfamily hydrolase, subfamily IA, variant 3; HAD-superfamily hydrolase, subfamily IA, variant 1; PFAM: Haloacid dehalogenase domain protein hydrolase; KEGG: ret:RHE_CH01779 hydrolase, haloacid dehalogenase-like family; HAD family hydrolase 339504 4583400 Pden_4839 Paracoccus denitrificans PD1222 HAD family hydrolase YP_918595.1 338830 R 318586 CDS YP_918596.1 119387562 4583401 complement(339581..340573) 1 NC_008688.1 PFAM: Alcohol dehydrogenase, zinc-binding domain protein; Alcohol dehydrogenase GroES domain protein; KEGG: atc:AGR_L_3295 hypothetical protein; alcohol dehydrogenase 340573 4583401 Pden_4840 Paracoccus denitrificans PD1222 alcohol dehydrogenase YP_918596.1 339581 R 318586 CDS YP_918597.1 119387563 4583402 complement(340631..341401) 1 NC_008688.1 Converts D-sorbitol to L-sorbose; sorbitol dehydrogenase 341401 4583402 Pden_4841 Paracoccus denitrificans PD1222 sorbitol dehydrogenase YP_918597.1 340631 R 318586 CDS YP_918598.1 119387564 4583403 complement(341398..342396) 1 NC_008688.1 PFAM: ABC transporter related; TOBE domain protein; Transport-associated OB domain protein; SMART: AAA ATPase; KEGG: rsp:RSP_0094 ABC sorbitol/mannitol transporter, ATPase subunit; ABC transporter related 342396 4583403 Pden_4842 Paracoccus denitrificans PD1222 ABC transporter related YP_918598.1 341398 R 318586 CDS YP_918599.1 119387565 4583404 complement(342404..343234) 1 NC_008688.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: rsp:RSP_0093 ABC sorbitol/mannitol transporter, inner membrane subunit; binding-protein-dependent transport systems inner membrane component 343234 4583404 Pden_4843 Paracoccus denitrificans PD1222 binding-protein-dependent transport systems inner membrane component YP_918599.1 342404 R 318586 CDS YP_918600.1 119387566 4583405 complement(343242..344114) 1 NC_008688.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: rsp:RSP_0092 ABC sorbitol/mannitol transporter, inner membrane subunit; binding-protein-dependent transport systems inner membrane component 344114 4583405 Pden_4844 Paracoccus denitrificans PD1222 binding-protein-dependent transport systems inner membrane component YP_918600.1 343242 R 318586 CDS YP_918601.1 119387567 4583406 complement(344219..345523) 1 NC_008688.1 PFAM: extracellular solute-binding protein, family 1; KEGG: atc:AGR_L_3289 periplasmic sorbitol-binding protein; extracellular solute-binding protein 345523 4583406 Pden_4845 Paracoccus denitrificans PD1222 extracellular solute-binding protein YP_918601.1 344219 R 318586 CDS YP_918602.1 119387568 4583407 complement(345633..346655) 1 NC_008688.1 PFAM: periplasmic binding protein/LacI transcriptional regulator; SMART: regulatory protein, LacI; KEGG: rde:RD1_1487 transcriptional regulator, LacI family; periplasmic binding protein/LacI transcriptional regulator 346655 4583407 Pden_4846 Paracoccus denitrificans PD1222 periplasmic binding protein/LacI transcriptional regulator YP_918602.1 345633 R 318586 CDS YP_918603.1 119387569 4583408 complement(346837..348114) 1 NC_008688.1 PFAM: D-tagatose-bisphosphate aldolase class II accessory protein AgaZ; KEGG: sme:SMb21373 sugar kinase; tagatose-6-phosphate kinase 348114 4583408 Pden_4847 Paracoccus denitrificans PD1222 tagatose-6-phosphate kinase YP_918603.1 346837 R 318586 CDS YP_918604.1 119387570 4583409 complement(348120..349061) 1 NC_008688.1 PFAM: PfkB domain protein; KEGG: sme:SMb21374 sugar kinase, PfkB family protein; ribokinase-like domain-containing protein 349061 4583409 Pden_4848 Paracoccus denitrificans PD1222 ribokinase-like domain-containing protein YP_918604.1 348120 R 318586 CDS YP_918605.1 119387571 4583410 complement(349066..350043) 1 NC_008688.1 PFAM: inner-membrane translocator; KEGG: sme:SMb21375 sugar uptake ABC transporter permease; inner-membrane translocator 350043 4583410 Pden_4849 Paracoccus denitrificans PD1222 inner-membrane translocator YP_918605.1 349066 R 318586 CDS YP_918606.1 119387572 4583411 complement(350040..351551) 1 NC_008688.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sme:SMb21376 sugar uptake ABC transporter ATP-binding protein; ABC transporter related 351551 4583411 Pden_4850 Paracoccus denitrificans PD1222 ABC transporter related YP_918606.1 350040 R 318586 CDS YP_918607.1 119387573 4583412 complement(351612..352499) 1 NC_008688.1 PFAM: periplasmic binding protein/LacI transcriptional regulator; KEGG: sme:SMb21377 sugar uptake ABC transporter periplasmic solute-binding protein precursor; periplasmic binding protein/LacI transcriptional regulator 352499 4583412 Pden_4851 Paracoccus denitrificans PD1222 periplasmic binding protein/LacI transcriptional regulator YP_918607.1 351612 R 318586 CDS YP_918608.1 119387574 4583413 complement(352963..355263) 1 NC_008688.1 PFAM: Sel1 domain protein repeat-containing protein; peptidase C14, caspase catalytic subunit p20; SMART: peptidase C14, caspase precursor p45; KEGG: ret:RHE_PE00124 hypothetical protein; peptidase C14, caspase catalytic subunit p20 355263 4583413 Pden_4852 Paracoccus denitrificans PD1222 peptidase C14, caspase catalytic subunit p20 YP_918608.1 352963 R 318586 CDS YP_918609.1 119387575 4583414 complement(355266..355892) 1 NC_008688.1 KEGG: rno:678915 hypothetical protein LOC678915; hypothetical protein 355892 4583414 Pden_4853 Paracoccus denitrificans PD1222 hypothetical protein YP_918609.1 355266 R 318586 CDS YP_918610.1 119387576 4583415 complement(355962..357653) 1 NC_008688.1 PFAM: protein of unknown function DUF126; protein of unknown function DUF521; KEGG: sme:SMb20269 hypothetical protein; hypothetical protein 357653 4583415 Pden_4854 Paracoccus denitrificans PD1222 hypothetical protein YP_918610.1 355962 R 318586 CDS YP_918611.1 119387577 4583416 complement(357807..358877) 1 NC_008688.1 PFAM: Malate/L-lactate dehydrogenase; KEGG: pau:PA14_48020 L-malate dehydrogenase; malate/L-lactate dehydrogenase 358877 4583416 Pden_4855 Paracoccus denitrificans PD1222 malate/L-lactate dehydrogenase YP_918611.1 357807 R 318586 CDS YP_918612.1 119387578 4583417 complement(358921..359907) 1 NC_008688.1 PFAM: TRAP dicarboxylate transporter- DctP subunit; KEGG: bja:bll4424 hypothetical protein; TRAP dicarboxylate transporter- DctP subunit 359907 4583417 Pden_4856 Paracoccus denitrificans PD1222 TRAP dicarboxylate transporter- DctP subunit YP_918612.1 358921 R 318586 CDS YP_918613.1 119387579 4583418 complement(359934..361199) 1 NC_008688.1 TIGRFAM: TRAP dicarboxylate transporter, DctM subunit; PFAM: TRAP C4-dicarboxylate transport system permease DctM subunit; KEGG: bja:bll4425 hypothetical protein; TRAP dicarboxylate transporter, DctM subunit 361199 4583418 Pden_4857 Paracoccus denitrificans PD1222 TRAP dicarboxylate transporter, DctM subunit YP_918613.1 359934 R 318586 CDS YP_918614.1 119387580 4583419 complement(361199..361816) 1 NC_008688.1 PFAM: Tripartite ATP-independent periplasmic transporter, DctQ component; KEGG: bja:bll4426 hypothetical protein; tripartite ATP-independent periplasmic transporter DctQ 361816 4583419 Pden_4858 Paracoccus denitrificans PD1222 tripartite ATP-independent periplasmic transporter DctQ YP_918614.1 361199 R 318586 CDS YP_918615.1 119387581 4583420 complement(361992..362996) 1 NC_008688.1 PFAM: proline racemase; KEGG: sme:SMb20268 proline racemase; hydroxyproline-2-epimerase 362996 4583420 Pden_4859 Paracoccus denitrificans PD1222 hydroxyproline-2-epimerase YP_918615.1 361992 R 318586 CDS YP_918616.1 119387582 4583421 complement(363004..364224) 1 NC_008688.1 PFAM: FAD dependent oxidoreductase; KEGG: sme:SMb20267 D-amino acid dehydrogenase; D-amino-acid dehydrogenase 364224 4583421 Pden_4860 Paracoccus denitrificans PD1222 D-amino-acid dehydrogenase YP_918616.1 363004 R 318586 CDS YP_918617.1 119387583 4583422 complement(364221..364946) 1 NC_008688.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: atc:AGR_L_402 probable ATP-binding component of ABC transporter; ABC transporter related 364946 4583422 Pden_4861 Paracoccus denitrificans PD1222 ABC transporter related YP_918617.1 364221 R 318586 CDS YP_918618.1 119387584 4583423 complement(364939..365592) 1 NC_008688.1 TIGRFAM: polar amino acid ABC transporter, inner membrane subunit; PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: atc:AGR_L_403 probable permease of ABC transporter; polar amino acid ABC transporter, inner membrane subunit 365592 4583423 Pden_4862 Paracoccus denitrificans PD1222 polar amino acid ABC transporter, inner membrane subunit YP_918618.1 364939 R 318586 CDS YP_918619.1 119387585 4583424 complement(365603..366295) 1 NC_008688.1 TIGRFAM: polar amino acid ABC transporter, inner membrane subunit; PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: atc:AGR_L_405 probable permease of ABC transporter; polar amino acid ABC transporter, inner membrane subunit 366295 4583424 Pden_4863 Paracoccus denitrificans PD1222 polar amino acid ABC transporter, inner membrane subunit YP_918619.1 365603 R 318586 CDS YP_918620.1 119387586 4583425 complement(366331..367137) 1 NC_008688.1 PFAM: extracellular solute-binding protein, family 3; KEGG: sme:SMb20263 ABC transporter periplasmic amino acid-binding protein; extracellular solute-binding protein 367137 4583425 Pden_4864 Paracoccus denitrificans PD1222 extracellular solute-binding protein YP_918620.1 366331 R 318586 CDS YP_918621.1 119387587 4583426 complement(367288..368802) 1 NC_008688.1 PFAM: aldehyde dehydrogenase; KEGG: sme:SMb20262 semialdehyde dehydrogenase; aldehyde dehydrogenase 368802 4583426 Pden_4865 Paracoccus denitrificans PD1222 aldehyde dehydrogenase YP_918621.1 367288 R 318586 CDS YP_918622.1 119387588 4583427 368936..369967 1 NC_008688.1 PFAM: Malate/L-lactate dehydrogenase; KEGG: sme:SMb20261 malate dehydrogenase; malate/L-lactate dehydrogenase 369967 4583427 Pden_4866 Paracoccus denitrificans PD1222 malate/L-lactate dehydrogenase YP_918622.1 368936 D 318586 CDS YP_918623.1 119387589 4583428 complement(370019..370981) 1 NC_008688.1 PFAM: dihydrodipicolinate synthetase; KEGG: sme:SMb20259 dihydrodipicolinate synthase; dihydrodipicolinate synthase 370981 4583428 Pden_4867 Paracoccus denitrificans PD1222 dihydrodipicolinate synthase YP_918623.1 370019 R 318586 CDS YP_918624.1 119387590 4583429 complement(371084..371782) 1 NC_008688.1 PFAM: regulatory protein GntR, HTH; GntR domain protein; KEGG: sme:SMb20258 transcriptional regulator protein; GntR family transcriptional regulator 371782 4583429 Pden_4868 Paracoccus denitrificans PD1222 GntR family transcriptional regulator YP_918624.1 371084 R 318586 CDS YP_918625.1 119387591 4583430 372107..372817 1 NC_008688.1 KEGG: mlo:mll7204 ABC transporter, substrate binding protein; ABC-type branched-chain amino acid transport systems periplasmic component-like 372817 4583430 Pden_4869 Paracoccus denitrificans PD1222 ABC-type branched-chain amino acid transport systems periplasmic component-like YP_918625.1 372107 D 318586 CDS YP_918626.1 119387592 4583431 complement(372730..373365) 1 NC_008688.1 PFAM: helix-turn-helix domain protein; Cupin 2, conserved barrel domain protein; KEGG: ppr:PBPRB1321 transcriptional regulator, HTH_3family; XRE family transcriptional regulator 373365 4583431 Pden_4870 Paracoccus denitrificans PD1222 XRE family transcriptional regulator YP_918626.1 372730 R 318586 CDS YP_918627.1 119387593 4583432 complement(373525..374331) 1 NC_008688.1 KEGG: rsp:RSP_3364 pyrroline-5-carboxylate reductase; TIGRFAM: pyrroline-5-carboxylate reductase; PFAM: NADP oxidoreductase, coenzyme F420-dependent; pyrroline-5-carboxylate reductase 374331 4583432 Pden_4871 Paracoccus denitrificans PD1222 pyrroline-5-carboxylate reductase YP_918627.1 373525 R 318586 CDS YP_918628.1 119387594 4583433 374536..375981 1 NC_008688.1 PFAM: FAD linked oxidase domain protein; KEGG: eba:ebA4737 FAD dependent oxidoreductase; FAD linked oxidase domain-containing protein 375981 4583433 Pden_4872 Paracoccus denitrificans PD1222 FAD linked oxidase domain-containing protein YP_918628.1 374536 D 318586 CDS YP_918629.1 119387595 4583434 376018..377100 1 NC_008688.1 KEGG: pae:PA4985 spermidine/putrescine transport system substrate-binding protein; spermidine/putrescine transport system substrate-binding protein 377100 4583434 Pden_4873 Paracoccus denitrificans PD1222 spermidine/putrescine transport system substrate-binding protein YP_918629.1 376018 D 318586 CDS YP_918630.1 119387596 4583435 377124..378206 1 NC_008688.1 KEGG: mes:Meso_2369 spermidine/putrescine ABC transporter ATPase subunit; TIGRFAM: spermidine/putrescine ABC transporter ATPase subunit; PFAM: ABC transporter related; Transport-associated OB domain protein; SMART: AAA ATPase; spermidine/putrescine ABC transporter ATPase subunit 378206 4583435 Pden_4874 Paracoccus denitrificans PD1222 spermidine/putrescine ABC transporter ATPase subunit YP_918630.1 377124 D 318586 CDS YP_918631.1 119387597 4583436 378206..379969 1 NC_008688.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: mes:Meso_1937 binding-protein-dependent transport systems inner membrane component; binding-protein-dependent transport systems inner membrane component 379969 4583436 Pden_4875 Paracoccus denitrificans PD1222 binding-protein-dependent transport systems inner membrane component YP_918631.1 378206 D 318586 CDS YP_918632.1 119387598 4583437 379987..380877 1 NC_008688.1 PFAM: dihydrodipicolinate synthetase; KEGG: bbr:BB1108 dihydrodipicolinate synthase; dihydrodipicolinate synthetase 380877 4583437 Pden_4876 Paracoccus denitrificans PD1222 dihydrodipicolinate synthetase YP_918632.1 379987 D 318586 CDS YP_918633.1 119387599 4583438 380890..382029 1 NC_008688.1 PFAM: FMN-dependent alpha-hydroxy acid dehydrogenase; KEGG: bpe:BP1669 lactate dehydrogenase; L-lactate dehydrogenase (cytochrome) 382029 4583438 Pden_4877 Paracoccus denitrificans PD1222 L-lactate dehydrogenase (cytochrome) YP_918633.1 380890 D 318586 CDS YP_918634.1 119387600 4583439 complement(382304..383257) 1 NC_008688.1 PFAM: pyruvate carboxyltransferase; KEGG: jan:Jann_3783 pyruvate carboxyltransferase; pyruvate carboxyltransferase 383257 4583439 Pden_4878 Paracoccus denitrificans PD1222 pyruvate carboxyltransferase YP_918634.1 382304 R 318586 CDS YP_918635.1 119387601 4583440 complement(383259..384446) 1 NC_008688.1 PFAM: L-carnitine dehydratase/bile acid-inducible protein F; KEGG: bja:blr0697 hypothetical protein; L-carnitine dehydratase/bile acid-inducible protein F 384446 4583440 Pden_4879 Paracoccus denitrificans PD1222 L-carnitine dehydratase/bile acid-inducible protein F YP_918635.1 383259 R 318586 CDS YP_918636.1 119387602 4583441 384553..385485 1 NC_008688.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: bja:bll0696 transcriptional regulatory protein; LysR family transcriptional regulator 385485 4583441 Pden_4880 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_918636.1 384553 D 318586 CDS YP_918637.1 119387603 4583442 complement(385533..386534) 1 NC_008688.1 PFAM: Substrate-binding region of ABC-type glycine betaine transport system; KEGG: rpd:RPD_2108 extracellular solute-binding protein, family 3; substrate-binding region of ABC-type glycine betaine transport system 386534 4583442 Pden_4881 Paracoccus denitrificans PD1222 substrate-binding region of ABC-type glycine betaine transport system YP_918637.1 385533 R 318586 CDS YP_918638.1 119387604 4583443 complement(386548..387327) 1 NC_008688.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: bja:bll6487 ABC transporter permease; binding-protein-dependent transport systems inner membrane component 387327 4583443 Pden_4882 Paracoccus denitrificans PD1222 binding-protein-dependent transport systems inner membrane component YP_918638.1 386548 R 318586 CDS YP_918639.1 119387605 4583444 complement(387324..388133) 1 NC_008688.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: bmb:BruAb2_0894 ABC transporter, ATP binding protein; ABC transporter related 388133 4583444 Pden_4883 Paracoccus denitrificans PD1222 ABC transporter related YP_918639.1 387324 R 318586 CDS YP_918640.1 119387606 4583445 complement(388334..388714) 1 NC_008688.1 hypothetical protein 388714 4583445 Pden_4884 Paracoccus denitrificans PD1222 hypothetical protein YP_918640.1 388334 R 318586 CDS YP_918641.1 119387607 4583446 388791..389441 1 NC_008688.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: csa:Csal_2353 binding-protein-dependent transport systems inner membrane component; binding-protein-dependent transport systems inner membrane component 389441 4583446 Pden_4885 Paracoccus denitrificans PD1222 binding-protein-dependent transport systems inner membrane component YP_918641.1 388791 D 318586 CDS YP_918642.1 119387608 4583447 389467..390615 1 NC_008688.1 KEGG: sme:SMa1466 probable ABC transporter ATP binding protein; TIGRFAM: glycine betaine/L-proline ABC transporter, ATPase subunit; PFAM: CBS domain containing protein; ABC transporter related; SMART: AAA ATPase; glycine betaine/L-proline ABC transporter, ATPase subunit 390615 4583447 Pden_4886 Paracoccus denitrificans PD1222 glycine betaine/L-proline ABC transporter, ATPase subunit YP_918642.1 389467 D 318586 CDS YP_918643.1 119387609 4583448 390612..391334 1 NC_008688.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: csa:Csal_2355 binding-protein-dependent transport systems inner membrane component; binding-protein-dependent transport systems inner membrane component 391334 4583448 Pden_4887 Paracoccus denitrificans PD1222 binding-protein-dependent transport systems inner membrane component YP_918643.1 390612 D 318586 CDS YP_918644.1 119387610 4583449 391373..392257 1 NC_008688.1 PFAM: Substrate-binding region of ABC-type glycine betaine transport system; KEGG: csa:Csal_2356 substrate-binding region of ABC-type glycine betaine transport system; substrate-binding region of ABC-type glycine betaine transport system 392257 4583449 Pden_4888 Paracoccus denitrificans PD1222 substrate-binding region of ABC-type glycine betaine transport system YP_918644.1 391373 D 318586 CDS YP_918645.1 119387611 4583450 392278..393198 1 NC_008688.1 PFAM: Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase; KEGG: csa:Csal_2359 nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase; Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase 393198 4583450 Pden_4889 Paracoccus denitrificans PD1222 Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase YP_918645.1 392278 D 318586 CDS YP_918646.1 119387612 4583451 393211..394401 1 NC_008688.1 PFAM: acyl-CoA dehydrogenase domain protein; Acyl-CoA dehydrogenase, type 2, C-terminal domain; KEGG: bxe:Bxe_B1084 butyryl-CoA dehydrogenase; acyl-CoA dehydrogenase 394401 4583451 Pden_4890 Paracoccus denitrificans PD1222 acyl-CoA dehydrogenase YP_918646.1 393211 D 318586 CDS YP_918647.1 119387613 4583452 394418..395980 1 NC_008688.1 PFAM: AMP-dependent synthetase and ligase; KEGG: bce:BC0890 acyl-CoA synthase; AMP-dependent synthetase/ligase 395980 4583452 Pden_4891 Paracoccus denitrificans PD1222 AMP-dependent synthetase/ligase YP_918647.1 394418 D 318586 CDS YP_918648.1 119387614 4583453 395991..397316 1 NC_008688.1 PFAM: MmgE/PrpD family protein; KEGG: csa:Csal_2358 MmgE/PrpD; MmgE/PrpD family protein 397316 4583453 Pden_4892 Paracoccus denitrificans PD1222 MmgE/PrpD family protein YP_918648.1 395991 D 318586 CDS YP_918649.1 119387615 4583454 complement(397338..398360) 1 NC_008688.1 PFAM: helix-turn-helix- domain containing protein, AraC type; ThiJ/PfpI domain protein; KEGG: mlo:mlr6509 transcriptional regulator; AraC family transcriptional regulator 398360 4583454 Pden_4893 Paracoccus denitrificans PD1222 AraC family transcriptional regulator YP_918649.1 397338 R 318586 CDS YP_918650.1 119387616 4583455 complement(398413..399606) 1 NC_008688.1 PFAM: FAD dependent oxidoreductase; KEGG: bxe:Bxe_B0746 oxidoreductase; FAD dependent oxidoreductase 399606 4583455 Pden_4894 Paracoccus denitrificans PD1222 FAD dependent oxidoreductase YP_918650.1 398413 R 318586 CDS YP_918651.1 119387617 4583456 complement(399593..401176) 1 NC_008688.1 PFAM: FAD-dependent pyridine nucleotide-disulphide oxidoreductase; FAD dependent oxidoreductase; BFD domain protein [2Fe-2S]-binding domain protein; KEGG: pol:Bpro_0689 BFD-like (2Fe-2S)-binding region; BFD/(2Fe-2S)-binding domain-containing protein 401176 4583456 Pden_4895 Paracoccus denitrificans PD1222 BFD/(2Fe-2S)-binding domain-containing protein YP_918651.1 399593 R 318586 CDS YP_918652.1 119387618 4583457 complement(401288..402316) 1 NC_008688.1 PFAM: ferredoxin; oxidoreductase FAD/NAD(P)-binding domain protein; Oxidoreductase FAD-binding domain protein; KEGG: mlo:mll5100 ferredoxin [2Fe-2S] I; oxidoreductase FAD/NAD(P)-binding subunit 402316 4583457 Pden_4896 Paracoccus denitrificans PD1222 oxidoreductase FAD/NAD(P)-binding subunit YP_918652.1 401288 R 318586 CDS YP_918653.1 119387619 4583458 complement(402322..403554) 1 NC_008688.1 PFAM: Rieske [2Fe-2S] domain protein; KEGG: ppu:PP_0315 rieske 2Fe-2S family protein; Rieske (2Fe-2S) domain-containing protein 403554 4583458 Pden_4897 Paracoccus denitrificans PD1222 Rieske (2Fe-2S) domain-containing protein YP_918653.1 402322 R 318586 CDS YP_918654.1 119387620 4583459 403708..403959 1 NC_008688.1 hypothetical protein 403959 4583459 Pden_4898 Paracoccus denitrificans PD1222 hypothetical protein YP_918654.1 403708 D 318586 CDS YP_918655.1 119387621 4583460 complement(403962..404570) 1 NC_008688.1 TIGRFAM: alkylhydroperoxidase like protein, AhpD family; uncharacterized peroxidase-related enzyme; PFAM: Carboxymuconolactone decarboxylase; KEGG: bja:bll6900 hypothetical protein; uncharacterized peroxidase-related enzyme 404570 4583460 Pden_4899 Paracoccus denitrificans PD1222 uncharacterized peroxidase-related enzyme YP_918655.1 403962 R 318586 CDS YP_918656.1 119387622 4583461 complement(404580..405149) 1 NC_008688.1 KEGG: bja:bll6901 hypothetical protein; hypothetical protein 405149 4583461 Pden_4900 Paracoccus denitrificans PD1222 hypothetical protein YP_918656.1 404580 R 318586 CDS YP_918657.1 119387623 4583462 complement(405160..406185) 1 NC_008688.1 PFAM: luciferase family protein; KEGG: bja:bll6902 hypothetical protein; luciferase family protein 406185 4583462 Pden_4901 Paracoccus denitrificans PD1222 luciferase family protein YP_918657.1 405160 R 318586 CDS YP_918658.1 119387624 4583463 complement(406182..406913) 1 NC_008688.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: eca:ECA0072 ABC transporter ATP-binding protein; ABC transporter related 406913 4583463 Pden_4902 Paracoccus denitrificans PD1222 ABC transporter related YP_918658.1 406182 R 318586 CDS YP_918659.1 119387625 4583464 complement(406910..407698) 1 NC_008688.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: eca:ECA0073 ABC transporter permease; binding-protein-dependent transport systems inner membrane component 407698 4583464 Pden_4903 Paracoccus denitrificans PD1222 binding-protein-dependent transport systems inner membrane component YP_918659.1 406910 R 318586 CDS YP_918660.1 119387626 4583465 complement(407735..408619) 1 NC_008688.1 produces formate from formyl-tetrahydrofolate which is the major source of formate for PurT in de novo purine nucleotide biosynthesis; has a role in one-carbon metabolism; forms a homohexamer; activated by methionine and inhibited by glycine; formyltetrahydrofolate deformylase 408619 4583465 Pden_4904 Paracoccus denitrificans PD1222 formyltetrahydrofolate deformylase YP_918660.1 407735 R 318586 CDS YP_918661.1 119387627 4583466 complement(408691..409599) 1 NC_008688.1 catalyzes the formation of 5,10-methenyltetrahydrofolate from 5,10-methylenetetrahydrofolate and subsequent formation of 10-formyltetrahydrofolate from 5,10-methenyltetrahydrofolate; bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase 409599 4583466 Pden_4905 Paracoccus denitrificans PD1222 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase YP_918661.1 408691 R 318586 CDS YP_918662.1 119387628 4583467 complement(409602..410168) 1 NC_008688.1 PFAM: Sarcosine oxidase, gamma subunit; KEGG: rde:RD1_0009 sarcosine oxidase, gamma subunit; sarcosine oxidase, gamma subunit 410168 4583467 Pden_4906 Paracoccus denitrificans PD1222 sarcosine oxidase, gamma subunit YP_918662.1 409602 R 318586 CDS YP_918663.1 119387629 4583468 complement(410161..413091) 1 NC_008688.1 TIGRFAM: sarcosine oxidase, alpha subunit family; PFAM: glycine cleavage T protein (aminomethyl transferase); FAD-dependent pyridine nucleotide-disulphide oxidoreductase; Glycine cleavage T-protein, C-terminal barrel; KEGG: sit:TM1040_3377 sarcosine oxidase, alpha subunit family; sarcosine oxidase alpha subunit family protein 413091 4583468 Pden_4907 Paracoccus denitrificans PD1222 sarcosine oxidase alpha subunit family protein YP_918663.1 410161 R 318586 CDS YP_918664.1 119387630 4583469 complement(413088..413402) 1 NC_008688.1 PFAM: Sarcosine oxidase, delta subunit, heterotetrameric; KEGG: rde:RD1_0011 sarcosine oxidase, delta subunit; sarcosine oxidase, delta subunit, heterotetrameric 413402 4583469 Pden_4908 Paracoccus denitrificans PD1222 sarcosine oxidase, delta subunit, heterotetrameric YP_918664.1 413088 R 318586 CDS YP_918665.1 119387631 4583470 complement(413380..414630) 1 NC_008688.1 TIGRFAM: sarcosine oxidase, beta subunit family; PFAM: FAD dependent oxidoreductase; KEGG: sit:TM1040_3375 sarcosine oxidase, beta subunit family; sarcosine oxidase beta subunit family protein 414630 4583470 Pden_4909 Paracoccus denitrificans PD1222 sarcosine oxidase beta subunit family protein YP_918665.1 413380 R 318586 CDS YP_918666.1 119387632 4583471 414756..415922 1 NC_008688.1 PFAM: helix-turn-helix- domain containing protein, AraC type; ThiJ/PfpI domain protein; KEGG: mlo:mlr6241 transcription regulator; AraC family transcriptional regulator 415922 4583471 Pden_4910 Paracoccus denitrificans PD1222 AraC family transcriptional regulator YP_918666.1 414756 D 318586 CDS YP_918667.1 119387633 4583472 complement(416120..417121) 1 NC_008688.1 KEGG: bbr:BB1042 extracellular solute-binding protein; extracellular solute-binding protein 417121 4583472 Pden_4911 Paracoccus denitrificans PD1222 extracellular solute-binding protein YP_918667.1 416120 R 318586 CDS YP_918668.1 119387634 4583473 complement(417208..418851) 1 NC_008688.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: bbr:BB1044 inner membrane component of ABC transporter; binding-protein-dependent transport systems inner membrane component 418851 4583473 Pden_4912 Paracoccus denitrificans PD1222 binding-protein-dependent transport systems inner membrane component YP_918668.1 417208 R 318586 CDS YP_918669.1 119387635 4583474 complement(418848..419909) 1 NC_008688.1 PFAM: ABC transporter related; Transport-associated OB domain protein; SMART: AAA ATPase; KEGG: bbr:BB1043 ATP-binding component of ABC transporter; ABC transporter related 419909 4583474 Pden_4913 Paracoccus denitrificans PD1222 ABC transporter related YP_918669.1 418848 R 318586 CDS YP_918670.1 119387636 4583475 complement(419938..420747) 1 NC_008688.1 PFAM: inositol monophosphatase; KEGG: sme:SMa0483 inositol monophosphatase; inositol monophosphatase 420747 4583475 Pden_4914 Paracoccus denitrificans PD1222 inositol monophosphatase YP_918670.1 419938 R 318586 CDS YP_918671.1 119387637 4583476 421058..421840 1 NC_008688.1 PFAM: regulatory protein, DeoR; Helix-turn-helix, type 11 domain protein; KEGG: bxe:Bxe_A4204 transcriptional regulator, DeoR family; DeoR family transcriptional regulator 421840 4583476 Pden_4915 Paracoccus denitrificans PD1222 DeoR family transcriptional regulator YP_918671.1 421058 D 318586 CDS YP_918672.1 119387638 4583477 complement(421864..424311) 1 NC_008688.1 PFAM: FAD dependent oxidoreductase; glycine cleavage T protein (aminomethyl transferase); Glycine cleavage T-protein, C-terminal barrel; KEGG: sme:SMc01662 sarcosine dehydrogenase; FAD dependent oxidoreductase 424311 4583477 Pden_4916 Paracoccus denitrificans PD1222 FAD dependent oxidoreductase YP_918672.1 421864 R 318586 CDS YP_918673.1 119387639 4583478 424551..425105 1 NC_008688.1 PFAM: helix-turn-helix domain protein; Cupin 2, conserved barrel domain protein; KEGG: sil:SPO3403 DNA-binding protein; XRE family transcriptional regulator 425105 4583478 Pden_4917 Paracoccus denitrificans PD1222 XRE family transcriptional regulator YP_918673.1 424551 D 318586 CDS YP_918674.1 119387640 4583479 complement(425252..425728) 1 NC_008688.1 KEGG: rru:Rru_B0014 transposase, mutator type; hypothetical protein 425728 4583479 Pden_4918 Paracoccus denitrificans PD1222 hypothetical protein YP_918674.1 425252 R 318586 CDS YP_918675.1 119387641 4583480 425785..426534 1 NC_008688.1 catalyzes the removal of N-terminal amino acids from peptides and arylamides; generally Co(II) however activity has been shown for some methionine aminopeptidases with Zn, Fe, or Mnin Bacillus subtilis the protein in this cluster is considered non-essential; methionine aminopeptidase 426534 4583480 Pden_4919 Paracoccus denitrificans PD1222 methionine aminopeptidase YP_918675.1 425785 D 318586 CDS YP_918676.1 119387642 4583481 426820..427398 1 NC_008688.1 KEGG: vvy:VV0790 hypothetical protein; hypothetical protein 427398 4583481 Pden_4920 Paracoccus denitrificans PD1222 hypothetical protein YP_918676.1 426820 D 318586 CDS YP_918677.1 119387643 4583482 complement(427353..428321) 1 NC_008688.1 PFAM: alpha/beta hydrolase fold; KEGG: lbl:LBL_2370 hydrolase; alpha/beta hydrolase 428321 4583482 Pden_4921 Paracoccus denitrificans PD1222 alpha/beta hydrolase YP_918677.1 427353 R 318586 CDS YP_918678.1 119387644 4583483 complement(428408..429511) 1 NC_008688.1 KEGG: gox:GOX0022 hypothetical protein; hypothetical protein 429511 4583483 Pden_4922 Paracoccus denitrificans PD1222 hypothetical protein YP_918678.1 428408 R 318586 CDS YP_918679.1 119387645 4583484 complement(429786..430586) 1 NC_008688.1 PFAM: regulatory proteins, IclR; KEGG: bam:Bamb_0518 transcriptional regulator, IclR family; regulatory proteins, IclR 430586 4583484 Pden_4923 Paracoccus denitrificans PD1222 regulatory proteins, IclR YP_918679.1 429786 R 318586 CDS YP_918680.1 119387646 4583485 430779..431534 1 NC_008688.1 TIGRFAM: polar amino acid ABC transporter, inner membrane subunit; PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: rfr:Rfer_1032 amino acid ABC transporter, permease, 3-TM region, His/Glu/Gln/Arg/opine; polar amino acid ABC transporter, inner membrane subunit 431534 4583485 Pden_4924 Paracoccus denitrificans PD1222 polar amino acid ABC transporter, inner membrane subunit YP_918680.1 430779 D 318586 CDS YP_918681.1 119387647 4583486 431545..432189 1 NC_008688.1 TIGRFAM: polar amino acid ABC transporter, inner membrane subunit; PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: rfr:Rfer_1031 amino acid ABC transporter, permease, 3-TM region, His/Glu/Gln/Arg/opine; polar amino acid ABC transporter, inner membrane subunit 432189 4583486 Pden_4925 Paracoccus denitrificans PD1222 polar amino acid ABC transporter, inner membrane subunit YP_918681.1 431545 D 318586 CDS YP_918682.1 119387648 4583487 432173..432907 1 NC_008688.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: mes:Meso_3975 ABC transporter related; ABC transporter related 432907 4583487 Pden_4926 Paracoccus denitrificans PD1222 ABC transporter related YP_918682.1 432173 D 318586 CDS YP_918683.1 119387649 4583488 432970..433770 1 NC_008688.1 PFAM: extracellular solute-binding protein, family 3; KEGG: rfr:Rfer_1029 extracellular solute-binding protein, family 3; extracellular solute-binding protein 433770 4583488 Pden_4927 Paracoccus denitrificans PD1222 extracellular solute-binding protein YP_918683.1 432970 D 318586 CDS YP_918684.1 119387650 4583489 433821..435347 1 NC_008688.1 PFAM: D-galactarate dehydratase/Altronate hydrolase domain protein; SAF domain; KEGG: rfr:Rfer_1027 galactarate dehydratase; galactarate dehydratase 435347 4583489 Pden_4928 Paracoccus denitrificans PD1222 galactarate dehydratase YP_918684.1 433821 D 318586 CDS YP_918685.1 119387651 4583490 435375..436289 1 NC_008688.1 PFAM: 2-keto-3-deoxy-galactonokinase; KEGG: ret:RHE_CH00854 2-dehydro-3-deoxygalactonokinase; 2-keto-3-deoxy-galactonokinase 436289 4583490 Pden_4929 Paracoccus denitrificans PD1222 2-keto-3-deoxy-galactonokinase YP_918685.1 435375 D 318586 CDS YP_918686.1 119387652 4583491 436286..436948 1 NC_008688.1 catalyzes the formation of D-glyceraldehyde 3-phosphate and pyruvate from 2-dehydro-3-deoxy-D-galactonate 6-phosphate; functions in galactonate metabolism; 2-dehydro-3-deoxy-6-phosphogalactonate aldolase 436948 4583491 Pden_4930 Paracoccus denitrificans PD1222 2-dehydro-3-deoxy-6-phosphogalactonate aldolase YP_918686.1 436286 D 318586 CDS YP_918687.1 119387653 4583492 437007..438020 1 NC_008688.1 PFAM: Alcohol dehydrogenase, zinc-binding domain protein; Alcohol dehydrogenase GroES domain protein; KEGG: bth:BT3617 sorbitol dehydrogenase; alcohol dehydrogenase 438020 4583492 Pden_4931 Paracoccus denitrificans PD1222 alcohol dehydrogenase YP_918687.1 437007 D 318586 CDS YP_918688.1 119387654 4583493 438017..438784 1 NC_008688.1 PFAM: short-chain dehydrogenase/reductase SDR; KR; KEGG: mmr:Mmar10_0232 2-deoxy-D-gluconate 3-dehydrogenase; short-chain dehydrogenase/reductase SDR 438784 4583493 Pden_4932 Paracoccus denitrificans PD1222 short-chain dehydrogenase/reductase SDR YP_918688.1 438017 D 318586 CDS YP_918689.1 119387655 4583494 complement(438858..439418) 1 NC_008688.1 KEGG: sme:SMa2229 hypothetical protein; hypothetical protein 439418 4583494 Pden_4933 Paracoccus denitrificans PD1222 hypothetical protein YP_918689.1 438858 R 318586 CDS YP_918690.1 119387656 4583495 complement(439421..440803) 1 NC_008688.1 PFAM: BFD domain protein [2Fe-2S]-binding domain protein; FAD-dependent pyridine nucleotide-disulphide oxidoreductase; KEGG: sme:SMa2225 opine oxidase subunit; BFD/(2Fe-2S)-binding domain-containing protein 440803 4583495 Pden_4934 Paracoccus denitrificans PD1222 BFD/(2Fe-2S)-binding domain-containing protein YP_918690.1 439421 R 318586 CDS YP_918691.1 119387657 4583496 complement(440800..441114) 1 NC_008688.1 KEGG: bxe:Bxe_B2707 hypothetical protein; hypothetical protein 441114 4583496 Pden_4935 Paracoccus denitrificans PD1222 hypothetical protein YP_918691.1 440800 R 318586 CDS YP_918692.1 119387658 4583497 complement(441095..442210) 1 NC_008688.1 PFAM: FAD dependent oxidoreductase; KEGG: sme:SMa2223 opine oxidase subunit; FAD dependent oxidoreductase 442210 4583497 Pden_4936 Paracoccus denitrificans PD1222 FAD dependent oxidoreductase YP_918692.1 441095 R 318586 CDS YP_918693.1 119387659 4583498 complement(442207..442920) 1 NC_008688.1 KEGG: sme:SMa2221 hypothetical protein; hypothetical protein 442920 4583498 Pden_4937 Paracoccus denitrificans PD1222 hypothetical protein YP_918693.1 442207 R 318586 CDS YP_918694.1 119387660 4583499 complement(442917..443510) 1 NC_008688.1 TIGRFAM: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; PFAM: flavoprotein; KEGG: sme:SMa2219 probable decarboxylase; 3-octaprenyl-4-hydroxybenzoate carboxy-lyase 443510 4583499 Pden_4938 Paracoccus denitrificans PD1222 3-octaprenyl-4-hydroxybenzoate carboxy-lyase YP_918694.1 442917 R 318586 CDS YP_918695.1 119387661 4583500 complement(443512..444843) 1 NC_008688.1 TIGRFAM: UbiD family decarboxylases; PFAM: Carboxylyase-related protein; KEGG: sme:SMa2217 decarboxylase; UbiD family decarboxylase 444843 4583500 Pden_4939 Paracoccus denitrificans PD1222 UbiD family decarboxylase YP_918695.1 443512 R 318586 CDS YP_918696.1 119387662 4583501 complement(444877..445641) 1 NC_008688.1 TIGRFAM: histidine utilization repressor; PFAM: regulatory protein GntR, HTH; UbiC transcription regulator-associated domain protein; KEGG: sme:SMa2215 GntR-family transcriptional regulator; histidine utilization repressor 445641 4583501 Pden_4940 Paracoccus denitrificans PD1222 histidine utilization repressor YP_918696.1 444877 R 318586 CDS YP_918697.1 119387663 4583502 445920..447416 1 NC_008688.1 PFAM: aldehyde dehydrogenase; KEGG: sme:SMA2213 aldehyde; betaine-aldehyde dehydrogenase 447416 4583502 Pden_4941 Paracoccus denitrificans PD1222 betaine-aldehyde dehydrogenase YP_918697.1 445920 D 318586 CDS YP_918698.1 119387664 4583503 447413..449116 1 NC_008688.1 catalyzes the formation of 2-acetolactate from pyruvate, leucine sensitive; also known as acetolactate synthase large subunit; thiamine pyrophosphate protein 449116 4583503 Pden_4942 Paracoccus denitrificans PD1222 thiamine pyrophosphate protein YP_918698.1 447413 D 318586 CDS YP_918699.1 119387665 4583504 449214..450236 1 NC_008688.1 PFAM: extracellular solute-binding protein, family 1; KEGG: sme:SMa2209 ABC transporter, periplasmic solute-binding protein; extracellular solute-binding protein 450236 4583504 Pden_4943 Paracoccus denitrificans PD1222 extracellular solute-binding protein YP_918699.1 449214 D 318586 CDS YP_918700.1 119387666 4583505 450315..451409 1 NC_008688.1 PFAM: ABC transporter related; TOBE domain protein; Transport-associated OB domain protein; SMART: AAA ATPase; KEGG: sme:SMa2207 ABC transporter, ATP-binding protein; ABC transporter related 451409 4583505 Pden_4944 Paracoccus denitrificans PD1222 ABC transporter related YP_918700.1 450315 D 318586 CDS YP_918701.1 119387667 4583506 451413..452273 1 NC_008688.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: sme:SMa2205 ABC transporter, permease; binding-protein-dependent transport systems inner membrane component 452273 4583506 Pden_4945 Paracoccus denitrificans PD1222 binding-protein-dependent transport systems inner membrane component YP_918701.1 451413 D 318586 CDS YP_918702.1 119387668 4583507 452270..453064 1 NC_008688.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: sme:SMa2203 ABC transporter, permease; binding-protein-dependent transport systems inner membrane component 453064 4583507 Pden_4946 Paracoccus denitrificans PD1222 binding-protein-dependent transport systems inner membrane component YP_918702.1 452270 D 318586 CDS YP_918703.1 119387669 4583508 453396..453593 1 NC_008688.1 PFAM: protein of unknown function DUF1127; KEGG: rde:RD1_2086 hypothetical protein; hypothetical protein 453593 4583508 Pden_4947 Paracoccus denitrificans PD1222 hypothetical protein YP_918703.1 453396 D 318586 CDS YP_918704.1 119387670 4583509 complement(453745..454716) 1 NC_008688.1 hypothetical protein 454716 4583509 Pden_4948 Paracoccus denitrificans PD1222 hypothetical protein YP_918704.1 453745 R 318586 CDS YP_918705.1 119387671 4583510 complement(454856..455650) 1 NC_008688.1 PFAM: protein of unknown function DUF72; KEGG: rsp:RSP_0939 hypothetical protein; hypothetical protein 455650 4583510 Pden_4949 Paracoccus denitrificans PD1222 hypothetical protein YP_918705.1 454856 R 318586 CDS YP_918706.1 119387672 4583511 455680..455967 1 NC_008688.1 hypothetical protein 455967 4583511 Pden_4950 Paracoccus denitrificans PD1222 hypothetical protein YP_918706.1 455680 D 318586 CDS YP_918707.1 119387673 4583512 complement(455943..457997) 1 NC_008688.1 PFAM: NADH:flavin oxidoreductase/NADH oxidase; FAD-dependent pyridine nucleotide-disulphide oxidoreductase; HI0933 family protein; KEGG: mlo:mlr8292 probable N-methylproline demethylase (stahydrine utilization protein StcD); NADH:flavin oxidoreductase/NADH oxidase 457997 4583512 Pden_4951 Paracoccus denitrificans PD1222 NADH:flavin oxidoreductase/NADH oxidase YP_918707.1 455943 R 318586 CDS YP_918708.1 119387674 4583513 complement(458149..459108) 1 NC_008688.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: bja:blr6829 transcriptional regulatory protein; LysR family transcriptional regulator 459108 4583513 Pden_4952 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_918708.1 458149 R 318586 CDS YP_918709.1 119387675 4583514 complement(459163..460233) 1 NC_008688.1 PFAM: ammonia monooxygenase; KEGG: rsp:RSP_7367 AbrB protein (AidB regulator); ammonia monooxygenase 460233 4583514 Pden_4953 Paracoccus denitrificans PD1222 ammonia monooxygenase YP_918709.1 459163 R 318586 CDS YP_918710.1 119387676 4583515 460383..461261 1 NC_008688.1 KEGG: ret:RHE_PF00334 acetyltransferase; acetyltransferase 461261 4583515 Pden_4954 Paracoccus denitrificans PD1222 acetyltransferase YP_918710.1 460383 D 318586 CDS YP_918711.1 119387677 4583516 complement(461312..462640) 1 NC_008688.1 PFAM: FAD dependent oxidoreductase; FAD-dependent pyridine nucleotide-disulphide oxidoreductase; KEGG: atc:AGR_L_1801 deaminase; FAD dependent oxidoreductase 462640 4583516 Pden_4955 Paracoccus denitrificans PD1222 FAD dependent oxidoreductase YP_918711.1 461312 R 318586 CDS YP_918712.1 119387678 4583517 complement(462656..463975) 1 NC_008688.1 PFAM: FAD dependent oxidoreductase; KEGG: ret:RHE_PF00361 probable deaminase; FAD dependent oxidoreductase 463975 4583517 Pden_4956 Paracoccus denitrificans PD1222 FAD dependent oxidoreductase YP_918712.1 462656 R 318586 CDS YP_918713.1 119387679 4583518 464212..464688 1 NC_008688.1 PFAM: regulatory protein, AsnC/Lrp family; KEGG: ret:RHE_PF00360 probable transcriptional regulator protein (leucine-responsive), AsnC family; AsnC family transcriptional regulator 464688 4583518 Pden_4957 Paracoccus denitrificans PD1222 AsnC family transcriptional regulator YP_918713.1 464212 D 318586 CDS YP_918714.1 119387680 4583519 complement(464707..466368) 1 NC_008688.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sme:SMa1864 ABC transporter, ATP-binding protein; ABC transporter related 466368 4583519 Pden_4958 Paracoccus denitrificans PD1222 ABC transporter related YP_918714.1 464707 R 318586 CDS YP_918715.1 119387681 4583520 complement(466368..467210) 1 NC_008688.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: ret:RHE_PF00353 probable oligopeptide ABC transporter, permease; binding-protein-dependent transport systems inner membrane component 467210 4583520 Pden_4959 Paracoccus denitrificans PD1222 binding-protein-dependent transport systems inner membrane component YP_918715.1 466368 R 318586 CDS YP_918716.1 119387682 4583521 complement(467210..468163) 1 NC_008688.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: sme:SMa1862 ABC transporter, permease; binding-protein-dependent transport systems inner membrane component 468163 4583521 Pden_4960 Paracoccus denitrificans PD1222 binding-protein-dependent transport systems inner membrane component YP_918716.1 467210 R 318586 CDS YP_918717.1 119387683 4583522 complement(468219..469832) 1 NC_008688.1 PFAM: extracellular solute-binding protein, family 5; KEGG: ret:RHE_PF00351 probable oligopeptide ABC transporter, substrate-binding protein; extracellular solute-binding protein 469832 4583522 Pden_4961 Paracoccus denitrificans PD1222 extracellular solute-binding protein YP_918717.1 468219 R 318586 CDS YP_918718.1 119387684 4583523 complement(469890..470690) 1 NC_008688.1 TIGRFAM: HAD-superfamily hydrolase, subfamily IA, variant 2 (HAD-like); PFAM: Haloacid dehalogenase domain protein hydrolase; KEGG: atc:AGR_L_2827 hypothetical protein; HAD family hydrolase 470690 4583523 Pden_4962 Paracoccus denitrificans PD1222 HAD family hydrolase YP_918718.1 469890 R 318586 CDS YP_918719.1 119387685 4583524 complement(470825..471739) 1 NC_008688.1 PFAM: D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding; KEGG: mlo:mll7048 probable dehydrogenase; D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding 471739 4583524 Pden_4963 Paracoccus denitrificans PD1222 D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding YP_918719.1 470825 R 318586 CDS YP_918720.1 119387686 4583525 complement(471739..473115) 1 NC_008688.1 PFAM: aminotransferase class-III; KEGG: sme:SMa1855 hypothetical protein; hypothetical protein 473115 4583525 Pden_4964 Paracoccus denitrificans PD1222 hypothetical protein YP_918720.1 471739 R 318586 CDS YP_918721.1 119387687 4583526 complement(473133..473966) 1 NC_008688.1 PFAM: GCN5-related N-acetyltransferase; KEGG: atc:AGR_L_2832 hypothetical protein; GCN5-related N-acetyltransferase 473966 4583526 Pden_4965 Paracoccus denitrificans PD1222 GCN5-related N-acetyltransferase YP_918721.1 473133 R 318586 CDS YP_918722.1 119387688 4583527 complement(474080..474433) 1 NC_008688.1 PFAM: protein of unknown function DUF861, cupin_3; KEGG: mlo:mll7047 hypothetical protein; hypothetical protein 474433 4583527 Pden_4966 Paracoccus denitrificans PD1222 hypothetical protein YP_918722.1 474080 R 318586 CDS YP_918723.1 119387689 4583528 complement(474442..475719) 1 NC_008688.1 PFAM: FAD dependent oxidoreductase; KEGG: mlo:mlr7042 probable oxidoreductase; FAD dependent oxidoreductase 475719 4583528 Pden_4967 Paracoccus denitrificans PD1222 FAD dependent oxidoreductase YP_918723.1 474442 R 318586 CDS YP_918724.1 119387690 4583529 complement(475722..476426) 1 NC_008688.1 TIGRFAM: haloacid dehalogenase, type II; HAD-superfamily hydrolase, subfamily IA, variant 2 (HAD-like); PFAM: Haloacid dehalogenase domain protein hydrolase; KEGG: ret:RHE_PF00342 probable dehalogenase; haloacid dehalogenase 476426 4583529 Pden_4968 Paracoccus denitrificans PD1222 haloacid dehalogenase YP_918724.1 475722 R 318586 CDS YP_918725.1 119387691 4583530 complement(476532..477980) 1 NC_008688.1 KEGG: sme:SMa1848 GabD5 succinate semialdehyde dehdyrogenase; TIGRFAM: succinic semialdehyde dehydrogenase; PFAM: aldehyde dehydrogenase; succinic semialdehyde dehydrogenase 477980 4583530 Pden_4969 Paracoccus denitrificans PD1222 succinic semialdehyde dehydrogenase YP_918725.1 476532 R 318586 CDS YP_918726.1 119387692 4583531 complement(477977..479017) 1 NC_008688.1 catalyzes the oxidation of 3-isopropylmalate to 3-carboxy-4-methyl-2-oxopentanoate in leucine biosynthesis; 3-isopropylmalate dehydrogenase 479017 4583531 Pden_4970 Paracoccus denitrificans PD1222 3-isopropylmalate dehydrogenase YP_918726.1 477977 R 318586 CDS YP_918727.1 119387693 4583532 complement(479029..480492) 1 NC_008688.1 PFAM: aldehyde dehydrogenase; KEGG: ret:RHE_PF00338 probable aldehyde dehydrogenase; aldehyde dehydrogenase 480492 4583532 Pden_4971 Paracoccus denitrificans PD1222 aldehyde dehydrogenase YP_918727.1 479029 R 318586 CDS YP_918728.1 119387694 4583533 complement(480618..481538) 1 NC_008688.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: mlo:mlr7023 transcriptional regulator; LysR family transcriptional regulator 481538 4583533 Pden_4972 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_918728.1 480618 R 318586 CDS YP_918729.1 119387695 4583534 complement(481546..483504) 1 NC_008688.1 PFAM: Hydantoinase B/oxoprolinase; KEGG: bpe:BP0821 hydantoin utilization protein B; 5-oxoprolinase 483504 4583534 Pden_4973 Paracoccus denitrificans PD1222 5-oxoprolinase YP_918729.1 481546 R 318586 CDS YP_918730.1 119387696 4583535 complement(483508..485547) 1 NC_008688.1 PFAM: Hydantoinase/oxoprolinase; Hydantoinaseoxoprolinase domain protein; KEGG: bbr:BB3858 hydantoin utilization protein A; 5-oxoprolinase 485547 4583535 Pden_4974 Paracoccus denitrificans PD1222 5-oxoprolinase YP_918730.1 483508 R 318586 CDS YP_918731.1 119387697 4583536 complement(485636..486100) 1 NC_008688.1 PFAM: GCN5-related N-acetyltransferase; KEGG: vpa:VP2001 hypothetical protein; GCN5-related N-acetyltransferase 486100 4583536 Pden_4975 Paracoccus denitrificans PD1222 GCN5-related N-acetyltransferase YP_918731.1 485636 R 318586 CDS YP_918732.1 119387698 4583537 486259..487389 1 NC_008688.1 catalyzes the formation of L-ornithine from N(2)-acetyl-L-ornithine; acetylornithine deacetylase 487389 4583537 Pden_4976 Paracoccus denitrificans PD1222 acetylornithine deacetylase YP_918732.1 486259 D 318586 CDS YP_918733.1 119387699 4583538 487592..487843 1 NC_008688.1 hypothetical protein 487843 4583538 Pden_4977 Paracoccus denitrificans PD1222 hypothetical protein YP_918733.1 487592 D 318586 CDS YP_918734.1 119387700 4583539 487868..489118 1 NC_008688.1 KEGG: pfa:PF10_0374 gene 11-1 protein precursor; hypothetical protein 489118 4583539 Pden_4978 Paracoccus denitrificans PD1222 hypothetical protein YP_918734.1 487868 D 318586 CDS YP_918735.1 119387701 4583540 complement(489237..491096) 1 NC_008688.1 PFAM: sigma-54 factor, interaction domain-containing protein; helix-turn-helix, Fis-type; GAF domain protein; ATPase associated with various cellular activities, AAA_5; SMART: AAA ATPase; KEGG: sil:SPO3788 acetoin catabolism regulatory protein; Fis family GAF modulated sigma54 specific transcriptional regulator 491096 4583540 Pden_4979 Paracoccus denitrificans PD1222 Fis family GAF modulated sigma54 specific transcriptional regulator YP_918735.1 489237 R 318586 CDS YP_918736.1 119387702 4583541 complement(491175..492248) 1 NC_008688.1 PFAM: Alcohol dehydrogenase, zinc-binding domain protein; Alcohol dehydrogenase GroES domain protein; KEGG: atc:AGR_L_281 hypothetical protein; alcohol dehydrogenase 492248 4583541 Pden_4980 Paracoccus denitrificans PD1222 alcohol dehydrogenase YP_918736.1 491175 R 318586 CDS YP_918737.1 119387703 4583542 complement(492258..492587) 1 NC_008688.1 TIGRFAM: alkylhydroperoxidase like protein, AhpD family; PFAM: Carboxymuconolactone decarboxylase; KEGG: sil:SPO3789 4-carboxymuconolactone decarboxylase domain/alkylhydroperoxidase AhpD family core domain protein; alkylhydroperoxidase 492587 4583542 Pden_4981 Paracoccus denitrificans PD1222 alkylhydroperoxidase YP_918737.1 492258 R 318586 CDS YP_918738.1 119387704 4583543 complement(492584..493372) 1 NC_008688.1 PFAM: NAD-dependent epimerase/dehydratase; short-chain dehydrogenase/reductase SDR; KR; KEGG: rha:RHA1_ro05279 acetoin dehydrogenase; short-chain dehydrogenase/reductase SDR 493372 4583543 Pden_4982 Paracoccus denitrificans PD1222 short-chain dehydrogenase/reductase SDR YP_918738.1 492584 R 318586 CDS YP_918739.1 119387705 4583544 complement(493422..494525) 1 NC_008688.1 PFAM: alpha/beta hydrolase fold; biotin/lipoyl attachment domain-containing protein; PGAP1 family protein; KEGG: sil:SPO3790 dihydrolipoamide acetyltransferase; branched-chain alpha-keto acid dehydrogenase subunit E2 494525 4583544 Pden_4983 Paracoccus denitrificans PD1222 branched-chain alpha-keto acid dehydrogenase subunit E2 YP_918739.1 493422 R 318586 CDS YP_918740.1 119387706 4583545 complement(494527..495534) 1 NC_008688.1 PFAM: Transketolase, central region; Transketolase domain protein; KEGG: sil:SPO3791 acetoin dehydrogenase complex, E1 component, beta subunit; transketolase, central region 495534 4583545 Pden_4984 Paracoccus denitrificans PD1222 transketolase, central region YP_918740.1 494527 R 318586 CDS YP_918741.1 119387707 4583546 complement(495557..496534) 1 NC_008688.1 PFAM: dehydrogenase, E1 component; KEGG: sil:SPO3792 acetoin dehydrogenase complex, E1 component, alpha subunit; pyruvate dehydrogenase (acetyl-transferring) 496534 4583546 Pden_4985 Paracoccus denitrificans PD1222 pyruvate dehydrogenase (acetyl-transferring) YP_918741.1 495557 R 318586 CDS YP_918742.1 119387708 4583547 complement(496555..497568) 1 NC_008688.1 PFAM: ATP-NAD/AcoX kinase; KEGG: sil:SPO3793 acetoin catabolism protein X; ATP-NAD/AcoX kinase 497568 4583547 Pden_4986 Paracoccus denitrificans PD1222 ATP-NAD/AcoX kinase YP_918742.1 496555 R 318586 CDS YP_918743.1 119387709 4583548 497659..498849 1 NC_008688.1 PFAM: sigma-54 factor, core-binding region; sigma-54, DNA-binding domain protein; KEGG: sil:SPO3795 RNA polymerase sigma-54 factor; RNA polymerase, sigma 54 subunit, RpoN 498849 4583548 Pden_4987 Paracoccus denitrificans PD1222 RNA polymerase, sigma 54 subunit, RpoN YP_918743.1 497659 D 318586 CDS YP_918744.1 119387710 4583549 complement(498993..500036) 1 NC_008688.1 PFAM: protein of unknown function UPF0118; KEGG: bms:BRA0460 hypothetical protein; hypothetical protein 500036 4583549 Pden_4988 Paracoccus denitrificans PD1222 hypothetical protein YP_918744.1 498993 R 318586 CDS YP_918745.1 119387711 4583550 complement(500225..500854) 1 NC_008688.1 PFAM: DSBA oxidoreductase; KEGG: sil:SPOA0362 27kDa outer membrane protein; Fis family transcriptional regulator 500854 4583550 Pden_4989 Paracoccus denitrificans PD1222 Fis family transcriptional regulator YP_918745.1 500225 R 318586 CDS YP_918746.1 119387712 4583551 complement(500906..501400) 1 NC_008688.1 PFAM: ErfK/YbiS/YcfS/YnhG family protein; KEGG: rsp:RSP_3073 ErfK/YbiS/YcfS/YnhG family protein; ErfK/YbiS/YcfS/YnhG family protein 501400 4583551 Pden_4990 Paracoccus denitrificans PD1222 ErfK/YbiS/YcfS/YnhG family protein YP_918746.1 500906 R 318586 CDS YP_918747.1 119387713 4583552 complement(502213..503199) 1 NC_008688.1 PFAM: Alcohol dehydrogenase, zinc-binding domain protein; Alcohol dehydrogenase GroES domain protein; KEGG: rfr:Rfer_1643 alcohol dehydrogenase, zinc-binding; alcohol dehydrogenase 503199 4583552 Pden_4991 Paracoccus denitrificans PD1222 alcohol dehydrogenase YP_918747.1 502213 R 318586 CDS YP_918748.1 119387714 4583553 complement(503222..504040) 1 NC_008688.1 PFAM: Enoyl-CoA hydratase/isomerase; KEGG: mes:Meso_1938 enoyl-CoA hydratase/isomerase; enoyl-CoA hydratase/isomerase 504040 4583553 Pden_4992 Paracoccus denitrificans PD1222 enoyl-CoA hydratase/isomerase YP_918748.1 503222 R 318586 CDS YP_918749.1 119387715 4583554 complement(504070..505269) 1 NC_008688.1 PFAM: major facilitator superfamily MFS_1; KEGG: mmr:Mmar10_2043 major facilitator superfamily MFS_1; major facilitator transporter 505269 4583554 Pden_4993 Paracoccus denitrificans PD1222 major facilitator transporter YP_918749.1 504070 R 318586 CDS YP_918750.1 119387716 4583555 complement(505308..506510) 1 NC_008688.1 PFAM: Extracellular ligand-binding receptor; KEGG: sit:TM1040_2237 extracellular ligand-binding receptor; extracellular ligand-binding receptor 506510 4583555 Pden_4994 Paracoccus denitrificans PD1222 extracellular ligand-binding receptor YP_918750.1 505308 R 318586 CDS YP_918751.1 119387717 4583556 complement(506611..507375) 1 NC_008688.1 PFAM: regulatory protein GntR, HTH; GntR domain protein; KEGG: sil:SPO2543 transcriptional regulator, GntR family; GntR family transcriptional regulator 507375 4583556 Pden_4995 Paracoccus denitrificans PD1222 GntR family transcriptional regulator YP_918751.1 506611 R 318586 CDS YP_918752.1 119387718 4583557 complement(507372..509489) 1 NC_008688.1 PFAM: CoA-binding domain protein; ATP-grasp domain protein; KEGG: sma:SAV1821 acyl-CoA synthetase (NDP forming type); CoA-binding domain-containing protein 509489 4583557 Pden_4996 Paracoccus denitrificans PD1222 CoA-binding domain-containing protein YP_918752.1 507372 R 318586 CDS YP_918753.1 119387719 4583558 complement(509578..510285) 1 NC_008688.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rfr:Rfer_2387 ABC transporter related; ABC transporter related 510285 4583558 Pden_4997 Paracoccus denitrificans PD1222 ABC transporter related YP_918753.1 509578 R 318586 CDS YP_918754.1 119387720 4583559 complement(510282..511034) 1 NC_008688.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: tth:TTC0969 branched-chain amino acid transport ATP-binding protein livG; ABC transporter related 511034 4583559 Pden_4998 Paracoccus denitrificans PD1222 ABC transporter related YP_918754.1 510282 R 318586 CDS YP_918755.1 119387721 4583560 complement(511031..512032) 1 NC_008688.1 PFAM: inner-membrane translocator; KEGG: reu:Reut_C6328 inner-membrane translocator; inner-membrane translocator 512032 4583560 Pden_4999 Paracoccus denitrificans PD1222 inner-membrane translocator YP_918755.1 511031 R 318586 CDS YP_918756.1 119387722 4583561 complement(512029..512994) 1 NC_008688.1 PFAM: inner-membrane translocator; KEGG: bja:bll6235 ABC transporter permease; inner-membrane translocator 512994 4583561 Pden_5000 Paracoccus denitrificans PD1222 inner-membrane translocator YP_918756.1 512029 R 318586 CDS YP_918757.1 119387723 4583562 complement(513391..513969) 1 NC_008688.1 PFAM: HupE/UreJ protein; KEGG: pfo:Pfl_0560 HupE/UreJ protein; HupE/UreJ protein 513969 4583562 Pden_5001 Paracoccus denitrificans PD1222 HupE/UreJ protein YP_918757.1 513391 R 318586 CDS YP_918758.1 119387724 4583563 complement(514015..514329) 1 NC_008688.1 SMART: Rhodanese domain protein; rhodanese domain-containing protein 514329 4583563 Pden_5002 Paracoccus denitrificans PD1222 rhodanese domain-containing protein YP_918758.1 514015 R 318586 CDS YP_918759.1 119387725 4583564 complement(514340..514846) 1 NC_008688.1 PFAM: Cupin domain protein; Cupin 2, conserved barrel domain protein; KEGG: bja:blr2407 hypothetical protein; cupin 2 domain-containing protein 514846 4583564 Pden_5003 Paracoccus denitrificans PD1222 cupin 2 domain-containing protein YP_918759.1 514340 R 318586 CDS YP_918760.1 119387726 4583565 complement(514961..515698) 1 NC_008688.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sma:SAV1559 ABC transporter ATP-binding protein; ABC transporter related 515698 4583565 Pden_5004 Paracoccus denitrificans PD1222 ABC transporter related YP_918760.1 514961 R 318586 CDS YP_918761.1 119387727 4583566 complement(515671..516540) 1 NC_008688.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: sma:SAV1558 ABC transporter transmembrane subunit, permease; binding-protein-dependent transport systems inner membrane component 516540 4583566 Pden_5005 Paracoccus denitrificans PD1222 binding-protein-dependent transport systems inner membrane component YP_918761.1 515671 R 318586 CDS YP_918762.1 119387728 4583567 complement(516542..517513) 1 NC_008688.1 TIGRFAM: aliphatic sulfonates family ABC transporter, periplsmic ligand-binding protein; SMART: extracellular solute-binding protein, family 3; KEGG: pau:PA14_30540 periplasmic aliphatic sulfonate-binding protein; aliphatic sulfonate ABC transporter periplasmic ligand-binding protein 517513 4583567 Pden_5006 Paracoccus denitrificans PD1222 aliphatic sulfonate ABC transporter periplasmic ligand-binding protein YP_918762.1 516542 R 318586 CDS YP_918763.1 119387729 4583568 complement(517529..518857) 1 NC_008688.1 KEGG: pst:PSPTO_2425 monooxygenase, NtaA/SnaA/SoxA family; NtaA/SnaA/SoxA family monooxygenase 518857 4583568 Pden_5007 Paracoccus denitrificans PD1222 NtaA/SnaA/SoxA family monooxygenase YP_918763.1 517529 R 318586 CDS YP_918764.1 119387730 4583569 complement(519031..520572) 1 NC_008688.1 PFAM: copper resistance protein CopC; copper resistance D domain protein; KEGG: rpa:RPA2929 copper resistance protein; copper resistance protein CopC 520572 4583569 Pden_5008 Paracoccus denitrificans PD1222 copper resistance protein CopC YP_918764.1 519031 R 318586 CDS YP_918765.1 119387731 4583570 complement(520569..521009) 1 NC_008688.1 KEGG: rpc:RPC_2425 nuclear export factor GLE1; nuclear export factor GLE1 521009 4583570 Pden_5009 Paracoccus denitrificans PD1222 nuclear export factor GLE1 YP_918765.1 520569 R 318586 CDS YP_918766.1 119387732 4583571 complement(521021..521812) 1 NC_008688.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: bam:Bamb_3676 ABC transporter related; ABC transporter related 521812 4583571 Pden_5010 Paracoccus denitrificans PD1222 ABC transporter related YP_918766.1 521021 R 318586 CDS YP_918767.1 119387733 4583572 complement(521806..522801) 1 NC_008688.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: bxe:Bxe_C0115 ABC nitrate/sulfonate/bicarbonate family transporter, inner membrane subunit; binding-protein-dependent transport systems inner membrane component 522801 4583572 Pden_5011 Paracoccus denitrificans PD1222 binding-protein-dependent transport systems inner membrane component YP_918767.1 521806 R 318586 CDS YP_918768.1 119387734 4583573 complement(522811..523842) 1 NC_008688.1 KEGG: bja:bll6455 ABC transporter substrate-binding protein; ABC transporter substrate-binding protein 523842 4583573 Pden_5012 Paracoccus denitrificans PD1222 ABC transporter substrate-binding protein YP_918768.1 522811 R 318586 CDS YP_918769.1 119387735 4583574 complement(523853..524959) 1 NC_008688.1 PFAM: luciferase family protein; KEGG: psb:Psyr_3599 alkanesulfonate monooxygenase; alkanesulfonate monooxygenase 524959 4583574 Pden_5013 Paracoccus denitrificans PD1222 alkanesulfonate monooxygenase YP_918769.1 523853 R 318586 CDS YP_918770.1 119387736 4583575 complement(524976..526130) 1 NC_008688.1 PFAM: acyl-CoA dehydrogenase domain protein; Acyl-CoA dehydrogenase, type 2, C-terminal domain; KEGG: bja:bll6452 acyl-CoA dehydrogenase; acyl-CoA dehydrogenase 526130 4583575 Pden_5014 Paracoccus denitrificans PD1222 acyl-CoA dehydrogenase YP_918770.1 524976 R 318586 CDS YP_918771.1 119387737 4583576 complement(526530..527465) 1 NC_008688.1 hypothetical protein 527465 4583576 Pden_5015 Paracoccus denitrificans PD1222 hypothetical protein YP_918771.1 526530 R 318586 CDS YP_918772.1 119387738 4583577 527529..528437 1 NC_008688.1 KEGG: rpc:RPC_3638 serine O-acetyltransferase; Serine O-acetyltransferase 528437 4583577 Pden_5016 Paracoccus denitrificans PD1222 Serine O-acetyltransferase YP_918772.1 527529 D 318586 CDS YP_918773.1 119387739 4583578 528519..529106 1 NC_008688.1 KEGG: bmb:BruAb2_0725 hypothetical protein; hypothetical protein 529106 4583578 Pden_5017 Paracoccus denitrificans PD1222 hypothetical protein YP_918773.1 528519 D 318586 CDS YP_918774.1 119387740 4583579 529599..530375 1 NC_008688.1 PFAM: Xylose isomerase domain protein TIM barrel; KEGG: rde:RD1_3783 hypothetical protein; hydroxypyruvate isomerase 530375 4583579 Pden_5018 Paracoccus denitrificans PD1222 hydroxypyruvate isomerase YP_918774.1 529599 D 318586 CDS YP_918775.1 119387741 4583580 complement(530421..531179) 1 NC_008688.1 TIGRFAM: beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family; PFAM: regulatory proteins, IclR; KEGG: atc:AGR_L_644 PcaR protein; beta-ketoadipate pathway transcription regulator 531179 4583580 Pden_5019 Paracoccus denitrificans PD1222 beta-ketoadipate pathway transcription regulator YP_918775.1 530421 R 318586 CDS YP_918776.1 119387742 4583581 531289..532038 1 NC_008688.1 KEGG: bmb:BruAb2_0588 PcaI, 3-oxoadipate CoA-transferase, alpha subunit; TIGRFAM: 3-oxoacid CoA-transferase, A subunit; PFAM: coenzyme A transferase; 3-oxoacid CoA-transferase subunit A 532038 4583581 Pden_5020 Paracoccus denitrificans PD1222 3-oxoacid CoA-transferase subunit A YP_918776.1 531289 D 318586 CDS YP_918777.1 119387743 4583582 532035..532706 1 NC_008688.1 KEGG: atc:AGR_L_642 3-oxoacid CoA-transferase subunit B; TIGRFAM: 3-oxoacid CoA-transferase, B subunit; PFAM: coenzyme A transferase; 3-oxoacid CoA-transferase subunit B 532706 4583582 Pden_5021 Paracoccus denitrificans PD1222 3-oxoacid CoA-transferase subunit B YP_918777.1 532035 D 318586 CDS YP_918778.1 119387744 4583583 532708..533907 1 NC_008688.1 catalyzes the thiolytic cleavage of beta-ketoadipyl-CoA to succinate and acetyl-CoA; beta-ketoadipyl CoA thiolase 533907 4583583 Pden_5022 Paracoccus denitrificans PD1222 beta-ketoadipyl CoA thiolase YP_918778.1 532708 D 318586 CDS YP_918779.1 119387745 4583584 complement(534012..534962) 1 NC_008688.1 PFAM: NAD-dependent epimerase/dehydratase; short-chain dehydrogenase/reductase SDR; 3-beta hydroxysteroid dehydrogenase/isomerase; polysaccharide biosynthesis protein CapD; dTDP-4-dehydrorhamnose reductase; Male sterility C-terminal domain; KEGG: mag:amb1437 nucleoside-diphosphate-sugar epimerase; NAD-dependent epimerase/dehydratase 534962 4583584 Pden_5023 Paracoccus denitrificans PD1222 NAD-dependent epimerase/dehydratase YP_918779.1 534012 R 318586 CDS YP_918780.1 119387746 4583585 535096..535398 1 NC_008688.1 hypothetical protein 535398 4583585 Pden_5024 Paracoccus denitrificans PD1222 hypothetical protein YP_918780.1 535096 D 318586 CDS YP_918781.1 119387747 4583586 535604..536038 1 NC_008688.1 TIGRFAM: cytidyltransferase-related domain; glycerol-3-phosphate cytidylyltransferase; PFAM: cytidylyltransferase; KEGG: blo:BL0210 probable glycerol-3-phosphate cytidylyltransferase; glycerol-3-phosphate cytidylyltransferase 536038 4583586 Pden_5025 Paracoccus denitrificans PD1222 glycerol-3-phosphate cytidylyltransferase YP_918781.1 535604 D 318586 CDS YP_918782.1 119387748 4583587 complement(536137..536541) 1 NC_008688.1 hypothetical protein 536541 4583587 Pden_5026 Paracoccus denitrificans PD1222 hypothetical protein YP_918782.1 536137 R 318586 CDS YP_918783.1 119387749 4583588 536632..539202 1 NC_008688.1 PFAM: glycosyl transferase, group 1; CDP-glycerol:poly(glycerophosphate) glycerophosphotransferase; KEGG: lxx:Lxx17460 teichoic acid synthase; glycosyl transferase, group 1 539202 4583588 Pden_5027 Paracoccus denitrificans PD1222 glycosyl transferase, group 1 YP_918783.1 536632 D 318586 CDS YP_918784.1 119387750 4583589 complement(539210..540220) 1 NC_008688.1 KEGG: sit:TM1040_1773 conserved hypothetical protein; hypothetical protein 540220 4583589 Pden_5028 Paracoccus denitrificans PD1222 hypothetical protein YP_918784.1 539210 R 318586 CDS YP_918785.1 119387751 4583590 complement(540232..541374) 1 NC_008688.1 KEGG: ecc:c3693 hypothetical protein; hypothetical protein 541374 4583590 Pden_5029 Paracoccus denitrificans PD1222 hypothetical protein YP_918785.1 540232 R 318586 CDS YP_918786.1 119387752 4583591 complement(541478..542752) 1 NC_008688.1 KEGG: ecc:c3695 hypothetical protein; hypothetical protein 542752 4583591 Pden_5030 Paracoccus denitrificans PD1222 hypothetical protein YP_918786.1 541478 R 318586 CDS YP_918787.1 119387753 4583592 543056..543865 1 NC_008688.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rsp:RSP_2175 ABC transporter, ATPase subunit; ABC transporter related 543865 4583592 Pden_5031 Paracoccus denitrificans PD1222 ABC transporter related YP_918787.1 543056 D 318586 CDS YP_918788.1 119387754 4583593 543840..544457 1 NC_008688.1 PFAM: cobalt transport protein; KEGG: rsp:RSP_2174 ABC transporter, inner membrane subunit; cobalt transport protein 544457 4583593 Pden_5032 Paracoccus denitrificans PD1222 cobalt transport protein YP_918788.1 543840 D 318586 CDS YP_918789.1 119387755 4583594 544464..545039 1 NC_008688.1 PFAM: BioY protein; KEGG: rsp:RSP_2173 biotin biosynthesis protein BioY; BioY protein 545039 4583594 Pden_5033 Paracoccus denitrificans PD1222 BioY protein YP_918789.1 544464 D 318586 CDS YP_918790.1 119387756 4583595 complement(545354..546376) 1 NC_008688.1 PFAM: initiator RepB protein; KEGG: cbu:CBUA0039 RepA protein; initiator RepB protein 546376 4583595 Pden_5034 Paracoccus denitrificans PD1222 initiator RepB protein YP_918790.1 545354 R 318586 CDS YP_918791.1 119387757 4583596 546983..548182 1 NC_008688.1 PFAM: Cobyrinic acid a,c-diamide synthase; KEGG: sme:SMb20046 probable replication protein A; cobyrinic acid a,c-diamide synthase 548182 4583596 Pden_5035 Paracoccus denitrificans PD1222 cobyrinic acid a,c-diamide synthase YP_918791.1 546983 D 318586 CDS YP_918792.1 119387758 4583597 548179..549144 1 NC_008688.1 TIGRFAM: parB-like partition proteins; PFAM: ParB domain protein nuclease; KEGG: cbu:CBUA0038 RepB protein; parB-like partition proteins 549144 4583597 Pden_5036 Paracoccus denitrificans PD1222 parB-like partition proteins YP_918792.1 548179 D 318586 CDS YP_918793.1 119387759 4583598 complement(549321..549998) 1 NC_008688.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sme:SMb20832 cell surface polysaccharide export ABC-2 transporter ATP-binding protein; ABC transporter related 549998 4583598 Pden_5037 Paracoccus denitrificans PD1222 ABC transporter related YP_918793.1 549321 R 318586 CDS YP_918794.1 119387760 4583599 complement(550003..551244) 1 NC_008688.1 KEGG: mes:Meso_2756 capsule polysaccharide export protein-like; capsule polysaccharide export protein-like 551244 4583599 Pden_5038 Paracoccus denitrificans PD1222 capsule polysaccharide export protein-like YP_918794.1 550003 R 318586 CDS YP_918795.1 119387761 4583600 552149..552901 1 NC_008688.1 PFAM: ABC-2 type transporter; KEGG: sme:SMb20833 cell surface polysaccharide export ABC-2 transporter permease, close relative of Y20822wzm2; ABC-2 type transporter 552901 4583600 Pden_5039 Paracoccus denitrificans PD1222 ABC-2 type transporter YP_918795.1 552149 D 318586 CDS YP_918796.1 119387762 4583601 complement(552932..554020) 1 NC_008688.1 PFAM: glycosyl transferase, group 1; KEGG: dvu:DVU0328 glycosyl transferase, group 1 family protein; glycosyl transferase, group 1 554020 4583601 Pden_5040 Paracoccus denitrificans PD1222 glycosyl transferase, group 1 YP_918796.1 552932 R 318586 CDS YP_918797.1 119387763 4583602 554121..555020 1 NC_008688.1 KEGG: msu:MS0656 hypothetical protein; hypothetical protein 555020 4583602 Pden_5041 Paracoccus denitrificans PD1222 hypothetical protein YP_918797.1 554121 D 318586 CDS YP_918798.1 119387764 4583603 complement(554998..555288) 1 NC_008688.1 hypothetical protein 555288 4583603 Pden_5042 Paracoccus denitrificans PD1222 hypothetical protein YP_918798.1 554998 R 318586 CDS YP_918799.1 119387765 4583604 555356..556501 1 NC_008688.1 PFAM: UDP-galactopyranose mutase; KEGG: atc:AGR_L_1762 probable UDP-galactopyranose mutase; UDP-galactopyranose mutase 556501 4583604 Pden_5043 Paracoccus denitrificans PD1222 UDP-galactopyranose mutase YP_918799.1 555356 D 318586 CDS YP_918800.1 119387766 4583605 complement(556550..557500) 1 NC_008688.1 PFAM: aldo/keto reductase; KEGG: mlo:mll3531 hypothetical protein; aldo/keto reductase 557500 4583605 Pden_5044 Paracoccus denitrificans PD1222 aldo/keto reductase YP_918800.1 556550 R 318586 CDS YP_918801.1 119387767 4583606 complement(557500..558684) 1 NC_008688.1 PFAM: FMN-dependent alpha-hydroxy acid dehydrogenase; KEGG: mes:Meso_3045 FMN-dependent alpha-hydroxy acid dehydrogenase; (S)-2-hydroxy-acid oxidase 558684 4583606 Pden_5045 Paracoccus denitrificans PD1222 (S)-2-hydroxy-acid oxidase YP_918801.1 557500 R 318586 CDS YP_918802.1 119387768 4583607 complement(558688..559206) 1 NC_008688.1 PFAM: regulatory protein, MarR; KEGG: mlo:mlr3448 regulatory protein (MarR-family); MarR family transcriptional regulator 559206 4583607 Pden_5046 Paracoccus denitrificans PD1222 MarR family transcriptional regulator YP_918802.1 558688 R 318586 CDS YP_918803.1 119387769 4583608 559396..560412 1 NC_008688.1 PFAM: extracellular solute-binding protein, family 1; KEGG: bja:bll3286 ABC transporter substrate-binding protein; extracellular solute-binding protein 560412 4583608 Pden_5047 Paracoccus denitrificans PD1222 extracellular solute-binding protein YP_918803.1 559396 D 318586 CDS YP_918804.1 119387770 4583609 560494..561555 1 NC_008688.1 PFAM: ABC transporter related; TOBE domain protein; Transport-associated OB domain protein; SMART: AAA ATPase; KEGG: rsp:RSP_3396 ABC opine/polyamine transporter, ATPase subunit; ABC transporter related 561555 4583609 Pden_5048 Paracoccus denitrificans PD1222 ABC transporter related YP_918804.1 560494 D 318586 CDS YP_918805.1 119387771 4583610 561552..562403 1 NC_008688.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: pol:Bpro_4378 binding-protein-dependent transport systems inner membrane component; binding-protein-dependent transport systems inner membrane component 562403 4583610 Pden_5049 Paracoccus denitrificans PD1222 binding-protein-dependent transport systems inner membrane component YP_918805.1 561552 D 318586 CDS YP_918806.1 119387772 4583611 562400..563188 1 NC_008688.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: rsp:RSP_3518 ABC polyamine/opine transporter, inner membrane subunit; binding-protein-dependent transport systems inner membrane component 563188 4583611 Pden_5050 Paracoccus denitrificans PD1222 binding-protein-dependent transport systems inner membrane component YP_918806.1 562400 D 318586 CDS YP_918807.1 119387773 4583612 563200..564021 1 NC_008688.1 PFAM: polysaccharide deacetylase; KEGG: bja:bll7202 hypothetical protein; polysaccharide deacetylase 564021 4583612 Pden_5051 Paracoccus denitrificans PD1222 polysaccharide deacetylase YP_918807.1 563200 D 318586 CDS YP_918808.1 119387774 4583613 564018..564758 1 NC_008688.1 PFAM: NAD-dependent epimerase/dehydratase; short-chain dehydrogenase/reductase SDR; KR; KEGG: rsp:RSP_7370 short-chain alcohol dehydrogenase; short-chain dehydrogenase/reductase SDR 564758 4583613 Pden_5052 Paracoccus denitrificans PD1222 short-chain dehydrogenase/reductase SDR YP_918808.1 564018 D 318586 CDS YP_918809.1 119387775 4583614 564766..565512 1 NC_008688.1 PFAM: NAD-dependent epimerase/dehydratase; short-chain dehydrogenase/reductase SDR; KEGG: rsp:RSP_3963 short-chain dehydrogenase/reductase SDR; short-chain dehydrogenase/reductase SDR 565512 4583614 Pden_5053 Paracoccus denitrificans PD1222 short-chain dehydrogenase/reductase SDR YP_918809.1 564766 D 318586 CDS YP_918810.1 119387776 4583615 565525..566901 1 NC_008688.1 PFAM: Amidase; KEGG: bja:blr3229 glutamyl-tRNA(Gln) amidotransferase subunit; amidase 566901 4583615 Pden_5054 Paracoccus denitrificans PD1222 amidase YP_918810.1 565525 D 318586 CDS YP_918811.1 119387777 4583616 complement(566911..568026) 1 NC_008688.1 PFAM: ABC-2 type transporter; KEGG: mlo:mlr4596 ABC transporter, ATP-binding protein; ABC-2 type transporter 568026 4583616 Pden_5055 Paracoccus denitrificans PD1222 ABC-2 type transporter YP_918811.1 566911 R 318586 CDS YP_918812.1 119387778 4583617 complement(568023..568931) 1 NC_008688.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: mlo:mlr4595 ATP-binding component of a transport system; ABC transporter related 568931 4583617 Pden_5056 Paracoccus denitrificans PD1222 ABC transporter related YP_918812.1 568023 R 318586 CDS YP_918813.1 119387779 4583618 complement(568928..569869) 1 NC_008688.1 PFAM: secretion protein HlyD family protein; KEGG: bmb:BruAb2_0759 HlyD family secretion protein; secretion protein HlyD family protein 569869 4583618 Pden_5057 Paracoccus denitrificans PD1222 secretion protein HlyD family protein YP_918813.1 568928 R 318586 CDS YP_918814.1 119387780 4583619 complement(569862..570503) 1 NC_008688.1 PFAM: regulatory protein, TetR; KEGG: mes:Meso_4073 transcriptional regulator, TetR family; TetR family transcriptional regulator 570503 4583619 Pden_5058 Paracoccus denitrificans PD1222 TetR family transcriptional regulator YP_918814.1 569862 R 318586 CDS YP_918815.1 119387781 4583620 complement(570617..571534) 1 NC_008688.1 PFAM: PfkB domain protein; KEGG: sil:SPO2420 2-dehydro-3-deoxygluconokinase; ribokinase-like domain-containing protein 571534 4583620 Pden_5059 Paracoccus denitrificans PD1222 ribokinase-like domain-containing protein YP_918815.1 570617 R 318586 CDS YP_918816.1 119387782 4583621 complement(571531..572982) 1 NC_008688.1 PFAM: Mannitol dehydrogenase, C-terminal domain; Mannitol dehydrogenase rossman, N-terminal domain; KEGG: sil:SPO1724 D-mannonate oxidoreductase; mannitol dehydrogenase 572982 4583621 Pden_5060 Paracoccus denitrificans PD1222 mannitol dehydrogenase YP_918816.1 571531 R 318586 CDS YP_918817.1 119387783 4583622 complement(572979..574187) 1 NC_008688.1 catalyzes the formation of 2-dehydro-3-deoxy-D-gluconate from mannonate; mannonate dehydratase 574187 4583622 Pden_5061 Paracoccus denitrificans PD1222 mannonate dehydratase YP_918817.1 572979 R 318586 CDS YP_918818.1 119387784 4583623 complement(574206..575363) 1 NC_008688.1 PFAM: FMN-dependent alpha-hydroxy acid dehydrogenase; KEGG: pau:PA14_33860 L-lactate dehydrogenase; L-lactate dehydrogenase (cytochrome) 575363 4583623 Pden_5062 Paracoccus denitrificans PD1222 L-lactate dehydrogenase (cytochrome) YP_918818.1 574206 R 318586 CDS YP_918819.1 119387785 4583624 complement(575368..576411) 1 NC_008688.1 PFAM: Alcohol dehydrogenase, zinc-binding domain protein; Alcohol dehydrogenase GroES domain protein; KEGG: sil:SPO2424 L-idonate 5-dehydrogenase; alcohol dehydrogenase 576411 4583624 Pden_5063 Paracoccus denitrificans PD1222 alcohol dehydrogenase YP_918819.1 575368 R 318586 CDS YP_918820.1 119387786 4583625 complement(576413..577693) 1 NC_008688.1 TIGRFAM: TRAP dicarboxylate transporter, DctM subunit; PFAM: TRAP C4-dicarboxylate transport system permease DctM subunit; KEGG: sil:SPO1719 TRAP dicarboxylate transporter, DctM subunit; TRAP dicarboxylate transporter, DctM subunit 577693 4583625 Pden_5064 Paracoccus denitrificans PD1222 TRAP dicarboxylate transporter, DctM subunit YP_918820.1 576413 R 318586 CDS YP_918821.1 119387787 4583626 complement(577698..578204) 1 NC_008688.1 PFAM: Tripartite ATP-independent periplasmic transporter, DctQ component; KEGG: sil:SPO1720 TRAP dicarboxylate transporter, DctQ subunit; tripartite ATP-independent periplasmic transporter DctQ 578204 4583626 Pden_5065 Paracoccus denitrificans PD1222 tripartite ATP-independent periplasmic transporter DctQ YP_918821.1 577698 R 318586 CDS YP_918822.1 119387788 4583627 complement(578272..579252) 1 NC_008688.1 TIGRFAM: TRAP dicarboxylate transporter, DctP subunit; PFAM: TRAP dicarboxylate transporter- DctP subunit; KEGG: rde:RD1_1052 C4-dicarboxylate transport system, substrate-binding protein; TRAP dicarboxylate transporter, DctP subunit 579252 4583627 Pden_5066 Paracoccus denitrificans PD1222 TRAP dicarboxylate transporter, DctP subunit YP_918822.1 578272 R 318586 CDS YP_918823.1 119387789 4583628 complement(579277..579957) 1 NC_008688.1 PFAM: regulatory protein GntR, HTH; GntR domain protein; KEGG: sme:SMa0065 GntR-family transcriptional regulator; GntR family transcriptional regulator 579957 4583628 Pden_5067 Paracoccus denitrificans PD1222 GntR family transcriptional regulator YP_918823.1 579277 R 318586 CDS YP_918824.1 119387790 4583629 complement(580126..581079) 1 NC_008688.1 PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: sme:SMc02596 transcription regulator protein; LysR family transcriptional regulator 581079 4583629 Pden_5068 Paracoccus denitrificans PD1222 LysR family transcriptional regulator YP_918824.1 580126 R 318586 CDS YP_918825.1 119387791 4583630 581257..582414 1 NC_008688.1 KEGG: nwi:Nwi_0592 O-succinylhomoserine (thiol)-lyase; TIGRFAM: O-succinylhomoserine (thiol)-lyase; PFAM: Cys/Met metabolism pyridoxal-phosphate-dependent enzymes; O-succinylhomoserine (thiol)-lyase 582414 4583630 Pden_5069 Paracoccus denitrificans PD1222 O-succinylhomoserine (thiol)-lyase YP_918825.1 581257 D 318586 CDS YP_918826.1 119387792 4583631 complement(582418..583371) 1 NC_008688.1 PFAM: helix-turn-helix- domain containing protein, AraC type; ThiJ/PfpI domain protein; KEGG: atc:AGR_pAT_bx241 hypothetical protein; AraC family transcriptional regulator 583371 4583631 Pden_5070 Paracoccus denitrificans PD1222 AraC family transcriptional regulator YP_918826.1 582418 R 318586 CDS YP_918827.1 119387793 4583632 583458..584345 1 NC_008688.1 PFAM: protein of unknown function DUF849; KEGG: atc:AGR_pAT_488 hypothetical protein; hypothetical protein 584345 4583632 Pden_5071 Paracoccus denitrificans PD1222 hypothetical protein YP_918827.1 583458 D 318586 CDS YP_918828.1 119387794 4583633 584405..585964 1 NC_008688.1 PFAM: extracellular solute-binding protein, family 5; KEGG: atc:AGR_pAT_490 OphA, peptide transport system substrate-binding protein; extracellular solute-binding protein 585964 4583633 Pden_5072 Paracoccus denitrificans PD1222 extracellular solute-binding protein YP_918828.1 584405 D 318586 CDS YP_918829.1 119387795 4583634 585961..587415 1 NC_008688.1 Converts (S)-3-hydroxyacyl-CoA to 3-oxyacyl-CoA; may also act as a thioesterase; bifunctional 3-hydroxyacyl-CoA dehydrogenase/thioesterase 587415 4583634 Pden_5073 Paracoccus denitrificans PD1222 bifunctional 3-hydroxyacyl-CoA dehydrogenase/thioesterase YP_918829.1 585961 D 318586 CDS YP_918830.1 119387796 4583635 587412..588389 1 NC_008688.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: atc:AGR_pAT_494 ABC transporter, permease; binding-protein-dependent transport systems inner membrane component 588389 4583635 Pden_5074 Paracoccus denitrificans PD1222 binding-protein-dependent transport systems inner membrane component YP_918830.1 587412 D 318586 CDS YP_918831.1 119387797 4583636 588394..589212 1 NC_008688.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: atc:AGR_pAT_496 ABC transporter, permease; binding-protein-dependent transport systems inner membrane component 589212 4583636 Pden_5075 Paracoccus denitrificans PD1222 binding-protein-dependent transport systems inner membrane component YP_918831.1 588394 D 318586 CDS YP_918832.1 119387798 4583637 589216..590832 1 NC_008688.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: atc:AGR_pAT_497 ABC transporter ATP-binding protein; ABC transporter related 590832 4583637 Pden_5076 Paracoccus denitrificans PD1222 ABC transporter related YP_918832.1 589216 D 318586 CDS YP_918833.1 119387799 4583638 590829..591707 1 NC_008688.1 PFAM: Alpha/beta hydrolase fold-3 domain protein; KEGG: atc:AGR_pAT_499 hypothetical protein; alpha/beta hydrolase 591707 4583638 Pden_5077 Paracoccus denitrificans PD1222 alpha/beta hydrolase YP_918833.1 590829 D 318586 CDS YP_918834.1 119387800 4583639 591783..592796 1 NC_008688.1 PFAM: regulatory protein, LacI; periplasmic binding protein/LacI transcriptional regulator; KEGG: sme:SMa0078 LacI-family transcriptional regulator; periplasmic binding protein/LacI transcriptional regulator 592796 4583639 Pden_5078 Paracoccus denitrificans PD1222 periplasmic binding protein/LacI transcriptional regulator YP_918834.1 591783 D 318586 CDS YP_918835.1 119387801 4583640 592864..593532 1 NC_008688.1 TIGRFAM: polar amino acid ABC transporter, inner membrane subunit; PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: sme:SMa0079 ABC transporter permease; polar amino acid ABC transporter, inner membrane subunit 593532 4583640 Pden_5079 Paracoccus denitrificans PD1222 polar amino acid ABC transporter, inner membrane subunit YP_918835.1 592864 D 318586 CDS YP_918836.1 119387802 4583641 593534..594190 1 NC_008688.1 TIGRFAM: polar amino acid ABC transporter, inner membrane subunit; PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: sme:SMa0081 ABC transporter permease; polar amino acid ABC transporter, inner membrane subunit 594190 4583641 Pden_5080 Paracoccus denitrificans PD1222 polar amino acid ABC transporter, inner membrane subunit YP_918836.1 593534 D 318586 CDS YP_918837.1 119387803 4583642 594227..595024 1 NC_008688.1 PFAM: extracellular solute-binding protein, family 3; KEGG: sme:SMa0082 ABC transporter, periplasmic solute-binding protein; extracellular solute-binding protein 595024 4583642 Pden_5081 Paracoccus denitrificans PD1222 extracellular solute-binding protein YP_918837.1 594227 D 318586 CDS YP_918838.1 119387804 4583643 595077..595811 1 NC_008688.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sme:SMa0083 ABC transporter ATP-binding protein; ABC transporter related 595811 4583643 Pden_5082 Paracoccus denitrificans PD1222 ABC transporter related YP_918838.1 595077 D 318586 CDS YP_918839.1 119387805 4583644 595808..596752 1 NC_008688.1 PFAM: D-isomer specific 2-hydroxyacid dehydrogenase, catalytic region; D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding; KEGG: atc:AGR_L_379 hypothetical protein; D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding 596752 4583644 Pden_5083 Paracoccus denitrificans PD1222 D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding YP_918839.1 595808 D 318586 CDS YP_918840.1 119387806 4583645 596730..597665 1 NC_008688.1 PFAM: PfkB domain protein; KEGG: psb:Psyr_2510 carbohydrate kinase, PfkB; ribokinase-like domain-containing protein 597665 4583645 Pden_5084 Paracoccus denitrificans PD1222 ribokinase-like domain-containing protein YP_918840.1 596730 D 318586 CDS YP_918841.1 119387807 4583646 597662..598402 1 NC_008688.1 KEGG: bte:BTH_II1322 hydratase/decarboxylase family protein; hydratase/decarboxylase family protein 598402 4583646 Pden_5085 Paracoccus denitrificans PD1222 hydratase/decarboxylase family protein YP_918841.1 597662 D 318586 CDS YP_918842.1 119387808 4583647 complement(598404..599519) 1 NC_008688.1 PFAM: 3-hydroxyacyl-CoA dehydrogenase domain protein; 6-phosphogluconate dehydrogenase, NAD-binding; 3-hydroxyacyl-CoA dehydrogenase, NAD-binding; KEGG: rxy:Rxyl_1761 3-hydroxybutyryl-CoA dehydrogenase; 3-hydroxybutyryl-CoA dehydrogenase 599519 4583647 Pden_5086 Paracoccus denitrificans PD1222 3-hydroxybutyryl-CoA dehydrogenase YP_918842.1 598404 R 318586 CDS YP_918843.1 119387809 4583648 599659..601944 1 NC_008688.1 catalyzes the conversion of salicylyl-CoA to gentisyl-CoA; salicylyl-CoA 5-hydroxylase 601944 4583648 Pden_5087 Paracoccus denitrificans PD1222 salicylyl-CoA 5-hydroxylase YP_918843.1 599659 D 318586 CDS YP_918844.1 119387810 4583649 601941..602678 1 NC_008688.1 PFAM: short-chain dehydrogenase/reductase SDR; KR; KEGG: mlo:mll5433 similar to granaticin polyketide ketoreductase; short-chain dehydrogenase/reductase SDR 602678 4583649 Pden_5088 Paracoccus denitrificans PD1222 short-chain dehydrogenase/reductase SDR YP_918844.1 601941 D 318586 CDS YP_918845.1 119387811 4583650 602675..603112 1 NC_008688.1 PFAM: regulatory protein, MarR; KEGG: mlo:mll5432 transcriptional regulator; MarR family transcriptional regulator 603112 4583650 Pden_5089 Paracoccus denitrificans PD1222 MarR family transcriptional regulator YP_918845.1 602675 D 318586 CDS YP_918846.1 119387812 4583651 603109..603921 1 NC_008688.1 Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA; enoyl-CoA hydratase 603921 4583651 Pden_5090 Paracoccus denitrificans PD1222 enoyl-CoA hydratase YP_918846.1 603109 D 318586 CDS YP_918847.1 119387813 4583652 603925..605061 1 NC_008688.1 PFAM: acyl-CoA dehydrogenase domain protein; Acyl-CoA dehydrogenase, type 2, C-terminal domain; KEGG: mlo:mll5430 acyl-CoA dehydrogenase; acyl-CoA dehydrogenase 605061 4583652 Pden_5091 Paracoccus denitrificans PD1222 acyl-CoA dehydrogenase YP_918847.1 603925 D 318586 CDS YP_918848.1 119387814 4583653 605058..605477 1 NC_008688.1 PFAM: thioesterase superfamily protein; KEGG: sil:SPO0786 thioesterase family protein; thioesterase superfamily protein 605477 4583653 Pden_5092 Paracoccus denitrificans PD1222 thioesterase superfamily protein YP_918848.1 605058 D 318586 CDS YP_918849.1 119387815 4583654 605467..605865 1 NC_008688.1 PFAM: Endoribonuclease L-PSP; KEGG: mlo:mll5429 hypothetical protein; endoribonuclease L-PSP 605865 4583654 Pden_5093 Paracoccus denitrificans PD1222 endoribonuclease L-PSP YP_918849.1 605467 D 318586 CDS YP_918850.1 119387816 4583655 605932..607572 1 NC_008688.1 PFAM: AMP-dependent synthetase and ligase; KEGG: sil:SPOA0401 benzoate-coenzyme A ligase; AMP-dependent synthetase/ligase 607572 4583655 Pden_5094 Paracoccus denitrificans PD1222 AMP-dependent synthetase/ligase YP_918850.1 605932 D 318586 CDS YP_918851.1 119387817 4583656 607669..608814 1 NC_008688.1 KEGG: rde:RD1_0540 ABC transporter substrate binding protei; ABC transporter substrate binding protei 608814 4583656 Pden_5095 Paracoccus denitrificans PD1222 ABC transporter substrate binding protei YP_918851.1 607669 D 318586 CDS YP_918852.1 119387818 4583657 608878..609789 1 NC_008688.1 PFAM: inner-membrane translocator; KEGG: sit:TM1040_2236 inner-membrane translocator; inner-membrane translocator 609789 4583657 Pden_5096 Paracoccus denitrificans PD1222 inner-membrane translocator YP_918852.1 608878 D 318586 CDS YP_918853.1 119387819 4583658 609793..610785 1 NC_008688.1 PFAM: inner-membrane translocator; KEGG: rde:RD1_0542 branched-chain amino acid ABC transporter, permease; inner-membrane translocator 610785 4583658 Pden_5097 Paracoccus denitrificans PD1222 inner-membrane translocator YP_918853.1 609793 D 318586 CDS YP_918854.1 119387820 4583659 610778..611542 1 NC_008688.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sit:TM1040_2234 ABC transporter related; ABC transporter related 611542 4583659 Pden_5098 Paracoccus denitrificans PD1222 ABC transporter related YP_918854.1 610778 D 318586 CDS YP_918855.1 119387821 4583660 611539..612228 1 NC_008688.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sit:TM1040_2233 ABC transporter related; ABC transporter related 612228 4583660 Pden_5099 Paracoccus denitrificans PD1222 ABC transporter related YP_918855.1 611539 D 318586 CDS YP_918856.1 119387822 4583661 612229..613047 1 NC_008688.1 KEGG: bcn:Bcen_1215 esterase/lipase-like protein; esterase/lipase-like protein 613047 4583661 Pden_5100 Paracoccus denitrificans PD1222 esterase/lipase-like protein YP_918856.1 612229 D 318586 CDS YP_918857.1 119387823 4583662 complement(613069..613356) 1 NC_008688.1 KEGG: sil:SPO0085 hypothetical protein; hypothetical protein 613356 4583662 Pden_5101 Paracoccus denitrificans PD1222 hypothetical protein YP_918857.1 613069 R 318586 CDS YP_918858.1 119387824 4583663 complement(613437..616136) 1 NC_008688.1 TIGRFAM: ATPase, P-type (transporting), HAD superfamily, subfamily IC; PFAM: cation transporting ATPase domain protein domain protein; Haloacid dehalogenase domain protein hydrolase; cation transporting ATPase domain protein; E1-E2 ATPase-associated domain protein; KEGG: rpb:RPB_1268 ATPase, E1-E2 type; ATPase, P-type (transporting), HAD superfamily, subfamily IC 616136 4583663 Pden_5102 Paracoccus denitrificans PD1222 ATPase, P-type (transporting), HAD superfamily, subfamily IC YP_918858.1 613437 R 318586 CDS YP_918859.1 119387825 4583664 complement(616216..618018) 1 NC_008688.1 PFAM: alpha/beta hydrolase fold; Poly-beta-hydroxybutyrate polymerase domain protein; KEGG: bxe:Bxe_B0358 poly-beta-hydroxyalkanoate synthasePhbC; poly-beta-hydroxybutyrate polymerase domain-containing protein 618018 4583664 Pden_5103 Paracoccus denitrificans PD1222 poly-beta-hydroxybutyrate polymerase domain-containing protein YP_918859.1 616216 R 318586 CDS YP_918860.1 119387826 4583665 complement(618213..618905) 1 NC_008688.1 PFAM: Surfeit locus 1 family protein; KEGG: sal:Sala_1504 surfeit locus 1; Surfeit locus 1 family protein 618905 4583665 Pden_5104 Paracoccus denitrificans PD1222 Surfeit locus 1 family protein YP_918860.1 618213 R 318586 CDS YP_918861.1 119387827 4583666 complement(618902..619285) 1 NC_008688.1 PFAM: cytochrome C oxidase subunit IV; KEGG: ret:RHE_PE00027 cytochrome o ubiquinol oxidase, subunit IV protein; cytochrome C oxidase subunit IV 619285 4583666 Pden_5105 Paracoccus denitrificans PD1222 cytochrome C oxidase subunit IV YP_918861.1 618902 R 318586 CDS YP_918862.1 119387828 4583667 complement(619285..619902) 1 NC_008688.1 PFAM: cytochrome c oxidase, subunit III; KEGG: rpb:RPB_0240 cytochrome c oxidase, subunit III; cytochrome c oxidase, subunit III 619902 4583667 Pden_5106 Paracoccus denitrificans PD1222 cytochrome c oxidase, subunit III YP_918862.1 619285 R 318586 CDS YP_918863.1 119387829 4583668 complement(619906..621912) 1 NC_008688.1 PFAM: cytochrome c oxidase, subunit I; KEGG: sal:Sala_1507 cytochrome-c oxidase; cytochrome-c oxidase 621912 4583668 Pden_5107 Paracoccus denitrificans PD1222 cytochrome-c oxidase YP_918863.1 619906 R 318586 CDS YP_918864.1 119387830 4583669 complement(621925..623127) 1 NC_008688.1 TIGRFAM: ubiquinol oxidase, subunit II; PFAM: cytochrome c oxidase, subunit II; COX aromatic rich domain protein; KEGG: bja:blr0149 cytochrome O ubiquinol oxidase subunit II; ubiquinol oxidase, subunit II 623127 4583669 Pden_5108 Paracoccus denitrificans PD1222 ubiquinol oxidase, subunit II YP_918864.1 621925 R 318586 CDS YP_918865.1 119387831 4583670 623349..624674 1 NC_008688.1 PFAM: General substrate transporter; major facilitator superfamily MFS_1; KEGG: bja:bll0148 MFS permease; major facilitator transporter 624674 4583670 Pden_5109 Paracoccus denitrificans PD1222 major facilitator transporter YP_918865.1 623349 D 318586 CDS YP_918866.1 119387832 4583671 624911..626368 1 NC_008688.1 PFAM: CBS domain containing protein; protein of unknown function DUF294, nucleotidyltransferase KEGG: rfr:Rfer_3783 cyclic nucleotide-binding domain (cNMP-BD) protein; signal-transduction protein 626368 4583671 Pden_5110 Paracoccus denitrificans PD1222 signal-transduction protein YP_918866.1 624911 D 318586 CDS YP_918867.1 119387833 4583672 626365..626610 1 NC_008688.1 KEGG: rfr:Rfer_3780 hypothetical protein; hypothetical protein 626610 4583672 Pden_5111 Paracoccus denitrificans PD1222 hypothetical protein YP_918867.1 626365 D 318586 CDS YP_918868.1 119387834 4583673 626607..629312 1 NC_008688.1 PFAM: ATP-binding region, ATPase domain protein domain protein; histidine kinase A domain protein domain protein; KEGG: rfr:Rfer_3779 periplasmic sensor signal transduction histidine kinase; integral membrane sensor signal transduction histidine kinase 629312 4583673 Pden_5112 Paracoccus denitrificans PD1222 integral membrane sensor signal transduction histidine kinase YP_918868.1 626607 D 318586 CDS YP_918869.1 119387835 4583674 629302..629667 1 NC_008688.1 PFAM: response regulator receiver; KEGG: eba:ebA168 protein containing response regulator domain, but no DNA binding domain; response regulator receiver protein 629667 4583674 Pden_5113 Paracoccus denitrificans PD1222 response regulator receiver protein YP_918869.1 629302 D 318586 CDS YP_918870.1 119387836 4583675 629664..631784 1 NC_008688.1 KEGG: rfr:Rfer_3777 DNA polymerase III, epsilon subunit; TIGRFAM: DNA polymerase III, epsilon subunit; PFAM: Exonuclease, RNase T and DNA polymerase III; SMART: Exonuclease; DNA polymerase III, epsilon subunit 631784 4583675 Pden_5114 Paracoccus denitrificans PD1222 DNA polymerase III, epsilon subunit YP_918870.1 629664 D 318586 CDS YP_918871.1 119387837 4583676 complement(631818..633980) 1 NC_008688.1 KEGG: rsp:RSP_1753 hypothetical protein; hypothetical protein 633980 4583676 Pden_5115 Paracoccus denitrificans PD1222 hypothetical protein YP_918871.1 631818 R 318586 CDS YP_918872.1 119387838 4583677 complement(634258..635226) 1 NC_008688.1 TIGRFAM: agmatinase; PFAM: Arginase/agmatinase/formiminoglutamase; KEGG: pfl:PFL_0325 agmatinase; agmatinase 635226 4583677 Pden_5116 Paracoccus denitrificans PD1222 agmatinase YP_918872.1 634258 R 318586 CDS YP_918873.1 119387839 4583678 635564..636178 1 NC_008688.1 PFAM: protein of unknown function DUF1234; KEGG: rsp:RSP_3119 conserved hypothetical protein / esterase; hypothetical protein 636178 4583678 Pden_5117 Paracoccus denitrificans PD1222 hypothetical protein YP_918873.1 635564 D 318586 CDS YP_918874.1 119387840 4583679 636385..637719 1 NC_008688.1 KEGG: rsp:RSP_3118 hypothetical protein; hypothetical protein 637719 4583679 Pden_5118 Paracoccus denitrificans PD1222 hypothetical protein YP_918874.1 636385 D 318586 CDS YP_918875.1 119387841 4583680 637973..638530 1 NC_008688.1 PFAM: NAD(P)H dehydrogenase (quinone); NADPH-dependent FMN reductase; KEGG: mlo:mlr5227 NADH-dependent FMN reductase MsuE; NADPH-dependent FMN reductase 638530 4583680 Pden_5119 Paracoccus denitrificans PD1222 NADPH-dependent FMN reductase YP_918875.1 637973 D 318586 CDS YP_918876.1 119387842 4583681 complement(638626..638979) 1 NC_008688.1 hypothetical protein 638979 4583681 Pden_5120 Paracoccus denitrificans PD1222 hypothetical protein YP_918876.1 638626 R 318586 CDS YP_918877.1 119387843 4583682 complement(638963..639214) 1 NC_008688.1 hypothetical protein 639214 4583682 Pden_5121 Paracoccus denitrificans PD1222 hypothetical protein YP_918877.1 638963 R 318586 CDS YP_918878.1 119387844 4583683 639347..639820 1 NC_008688.1 PFAM: regulatory protein, AsnC/Lrp family; KEGG: bja:blr8125 transcriptional regulatory protein; AsnC family transcriptional regulator 639820 4583683 Pden_5122 Paracoccus denitrificans PD1222 AsnC family transcriptional regulator YP_918878.1 639347 D 318586 CDS YP_918879.1 119387845 4583684 complement(639969..640247) 1 NC_008688.1 hypothetical protein 640247 4583684 Pden_5123 Paracoccus denitrificans PD1222 hypothetical protein YP_918879.1 639969 R 318586 CDS YP_918880.1 119387846 4583685 640248..640676 1 NC_008688.1 hypothetical protein 640676 4583685 Pden_5124 Paracoccus denitrificans PD1222 hypothetical protein YP_918880.1 640248 D 318586 CDS YP_918881.1 119387847 4583686 640801..642153 1 NC_008688.1 KEGG: ret:RHE_PC00169 probable monooxygenase; monooxygenase 642153 4583686 Pden_5125 Paracoccus denitrificans PD1222 monooxygenase YP_918881.1 640801 D 318586 CDS YP_918882.1 119387848 4583687 642158..643000 1 NC_008688.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: sme:SMb20571 aliphatic sulfonate uptake ABC transporter permease; binding-protein-dependent transport systems inner membrane component 643000 4583687 Pden_5126 Paracoccus denitrificans PD1222 binding-protein-dependent transport systems inner membrane component YP_918882.1 642158 D 318586 CDS YP_918883.1 119387849 4583688 643025..644002 1 NC_008688.1 KEGG: ret:RHE_PC00167 probable aliphatic sulphonate ABC transporter, substrate-binding protein; Fis family transcriptional regulator 644002 4583688 Pden_5127 Paracoccus denitrificans PD1222 Fis family transcriptional regulator YP_918883.1 643025 D 318586 CDS YP_918884.1 119387850 4583689 644002..644772 1 NC_008688.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sme:SMb20569 ABC transporter ATP-binding protein; ABC transporter related 644772 4583689 Pden_5128 Paracoccus denitrificans PD1222 ABC transporter related YP_918884.1 644002 D 318586 CDS YP_918885.1 119387851 4583690 645014..645514 1 NC_008688.1 PFAM: sigma-70 region 2 domain protein; sigma-70 region 4 domain protein; Sigma-70, region 4 type 2; KEGG: neu:NE1071 probable sigma-70 factor, ECF subfamily; ECF subfamily RNA polymerase sigma-24 factor 645514 4583690 Pden_5129 Paracoccus denitrificans PD1222 ECF subfamily RNA polymerase sigma-24 factor YP_918885.1 645014 D 318586 CDS YP_918886.1 119387852 4583691 645516..646472 1 NC_008688.1 PFAM: FecR protein; KEGG: neu:NE1070 transmembrane sensor; FecR 646472 4583691 Pden_5130 Paracoccus denitrificans PD1222 FecR YP_918886.1 645516 D 318586 CDS YP_918887.1 119387853 4583692 646603..649128 1 NC_008688.1 TIGRFAM: TonB-dependent siderophore receptor; PFAM: TonB-dependent receptor; Secretin/TonB, short N-terminal domain; TonB-dependent receptor, plug; KEGG: nwi:Nwi_1732 TonB-dependent siderophore receptor; TonB-dependent siderophore receptor 649128 4583692 Pden_5131 Paracoccus denitrificans PD1222 TonB-dependent siderophore receptor YP_918887.1 646603 D 318586 CDS YP_918888.1 119387854 4583693 649292..650629 1 NC_008688.1 TIGRFAM: efflux transporter, RND family, MFP subunit; KEGG: nwi:Nwi_2042 secretion protein HlyD; RND family efflux transporter MFP subunit 650629 4583693 Pden_5132 Paracoccus denitrificans PD1222 RND family efflux transporter MFP subunit YP_918888.1 649292 D 318586 CDS YP_918889.1 119387855 4583694 650650..652572 1 NC_008688.1 PFAM: ABC transporter related; protein of unknown function DUF214; SMART: AAA ATPase; KEGG: nwi:Nwi_2041 ABC transporter, ATPase subunit; ABC transporter 652572 4583694 Pden_5133 Paracoccus denitrificans PD1222 ABC transporter YP_918889.1 650650 D 318586 CDS YP_918890.1 119387856 4583695 652635..653789 1 NC_008688.1 KEGG: ssn:SSO_1681 receptor; hypothetical protein 653789 4583695 Pden_5134 Paracoccus denitrificans PD1222 hypothetical protein YP_918890.1 652635 D 318586 CDS