-- dump date 20140619_231450 -- class Genbank::Feature -- table feature -- table main -- field 1 id -- field 2 type -- field 3 name -- field 4 contig -- field 5 start_pos -- field 6 end_pos -- field 7 strand -- field 8 description -- field 9 chrom_position -- field 10 organism -- field 11 GeneID -- header -- id type name contig start_pos end_pos strand description chrom_position organism GeneID 318586000001 SEQ_END SEQ_END NC_008686.1 2852282 2852282 DR NC_008686.1; contig end 2852282..2852282 Paracoccus denitrificans PD1222 318586000002 SEQ_END SEQ_END NC_008687.1 1730097 1730097 DR NC_008687.1; contig end 1730097..1730097 Paracoccus denitrificans PD1222 318586000003 SEQ_END SEQ_END NC_008688.1 653815 653815 DR NC_008688.1; contig end 653815..653815 Paracoccus denitrificans PD1222 YP_913814.1 CDS Pden_0001 NC_008686.1 170 616 D PFAM: conserved hypothetical protein 701; KEGG: sil:SPO3893 hypothetical protein; hypothetical protein 170..616 Paracoccus denitrificans PD1222 4579419 YP_913815.1 CDS rho NC_008686.1 709 2013 D An RNA-DNA helicase that actively releases nascent mRNAs from paused transcription complexes; transcription termination factor Rho 709..2013 Paracoccus denitrificans PD1222 4579420 YP_913816.1 CDS Pden_0003 NC_008686.1 2030 3289 D 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 2030..3289 Paracoccus denitrificans PD1222 4579421 YP_913817.1 CDS Pden_0004 NC_008686.1 3298 5157 D 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 3298..5157 Paracoccus denitrificans PD1222 4578545 YP_913818.1 CDS Pden_0005 NC_008686.1 5157 5738 D TIGRFAM: methyltransferase GidB; PFAM: glucose inhibited division protein; KEGG: rde:RD1_0431 methyltransferase GidB; methyltransferase GidB 5157..5738 Paracoccus denitrificans PD1222 4578546 YP_913819.1 CDS Pden_0006 NC_008686.1 5731 6507 D PFAM: Cobyrinic acid a,c-diamide synthase; KEGG: sit:TM1040_2867 cobyrinic acid a,c-diamide synthase; cobyrinic acid a,c-diamide synthase 5731..6507 Paracoccus denitrificans PD1222 4578547 YP_913820.1 CDS Pden_0007 NC_008686.1 6517 7395 D TIGRFAM: parB-like partition proteins; PFAM: ParB domain protein nuclease; KEGG: rsp:RSP_1225 ParB-like partition protein; parB-like partition proteins 6517..7395 Paracoccus denitrificans PD1222 4578548 YP_913821.1 CDS Pden_0008 NC_008686.1 7526 8065 R PFAM: GrpE protein; KEGG: rsp:RSP_1219 chaperone protein GrpE (heat shock protein); heat shock protein GrpE complement(7526..8065) Paracoccus denitrificans PD1222 4578549 YP_913822.1 CDS hrcA NC_008686.1 8073 9128 R 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 complement(8073..9128) Paracoccus denitrificans PD1222 4578550 YP_913823.1 CDS rph NC_008686.1 9211 9936 D 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 9211..9936 Paracoccus denitrificans PD1222 4578551 YP_913824.1 CDS Pden_0011 NC_008686.1 9924 10529 D 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 9924..10529 Paracoccus denitrificans PD1222 4578552 YP_913825.1 CDS Pden_0012 NC_008686.1 10522 10896 D PFAM: Endoribonuclease L-PSP; KEGG: rsp:RSP_1223 translation initiation inhibitor, YjgF family / endoribonuclease L-PSP; endoribonuclease L-PSP 10522..10896 Paracoccus denitrificans PD1222 4578553 YP_913826.1 CDS Pden_0013 NC_008686.1 10905 12089 D catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III; coproporphyrinogen III oxidase 10905..12089 Paracoccus denitrificans PD1222 4578554 YP_913827.1 CDS Pden_0014 NC_008686.1 12091 12444 D PFAM: protein of unknown function DUF454; KEGG: atc:AGR_C_4462 hypothetical protein; hypothetical protein 12091..12444 Paracoccus denitrificans PD1222 4578555 YP_913828.1 CDS Pden_0015 NC_008686.1 12535 13119 D catalyzes the reaction of formaldehyde with glutathione to form S-hydroxymethylglutathione; glutathione-dependent formaldehyde-activating protein 12535..13119 Paracoccus denitrificans PD1222 4578556 YP_913829.1 CDS Pden_0016 NC_008686.1 13223 14350 D PFAM: Alcohol dehydrogenase, zinc-binding domain protein; Alcohol dehydrogenase GroES domain protein; KEGG: rsp:RSP_2576 alcohol dehydrogenase class III; alcohol dehydrogenase 13223..14350 Paracoccus denitrificans PD1222 4578557 YP_913830.1 CDS Pden_0017 NC_008686.1 14426 15061 D PFAM: peptidase S14, ClpP; KEGG: hne:HNE_0542 ATP-dependent Clp protease, proteolytic subunit ClpP; endopeptidase Clp 14426..15061 Paracoccus denitrificans PD1222 4578558 YP_913831.1 CDS Pden_0018 NC_008686.1 15058 15579 D PFAM: GCN5-related N-acetyltransferase; KEGG: sus:Acid_2411 GCN5-related N-acetyltransferase; N-acetyltransferase 15058..15579 Paracoccus denitrificans PD1222 4578559 YP_913832.1 CDS Pden_0019 NC_008686.1 15576 16415 D PFAM: esterase; KEGG: sil:SPO3829 S-formylglutathione hydrolase; carboxylesterase 15576..16415 Paracoccus denitrificans PD1222 4578560 YP_913833.1 CDS Pden_0020 NC_008686.1 16615 18417 D PFAM: Pyrrolo-quinoline quinone; KEGG: rsp:RSP_2578 pqq dehydrogenase protein; Pyrrolo-quinoline quinone 16615..18417 Paracoccus denitrificans PD1222 4578561 YP_913834.1 CDS Pden_0021 NC_008686.1 18519 19199 D KEGG: sme:SMb20174 cytochrome c protein; hypothetical protein 18519..19199 Paracoccus denitrificans PD1222 4578562 YP_913835.1 CDS Pden_0022 NC_008686.1 19196 20008 D SMART: extracellular solute-binding protein, family 3; KEGG: rsp:RSP_2580 methanol oxidation protein; extracellular solute-binding protein 19196..20008 Paracoccus denitrificans PD1222 4578563 YP_913836.1 CDS Pden_0023 NC_008686.1 20005 20535 D KEGG: rsp:RSP_2581 rhodanese; rhodanese 20005..20535 Paracoccus denitrificans PD1222 4578877 YP_913837.1 CDS Pden_0024 NC_008686.1 20567 21118 R KEGG: rde:RD1_0896 hypothetical protein; hypothetical protein complement(20567..21118) Paracoccus denitrificans PD1222 4578878 YP_913838.1 CDS Pden_0025 NC_008686.1 21122 21679 R KEGG: rsp:RSP_2574 hypothetical protein; hypothetical protein complement(21122..21679) Paracoccus denitrificans PD1222 4578879 YP_913839.1 CDS Pden_0026 NC_008686.1 21795 22982 D KEGG: rsp:RSP_2582 hypothetical protein; hypothetical protein 21795..22982 Paracoccus denitrificans PD1222 4578880 YP_913840.1 CDS Pden_0027 NC_008686.1 22991 23962 D TIGRFAM: 40-residue YVTN family beta-propeller repeat protein; KEGG: rsp:RSP_2583 hypothetical protein; hypothetical protein 22991..23962 Paracoccus denitrificans PD1222 4578881 YP_913841.1 CDS Pden_0028 NC_008686.1 23986 24555 D KEGG: rsp:RSP_2584 hypothetical protein; hypothetical protein 23986..24555 Paracoccus denitrificans PD1222 4578882 YP_913842.1 CDS Pden_0029 NC_008686.1 24593 25312 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rsp:RSP_2586 ABC multidrug efflux transporter, ATPase subunit; ABC transporter 24593..25312 Paracoccus denitrificans PD1222 4578883 YP_913843.1 CDS Pden_0030 NC_008686.1 25309 26127 D PFAM: ABC-2 type transporter; KEGG: rsp:RSP_2587 ABC multidrug efflux transporter, inner membrane subunit; ABC transporter 25309..26127 Paracoccus denitrificans PD1222 4578884 YP_913844.1 CDS Pden_0031 NC_008686.1 26124 26714 D KEGG: rsp:RSP_2588 hypothetical protein; hypothetical protein 26124..26714 Paracoccus denitrificans PD1222 4578885 YP_913845.1 CDS Pden_0032 NC_008686.1 26711 27313 D 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 26711..27313 Paracoccus denitrificans PD1222 4578886 YP_913846.1 CDS Pden_0033 NC_008686.1 27310 28041 R 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 complement(27310..28041) Paracoccus denitrificans PD1222 4578887 YP_913847.1 CDS Pden_0034 NC_008686.1 28038 28796 R PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sil:SPO0052 ABC transporter, ATP-binding protein; ABC transporter complement(28038..28796) Paracoccus denitrificans PD1222 4578888 YP_913848.1 CDS Pden_0035 NC_008686.1 28793 29467 R PFAM: TENA/THI-4 domain protein; KEGG: rde:RD1_3613 transcriptional regulator; TenA family transcription regulator complement(28793..29467) Paracoccus denitrificans PD1222 4578889 YP_913849.1 CDS Pden_0036 NC_008686.1 29464 30435 R KEGG: sit:TM1040_3655 NlpA lipoprotein; NlpA lipoprotein complement(29464..30435) Paracoccus denitrificans PD1222 4578890 YP_913850.1 CDS Pden_0037 NC_008686.1 30432 31394 R 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 complement(30432..31394) Paracoccus denitrificans PD1222 4578891 YP_913851.1 CDS thiE NC_008686.1 31391 31987 R Condenses 4-methyl-5-(beta-hydroxyethyl)-thiazole monophosphate and 4-amino-5-hydroxymethyl pyrimidine pyrophosphate to form thiamine monophosphate; thiamine-phosphate pyrophosphorylase complement(31391..31987) Paracoccus denitrificans PD1222 4578892 YP_913852.1 CDS thiG NC_008686.1 31984 32748 R 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 complement(31984..32748) Paracoccus denitrificans PD1222 4578893 YP_913853.1 CDS Pden_0040 NC_008686.1 32750 32947 R TIGRFAM: thiamine biosynthesis protein ThiS; PFAM: thiamineS protein; KEGG: bmb:BruAb1_0211 thiamine biosynthesis ThiS; thiamine biosynthesis protein ThiS complement(32750..32947) Paracoccus denitrificans PD1222 4578894 YP_913854.1 CDS Pden_0041 NC_008686.1 32931 33908 R PFAM: FAD dependent oxidoreductase; KEGG: rde:RD1_0747 thiamine biosynthesis oxidoreductase ThiO; FAD dependent oxidoreductase complement(32931..33908) Paracoccus denitrificans PD1222 4578895 YP_913855.1 CDS Pden_0042 NC_008686.1 33905 34759 R KEGG: sil:SPO0045 phosphomethylpyrimidine kinase; TIGRFAM: phosphomethylpyrimidine kinase; PFAM: Phosphomethylpyrimidine kinase type-1; phosphomethylpyrimidine kinase complement(33905..34759) Paracoccus denitrificans PD1222 4578896 YP_913856.1 CDS Pden_0043 NC_008686.1 35028 35630 D 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 35028..35630 Paracoccus denitrificans PD1222 4579074 YP_913857.1 CDS Pden_0044 NC_008686.1 35726 36292 D KEGG: sit:TM1040_3505 conserved hypothetical protein; hypothetical protein 35726..36292 Paracoccus denitrificans PD1222 4579075 YP_913858.1 CDS Pden_0045 NC_008686.1 36357 36791 R KEGG: bja:bll6386 3-dehydroquinate dehydratase; TIGRFAM: 3-dehydroquinate dehydratase, type II; PFAM: dehydroquinase, class II; 3-dehydroquinate dehydratase complement(36357..36791) Paracoccus denitrificans PD1222 4579076 YP_913859.1 CDS Pden_0046 NC_008686.1 36818 37519 R PFAM: response regulator receiver; transcriptional regulator domain protein; KEGG: rsp:RSP_2281 two-component trancriptional regulator, winged helix family; two component transcriptional regulator complement(36818..37519) Paracoccus denitrificans PD1222 4579077 YP_913860.1 CDS Pden_0047 NC_008686.1 37512 39392 R 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 complement(37512..39392) Paracoccus denitrificans PD1222 4579078 YP_913861.1 CDS Pden_0048 NC_008686.1 39505 41481 D PFAM: AMP-dependent synthetase and ligase; KEGG: rsp:RSP_2279 long chain acyl-CoA synthetase; AMP-dependent synthetase/ligase 39505..41481 Paracoccus denitrificans PD1222 4579079 YP_913862.1 CDS Pden_0049 NC_008686.1 41478 42287 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sit:TM1040_0114 ABC transporter related; ABC transporter 41478..42287 Paracoccus denitrificans PD1222 4579080 YP_913863.1 CDS Pden_0050 NC_008686.1 42298 43278 D PFAM: inner-membrane translocator; KEGG: rsp:RSP_2277 ABC branched amino acid transporter family, inner membrane subunit; inner-membrane translocator 42298..43278 Paracoccus denitrificans PD1222 4579081 YP_913864.1 CDS Pden_0051 NC_008686.1 43354 44460 D PFAM: inner-membrane translocator; KEGG: rsp:RSP_2276 ABC branched amino acid transporter family, inner membrane subunit; inner-membrane translocator 43354..44460 Paracoccus denitrificans PD1222 4579082 YP_913865.1 CDS Pden_0052 NC_008686.1 44505 45785 D KEGG: rsp:RSP_2275 ABC branched amino acid transporter family, periplasmic substrate-binding subunit; Fis family transcriptional regulator 44505..45785 Paracoccus denitrificans PD1222 4579083 YP_913866.1 CDS Pden_0053 NC_008686.1 45839 46663 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rsp:RSP_2274 ABC branched amino acid transporter family, ATPase subunit; ABC transporter 45839..46663 Paracoccus denitrificans PD1222 4579084 YP_913867.1 CDS Pden_0054 NC_008686.1 46682 47899 D KEGG: sil:SPO3289 phenylacetate-CoA ligase; phenylacetate-CoA ligase 46682..47899 Paracoccus denitrificans PD1222 4579085 YP_913868.1 CDS Pden_0055 NC_008686.1 48379 48504 R PFAM: ribosomal protein L36; KEGG: hne:HNE_3350 ribosomal protein L36; 50S ribosomal protein L36 complement(48379..48504) Paracoccus denitrificans PD1222 4579086 YP_913869.1 CDS Pden_0056 NC_008686.1 48847 49710 D PFAM: N-formylglutamate amidohydrolase; KEGG: rde:RD1_0718 N-formylglutamate amidohydrolase; N-formylglutamate amidohydrolase 48847..49710 Paracoccus denitrificans PD1222 4579087 YP_913870.1 CDS Pden_0057 NC_008686.1 49729 50616 D PFAM: band 7 protein; KEGG: rsp:RSP_1401 band 7 protein; hypothetical protein 49729..50616 Paracoccus denitrificans PD1222 4579088 YP_913871.1 CDS Pden_0058 NC_008686.1 50750 51301 D PFAM: NUDIX hydrolase; KEGG: sil:SPO3279 NUDIX domain protein; NUDIX hydrolase 50750..51301 Paracoccus denitrificans PD1222 4579089 YP_913872.1 CDS Pden_0059 NC_008686.1 51353 51982 D PFAM: Glutathione S-transferase, N-terminal domain; KEGG: bpe:BP1270 glutathione S-transferase; glutathione S-transferase domain-containing protein 51353..51982 Paracoccus denitrificans PD1222 4579090 YP_913873.1 CDS Pden_0060 NC_008686.1 51983 52687 R 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 complement(51983..52687) Paracoccus denitrificans PD1222 4579091 YP_913874.1 CDS Pden_0061 NC_008686.1 52790 53563 D KEGG: mmr:Mmar10_0746 hypothetical protein; hypothetical protein 52790..53563 Paracoccus denitrificans PD1222 4579092 YP_913875.1 CDS Pden_0062 NC_008686.1 53670 56297 D 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 53670..56297 Paracoccus denitrificans PD1222 4580939 YP_913876.1 CDS Pden_0063 NC_008686.1 56428 57324 D 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 56428..57324 Paracoccus denitrificans PD1222 4580940 YP_913877.1 CDS Pden_0064 NC_008686.1 57324 57950 D PFAM: Ferric reductase domain protein transmembrane component, N-terminal domain; KEGG: sit:TM1040_0134 ferric reductase-like transmembrane component-like; ferric reductase 57324..57950 Paracoccus denitrificans PD1222 4580941 YP_913878.1 CDS Pden_0065 NC_008686.1 57925 58224 D hypothetical protein 57925..58224 Paracoccus denitrificans PD1222 4580942 YP_913879.1 CDS Pden_0066 NC_008686.1 64006 64503 R KEGG: bhe:BH15450 hypothetical protein; hypothetical protein complement(64006..64503) Paracoccus denitrificans PD1222 4580943 YP_913880.1 CDS Pden_0067 NC_008686.1 64712 65059 D PFAM: IS66 Orf2 family protein; KEGG: sme:SMa1613 hypothetical protein; IS66 Orf2 family protein 64712..65059 Paracoccus denitrificans PD1222 4580944 YP_913881.1 CDS Pden_0068 NC_008686.1 65122 66750 D PFAM: transposase IS66; KEGG: sme:SMa2171 hypothetical protein; transposase IS66 65122..66750 Paracoccus denitrificans PD1222 4580945 YP_913882.1 CDS Pden_0069 NC_008686.1 66750 67046 D KEGG: sme:SMa1608 hypothetical protein; hypothetical protein 66750..67046 Paracoccus denitrificans PD1222 4580946 YP_913883.1 CDS Pden_0070 NC_008686.1 67024 67266 R KEGG: nma:NMA2178 hypothetical protein; hypothetical protein complement(67024..67266) Paracoccus denitrificans PD1222 4580947 YP_913884.1 CDS Pden_0071 NC_008686.1 67303 67578 D hypothetical protein 67303..67578 Paracoccus denitrificans PD1222 4580948 YP_913885.1 CDS Pden_0072 NC_008686.1 67679 69196 D PFAM: CHAD domain containing protein; KEGG: neu:NE1494 hypothetical protein; CHAD domain-containing protein 67679..69196 Paracoccus denitrificans PD1222 4580949 YP_913886.1 CDS Pden_0073 NC_008686.1 69196 69945 D PFAM: Cobyrinic acid a,c-diamide synthase; KEGG: neu:NE1495 ParA family ATPase; cobyrinic acid a,c-diamide synthase 69196..69945 Paracoccus denitrificans PD1222 4580950 YP_913887.1 CDS Pden_0074 NC_008686.1 69942 70397 D PFAM: adenylate cyclase; KEGG: neu:NE1496 hypothetical protein; adenylate cyclase 69942..70397 Paracoccus denitrificans PD1222 4580951 YP_913888.1 CDS Pden_0075 NC_008686.1 70419 70706 R KEGG: jan:Jann_1003 hypothetical protein; hypothetical protein complement(70419..70706) Paracoccus denitrificans PD1222 4580952 YP_913889.1 CDS Pden_0076 NC_008686.1 70813 71199 R hypothetical protein complement(70813..71199) Paracoccus denitrificans PD1222 4580953 YP_913890.1 CDS Pden_0077 NC_008686.1 71248 71667 D KEGG: gox:GOX2729 transposase; transposase 71248..71667 Paracoccus denitrificans PD1222 4580954 YP_913891.1 CDS Pden_0078 NC_008686.1 71795 72022 D KEGG: gox:GOX2722 truncated transposase; transposase 71795..72022 Paracoccus denitrificans PD1222 4580955 YP_913892.1 CDS Pden_0079 NC_008686.1 72151 72867 D PFAM: response regulator receiver; transcriptional regulator domain protein; KEGG: nar:Saro_0441 two component transcriptional regulator, winged helix family; two component transcriptional regulator 72151..72867 Paracoccus denitrificans PD1222 4580956 YP_913893.1 CDS Pden_0080 NC_008686.1 72869 75208 D 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 72869..75208 Paracoccus denitrificans PD1222 4580957 YP_913894.1 CDS Pden_0081 NC_008686.1 75555 77324 D PFAM: regulatory protein, LuxR; KEGG: sil:SPO1388 transcriptional regulator, LuxR family/hydrolase, alpha/beta fold family; LuxR family transcriptional regulator 75555..77324 Paracoccus denitrificans PD1222 4580958 YP_913895.1 CDS Pden_0082 NC_008686.1 77426 77737 D hypothetical protein 77426..77737 Paracoccus denitrificans PD1222 4578604 YP_913896.1 CDS Pden_0083 NC_008686.1 77791 78135 R hypothetical protein complement(77791..78135) Paracoccus denitrificans PD1222 4578605 YP_913897.1 CDS Pden_0084 NC_008686.1 78314 78568 D KEGG: rso:RSc2496 hypothetical signal peptide protein; hypothetical protein 78314..78568 Paracoccus denitrificans PD1222 4578606 YP_913898.1 CDS Pden_0085 NC_008686.1 79049 79255 D hypothetical protein 79049..79255 Paracoccus denitrificans PD1222 4578607 YP_913899.1 CDS Pden_0086 NC_008686.1 79239 79514 D hypothetical protein 79239..79514 Paracoccus denitrificans PD1222 4578608 YP_913900.1 CDS Pden_0087 NC_008686.1 79557 80267 D PFAM: acylneuraminate cytidylyltransferase; KEGG: aeh:Mlg_2324 acylneuraminate cytidylyltransferase; acylneuraminate cytidylyltransferase 79557..80267 Paracoccus denitrificans PD1222 4578609 YP_913901.1 CDS Pden_0088 NC_008686.1 80264 81310 D KEGG: ccr:CC2854 flagellin modification protein FlmD; flagellin modification protein FlmD 80264..81310 Paracoccus denitrificans PD1222 4578610 YP_913902.1 CDS Pden_0089 NC_008686.1 81485 82816 D KEGG: dvu:DVU1387 hypothetical protein; hypothetical protein 81485..82816 Paracoccus denitrificans PD1222 4578611 YP_913903.1 CDS Pden_0090 NC_008686.1 82819 83619 D KEGG: eca:ECA3144 hypothetical protein; hypothetical protein 82819..83619 Paracoccus denitrificans PD1222 4578612 YP_913904.1 CDS Pden_0091 NC_008686.1 83710 84885 R hypothetical protein complement(83710..84885) Paracoccus denitrificans PD1222 4578613 YP_913905.1 CDS Pden_0092 NC_008686.1 85055 86716 R hypothetical protein complement(85055..86716) Paracoccus denitrificans PD1222 4578614 YP_913906.1 CDS Pden_0093 NC_008686.1 86854 87855 R 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 complement(86854..87855) Paracoccus denitrificans PD1222 4578615 YP_913907.1 CDS Pden_0094 NC_008686.1 88201 88311 R KEGG: nha:Nham_3939 transposase IS116/IS110/IS902; transposase IS116/IS110/IS902 complement(88201..88311) Paracoccus denitrificans PD1222 4578616 YP_913908.1 CDS Pden_0095 NC_008686.1 88450 89019 R PFAM: Resolvase, N-terminal domain; Resolvase helix-turn-helix domain protein; KEGG: bpm:BURPS1710b_2170 DNA invertase; resolvase domain-containing protein complement(88450..89019) Paracoccus denitrificans PD1222 4578617 YP_913909.1 CDS Pden_0096 NC_008686.1 89344 89625 D KEGG: bmb:BruAb1_1581 hypothetical protein; hypothetical protein 89344..89625 Paracoccus denitrificans PD1222 4578618 YP_913910.1 CDS Pden_0097 NC_008686.1 89793 90434 R hypothetical protein complement(89793..90434) Paracoccus denitrificans PD1222 4578619 YP_913911.1 CDS Pden_0098 NC_008686.1 90443 90688 R PFAM: Conjugal transfer TraD family protein; KEGG: rpc:RPC_4518 conjugal transfer TraD; conjugal transfer TraD family protein complement(90443..90688) Paracoccus denitrificans PD1222 4578620 YP_913912.1 CDS Pden_0099 NC_008686.1 90690 91028 R KEGG: rpe:RPE_3258 hypothetical protein; hypothetical protein complement(90690..91028) Paracoccus denitrificans PD1222 4578621 YP_913913.1 CDS Pden_0100 NC_008686.1 91189 94185 D MobA/MobL family protein; conjugal transfer relaxase TraA 91189..94185 Paracoccus denitrificans PD1222 4578622 YP_913914.1 CDS Pden_0101 NC_008686.1 94406 94681 R hypothetical protein complement(94406..94681) Paracoccus denitrificans PD1222 4580879 YP_913915.1 CDS Pden_0102 NC_008686.1 94879 95094 D PFAM: Prophage CP4-57 regulatory; KEGG: rpe:RPE_3260 phage transcriptional regulator, AlpA; phage transcriptional regulator AlpA 94879..95094 Paracoccus denitrificans PD1222 4580880 YP_913916.1 CDS Pden_0103 NC_008686.1 95326 95817 D KEGG: rru:Rru_A1415 protein of unknown function DUF132; hypothetical protein 95326..95817 Paracoccus denitrificans PD1222 4580881 YP_913917.1 CDS Pden_0104 NC_008686.1 95814 96074 D KEGG: sus:Acid_1920 conserved hypothetical protein; hypothetical protein 95814..96074 Paracoccus denitrificans PD1222 4580882 YP_913918.1 CDS Pden_0105 NC_008686.1 96094 97743 D PFAM: Resolvase, N-terminal domain; Recombinase; KEGG: nwi:Nwi_2841 resolvase; recombinase 96094..97743 Paracoccus denitrificans PD1222 4580883 YP_913919.1 CDS Pden_0106 NC_008686.1 97636 99429 R PFAM: Resolvase, N-terminal domain; Recombinase; KEGG: nha:Nham_3864 recombinase; recombinase complement(97636..99429) Paracoccus denitrificans PD1222 4580884 YP_913920.1 CDS Pden_0107 NC_008686.1 99430 99915 D hypothetical protein 99430..99915 Paracoccus denitrificans PD1222 4580885 YP_913921.1 CDS Pden_0108 NC_008686.1 100054 101091 R PFAM: aldo/keto reductase; KEGG: rsp:RSP_3201 oxidoreductase; aldo/keto reductase complement(100054..101091) Paracoccus denitrificans PD1222 4580886 YP_913922.1 CDS Pden_0109 NC_008686.1 101268 102167 D 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 101268..102167 Paracoccus denitrificans PD1222 4580887 YP_913923.1 CDS Pden_0110 NC_008686.1 102305 102685 R hypothetical protein complement(102305..102685) Paracoccus denitrificans PD1222 4580888 YP_913924.1 CDS Pden_0111 NC_008686.1 102697 103602 R hypothetical protein complement(102697..103602) Paracoccus denitrificans PD1222 4580889 YP_913925.1 CDS Pden_0112 NC_008686.1 103599 105035 R KEGG: mmc:Mmcs_3174 hypothetical protein; hypothetical protein complement(103599..105035) Paracoccus denitrificans PD1222 4580890 YP_913926.1 CDS Pden_0113 NC_008686.1 105698 106597 R SMART: TIR protein; KEGG: bmb:BruAb1_0274 hypothetical protein; TIR protein complement(105698..106597) Paracoccus denitrificans PD1222 4580891 YP_913927.1 CDS Pden_0114 NC_008686.1 106933 107211 R PFAM: SH3, type 3 domain protein; KEGG: rsp:RSP_6161 hypothetical protein; SH3 type 3 domain-containing protein complement(106933..107211) Paracoccus denitrificans PD1222 4580892 YP_913928.1 CDS Pden_0115 NC_008686.1 107337 108014 R TIGRFAM: yecA family protein; PFAM: SEC-C motif domain protein; KEGG: rpe:RPE_2282 YecA family protein; hypothetical protein complement(107337..108014) Paracoccus denitrificans PD1222 4580893 YP_913929.1 CDS Pden_0116 NC_008686.1 108141 108776 R PFAM: transferase hexapeptide repeat containing protein; KEGG: atc:AGR_L_286 chloramphenicol acetyltransferase; hexapaptide repeat-containing transferase complement(108141..108776) Paracoccus denitrificans PD1222 4580894 YP_913930.1 CDS Pden_0117 NC_008686.1 109037 109393 D hypothetical protein 109037..109393 Paracoccus denitrificans PD1222 4580895 YP_913931.1 CDS Pden_0118 NC_008686.1 109402 109755 D KEGG: bcl:ABC1987 hypothetical protein; hypothetical protein 109402..109755 Paracoccus denitrificans PD1222 4580896 YP_913932.1 CDS Pden_0119 NC_008686.1 109994 110410 D KEGG: mes:Meso_3831 hypothetical protein; hypothetical protein 109994..110410 Paracoccus denitrificans PD1222 4580897 YP_913933.1 CDS Pden_0120 NC_008686.1 110943 111620 D 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 110943..111620 Paracoccus denitrificans PD1222 4580898 YP_913934.1 CDS Pden_0121 NC_008686.1 111692 111982 D hypothetical protein 111692..111982 Paracoccus denitrificans PD1222 4579500 YP_913935.1 CDS Pden_0122 NC_008686.1 112280 112741 D PFAM: GCN5-related N-acetyltransferase; KEGG: atc:AGR_L_1711 acetyltransferase; hypothetical protein 112280..112741 Paracoccus denitrificans PD1222 4579501 YP_913936.1 CDS Pden_0123 NC_008686.1 113488 113898 D 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 113488..113898 Paracoccus denitrificans PD1222 4579502 YP_913937.1 CDS Pden_0124 NC_008686.1 113876 114208 D hypothetical protein 113876..114208 Paracoccus denitrificans PD1222 4579503 YP_913938.1 CDS Pden_0125 NC_008686.1 114444 114647 D hypothetical protein 114444..114647 Paracoccus denitrificans PD1222 4579504 YP_913939.1 CDS Pden_0126 NC_008686.1 115048 115260 D hypothetical protein 115048..115260 Paracoccus denitrificans PD1222 4579505 YP_913940.1 CDS Pden_0127 NC_008686.1 115281 115730 R KEGG: mes:Meso_3838 hypothetical protein; hypothetical protein complement(115281..115730) Paracoccus denitrificans PD1222 4579506 YP_913941.1 CDS Pden_0128 NC_008686.1 115825 116091 R hypothetical protein complement(115825..116091) Paracoccus denitrificans PD1222 4579507 YP_913942.1 CDS Pden_0129 NC_008686.1 116238 116501 R KEGG: nwi:Nwi_0844 hypothetical protein; hypothetical protein complement(116238..116501) Paracoccus denitrificans PD1222 4579508 YP_913943.1 CDS Pden_0130 NC_008686.1 116687 116923 R PFAM: helix-turn-helix domain protein; KEGG: mlo:msr6108 transcriptional regulator; XRE family transcriptional regulator complement(116687..116923) Paracoccus denitrificans PD1222 4579509 YP_913944.1 CDS Pden_0131 NC_008686.1 117115 117384 D KEGG: nwi:Nwi_0845 hypothetical protein; hypothetical protein 117115..117384 Paracoccus denitrificans PD1222 4579510 YP_913945.1 CDS Pden_0132 NC_008686.1 117381 118250 D KEGG: nwi:Nwi_0846 possible replication protein A; replication protein A 117381..118250 Paracoccus denitrificans PD1222 4579511 YP_913946.1 CDS Pden_0133 NC_008686.1 118506 119006 D KEGG: mes:Meso_2334 hypothetical protein; hypothetical protein 118506..119006 Paracoccus denitrificans PD1222 4579512 YP_913947.1 CDS Pden_0134 NC_008686.1 119003 120622 D PFAM: C-5 cytosine-specific DNA methylase; transposase IS116/IS110/IS902 family protein; KEGG: mlo:mll5964 transposase; transposase IS116/IS110/IS902 family protein 119003..120622 Paracoccus denitrificans PD1222 4579513 YP_913948.1 CDS Pden_0135 NC_008686.1 121111 121665 D hypothetical protein 121111..121665 Paracoccus denitrificans PD1222 4579514 YP_913949.1 CDS Pden_0136 NC_008686.1 121919 122851 D PFAM: protein of unknown function DUF736; KEGG: mes:Meso_3845 conjugal transfer protein precursor; hypothetical protein 121919..122851 Paracoccus denitrificans PD1222 4579515 YP_913950.1 CDS Pden_0137 NC_008686.1 122855 123550 D PFAM: Lytic transglycosylase, catalytic; KEGG: mes:Meso_0517 lytic transglycosylase, catalytic; lytic transglycosylase, catalytic 122855..123550 Paracoccus denitrificans PD1222 4579516 YP_913951.1 CDS Pden_0138 NC_008686.1 123600 124181 D hypothetical protein 123600..124181 Paracoccus denitrificans PD1222 4579517 YP_913952.1 CDS Pden_0139 NC_008686.1 124423 126159 D KEGG: bja:bll0044 hypothetical protein; hypothetical protein 124423..126159 Paracoccus denitrificans PD1222 4579518 YP_913953.1 CDS Pden_0140 NC_008686.1 126242 126493 D 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 126242..126493 Paracoccus denitrificans PD1222 4580164 YP_913954.1 CDS Pden_0141 NC_008686.1 126578 126934 D KEGG: rru:Rru_A0091 PilT protein-like; twitching motility protein PilT 126578..126934 Paracoccus denitrificans PD1222 4580165 YP_913955.1 CDS Pden_0142 NC_008686.1 127107 129131 D type IV secretion VirD4 coupling protein family; conjugal transfer protein TraG 127107..129131 Paracoccus denitrificans PD1222 4580166 YP_913956.1 CDS Pden_0143 NC_008686.1 129135 129545 D KEGG: bja:bll0042 hypothetical protein; hypothetical protein 129135..129545 Paracoccus denitrificans PD1222 4580167 YP_913957.1 CDS Pden_0144 NC_008686.1 129586 129894 R PFAM: plasmid stabilization system; KEGG: sme:SMb20627 hypothetical protein; plasmid stabilization system protein complement(129586..129894) Paracoccus denitrificans PD1222 4580168 YP_913958.1 CDS Pden_0145 NC_008686.1 129891 130160 R PFAM: CopG domain protein DNA-binding domain protein; KEGG: sme:SMb20628 hypothetical protein; CopG family transcriptional regulator complement(129891..130160) Paracoccus denitrificans PD1222 4580169 YP_913959.1 CDS Pden_0146 NC_008686.1 130357 130599 R KEGG: mes:Meso_0499 hypothetical protein; hypothetical protein complement(130357..130599) Paracoccus denitrificans PD1222 4580170 YP_913960.1 CDS Pden_0147 NC_008686.1 130604 131779 R PFAM: conjugation TrbI family protein; KEGG: mes:Meso_0500 conjugation TrbI-like protein; conjugation TrbI family protein complement(130604..131779) Paracoccus denitrificans PD1222 4580171 YP_913961.1 CDS Pden_0148 NC_008686.1 131779 132783 R PFAM: Conjugal transfer protein TrbG/VirB9/CagX; KEGG: mes:Meso_0501 conjugal transfer protein TrbG/VirB9/CagX; conjugal transfer protein TrbG/VirB9/CagX complement(131779..132783) Paracoccus denitrificans PD1222 4580172 YP_913962.1 CDS Pden_0149 NC_008686.1 132780 133469 R PFAM: Conjugal transfer protein; KEGG: mes:Meso_0502 conjugal transfer protein; conjugal transfer protein TrbF complement(132780..133469) Paracoccus denitrificans PD1222 4580173 YP_913963.1 CDS Pden_0150 NC_008686.1 133466 134785 R type IV secretion VirB6 family; conjugal transfer protein TrbL complement(133466..134785) Paracoccus denitrificans PD1222 4580174 YP_913964.1 CDS Pden_0151 NC_008686.1 134793 135080 R KEGG: mes:Meso_2319 hypothetical protein; hypothetical protein complement(134793..135080) Paracoccus denitrificans PD1222 4580175 YP_913965.1 CDS Pden_0152 NC_008686.1 135101 135901 R KEGG: mes:Meso_3855 conjugal transfer protein TrbJ; conjugal transfer protein TrbJ complement(135101..135901) Paracoccus denitrificans PD1222 4580176 YP_913966.1 CDS Pden_0153 NC_008686.1 135898 138516 R type IV secretion system VirB4 family; conjugal transfer ATPase TrbE complement(135898..138516) Paracoccus denitrificans PD1222 4580177 YP_913967.1 CDS Pden_0154 NC_008686.1 138528 138809 R KEGG: mes:Meso_0507 conjugal transfer protein TrbB; conjugal transfer protein TrbB complement(138528..138809) Paracoccus denitrificans PD1222 4580178 YP_913968.1 CDS Pden_0155 NC_008686.1 138809 139138 R PFAM: Conjugal transfer protein TrbC; KEGG: mes:Meso_2323 conjugal transfer protein TrbC; conjugal transfer protein TrbC complement(138809..139138) Paracoccus denitrificans PD1222 4580179 YP_913969.1 CDS Pden_0156 NC_008686.1 139135 140139 R PFAM: type II secretion system protein E; KEGG: mes:Meso_2324 type II secretion system protein E; type II secretion system protein E complement(139135..140139) Paracoccus denitrificans PD1222 4580180 YP_913970.1 CDS Pden_0157 NC_008686.1 140328 141215 R PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: nwi:Nwi_0252 transcriptional regulatory protein, LysR family; LysR family transcriptional regulator complement(140328..141215) Paracoccus denitrificans PD1222 4580181 YP_913971.1 CDS Pden_0158 NC_008686.1 141246 141467 R KEGG: mlo:mlr6069 transposase; hypothetical protein complement(141246..141467) Paracoccus denitrificans PD1222 4580182 YP_913972.1 CDS Pden_0159 NC_008686.1 141627 141974 R hypothetical protein complement(141627..141974) Paracoccus denitrificans PD1222 4580183 YP_913973.1 CDS Pden_0160 NC_008686.1 142033 145134 R PFAM: acriflavin resistance protein; KEGG: atc:AGR_L_494 RND pump protein; acriflavin resistance protein complement(142033..145134) Paracoccus denitrificans PD1222 4579714 YP_913974.1 CDS Pden_0161 NC_008686.1 145138 146280 R 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 complement(145138..146280) Paracoccus denitrificans PD1222 4579715 YP_913975.1 CDS Pden_0162 NC_008686.1 146505 147182 R PFAM: MltA-interacting MipA family protein; KEGG: ccr:CC0351 outer membrane protein; MltA-interacting MipA family protein complement(146505..147182) Paracoccus denitrificans PD1222 4579716 YP_913976.1 CDS Pden_0163 NC_008686.1 147265 147627 D hypothetical protein 147265..147627 Paracoccus denitrificans PD1222 4579717 YP_913977.1 CDS Pden_0164 NC_008686.1 147614 148240 D PFAM: regulatory protein, TetR; KEGG: sco:SCO1193 TetR-family transcriptional regulator; TetR family transcriptional regulator 147614..148240 Paracoccus denitrificans PD1222 4579718 YP_913978.1 CDS Pden_0166 NC_008686.1 148664 149005 R SMART: regulatory protein, ArsR; KEGG: nwi:Nwi_3123 transcriptional regulatory protein, ArsR family; regulatory protein ArsR complement(148664..149005) Paracoccus denitrificans PD1222 4579719 YP_913979.1 CDS Pden_0167 NC_008686.1 149251 150348 D PFAM: Cupin 2, conserved barrel domain protein; KEGG: mes:Meso_3565 cupin 2, conserved barrel; cupin 149251..150348 Paracoccus denitrificans PD1222 4579720 YP_913980.1 CDS Pden_0168 NC_008686.1 150370 151140 D KEGG: mes:Meso_3566 hypothetical protein; hypothetical protein 150370..151140 Paracoccus denitrificans PD1222 4579721 YP_913981.1 CDS Pden_0169 NC_008686.1 151137 151964 R PFAM: regulatory proteins, IclR; KEGG: dar:Daro_0384 regulatory proteins, IclR; regulatory proteins, IclR complement(151137..151964) Paracoccus denitrificans PD1222 4579722 YP_913982.1 CDS Pden_0170 NC_008686.1 151979 152380 R PFAM: thioesterase superfamily protein; KEGG: gka:GK1990 4-hydroxybenzoyl-CoA thioesterase; thioesterase complement(151979..152380) Paracoccus denitrificans PD1222 4579723 YP_913983.1 CDS Pden_0171 NC_008686.1 152463 153608 D PFAM: monooxygenase, FAD-binding; KEGG: bja:blr0106 probable monooxygenase; FAD-binding monooxygenase 152463..153608 Paracoccus denitrificans PD1222 4579724 YP_913984.1 CDS Pden_0172 NC_008686.1 153619 155283 D TIGRFAM: benzoate-CoA ligase family; PFAM: AMP-dependent synthetase and ligase; KEGG: bja:blr0107 probable coenzyme A ligase; benzoate-CoA ligase family 153619..155283 Paracoccus denitrificans PD1222 4579725 YP_913985.1 CDS Pden_0173 NC_008686.1 155383 156093 D PFAM: fumarylacetoacetate (FAA) hydrolase; KEGG: rme:Rmet_4907 fumarylacetoacetate (FAA) hydrolase; fumarylacetoacetate (FAA) hydrolase 155383..156093 Paracoccus denitrificans PD1222 4579726 YP_913986.1 CDS Pden_0174 NC_008686.1 156090 156743 D TIGRFAM: maleylacetoacetate isomerase; PFAM: Glutathione S-transferase, N-terminal domain; KEGG: mlo:mlr1135 maleylacetoacetate isomerase; maleylacetoacetate isomerase 156090..156743 Paracoccus denitrificans PD1222 4579727 YP_913987.1 CDS Pden_0175 NC_008686.1 156769 157950 D KEGG: bja:blr1052 ABC transporter binding protein; ABC transporter binding protein 156769..157950 Paracoccus denitrificans PD1222 4579728 YP_913988.1 CDS Pden_0176 NC_008686.1 157992 158912 D PFAM: inner-membrane translocator; KEGG: bja:blr1064 ABC transporter permease protein; inner-membrane translocator 157992..158912 Paracoccus denitrificans PD1222 4579729 YP_913989.1 CDS Pden_0177 NC_008686.1 158917 159918 D PFAM: inner-membrane translocator; KEGG: bja:blr1065 ABC transporter permease protein; inner-membrane translocator 158917..159918 Paracoccus denitrificans PD1222 4579730 YP_913990.1 CDS Pden_0178 NC_008686.1 159915 160664 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: bja:blr1066 ABC transporter ATP-binding protein; ABC transporter 159915..160664 Paracoccus denitrificans PD1222 4579731 YP_913991.1 CDS Pden_0179 NC_008686.1 160664 161365 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: bja:blr1067 ABC transporter ATP-binding protein; ABC transporter 160664..161365 Paracoccus denitrificans PD1222 4579732 YP_913992.1 CDS Pden_0180 NC_008686.1 161423 162874 D PFAM: aldehyde dehydrogenase; KEGG: mlo:mll7197 dehydrogenase; aldehyde dehydrogenase 161423..162874 Paracoccus denitrificans PD1222 4578818 YP_913993.1 CDS Pden_0181 NC_008686.1 162937 164652 D PFAM: glucose-methanol-choline oxidoreductase; GMC oxidoreductase; KEGG: xcv:XCV2149 choline dehydrogenase; glucose-methanol-choline oxidoreductase 162937..164652 Paracoccus denitrificans PD1222 4578819 YP_913994.1 CDS Pden_0182 NC_008686.1 164730 165875 D KEGG: rme:Rmet_3785 beta-lactamase-like protein; beta-lactamase-like protein 164730..165875 Paracoccus denitrificans PD1222 4578820 YP_913995.1 CDS Pden_0183 NC_008686.1 165932 167233 R catalyzes the oxidative deamination of D-amino acids; D-amino acid dehydrogenase small subunit complement(165932..167233) Paracoccus denitrificans PD1222 4578821 YP_913996.1 CDS Pden_0184 NC_008686.1 167506 168204 R KEGG: oih:OB0952 hypothetical protein; hypothetical protein complement(167506..168204) Paracoccus denitrificans PD1222 4578822 YP_913997.1 CDS Pden_0185 NC_008686.1 168231 168968 R KEGG: oih:OB0951 hypothetical protein; hypothetical protein complement(168231..168968) Paracoccus denitrificans PD1222 4578823 YP_913998.1 CDS Pden_0186 NC_008686.1 169001 170164 R KEGG: bja:blr5691 amidohydrolase; TIGRFAM: amidohydrolase; PFAM: peptidase M20; peptidase dimerisation domain protein; amidohydrolase complement(169001..170164) Paracoccus denitrificans PD1222 4578824 YP_913999.1 CDS Pden_0187 NC_008686.1 170313 170816 D PFAM: regulatory protein, MarR; KEGG: sil:SPO1261 transcriptional regulator, MarR family; MarR family transcriptional regulator 170313..170816 Paracoccus denitrificans PD1222 4578825 YP_914000.1 CDS Pden_0188 NC_008686.1 170847 171662 R PFAM: regulatory proteins, IclR; KEGG: bps:BPSS2127 IclR transcriptional regulator protein; regulatory proteins, IclR complement(170847..171662) Paracoccus denitrificans PD1222 4578826 YP_914001.1 CDS Pden_0189 NC_008686.1 171675 173552 R 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 complement(171675..173552) Paracoccus denitrificans PD1222 4578827 YP_914002.1 CDS Pden_0190 NC_008686.1 173552 174082 R PFAM: Tripartite ATP-independent periplasmic transporter, DctQ component; KEGG: mlo:mll5171 hypothetical protein; tripartite ATP-independent periplasmic transporter DctQ complement(173552..174082) Paracoccus denitrificans PD1222 4578828 YP_914003.1 CDS Pden_0191 NC_008686.1 174180 174593 R PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase; KEGG: cme:CMP184C hypothetical protein, conserved Pfam: Glyoxalase; glyoxalase/bleomycin resistance protein/dioxygenase complement(174180..174593) Paracoccus denitrificans PD1222 4578829 YP_914004.1 CDS Pden_0192 NC_008686.1 174620 175390 R PFAM: short-chain dehydrogenase/reductase SDR; KR; KEGG: tma:TM1724 3-oxoacyl-(acyl carrier protein) reductase; short-chain dehydrogenase/reductase SDR complement(174620..175390) Paracoccus denitrificans PD1222 4578830 YP_914005.1 CDS Pden_0193 NC_008686.1 175536 176624 R PFAM: TRAP dicarboxylate transporter- DctP subunit; KEGG: mlo:mlr5166 periplasmic mannitol-binding protein; SmoM; TRAP dicarboxylate transporter- DctP subunit complement(175536..176624) Paracoccus denitrificans PD1222 4578831 YP_914006.1 CDS Pden_0194 NC_008686.1 176899 177723 D KEGG: bxe:Bxe_C0656 hypothetical protein; hypothetical protein 176899..177723 Paracoccus denitrificans PD1222 4578832 YP_914007.1 CDS Pden_0195 NC_008686.1 177720 178925 D PFAM: L-carnitine dehydratase/bile acid-inducible protein F; KEGG: rpa:RPA4557 hypothetical protein; L-carnitine dehydratase/bile acid-inducible protein F 177720..178925 Paracoccus denitrificans PD1222 4578833 YP_914008.1 CDS Pden_0196 NC_008686.1 178909 179730 D PFAM: short-chain dehydrogenase/reductase SDR; KEGG: psp:PSPPH_1258 3-oxoacyl-(acyl-carrier-protein) reductase; short-chain dehydrogenase/reductase SDR 178909..179730 Paracoccus denitrificans PD1222 4578834 YP_914009.1 CDS Pden_0197 NC_008686.1 179751 181280 D converts 3-hydroxyadipyl-CoA to beta-ketoadipyl-CoA in phenylacetate degradation; 3-hydroxyacyl-CoA dehydrogenase 179751..181280 Paracoccus denitrificans PD1222 4578835 YP_914010.1 CDS Pden_0198 NC_008686.1 181335 182495 R PFAM: acyl-CoA dehydrogenase domain protein; Acyl-CoA dehydrogenase, type 2, C-terminal domain; KEGG: mag:amb2599 acyl-CoA dehydrogenase; butyryl-CoA dehydrogenase complement(181335..182495) Paracoccus denitrificans PD1222 4578836 YP_914011.1 CDS Pden_0201 NC_008686.1 183912 185984 R 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 complement(183912..185984) Paracoccus denitrificans PD1222 4579016 YP_914012.1 CDS Pden_0202 NC_008686.1 186326 186856 D PFAM: flavin reductase domain protein, FMN-binding; KEGG: bte:BTH_II2298 flavin reductase domain protein; flavin reductase domain-containing protein 186326..186856 Paracoccus denitrificans PD1222 4579017 YP_914013.1 CDS Pden_0203 NC_008686.1 186916 188004 D PFAM: luciferase family protein; KEGG: jan:Jann_2939 luciferase-like; luciferase family protein 186916..188004 Paracoccus denitrificans PD1222 4579018 YP_914014.1 CDS Pden_0204 NC_008686.1 188036 188707 D 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 188036..188707 Paracoccus denitrificans PD1222 4579019 YP_914015.1 CDS Pden_0205 NC_008686.1 188774 189028 R hypothetical protein complement(188774..189028) Paracoccus denitrificans PD1222 4579020 YP_914016.1 CDS Pden_0206 NC_008686.1 189154 189945 R PFAM: short-chain dehydrogenase/reductase SDR; KR; KEGG: pau:PA14_10280 short-chain dehydrogenase; short-chain dehydrogenase/reductase SDR complement(189154..189945) Paracoccus denitrificans PD1222 4579021 YP_914017.1 CDS Pden_0207 NC_008686.1 190129 191124 R PFAM: alpha/beta hydrolase fold; KEGG: rso:RS05450 hydrolase signal peptide protein; alpha/beta hydrolase complement(190129..191124) Paracoccus denitrificans PD1222 4579022 YP_914018.1 CDS Pden_0208 NC_008686.1 191172 191351 R PFAM: 4-oxalocrotonate tautomerase; KEGG: rso:RS05436 hypothetical protein; 4-oxalocrotonate tautomerase complement(191172..191351) Paracoccus denitrificans PD1222 4579023 YP_914019.1 CDS Pden_0209 NC_008686.1 191454 192362 D PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: psb:Psyr_2945 regulatory protein, LysR:LysR, substrate-binding; LysR family transcriptional regulator 191454..192362 Paracoccus denitrificans PD1222 4579024 YP_914020.1 CDS Pden_0210 NC_008686.1 192405 193013 R KEGG: rso:RS05437 hypothetical protein; hypothetical protein complement(192405..193013) Paracoccus denitrificans PD1222 4579025 YP_914021.1 CDS Pden_0211 NC_008686.1 193178 193600 R PFAM: regulatory protein, MerR; KEGG: rsp:RSP_1790 probable transcriptional regulator; MerR family transcriptional regulator complement(193178..193600) Paracoccus denitrificans PD1222 4579026 YP_914022.1 CDS Pden_0212 NC_008686.1 193651 195927 D 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 193651..195927 Paracoccus denitrificans PD1222 4579027 YP_914023.1 CDS Pden_0213 NC_008686.1 195927 196523 D KEGG: tfu:Tfu_1571 hypothetical protein; S-isoprenylcysteine methyltransferase-like protein 195927..196523 Paracoccus denitrificans PD1222 4579028 YP_914024.1 CDS Pden_0214 NC_008686.1 196604 197680 R TIGRFAM: arsenical-resistance protein; PFAM: Bile acid:sodium symporter; KEGG: sal:Sala_2405 arsenical-resistance protein; arsenical-resistance protein complement(196604..197680) Paracoccus denitrificans PD1222 4579029 YP_914025.1 CDS Pden_0215 NC_008686.1 197709 198137 R TIGRFAM: arsenate reductase; PFAM: arsenate reductase and related; KEGG: rpa:RPA3554 arsenate reductase; arsenate reductase complement(197709..198137) Paracoccus denitrificans PD1222 4579030 YP_914026.1 CDS Pden_0216 NC_008686.1 198147 198683 R PFAM: low molecular weight phosphotyrosine protein phosphatase; KEGG: nwi:Nwi_3124 low molecular weight phosphotyrosine protein phosphatase; protein tyrosine phosphatase complement(198147..198683) Paracoccus denitrificans PD1222 4579031 YP_914027.1 CDS Pden_0217 NC_008686.1 198676 199038 R SMART: regulatory protein, ArsR; KEGG: nwi:Nwi_3123 transcriptional regulatory protein, ArsR family; regulatory protein ArsR complement(198676..199038) Paracoccus denitrificans PD1222 4579032 YP_914028.1 CDS Pden_0218 NC_008686.1 199089 199535 D PFAM: regulatory protein, LysR; KEGG: gvi:glr3360 LysR family transcriptional regulatory protein; LysR family transcriptional regulator 199089..199535 Paracoccus denitrificans PD1222 4579033 YP_914029.1 CDS Pden_0219 NC_008686.1 199766 200146 D KEGG: ttj:TTHB244 phenol hydroxylase component B; hypothetical protein 199766..200146 Paracoccus denitrificans PD1222 4579034 YP_914030.1 CDS Pden_0220 NC_008686.1 200561 201643 D PFAM: luciferase family protein; KEGG: jan:Jann_2939 luciferase-like; luciferase family protein 200561..201643 Paracoccus denitrificans PD1222 4580800 YP_914031.1 CDS Pden_0221 NC_008686.1 201702 202565 D KEGG: bxe:Bxe_C0656 hypothetical protein; hypothetical protein 201702..202565 Paracoccus denitrificans PD1222 4580801 YP_914032.1 CDS Pden_0222 NC_008686.1 202555 203775 D 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 202555..203775 Paracoccus denitrificans PD1222 4580802 YP_914033.1 CDS Pden_0223 NC_008686.1 203895 205325 D PFAM: aldehyde dehydrogenase; KEGG: bmb:BruAb2_0802 aldehyde dehydrogenase family protein; succinate-semialdehyde dehydrogenase (NAD(P)(+)) 203895..205325 Paracoccus denitrificans PD1222 4580803 YP_914034.1 CDS Pden_0224 NC_008686.1 205387 207240 R 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 complement(205387..207240) Paracoccus denitrificans PD1222 4580804 YP_914035.1 CDS Pden_0225 NC_008686.1 207290 207832 R PFAM: flavin reductase domain protein, FMN-binding; KEGG: rsp:RSP_3957 flavoprotein oxidoreductase; flavin reductase domain-containing protein complement(207290..207832) Paracoccus denitrificans PD1222 4580805 YP_914036.1 CDS Pden_0226 NC_008686.1 208050 208970 R PFAM: luciferase family protein; KEGG: ppu:PP_3171 hypothetical protein; luciferase family protein complement(208050..208970) Paracoccus denitrificans PD1222 4580806 YP_914037.1 CDS Pden_0227 NC_008686.1 209038 209307 R hypothetical protein complement(209038..209307) Paracoccus denitrificans PD1222 4580807 YP_914038.1 CDS Pden_0228 NC_008686.1 209307 209846 R PFAM: Xylose isomerase domain protein TIM barrel; KEGG: sus:Acid_5864 xylose isomerase domain protein TIM barrel; xylose isomerase domain-containing protein complement(209307..209846) Paracoccus denitrificans PD1222 4580808 YP_914039.1 CDS Pden_0229 NC_008686.1 209861 210658 R PFAM: Xylose isomerase domain protein TIM barrel; KEGG: sus:Acid_5864 xylose isomerase domain protein TIM barrel; xylose isomerase domain-containing protein complement(209861..210658) Paracoccus denitrificans PD1222 4580809 YP_914040.1 CDS Pden_0230 NC_008686.1 210655 211734 R PFAM: luciferase family protein; KEGG: psb:Psyr_1559 luciferase; luciferase family protein complement(210655..211734) Paracoccus denitrificans PD1222 4580810 YP_914041.1 CDS Pden_0231 NC_008686.1 211824 212726 D PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: bcn:Bcen_1980 transcriptional regulator, LysR family; LysR family transcriptional regulator 211824..212726 Paracoccus denitrificans PD1222 4580811 YP_914042.1 CDS Pden_0232 NC_008686.1 212737 213429 R PFAM: regulatory protein, TetR; KEGG: pae:PA3678 probable transcriptional regulator; TetR family transcriptional regulator complement(212737..213429) Paracoccus denitrificans PD1222 4580812 YP_914043.1 CDS Pden_0233 NC_008686.1 213456 215417 D KEGG: gme:Gmet_2060 fusaric acid resistance protein conserved region; hypothetical protein 213456..215417 Paracoccus denitrificans PD1222 4580813 YP_914044.1 CDS Pden_0234 NC_008686.1 215564 215908 D KEGG: xcb:XC_0382 b-ketoadipate enol-lactone hydrolase; hypothetical protein 215564..215908 Paracoccus denitrificans PD1222 4580814 YP_914045.1 CDS Pden_0235 NC_008686.1 215905 216918 R 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 complement(215905..216918) Paracoccus denitrificans PD1222 4580815 YP_914046.1 CDS Pden_0236 NC_008686.1 216915 217913 R 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 complement(216915..217913) Paracoccus denitrificans PD1222 4580816 YP_914047.1 CDS Pden_0237 NC_008686.1 217913 218785 R 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 complement(217913..218785) Paracoccus denitrificans PD1222 4580817 YP_914048.1 CDS Pden_0238 NC_008686.1 218785 219720 R 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 complement(218785..219720) Paracoccus denitrificans PD1222 4580818 YP_914049.1 CDS Pden_0239 NC_008686.1 219738 221327 R PFAM: extracellular solute-binding protein, family 5; KEGG: pol:Bpro_4344 extracellular solute-binding protein, family 5; extracellular solute-binding protein complement(219738..221327) Paracoccus denitrificans PD1222 4580819 YP_914050.1 CDS Pden_0240 NC_008686.1 221408 222094 R PFAM: regulatory protein GntR, HTH; GntR domain protein; KEGG: mes:Meso_4461 transcriptional regulator, GntR family; GntR family transcriptional regulator complement(221408..222094) Paracoccus denitrificans PD1222 4579733 YP_914051.1 CDS Pden_0241 NC_008686.1 222145 223182 D PFAM: Malate/L-lactate dehydrogenase; KEGG: mes:Meso_4453 malate/L-lactate dehydrogenase; (R)-2-hydroxyacid dehydrogenase 222145..223182 Paracoccus denitrificans PD1222 4579734 YP_914052.1 CDS Pden_0242 NC_008686.1 223208 224464 D PFAM: iron-containing alcohol dehydrogenase; KEGG: rpc:RPC_0105 alcohol dehydrogenase; iron-containing alcohol dehydrogenase 223208..224464 Paracoccus denitrificans PD1222 4579735 YP_914053.1 CDS Pden_0243 NC_008686.1 224461 225939 D PFAM: aldehyde dehydrogenase; KEGG: mes:Meso_4451 aldehyde dehydrogenase; succinate-semialdehyde dehydrogenase (NAD(P)(+)) 224461..225939 Paracoccus denitrificans PD1222 4579736 YP_914054.1 CDS Pden_0244 NC_008686.1 225977 227128 D 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 225977..227128 Paracoccus denitrificans PD1222 4579737 YP_914055.1 CDS Pden_0245 NC_008686.1 227187 228044 D PFAM: fumarylacetoacetate (FAA) hydrolase; KEGG: reu:Reut_A0050 5-carboxymethyl-2-hydroxymuconate delta-isomerase; 5-carboxymethyl-2-hydroxymuconate delta-isomerase 227187..228044 Paracoccus denitrificans PD1222 4579738 YP_914056.1 CDS Pden_0246 NC_008686.1 228259 229149 D PFAM: Xylose isomerase domain protein TIM barrel; KEGG: msu:MS0202 hypothetical protein; xylose isomerase domain-containing protein 228259..229149 Paracoccus denitrificans PD1222 4579739 YP_914057.1 CDS Pden_0247 NC_008686.1 229193 230239 D PFAM: periplasmic binding protein/LacI transcriptional regulator; KEGG: msu:MS0201 RbsB protein; periplasmic binding protein/LacI transcriptional regulator 229193..230239 Paracoccus denitrificans PD1222 4579740 YP_914058.1 CDS Pden_0248 NC_008686.1 230457 231896 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: msu:MS0200 MglA protein; ABC transporter 230457..231896 Paracoccus denitrificans PD1222 4579741 YP_914059.1 CDS Pden_0249 NC_008686.1 231893 232855 D PFAM: inner-membrane translocator; KEGG: msu:MS0199 ribose/xylose/arabinose/galactoside ABC-type transport systems, permease components; inner-membrane translocator 231893..232855 Paracoccus denitrificans PD1222 4579742 YP_914060.1 CDS Pden_0250 NC_008686.1 232852 233715 D involved in rpiB and als operon repression; DNA-binding transcriptional repressor RpiR 232852..233715 Paracoccus denitrificans PD1222 4579743 YP_914061.1 CDS Pden_0251 NC_008686.1 233732 234574 D PFAM: PfkB domain protein; KEGG: msu:MS0197 RbsK protein; ribokinase-like domain-containing protein 233732..234574 Paracoccus denitrificans PD1222 4579744 YP_914062.1 CDS Pden_0252 NC_008686.1 234598 234849 R KEGG: gox:GOX2677 transposase (class I); transposase (class I) complement(234598..234849) Paracoccus denitrificans PD1222 4579745 YP_914063.1 CDS Pden_0253 NC_008686.1 234955 235479 R hypothetical protein complement(234955..235479) Paracoccus denitrificans PD1222 4579746 YP_914064.1 CDS Pden_0254 NC_008686.1 235511 235789 D hypothetical protein 235511..235789 Paracoccus denitrificans PD1222 4579747 YP_914065.1 CDS Pden_0255 NC_008686.1 236307 236864 D hypothetical protein 236307..236864 Paracoccus denitrificans PD1222 4579748 YP_914066.1 CDS Pden_0256 NC_008686.1 236988 237242 D hypothetical protein 236988..237242 Paracoccus denitrificans PD1222 4579749 YP_914067.1 CDS Pden_0257 NC_008686.1 237429 237779 R KEGG: nfa:nfa39970 hypothetical protein; hypothetical protein complement(237429..237779) Paracoccus denitrificans PD1222 4579750 YP_914068.1 CDS Pden_0258 NC_008686.1 237776 238126 R hypothetical protein complement(237776..238126) Paracoccus denitrificans PD1222 4579751 YP_914069.1 CDS Pden_0259 NC_008686.1 238183 238512 D hypothetical protein 238183..238512 Paracoccus denitrificans PD1222 4578897 YP_914070.1 CDS Pden_0260 NC_008686.1 238789 239064 R hypothetical protein complement(238789..239064) Paracoccus denitrificans PD1222 4578898 YP_914071.1 CDS Pden_0261 NC_008686.1 239190 239984 R PFAM: D12 class N6 adenine-specific DNA methyltransferase; KEGG: ypm:YP_1932 methyltransferase; D12 class N6 adenine-specific DNA methyltransferase complement(239190..239984) Paracoccus denitrificans PD1222 4578899 YP_914072.1 CDS Pden_0262 NC_008686.1 239981 240562 R KEGG: mes:Meso_0232 hypothetical protein; hypothetical protein complement(239981..240562) Paracoccus denitrificans PD1222 4578900 YP_914073.1 CDS Pden_0263 NC_008686.1 240559 242226 R TIGRFAM: DNA-cytosine methyltransferase; PFAM: C-5 cytosine-specific DNA methylase; KEGG: bte:BTH_II1364 DNA methyltransferase; DNA-cytosine methyltransferase complement(240559..242226) Paracoccus denitrificans PD1222 4578901 YP_914074.1 CDS Pden_0264 NC_008686.1 242420 242716 D KEGG: sme:SMc00822 hypothetical protein; hypothetical protein 242420..242716 Paracoccus denitrificans PD1222 4578902 YP_914075.1 CDS Pden_0265 NC_008686.1 242716 243093 D KEGG: sit:TM1040_0815 transcriptional regulator, XRE family; XRE family transcriptional regulator 242716..243093 Paracoccus denitrificans PD1222 4578903 YP_914076.1 CDS Pden_0266 NC_008686.1 243083 243817 D hypothetical protein 243083..243817 Paracoccus denitrificans PD1222 4578904 YP_914077.1 CDS Pden_0267 NC_008686.1 243957 244910 R PFAM: Peptidoglycan-binding domain 1 protein; KEGG: eli:ELI_07940 bacteriophage-acquired protein; peptidoglycan binding domain-containing protein complement(243957..244910) Paracoccus denitrificans PD1222 4578905 YP_914078.1 CDS Pden_0268 NC_008686.1 244980 245237 R hypothetical protein complement(244980..245237) Paracoccus denitrificans PD1222 4578906 YP_914079.1 CDS Pden_0269 NC_008686.1 245264 245617 R KEGG: sil:SPO2726 hypothetical protein; hypothetical protein complement(245264..245617) Paracoccus denitrificans PD1222 4578907 YP_914080.1 CDS Pden_0270 NC_008686.1 245625 249644 R KEGG: nwi:Nwi_0792 gene transfer agent (GTA) like protein; gene transfer agent (GTA) like protein complement(245625..249644) Paracoccus denitrificans PD1222 4578908 YP_914081.1 CDS Pden_0271 NC_008686.1 249649 250086 R TIGRFAM: phage cell wall peptidase, NlpC/P60 family; PFAM: NLP/P60 protein; KEGG: sil:SPO2729 hypothetical protein; NlpC/P60 family phage cell wall peptidase complement(249649..250086) Paracoccus denitrificans PD1222 4578909 YP_914082.1 CDS Pden_0272 NC_008686.1 250083 250967 R KEGG: rpb:RPB_3460 phage conserved hypothetical protein BR0599; phage protein complement(250083..250967) Paracoccus denitrificans PD1222 4578910 YP_914083.1 CDS Pden_0273 NC_008686.1 250964 251590 R KEGG: mmr:Mmar10_0930 hypothetical protein; hypothetical protein complement(250964..251590) Paracoccus denitrificans PD1222 4578911 YP_914084.1 CDS Pden_0274 NC_008686.1 251590 252849 R KEGG: dvu:DVU1490 tail tape measure protein; hypothetical protein complement(251590..252849) Paracoccus denitrificans PD1222 4578912 YP_914085.1 CDS Pden_0275 NC_008686.1 252834 253898 R hypothetical protein complement(252834..253898) Paracoccus denitrificans PD1222 4578913 YP_914086.1 CDS Pden_0276 NC_008686.1 254344 254865 D KEGG: bmb:BruAb2_0879 hypothetical sugar-binding protein; sugar-binding protein 254344..254865 Paracoccus denitrificans PD1222 4578914 YP_914087.1 CDS Pden_0277 NC_008686.1 254938 255678 R PFAM: ChaC family protein; KEGG: mlo:mll2256 cation transport protein; ChaC family protein complement(254938..255678) Paracoccus denitrificans PD1222 4578915 YP_914088.1 CDS Pden_0278 NC_008686.1 256203 257528 D PFAM: General substrate transporter; major facilitator superfamily MFS_1; KEGG: rxy:Rxyl_2255 general substrate transporter; major facilitator superfamily transporter 256203..257528 Paracoccus denitrificans PD1222 4578916 YP_914089.1 CDS Pden_0279 NC_008686.1 257705 259090 D PFAM: regulatory protein GntR, HTH; aminotransferase, class I and II; KEGG: ret:RHE_PF00188 transcriptional regulator protein, GntR family; GntR family transcriptional regulator 257705..259090 Paracoccus denitrificans PD1222 4580184 YP_914090.1 CDS Pden_0280 NC_008686.1 259188 259973 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sme:SMb20427 amino acid ABC transporter ATP-binding protein; ABC transporter 259188..259973 Paracoccus denitrificans PD1222 4580185 YP_914091.1 CDS Pden_0281 NC_008686.1 259973 260818 D PFAM: extracellular solute-binding protein, family 3; KEGG: mlo:mlr7133 amino acid ABC transporter protein, solute-binding component; extracellular solute-binding protein 259973..260818 Paracoccus denitrificans PD1222 4580186 YP_914092.1 CDS Pden_0282 NC_008686.1 260877 261533 D 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 260877..261533 Paracoccus denitrificans PD1222 4580187 YP_914093.1 CDS Pden_0283 NC_008686.1 261535 262194 D 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 261535..262194 Paracoccus denitrificans PD1222 4580188 YP_914094.1 CDS Pden_0284 NC_008686.1 262191 262934 D PFAM: Asp/Glu racemase; KEGG: sme:SMb20431 hypothetical arylmalonate decarboxylase protein; Asp/Glu racemase 262191..262934 Paracoccus denitrificans PD1222 4580189 YP_914095.1 CDS eutB NC_008686.1 262931 263887 D catalyzes the formation of 2-oxobutanoate from L-threonine; involved in ectoine utilization; threonine dehydratase 262931..263887 Paracoccus denitrificans PD1222 4580190 YP_914096.1 CDS Pden_0286 NC_008686.1 263884 264861 D cyclodeaminase; ectoine utilization protein EutC 263884..264861 Paracoccus denitrificans PD1222 4580191 YP_914097.1 CDS Pden_0287 NC_008686.1 264873 266054 D PFAM: peptidase M24; KEGG: sme:SMb20434 hydrolasepeptidase protein; peptidase M24 264873..266054 Paracoccus denitrificans PD1222 4580192 YP_914098.1 CDS Pden_0288 NC_008686.1 266068 267069 D PFAM: Succinylglutamate desuccinylase/aspartoacylase; KEGG: sme:SMb20435 hypothetical protein; succinylglutamate desuccinylase/aspartoacylase 266068..267069 Paracoccus denitrificans PD1222 4580193 YP_914099.1 CDS Pden_0289 NC_008686.1 267066 268517 D PFAM: aldehyde dehydrogenase; KEGG: sil:SPO1137 succinate-semialdehyde dehydrogenase; succinate-semialdehyde dehydrogenase (NAD(P)(+)) 267066..268517 Paracoccus denitrificans PD1222 4580194 YP_914100.1 CDS Pden_0290 NC_008686.1 268517 269887 D PFAM: aminotransferase class-III; KEGG: sit:TM1040_2691 aminotransferase class-III; hypothetical protein 268517..269887 Paracoccus denitrificans PD1222 4580195 YP_914101.1 CDS Pden_0291 NC_008686.1 269891 271033 D PFAM: Alcohol dehydrogenase, zinc-binding domain protein; Alcohol dehydrogenase GroES domain protein; KEGG: csa:Csal_2340 alcohol dehydrogenase, zinc-binding; alcohol dehydrogenase 269891..271033 Paracoccus denitrificans PD1222 4580196 YP_914102.1 CDS Pden_0292 NC_008686.1 271049 272245 R PFAM: protein of unknown function DUF1006; KEGG: jan:Jann_2912 protein of unknown function DUF1006; hypothetical protein complement(271049..272245) Paracoccus denitrificans PD1222 4580197 YP_914103.1 CDS Pden_0293 NC_008686.1 272403 272990 R hypothetical protein complement(272403..272990) Paracoccus denitrificans PD1222 4580198 YP_914104.1 CDS Pden_0294 NC_008686.1 273336 275105 R PFAM: Hemolysin-type calcium-binding region; KEGG: sil:SPO1617 type I secretion target repeat protein; hemolysin-type calcium-binding protein complement(273336..275105) Paracoccus denitrificans PD1222 4580199 YP_914105.1 CDS Pden_0295 NC_008686.1 275682 276158 D KEGG: rsp:RSP_3055 transcriptional regulator, MarR family; MarR family transcriptional regulator 275682..276158 Paracoccus denitrificans PD1222 4580200 YP_914106.1 CDS Pden_0296 NC_008686.1 276190 278148 R PFAM: TonB-dependent receptor; TonB-dependent receptor, plug; KEGG: rsp:RSP_3056 TonB dependent-iron siderophore receptor; TonB-dependent receptor complement(276190..278148) Paracoccus denitrificans PD1222 4580201 YP_914107.1 CDS Pden_0297 NC_008686.1 278251 279009 R PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: atc:AGR_C_4492 ferrichrome ABC transporter (ATP-binding protein); ABC transporter complement(278251..279009) Paracoccus denitrificans PD1222 4580202 YP_914108.1 CDS Pden_0298 NC_008686.1 279006 279965 R PFAM: transport system permease protein; KEGG: atc:AGR_C_4491 ferrichrome ABC transporter (permease) homolog; transport system permease complement(279006..279965) Paracoccus denitrificans PD1222 4579694 YP_914109.1 CDS Pden_0299 NC_008686.1 279955 280911 R PFAM: transport system permease protein; KEGG: atc:AGR_C_4489 ferrichrome ABC transporter (permease); transport system permease complement(279955..280911) Paracoccus denitrificans PD1222 4579695 YP_914110.1 CDS Pden_0300 NC_008686.1 280913 281818 R PFAM: periplasmic binding protein; KEGG: atc:AGR_C_4488 unknown conserved protein; periplasmic binding protein complement(280913..281818) Paracoccus denitrificans PD1222 4579696 YP_914111.1 CDS Pden_0301 NC_008686.1 282034 283434 D 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 282034..283434 Paracoccus denitrificans PD1222 4579697 YP_914112.1 CDS Pden_0302 NC_008686.1 283449 284342 R PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: sme:SMa1782 LysR-family transcriptional regulator; LysR family transcriptional regulator complement(283449..284342) Paracoccus denitrificans PD1222 4579698 YP_914113.1 CDS Pden_0303 NC_008686.1 284436 284876 D PFAM: transmembrane pair domain protein; KEGG: sme:SMa1780 hypothetical protein; transmembrane pair domain-containing protein 284436..284876 Paracoccus denitrificans PD1222 4579699 YP_914114.1 CDS Pden_0304 NC_008686.1 284873 285757 R PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: mlo:mll4929 transcriptional regulator; LysR family transcriptional regulator complement(284873..285757) Paracoccus denitrificans PD1222 4579700 YP_914115.1 CDS Pden_0305 NC_008686.1 285838 286125 D hypothetical protein 285838..286125 Paracoccus denitrificans PD1222 4579701 YP_914116.1 CDS Pden_0306 NC_008686.1 286535 288052 R PFAM: protein of unknown function DUF112, transmembrane; KEGG: sme:SMb20726 conserved hypothetical membrane protein; hypothetical protein complement(286535..288052) Paracoccus denitrificans PD1222 4579702 YP_914117.1 CDS Pden_0307 NC_008686.1 288056 288550 R KEGG: atc:AGR_C_4484 tricarboxylic transport membrane protein; tricarboxylic transport membrane protein complement(288056..288550) Paracoccus denitrificans PD1222 4579703 YP_914118.1 CDS Pden_0308 NC_008686.1 288547 289488 R PFAM: Uncharacterized protein UPF0065; KEGG: sme:SMb20724 tricarboxylic transport membrane protein; hypothetical protein complement(288547..289488) Paracoccus denitrificans PD1222 4579704 YP_914119.1 CDS Pden_0309 NC_008686.1 289661 290758 R KEGG: atc:AGR_C_4480 periplasmic iron-binding protein; periplasmic iron-binding protein complement(289661..290758) Paracoccus denitrificans PD1222 4579705 YP_914120.1 CDS Pden_0310 NC_008686.1 290820 291491 D PFAM: response regulator receiver; transcriptional regulator domain protein; KEGG: sme:SMb20722 two-component response regulator protein; two component transcriptional regulator 290820..291491 Paracoccus denitrificans PD1222 4579706 YP_914121.1 CDS Pden_0311 NC_008686.1 291488 292918 D 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 291488..292918 Paracoccus denitrificans PD1222 4579707 YP_914122.1 CDS Pden_0312 NC_008686.1 293052 294146 D PFAM: protein of unknown function DUF475; KEGG: rsp:RSP_0459 hypothetical protein; hypothetical protein 293052..294146 Paracoccus denitrificans PD1222 4579708 YP_914123.1 CDS Pden_0313 NC_008686.1 294237 295178 D KEGG: sil:SPO0845 hypothetical protein; hypothetical protein 294237..295178 Paracoccus denitrificans PD1222 4579709 YP_914124.1 CDS Pden_0314 NC_008686.1 295262 295834 D PFAM: AmiS/UreI transporter; KEGG: bpa:BPP1188 transporter protein; AmiS/UreI transporter 295262..295834 Paracoccus denitrificans PD1222 4579710 YP_914125.1 CDS Pden_0315 NC_008686.1 295835 297919 R 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 complement(295835..297919) Paracoccus denitrificans PD1222 4579711 YP_914126.1 CDS Pden_0316 NC_008686.1 297929 298891 R PFAM: glycosyl transferase, family 2; KEGG: sil:SPO0853 glycosyl transferase, group 2 family protein; glycosyl transferase family protein complement(297929..298891) Paracoccus denitrificans PD1222 4579712 YP_914127.1 CDS Pden_0317 NC_008686.1 298982 300166 R PFAM: CBS domain containing protein; HPP family protein+B94; KEGG: rsp:RSP_0830 CBS-domain-containing membrane protein; hypothetical protein complement(298982..300166) Paracoccus denitrificans PD1222 4579713 YP_914128.1 CDS Pden_0318 NC_008686.1 300271 300927 R PFAM: regulatory protein GntR, HTH; GntR domain protein; KEGG: psb:Psyr_0495 regulatory protein, GntR:bacterial regulatory protein, GntR; GntR family transcriptional regulator complement(300271..300927) Paracoccus denitrificans PD1222 4578799 YP_914129.1 CDS Pden_0319 NC_008686.1 301221 302456 D KEGG: atc:AGR_L_1874 hypothetical protein; hypothetical protein 301221..302456 Paracoccus denitrificans PD1222 4578800 YP_914130.1 CDS Pden_0320 NC_008686.1 302525 303298 D PFAM: LamB/YcsF family protein; KEGG: pst:PSPTO_5378 LamB/YcsF family protein; LamB/YcsF family protein 302525..303298 Paracoccus denitrificans PD1222 4578801 YP_914131.1 CDS Pden_0321 NC_008686.1 303295 304086 D PFAM: protein of unknown function DUF1445; KEGG: atc:AGR_L_1868 hypothetical protein; hypothetical protein 303295..304086 Paracoccus denitrificans PD1222 4578802 YP_914132.1 CDS Pden_0322 NC_008686.1 304074 305642 D PFAM: Allophanate hydrolase subunit 2; Allophanate hydrolase subunit 1; KEGG: atc:AGR_L_1866 hypothetical protein; allophanate hydrolase subunit 2 304074..305642 Paracoccus denitrificans PD1222 4578803 YP_914133.1 CDS Pden_0323 NC_008686.1 305639 307405 D 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 305639..307405 Paracoccus denitrificans PD1222 4578804 YP_914134.1 CDS Pden_0324 NC_008686.1 307485 308516 D PFAM: ammonia monooxygenase; KEGG: jan:Jann_2088 ammonia monooxygenase; ammonia monooxygenase 307485..308516 Paracoccus denitrificans PD1222 4578805 YP_914135.1 CDS Pden_0325 NC_008686.1 308566 309129 D PFAM: protein of unknown function DUF886; KEGG: mlo:mlr8324 hypothetical protein; hypothetical protein 308566..309129 Paracoccus denitrificans PD1222 4578806 YP_914136.1 CDS Pden_0326 NC_008686.1 309179 310213 R PFAM: luciferase family protein; KEGG: mlo:mll2315 alkanal monooxygenase (bacterial liciferase alpha chain) like protein; luciferase family protein complement(309179..310213) Paracoccus denitrificans PD1222 4578807 YP_914137.1 CDS Pden_0327 NC_008686.1 310210 311184 R PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: pau:PA14_48770 transcriptional regulator; LysR family transcriptional regulator complement(310210..311184) Paracoccus denitrificans PD1222 4578808 YP_914138.1 CDS Pden_0328 NC_008686.1 311304 312248 D PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase; KEGG: sme:SMc01961 hypothetical protein; glyoxalase/bleomycin resistance protein/dioxygenase 311304..312248 Paracoccus denitrificans PD1222 4578809 YP_914139.1 CDS Pden_0329 NC_008686.1 312401 312802 D KEGG: bja:blr6753 hypothetical protein; hypothetical protein 312401..312802 Paracoccus denitrificans PD1222 4578810 YP_914140.1 CDS Pden_0330 NC_008686.1 312834 313427 R PFAM: NADPH-dependent FMN reductase; KEGG: mlo:mll2599 probable reductase; NADPH-dependent FMN reductase complement(312834..313427) Paracoccus denitrificans PD1222 4578811 YP_914141.1 CDS Pden_0331 NC_008686.1 313684 315213 R PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase; KEGG: sme:SMc01956 hypothetical protein; glyoxalase/bleomycin resistance protein/dioxygenase complement(313684..315213) Paracoccus denitrificans PD1222 4578812 YP_914142.1 CDS Pden_0332 NC_008686.1 315226 315843 R 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 complement(315226..315843) Paracoccus denitrificans PD1222 4578813 YP_914143.1 CDS trpA NC_008686.1 315957 316754 R catalyzes the formation of indole and glyceraldehyde 3-phosphate from indoleglycerol phosphate in tryptophan biosynthesis; tryptophan synthase subunit alpha complement(315957..316754) Paracoccus denitrificans PD1222 4578814 YP_914144.1 CDS Pden_0334 NC_008686.1 316884 317981 D 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 316884..317981 Paracoccus denitrificans PD1222 4578815 YP_914145.1 CDS Pden_0335 NC_008686.1 318371 319441 R PFAM: phage integrase family protein; KEGG: gox:GOX2318 prophage integrase; phage integrase family protein complement(318371..319441) Paracoccus denitrificans PD1222 4578816 YP_914146.1 CDS Pden_0336 NC_008686.1 319640 319954 R hypothetical protein complement(319640..319954) Paracoccus denitrificans PD1222 4578817 YP_914147.1 CDS Pden_0337 NC_008686.1 319992 320720 R KEGG: rsp:RSP_3624 hypothetical protein; hypothetical protein complement(319992..320720) Paracoccus denitrificans PD1222 4579035 YP_914148.1 CDS Pden_0338 NC_008686.1 320717 321160 R hypothetical protein complement(320717..321160) Paracoccus denitrificans PD1222 4579036 YP_914149.1 CDS Pden_0339 NC_008686.1 321356 322261 R KEGG: pst:PSPTO_3428 hypothetical protein; hypothetical protein complement(321356..322261) Paracoccus denitrificans PD1222 4579037 YP_914150.1 CDS Pden_0340 NC_008686.1 322258 322677 R hypothetical protein complement(322258..322677) Paracoccus denitrificans PD1222 4579038 YP_914151.1 CDS Pden_0341 NC_008686.1 322674 325319 R PFAM: DNA methylase N-4/N-6 domain protein; KEGG: mes:Meso_1199 helicase-like; DNA methylase N-4/N-6 domain-containing protein complement(322674..325319) Paracoccus denitrificans PD1222 4579039 YP_914152.1 CDS Pden_0342 NC_008686.1 325323 326441 R 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 complement(325323..326441) Paracoccus denitrificans PD1222 4579040 YP_914153.1 CDS Pden_0343 NC_008686.1 326577 326789 R hypothetical protein complement(326577..326789) Paracoccus denitrificans PD1222 4579041 YP_914154.1 CDS Pden_0344 NC_008686.1 327011 327613 D hypothetical protein 327011..327613 Paracoccus denitrificans PD1222 4579042 YP_914155.1 CDS Pden_0345 NC_008686.1 328067 328573 D hypothetical protein 328067..328573 Paracoccus denitrificans PD1222 4579043 YP_914156.1 CDS Pden_0346 NC_008686.1 328573 329100 D hypothetical protein 328573..329100 Paracoccus denitrificans PD1222 4579044 YP_914157.1 CDS Pden_0347 NC_008686.1 329084 329443 R hypothetical protein complement(329084..329443) Paracoccus denitrificans PD1222 4579045 YP_914158.1 CDS Pden_0348 NC_008686.1 329665 329997 D hypothetical protein 329665..329997 Paracoccus denitrificans PD1222 4579046 YP_914159.1 CDS Pden_0349 NC_008686.1 329990 330304 D hypothetical protein 329990..330304 Paracoccus denitrificans PD1222 4579047 YP_914160.1 CDS Pden_0350 NC_008686.1 330301 330513 D hypothetical protein 330301..330513 Paracoccus denitrificans PD1222 4579048 YP_914161.1 CDS Pden_0351 NC_008686.1 330675 331004 R hypothetical protein complement(330675..331004) Paracoccus denitrificans PD1222 4579049 YP_914162.1 CDS Pden_0352 NC_008686.1 331125 332267 D KEGG: sit:TM1040_1631 hypothetical protein; hypothetical protein 331125..332267 Paracoccus denitrificans PD1222 4579050 YP_914163.1 CDS Pden_0353 NC_008686.1 332260 334101 D TIGRFAM: phage/plasmid primase, P4 family; PFAM: Poxvirus D5 protein; KEGG: bld:BLi03629 hypothetical protein; P4 family phage/plasmid primase 332260..334101 Paracoccus denitrificans PD1222 4579051 YP_914164.1 CDS Pden_0354 NC_008686.1 334153 334449 R hypothetical protein complement(334153..334449) Paracoccus denitrificans PD1222 4579052 YP_914165.1 CDS Pden_0355 NC_008686.1 334560 335318 D KEGG: rsp:RSP_3778 hypothetical protein; hypothetical protein 334560..335318 Paracoccus denitrificans PD1222 4579053 YP_914166.1 CDS Pden_0356 NC_008686.1 335488 335838 D PFAM: HNH endonuclease; SMART: HNH nuclease; KEGG: rsp:RSP_2072 phage-related holin protein; HNH endonuclease 335488..335838 Paracoccus denitrificans PD1222 4579054 YP_914167.1 CDS Pden_0357 NC_008686.1 335888 336148 D hypothetical protein 335888..336148 Paracoccus denitrificans PD1222 4580514 YP_914168.1 CDS Pden_0358 NC_008686.1 336322 336825 D PFAM: Resolvase helix-turn-helix domain protein; KEGG: sit:TM1040_1626 hypothetical protein; resolvase domain-containing protein 336322..336825 Paracoccus denitrificans PD1222 4580515 YP_914169.1 CDS Pden_0359 NC_008686.1 336815 338536 D PFAM: phage Terminase; KEGG: rsp:RSP_2070 phage-related terminase; phage terminase 336815..338536 Paracoccus denitrificans PD1222 4580516 YP_914170.1 CDS Pden_0360 NC_008686.1 338536 339873 D TIGRFAM: phage portal protein, HK97 family; PFAM: phage portal protein; KEGG: rsp:RSP_2069 phage portal protein, HK97 family; HK97 family phage portal protein 338536..339873 Paracoccus denitrificans PD1222 4580517 YP_914171.1 CDS Pden_0361 NC_008686.1 339860 340702 D PFAM: peptidase S14, ClpP; KEGG: rsp:RSP_2068 ClpP-like protease; peptidase S14, ClpP 339860..340702 Paracoccus denitrificans PD1222 4580518 YP_914172.1 CDS Pden_0362 NC_008686.1 340714 342063 D TIGRFAM: phage major capsid protein, HK97 family; KEGG: rsp:RSP_2067 prophage LambdaSo, major capsid protein, HK97 family; HK97 family phage major capsid protein 340714..342063 Paracoccus denitrificans PD1222 4580519 YP_914173.1 CDS Pden_0363 NC_008686.1 342121 342429 D hypothetical protein 342121..342429 Paracoccus denitrificans PD1222 4580520 YP_914174.1 CDS Pden_0364 NC_008686.1 342471 342965 D hypothetical protein 342471..342965 Paracoccus denitrificans PD1222 4580521 YP_914175.1 CDS Pden_0365 NC_008686.1 342934 343482 D KEGG: sit:TM1040_1619 phage conserved hypothetical protein, phiE125 gp8; hypothetical protein 342934..343482 Paracoccus denitrificans PD1222 4580522 YP_914176.1 CDS Pden_0366 NC_008686.1 343476 343835 D TIGRFAM: phage head-tail adaptor; phage head-tail adaptor 343476..343835 Paracoccus denitrificans PD1222 4580523 YP_914177.1 CDS Pden_0367 NC_008686.1 343922 344218 D hypothetical protein 343922..344218 Paracoccus denitrificans PD1222 4580524 YP_914178.1 CDS Pden_0368 NC_008686.1 344215 344742 R hypothetical protein complement(344215..344742) Paracoccus denitrificans PD1222 4580525 YP_914179.1 CDS Pden_0369 NC_008686.1 344752 345042 D hypothetical protein 344752..345042 Paracoccus denitrificans PD1222 4580526 YP_914180.1 CDS Pden_0370 NC_008686.1 345234 345695 D hypothetical protein 345234..345695 Paracoccus denitrificans PD1222 4580527 YP_914181.1 CDS Pden_0371 NC_008686.1 345695 346084 D hypothetical protein 345695..346084 Paracoccus denitrificans PD1222 4580528 YP_914182.1 CDS Pden_0372 NC_008686.1 346245 349151 D KEGG: rsp:RSP_3791 hypothetical protein; hypothetical protein 346245..349151 Paracoccus denitrificans PD1222 4580529 YP_914183.1 CDS Pden_0373 NC_008686.1 349151 349831 D hypothetical protein 349151..349831 Paracoccus denitrificans PD1222 4580530 YP_914184.1 CDS Pden_0374 NC_008686.1 349828 350394 D hypothetical protein 349828..350394 Paracoccus denitrificans PD1222 4580531 YP_914185.1 CDS Pden_0375 NC_008686.1 350379 350750 D KEGG: mes:Meso_1234 hypothetical protein; hypothetical protein 350379..350750 Paracoccus denitrificans PD1222 4580532 YP_914186.1 CDS Pden_0376 NC_008686.1 350750 352792 D KEGG: nar:Saro_2739 hypothetical protein; hypothetical protein 350750..352792 Paracoccus denitrificans PD1222 4579558 YP_914187.1 CDS Pden_0377 NC_008686.1 352856 354613 D hypothetical protein 352856..354613 Paracoccus denitrificans PD1222 4579559 YP_914188.1 CDS Pden_0378 NC_008686.1 354623 355363 D hypothetical protein 354623..355363 Paracoccus denitrificans PD1222 4579560 YP_914189.1 CDS Pden_0379 NC_008686.1 355399 355695 D hypothetical protein 355399..355695 Paracoccus denitrificans PD1222 4579561 YP_914190.1 CDS Pden_0380 NC_008686.1 355711 355959 R hypothetical protein complement(355711..355959) Paracoccus denitrificans PD1222 4579562 YP_914191.1 CDS Pden_0381 NC_008686.1 356004 356636 D KEGG: syw:SYNW0477 hypothetical protein; hypothetical protein 356004..356636 Paracoccus denitrificans PD1222 4579563 YP_914192.1 CDS Pden_0382 NC_008686.1 356648 357043 D KEGG: rsp:RSP_6192 hypothetical protein; hypothetical protein 356648..357043 Paracoccus denitrificans PD1222 4579564 YP_914193.1 CDS Pden_0383 NC_008686.1 357161 357364 R hypothetical protein complement(357161..357364) Paracoccus denitrificans PD1222 4579565 YP_914194.1 CDS Pden_0384 NC_008686.1 357761 357928 R hypothetical protein complement(357761..357928) Paracoccus denitrificans PD1222 4579566 YP_914195.1 CDS Pden_0385 NC_008686.1 358047 359285 R PFAM: Resolvase, N-terminal domain; Recombinase; KEGG: nwi:Nwi_1951 resolvase; recombinase complement(358047..359285) Paracoccus denitrificans PD1222 4579567 YP_914196.1 CDS Pden_0386 NC_008686.1 359492 360115 D PFAM: protein of unknown function DUF159; KEGG: sit:TM1040_1580 protein of unknown function DUF159; hypothetical protein 359492..360115 Paracoccus denitrificans PD1222 4579568 YP_914197.1 CDS Pden_0387 NC_008686.1 360185 360424 D hypothetical protein 360185..360424 Paracoccus denitrificans PD1222 4579569 YP_914198.1 CDS Pden_0388 NC_008686.1 360445 360705 D hypothetical protein 360445..360705 Paracoccus denitrificans PD1222 4579570 YP_914199.1 CDS Pden_0389 NC_008686.1 361152 361484 D hypothetical protein 361152..361484 Paracoccus denitrificans PD1222 4579571 YP_914200.1 CDS Pden_0390 NC_008686.1 361651 362016 D PFAM: protein of unknown function DUF983; KEGG: ccr:CC1021 hypothetical protein; hypothetical protein 361651..362016 Paracoccus denitrificans PD1222 4579572 YP_914201.1 CDS Pden_0391 NC_008686.1 362346 362717 R hypothetical protein complement(362346..362717) Paracoccus denitrificans PD1222 4579573 YP_914202.1 CDS Pden_0392 NC_008686.1 362922 363236 D KEGG: jan:Jann_0243 hypothetical protein; hypothetical protein 362922..363236 Paracoccus denitrificans PD1222 4579574 YP_914203.1 CDS Pden_0393 NC_008686.1 363233 363715 D KEGG: bms:BR0799 hypothetical protein; hypothetical protein 363233..363715 Paracoccus denitrificans PD1222 4579575 YP_914204.1 CDS Pden_0394 NC_008686.1 364225 364824 D KEGG: rde:RD1_A0063 succinoglycan biosynthesis protein ExoI; hypothetical protein 364225..364824 Paracoccus denitrificans PD1222 4579576 YP_914205.1 CDS Pden_0395 NC_008686.1 365115 365942 D PFAM: diaminopimelate epimerase; KEGG: sil:SPO0278 diaminopimelate epimerase; diaminopimelate epimerase 365115..365942 Paracoccus denitrificans PD1222 4579577 YP_914206.1 CDS Pden_0396 NC_008686.1 365939 367201 D 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 365939..367201 Paracoccus denitrificans PD1222 4578683 YP_914207.1 CDS Pden_0397 NC_008686.1 367359 368318 D PFAM: histone deacetylase superfamily; KEGG: rsp:RSP_1137 histone deacetylase family protein; histone deacetylase superfamily protein 367359..368318 Paracoccus denitrificans PD1222 4578684 YP_914208.1 CDS Pden_0398 NC_008686.1 368315 368557 D TIGRFAM: exodeoxyribonuclease VII, small subunit; PFAM: Exonuclease VII, small subunit; KEGG: jan:Jann_0090 exodeoxyribonuclease VII, small subunit; exodeoxyribonuclease VII small subunit 368315..368557 Paracoccus denitrificans PD1222 4578685 YP_914209.1 CDS Pden_0399 NC_008686.1 368557 369420 D PFAM: Polyprenyl synthetase; KEGG: rsp:RSP_1135 geranylgeranyl pyrophosphate synthetase; polyprenyl synthetase 368557..369420 Paracoccus denitrificans PD1222 4578686 YP_914210.1 CDS Pden_0400 NC_008686.1 369446 371368 D catalyzes the formation of 1-deoxy-D-xylulose 5-phosphate from pyruvate and D-glyceraldehyde 3-phosphate; 1-deoxy-D-xylulose-5-phosphate synthase 369446..371368 Paracoccus denitrificans PD1222 4578687 YP_914211.1 CDS Pden_0401 NC_008686.1 371378 371998 D PFAM: SH3, type 3 domain protein; KEGG: sil:SPO0041 hypothetical protein; SH3 type 3 domain-containing protein 371378..371998 Paracoccus denitrificans PD1222 4578688 YP_914212.1 CDS Pden_0402 NC_008686.1 371995 372858 R PFAM: NAD-dependent epimerase/dehydratase; dTDP-4-dehydrorhamnose reductase; KEGG: jan:Jann_0273 NAD-dependent epimerase/dehydratase; NAD-dependent epimerase/dehydratase complement(371995..372858) Paracoccus denitrificans PD1222 4578689 YP_914213.1 CDS Pden_0403 NC_008686.1 372855 373841 R PFAM: luciferase family protein; KEGG: sil:SPO2518 bacterial luciferase family protein; luciferase family protein complement(372855..373841) Paracoccus denitrificans PD1222 4578690 YP_914214.1 CDS Pden_0404 NC_008686.1 373937 375421 D Catalyzes the hydrolysis of AMP to form adenine and ribose 5-phosphate using water as the nucleophile; AMP nucleosidase 373937..375421 Paracoccus denitrificans PD1222 4578691 YP_914215.1 CDS Pden_0405 NC_008686.1 375573 375872 D PFAM: histone family protein DNA-binding protein; KEGG: rsp:RSP_1388 DNA-binding protein HU, form N; histone family protein DNA-binding protein 375573..375872 Paracoccus denitrificans PD1222 4578692 YP_914216.1 CDS Pden_0406 NC_008686.1 376017 376937 D PFAM: protein of unknown function DUF6, transmembrane; KEGG: rsp:RSP_1390 transporter, DMT superfamily; hypothetical protein 376017..376937 Paracoccus denitrificans PD1222 4578693 YP_914217.1 CDS Pden_0407 NC_008686.1 376892 377485 R KEGG: hne:HNE_1223 glutathione S-transferase; glutathione S-transferase complement(376892..377485) Paracoccus denitrificans PD1222 4578694 YP_914218.1 CDS Pden_0408 NC_008686.1 377546 378247 D PFAM: Helix-turn-helix, type 11 domain protein; KEGG: hne:HNE_1222 hypothetical protein; helix-turn-helix, type 11 domain-containing protein 377546..378247 Paracoccus denitrificans PD1222 4578695 YP_914219.1 CDS Pden_0409 NC_008686.1 378225 379646 R PFAM: aminotransferase, class V; KEGG: ret:RHE_PE00221 hypothetical protein; class V aminotransferase complement(378225..379646) Paracoccus denitrificans PD1222 4578696 YP_914220.1 CDS Pden_0410 NC_008686.1 379720 380193 D PFAM: regulatory protein, AsnC/Lrp family; KEGG: ret:RHE_PE00222 probable transcriptional regulator protein, AsnC family; AsnC family transcriptional regulator 379720..380193 Paracoccus denitrificans PD1222 4578697 YP_914221.1 CDS Pden_0411 NC_008686.1 380224 381213 D KEGG: ret:RHE_CH01163 exonuclease protein involved in mRNA processing; exonuclease protein involved in mRNA processing 380224..381213 Paracoccus denitrificans PD1222 4578698 YP_914222.1 CDS Pden_0412 NC_008686.1 381210 382754 D PFAM: ATP dependent DNA ligase domain protein; ATP dependent DNA ligase; KEGG: ccr:CC3610 DNA ligase, ATP-dependent; ATP dependent DNA ligase 381210..382754 Paracoccus denitrificans PD1222 4578699 YP_914223.1 CDS Pden_0413 NC_008686.1 382751 385186 D 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 382751..385186 Paracoccus denitrificans PD1222 4578700 YP_914224.1 CDS Pden_0414 NC_008686.1 385183 385839 D KEGG: rsp:RSP_0659 metallo-phosphoesterase; metallo-phosphoesterase 385183..385839 Paracoccus denitrificans PD1222 4578701 YP_914225.1 CDS Pden_0415 NC_008686.1 385901 386668 R KEGG: mlo:mll1390 outer membrane protein; outer membrane protein complement(385901..386668) Paracoccus denitrificans PD1222 4579461 YP_914226.1 CDS gyrB NC_008686.1 386880 389318 R negatively supercoils closed circular double-stranded DNA; DNA gyrase subunit B complement(386880..389318) Paracoccus denitrificans PD1222 4579462 YP_914227.1 CDS Pden_0417 NC_008686.1 389505 389840 R PFAM: protein of unknown function DUF1491; KEGG: rsp:RSP_1677 hypothetical protein; hypothetical protein complement(389505..389840) Paracoccus denitrificans PD1222 4579463 YP_914228.1 CDS era NC_008686.1 389833 390744 R 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 complement(389833..390744) Paracoccus denitrificans PD1222 4579464 YP_914229.1 CDS Pden_0419 NC_008686.1 390741 391466 R PFAM: ribonuclease III; double-stranded RNA binding domain protein; KEGG: rsp:RSP_1675 ribonuclease III; ribonuclease III complement(390741..391466) Paracoccus denitrificans PD1222 4579465 YP_914230.1 CDS Pden_0420 NC_008686.1 391475 392266 R KEGG: rsp:RSP_1674 type 1 signal peptidase; TIGRFAM: signal peptidase I; PFAM: peptidase S24, S26A and S26B; signal peptidase I complement(391475..392266) Paracoccus denitrificans PD1222 4579466 YP_914231.1 CDS acpS NC_008686.1 392326 392745 R 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 complement(392326..392745) Paracoccus denitrificans PD1222 4579467 YP_914232.1 CDS Pden_0422 NC_008686.1 392794 393528 R involved in the de novo synthesis of pyridoxine (Vitamin B6); pyridoxine 5'-phosphate synthase complement(392794..393528) Paracoccus denitrificans PD1222 4579468 YP_914233.1 CDS Pden_0423 NC_008686.1 393559 394380 R 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 complement(393559..394380) Paracoccus denitrificans PD1222 4579469 YP_914234.1 CDS Pden_0424 NC_008686.1 394384 396312 R PFAM: TPR repeat-containing protein; Tetratricopeptide TPR_2 repeat protein; SMART: Tetratricopeptide domain protein; KEGG: rde:RD1_3403 TPR domain protein; hypothetical protein complement(394384..396312) Paracoccus denitrificans PD1222 4579470 YP_914235.1 CDS Pden_0425 NC_008686.1 396309 397955 R 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 complement(396309..397955) Paracoccus denitrificans PD1222 4579471 YP_914236.1 CDS greA NC_008686.1 398232 398702 D 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 398232..398702 Paracoccus denitrificans PD1222 4579472 YP_914237.1 CDS Pden_0427 NC_008686.1 398720 399667 D KEGG: sil:SPO0311 hypothetical protein; hypothetical protein 398720..399667 Paracoccus denitrificans PD1222 4579473 YP_914238.1 CDS Pden_0428 NC_008686.1 399664 400251 R PFAM: GCN5-related N-acetyltransferase; KEGG: rsp:RSP_0736 MobC protein; N-acetyltransferase complement(399664..400251) Paracoccus denitrificans PD1222 4579474 YP_914239.1 CDS Pden_0429 NC_008686.1 400357 401133 D PFAM: AzlC family protein; KEGG: rsp:RSP_0739 branched chain amino acid efflux pump, large (AzlC) subunit; AzlC family protein 400357..401133 Paracoccus denitrificans PD1222 4579475 YP_914240.1 CDS Pden_0430 NC_008686.1 401130 401462 D PFAM: branched-chain amino acid transport; KEGG: rde:RD1_3412 hypothetical protein; branched-chain amino acid transport 401130..401462 Paracoccus denitrificans PD1222 4579476 YP_914241.1 CDS Pden_0431 NC_008686.1 401447 402094 R KEGG: rsp:RSP_6127 hypothetical protein; hypothetical protein complement(401447..402094) Paracoccus denitrificans PD1222 4579477 YP_914242.1 CDS Pden_0432 NC_008686.1 402118 402318 R 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 complement(402118..402318) Paracoccus denitrificans PD1222 4579478 YP_914243.1 CDS Pden_0433 NC_008686.1 402332 403354 R PFAM: beta-lactamase domain protein; KEGG: rsp:RSP_0741 metallo-beta-lactamase family protein; beta-lactamase domain-containing protein complement(402332..403354) Paracoccus denitrificans PD1222 4579479 YP_914244.1 CDS Pden_0434 NC_008686.1 403351 405042 R 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 complement(403351..405042) Paracoccus denitrificans PD1222 4579480 YP_914245.1 CDS Pden_0435 NC_008686.1 405159 406109 D 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 405159..406109 Paracoccus denitrificans PD1222 4578838 YP_914246.1 CDS Pden_0436 NC_008686.1 406113 406685 R PFAM: protein of unknown function DUF179; KEGG: sil:SPO0296 transcriptional regulator; hypothetical protein complement(406113..406685) Paracoccus denitrificans PD1222 4578839 YP_914247.1 CDS Pden_0437 NC_008686.1 406794 407576 D KEGG: rde:RD1_3420 hypothetical protein; hypothetical protein 406794..407576 Paracoccus denitrificans PD1222 4578840 YP_914248.1 CDS Pden_0438 NC_008686.1 407573 408388 R 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 complement(407573..408388) Paracoccus denitrificans PD1222 4578841 YP_914249.1 CDS Pden_0439 NC_008686.1 408494 408895 R hypothetical protein complement(408494..408895) Paracoccus denitrificans PD1222 4578842 YP_914250.1 CDS Pden_0440 NC_008686.1 409050 410171 D catalyzes the oxidation of 3-isopropylmalate to 3-carboxy-4-methyl-2-oxopentanoate in leucine biosynthesis; 3-isopropylmalate dehydrogenase 409050..410171 Paracoccus denitrificans PD1222 4578843 YP_914251.1 CDS Pden_0441 NC_008686.1 410232 411185 D PFAM: protein of unknown function DUF6, transmembrane; KEGG: rsp:RSP_0858 transporter, RhaT family, DMT superfamily; hypothetical protein 410232..411185 Paracoccus denitrificans PD1222 4578844 YP_914252.1 CDS Pden_0442 NC_008686.1 411827 412228 D hypothetical protein 411827..412228 Paracoccus denitrificans PD1222 4578845 YP_914253.1 CDS Pden_0443 NC_008686.1 412240 412752 D PFAM: protein of unknown function DUF955; KEGG: gbe:GbCGDNIH1_1521 hypothetical protein; hypothetical protein 412240..412752 Paracoccus denitrificans PD1222 4578846 YP_914254.1 CDS Pden_0444 NC_008686.1 412764 413840 D KEGG: gbe:GbCGDNIH1_1520 hypothetical protein; hypothetical protein 412764..413840 Paracoccus denitrificans PD1222 4578847 YP_914255.1 CDS Pden_0445 NC_008686.1 414070 414585 D KEGG: sil:SPOA0122 ISSpo9, transposase; hypothetical protein 414070..414585 Paracoccus denitrificans PD1222 4578848 YP_914256.1 CDS Pden_0446 NC_008686.1 415141 416178 D PFAM: zinc finger, CHC2-family protein; KEGG: bpa:BPP0490 DNA primase; CHC2-family zinc finger protein 415141..416178 Paracoccus denitrificans PD1222 4578849 YP_914257.1 CDS Pden_0447 NC_008686.1 416175 419363 D KEGG: bpa:BPP0491 hypothetical protein; hypothetical protein 416175..419363 Paracoccus denitrificans PD1222 4578850 YP_914258.1 CDS Pden_0448 NC_008686.1 419360 420268 D KEGG: bpa:BPP0493 hypothetical protein; hypothetical protein 419360..420268 Paracoccus denitrificans PD1222 4578851 YP_914259.1 CDS Pden_0449 NC_008686.1 420268 421179 D PFAM: Exonuclease, RNase T and DNA polymerase III; SMART: Exonuclease; KEGG: ret:RHE_PE00402 probable polymerase epsilon subunit protein; exonuclease 420268..421179 Paracoccus denitrificans PD1222 4578852 YP_914260.1 CDS Pden_0450 NC_008686.1 421270 421986 R KEGG: bmb:BruAb2_0399 hypothetical protein; hypothetical protein complement(421270..421986) Paracoccus denitrificans PD1222 4578853 YP_914261.1 CDS Pden_0451 NC_008686.1 421964 422515 R KEGG: bmb:BruAb2_0400 hypothetical protein; hypothetical protein complement(421964..422515) Paracoccus denitrificans PD1222 4578854 YP_914262.1 CDS Pden_0453 NC_008686.1 423504 423761 R hypothetical protein complement(423504..423761) Paracoccus denitrificans PD1222 4578855 YP_914263.1 CDS Pden_0454 NC_008686.1 423758 424588 R hypothetical protein complement(423758..424588) Paracoccus denitrificans PD1222 4578856 YP_914264.1 CDS Pden_0455 NC_008686.1 424675 424929 D PFAM: helix-turn-helix domain protein; KEGG: rde:RD1_0810 DNA-binding protein; helix-turn-helix domain-containing protein 424675..424929 Paracoccus denitrificans PD1222 4580027 YP_914265.1 CDS Pden_0456 NC_008686.1 425445 425816 R hypothetical protein complement(425445..425816) Paracoccus denitrificans PD1222 4580028 YP_914266.1 CDS Pden_0457 NC_008686.1 425929 426456 D KEGG: rpb:RPB_2539 hypothetical protein; hypothetical protein 425929..426456 Paracoccus denitrificans PD1222 4580029 YP_914267.1 CDS Pden_0458 NC_008686.1 426466 428598 D PFAM: Integrase, catalytic region; KEGG: bmb:BruAb1_0746 transposase, hypothetical; integrase catalytic subunit 426466..428598 Paracoccus denitrificans PD1222 4580030 YP_914268.1 CDS Pden_0459 NC_008686.1 428588 429586 D KEGG: rde:RD1_0796 transposition protein; transposition protein 428588..429586 Paracoccus denitrificans PD1222 4580031 YP_914269.1 CDS Pden_0460 NC_008686.1 429588 431069 D KEGG: nha:Nham_2090 hypothetical protein; hypothetical protein 429588..431069 Paracoccus denitrificans PD1222 4580032 YP_914270.1 CDS Pden_0461 NC_008686.1 431234 432751 D PFAM: Integrase, catalytic region; KEGG: sme:SMc03282 transposase number 1 for insertion sequence ISRM27; integrase catalytic subunit 431234..432751 Paracoccus denitrificans PD1222 4580033 YP_914271.1 CDS Pden_0462 NC_008686.1 432748 433326 D PFAM: IstB domain protein ATP-binding protein; KEGG: sme:SMc03281 transposase; IstB ATP binding domain-containing protein 432748..433326 Paracoccus denitrificans PD1222 4580034 YP_914272.1 CDS Pden_0463 NC_008686.1 433296 434282 D PFAM: Recombinase; KEGG: rsp:RSP_3812 recombinase; recombinase 433296..434282 Paracoccus denitrificans PD1222 4580035 YP_914273.1 CDS Pden_0464 NC_008686.1 434326 435324 D 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 434326..435324 Paracoccus denitrificans PD1222 4580036 YP_914274.1 CDS Pden_0466 NC_008686.1 436286 437371 D 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 436286..437371 Paracoccus denitrificans PD1222 4580037 YP_914275.1 CDS Pden_0467 NC_008686.1 437384 438448 D KEGG: bmb:BruAb2_0855 hypothetical spermidine/putrescine ABC transporter, periplasmic spermidine/putrescine-binding protein; spermidine/putrescine-binding protein 437384..438448 Paracoccus denitrificans PD1222 4580038 YP_914276.1 CDS Pden_0468 NC_008686.1 438445 439695 D 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 438445..439695 Paracoccus denitrificans PD1222 4580039 YP_914277.1 CDS Pden_0469 NC_008686.1 439692 440477 D 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 439692..440477 Paracoccus denitrificans PD1222 4580040 YP_914278.1 CDS Pden_0470 NC_008686.1 440577 441365 D PFAM: regulatory protein GntR, HTH; GntR domain protein; KEGG: pau:PA14_72890 transcriptional regulator; GntR family transcriptional regulator 440577..441365 Paracoccus denitrificans PD1222 4580041 YP_914279.1 CDS Pden_0471 NC_008686.1 441610 442539 D PFAM: protein of unknown function DUF849; KEGG: bur:Bcep18194_C7701 protein of unknown function DUF849; hypothetical protein 441610..442539 Paracoccus denitrificans PD1222 4580042 YP_914280.1 CDS Pden_0472 NC_008686.1 442556 444619 D PFAM: Hydantoinase/oxoprolinase; Hydantoinaseoxoprolinase domain protein; KEGG: reu:Reut_C6223 5-oxoprolinase (ATP-hydrolyzing); 5-oxoprolinase 442556..444619 Paracoccus denitrificans PD1222 4580043 YP_914281.1 CDS Pden_0473 NC_008686.1 444631 446397 D PFAM: Hydantoinase B/oxoprolinase; KEGG: reu:Reut_C6222 hydantoinase B/oxoprolinase; hydantoinase B/oxoprolinase 444631..446397 Paracoccus denitrificans PD1222 4580044 YP_914282.1 CDS fabG NC_008686.1 446394 447158 D catalyzes the first of the two reduction steps in the elongation cycle of fatty acid synthesis; 3-ketoacyl-ACP reductase 446394..447158 Paracoccus denitrificans PD1222 4580045 YP_914283.1 CDS Pden_0475 NC_008686.1 447146 447538 D hypothetical protein 447146..447538 Paracoccus denitrificans PD1222 4580046 YP_914284.1 CDS Pden_0476 NC_008686.1 447538 447990 D PFAM: thioesterase superfamily protein; KEGG: bja:blr1345 hypothetical protein; thioesterase 447538..447990 Paracoccus denitrificans PD1222 4579093 YP_914285.1 CDS Pden_0477 NC_008686.1 448044 448658 D 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 448044..448658 Paracoccus denitrificans PD1222 4579094 YP_914286.1 CDS Pden_0478 NC_008686.1 448844 450010 D PFAM: protein of unknown function DUF1100, hydrolase family protein; KEGG: ppu:PP_3195 hypothetical protein; hypothetical protein 448844..450010 Paracoccus denitrificans PD1222 4579095 YP_914287.1 CDS Pden_0479 NC_008686.1 450007 450780 D PFAM: short-chain dehydrogenase/reductase SDR; KEGG: reu:Reut_C6224 short-chain dehydrogenase/reductase SDR; short-chain dehydrogenase/reductase SDR 450007..450780 Paracoccus denitrificans PD1222 4579096 YP_914288.1 CDS Pden_0480 NC_008686.1 450916 452154 D PFAM: major facilitator superfamily MFS_1; KEGG: rha:RHA1_ro04907 transporter, MFS superfamily; major facilitator superfamily transporter 450916..452154 Paracoccus denitrificans PD1222 4579097 YP_914289.1 CDS Pden_0481 NC_008686.1 452349 452849 R KEGG: gbe:GbCGDNIH1_1799 transposase; hypothetical protein complement(452349..452849) Paracoccus denitrificans PD1222 4579098 YP_914290.1 CDS Pden_0482 NC_008686.1 453006 453269 D PFAM: SpoVT/AbrB domain protein; KEGG: sme:SMc03949 nitrogen regulatory protein; SpoVT/AbrB domain-containing protein 453006..453269 Paracoccus denitrificans PD1222 4579099 YP_914291.1 CDS Pden_0483 NC_008686.1 453266 453667 D PFAM: PilT protein domain protein; SMART: Nucleotide binding protein, PINc; KEGG: sme:SMa0981 probable NtrR2 transcription regulator; twitching motility protein PilT 453266..453667 Paracoccus denitrificans PD1222 4579100 YP_914292.1 CDS Pden_0484 NC_008686.1 454495 454833 D KEGG: eba:ebB86 RelE-like cytotoxic translational repressor of toxin-antitoxin stability system; RelE-like cytotoxic translational repressor of toxin-antitoxin stability system 454495..454833 Paracoccus denitrificans PD1222 4579101 YP_914293.1 CDS Pden_0485 NC_008686.1 454815 455108 D KEGG: noc:Noc_2738 transcriptional regulator, XRE family; XRE family transcriptional regulator 454815..455108 Paracoccus denitrificans PD1222 4579102 YP_914294.1 CDS Pden_0486 NC_008686.1 455218 455601 D KEGG: sme:SMc01416 hypothetical protein; hypothetical protein 455218..455601 Paracoccus denitrificans PD1222 4579103 YP_914295.1 CDS Pden_0487 NC_008686.1 455768 456088 R hypothetical protein complement(455768..456088) Paracoccus denitrificans PD1222 4579104 YP_914296.1 CDS Pden_0488 NC_008686.1 456189 460739 R 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 complement(456189..460739) Paracoccus denitrificans PD1222 4579105 YP_914297.1 CDS Pden_0489 NC_008686.1 460736 461500 R KEGG: rsp:RSP_1148 hypothetical protein; hypothetical protein complement(460736..461500) Paracoccus denitrificans PD1222 4579106 YP_914298.1 CDS Pden_0490 NC_008686.1 461513 463006 R function undetermined; similar to glutamate synthase beta subunit and related oxidoreductases which transfer electrons from NADPH to an acceptor protein or protein domain; oxidoreductase complement(461513..463006) Paracoccus denitrificans PD1222 4579107 YP_914299.1 CDS Pden_0491 NC_008686.1 463157 463960 R 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 complement(463157..463960) Paracoccus denitrificans PD1222 4579108 YP_914300.1 CDS Pden_0492 NC_008686.1 463960 464952 R 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 complement(463960..464952) Paracoccus denitrificans PD1222 4579109 YP_914301.1 CDS Pden_0493 NC_008686.1 464983 466581 R PFAM: glucose-methanol-choline oxidoreductase; GMC oxidoreductase; KEGG: ter:Tery_1077 glucose-methanol-choline oxidoreductase; glucose-methanol-choline oxidoreductase complement(464983..466581) Paracoccus denitrificans PD1222 4579110 YP_914302.1 CDS Pden_0494 NC_008686.1 467184 467624 D PFAM: NUDIX hydrolase; KEGG: rsp:RSP_1208 NUDIX hydrolase; NUDIX hydrolase 467184..467624 Paracoccus denitrificans PD1222 4579111 YP_914303.1 CDS Pden_0495 NC_008686.1 467633 468904 R 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 complement(467633..468904) Paracoccus denitrificans PD1222 4581037 YP_914304.1 CDS Pden_0496 NC_008686.1 469024 469374 D PFAM: Hpt domain protein; KEGG: sit:TM1040_2886 Hpt protein; Hpt protein 469024..469374 Paracoccus denitrificans PD1222 4581038 YP_914305.1 CDS Pden_0497 NC_008686.1 469382 470620 R catalyzes the formation of 2-oxobutanoate from L-threonine; biosynthetic; threonine dehydratase complement(469382..470620) Paracoccus denitrificans PD1222 4581039 YP_914306.1 CDS Pden_0498 NC_008686.1 470699 471541 R hypothetical protein complement(470699..471541) Paracoccus denitrificans PD1222 4581040 YP_914307.1 CDS Pden_0499 NC_008686.1 471591 472817 D catalyzes the formation of 2-N(omega)-(L-arginino)succinate from L-citrulline and L-aspartate in arginine biosynthesis, AMP-forming; argininosuccinate synthase 471591..472817 Paracoccus denitrificans PD1222 4581041 YP_914308.1 CDS Pden_0500 NC_008686.1 472955 473434 D PFAM: 3-demethylubiquinone-9 3-methyltransferase; KEGG: nwi:Nwi_0688 3-demethylubiquinone-9 3-methyltransferase; 3-demethylubiquinone-9 3-methyltransferase 472955..473434 Paracoccus denitrificans PD1222 4581042 YP_914309.1 CDS Pden_0501 NC_008686.1 473477 474028 D TIGRFAM: molybdenum cofactor synthesis domain; PFAM: molybdopterin binding domain; KEGG: bmb:BruAb2_0726 MogA, molybdenum cofactor biosynthesis protein; molybdenum cofactor synthesis domain-containing protein 473477..474028 Paracoccus denitrificans PD1222 4581043 YP_914310.1 CDS Pden_0502 NC_008686.1 474003 474617 R KEGG: rsp:RSP_0986 hypothetical protein; hypothetical protein complement(474003..474617) Paracoccus denitrificans PD1222 4581044 YP_914311.1 CDS Pden_0503 NC_008686.1 474658 475452 R PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sme:SMc02169 ATP-binding ABC transporter protein; ABC transporter complement(474658..475452) Paracoccus denitrificans PD1222 4581045 YP_914312.1 CDS Pden_0504 NC_008686.1 475449 476522 R PFAM: inner-membrane translocator; KEGG: rsp:RSP_0989 ABC sugar transporter, inner membrane subunit; inner-membrane translocator complement(475449..476522) Paracoccus denitrificans PD1222 4581046 YP_914313.1 CDS Pden_0505 NC_008686.1 476615 477634 R PFAM: periplasmic binding protein/LacI transcriptional regulator; KEGG: rsp:RSP_0990 ABC sugar transporter, periplasmic sugar binding subunit; periplasmic binding protein/LacI transcriptional regulator complement(476615..477634) Paracoccus denitrificans PD1222 4581047 YP_914314.1 CDS Pden_0506 NC_008686.1 477754 478944 D PFAM: ROK family protein; regulatory protein, MarR; KEGG: rsp:RSP_0991 transcriptional regulator, ROK family; ROK family protein 477754..478944 Paracoccus denitrificans PD1222 4581048 YP_914315.1 CDS Pden_0507 NC_008686.1 478963 479877 D PFAM: heat shock protein DnaJ domain protein; chaperone DnaJ domain protein; KEGG: sme:SMa0116 DnaJ/CbpA-type protein; molecular chaperone DnaJ 478963..479877 Paracoccus denitrificans PD1222 4581049 YP_914316.1 CDS Pden_0508 NC_008686.1 479874 480221 D KEGG: rru:Rru_A2016 hypothetical protein; hypothetical protein 479874..480221 Paracoccus denitrificans PD1222 4581050 YP_914317.1 CDS Pden_0509 NC_008686.1 480218 480385 R PFAM: protein of unknown function DUF1289; KEGG: jan:Jann_2180 protein of unknown function DUF1289; hypothetical protein complement(480218..480385) Paracoccus denitrificans PD1222 4581051 YP_914318.1 CDS Pden_0510 NC_008686.1 480382 480858 R similar to RuvC resolvase with substantial differences; NMR structural information suggests this protein is monomeric; unknown cellular function; Holliday junction resolvase-like protein complement(480382..480858) Paracoccus denitrificans PD1222 4581052 YP_914319.1 CDS Pden_0511 NC_008686.1 480855 482102 R KEGG: rsp:RSP_2685 cytochrome c-type biogenesis protein, CycH; cytochrome c-type biogenesis protein, CycH complement(480855..482102) Paracoccus denitrificans PD1222 4581053 YP_914320.1 CDS Pden_0512 NC_008686.1 482305 483576 D TIGRFAM: sarcosine oxidase, beta subunit family; PFAM: FAD dependent oxidoreductase; KEGG: rsp:RSP_2686 sarcosine oxidase beta subunit; sarcosine oxidase subunit beta 482305..483576 Paracoccus denitrificans PD1222 4581054 YP_914321.1 CDS Pden_0513 NC_008686.1 483734 483985 D KEGG: rsp:RSP_1403 conserved hypoothetical protein; hypothetical protein 483734..483985 Paracoccus denitrificans PD1222 4581055 YP_914322.1 CDS Pden_0514 NC_008686.1 484296 484676 D PFAM: Sarcosine oxidase, delta subunit, heterotetrameric; KEGG: rsp:RSP_2688 sarcosine oxidase delta subunit protein; sarcosine oxidase, delta subunit, heterotetrameric 484296..484676 Paracoccus denitrificans PD1222 4581056 YP_914323.1 CDS Pden_0515 NC_008686.1 484673 487606 D 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 484673..487606 Paracoccus denitrificans PD1222 4578702 YP_914324.1 CDS Pden_0516 NC_008686.1 487599 488117 D PFAM: Sarcosine oxidase, gamma subunit; KEGG: rsp:RSP_2690 sarcosine oxidase gamma subunit; sarcosine oxidase, gamma subunit 487599..488117 Paracoccus denitrificans PD1222 4578703 YP_914325.1 CDS Pden_0517 NC_008686.1 488190 488645 D KEGG: rde:RD1_1770 hypothetical protein; hypothetical protein 488190..488645 Paracoccus denitrificans PD1222 4578704 YP_914326.1 CDS Pden_0518 NC_008686.1 488754 489353 D PFAM: manganese and iron superoxide dismutase; KEGG: rsp:RSP_2693 superoxide dismutase, Fe-Mn family; superoxide dismutase 488754..489353 Paracoccus denitrificans PD1222 4578705 YP_914327.1 CDS Pden_0519 NC_008686.1 489405 489929 D PFAM: protein of unknown function DUF461; KEGG: rde:RD1_1682 hypothetical protein; hypothetical protein 489405..489929 Paracoccus denitrificans PD1222 4578706 YP_914328.1 CDS Pden_0520 NC_008686.1 489926 490564 R PFAM: lipolytic enzyme, G-D-S-L family; KEGG: rsp:RSP_3601 lipolytic enzyme, G-D-S-L family; GDSL family lipase complement(489926..490564) Paracoccus denitrificans PD1222 4578707 YP_914329.1 CDS Pden_0521 NC_008686.1 490561 492984 R 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 complement(490561..492984) Paracoccus denitrificans PD1222 4578708 YP_914330.1 CDS Pden_0522 NC_008686.1 493412 493990 D PFAM: ErfK/YbiS/YcfS/YnhG family protein; KEGG: mes:Meso_4112 ErfK/YbiS/YcfS/YnhG; ErfK/YbiS/YcfS/YnhG family protein 493412..493990 Paracoccus denitrificans PD1222 4578709 YP_914331.1 CDS Pden_0523 NC_008686.1 493991 495088 D 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 493991..495088 Paracoccus denitrificans PD1222 4578710 YP_914332.1 CDS Pden_0524 NC_008686.1 495107 495910 R 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 complement(495107..495910) Paracoccus denitrificans PD1222 4578711 YP_914333.1 CDS Pden_0525 NC_008686.1 495894 496859 R PFAM: inner-membrane translocator; KEGG: rsp:RSP_2208 ABC sugar transporter, inner membrane subunit; inner-membrane translocator complement(495894..496859) Paracoccus denitrificans PD1222 4578712 YP_914334.1 CDS Pden_0526 NC_008686.1 496859 498037 R PFAM: inner-membrane translocator; KEGG: rsp:RSP_2209 ABC sugar transporter, inner membrane subunit; inner-membrane translocator complement(496859..498037) Paracoccus denitrificans PD1222 4578713 YP_914335.1 CDS Pden_0527 NC_008686.1 498015 499640 R PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sil:SPO0378 sugar ABC transporter, ATP-binding protein; ABC transporter complement(498015..499640) Paracoccus denitrificans PD1222 4578714 YP_914336.1 CDS Pden_0528 NC_008686.1 499640 500626 R PFAM: basic membrane lipoprotein; KEGG: rsp:RSP_2211 ABC transporter, periplasmic substrate-binding protein; basic membrane lipoprotein complement(499640..500626) Paracoccus denitrificans PD1222 4578715 YP_914337.1 CDS Pden_0529 NC_008686.1 500718 501119 R TIGRFAM: ribosomal-protein-alanine acetyltransferase; PFAM: GCN5-related N-acetyltransferase; KEGG: rsp:RSP_2212 acetyltransferase; ribosomal-protein-alanine acetyltransferase complement(500718..501119) Paracoccus denitrificans PD1222 4578716 YP_914338.1 CDS Pden_0530 NC_008686.1 501116 501709 R PFAM: peptidase M22, glycoprotease; KEGG: rsp:RSP_2213 hypothetical protein; peptidase M22, glycoprotease complement(501116..501709) Paracoccus denitrificans PD1222 4578717 YP_914339.1 CDS Pden_0531 NC_008686.1 501702 502256 R PFAM: nitrogen-fixing NifU domain protein; KEGG: sit:TM1040_3091 nitrogen-fixing NifU-like; NifU domain-containing protein complement(501702..502256) Paracoccus denitrificans PD1222 4578718 YP_914340.1 CDS Pden_0532 NC_008686.1 502470 502925 R PFAM: UspA domain protein; KEGG: sit:TM1040_3730 UspA; UspA domain-containing protein complement(502470..502925) Paracoccus denitrificans PD1222 4578719 YP_914341.1 CDS Pden_0533 NC_008686.1 503082 503831 D PFAM: sugar transferase; KEGG: rsp:RSP_1189 sugar transferase; sugar transferase 503082..503831 Paracoccus denitrificans PD1222 4578720 YP_914342.1 CDS truA NC_008686.1 504029 504814 R mediates pseudouridylation (positions 38, 39, 40) at the tRNA anticodon region which contributes to the structural stability; tRNA pseudouridine synthase A complement(504029..504814) Paracoccus denitrificans PD1222 4579772 YP_914343.1 CDS Pden_0535 NC_008686.1 504818 505792 R KEGG: sil:SPO2985 hypothetical protein; hypothetical protein complement(504818..505792) Paracoccus denitrificans PD1222 4579773 YP_914344.1 CDS Pden_0536 NC_008686.1 506263 507711 D PFAM: cation transporter; KEGG: rsp:RSP_1854 potassium uptake transporter, transmembrane component, TrkH; cation transporter 506263..507711 Paracoccus denitrificans PD1222 4579774 YP_914345.1 CDS Pden_0537 NC_008686.1 507708 508946 R PFAM: Peptidoglycan-binding domain 1 protein; KEGG: rsp:RSP_1855 hypothetical protein; peptidoglycan binding domain-containing protein complement(507708..508946) Paracoccus denitrificans PD1222 4579775 YP_914346.1 CDS glyQ NC_008686.1 509237 510187 D 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 509237..510187 Paracoccus denitrificans PD1222 4579776 YP_914347.1 CDS Pden_0539 NC_008686.1 510184 510666 D KEGG: sit:TM1040_2311 conserved hypothetical protein; signal transduction histidine kinase regulating citrate/malate metabolism 510184..510666 Paracoccus denitrificans PD1222 4579777 YP_914348.1 CDS Pden_0540 NC_008686.1 510666 512723 D KEGG: rsp:RSP_1858 glycyl-tRNA synthetase beta subunit; glycine--tRNA ligase 510666..512723 Paracoccus denitrificans PD1222 4579778 YP_914349.1 CDS Pden_0541 NC_008686.1 512830 515391 D catalyzes the formation of phosphoenolpyruvate from pyruvate; pyruvate phosphate dikinase 512830..515391 Paracoccus denitrificans PD1222 4579779 YP_914350.1 CDS Pden_0542 NC_008686.1 515619 516158 D PFAM: cell wall hydrolase, SleB; KEGG: rsp:RSP_1860 hypothetical protein; cell wall hydrolase SleB 515619..516158 Paracoccus denitrificans PD1222 4579780 YP_914351.1 CDS Pden_0543 NC_008686.1 516201 517019 D PFAM: dihydroneopterin aldolase; KEGG: rsp:RSP_1861 probable dihydroneopterin aldolase; dihydroneopterin aldolase 516201..517019 Paracoccus denitrificans PD1222 4579781 YP_914352.1 CDS Pden_0544 NC_008686.1 517064 518035 D KEGG: rsp:RSP_1862 dihydropteroate synthase, DhpS; TIGRFAM: dihydropteroate synthase; PFAM: dihydropteroate synthase, DHPS; dihydropteroate synthase 517064..518035 Paracoccus denitrificans PD1222 4579782 YP_914353.1 CDS glmM NC_008686.1 518046 519389 D catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate; phosphoglucosamine mutase 518046..519389 Paracoccus denitrificans PD1222 4579783 YP_914354.1 CDS Pden_0546 NC_008686.1 519472 520593 R PFAM: monooxygenase, FAD-binding; KEGG: rsp:RSP_2656 salicylate hydroxylase (salicylate 1-monooxygenase); FAD-binding monooxygenase complement(519472..520593) Paracoccus denitrificans PD1222 4579784 YP_914355.1 CDS Pden_0547 NC_008686.1 520635 521057 R 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 complement(520635..521057) Paracoccus denitrificans PD1222 4579785 YP_914356.1 CDS Pden_0548 NC_008686.1 521219 522058 D 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 521219..522058 Paracoccus denitrificans PD1222 4579786 YP_914357.1 CDS Pden_0549 NC_008686.1 522070 522510 D PFAM: GCN5-related N-acetyltransferase; KEGG: rde:RD1_2794 acetyltransferase; N-acetyltransferase 522070..522510 Paracoccus denitrificans PD1222 4579787 YP_914358.1 CDS Pden_0550 NC_008686.1 522559 523053 R PFAM: Lytic transglycosylase, catalytic; KEGG: sil:SPO2284 transglycosylase SLT domain protein; lytic transglycosylase, catalytic complement(522559..523053) Paracoccus denitrificans PD1222 4579788 YP_914359.1 CDS Pden_0551 NC_008686.1 523200 524594 R 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 complement(523200..524594) Paracoccus denitrificans PD1222 4579789 YP_914360.1 CDS Pden_0552 NC_008686.1 524645 525037 R KEGG: jan:Jann_0835 inner membrane protein; inner membrane protein complement(524645..525037) Paracoccus denitrificans PD1222 4579790 YP_914361.1 CDS Pden_0553 NC_008686.1 525037 525294 R hypothetical protein complement(525037..525294) Paracoccus denitrificans PD1222 4579791 YP_914362.1 CDS Pden_0554 NC_008686.1 525437 526969 R 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 complement(525437..526969) Paracoccus denitrificans PD1222 4579675 YP_914363.1 CDS sucA NC_008686.1 526971 529937 R 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 complement(526971..529937) Paracoccus denitrificans PD1222 4579676 YP_914364.1 CDS Pden_0556 NC_008686.1 529934 530182 R hypothetical protein complement(529934..530182) Paracoccus denitrificans PD1222 4579677 YP_914365.1 CDS Pden_0557 NC_008686.1 530201 530545 D hypothetical protein 530201..530545 Paracoccus denitrificans PD1222 4579678 YP_914366.1 CDS Pden_0558 NC_008686.1 530589 531473 R 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 complement(530589..531473) Paracoccus denitrificans PD1222 4579679 YP_914367.1 CDS sucC NC_008686.1 531478 532671 R catalyzes the interconversion of succinyl-CoA and succinate; succinyl-CoA synthetase subunit beta complement(531478..532671) Paracoccus denitrificans PD1222 4579680 YP_914368.1 CDS Pden_0560 NC_008686.1 532894 536133 D PFAM: Hemolysin-type calcium-binding region; KEGG: pol:Bpro_4929 hemolysin-type calcium-binding region; hemolysin-type calcium-binding protein 532894..536133 Paracoccus denitrificans PD1222 4579681 YP_914369.1 CDS Pden_0561 NC_008686.1 536193 537155 R Catalyzes the reversible oxidation of malate to oxaloacetate; malate dehydrogenase complement(536193..537155) Paracoccus denitrificans PD1222 4579682 YP_914370.1 CDS Pden_0562 NC_008686.1 537341 538075 D PFAM: protein of unknown function DUF81; KEGG: rsp:RSP_0969 integral membrane protein; hypothetical protein 537341..538075 Paracoccus denitrificans PD1222 4579683 YP_914371.1 CDS Pden_0563 NC_008686.1 538156 538995 D PFAM: HpcH/HpaI aldolase; KEGG: rsp:RSP_0970 citrate lyase beta chain; citryl-CoA lyase 538156..538995 Paracoccus denitrificans PD1222 4579684 YP_914372.1 CDS Pden_0564 NC_008686.1 539041 539592 D PFAM: NnrUfamily protein; KEGG: jan:Jann_0815 NnrU; NnrU family protein 539041..539592 Paracoccus denitrificans PD1222 4579685 YP_914373.1 CDS Pden_0565 NC_008686.1 539594 539800 D KEGG: sil:SPO0354 hypothetical protein; hypothetical protein 539594..539800 Paracoccus denitrificans PD1222 4579686 YP_914374.1 CDS Pden_0566 NC_008686.1 539810 540844 D PFAM: MaoC domain protein dehydratase; KEGG: sil:SPO0355 hypothetical protein; dehydratase 539810..540844 Paracoccus denitrificans PD1222 4579687 YP_914375.1 CDS Pden_0567 NC_008686.1 541157 541549 D PFAM: succinate dehydrogenase, cytochrome b subunit; KEGG: rsp:RSP_0974 succinate dehydrogenase cytochrome b-556 subunit; succinate dehydrogenase, cytochrome b subunit 541157..541549 Paracoccus denitrificans PD1222 4579688 YP_914376.1 CDS Pden_0568 NC_008686.1 541566 541955 D KEGG: rsp:RSP_0975 succinate dehydrogenase, hydrophobic membrane anchor protein; succinate dehydrogenase, hydrophobic membrane anchor protein 541566..541955 Paracoccus denitrificans PD1222 4579689 YP_914377.1 CDS sdhA NC_008686.1 541965 543767 D 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 541965..543767 Paracoccus denitrificans PD1222 4579690 YP_914378.1 CDS Pden_0570 NC_008686.1 543767 544123 D KEGG: jan:Jann_0807 hypothetical protein; hypothetical protein 543767..544123 Paracoccus denitrificans PD1222 4579691 YP_914379.1 CDS Pden_0571 NC_008686.1 544123 544449 D KEGG: rsp:RSP_0978 hypothetical protein; hypothetical protein 544123..544449 Paracoccus denitrificans PD1222 4579692 YP_914380.1 CDS sdhB NC_008686.1 544520 545299 D 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 544520..545299 Paracoccus denitrificans PD1222 4579693 YP_914381.1 CDS Pden_0573 NC_008686.1 545816 546649 D KEGG: rde:RD1_1633 hypothetical protein; hypothetical protein 545816..546649 Paracoccus denitrificans PD1222 4579617 YP_914382.1 CDS Pden_0574 NC_008686.1 546646 547338 R PFAM: beta-lactamase domain protein; KEGG: rsp:RSP_2268 metallo beta lactamase superfamily; beta-lactamase domain-containing protein complement(546646..547338) Paracoccus denitrificans PD1222 4579618 YP_914383.1 CDS gatC NC_008686.1 547470 547757 D 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 547470..547757 Paracoccus denitrificans PD1222 4579619 YP_914384.1 CDS gatA NC_008686.1 547754 549235 D 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 547754..549235 Paracoccus denitrificans PD1222 4579620 YP_914385.1 CDS Pden_0577 NC_008686.1 549259 549783 D KEGG: rsp:RSP_2271 hypothetical protein; hypothetical protein 549259..549783 Paracoccus denitrificans PD1222 4579621 YP_914386.1 CDS Pden_0578 NC_008686.1 549780 550406 D PFAM: N-acetylmuramoyl-L-alanine amidase, family 2; KEGG: rsp:RSP_2272 N-acetylmuramoyl-L-alanine amidase, family 2; N-acetylmuramoyl-L-alanine amidase 549780..550406 Paracoccus denitrificans PD1222 4579622 YP_914387.1 CDS Pden_0579 NC_008686.1 550394 551167 R PFAM: protein of unknown function DUF519; KEGG: sil:SPO0421 hypothetical protein; hypothetical protein complement(550394..551167) Paracoccus denitrificans PD1222 4579623 YP_914388.1 CDS Pden_0580 NC_008686.1 551716 552015 R PFAM: protein of unknown function DUF1127; KEGG: sit:TM1040_2023 protein of unknown function DUF1127; hypothetical protein complement(551716..552015) Paracoccus denitrificans PD1222 4579624 YP_914389.1 CDS Pden_0581 NC_008686.1 552277 553380 D KEGG: rsp:RSP_2093 Mrp (multidrug resistance-associated proteins) family protein; Mrp (multidrug resistance-associated proteins) family protein 552277..553380 Paracoccus denitrificans PD1222 4579625 YP_914390.1 CDS Pden_0582 NC_008686.1 554021 554530 D MraZ; UPF0040; crystal structure shows similarity to AbrB; cell division protein MraZ 554021..554530 Paracoccus denitrificans PD1222 4579626 YP_914391.1 CDS mraW NC_008686.1 554532 555500 D TIGRFAM: S-adenosyl-methyltransferase MraW; PFAM: methyltransferase; KEGG: rsp:RSP_6038 methyltransferase MraW/YabC; S-adenosyl-methyltransferase MraW 554532..555500 Paracoccus denitrificans PD1222 4579627 YP_914392.1 CDS Pden_0584 NC_008686.1 555500 555883 D KEGG: sil:SPO1180 hypothetical protein; hypothetical protein 555500..555883 Paracoccus denitrificans PD1222 4579628 YP_914393.1 CDS Pden_0585 NC_008686.1 555880 557685 D PFAM: penicillin-binding protein, transpeptidase; Penicillin-binding protein, dimerisation domain; KEGG: rsp:RSP_2098 cell division protein FtsI/penicillin-binding protein 2; peptidoglycan glycosyltransferase 555880..557685 Paracoccus denitrificans PD1222 4579629 YP_914394.1 CDS murE NC_008686.1 557715 559184 D 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 557715..559184 Paracoccus denitrificans PD1222 4579630 YP_914395.1 CDS Pden_0587 NC_008686.1 559181 560566 D 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 559181..560566 Paracoccus denitrificans PD1222 4579631 YP_914396.1 CDS mraY NC_008686.1 560566 561648 D First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan; phospho-N-acetylmuramoyl-pentapeptide- transferase 560566..561648 Paracoccus denitrificans PD1222 4579632 YP_914397.1 CDS murD NC_008686.1 561731 563131 D 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 561731..563131 Paracoccus denitrificans PD1222 4579633 YP_914398.1 CDS Pden_0590 NC_008686.1 563332 564489 R PFAM: membrane protein involved in aromatic hydrocarbon degradation; KEGG: rsp:RSP_0007 outer membrane protein; aromatic hydrocarbon degradation membrane protein complement(563332..564489) Paracoccus denitrificans PD1222 4579634 YP_914399.1 CDS Pden_0591 NC_008686.1 564656 565627 D KEGG: rsp:RSP_2869 possible tellurite resistance protein; tellurite resistance protein 564656..565627 Paracoccus denitrificans PD1222 4579635 YP_914400.1 CDS Pden_0592 NC_008686.1 565697 567145 D 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 565697..567145 Paracoccus denitrificans PD1222 4579636 YP_914401.1 CDS Pden_0593 NC_008686.1 567470 568273 D KEGG: rsp:RSP_1319 possible invasion protein; hypothetical protein 567470..568273 Paracoccus denitrificans PD1222 4579637 YP_914402.1 CDS Pden_0594 NC_008686.1 568349 569500 D PFAM: Fmu (Sun) domain protein; KEGG: rsp:RSP_0455 possible NOL1/NOP2/sun family protein; Fmu (Sun) domain-containing protein 568349..569500 Paracoccus denitrificans PD1222 4579638 YP_914403.1 CDS Pden_0595 NC_008686.1 569558 571600 D 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 569558..571600 Paracoccus denitrificans PD1222 4579639 YP_914404.1 CDS Pden_0596 NC_008686.1 571624 572208 R KEGG: rsp:RSP_0453 hypothetical protein; hypothetical protein complement(571624..572208) Paracoccus denitrificans PD1222 4579640 YP_914405.1 CDS recA NC_008686.1 572452 573522 D 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 572452..573522 Paracoccus denitrificans PD1222 4579641 YP_914406.1 CDS alaS NC_008686.1 573749 576406 D 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 573749..576406 Paracoccus denitrificans PD1222 4579642 YP_914407.1 CDS Pden_0599 NC_008686.1 576403 576693 D PFAM: protein of unknown function DUF1330; KEGG: rsp:RSP_0450 hypothetical protein; hypothetical protein 576403..576693 Paracoccus denitrificans PD1222 4579643 YP_914408.1 CDS Pden_0600 NC_008686.1 576760 577554 D KEGG: rsp:RSP_0449 glutamine amidotransferase; glutamine amidotransferase 576760..577554 Paracoccus denitrificans PD1222 4579644 YP_914409.1 CDS Pden_0601 NC_008686.1 577694 577939 R hypothetical protein complement(577694..577939) Paracoccus denitrificans PD1222 4579645 YP_914410.1 CDS Pden_0602 NC_008686.1 577960 578181 R hypothetical protein complement(577960..578181) Paracoccus denitrificans PD1222 4579646 YP_914411.1 CDS Pden_0603 NC_008686.1 578569 579861 D catalyzes the formation of N6-(1,2,-dicarboxyethyl)-AMP from L-aspartate, inosine monophosphate and GTP in AMP biosynthesis; adenylosuccinate synthetase 578569..579861 Paracoccus denitrificans PD1222 4579647 YP_914412.1 CDS Pden_0604 NC_008686.1 579873 580085 D KEGG: sil:SPO1317 hypothetical protein; hypothetical protein 579873..580085 Paracoccus denitrificans PD1222 4579648 YP_914413.1 CDS Pden_0605 NC_008686.1 580103 580738 D TIGRFAM: thiamine pyrophosphokinase; PFAM: Thiamin pyrophosphokinase, catalytic region; KEGG: rde:RD1_1915 thiamine pyrophosphokinase; thiamine pyrophosphokinase 580103..580738 Paracoccus denitrificans PD1222 4579649 YP_914414.1 CDS Pden_0606 NC_008686.1 580824 581795 R 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 complement(580824..581795) Paracoccus denitrificans PD1222 4579650 YP_914415.1 CDS Pden_0607 NC_008686.1 581788 582795 R 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 complement(581788..582795) Paracoccus denitrificans PD1222 4579651 YP_914416.1 CDS Pden_0608 NC_008686.1 582803 584503 R 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 complement(582803..584503) Paracoccus denitrificans PD1222 4579652 YP_914417.1 CDS Pden_0609 NC_008686.1 584724 586553 D 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 584724..586553 Paracoccus denitrificans PD1222 4579653 YP_914418.1 CDS Pden_0610 NC_008686.1 586652 587821 D KEGG: sit:TM1040_0719 peptidase M20D, amidohydrolase; TIGRFAM: amidohydrolase; PFAM: peptidase M20; peptidase dimerisation domain protein; amidohydrolase 586652..587821 Paracoccus denitrificans PD1222 4579654 YP_914419.1 CDS Pden_0611 NC_008686.1 587908 589299 R E3 component of pyruvate complex; catalyzes the oxidation of dihydrolipoamide to lipoamide; dihydrolipoamide dehydrogenase complement(587908..589299) Paracoccus denitrificans PD1222 4579655 YP_914420.1 CDS Pden_0612 NC_008686.1 589345 589926 R PFAM: protein of unknown function DUF924; KEGG: sil:SPO2224 hypothetical protein; hypothetical protein complement(589345..589926) Paracoccus denitrificans PD1222 4578996 YP_914421.1 CDS Pden_0613 NC_008686.1 589984 591234 R PFAM: major facilitator superfamily MFS_1; KEGG: rsp:RSP_2970 transporter, major facilitator superfamily (MFS); major facilitator superfamily transporter complement(589984..591234) Paracoccus denitrificans PD1222 4578997 YP_914422.1 CDS queA NC_008686.1 591234 592313 R Synthesizes oQ from preQ1 in a single S-adenosylmethionine-requiring step; S-adenosylmethionine--tRNA ribosyltransferase-isomerase complement(591234..592313) Paracoccus denitrificans PD1222 4578998 YP_914423.1 CDS Pden_0615 NC_008686.1 592411 592701 D KEGG: sit:TM1040_2200 bacterioferritin-associated ferredoxin; bacterioferritin-associated ferredoxin 592411..592701 Paracoccus denitrificans PD1222 4578999 YP_914424.1 CDS Pden_0616 NC_008686.1 592649 593134 D TIGRFAM: bacterioferritin; PFAM: Rubrerythrin; Ferritin, Dps family protein; KEGG: rsp:RSP_3342 bacterioferritin; bacterioferritin 592649..593134 Paracoccus denitrificans PD1222 4579000 YP_914425.1 CDS Pden_0617 NC_008686.1 593194 593868 R 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 complement(593194..593868) Paracoccus denitrificans PD1222 4579001 YP_914426.1 CDS glmU NC_008686.1 593973 595313 D 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 593973..595313 Paracoccus denitrificans PD1222 4579002 YP_914427.1 CDS Pden_0619 NC_008686.1 595315 597132 D Catalyzes the first step in hexosamine metabolism, converting fructose-6P into glucosamine-6P using glutamine as a nitrogen source; glucosamine--fructose-6-phosphate aminotransferase 595315..597132 Paracoccus denitrificans PD1222 4579003 YP_914428.1 CDS Pden_0620 NC_008686.1 597136 598119 R PFAM: peptidase S58, DmpA; KEGG: sit:TM1040_2667 peptidase S58, DmpA; peptidase S58, DmpA complement(597136..598119) Paracoccus denitrificans PD1222 4579004 YP_914429.1 CDS Pden_0621 NC_008686.1 598259 598843 D KEGG: rpa:RPA4834 peptide methionine sulfoxide reductase; TIGRFAM: peptide methionine sulfoxide reductase; PFAM: Methionine sulfoxide reductase A; peptide methionine sulfoxide reductase 598259..598843 Paracoccus denitrificans PD1222 4579005 YP_914430.1 CDS Pden_0622 NC_008686.1 598844 599713 D PFAM: methyltransferase small; ribosomal L11 methyltransferase; Methyltransferase type 11; KEGG: sit:TM1040_2376 ribosomal L11 methyltransferase; ribosomal L11 methyltransferase 598844..599713 Paracoccus denitrificans PD1222 4579006 YP_914431.1 CDS Pden_0623 NC_008686.1 599834 600028 R PFAM: protein of unknown function DUF1127; KEGG: sit:TM1040_2374 protein of unknown function DUF1127; hypothetical protein complement(599834..600028) Paracoccus denitrificans PD1222 4579007 YP_914432.1 CDS Pden_0624 NC_008686.1 600267 600986 R 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 complement(600267..600986) Paracoccus denitrificans PD1222 4579008 YP_914433.1 CDS ubiA NC_008686.1 601003 601974 D 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 601003..601974 Paracoccus denitrificans PD1222 4579009 YP_914434.1 CDS Pden_0626 NC_008686.1 602001 604307 D PFAM: OmpA/MotB domain protein; KEGG: rde:RD1_4081 OmpA domain protein; OmpA/MotB domain-containing protein 602001..604307 Paracoccus denitrificans PD1222 4579010 YP_914435.1 CDS Pden_0627 NC_008686.1 604338 604664 D KEGG: rsp:RSP_1011 hypothetical protein; hypothetical protein 604338..604664 Paracoccus denitrificans PD1222 4579011 YP_914436.1 CDS Pden_0628 NC_008686.1 604661 605521 R hypothetical protein complement(604661..605521) Paracoccus denitrificans PD1222 4579012 YP_914437.1 CDS Pden_0629 NC_008686.1 605518 605964 R hypothetical protein complement(605518..605964) Paracoccus denitrificans PD1222 4579013 YP_914438.1 CDS Pden_0630 NC_008686.1 606107 607291 R catalyzes the formation of L-glutamate and an aromatic oxo acid from an aromatic amino acid and 2-oxoglutarate; aromatic amino acid aminotransferase complement(606107..607291) Paracoccus denitrificans PD1222 4579014 YP_914439.1 CDS Pden_0631 NC_008686.1 607291 608151 R PFAM: Rhodanese domain protein; KEGG: rsp:RSP_0885 thiosulfate sulfurtransferase, rhodanese-like; 3-mercaptopyruvate sulfurtransferase complement(607291..608151) Paracoccus denitrificans PD1222 4579015 YP_914440.1 CDS smpB NC_008686.1 608217 608687 R 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 complement(608217..608687) Paracoccus denitrificans PD1222 4580243 YP_914441.1 CDS Pden_0633 NC_008686.1 608839 610500 D catalyzes the formation of 2-acetolactate from pyruvate, leucine sensitive; also known as acetolactate synthase large subunit; thiamine pyrophosphate protein 608839..610500 Paracoccus denitrificans PD1222 4580244 YP_914442.1 CDS Pden_0634 NC_008686.1 610511 611935 R PFAM: phosphate transporter; KEGG: rsp:RSP_2170 phosphate transporter, Pit family; phosphate transporter complement(610511..611935) Paracoccus denitrificans PD1222 4580245 YP_914443.1 CDS Pden_0635 NC_008686.1 611932 612402 R PFAM: NUDIX hydrolase; KEGG: sit:TM1040_0668 NUDIX hydrolase; NUDIX hydrolase complement(611932..612402) Paracoccus denitrificans PD1222 4580246 YP_914444.1 CDS Pden_0636 NC_008686.1 612399 612830 R PFAM: Class I peptide chain release factor; KEGG: rsp:RSP_1366 hypothetical protein; peptidyl-tRNA hydrolase domain-containing protein complement(612399..612830) Paracoccus denitrificans PD1222 4580247 YP_914445.1 CDS Pden_0637 NC_008686.1 612897 614948 R 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 complement(612897..614948) Paracoccus denitrificans PD1222 4580248 YP_914446.1 CDS Pden_0638 NC_008686.1 615033 616142 R PFAM: conserved hypothetical protein 1620; KEGG: sil:SPO3140 hypothetical protein; hypothetical protein complement(615033..616142) Paracoccus denitrificans PD1222 4580249 YP_914447.1 CDS Pden_0639 NC_008686.1 616152 617519 R PFAM: protein of unknown function DUF463, YcjX family protein; KEGG: sil:SPO3142 hypothetical protein; hypothetical protein complement(616152..617519) Paracoccus denitrificans PD1222 4580250 YP_914448.1 CDS Pden_0640 NC_008686.1 617618 620026 D 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 617618..620026 Paracoccus denitrificans PD1222 4580251 YP_914449.1 CDS Pden_0641 NC_008686.1 620066 620614 R KEGG: bpe:BP1216 hypothetical protein; hypothetical protein complement(620066..620614) Paracoccus denitrificans PD1222 4580252 YP_914450.1 CDS Pden_0642 NC_008686.1 620768 621661 R TIGRFAM: methionyl-tRNA formyltransferase; PFAM: formyl transferase domain protein; KEGG: rsp:RSP_0875 methionyl-tRNA formyl transferase; methionyl-tRNA formyltransferase complement(620768..621661) Paracoccus denitrificans PD1222 4580253 YP_914451.1 CDS Pden_0643 NC_008686.1 621688 622566 R KEGG: mmr:Mmar10_2929 dienelactone hydrolase; dienelactone hydrolase complement(621688..622566) Paracoccus denitrificans PD1222 4580254 YP_914452.1 CDS Pden_0644 NC_008686.1 622551 624188 R KEGG: sit:TM1040_1832 conserved hypothetical protein; hypothetical protein complement(622551..624188) Paracoccus denitrificans PD1222 4580255 YP_914453.1 CDS Pden_0645 NC_008686.1 624493 624993 R TIGRFAM: peptide deformylase; PFAM: formylmethionine deformylase; KEGG: rsp:RSP_0874 formylmethionine deformylase; peptide deformylase complement(624493..624993) Paracoccus denitrificans PD1222 4580256 YP_914454.1 CDS Pden_0646 NC_008686.1 625277 625834 R PFAM: formylmethionine deformylase; KEGG: rsp:RSP_0872 formylmethionine deformylase; peptide deformylase complement(625277..625834) Paracoccus denitrificans PD1222 4580257 YP_914455.1 CDS Pden_0647 NC_008686.1 625827 626348 R KEGG: rsp:RSP_0872 formylmethionine deformylase; TIGRFAM: peptide deformylase; PFAM: formylmethionine deformylase; peptide deformylase complement(625827..626348) Paracoccus denitrificans PD1222 4580258 YP_914456.1 CDS Pden_0648 NC_008686.1 626439 627623 D PFAM: aminotransferase, class I and II; KEGG: rsp:RSP_0871 aminotransferase; class I and II aminotransferase 626439..627623 Paracoccus denitrificans PD1222 4580259 YP_914457.1 CDS Pden_0649 NC_008686.1 627620 628249 D PFAM: ErfK/YbiS/YcfS/YnhG family protein; KEGG: sat:SYN_02183 protein ErfK; ErfK/YbiS/YcfS/YnhG family protein 627620..628249 Paracoccus denitrificans PD1222 4580260 YP_914458.1 CDS Pden_0650 NC_008686.1 628306 629682 D 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 628306..629682 Paracoccus denitrificans PD1222 4580261 YP_914459.1 CDS Pden_0651 NC_008686.1 629713 629949 D PFAM: regulatory protein, AsnC/Lrp family; KEGG: rsp:RSP_0958 RAM domain protein; AsnC family transcriptional regulator 629713..629949 Paracoccus denitrificans PD1222 4578956 YP_914460.1 CDS Pden_0652 NC_008686.1 629991 631136 D catalyzes the formation of histidinol phosphate and 2-oxoglutarate from glutamate and imidazole acetol-phosphate; histidinol-phosphate aminotransferase 629991..631136 Paracoccus denitrificans PD1222 4578957 YP_914461.1 CDS Pden_0653 NC_008686.1 631186 631668 R PFAM: regulatory protein, AsnC/Lrp family; KEGG: rde:RD1_2963 glutamate uptake regulatory protein; AsnC family transcriptional regulator complement(631186..631668) Paracoccus denitrificans PD1222 4578958 YP_914462.1 CDS Pden_0654 NC_008686.1 631740 632120 D KEGG: rsp:RSP_1943 hypothetical protein; hypothetical protein 631740..632120 Paracoccus denitrificans PD1222 4578959 YP_914463.1 CDS Pden_0655 NC_008686.1 632113 633768 D 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 632113..633768 Paracoccus denitrificans PD1222 4578960 YP_914464.1 CDS Pden_0656 NC_008686.1 633761 634492 D catalyzes the reduction of 3'-phosphoadenylyl sulfate into sulfite; phosphoadenosine phosphosulfate reductase 633761..634492 Paracoccus denitrificans PD1222 4578961 YP_914465.1 CDS Pden_0657 NC_008686.1 634489 634860 D KEGG: rsp:RSP_1940 hypothetical protein; hypothetical protein 634489..634860 Paracoccus denitrificans PD1222 4578962 YP_914466.1 CDS Pden_0658 NC_008686.1 634914 635750 D PFAM: oxidoreductase FAD/NAD(P)-binding domain protein; Oxidoreductase FAD-binding domain protein; KEGG: rsp:RSP_1939 NADPH-ferredoxin reductase; ferredoxin-NADP reductase 634914..635750 Paracoccus denitrificans PD1222 4578963 YP_914467.1 CDS Pden_0659 NC_008686.1 635875 638430 D catalyzes the ATP-dependent breakage of single-stranded DNA followed by passage and rejoining, maintains net negative superhelicity; DNA topoisomerase I 635875..638430 Paracoccus denitrificans PD1222 4578964 YP_914468.1 CDS Pden_0660 NC_008686.1 638639 640381 D KEGG: rru:Rru_A0385 gamma-glutamyltransferase; TIGRFAM: gamma-glutamyltransferase; PFAM: gamma-glutamyltranspeptidase; gamma-glutamyltransferase 638639..640381 Paracoccus denitrificans PD1222 4578965 YP_914469.1 CDS Pden_0661 NC_008686.1 640375 640722 R PFAM: protein of unknown function DUF488; KEGG: rfr:Rfer_4130 protein of unknown function DUF488; hypothetical protein complement(640375..640722) Paracoccus denitrificans PD1222 4578966 YP_914470.1 CDS Pden_0662 NC_008686.1 641089 642597 R TIGRFAM: amino acid carrier protein; PFAM: sodium:alanine symporter; KEGG: sme:SMc04263 amino acid carrier transmembrane protein; amino acid carrier protein complement(641089..642597) Paracoccus denitrificans PD1222 4578967 YP_914471.1 CDS Pden_0663 NC_008686.1 642700 644766 R 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 complement(642700..644766) Paracoccus denitrificans PD1222 4578968 YP_914472.1 CDS Pden_0664 NC_008686.1 644849 645850 R TIGRFAM: TRAP transporter solute receptor, TAXI family; KEGG: bmb:BruAb1_1199 outer membrane protein, hypothetical; TRAP transporter solute receptor TAXI family protein complement(644849..645850) Paracoccus denitrificans PD1222 4578969 YP_914473.1 CDS Pden_0665 NC_008686.1 646155 647639 D PFAM: phosphate transporter; KEGG: sit:TM1040_0608 phosphate transporter; phosphate transporter 646155..647639 Paracoccus denitrificans PD1222 4578970 YP_914474.1 CDS Pden_0666 NC_008686.1 647851 649314 D TIGRFAM: amino acid carrier protein; PFAM: sodium:alanine symporter; KEGG: cjk:jk0467 Na+/alanine symporter; amino acid carrier protein 647851..649314 Paracoccus denitrificans PD1222 4578971 YP_914475.1 CDS Pden_0667 NC_008686.1 649453 650526 R hypothetical protein complement(649453..650526) Paracoccus denitrificans PD1222 4578972 YP_914476.1 CDS Pden_0668 NC_008686.1 650523 651113 R PFAM: regulatory protein, TetR; KEGG: sit:TM1040_1583 transcriptional regulator, TetR family; TetR family transcriptional regulator complement(650523..651113) Paracoccus denitrificans PD1222 4578973 YP_914477.1 CDS Pden_0669 NC_008686.1 651205 652191 D 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 651205..652191 Paracoccus denitrificans PD1222 4578974 YP_914478.1 CDS Pden_0670 NC_008686.1 652191 653123 D 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 652191..653123 Paracoccus denitrificans PD1222 4578975 YP_914479.1 CDS Pden_0671 NC_008686.1 653111 653893 D PFAM: beta-lactamase domain protein; KEGG: pfl:PFL_6134 metallo-beta-lactamase protein; beta-lactamase domain-containing protein 653111..653893 Paracoccus denitrificans PD1222 4578741 YP_914480.1 CDS Pden_0672 NC_008686.1 653890 655170 D TIGRFAM: adenylate-forming enzyme; KEGG: pfl:PFL_6135 PF5220; adenylate-forming enzyme 653890..655170 Paracoccus denitrificans PD1222 4578742 YP_914481.1 CDS Pden_0673 NC_008686.1 655286 656311 R PFAM: regulatory protein, LacI; periplasmic binding protein/LacI transcriptional regulator; KEGG: sme:SMb20290 transcriptional regulator protein; regulatory protein, LacI complement(655286..656311) Paracoccus denitrificans PD1222 4578743 YP_914482.1 CDS Pden_0674 NC_008686.1 656409 657740 D PFAM: Benzoate membrane transport protein; Xanthine/uracil/vitamin C permease; KEGG: sme:SMb20289 permease protein; xanthine/uracil/vitamin C permease 656409..657740 Paracoccus denitrificans PD1222 4578744 YP_914483.1 CDS Pden_0675 NC_008686.1 657740 659137 D PFAM: amidohydrolase; Amidohydrolase 3; KEGG: sme:SMb20288 hypothetical protein; amidohydrolase 657740..659137 Paracoccus denitrificans PD1222 4578745 YP_914484.1 CDS Pden_0676 NC_008686.1 659134 659844 D PFAM: protein of unknown function DUF81; KEGG: sme:SMb20287 hypothetical protein; hypothetical protein 659134..659844 Paracoccus denitrificans PD1222 4578746 YP_914485.1 CDS Pden_0677 NC_008686.1 659972 660733 R KEGG: sme:SMc04361 hydantoin racemase protein; hydantoin racemase protein complement(659972..660733) Paracoccus denitrificans PD1222 4578747 YP_914486.1 CDS Pden_0678 NC_008686.1 660737 662089 R 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 complement(660737..662089) Paracoccus denitrificans PD1222 4578748 YP_914487.1 CDS Pden_0679 NC_008686.1 662118 662828 R PFAM: Asp/Glu racemase; KEGG: pcr:Pcryo_0404 Asp/Glu racemase; Asp/Glu racemase complement(662118..662828) Paracoccus denitrificans PD1222 4578749 YP_914488.1 CDS Pden_0680 NC_008686.1 662953 663633 D PFAM: regulatory protein GntR, HTH; GntR domain protein; KEGG: pcr:Pcryo_0403 transcriptional regulator, GntR family; GntR family transcriptional regulator 662953..663633 Paracoccus denitrificans PD1222 4578750 YP_914489.1 CDS Pden_0681 NC_008686.1 663687 664271 D KEGG: rsp:RSP_6118 hypothetical protein; hypothetical protein 663687..664271 Paracoccus denitrificans PD1222 4578751 YP_914490.1 CDS Pden_0682 NC_008686.1 664351 664755 D TIGRFAM: 4-hydroxybenzoyl-CoA thioesterase; PFAM: thioesterase superfamily protein; KEGG: rsp:RSP_0673 thioesterase; 4-hydroxybenzoyl-CoA thioesterase 664351..664755 Paracoccus denitrificans PD1222 4578752 YP_914491.1 CDS Pden_0683 NC_008686.1 664857 665552 D PFAM: MotA/TolQ/ExbB proton channel; KEGG: sil:SPO3112 proton transporter TolQ; MotA/TolQ/ExbB proton channel 664857..665552 Paracoccus denitrificans PD1222 4578753 YP_914492.1 CDS Pden_0684 NC_008686.1 665554 666018 D PFAM: Biopolymer transport protein ExbD/TolR; KEGG: sil:SPO3111 biopolymer transport protein, ExbD/TolR family; biopolymer transport protein ExbD/TolR 665554..666018 Paracoccus denitrificans PD1222 4578754 YP_914493.1 CDS Pden_0685 NC_008686.1 666022 667566 D PFAM: TolA family protein; KEGG: rsp:RSP_0670 possible TolA protein; TolA family protein 666022..667566 Paracoccus denitrificans PD1222 4578755 YP_914494.1 CDS tolB NC_008686.1 667568 668953 D 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 667568..668953 Paracoccus denitrificans PD1222 4578756 YP_914495.1 CDS Pden_0687 NC_008686.1 668964 669485 D TIGRFAM: OmpA domain protein; PFAM: OmpA/MotB domain protein; KEGG: jan:Jann_0976 OmpA/MotB; OmpA domain-containing protein 668964..669485 Paracoccus denitrificans PD1222 4578757 YP_914496.1 CDS Pden_0688 NC_008686.1 669482 670411 D KEGG: rsp:RSP_0667 hypothetical protein; hypothetical protein 669482..670411 Paracoccus denitrificans PD1222 4578758 YP_914497.1 CDS Pden_0689 NC_008686.1 670401 671630 D TIGRFAM: tRNA(Ile)-lysidine synthetase; PFAM: PP-loop domain protein; KEGG: rsp:RSP_0666 probable cell cycle protein; tRNA(Ile)-lysidine synthetase 670401..671630 Paracoccus denitrificans PD1222 4578759 YP_914498.1 CDS Pden_0690 NC_008686.1 671691 673586 D 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 671691..673586 Paracoccus denitrificans PD1222 4580631 YP_914499.1 CDS Pden_0691 NC_008686.1 673915 674232 D PFAM: Chorismate mutase; KEGG: rsp:RSP_0662 chorismate mutase; chorismate mutase 673915..674232 Paracoccus denitrificans PD1222 4580632 YP_914500.1 CDS Pden_0692 NC_008686.1 674269 674679 R TIGRFAM: uncharacterized domain 1; PFAM: thioesterase superfamily protein; KEGG: rde:RD1_2106 hypothetical protein; hypothetical protein complement(674269..674679) Paracoccus denitrificans PD1222 4580633 YP_914501.1 CDS ruvB NC_008686.1 674672 675697 R 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 complement(674672..675697) Paracoccus denitrificans PD1222 4580634 YP_914502.1 CDS Pden_0694 NC_008686.1 675694 676572 R PFAM: peptidase M48, Ste24p; KEGG: rsp:RSP_0554 heat shock protein HtpX; peptidase M48, Ste24p complement(675694..676572) Paracoccus denitrificans PD1222 4580635 YP_914503.1 CDS ruvA NC_008686.1 676578 677249 R plays an essential role in ATP-dependent branch migration of the Holliday junction; Holliday junction DNA helicase RuvA complement(676578..677249) Paracoccus denitrificans PD1222 4580636 YP_914504.1 CDS Pden_0696 NC_008686.1 677260 677754 R TIGRFAM: crossover junction endodeoxyribonuclease RuvC; PFAM: Crossover junction endodeoxyribonuclease RuvC; KEGG: rsp:RSP_0556 Holliday junction resolvase; crossover junction endodeoxyribonuclease RuvC complement(677260..677754) Paracoccus denitrificans PD1222 4580637 YP_914505.1 CDS Pden_0697 NC_008686.1 677879 680719 D 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 677879..680719 Paracoccus denitrificans PD1222 4580638 YP_914506.1 CDS Pden_0698 NC_008686.1 680719 681072 D subunit C of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; monovalent cation/H+ antiporter subunit C 680719..681072 Paracoccus denitrificans PD1222 4580639 YP_914507.1 CDS Pden_0699 NC_008686.1 681069 682661 D 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 681069..682661 Paracoccus denitrificans PD1222 4580640 YP_914508.1 CDS Pden_0700 NC_008686.1 682658 683149 D 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 682658..683149 Paracoccus denitrificans PD1222 4580641 YP_914509.1 CDS Pden_0701 NC_008686.1 683146 683415 D 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 683146..683415 Paracoccus denitrificans PD1222 4580642 YP_914510.1 CDS Pden_0702 NC_008686.1 683425 683808 D 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 683425..683808 Paracoccus denitrificans PD1222 4580643 YP_914511.1 CDS Pden_0703 NC_008686.1 683815 684087 D hypothetical protein 683815..684087 Paracoccus denitrificans PD1222 4580644 YP_914512.1 CDS Pden_0704 NC_008686.1 684138 685013 R catalyzes the formation of dihydrodipicolinate from L-aspartate 4-semialdehyde and pyruvate in lysine and diaminopimelate biosynthesis; dihydrodipicolinate synthase complement(684138..685013) Paracoccus denitrificans PD1222 4580645 YP_914513.1 CDS Pden_0705 NC_008686.1 685120 687270 D PFAM: Lytic transglycosylase, catalytic; KEGG: rsp:RSP_0881 soluble lytic transglycosylase; lytic transglycosylase, catalytic 685120..687270 Paracoccus denitrificans PD1222 4580646 YP_914514.1 CDS Pden_0706 NC_008686.1 687224 688183 R PFAM: protein of unknown function DUF6, transmembrane; KEGG: jan:Jann_0141 protein of unknown function DUF6, transmembrane; hypothetical protein complement(687224..688183) Paracoccus denitrificans PD1222 4580647 YP_914515.1 CDS Pden_0707 NC_008686.1 688246 689034 R PFAM: inositol monophosphatase; KEGG: rsp:RSP_2169 inositol monophosphatase family protein; inositol monophosphatase complement(688246..689034) Paracoccus denitrificans PD1222 4580648 YP_914516.1 CDS Pden_0708 NC_008686.1 689103 689804 R 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 complement(689103..689804) Paracoccus denitrificans PD1222 4580649 YP_914517.1 CDS Pden_0709 NC_008686.1 689801 691162 R catalyzes the deimination of N-formimino-L-glutamate to ammonia and N-formyl-L-glutamate; N-formimino-L-glutamate deiminase complement(689801..691162) Paracoccus denitrificans PD1222 4580650 YP_914518.1 CDS Pden_0710 NC_008686.1 691259 692461 D catalyzing the hydrolysis of 4-imidazolone-5-propionate to N-formimidoyl-L-glutamate, the third step in the histidine degradation pathway; imidazolonepropionase 691259..692461 Paracoccus denitrificans PD1222 4579519 YP_914519.1 CDS Pden_0711 NC_008686.1 692454 693995 D catalyzes the degradation of histidine to urocanate and ammmonia; histidine ammonia-lyase 692454..693995 Paracoccus denitrificans PD1222 4579520 YP_914520.1 CDS Pden_0712 NC_008686.1 693992 694783 D PFAM: N-formylglutamate amidohydrolase; KEGG: bme:BMEII0366 formiminoglutamase; N-formylglutamate amidohydrolase 693992..694783 Paracoccus denitrificans PD1222 4579521 YP_914521.1 CDS Pden_0713 NC_008686.1 694780 695928 D 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 694780..695928 Paracoccus denitrificans PD1222 4579522 YP_914522.1 CDS Pden_0714 NC_008686.1 695925 697079 D PFAM: acyl-CoA dehydrogenase domain protein; Acyl-CoA dehydrogenase, type 2, C-terminal domain; KEGG: rde:RD1_3681 acyl-CoA dehydrogenase; butyryl-CoA dehydrogenase 695925..697079 Paracoccus denitrificans PD1222 4579523 YP_914523.1 CDS Pden_0715 NC_008686.1 697092 698756 D catalyzes the formation of 4-imidazolone-5-propanoate from urocanate during histidine metabolism; urocanate hydratase 697092..698756 Paracoccus denitrificans PD1222 4579524 YP_914524.1 CDS Pden_0716 NC_008686.1 698821 699639 D 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 698821..699639 Paracoccus denitrificans PD1222 4579525 YP_914525.1 CDS Pden_0717 NC_008686.1 699697 700344 D 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 699697..700344 Paracoccus denitrificans PD1222 4579526 YP_914526.1 CDS Pden_0718 NC_008686.1 700344 701006 D 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 700344..701006 Paracoccus denitrificans PD1222 4579527 YP_914527.1 CDS Pden_0719 NC_008686.1 701011 701781 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rru:Rru_A1298 ABC transporter component; ABC transporter 701011..701781 Paracoccus denitrificans PD1222 4579528 YP_914528.1 CDS Pden_0720 NC_008686.1 701997 703100 D PFAM: NADH:flavin oxidoreductase/NADH oxidase; KEGG: mes:Meso_1173 NADH:flavin oxidoreductase/NADH oxidase; NADH:flavin oxidoreductase 701997..703100 Paracoccus denitrificans PD1222 4579529 YP_914529.1 CDS Pden_0721 NC_008686.1 703138 704292 R PFAM: Patatin; KEGG: rpa:RPA4207 patatin-like phospholipase domain; patatin complement(703138..704292) Paracoccus denitrificans PD1222 4579530 YP_914530.1 CDS Pden_0722 NC_008686.1 704289 704567 R hypothetical protein complement(704289..704567) Paracoccus denitrificans PD1222 4579531 YP_914531.1 CDS Pden_0723 NC_008686.1 704594 705871 D PFAM: CBS domain containing protein; protein of unknown function DUF21; transporter-associated region; KEGG: atc:AGR_L_2203 TlyC; hemolysin; hypothetical protein 704594..705871 Paracoccus denitrificans PD1222 4579532 YP_914532.1 CDS Pden_0724 NC_008686.1 705953 706936 D PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: mlo:mll6938 transcriptional regulator; LysR family transcriptional regulator 705953..706936 Paracoccus denitrificans PD1222 4579533 YP_914533.1 CDS Pden_0725 NC_008686.1 706917 707765 R TIGRFAM: TonB family protein; KEGG: rpb:RPB_1657 TonB-like protein; TonB family protein complement(706917..707765) Paracoccus denitrificans PD1222 4579534 YP_914534.1 CDS Pden_0726 NC_008686.1 707762 708325 R PFAM: Biopolymer transport protein ExbD/TolR; KEGG: atc:AGR_C_265 biopolymer transport ExbD protein; biopolymer transport protein ExbD/TolR complement(707762..708325) Paracoccus denitrificans PD1222 4579535 YP_914535.1 CDS Pden_0727 NC_008686.1 708329 709624 R PFAM: MotA/TolQ/ExbB proton channel; KEGG: atc:AGR_C_264 biopolymer transport ExbB protein; MotA/TolQ/ExbB proton channel complement(708329..709624) Paracoccus denitrificans PD1222 4579536 YP_914536.1 CDS Pden_0728 NC_008686.1 709715 710752 R 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 complement(709715..710752) Paracoccus denitrificans PD1222 4579537 YP_914537.1 CDS Pden_0729 NC_008686.1 710813 711985 R PFAM: aminotransferase, class V; KEGG: rsp:RSP_0245 serine-pyruvate aminotransferase/aspartate aminotransferase; class V aminotransferase complement(710813..711985) Paracoccus denitrificans PD1222 4579597 YP_914538.1 CDS Pden_0730 NC_008686.1 712246 713985 D 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 712246..713985 Paracoccus denitrificans PD1222 4579598 YP_914539.1 CDS Pden_0731 NC_008686.1 713985 714701 D PFAM: glycine cleavage T protein (aminomethyl transferase); KEGG: sit:TM1040_1985 glycine cleavage T protein (aminomethyl transferase); glycine cleavage T protein (aminomethyl transferase) 713985..714701 Paracoccus denitrificans PD1222 4579599 YP_914540.1 CDS Pden_0732 NC_008686.1 714698 715789 D PFAM: UMUC domain protein DNA-repair protein; KEGG: sme:SMa2355 DNA polymerase IV; DNA-directed DNA polymerase 714698..715789 Paracoccus denitrificans PD1222 4579600 YP_914541.1 CDS Pden_0733 NC_008686.1 715780 716727 R KEGG: jan:Jann_1800 hypothetical protein; hypothetical protein complement(715780..716727) Paracoccus denitrificans PD1222 4579601 YP_914542.1 CDS Pden_0734 NC_008686.1 716936 718111 D 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 716936..718111 Paracoccus denitrificans PD1222 4579602 YP_914543.1 CDS Pden_0735 NC_008686.1 718358 719248 D PFAM: dienelactone hydrolase; KEGG: mmr:Mmar10_2526 carboxymethylenebutenolidase; carboxymethylenebutenolidase 718358..719248 Paracoccus denitrificans PD1222 4579603 YP_914544.1 CDS Pden_0736 NC_008686.1 719300 719692 D PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase; KEGG: bja:blr0519 hypothetical protein; glyoxalase/bleomycin resistance protein/dioxygenase 719300..719692 Paracoccus denitrificans PD1222 4579604 YP_914545.1 CDS Pden_0737 NC_008686.1 719689 720102 D PFAM: glutathione-dependent formaldehyde-activating, GFA; KEGG: sme:SMc04046 hypothetical protein; glutathione-dependent formaldehyde-activating protein 719689..720102 Paracoccus denitrificans PD1222 4579605 YP_914546.1 CDS Pden_0738 NC_008686.1 720338 720991 D PFAM: transferase hexapeptide repeat containing protein; KEGG: rsp:RSP_1706 acetyltransferase; hexapaptide repeat-containing transferase 720338..720991 Paracoccus denitrificans PD1222 4579606 YP_914547.1 CDS Pden_0739 NC_008686.1 721049 722890 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: bme:BMEI0471 ABC transporter ATP-binding protein; ABC transporter 721049..722890 Paracoccus denitrificans PD1222 4579607 YP_914548.1 CDS Pden_0740 NC_008686.1 723027 723938 D KEGG: jan:Jann_3368 hypothetical protein; hypothetical protein 723027..723938 Paracoccus denitrificans PD1222 4579608 YP_914549.1 CDS Pden_0741 NC_008686.1 723963 724208 D 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 723963..724208 Paracoccus denitrificans PD1222 4579609 YP_914550.1 CDS Pden_0742 NC_008686.1 724404 724943 D 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 724404..724943 Paracoccus denitrificans PD1222 4579610 YP_914551.1 CDS rplK NC_008686.1 725043 725495 D binds directly to 23S ribosomal RNA; 50S ribosomal protein L11 725043..725495 Paracoccus denitrificans PD1222 4579611 YP_914552.1 CDS rplA NC_008686.1 725499 726200 D 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 725499..726200 Paracoccus denitrificans PD1222 4579612 YP_914553.1 CDS rplJ NC_008686.1 726682 727197 D binds the two ribosomal protein L7/L12 dimers and anchors them to the large ribosomal subunit; 50S ribosomal protein L10 726682..727197 Paracoccus denitrificans PD1222 4579613 YP_914554.1 CDS rplL NC_008686.1 727265 727639 D 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 727265..727639 Paracoccus denitrificans PD1222 4579614 YP_914555.1 CDS rpoB NC_008686.1 727881 732029 D 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 727881..732029 Paracoccus denitrificans PD1222 4579615 YP_914556.1 CDS Pden_0748 NC_008686.1 732032 732343 D hypothetical protein 732032..732343 Paracoccus denitrificans PD1222 4579616 YP_914557.1 CDS Pden_0749 NC_008686.1 732340 736548 D 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' 732340..736548 Paracoccus denitrificans PD1222 4580047 YP_914558.1 CDS Pden_0750 NC_008686.1 736780 737055 D hypothetical protein 736780..737055 Paracoccus denitrificans PD1222 4580048 YP_914559.1 CDS Pden_0751 NC_008686.1 737215 738156 D PFAM: protein of unknown function DUF6, transmembrane; KEGG: rsp:RSP_1711 possible transporter, RhaT family, DMT superfamily; hypothetical protein 737215..738156 Paracoccus denitrificans PD1222 4580049 YP_914560.1 CDS Pden_0752 NC_008686.1 738156 738995 D KEGG: jan:Jann_0574 hypothetical protein; hypothetical protein 738156..738995 Paracoccus denitrificans PD1222 4580050 YP_914561.1 CDS rpsL NC_008686.1 739289 739660 D 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 739289..739660 Paracoccus denitrificans PD1222 4580051 YP_914562.1 CDS Pden_0754 NC_008686.1 739673 740143 D binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit; 30S ribosomal protein S7 739673..740143 Paracoccus denitrificans PD1222 4580052 YP_914563.1 CDS Pden_0755 NC_008686.1 740162 742285 D EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene; elongation factor G 740162..742285 Paracoccus denitrificans PD1222 4580053 YP_914564.1 CDS Pden_0756 NC_008686.1 742372 743547 D 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 742372..743547 Paracoccus denitrificans PD1222 4580054 YP_914565.1 CDS Pden_0757 NC_008686.1 743731 744531 R hypothetical protein complement(743731..744531) Paracoccus denitrificans PD1222 4580055 YP_914566.1 CDS rpsJ NC_008686.1 744795 745103 D 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 744795..745103 Paracoccus denitrificans PD1222 4580056 YP_914567.1 CDS rplC NC_008686.1 745114 745851 D 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 745114..745851 Paracoccus denitrificans PD1222 4580057 YP_914568.1 CDS rplD NC_008686.1 745851 746471 D 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 745851..746471 Paracoccus denitrificans PD1222 4580058 YP_914569.1 CDS rplW NC_008686.1 746468 746764 D binds third domain of 23S rRNA and protein L29; part of exit tunnel; 50S ribosomal protein L23 746468..746764 Paracoccus denitrificans PD1222 4580059 YP_914570.1 CDS rplB NC_008686.1 746860 747699 D 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 746860..747699 Paracoccus denitrificans PD1222 4580060 YP_914571.1 CDS rpsS NC_008686.1 747703 747981 D protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA; 30S ribosomal protein S19 747703..747981 Paracoccus denitrificans PD1222 4580061 YP_914572.1 CDS rplV NC_008686.1 747987 748367 D 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 747987..748367 Paracoccus denitrificans PD1222 4580062 YP_914573.1 CDS rpsC NC_008686.1 748367 749089 D 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 748367..749089 Paracoccus denitrificans PD1222 4580063 YP_914574.1 CDS rplP NC_008686.1 749102 749515 D located in the peptidyl transferase center and may be involved in peptidyl transferase activity; similar to archaeal L10e; 50S ribosomal protein L16 749102..749515 Paracoccus denitrificans PD1222 4580064 YP_914575.1 CDS Pden_0767 NC_008686.1 749633 749911 D PFAM: ribosomal protein L29; KEGG: jan:Jann_0599 ribosomal protein L29; 50S ribosomal protein L29 749633..749911 Paracoccus denitrificans PD1222 4580065 YP_914576.1 CDS rpsQ NC_008686.1 749924 750172 D primary binding protein; helps mediate assembly; involved in translation fidelity; 30S ribosomal protein S17 749924..750172 Paracoccus denitrificans PD1222 4579987 YP_914577.1 CDS rplN NC_008686.1 750236 750604 D binds to the 23S rRNA between the centers for peptidyl transferase and GTPase; 50S ribosomal protein L14 750236..750604 Paracoccus denitrificans PD1222 4579988 YP_914578.1 CDS rplX NC_008686.1 750604 750909 D assembly initiator protein; binds to 5' end of 23S rRNA and nucleates assembly of the 50S; surrounds polypeptide exit tunnel; 50S ribosomal protein L24 750604..750909 Paracoccus denitrificans PD1222 4579989 YP_914579.1 CDS rplE NC_008686.1 750909 751469 D 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 750909..751469 Paracoccus denitrificans PD1222 4579990 YP_914580.1 CDS rpsN NC_008686.1 751488 751793 D 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 751488..751793 Paracoccus denitrificans PD1222 4579991 YP_914581.1 CDS rpsH NC_008686.1 751803 752201 D binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit; 30S ribosomal protein S8 751803..752201 Paracoccus denitrificans PD1222 4579992 YP_914582.1 CDS rplF NC_008686.1 752213 752746 D 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 752213..752746 Paracoccus denitrificans PD1222 4579993 YP_914583.1 CDS rplR NC_008686.1 752758 753117 D binds 5S rRNA along with protein L5 and L25; 50S ribosomal protein L18 752758..753117 Paracoccus denitrificans PD1222 4579994 YP_914584.1 CDS rpsE NC_008686.1 753236 753802 D 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 753236..753802 Paracoccus denitrificans PD1222 4579995 YP_914585.1 CDS rpmD NC_008686.1 753815 754003 D L30 binds domain II of the 23S rRNA and the 5S rRNA; similar to eukaryotic protein L7; 50S ribosomal protein L30 753815..754003 Paracoccus denitrificans PD1222 4579996 YP_914586.1 CDS Pden_0778 NC_008686.1 754133 754855 D KEGG: rsp:RSP_2084 hypothetical protein; hypothetical protein 754133..754855 Paracoccus denitrificans PD1222 4579997 YP_914587.1 CDS rplO NC_008686.1 755010 755495 D late assembly protein; 50S ribosomal protein L15 755010..755495 Paracoccus denitrificans PD1222 4579998 YP_914588.1 CDS secY NC_008686.1 755600 756973 D 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 755600..756973 Paracoccus denitrificans PD1222 4579999 YP_914589.1 CDS adk NC_008686.1 757011 757667 D essential enzyme that recycles AMP in active cells; converts ATP and AMP to two molecules of ADP; adenylate kinase 757011..757667 Paracoccus denitrificans PD1222 4580000 YP_914590.2 CDS rpsM NC_008686.1 757831 758199 D 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 757831..758199 Paracoccus denitrificans PD1222 4580001 YP_914591.1 CDS Pden_0783 NC_008686.1 758212 758601 D 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 758212..758601 Paracoccus denitrificans PD1222 4580002 YP_914592.1 CDS Pden_0784 NC_008686.1 758721 759737 D 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 758721..759737 Paracoccus denitrificans PD1222 4580003 YP_914593.1 CDS rplQ NC_008686.1 759854 760276 D is a component of the macrolide binding site in the peptidyl transferase center; 50S ribosomal protein L17 759854..760276 Paracoccus denitrificans PD1222 4580004 YP_914594.1 CDS Pden_0786 NC_008686.1 760626 761237 D PFAM: regulatory protein, LuxR; Autoinducer-binding domain protein; KEGG: jan:Jann_0619 transcriptional regulator, LuxR family; response regulator receiver protein 760626..761237 Paracoccus denitrificans PD1222 4580005 YP_914595.1 CDS Pden_0787 NC_008686.1 761305 761895 D KEGG: jan:Jann_0620 N-acyl-L-homoserine lactone synthetase-like; N-acyl-L-homoserine lactone synthetase-like 761305..761895 Paracoccus denitrificans PD1222 4580006 YP_914596.1 CDS Pden_0788 NC_008686.1 761957 763285 D 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 761957..763285 Paracoccus denitrificans PD1222 4580612 YP_914597.1 CDS Pden_0789 NC_008686.1 763282 763656 D TIGRFAM: CrcB protein; PFAM: Camphor resistance CrcB protein; KEGG: rsp:RSP_1744 CrcB-like protein; CrcB protein 763282..763656 Paracoccus denitrificans PD1222 4580613 YP_914598.1 CDS Pden_0790 NC_008686.1 763653 764699 D TIGRFAM: pseudouridine synthase, RluA family; PFAM: RNA-binding S4 domain protein; pseudouridine synthase; KEGG: rsp:RSP_1745 pseudouridine synthase; RluA family pseudouridine synthase 763653..764699 Paracoccus denitrificans PD1222 4580614 YP_914599.1 CDS Pden_0791 NC_008686.1 764696 765358 D 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 764696..765358 Paracoccus denitrificans PD1222 4580615 YP_914600.1 CDS Pden_0792 NC_008686.1 765351 766061 D PFAM: ATP12 ATPase; KEGG: jan:Jann_0626 ATP12 ATPase; ATP12 ATPase 765351..766061 Paracoccus denitrificans PD1222 4580616 YP_914601.1 CDS Pden_0793 NC_008686.1 766214 767239 D 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 766214..767239 Paracoccus denitrificans PD1222 4580617 YP_914602.1 CDS Pden_0794 NC_008686.1 767355 768608 D 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 767355..768608 Paracoccus denitrificans PD1222 4580618 YP_914603.1 CDS Pden_0795 NC_008686.1 768610 770064 D 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 768610..770064 Paracoccus denitrificans PD1222 4580619 YP_914604.1 CDS Pden_0796 NC_008686.1 770075 770848 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sil:SPO0522 glutamate/glutamine/aspartate/asparagine ABC transporter, ATP-binding protein; ABC transporter 770075..770848 Paracoccus denitrificans PD1222 4580620 YP_914605.1 CDS Pden_0797 NC_008686.1 770948 771850 D KEGG: rde:RD1_B0053 rhizobiocin; hypothetical protein 770948..771850 Paracoccus denitrificans PD1222 4580621 YP_914606.1 CDS Pden_0798 NC_008686.1 771923 772783 R PFAM: aminotransferase, class IV; KEGG: rsp:RSP_1768 aminotransferase class IV , D-alanine aminotransferase; aminotransferase, class IV complement(771923..772783) Paracoccus denitrificans PD1222 4580622 YP_914607.1 CDS Pden_0799 NC_008686.1 772881 773906 D PFAM: HpcH/HpaI aldolase; KEGG: rde:RD1_1001 citrate lyase, beta subunit; citrate (pro-3S)-lyase 772881..773906 Paracoccus denitrificans PD1222 4580623 YP_914608.1 CDS Pden_0800 NC_008686.1 774324 775946 R 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 complement(774324..775946) Paracoccus denitrificans PD1222 4580624 YP_914609.1 CDS Pden_0801 NC_008686.1 775943 776755 R 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 complement(775943..776755) Paracoccus denitrificans PD1222 4580625 YP_914610.1 CDS Pden_0802 NC_008686.1 776752 777690 R 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 complement(776752..777690) Paracoccus denitrificans PD1222 4580626 YP_914611.1 CDS Pden_0803 NC_008686.1 777739 779373 R PFAM: protein of unknown function DUF894, DitE; major facilitator superfamily MFS_1; KEGG: bms:BRA0311 transporter; hypothetical protein complement(777739..779373) Paracoccus denitrificans PD1222 4580627 YP_914612.1 CDS Pden_0804 NC_008686.1 779632 780933 D catalyzes the oxidative deamination of D-amino acids; D-amino acid dehydrogenase small subunit 779632..780933 Paracoccus denitrificans PD1222 4580628 YP_914613.1 CDS Pden_0805 NC_008686.1 780997 781257 R PFAM: Transglycosylase-associated protein; KEGG: bur:Bcep18194_B2685 transglycosylase-associated protein; transglycosylase-associated protein complement(780997..781257) Paracoccus denitrificans PD1222 4580629 YP_914614.1 CDS Pden_0806 NC_008686.1 781254 781526 R hypothetical protein complement(781254..781526) Paracoccus denitrificans PD1222 4580630 YP_914615.1 CDS Pden_0807 NC_008686.1 781572 782318 D PFAM: ErfK/YbiS/YcfS/YnhG family protein; KEGG: rsp:RSP_1754 hypothetical protein; ErfK/YbiS/YcfS/YnhG family protein 781572..782318 Paracoccus denitrificans PD1222 4580553 YP_914616.1 CDS Pden_0808 NC_008686.1 782443 782997 D KEGG: tpa:TP0470 hypothetical protein; hypothetical protein 782443..782997 Paracoccus denitrificans PD1222 4580554 YP_914617.1 CDS Pden_0809 NC_008686.1 783068 783979 D PFAM: Lytic transglycosylase, catalytic; KEGG: sme:SMc01230 transglycosylase transmembrane protein; lytic transglycosylase, catalytic 783068..783979 Paracoccus denitrificans PD1222 4580555 YP_914618.1 CDS Pden_0810 NC_008686.1 784055 785524 R PFAM: extracellular solute-binding protein, family 5; KEGG: jan:Jann_0782 extracellular solute-binding protein, family 5; extracellular solute-binding protein complement(784055..785524) Paracoccus denitrificans PD1222 4580556 YP_914619.1 CDS Pden_0811 NC_008686.1 785581 786273 R PFAM: CDP-alcohol phosphatidyltransferase; KEGG: rsp:RSP_0565 phosphatidylcholine synthase; phosphatidylcholine synthase complement(785581..786273) Paracoccus denitrificans PD1222 4580557 YP_914620.1 CDS Pden_0812 NC_008686.1 786368 787243 R 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 complement(786368..787243) Paracoccus denitrificans PD1222 4580558 YP_914621.1 CDS Pden_0813 NC_008686.1 787437 788591 D catalyzes the formation of 3-phosphonooxypyruvate and glutamate from O-phospho-L-serine and 2-oxoglutarate; phosphoserine aminotransferase 787437..788591 Paracoccus denitrificans PD1222 4580559 YP_914622.1 CDS Pden_0814 NC_008686.1 788704 790293 D 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 788704..790293 Paracoccus denitrificans PD1222 4580560 YP_914623.1 CDS Pden_0815 NC_008686.1 790346 791074 D PFAM: metallophosphoesterase; KEGG: rsp:RSP_1353 protein phosphatase; metallophosphoesterase 790346..791074 Paracoccus denitrificans PD1222 4580561 YP_914624.1 CDS Pden_0816 NC_008686.1 791211 792839 D 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 791211..792839 Paracoccus denitrificans PD1222 4580562 YP_914625.1 CDS Pden_0817 NC_008686.1 793035 793496 D PFAM: CreA family protein; KEGG: rsp:RSP_2505 possible CreA protein; CreA family protein 793035..793496 Paracoccus denitrificans PD1222 4580563 YP_914626.1 CDS Pden_0818 NC_008686.1 793728 794060 D TIGRFAM: hemimethylated DNA binding protein; KEGG: rsp:RSP_1498 hypothetical protein; hemimethylated DNA binding protein 793728..794060 Paracoccus denitrificans PD1222 4580564 YP_914627.1 CDS Pden_0819 NC_008686.1 794073 794630 R KEGG: jan:Jann_4052 anti-sigma regulatory factor (serine/threonine protein kinase); anti-sigma regulatory factor complement(794073..794630) Paracoccus denitrificans PD1222 4580565 YP_914628.1 CDS Pden_0820 NC_008686.1 794627 794992 R 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 complement(794627..794992) Paracoccus denitrificans PD1222 4580566 YP_914629.1 CDS Pden_0821 NC_008686.1 795231 795608 D hypothetical protein 795231..795608 Paracoccus denitrificans PD1222 4580567 YP_914630.1 CDS Pden_0822 NC_008686.1 795629 798091 D 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 795629..798091 Paracoccus denitrificans PD1222 4580568 YP_914631.1 CDS Pden_0823 NC_008686.1 798302 799714 D PFAM: protein of unknown function DUF404; protein of unknown function DUF407; KEGG: rsp:RSP_2415 hypothetical protein; hypothetical protein 798302..799714 Paracoccus denitrificans PD1222 4580569 YP_914632.1 CDS Pden_0824 NC_008686.1 799729 800688 D PFAM: protein of unknown function DUF403; KEGG: rsp:RSP_2416 hypothetical protein; hypothetical protein 799729..800688 Paracoccus denitrificans PD1222 4580570 YP_914633.1 CDS Pden_0825 NC_008686.1 800699 801505 D PFAM: transglutaminase domain protein; transglutaminase, N-terminal domain protein; KEGG: rsp:RSP_2417 hypothetical protein; transglutaminase domain-containing protein 800699..801505 Paracoccus denitrificans PD1222 4580571 YP_914634.1 CDS Pden_0826 NC_008686.1 801536 802294 D PFAM: 20S proteasome, A and B subunits; KEGG: rsp:RSP_2420 proteasome-type protease; 20S proteasome subunits A/B 801536..802294 Paracoccus denitrificans PD1222 4580572 YP_914635.1 CDS Pden_0827 NC_008686.1 802307 804943 R This protein performs the mismatch recognition step during the DNA repair process; DNA mismatch repair protein MutS complement(802307..804943) Paracoccus denitrificans PD1222 4579442 YP_914636.1 CDS Pden_0828 NC_008686.1 805100 805939 D KEGG: sit:TM1040_2771 hydratase/decarboxylase; hydratase/decarboxylase 805100..805939 Paracoccus denitrificans PD1222 4579443 YP_914637.1 CDS Pden_0829 NC_008686.1 806084 807190 D PFAM: extracellular solute-binding protein, family 1; KEGG: rsp:RSP_0346 ABC transporter, substrate binding protein; extracellular solute-binding protein 806084..807190 Paracoccus denitrificans PD1222 4579444 YP_914638.1 CDS Pden_0830 NC_008686.1 807211 808092 D 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 807211..808092 Paracoccus denitrificans PD1222 4579445 YP_914639.1 CDS Pden_0831 NC_008686.1 808089 808871 D 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 808089..808871 Paracoccus denitrificans PD1222 4579446 YP_914640.1 CDS Pden_0832 NC_008686.1 808868 809902 D PFAM: ABC transporter related; Transport-associated OB domain protein; SMART: AAA ATPase; KEGG: rsp:RSP_0349 ABC transporter, ATPase subunit; ABC transporter 808868..809902 Paracoccus denitrificans PD1222 4579447 YP_914641.1 CDS Pden_0833 NC_008686.1 810408 812123 D PFAM: Hemolysin-type calcium-binding region; KEGG: bja:bll7673 hypothetical protein; hemolysin-type calcium-binding protein 810408..812123 Paracoccus denitrificans PD1222 4579448 YP_914642.1 CDS Pden_0834 NC_008686.1 812160 812933 R 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 complement(812160..812933) Paracoccus denitrificans PD1222 4579449 YP_914643.1 CDS Pden_0835 NC_008686.1 813051 814475 D KEGG: sit:TM1040_2399 membrane protein; hypothetical protein 813051..814475 Paracoccus denitrificans PD1222 4579450 YP_914644.1 CDS Pden_0836 NC_008686.1 814575 820856 D 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 814575..820856 Paracoccus denitrificans PD1222 4579451 YP_914645.1 CDS Pden_0837 NC_008686.1 820859 821851 D PFAM: glycosyl transferase, family 2; KEGG: sil:SPO0848 glycosyl transferase, group 2 family protein; glycosyl transferase family protein 820859..821851 Paracoccus denitrificans PD1222 4579452 YP_914646.1 CDS Pden_0838 NC_008686.1 821848 826473 D 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 821848..826473 Paracoccus denitrificans PD1222 4579453 YP_914647.1 CDS Pden_0839 NC_008686.1 826470 827093 D PFAM: 4'-phosphopantetheinyl transferase; KEGG: sma:SAV1748 phosphopantetheinyl transferase; 4'-phosphopantetheinyl transferase 826470..827093 Paracoccus denitrificans PD1222 4579454 YP_914648.1 CDS Pden_0840 NC_008686.1 827074 828279 R PFAM: glycosyl transferase, group 1; KEGG: sil:SPO0842 glycosyl transferase, group 1 family protein; group 1 glycosyl transferase complement(827074..828279) Paracoccus denitrificans PD1222 4579455 YP_914649.1 CDS Pden_0841 NC_008686.1 828462 828674 D hypothetical protein 828462..828674 Paracoccus denitrificans PD1222 4579456 YP_914650.1 CDS Pden_0842 NC_008686.1 828668 829366 R PFAM: sugar transferase; KEGG: jan:Jann_4237 undecaprenyl-phosphate galactosephosphotransferase; undecaprenyl-phosphate galactose phosphotransferase complement(828668..829366) Paracoccus denitrificans PD1222 4579457 YP_914651.1 CDS Pden_0843 NC_008686.1 829672 830442 D KEGG: sil:SPO0844 hypothetical protein; hypothetical protein 829672..830442 Paracoccus denitrificans PD1222 4579458 YP_914652.1 CDS Pden_0844 NC_008686.1 830439 831266 R PFAM: glycosyl transferase, family 2; KEGG: sil:SPO0843 glycosyl transferase, group 2 family protein; glycosyl transferase family protein complement(830439..831266) Paracoccus denitrificans PD1222 4579459 YP_914653.1 CDS Pden_0845 NC_008686.1 831535 832272 D KEGG: sil:SPO0839 exopolysaccharide biosynthesis domain protein; chromosome partitioning ATPase-like protein 831535..832272 Paracoccus denitrificans PD1222 4579460 YP_914654.1 CDS Pden_0846 NC_008686.1 832333 833799 D PFAM: lipopolysaccharide biosynthesis; KEGG: pen:PSEEN2947 exopolysaccharide transport protein; lipopolysaccharide biosynthesis protein 832333..833799 Paracoccus denitrificans PD1222 4578643 YP_914655.1 CDS Pden_0847 NC_008686.1 833799 835172 D PFAM: polysaccharide biosynthesis protein; KEGG: sil:SPO0841 polysaccharide biosynthesis protein; polysaccharide biosynthesis protein 833799..835172 Paracoccus denitrificans PD1222 4578644 YP_914656.1 CDS Pden_0848 NC_008686.1 835257 837539 D NADP-dependent; catalyzes the oxidative decarboxylation of malate to form pyruvate; decarboxylates oxaloacetate; malic enzyme 835257..837539 Paracoccus denitrificans PD1222 4578645 YP_914657.1 CDS Pden_0849 NC_008686.1 837600 838199 R KEGG: rsp:RSP_2718 possible outer membrane protein; outer membrane protein complement(837600..838199) Paracoccus denitrificans PD1222 4578646 YP_914658.1 CDS Pden_0850 NC_008686.1 838421 839389 R PFAM: Rhodanese domain protein; KEGG: sil:SPO0091 rhodanese-like domain protein; rhodanese domain-containing protein complement(838421..839389) Paracoccus denitrificans PD1222 4578647 YP_914659.1 CDS Pden_0851 NC_008686.1 839444 840040 D PFAM: isochorismatase hydrolase; KEGG: rde:RD1_0585 pyrazinamidase/nicotinamidase; nicotinamidase 839444..840040 Paracoccus denitrificans PD1222 4578648 YP_914660.1 CDS Pden_0852 NC_008686.1 840040 841347 D catalyzes the formation of nictonate and 5-phospho-alpha-D-ribose 1-diphosphate from nicotinate D-ribonucleotide and diphosphate; nicotinate phosphoribosyltransferase 840040..841347 Paracoccus denitrificans PD1222 4578649 YP_914661.1 CDS nadE NC_008686.1 841517 843187 R 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 complement(841517..843187) Paracoccus denitrificans PD1222 4578650 YP_914662.1 CDS Pden_0854 NC_008686.1 843319 844785 D PFAM: MORN repeat-containing protein; KEGG: rsp:RSP_2332 hypothetical protein; MORN repeat-containing protein 843319..844785 Paracoccus denitrificans PD1222 4578651 YP_914663.1 CDS Pden_0855 NC_008686.1 844892 845389 R catalyzes the conversion of guanine, xanthine and, to a lesser extent, hypoxanthine to GMP, XMP and IMP, respectively; xanthine-guanine phosphoribosyltransferase complement(844892..845389) Paracoccus denitrificans PD1222 4578652 YP_914664.1 CDS Pden_0856 NC_008686.1 845399 846001 R PFAM: Lysine exporter protein (LYSE/YGGA); KEGG: rde:RD1_3200 threonine efflux protein; lysine exporter protein LysE/YggA complement(845399..846001) Paracoccus denitrificans PD1222 4578653 YP_914665.1 CDS Pden_0857 NC_008686.1 846011 846838 R Catalyzes a key regulatory step in fatty acid biosynthesis; enoyl-ACP reductase complement(846011..846838) Paracoccus denitrificans PD1222 4578654 YP_914666.1 CDS Pden_0858 NC_008686.1 846922 847584 D PFAM: pyridoxamine 5'-phosphate oxidase-related, FMN-binding; KEGG: sil:SPO2141 pyridoxamine 5''-phosphate oxidase; pyridoxamine-phosphate oxidase 846922..847584 Paracoccus denitrificans PD1222 4578655 YP_914667.1 CDS Pden_0859 NC_008686.1 847715 848308 D 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 847715..848308 Paracoccus denitrificans PD1222 4578656 YP_914668.1 CDS Pden_0860 NC_008686.1 848305 848799 D PFAM: protein of unknown function DUF192; KEGG: sil:SPO2139 hypothetical protein; hypothetical protein 848305..848799 Paracoccus denitrificans PD1222 4578657 YP_914669.1 CDS Pden_0862 NC_008686.1 849700 850956 D KEGG: rsp:RSP_1849 aspartate kinase; TIGRFAM: aspartate kinase; PFAM: aspartate/glutamate/uridylate kinase; amino acid-binding ACT domain protein; aspartate kinase 849700..850956 Paracoccus denitrificans PD1222 4578658 YP_914670.1 CDS Pden_0863 NC_008686.1 850988 853231 D 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 850988..853231 Paracoccus denitrificans PD1222 4578659 YP_914671.1 CDS Pden_0864 NC_008686.1 853260 854033 R PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rpd:RPD_2478 ABC transporter related; ABC transporter complement(853260..854033) Paracoccus denitrificans PD1222 4578660 YP_914672.1 CDS Pden_0865 NC_008686.1 854021 854989 R PFAM: transport system permease protein; ABC-3 protein; KEGG: rpd:RPD_2479 transport system permease protein; transport system permease complement(854021..854989) Paracoccus denitrificans PD1222 4578661 YP_914673.1 CDS Pden_0866 NC_008686.1 855006 856037 R PFAM: periplasmic binding protein; KEGG: rpa:RPA0151 possible iron ABC transporter periplasmic binding protein; periplasmic binding protein complement(855006..856037) Paracoccus denitrificans PD1222 4578662 YP_914674.1 CDS Pden_0867 NC_008686.1 856034 856495 R PFAM: protein of unknown function UPF0066; KEGG: bja:bll5136 VirR; hypothetical protein complement(856034..856495) Paracoccus denitrificans PD1222 4579263 YP_914675.1 CDS Pden_0868 NC_008686.1 856488 856622 R hypothetical protein complement(856488..856622) Paracoccus denitrificans PD1222 4579264 YP_914676.1 CDS Pden_0869 NC_008686.1 856647 857168 R KEGG: sit:TM1040_2053 conserved hypothetical protein; hypothetical protein complement(856647..857168) Paracoccus denitrificans PD1222 4579265 YP_914677.1 CDS Pden_0870 NC_008686.1 857422 857712 D hypothetical protein 857422..857712 Paracoccus denitrificans PD1222 4579266 YP_914678.1 CDS Pden_0871 NC_008686.1 857878 859314 R 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 complement(857878..859314) Paracoccus denitrificans PD1222 4579267 YP_914679.1 CDS rpmH NC_008686.1 859553 859690 D in Escherichia coli transcription of this gene is enhanced by polyamines; 50S ribosomal protein L34 859553..859690 Paracoccus denitrificans PD1222 4579268 YP_914680.1 CDS Pden_0873 NC_008686.1 859720 860169 D TIGRFAM: ribonuclease P protein component; PFAM: ribonuclease P protein; KEGG: rsp:RSP_1060 ribonuclease P protein component; ribonuclease P protein component 859720..860169 Paracoccus denitrificans PD1222 4579269 YP_914681.1 CDS Pden_0874 NC_008686.1 860166 860408 D PFAM: protein of unknown function DUF37; KEGG: rsp:RSP_1061 hypothetical protein; hypothetical protein 860166..860408 Paracoccus denitrificans PD1222 4579270 YP_914682.1 CDS Pden_0875 NC_008686.1 860460 861353 D TtcA; YdaO; catalyzes the thiolation of cytosine 32 in specific tRNAs; C32 tRNA thiolase 860460..861353 Paracoccus denitrificans PD1222 4579271 YP_914683.1 CDS Pden_0876 NC_008686.1 861414 862685 D PFAM: EAL domain protein; KEGG: rde:RD1_1456 EAL domain protein; diguanylate phosphodiesterase 861414..862685 Paracoccus denitrificans PD1222 4579272 YP_914684.1 CDS Pden_0877 NC_008686.1 862908 864815 D 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 862908..864815 Paracoccus denitrificans PD1222 4579273 YP_914685.1 CDS Pden_0878 NC_008686.1 864812 865570 D PFAM: MOSC domain containing protein; KEGG: rsp:RSP_1065 hypothetical protein; MOSC domain-containing protein 864812..865570 Paracoccus denitrificans PD1222 4579274 YP_914686.1 CDS engB NC_008686.1 865567 866217 D 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 865567..866217 Paracoccus denitrificans PD1222 4579275 YP_914687.1 CDS Pden_0880 NC_008686.1 866295 867209 D catalyzes the phosphorylation of N-acetyl-L-glutamate to form N-acetyl-L-glutamate 5-phosphate; acetylglutamate kinase 866295..867209 Paracoccus denitrificans PD1222 4579276 YP_914688.1 CDS Pden_0881 NC_008686.1 867318 867836 D PFAM: Phosphoglycerate mutase; KEGG: rsp:RSP_1070 hypothetical protein; phosphohistidine phosphatase, SixA 867318..867836 Paracoccus denitrificans PD1222 4579277 YP_914689.1 CDS Pden_0882 NC_008686.1 867833 868792 R PFAM: PfkB domain protein; KEGG: rsp:RSP_2334 carbohydrate kinase, PfkB; ribokinase-like domain-containing protein complement(867833..868792) Paracoccus denitrificans PD1222 4579278 YP_914690.1 CDS Pden_0883 NC_008686.1 868792 869199 R PFAM: protein of unknown function DUF1025; KEGG: jan:Jann_3637 protein of unknown function DUF1025; hypothetical protein complement(868792..869199) Paracoccus denitrificans PD1222 4579279 YP_914691.1 CDS gltX NC_008686.1 869278 870603 D Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation; glutamyl-tRNA synthetase 869278..870603 Paracoccus denitrificans PD1222 4579280 YP_914692.1 CDS Pden_0885 NC_008686.1 870566 870937 R hypothetical protein complement(870566..870937) Paracoccus denitrificans PD1222 4579281 YP_914693.1 CDS Pden_0886 NC_008686.1 871051 871317 D hypothetical protein 871051..871317 Paracoccus denitrificans PD1222 4578564 YP_914694.1 CDS tig NC_008686.1 871325 872704 D Tig; RopA; peptidyl-prolyl cis/trans isomerase; promotes folding of newly synthesized proteins; binds ribosomal 50S subunit; forms a homodimer; trigger factor 871325..872704 Paracoccus denitrificans PD1222 4578565 YP_914695.1 CDS Pden_0888 NC_008686.1 872907 873701 R KEGG: afm:Afu1g11690 hypothetical protein; hypothetical protein complement(872907..873701) Paracoccus denitrificans PD1222 4578566 YP_914696.1 CDS rplI NC_008686.1 873862 874446 R in Escherichia coli this protein is wrapped around the base of the L1 stalk; 50S ribosomal protein L9 complement(873862..874446) Paracoccus denitrificans PD1222 4578567 YP_914697.1 CDS rpsR NC_008686.1 874459 874686 R 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 complement(874459..874686) Paracoccus denitrificans PD1222 4578568 YP_914698.1 CDS rpsF NC_008686.1 874705 875100 R binds cooperatively with S18 to the S15-16S complex, allowing platform assembly to continue with S11 and S21; 30S ribosomal protein S6 complement(874705..875100) Paracoccus denitrificans PD1222 4578569 YP_914699.1 CDS Pden_0892 NC_008686.1 875389 875970 D PFAM: YceI family protein; KEGG: sil:SPO2279 hypothetical protein; hypothetical protein 875389..875970 Paracoccus denitrificans PD1222 4578570 YP_914700.1 CDS Pden_0893 NC_008686.1 876043 877065 R PFAM: Di-haem cytochrome c peroxidase; KEGG: sil:SPO0330 cytochrome c peroxidase; cytochrome-c peroxidase complement(876043..877065) Paracoccus denitrificans PD1222 4578571 YP_914701.1 CDS prfA NC_008686.1 877258 878313 D 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 877258..878313 Paracoccus denitrificans PD1222 4578572 YP_914702.1 CDS Pden_0895 NC_008686.1 878318 879145 D 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 878318..879145 Paracoccus denitrificans PD1222 4578573 YP_914703.1 CDS Pden_0896 NC_008686.1 879393 880181 D KEGG: rsp:RSP_6078 hypothetical protein; hypothetical protein 879393..880181 Paracoccus denitrificans PD1222 4578574 YP_914704.1 CDS ksgA NC_008686.1 880185 881033 R 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 complement(880185..881033) Paracoccus denitrificans PD1222 4578575 YP_914705.1 CDS pdxA NC_008686.1 881030 881998 R 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 complement(881030..881998) Paracoccus denitrificans PD1222 4578576 YP_914706.1 CDS Pden_0899 NC_008686.1 882066 883337 R 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 complement(882066..883337) Paracoccus denitrificans PD1222 4578577 YP_914707.1 CDS Pden_0900 NC_008686.1 883369 885783 R PFAM: Organic solvent tolerance protein; KEGG: rsp:RSP_2902 organic solvent tolerance protein; organic solvent tolerance protein complement(883369..885783) Paracoccus denitrificans PD1222 4578578 YP_914708.1 CDS Pden_0901 NC_008686.1 885783 886904 R PFAM: permease YjgP/YjgQ family protein; KEGG: rsp:RSP_2901 permease; YjgP/YjgQ family permease complement(885783..886904) Paracoccus denitrificans PD1222 4578579 YP_914709.1 CDS Pden_0902 NC_008686.1 886901 888049 R PFAM: permease YjgP/YjgQ family protein; KEGG: rsp:RSP_2900 predicted permease; YjgP/YjgQ family permease complement(886901..888049) Paracoccus denitrificans PD1222 4578580 YP_914710.1 CDS Pden_0903 NC_008686.1 888179 889780 D catalyzes the removal of N-terminal amino acids preferably leucine from various peptides; leucyl aminopeptidase 888179..889780 Paracoccus denitrificans PD1222 4578581 YP_914711.1 CDS Pden_0904 NC_008686.1 889780 890229 D 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 889780..890229 Paracoccus denitrificans PD1222 4578582 YP_914712.1 CDS Pden_0905 NC_008686.1 890283 890858 R KEGG: sit:TM1040_0952 conserved hypothetical protein; hypothetical protein complement(890283..890858) Paracoccus denitrificans PD1222 4578583 YP_914713.1 CDS Pden_0906 NC_008686.1 890858 891469 R PFAM: multiple antibiotic resistance (MarC)-related proteins; KEGG: rsp:RSP_2896 multiple antibiotic transporter; multiple antibiotic resistance (MarC)-like proteins complement(890858..891469) Paracoccus denitrificans PD1222 4579055 YP_914714.1 CDS Pden_0907 NC_008686.1 891636 891914 D PFAM: sec-independent translocation protein mttA/Hcf106; KEGG: rde:RD1_3255 twin-arginine translocation protein, TatA/E family; sec-independent translocation protein mttA/Hcf106 891636..891914 Paracoccus denitrificans PD1222 4579056 YP_914715.1 CDS Pden_0908 NC_008686.1 891933 892436 D 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 891933..892436 Paracoccus denitrificans PD1222 4579057 YP_914716.1 CDS Pden_0909 NC_008686.1 892437 893279 D 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 892437..893279 Paracoccus denitrificans PD1222 4579058 YP_914717.1 CDS Pden_0910 NC_008686.1 893272 894114 D PFAM: protein of unknown function DUF815; KEGG: rsp:RSP_2542 ATPase; hypothetical protein 893272..894114 Paracoccus denitrificans PD1222 4579059 YP_914718.1 CDS Pden_0911 NC_008686.1 894663 895712 R PFAM: Choloylglycine hydrolase; KEGG: atc:AGR_L_573 probable hydrolase VCA0877; choloylglycine hydrolase complement(894663..895712) Paracoccus denitrificans PD1222 4579060 YP_914719.1 CDS Pden_0912 NC_008686.1 895740 896078 R hypothetical protein complement(895740..896078) Paracoccus denitrificans PD1222 4579061 YP_914720.1 CDS Pden_0913 NC_008686.1 896404 897765 R 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 complement(896404..897765) Paracoccus denitrificans PD1222 4579062 YP_914721.1 CDS Pden_0914 NC_008686.1 897908 898339 D PFAM: regulatory protein, MarR; KEGG: rde:RD1_3650 transcriptional regulator MarR/EmrR family; MarR family transcriptional regulator 897908..898339 Paracoccus denitrificans PD1222 4579063 YP_914722.1 CDS Pden_0915 NC_008686.1 898445 898843 R PFAM: Entericidin EcnAB; entericidin A/B complement(898445..898843) Paracoccus denitrificans PD1222 4579064 YP_914723.1 CDS Pden_0916 NC_008686.1 898903 899223 D KEGG: rde:RD1_1084 hypothetical protein; TraR/DksA family transcriptional regulator 898903..899223 Paracoccus denitrificans PD1222 4579065 YP_914724.1 CDS Pden_0917 NC_008686.1 899233 899382 R PFAM: Entericidin EcnAB; KEGG: rsp:RSP_6220 hypothetical protein; entericidin EcnAB complement(899233..899382) Paracoccus denitrificans PD1222 4579066 YP_914725.1 CDS Pden_0918 NC_008686.1 899825 900592 R PFAM: alpha/beta hydrolase fold; Thioesterase; PGAP1 family protein; KEGG: rsp:RSP_0821 esterase/lipase/thioesterase; alpha/beta hydrolase complement(899825..900592) Paracoccus denitrificans PD1222 4579067 YP_914726.1 CDS Pden_0919 NC_008686.1 900663 901046 D KEGG: rsp:RSP_0822 hypothetical protein; hypothetical protein 900663..901046 Paracoccus denitrificans PD1222 4579068 YP_914727.1 CDS glyA NC_008686.1 901497 902780 R catalyzes the reaction of glycine with 5,10-methylenetetrahydrofolate to form L-serine and tetrahydrofolate; serine hydroxymethyltransferase complement(901497..902780) Paracoccus denitrificans PD1222 4579069 YP_914728.1 CDS ppnK NC_008686.1 902924 903673 D catalyzes the phosphorylation of NAD to NADP; inorganic polyphosphate/ATP-NAD kinase 902924..903673 Paracoccus denitrificans PD1222 4579070 YP_914729.1 CDS Pden_0922 NC_008686.1 903740 905335 D 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 903740..905335 Paracoccus denitrificans PD1222 4579071 YP_914730.1 CDS Pden_0923 NC_008686.1 905484 905984 D hypothetical protein 905484..905984 Paracoccus denitrificans PD1222 4579072 YP_914731.1 CDS Pden_0924 NC_008686.1 906075 906497 R PFAM: OsmC family protein; KEGG: rpa:RPA4194 osmotically inducible protein OsmC; OsmC family protein complement(906075..906497) Paracoccus denitrificans PD1222 4579073 YP_914732.1 CDS Pden_0925 NC_008686.1 906605 907498 D PFAM: protein of unknown function DUF6, transmembrane; KEGG: bmb:BruAb2_0942 hypothetical membrane protein; hypothetical protein 906605..907498 Paracoccus denitrificans PD1222 4579399 YP_914733.1 CDS Pden_0926 NC_008686.1 907568 907921 D PFAM: protein of unknown function DUF305; KEGG: mes:Meso_3895 protein of unknown function DUF305; hypothetical protein 907568..907921 Paracoccus denitrificans PD1222 4579400 YP_914734.1 CDS Pden_0927 NC_008686.1 907993 909129 R KEGG: rsp:RSP_2659 deoxyguanosinetriphosphate triphosphohydrolase; TIGRFAM: deoxyguanosinetriphosphate triphosphohydrolase; PFAM: metal-dependent phosphohydrolase, HD sub domain; SMART: metal-dependent phosphohydrolase, HD region; deoxyguanosinetriphosphate triphosphohydrolase complement(907993..909129) Paracoccus denitrificans PD1222 4579401 YP_914735.1 CDS Pden_0928 NC_008686.1 909205 909540 D 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 909205..909540 Paracoccus denitrificans PD1222 4579402 YP_914736.1 CDS Pden_0929 NC_008686.1 909579 910364 D TIGRFAM: exodeoxyribonuclease III; exodeoxyribonuclease III Xth; PFAM: Endonuclease/exonuclease/phosphatase; KEGG: rsp:RSP_2657 exodeoxyribonuclease III; exodeoxyribonuclease III 909579..910364 Paracoccus denitrificans PD1222 4579403 YP_914737.1 CDS Pden_0930 NC_008686.1 910464 910817 R hypothetical protein complement(910464..910817) Paracoccus denitrificans PD1222 4579404 YP_914738.1 CDS Pden_0931 NC_008686.1 910948 912804 R PFAM: extracellular solute-binding protein, family 5; KEGG: rsp:RSP_2856 oligopeptide ABC transporter, periplasmic-binding protein; extracellular solute-binding protein complement(910948..912804) Paracoccus denitrificans PD1222 4579405 YP_914739.1 CDS Pden_0932 NC_008686.1 913215 913997 D TIGRFAM: 3-hydroxybutyrate dehydrogenase; PFAM: short-chain dehydrogenase/reductase SDR; KR; KEGG: rde:RD1_2738 D-beta-hydroxybutyrate dehydrogenase; 3-hydroxybutyrate dehydrogenase 913215..913997 Paracoccus denitrificans PD1222 4579406 YP_914740.1 CDS Pden_0933 NC_008686.1 914019 915005 R PFAM: basic membrane lipoprotein; KEGG: rha:RHA1_ro04986 hypothetical protein; basic membrane lipoprotein complement(914019..915005) Paracoccus denitrificans PD1222 4579407 YP_914741.1 CDS thyX NC_008686.1 915121 916053 R 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 complement(915121..916053) Paracoccus denitrificans PD1222 4579408 YP_914742.1 CDS Pden_0935 NC_008686.1 916203 916631 D PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase; KEGG: rde:RD1_1872 lactoylglutathione lyase; glyoxalase/bleomycin resistance protein/dioxygenase 916203..916631 Paracoccus denitrificans PD1222 4579409 YP_914743.1 CDS Pden_0936 NC_008686.1 916811 917329 R PFAM: regulatory protein, MarR; KEGG: sil:SPO1267 transcriptional regulator, MarR family; MarR family transcriptional regulator complement(916811..917329) Paracoccus denitrificans PD1222 4579410 YP_914744.1 CDS Pden_0937 NC_008686.1 917421 917666 R PFAM: protein of unknown function DUF339; KEGG: rsp:RSP_0761 hypothetical protein; hypothetical protein complement(917421..917666) Paracoccus denitrificans PD1222 4579411 YP_914745.1 CDS Pden_0938 NC_008686.1 917772 918974 D PFAM: aminotransferase, class I and II; KEGG: rsp:RSP_0763 aspartate aminotransferase; class I and II aminotransferase 917772..918974 Paracoccus denitrificans PD1222 4579412 YP_914746.1 CDS aspA NC_008686.1 919032 920438 R catalyzes the formation of fumarate from aspartate; aspartate ammonia-lyase complement(919032..920438) Paracoccus denitrificans PD1222 4579413 YP_914747.1 CDS Pden_0940 NC_008686.1 920599 921495 R PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: sil:SPO2668 transcriptional regulator, LysR family; LysR family transcriptional regulator complement(920599..921495) Paracoccus denitrificans PD1222 4579414 YP_914748.1 CDS Pden_0941 NC_008686.1 921708 922742 D PFAM: Malate/L-lactate dehydrogenase; KEGG: atc:AGR_L_410 probable L-malate dehydrogenase; malate/L-lactate dehydrogenase 921708..922742 Paracoccus denitrificans PD1222 4579415 YP_914749.1 CDS Pden_0942 NC_008686.1 922739 923203 R PFAM: regulatory protein, AsnC/Lrp family; KEGG: jan:Jann_3495 transcriptional regulator, AsnC family; AsnC family transcriptional regulator complement(922739..923203) Paracoccus denitrificans PD1222 4579416 YP_914750.1 CDS Pden_0943 NC_008686.1 923313 926732 D 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 923313..926732 Paracoccus denitrificans PD1222 4579417 YP_914751.1 CDS Pden_0944 NC_008686.1 926862 927233 D KEGG: rsp:RSP_3680 transcriptional regulator, TetR family; TetR family transcriptional regulator 926862..927233 Paracoccus denitrificans PD1222 4579418 YP_914752.1 CDS Pden_0945 NC_008686.1 927765 928766 D 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 927765..928766 Paracoccus denitrificans PD1222 4579656 YP_914753.1 CDS Pden_0946 NC_008686.1 928843 929733 D PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: sme:SMc02379 permease protein; binding-protein-dependent transport system inner membrane protein 928843..929733 Paracoccus denitrificans PD1222 4579657 YP_914754.1 CDS Pden_0947 NC_008686.1 929726 930772 D 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 929726..930772 Paracoccus denitrificans PD1222 4579658 YP_914755.1 CDS Pden_0948 NC_008686.1 930853 932481 D 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 930853..932481 Paracoccus denitrificans PD1222 4579659 YP_914756.1 CDS Pden_0949 NC_008686.1 932488 933501 R PFAM: DNA/RNA non-specific endonuclease; KEGG: rha:RHA1_ro05345 hypothetical protein; DNA/RNA non-specific endonuclease complement(932488..933501) Paracoccus denitrificans PD1222 4579660 YP_914757.1 CDS Pden_0950 NC_008686.1 933691 935244 R PFAM: peptidase S8 and S53, subtilisin, kexin, sedolisin; KEGG: bha:BH0684 prepro-alkaline protease; peptidase S8/S53 subtilisin kexin sedolisin complement(933691..935244) Paracoccus denitrificans PD1222 4579661 YP_914758.1 CDS Pden_0951 NC_008686.1 935339 937603 R 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 complement(935339..937603) Paracoccus denitrificans PD1222 4579662 YP_914759.1 CDS Pden_0952 NC_008686.1 937769 938428 R PFAM: DSBA oxidoreductase; KEGG: rsp:RSP_2852 predicted polyketide biosynthesis associated protein; DSBA oxidoreductase complement(937769..938428) Paracoccus denitrificans PD1222 4579663 YP_914760.1 CDS Pden_0953 NC_008686.1 938429 939892 R PFAM: AMP-dependent synthetase and ligase; KEGG: sil:SPO2069 benzoate-coenzyme A ligase; AMP-dependent synthetase/ligase complement(938429..939892) Paracoccus denitrificans PD1222 4579664 YP_914761.1 CDS Pden_0954 NC_008686.1 940098 940304 R 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 complement(940098..940304) Paracoccus denitrificans PD1222 4579665 YP_914762.1 CDS thrS NC_008686.1 940532 942478 R 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 complement(940532..942478) Paracoccus denitrificans PD1222 4579666 YP_914763.1 CDS Pden_0956 NC_008686.1 942649 943398 D KEGG: sit:TM1040_1720 conserved hypothetical protein; hypothetical protein 942649..943398 Paracoccus denitrificans PD1222 4579667 YP_914764.1 CDS Pden_0957 NC_008686.1 943441 944784 R TIGRFAM: polyhydroxyalkanoate depolymerase, intracellular; PFAM: PHB de-polymerase domain protein; KEGG: rde:RD1_1887 polyhydroxyalkanoate depolymerase, intracellular; polyhydroxyalkanoate depolymerase complement(943441..944784) Paracoccus denitrificans PD1222 4579668 YP_914765.1 CDS Pden_0958 NC_008686.1 944898 947219 D 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 944898..947219 Paracoccus denitrificans PD1222 4579669 YP_914766.1 CDS Pden_0959 NC_008686.1 947333 947806 D KEGG: rsp:RSP_0381 hypothetical protein; hypothetical protein 947333..947806 Paracoccus denitrificans PD1222 4579670 YP_914767.1 CDS Pden_0960 NC_008686.1 947955 948542 D 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 947955..948542 Paracoccus denitrificans PD1222 4579671 YP_914768.1 CDS Pden_0961 NC_008686.1 948709 949788 R PFAM: phage integrase family protein; KEGG: rsp:RSP_1662 integrase/recombinase; phage integrase family protein complement(948709..949788) Paracoccus denitrificans PD1222 4579672 YP_914769.1 CDS Pden_0962 NC_008686.1 949785 950018 R KEGG: rsp:RSP_6015 hypothetical protein; hypothetical protein complement(949785..950018) Paracoccus denitrificans PD1222 4579673 YP_914770.1 CDS Pden_0963 NC_008686.1 950015 950743 R KEGG: rsp:RSP_3624 hypothetical protein; hypothetical protein complement(950015..950743) Paracoccus denitrificans PD1222 4579674 YP_914771.1 CDS Pden_0964 NC_008686.1 950740 951180 R hypothetical protein complement(950740..951180) Paracoccus denitrificans PD1222 4579538 YP_914772.1 CDS Pden_0965 NC_008686.1 951170 951442 R hypothetical protein complement(951170..951442) Paracoccus denitrificans PD1222 4579539 YP_914773.1 CDS Pden_0966 NC_008686.1 951442 952170 R hypothetical protein complement(951442..952170) Paracoccus denitrificans PD1222 4579540 YP_914774.1 CDS Pden_0967 NC_008686.1 952167 952967 R KEGG: ecc:c1524 hypothetical protein; hypothetical protein complement(952167..952967) Paracoccus denitrificans PD1222 4579541 YP_914775.1 CDS Pden_0968 NC_008686.1 952964 953392 R KEGG: bxe:Bxe_A3103 bacteriophage hypothetical protein; hypothetical protein complement(952964..953392) Paracoccus denitrificans PD1222 4579542 YP_914776.1 CDS Pden_0969 NC_008686.1 953392 956043 R PFAM: DNA methylase N-4/N-6 domain protein; KEGG: mes:Meso_1199 helicase-like; DNA methylase N-4/N-6 domain-containing protein complement(953392..956043) Paracoccus denitrificans PD1222 4579543 YP_914777.1 CDS Pden_0970 NC_008686.1 956047 957165 R 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 complement(956047..957165) Paracoccus denitrificans PD1222 4579544 YP_914778.1 CDS Pden_0971 NC_008686.1 957302 957514 R hypothetical protein complement(957302..957514) Paracoccus denitrificans PD1222 4579545 YP_914779.1 CDS Pden_0972 NC_008686.1 957514 957774 R hypothetical protein complement(957514..957774) Paracoccus denitrificans PD1222 4579546 YP_914780.1 CDS Pden_0973 NC_008686.1 958079 958315 D hypothetical protein 958079..958315 Paracoccus denitrificans PD1222 4579547 YP_914781.1 CDS Pden_0974 NC_008686.1 958305 958832 R hypothetical protein complement(958305..958832) Paracoccus denitrificans PD1222 4579548 YP_914782.1 CDS Pden_0975 NC_008686.1 959004 959615 R PFAM: helix-turn-helix domain protein; peptidase S24, S26A and S26B; KEGG: rsp:RSP_3771 hypothetical protein; phage repressor complement(959004..959615) Paracoccus denitrificans PD1222 4579549 YP_914783.1 CDS Pden_0976 NC_008686.1 959622 959930 R hypothetical protein complement(959622..959930) Paracoccus denitrificans PD1222 4579550 YP_914784.1 CDS Pden_0977 NC_008686.1 959968 960303 D hypothetical protein 959968..960303 Paracoccus denitrificans PD1222 4579551 YP_914785.1 CDS Pden_0978 NC_008686.1 960623 960958 R hypothetical protein complement(960623..960958) Paracoccus denitrificans PD1222 4579552 YP_914786.1 CDS Pden_0979 NC_008686.1 961090 961365 D hypothetical protein 961090..961365 Paracoccus denitrificans PD1222 4579553 YP_914787.1 CDS Pden_0980 NC_008686.1 961362 961556 D hypothetical protein 961362..961556 Paracoccus denitrificans PD1222 4579554 YP_914788.1 CDS Pden_0981 NC_008686.1 961553 962695 D KEGG: sit:TM1040_1631 hypothetical protein; hypothetical protein 961553..962695 Paracoccus denitrificans PD1222 4579555 YP_914789.1 CDS Pden_0982 NC_008686.1 962688 962936 D hypothetical protein 962688..962936 Paracoccus denitrificans PD1222 4579556 YP_914790.1 CDS Pden_0983 NC_008686.1 962933 964771 D TIGRFAM: phage/plasmid primase, P4 family; PFAM: Poxvirus D5 protein; KEGG: lin:lin2587 similar to bacteriophage protein; P4 family phage/plasmid primase 962933..964771 Paracoccus denitrificans PD1222 4579557 YP_914791.1 CDS Pden_0984 NC_008686.1 965147 965905 D KEGG: rsp:RSP_3778 hypothetical protein; hypothetical protein 965147..965905 Paracoccus denitrificans PD1222 4578760 YP_914792.1 CDS Pden_0985 NC_008686.1 966075 966425 D PFAM: HNH endonuclease; SMART: HNH nuclease; KEGG: rsp:RSP_2072 phage-related holin protein; HNH endonuclease 966075..966425 Paracoccus denitrificans PD1222 4578761 YP_914793.1 CDS Pden_0986 NC_008686.1 966475 966735 D hypothetical protein 966475..966735 Paracoccus denitrificans PD1222 4578762 YP_914794.1 CDS Pden_0987 NC_008686.1 966910 967413 D PFAM: Resolvase helix-turn-helix domain protein; KEGG: sit:TM1040_1626 hypothetical protein; resolvase domain-containing protein 966910..967413 Paracoccus denitrificans PD1222 4578763 YP_914795.1 CDS Pden_0988 NC_008686.1 967403 969124 D PFAM: phage Terminase; KEGG: rsp:RSP_2070 phage-related terminase; phage terminase 967403..969124 Paracoccus denitrificans PD1222 4578764 YP_914796.1 CDS Pden_0989 NC_008686.1 969124 970461 D TIGRFAM: phage portal protein, HK97 family; PFAM: phage portal protein; KEGG: rsp:RSP_2069 phage portal protein, HK97 family; HK97 family phage portal protein 969124..970461 Paracoccus denitrificans PD1222 4578765 YP_914797.1 CDS Pden_0990 NC_008686.1 970448 971290 D PFAM: peptidase S14, ClpP; KEGG: rsp:RSP_2068 ClpP-like protease; peptidase S14, ClpP 970448..971290 Paracoccus denitrificans PD1222 4578766 YP_914798.1 CDS Pden_0991 NC_008686.1 971302 972651 D TIGRFAM: phage major capsid protein, HK97 family; KEGG: rsp:RSP_2067 prophage LambdaSo, major capsid protein, HK97 family; HK97 family phage major capsid protein 971302..972651 Paracoccus denitrificans PD1222 4578767 YP_914799.1 CDS Pden_0992 NC_008686.1 972709 973017 D hypothetical protein 972709..973017 Paracoccus denitrificans PD1222 4578768 YP_914800.1 CDS Pden_0993 NC_008686.1 973059 973553 D hypothetical protein 973059..973553 Paracoccus denitrificans PD1222 4578769 YP_914801.1 CDS Pden_0994 NC_008686.1 973522 974070 D KEGG: sit:TM1040_1619 phage conserved hypothetical protein, phiE125 gp8; hypothetical protein 973522..974070 Paracoccus denitrificans PD1222 4578770 YP_914802.1 CDS Pden_0995 NC_008686.1 974064 974414 D KEGG: sit:TM1040_1666 conserved hypothetical protein; hypothetical protein 974064..974414 Paracoccus denitrificans PD1222 4578771 YP_914803.1 CDS Pden_0996 NC_008686.1 974411 974818 D KEGG: rpa:RPA1898 homologue of rhodobacter capsulatus gene transfer agent (GTA) orfg8 (32% identity); hypothetical protein 974411..974818 Paracoccus denitrificans PD1222 4578772 YP_914804.1 CDS Pden_0997 NC_008686.1 975002 975460 D 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 975002..975460 Paracoccus denitrificans PD1222 4578773 YP_914805.1 CDS Pden_0998 NC_008686.1 975521 975982 D hypothetical protein 975521..975982 Paracoccus denitrificans PD1222 4578774 YP_914806.1 CDS Pden_0999 NC_008686.1 975982 976437 D hypothetical protein 975982..976437 Paracoccus denitrificans PD1222 4578775 YP_914807.1 CDS Pden_1000 NC_008686.1 976763 979738 D TIGRFAM: phage tape measure protein; KEGG: rso:RSc0873 bacteriophage-related transmembrane protein; phage tape measure protein 976763..979738 Paracoccus denitrificans PD1222 4578776 YP_914808.1 CDS Pden_1001 NC_008686.1 979738 980418 D hypothetical protein 979738..980418 Paracoccus denitrificans PD1222 4578777 YP_914809.1 CDS Pden_1002 NC_008686.1 980415 980981 D hypothetical protein 980415..980981 Paracoccus denitrificans PD1222 4578778 YP_914810.1 CDS Pden_1003 NC_008686.1 980966 981337 D KEGG: mes:Meso_1234 hypothetical protein; hypothetical protein 980966..981337 Paracoccus denitrificans PD1222 4579752 YP_914811.1 CDS Pden_1004 NC_008686.1 981337 983379 D KEGG: nar:Saro_2739 hypothetical protein; hypothetical protein 981337..983379 Paracoccus denitrificans PD1222 4579753 YP_914812.1 CDS Pden_1005 NC_008686.1 983443 983823 D hypothetical protein 983443..983823 Paracoccus denitrificans PD1222 4579754 YP_914813.1 CDS Pden_1006 NC_008686.1 983811 984200 R PFAM: transposase, IS4 family protein; KEGG: sit:TM1040_0174 transposase, IS4; transposase, IS4 family protein complement(983811..984200) Paracoccus denitrificans PD1222 4579755 YP_914814.1 CDS Pden_1007 NC_008686.1 984197 984568 R KEGG: nar:Saro_2759 transposase orfA IS5 family element; IS5 family transposase OrfA complement(984197..984568) Paracoccus denitrificans PD1222 4579756 YP_914815.1 CDS Pden_1008 NC_008686.1 984674 985630 R KEGG: rsp:RSP_4009 phosphate acetyl/butaryl transferase; TIGRFAM: phosphate acetyltransferase; PFAM: phosphate acetyl/butaryl transferase; phosphate acetyltransferase complement(984674..985630) Paracoccus denitrificans PD1222 4579757 YP_914816.1 CDS Pden_1009 NC_008686.1 985643 986659 R PFAM: conserved hypothetical protein 698; KEGG: rsp:RSP_4010 conserved hypothetical protein 698; hypothetical protein complement(985643..986659) Paracoccus denitrificans PD1222 4579758 YP_914817.1 CDS Pden_1010 NC_008686.1 986933 988714 R catalyzes the formation of acetyl phosphate and sulfite from 2-sulfoacetaldehyde; is active when grown on taurine as a sole carbon source; sulfoacetaldehyde acetyltransferase complement(986933..988714) Paracoccus denitrificans PD1222 4579759 YP_914818.1 CDS Pden_1011 NC_008686.1 988911 990215 R PFAM: major facilitator superfamily MFS_1; KEGG: bja:bll6038 hypothetical transport protein; major facilitator superfamily transporter complement(988911..990215) Paracoccus denitrificans PD1222 4579760 YP_914819.1 CDS Pden_1012 NC_008686.1 990373 991899 R PFAM: AMP-dependent synthetase and ligase; KEGG: rde:RD1_2917 hypothetical protein; AMP-dependent synthetase/ligase complement(990373..991899) Paracoccus denitrificans PD1222 4579761 YP_914820.1 CDS Pden_1013 NC_008686.1 991896 993305 R KEGG: jan:Jann_1566 aldehyde dehydrogenase; succinate-semialdehyde dehydrogenase (NAD(P)(+)) complement(991896..993305) Paracoccus denitrificans PD1222 4579762 YP_914821.1 CDS Pden_1014 NC_008686.1 993512 994546 D PFAM: regulatory protein, LacI; periplasmic binding protein/LacI transcriptional regulator; KEGG: rde:RD1_2923 transcriptional regulator, LacI family; periplasmic binding protein/LacI transcriptional regulator 993512..994546 Paracoccus denitrificans PD1222 4579763 YP_914822.1 CDS Pden_1015 NC_008686.1 994548 994751 R KEGG: ccr:CC2592 ISCc1, transposase OrfB; ISCc1, transposase OrfB complement(994548..994751) Paracoccus denitrificans PD1222 4579764 YP_914823.1 CDS Pden_1016 NC_008686.1 994798 995172 R hypothetical protein complement(994798..995172) Paracoccus denitrificans PD1222 4579765 YP_914824.1 CDS Pden_1017 NC_008686.1 995578 996606 D 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 995578..996606 Paracoccus denitrificans PD1222 4579766 YP_914825.1 CDS Pden_1018 NC_008686.1 997017 998231 D PFAM: creatinase; peptidase M24; KEGG: ppu:PP_3667 creatinase; creatinase 997017..998231 Paracoccus denitrificans PD1222 4579767 YP_914826.1 CDS Pden_1019 NC_008686.1 998293 999084 R PFAM: Creatininase; KEGG: rxy:Rxyl_0459 creatininase; creatininase complement(998293..999084) Paracoccus denitrificans PD1222 4579768 YP_914827.1 CDS Pden_1020 NC_008686.1 999184 1000077 D PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: rde:RD1_2370 transcriptional regulator, LysR family; LysR family transcriptional regulator 999184..1000077 Paracoccus denitrificans PD1222 4579769 YP_914828.1 CDS Pden_1021 NC_008686.1 1000194 1001321 D KEGG: rde:RD1_2369 spermidine/putrescine ABC transporter, periplasmic binding protein; spermidine/putrescine ABC transporter, periplasmic binding protein 1000194..1001321 Paracoccus denitrificans PD1222 4579770 YP_914829.1 CDS Pden_1022 NC_008686.1 1001379 1002224 D 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 1001379..1002224 Paracoccus denitrificans PD1222 4579771 YP_914830.1 CDS Pden_1023 NC_008686.1 1002221 1003039 D 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 1002221..1003039 Paracoccus denitrificans PD1222 4579578 YP_914831.1 CDS Pden_1024 NC_008686.1 1003043 1004131 D 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 1003043..1004131 Paracoccus denitrificans PD1222 4579579 YP_914832.1 CDS Pden_1025 NC_008686.1 1004440 1005285 D PFAM: extracellular solute-binding protein, family 3; KEGG: atc:AGR_L_407 probable binding protein component of ABC transporter; extracellular solute-binding protein 1004440..1005285 Paracoccus denitrificans PD1222 4579580 YP_914833.1 CDS Pden_1026 NC_008686.1 1005295 1005960 D 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 1005295..1005960 Paracoccus denitrificans PD1222 4579581 YP_914834.1 CDS Pden_1027 NC_008686.1 1005950 1006621 D 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 1005950..1006621 Paracoccus denitrificans PD1222 4579582 YP_914835.1 CDS Pden_1028 NC_008686.1 1006618 1007340 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sme:SMb20266 amino acid ABC transporter ATP-binding protein; ABC transporter 1006618..1007340 Paracoccus denitrificans PD1222 4579583 YP_914836.1 CDS Pden_1029 NC_008686.1 1007353 1007610 D hypothetical protein 1007353..1007610 Paracoccus denitrificans PD1222 4579584 YP_914837.1 CDS Pden_1030 NC_008686.1 1007692 1008927 D PFAM: major facilitator superfamily MFS_1; KEGG: rru:Rru_A1180 major facilitator superfamily MFS_1; major facilitator superfamily transporter 1007692..1008927 Paracoccus denitrificans PD1222 4579585 YP_914838.1 CDS Pden_1031 NC_008686.1 1009116 1010735 D PFAM: glucose-methanol-choline oxidoreductase; GMC oxidoreductase; KEGG: mes:Meso_3754 glucose-methanol-choline oxidoreductase; glucose-methanol-choline oxidoreductase 1009116..1010735 Paracoccus denitrificans PD1222 4579586 YP_914839.1 CDS Pden_1032 NC_008686.1 1010907 1011980 D PFAM: periplasmic binding protein/LacI transcriptional regulator; KEGG: rha:RHA1_ro00226 ABC sugar transporter, periplasmic solute-binding protein; periplasmic binding protein/LacI transcriptional regulator 1010907..1011980 Paracoccus denitrificans PD1222 4579587 YP_914840.1 CDS Pden_1033 NC_008686.1 1012013 1012810 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sco:SCO6010 probable ABC-transport system ATP binding protein; ABC transporter 1012013..1012810 Paracoccus denitrificans PD1222 4579588 YP_914841.1 CDS Pden_1034 NC_008686.1 1012803 1014017 D PFAM: inner-membrane translocator; KEGG: tfu:Tfu_1920 ABC transporter transmembrane transport protein; inner-membrane translocator 1012803..1014017 Paracoccus denitrificans PD1222 4579589 YP_914842.1 CDS Pden_1035 NC_008686.1 1014024 1014977 R PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: bms:BR1086 transcriptional regulator, LysR family; LysR family transcriptional regulator complement(1014024..1014977) Paracoccus denitrificans PD1222 4579590 YP_914843.1 CDS Pden_1036 NC_008686.1 1015071 1016027 D PFAM: amidohydrolase 2; KEGG: mlo:mll5767 hypothetical protein; amidohydrolase 1015071..1016027 Paracoccus denitrificans PD1222 4579591 YP_914844.1 CDS Pden_1037 NC_008686.1 1016024 1017241 D PFAM: amidohydrolase; Amidohydrolase 3; KEGG: mes:Meso_4503 amidohydrolase; amidohydrolase 1016024..1017241 Paracoccus denitrificans PD1222 4579592 YP_914845.1 CDS Pden_1038 NC_008686.1 1017249 1018118 R PFAM: protein of unknown function DUF6, transmembrane; KEGG: mlo:mlr0545 hypothetical protein; hypothetical protein complement(1017249..1018118) Paracoccus denitrificans PD1222 4579593 YP_914846.1 CDS Pden_1039 NC_008686.1 1018118 1018432 R PFAM: NIPSNAP family containing protein; KEGG: bbr:BB1741 hypothetical protein; NIPSNAP family protein complement(1018118..1018432) Paracoccus denitrificans PD1222 4579594 YP_914847.1 CDS Pden_1040 NC_008686.1 1018437 1019198 R PFAM: short-chain dehydrogenase/reductase SDR; KR; KEGG: bbr:BB1748 short chain dehydrogenase; short chain dehydrogenase complement(1018437..1019198) Paracoccus denitrificans PD1222 4579595 YP_914848.1 CDS Pden_1041 NC_008686.1 1019202 1019999 R PFAM: aspartate dehydrogenase; homoserine dehydrogenase, NAD-binding; KEGG: rso:RS01727 L-aspartate dehydrogenase; aspartate dehydrogenase complement(1019202..1019999) Paracoccus denitrificans PD1222 4579596 YP_914849.1 CDS Pden_1042 NC_008686.1 1019996 1020793 R PFAM: alpha/beta hydrolase fold; KEGG: bbr:BB1746 hydrolase; alpha/beta hydrolase complement(1019996..1020793) Paracoccus denitrificans PD1222 4578623 YP_914850.1 CDS Pden_1043 NC_008686.1 1020799 1021344 R PFAM: Cupin 2, conserved barrel domain protein; KEGG: bpa:BPP2288 hypothetical protein; cupin complement(1020799..1021344) Paracoccus denitrificans PD1222 4578624 YP_914851.1 CDS Pden_1044 NC_008686.1 1021341 1023008 R PFAM: glucose-methanol-choline oxidoreductase; GMC oxidoreductase; KEGG: pfo:Pfl_5244 choline dehydrogenase; glucose-methanol-choline oxidoreductase complement(1021341..1023008) Paracoccus denitrificans PD1222 4578625 YP_914852.1 CDS Pden_1045 NC_008686.1 1023021 1024043 R PFAM: proline racemase; KEGG: rha:RHA1_ro05288 probable proline racemase; proline racemase complement(1023021..1024043) Paracoccus denitrificans PD1222 4578626 YP_914853.1 CDS Pden_1046 NC_008686.1 1024119 1025192 R PFAM: regulatory protein, LacI; periplasmic binding protein/LacI transcriptional regulator; KEGG: sil:SPO0590 transcriptional regulator, LacI family; regulatory protein, LacI complement(1024119..1025192) Paracoccus denitrificans PD1222 4578627 YP_914854.1 CDS Pden_1047 NC_008686.1 1025338 1026639 D PFAM: extracellular solute-binding protein, family 1; KEGG: rxy:Rxyl_0062 extracellular solute-binding protein, family 1; extracellular solute-binding protein 1025338..1026639 Paracoccus denitrificans PD1222 4578628 YP_914855.1 CDS Pden_1048 NC_008686.1 1026700 1027626 D 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 1026700..1027626 Paracoccus denitrificans PD1222 4578629 YP_914856.1 CDS Pden_1049 NC_008686.1 1027639 1028481 D 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 1027639..1028481 Paracoccus denitrificans PD1222 4578630 YP_914857.1 CDS Pden_1050 NC_008686.1 1028486 1029556 D PFAM: ABC transporter related; Transport-associated OB domain protein; SMART: AAA ATPase; KEGG: sth:STH1782 sugar ABC transportor ATP-binding protein; ABC transporter 1028486..1029556 Paracoccus denitrificans PD1222 4578631 YP_914858.1 CDS Pden_1051 NC_008686.1 1029578 1031062 D PFAM: aldehyde dehydrogenase; KEGG: mlo:mll1015 aldehyde dehydrogenase; aldehyde dehydrogenase 1029578..1031062 Paracoccus denitrificans PD1222 4578632 YP_914859.1 CDS Pden_1054 NC_008686.1 1032328 1033653 D PFAM: aldehyde dehydrogenase; KEGG: jan:Jann_3747 aldehyde dehydrogenase; aldehyde dehydrogenase 1032328..1033653 Paracoccus denitrificans PD1222 4578634 YP_914860.1 CDS Pden_1055 NC_008686.1 1033801 1034103 R hypothetical protein complement(1033801..1034103) Paracoccus denitrificans PD1222 4578635 YP_914861.1 CDS Pden_1056 NC_008686.1 1034464 1035075 D KEGG: nha:Nham_3600 AMP-dependent synthetase and ligase; hypothetical protein 1034464..1035075 Paracoccus denitrificans PD1222 4578636 YP_914862.1 CDS Pden_1057 NC_008686.1 1035142 1036530 R metallo-dependent hydrolase superfamily; deaminase with metallo-dependent hydrolase domain; deaminase complement(1035142..1036530) Paracoccus denitrificans PD1222 4578637 YP_914863.1 CDS Pden_1058 NC_008686.1 1036643 1037509 D PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: pau:PA14_32360 LysR-family transcriptional regulator; LysR family transcriptional regulator 1036643..1037509 Paracoccus denitrificans PD1222 4578638 YP_914864.1 CDS Pden_1059 NC_008686.1 1037570 1037839 D hypothetical protein 1037570..1037839 Paracoccus denitrificans PD1222 4578639 YP_914865.1 CDS Pden_1060 NC_008686.1 1037869 1038864 R 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 complement(1037869..1038864) Paracoccus denitrificans PD1222 4578640 YP_914866.1 CDS Pden_1061 NC_008686.1 1038928 1039539 R PFAM: protein of unknown function DUF224, cysteine-rich region domain protein; KEGG: bja:blr6041 glycolate oxidase; hypothetical protein complement(1038928..1039539) Paracoccus denitrificans PD1222 4578641 YP_914867.1 CDS Pden_1062 NC_008686.1 1039892 1040434 R PFAM: flavin reductase domain protein, FMN-binding; KEGG: dar:Daro_1187 hypothetical protein; flavin reductase domain-containing protein complement(1039892..1040434) Paracoccus denitrificans PD1222 4578642 YP_914868.1 CDS Pden_1063 NC_008686.1 1040964 1041296 D KEGG: atc:AGR_L_3474 hypothetical protein; aspartate racemase 1040964..1041296 Paracoccus denitrificans PD1222 4580262 YP_914869.1 CDS Pden_1064 NC_008686.1 1041329 1042243 R 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 complement(1041329..1042243) Paracoccus denitrificans PD1222 4580263 YP_914870.1 CDS Pden_1065 NC_008686.1 1042377 1043132 D PFAM: short-chain dehydrogenase/reductase SDR; KR; KEGG: eca:ECA3214 probable short chain dehydrogenase; short-chain dehydrogenase/reductase SDR 1042377..1043132 Paracoccus denitrificans PD1222 4580264 YP_914871.1 CDS Pden_1066 NC_008686.1 1043153 1043650 R KEGG: atc:AGR_C_479 hypothetical protein; hypothetical protein complement(1043153..1043650) Paracoccus denitrificans PD1222 4580265 YP_914872.1 CDS Pden_1067 NC_008686.1 1043791 1044216 R PFAM: OsmC family protein; KEGG: gbe:GbCGDNIH1_0067 organic hydroperoxide resistance protein; OsmC family protein complement(1043791..1044216) Paracoccus denitrificans PD1222 4580266 YP_914873.1 CDS Pden_1068 NC_008686.1 1044336 1044779 D PFAM: regulatory protein, MarR; KEGG: mlo:mlr2690 probable transcriptional regulator; MarR family transcriptional regulator 1044336..1044779 Paracoccus denitrificans PD1222 4580267 YP_914874.1 CDS Pden_1069 NC_008686.1 1044898 1045320 D KEGG: aba:Acid345_1171 hypothetical protein; hypothetical protein 1044898..1045320 Paracoccus denitrificans PD1222 4580268 YP_914875.1 CDS Pden_1070 NC_008686.1 1045344 1045961 D PFAM: regulatory proteins, IclR; KEGG: bja:bll3094 transcriptional regulatory protein; regulatory proteins, IclR 1045344..1045961 Paracoccus denitrificans PD1222 4580269 YP_914876.1 CDS Pden_1071 NC_008686.1 1046186 1047334 D PFAM: aminotransferase, class V; KEGG: bja:blr3095 probable aminotransferase; class V aminotransferase 1046186..1047334 Paracoccus denitrificans PD1222 4580270 YP_914877.1 CDS Pden_1072 NC_008686.1 1047405 1048292 D PFAM: extracellular solute-binding protein, family 3; KEGG: bja:blr3096 ABC transporter substrate-binding protein; extracellular solute-binding protein 1047405..1048292 Paracoccus denitrificans PD1222 4580271 YP_914878.1 CDS Pden_1073 NC_008686.1 1048349 1049110 D 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 1048349..1049110 Paracoccus denitrificans PD1222 4580272 YP_914879.1 CDS Pden_1074 NC_008686.1 1049107 1049799 D 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 1049107..1049799 Paracoccus denitrificans PD1222 4580273 YP_914880.1 CDS Pden_1075 NC_008686.1 1049814 1050566 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: psp:PSPPH_1133 amino acid ABC transporter, ATP-binding protein; ABC transporter 1049814..1050566 Paracoccus denitrificans PD1222 4580274 YP_914881.1 CDS Pden_1076 NC_008686.1 1050707 1051222 R PFAM: protein of unknown function DUF1697; KEGG: bja:bll4334 hypothetical protein; hypothetical protein complement(1050707..1051222) Paracoccus denitrificans PD1222 4580275 YP_914882.1 CDS Pden_1077 NC_008686.1 1051385 1052533 D PFAM: ABC transporter related; Transport-associated OB domain protein; SMART: AAA ATPase; KEGG: mlo:mll3624 ATP-binding component of transport system; ABC transporter 1051385..1052533 Paracoccus denitrificans PD1222 4580276 YP_914883.1 CDS Pden_1078 NC_008686.1 1052524 1053492 D PFAM: extracellular solute-binding protein, family 1; KEGG: sit:TM1040_0544 extracellular solute-binding protein, family 1; extracellular solute-binding protein 1052524..1053492 Paracoccus denitrificans PD1222 4580277 YP_914884.1 CDS Pden_1079 NC_008686.1 1053498 1055225 D 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 1053498..1055225 Paracoccus denitrificans PD1222 4580278 YP_914885.1 CDS Pden_1080 NC_008686.1 1055213 1056331 D PFAM: beta-lactamase domain protein; KEGG: sit:TM1040_0541 beta-lactamase-like; beta-lactamase domain-containing protein 1055213..1056331 Paracoccus denitrificans PD1222 4580279 YP_914886.1 CDS Pden_1081 NC_008686.1 1056489 1056848 D KEGG: sme:SMb20160 hypothetical protein; dual specificity protein phosphatase 1056489..1056848 Paracoccus denitrificans PD1222 4580280 YP_914887.1 CDS Pden_1082 NC_008686.1 1056891 1057169 D hypothetical protein 1056891..1057169 Paracoccus denitrificans PD1222 4578779 YP_914888.1 CDS Pden_1083 NC_008686.1 1057189 1058175 D PFAM: beta-lactamase; KEGG: rsp:RSP_2235 hypothetical protein; beta-lactamase 1057189..1058175 Paracoccus denitrificans PD1222 4578780 YP_914889.1 CDS Pden_1084 NC_008686.1 1058320 1058490 D KEGG: mes:Meso_0502 conjugal transfer protein; conjugal transfer protein 1058320..1058490 Paracoccus denitrificans PD1222 4578781 YP_914890.1 CDS Pden_1086 NC_008686.1 1058907 1060412 R PFAM: glucose-methanol-choline oxidoreductase; KEGG: mlo:mlr6655 similar to dehydrogenase subunit; glucose-methanol-choline oxidoreductase complement(1058907..1060412) Paracoccus denitrificans PD1222 4578782 YP_914891.1 CDS Pden_1087 NC_008686.1 1060420 1061517 R 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 complement(1060420..1061517) Paracoccus denitrificans PD1222 4578783 YP_914892.1 CDS Pden_1088 NC_008686.1 1061523 1062401 R PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: mlo:mlr6653 ABC transporter (permease protein); binding-protein-dependent transport system inner membrane protein complement(1061523..1062401) Paracoccus denitrificans PD1222 4578784 YP_914893.1 CDS Pden_1089 NC_008686.1 1062391 1063287 R PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: mlo:mlr6652 ABC transporter (permease protein); binding-protein-dependent transport system inner membrane protein complement(1062391..1063287) Paracoccus denitrificans PD1222 4578785 YP_914894.1 CDS Pden_1090 NC_008686.1 1063371 1064624 R PFAM: extracellular solute-binding protein, family 1; KEGG: mlo:mlr6651 ABC transporter (substrate-binding protein); extracellular solute-binding protein complement(1063371..1064624) Paracoccus denitrificans PD1222 4578786 YP_914895.1 CDS Pden_1091 NC_008686.1 1064693 1066000 R catalyzes the oxidation of L-histidinol to L-histidinaldehyde and then to L-histidine in histidine biosynthesis; functions as a dimer; histidinol dehydrogenase complement(1064693..1066000) Paracoccus denitrificans PD1222 4578787 YP_914896.1 CDS Pden_1092 NC_008686.1 1066114 1067916 R 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 complement(1066114..1067916) Paracoccus denitrificans PD1222 4578788 YP_914897.1 CDS Pden_1093 NC_008686.1 1068069 1068911 D SMART: helix-turn-helix domain protein; KEGG: mlo:mlr6646 hypothetical protein; XRE family transcriptional regulator 1068069..1068911 Paracoccus denitrificans PD1222 4578789 YP_914898.1 CDS Pden_1094 NC_008686.1 1068972 1069730 D KEGG: mlo:mll6647 hypothetical protein; hypothetical protein 1068972..1069730 Paracoccus denitrificans PD1222 4578790 YP_914899.1 CDS Pden_1095 NC_008686.1 1069750 1071117 D PFAM: fumarate lyase; KEGG: bms:BR1958 aspartate ammonia-lyase; aspartate ammonia-lyase 1069750..1071117 Paracoccus denitrificans PD1222 4578791 YP_914900.1 CDS Pden_1096 NC_008686.1 1071142 1072143 D PFAM: glycoside hydrolase, family 3 domain protein; KEGG: bcn:Bcen_1514 glycoside hydrolase, family 3-like; glycoside hydrolase family protein 1071142..1072143 Paracoccus denitrificans PD1222 4578792 YP_914901.1 CDS Pden_1097 NC_008686.1 1072164 1072523 R KEGG: mlo:mlr6657 hypothetical protein; hypothetical protein complement(1072164..1072523) Paracoccus denitrificans PD1222 4578793 YP_914902.1 CDS Pden_1098 NC_008686.1 1072561 1074150 R PFAM: glucose-methanol-choline oxidoreductase; FAD dependent oxidoreductase; GMC oxidoreductase; KEGG: mlo:mlr6656 dehydrogenase; glucose-methanol-choline oxidoreductase complement(1072561..1074150) Paracoccus denitrificans PD1222 4578794 YP_914903.1 CDS Pden_1099 NC_008686.1 1074342 1075223 D PFAM: Xylose isomerase domain protein TIM barrel; KEGG: bcn:Bcen_1508 xylose isomerase-like TIM barrel; xylose isomerase domain-containing protein 1074342..1075223 Paracoccus denitrificans PD1222 4578795 YP_914904.1 CDS Pden_1100 NC_008686.1 1075249 1076409 D PFAM: major facilitator superfamily MFS_1; KEGG: rha:RHA1_ro01579 possible transporter, MFS superfamily; major facilitator superfamily transporter 1075249..1076409 Paracoccus denitrificans PD1222 4578796 YP_914905.1 CDS Pden_1101 NC_008686.1 1076527 1076964 R KEGG: sme:SMb20276 transcriptional regulator protein; RpiR family transcriptional regulator complement(1076527..1076964) Paracoccus denitrificans PD1222 4578797 YP_914906.1 CDS Pden_1102 NC_008686.1 1077084 1077986 R PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: gvi:glr2986 LysR family transcriptional regulatory protein; LysR family transcriptional regulator complement(1077084..1077986) Paracoccus denitrificans PD1222 4578798 YP_914907.1 CDS Pden_1103 NC_008686.1 1078420 1079778 D PFAM: General substrate transporter; major facilitator superfamily MFS_1; KEGG: ppu:PP_2411 major facilitator family transporter; major facilitator superfamily transporter 1078420..1079778 Paracoccus denitrificans PD1222 4580437 YP_914908.1 CDS Pden_1104 NC_008686.1 1079858 1080391 D PFAM: 4-vinyl reductase, 4VR; KEGG: reu:Reut_B4820 4-vinyl reductase, 4VR; 4-vinyl reductase, 4VR 1079858..1080391 Paracoccus denitrificans PD1222 4580438 YP_914909.1 CDS Pden_1105 NC_008686.1 1080449 1081447 D PFAM: peptidase M19, renal dipeptidase; KEGG: cps:CPS_4019 peptidase, M19 family; peptidase M19 1080449..1081447 Paracoccus denitrificans PD1222 4580439 YP_914910.1 CDS Pden_1106 NC_008686.1 1082126 1082881 D PFAM: regulatory protein GntR, HTH; GntR domain protein; KEGG: sil:SPO1912 transcriptional regulator, GntR family; GntR family transcriptional regulator 1082126..1082881 Paracoccus denitrificans PD1222 4580440 YP_914911.1 CDS Pden_1107 NC_008686.1 1082878 1083873 D PFAM: Alcohol dehydrogenase, zinc-binding domain protein; Alcohol dehydrogenase GroES domain protein; KEGG: pol:Bpro_2634 alcohol dehydrogenase, zinc-binding; alcohol dehydrogenase 1082878..1083873 Paracoccus denitrificans PD1222 4580441 YP_914912.1 CDS Pden_1108 NC_008686.1 1083927 1085582 R activates fatty acids by binding to coenzyme A; acyl-CoA synthetase complement(1083927..1085582) Paracoccus denitrificans PD1222 4580442 YP_914913.1 CDS Pden_1109 NC_008686.1 1085622 1085837 R KEGG: mes:Meso_2537 rhodanese-like; rhodanese-like protein complement(1085622..1085837) Paracoccus denitrificans PD1222 4580443 YP_914914.1 CDS Pden_1110 NC_008686.1 1086247 1086537 R PFAM: protein of unknown function DUF1330; KEGG: mes:Meso_0684 protein of unknown function DUF1330; hypothetical protein complement(1086247..1086537) Paracoccus denitrificans PD1222 4580444 YP_914915.1 CDS Pden_1111 NC_008686.1 1086592 1088076 R TIGRFAM: NCS1 nucleoside transporter family; PFAM: permease for cytosine/purines, uracil, thiamine, allantoin; KEGG: sit:TM1040_0338 NCS1 nucleoside transporter family; NCS1 nucleoside transporter complement(1086592..1088076) Paracoccus denitrificans PD1222 4580445 YP_914916.1 CDS Pden_1112 NC_008686.1 1088170 1089639 R catalyzes the hydrolytic cleavage of hydantoin with aromatic side chains at the 5'position; phenylhydantoinase complement(1088170..1089639) Paracoccus denitrificans PD1222 4580446 YP_914917.1 CDS Pden_1113 NC_008686.1 1089636 1090886 R 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 complement(1089636..1090886) Paracoccus denitrificans PD1222 4580447 YP_914918.1 CDS cofG NC_008686.1 1091275 1092417 D 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 1091275..1092417 Paracoccus denitrificans PD1222 4580448 YP_914919.1 CDS Pden_1115 NC_008686.1 1092414 1093670 D PFAM: Radical SAM domain protein; SMART: Elongator protein 3/MiaB/NifB; KEGG: cps:CPS_4048 conserved hypothetical protein TIGR00423; radical SAM domain-containing protein 1092414..1093670 Paracoccus denitrificans PD1222 4580449 YP_914920.1 CDS Pden_1116 NC_008686.1 1093667 1094620 D 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 1093667..1094620 Paracoccus denitrificans PD1222 4580450 YP_914921.1 CDS Pden_1117 NC_008686.1 1094617 1095267 D PFAM: protein of unknown function DUF121; KEGG: cps:CPS_4046 hypothetical protein; hypothetical protein 1094617..1095267 Paracoccus denitrificans PD1222 4580451 YP_914922.1 CDS Pden_1118 NC_008686.1 1095264 1096037 D TIGRFAM: F420-dependent oxidoreductase, PFAM: protein of unknown function DUF129; KEGG: cps:CPS_4045 F420-dependent oxidoreductase; F420-dependent oxidoreductase 1095264..1096037 Paracoccus denitrificans PD1222 4580452 YP_914923.1 CDS Pden_1119 NC_008686.1 1096034 1096702 D 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 1096034..1096702 Paracoccus denitrificans PD1222 4580453 YP_914924.1 CDS Pden_1120 NC_008686.1 1096737 1097738 D PFAM: luciferase family protein; KEGG: cps:CPS_4043 methylenetetrahydromethanopterin reductase; luciferase family protein 1096737..1097738 Paracoccus denitrificans PD1222 4580454 YP_914925.1 CDS Pden_1121 NC_008686.1 1097832 1098497 D PFAM: regulatory protein, TetR; Tetracycline transcriptional regulator YcdC, C-terminal domain protein; KEGG: mlo:mlr1634 probable transcriptional regulator; TetR family transcriptional regulator 1097832..1098497 Paracoccus denitrificans PD1222 4580455 YP_914926.1 CDS Pden_1122 NC_008686.1 1098969 1099472 R PFAM: protein of unknown function DUF336; KEGG: atc:AGR_C_2067 hypothetical protein; hypothetical protein complement(1098969..1099472) Paracoccus denitrificans PD1222 4578857 YP_914927.1 CDS Pden_1123 NC_008686.1 1099543 1100151 R PFAM: regulatory protein, LuxR; response regulator receiver; Sigma-70, region 4 type 2; KEGG: atc:AGR_C_2066 hypothetical protein; Fis family transcriptional regulator complement(1099543..1100151) Paracoccus denitrificans PD1222 4578858 YP_914928.1 CDS Pden_1124 NC_008686.1 1100148 1101599 R 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 complement(1100148..1101599) Paracoccus denitrificans PD1222 4578859 YP_914929.1 CDS Pden_1125 NC_008686.1 1101981 1102979 D 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 1101981..1102979 Paracoccus denitrificans PD1222 4578860 YP_914930.1 CDS Pden_1126 NC_008686.1 1103117 1103815 D KEGG: rsp:RSP_3276 hypothetical protein; hypothetical protein 1103117..1103815 Paracoccus denitrificans PD1222 4578861 YP_914931.1 CDS Pden_1127 NC_008686.1 1103802 1104131 D KEGG: rsp:RSP_6252 hypothetical protein; hypothetical protein 1103802..1104131 Paracoccus denitrificans PD1222 4578862 YP_914932.1 CDS Pden_1128 NC_008686.1 1104128 1104976 D PFAM: von Willebrand factor, type A; KEGG: rsp:RSP_3278 Von Willebrand domain containing protein; von Willebrand factor type A domain-containing protein 1104128..1104976 Paracoccus denitrificans PD1222 4578863 YP_914933.1 CDS Pden_1129 NC_008686.1 1104973 1105920 D PFAM: von Willebrand factor, type A; KEGG: rsp:RSP_3280 hypothetical protein; von Willebrand factor A 1104973..1105920 Paracoccus denitrificans PD1222 4578864 YP_914934.1 CDS Pden_1130 NC_008686.1 1105917 1106528 D KEGG: rsp:RSP_3281 hypothetical protein; hypothetical protein 1105917..1106528 Paracoccus denitrificans PD1222 4578865 YP_914935.1 CDS Pden_1131 NC_008686.1 1106522 1107718 D KEGG: rsp:RSP_3282 hypothetical protein; hypothetical protein 1106522..1107718 Paracoccus denitrificans PD1222 4578866 YP_914936.1 CDS Pden_1132 NC_008686.1 1107943 1108827 R KEGG: mes:Meso_3101 PRC-barrel; PRC-barrel containing protein complement(1107943..1108827) Paracoccus denitrificans PD1222 4578867 YP_914937.1 CDS Pden_1133 NC_008686.1 1108967 1109188 R KEGG: rsp:RSP_2379 hypothetical protein; hypothetical protein complement(1108967..1109188) Paracoccus denitrificans PD1222 4578868 YP_914938.1 CDS Pden_1134 NC_008686.1 1109204 1110061 R PFAM: short-chain dehydrogenase/reductase SDR; KR; KEGG: ret:RHE_PE00299 oxidoreductase protein, short-chain dehydrogenase reductase (SDR)family; short-chain dehydrogenase/reductase SDR complement(1109204..1110061) Paracoccus denitrificans PD1222 4578869 YP_914939.1 CDS Pden_1135 NC_008686.1 1110058 1110744 R KEGG: sme:SMb20339 hypothetical protein; hypothetical protein complement(1110058..1110744) Paracoccus denitrificans PD1222 4578870 YP_914940.1 CDS Pden_1136 NC_008686.1 1110901 1111398 D PFAM: protein of unknown function DUF892; KEGG: sme:SMc00371 hypothetical protein; hypothetical protein 1110901..1111398 Paracoccus denitrificans PD1222 4578871 YP_914941.1 CDS Pden_1137 NC_008686.1 1111575 1112048 R 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 complement(1111575..1112048) Paracoccus denitrificans PD1222 4578872 YP_914942.1 CDS Pden_1138 NC_008686.1 1112662 1113549 D PFAM: helix-turn-helix- domain containing protein, AraC type; KEGG: sme:SMc01610 transcription regulator protein; helix-turn-helix domain-containing protein 1112662..1113549 Paracoccus denitrificans PD1222 4578873 YP_914943.1 CDS Pden_1139 NC_008686.1 1113565 1115775 D 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 1113565..1115775 Paracoccus denitrificans PD1222 4578874 YP_914944.1 CDS Pden_1140 NC_008686.1 1115769 1116647 D PFAM: periplasmic binding protein; KEGG: rsp:RSP_1439 ABC Fe+3 hydroxamate (ferrichrome) transporter, periplasmic siderophore binding protein; periplasmic binding protein 1115769..1116647 Paracoccus denitrificans PD1222 4578875 YP_914945.1 CDS Pden_1141 NC_008686.1 1116644 1118614 D 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 1116644..1118614 Paracoccus denitrificans PD1222 4578876 YP_914946.1 CDS Pden_1142 NC_008686.1 1118611 1119378 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rsp:RSP_1437 ABC Fe+3 hydroxamate (ferrichrome) transporter, ATPase subunit; ABC transporter 1118611..1119378 Paracoccus denitrificans PD1222 4580456 YP_914947.1 CDS Pden_1143 NC_008686.1 1119400 1121097 D 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 1119400..1121097 Paracoccus denitrificans PD1222 4580457 YP_914948.1 CDS Pden_1144 NC_008686.1 1121215 1121577 R KEGG: ret:RHE_CH03726 hypothetical protein; hypothetical protein complement(1121215..1121577) Paracoccus denitrificans PD1222 4580458 YP_914949.1 CDS Pden_1145 NC_008686.1 1121604 1122161 R TIGRFAM: intracellular protease, PfpI family; PFAM: ThiJ/PfpI domain protein; KEGG: ret:RHE_CH03725 hypothetical protein; PfpI family intracellular peptidase complement(1121604..1122161) Paracoccus denitrificans PD1222 4580459 YP_914950.1 CDS Pden_1146 NC_008686.1 1122331 1123320 R PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: bmb:BruAb1_1927 transcriptional regulator, LysR family; LysR family transcriptional regulator complement(1122331..1123320) Paracoccus denitrificans PD1222 4580460 YP_914951.1 CDS Pden_1147 NC_008686.1 1123561 1124403 D PFAM: extracellular solute-binding protein, family 3; KEGG: bmb:BruAb1_1929 amino acid ABC transporter, periplasmic amino acid-binding protein; extracellular solute-binding protein 1123561..1124403 Paracoccus denitrificans PD1222 4580461 YP_914952.1 CDS Pden_1148 NC_008686.1 1124465 1125124 D 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 1124465..1125124 Paracoccus denitrificans PD1222 4580462 YP_914953.1 CDS Pden_1149 NC_008686.1 1125128 1125850 D 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 1125128..1125850 Paracoccus denitrificans PD1222 4580463 YP_914954.1 CDS Pden_1150 NC_008686.1 1125898 1126653 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: bmb:BruAb1_1932 amino acid ABC transporter, ATP-binding protein; ABC transporter 1125898..1126653 Paracoccus denitrificans PD1222 4580464 YP_914955.1 CDS Pden_1151 NC_008686.1 1126673 1127662 D PFAM: Arginase/agmatinase/formiminoglutamase; KEGG: bms:BR1957 arginase family protein; arginase 1126673..1127662 Paracoccus denitrificans PD1222 4580465 YP_914956.1 CDS Pden_1152 NC_008686.1 1127743 1128501 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: bms:BR1959 amino acid ABC transporter, ATP-binding protein; ABC transporter 1127743..1128501 Paracoccus denitrificans PD1222 4580466 YP_914957.1 CDS Pden_1153 NC_008686.1 1128513 1129523 D PFAM: Asparaginase/glutaminase; KEGG: bmb:BruAb1_1936 L-asparaginase type II, hypothetical; asparaginase/glutaminase 1128513..1129523 Paracoccus denitrificans PD1222 4580467 YP_914958.1 CDS Pden_1154 NC_008686.1 1129819 1130460 D KEGG: mag:amb4044 site-specific recombinase; hypothetical protein 1129819..1130460 Paracoccus denitrificans PD1222 4580468 YP_914959.1 CDS Pden_1155 NC_008686.1 1130501 1130773 D hypothetical protein 1130501..1130773 Paracoccus denitrificans PD1222 4580469 YP_914960.1 CDS Pden_1157 NC_008686.1 1131251 1131565 D KEGG: swo:Swol_1691 periplasmic binding protein; periplasmic binding protein 1131251..1131565 Paracoccus denitrificans PD1222 4580470 YP_914961.1 CDS Pden_1158 NC_008686.1 1131562 1132419 D KEGG: mta:Moth_1420 hypothetical protein; hypothetical protein 1131562..1132419 Paracoccus denitrificans PD1222 4580471 YP_914962.1 CDS Pden_1159 NC_008686.1 1132445 1132687 D KEGG: nwi:Nwi_2070 hypothetical protein; hypothetical protein 1132445..1132687 Paracoccus denitrificans PD1222 4580472 YP_914963.1 CDS Pden_1160 NC_008686.1 1132706 1133068 R PFAM: HPP family protein+B94; KEGG: son:SO1392 hypothetical protein; HPP family protein complement(1132706..1133068) Paracoccus denitrificans PD1222 4580473 YP_914964.1 CDS Pden_1161 NC_008686.1 1133256 1134461 R 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 complement(1133256..1134461) Paracoccus denitrificans PD1222 4580474 YP_914965.1 CDS Pden_1162 NC_008686.1 1134577 1135359 D PFAM: Arginase/agmatinase/formiminoglutamase; KEGG: csa:Csal_1087 arginase/agmatinase/formiminoglutamase; arginase 1134577..1135359 Paracoccus denitrificans PD1222 4579928 YP_914966.1 CDS Pden_1163 NC_008686.1 1135367 1135786 R PFAM: NUDIX hydrolase; KEGG: pfl:PFL_4894 hydrolase, NUDIX family; NUDIX hydrolase complement(1135367..1135786) Paracoccus denitrificans PD1222 4579929 YP_914967.1 CDS Pden_1166 NC_008686.1 1136932 1138197 D PFAM: major facilitator superfamily MFS_1; KEGG: rsp:RSP_4025 major facilitator superfamily, fosmidomycin resistant protein; major facilitator superfamily transporter 1136932..1138197 Paracoccus denitrificans PD1222 4579931 YP_914968.1 CDS Pden_1167 NC_008686.1 1138212 1138949 R TIGRFAM: molybdenum ABC transporter, periplasmic molybdate-binding protein; KEGG: ava:Ava_4058 hypothetical protein; molybdenum ABC transporter periplasmic molybdate-binding protein complement(1138212..1138949) Paracoccus denitrificans PD1222 4579932 YP_914969.1 CDS Pden_1168 NC_008686.1 1139024 1140085 D PFAM: periplasmic binding protein; KEGG: hin:HI1472 iron transport system substrate-binding protein; periplasmic binding protein 1139024..1140085 Paracoccus denitrificans PD1222 4579933 YP_914970.1 CDS Pden_1169 NC_008686.1 1140148 1141122 D PFAM: transport system permease protein; KEGG: eca:ECA3095 ABC transporter permease protein; transport system permease 1140148..1141122 Paracoccus denitrificans PD1222 4579934 YP_914971.1 CDS Pden_1170 NC_008686.1 1141115 1141867 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rpa:RPA2310 iron ABC transporter ATP-binding protein; ABC transporter 1141115..1141867 Paracoccus denitrificans PD1222 4579935 YP_914972.1 CDS Pden_1171 NC_008686.1 1141928 1144021 R PFAM: TonB-dependent receptor; TonB-dependent receptor, plug; KEGG: nha:Nham_3366 TonB-dependent receptor; TonB-dependent receptor complement(1141928..1144021) Paracoccus denitrificans PD1222 4579936 YP_914973.1 CDS Pden_1172 NC_008686.1 1144375 1144584 D PFAM: TOBE domain protein; KEGG: mlo:msr1466 molybdo-pterin binding protein; TOBE domain-containing protein 1144375..1144584 Paracoccus denitrificans PD1222 4579937 YP_914974.1 CDS Pden_1173 NC_008686.1 1144701 1145660 R PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: bpm:BURPS1710b_A0985 transcriptional regulator CatR; LysR family transcriptional regulator complement(1144701..1145660) Paracoccus denitrificans PD1222 4579938 YP_914975.1 CDS Pden_1174 NC_008686.1 1145826 1147016 D 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 1145826..1147016 Paracoccus denitrificans PD1222 4579939 YP_914976.1 CDS Pden_1175 NC_008686.1 1147019 1147309 D PFAM: Muconolactone delta-isomerase; KEGG: bam:Bamb_6586 muconolactone delta-isomerase; muconolactone delta-isomerase 1147019..1147309 Paracoccus denitrificans PD1222 4579940 YP_914977.1 CDS Pden_1176 NC_008686.1 1147377 1148315 D 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 1147377..1148315 Paracoccus denitrificans PD1222 4579941 YP_914978.1 CDS Pden_1177 NC_008686.1 1148433 1149791 D 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 1148433..1149791 Paracoccus denitrificans PD1222 4579942 YP_914979.1 CDS Pden_1178 NC_008686.1 1149788 1150276 D PFAM: aromatic-ring-hydroxylating dioxygenase, beta subunit; KEGG: bur:Bcep18194_C7047 2-chlorobenzoate 1,2-dioxygenase; 2-chlorobenzoate 1,2-dioxygenase 1149788..1150276 Paracoccus denitrificans PD1222 4579943 YP_914980.1 CDS Pden_1179 NC_008686.1 1150318 1151346 D 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 1150318..1151346 Paracoccus denitrificans PD1222 4579944 YP_914981.1 CDS benD NC_008686.1 1151343 1152128 D catalyzes the degradation of 2-hydro-1,2-dihydroxy benzoate to catechol; 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase 1151343..1152128 Paracoccus denitrificans PD1222 4579945 YP_914982.1 CDS Pden_1181 NC_008686.1 1152170 1153501 D PFAM: General substrate transporter; major facilitator superfamily MFS_1; KEGG: ppu:PP_3165 benzoate MFS transporter BenK; major facilitator superfamily transporter 1152170..1153501 Paracoccus denitrificans PD1222 4579946 YP_914983.1 CDS Pden_1182 NC_008686.1 1153562 1154359 D TIGRFAM: 3-oxoadipate enol-lactonase; PFAM: alpha/beta hydrolase fold; KEGG: xcb:XC_0382 b-ketoadipate enol-lactone hydrolase; 3-oxoadipate enol-lactonase 1153562..1154359 Paracoccus denitrificans PD1222 4579947 YP_914984.1 CDS Pden_1183 NC_008686.1 1154430 1155110 R PFAM: regulatory protein GntR, HTH; GntR domain protein; KEGG: pau:PA14_47820 transcriptional regulator; GntR family transcriptional regulator complement(1154430..1155110) Paracoccus denitrificans PD1222 4580066 YP_914985.1 CDS Pden_1184 NC_008686.1 1155325 1156353 D PFAM: proline racemase; KEGG: bmb:BruAb1_0363 hypothetical proline racemase; proline racemase 1155325..1156353 Paracoccus denitrificans PD1222 4580067 YP_914986.1 CDS Pden_1185 NC_008686.1 1156370 1157320 D PFAM: ornithine cyclodeaminase/mu-crystallin; Shikimate/quinate 5-dehydrogenase; KEGG: rsp:RSP_0854 predicted ornithine cyclodeaminase; ornithine cyclodeaminase/mu-crystallin 1156370..1157320 Paracoccus denitrificans PD1222 4580068 YP_914987.1 CDS Pden_1186 NC_008686.1 1157466 1158650 R PFAM: Alcohol dehydrogenase, zinc-binding domain protein; Alcohol dehydrogenase GroES domain protein; KEGG: atc:AGR_C_2885 hypothetical protein; alcohol dehydrogenase complement(1157466..1158650) Paracoccus denitrificans PD1222 4580069 YP_914988.1 CDS Pden_1187 NC_008686.1 1158682 1159791 R 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 complement(1158682..1159791) Paracoccus denitrificans PD1222 4580070 YP_914989.1 CDS Pden_1188 NC_008686.1 1159855 1160922 R PFAM: ferredoxin; oxidoreductase FAD/NAD(P)-binding domain protein; Oxidoreductase FAD-binding domain protein; KEGG: sme:SMa0752 possible dioxygenase reductase subunit; ferredoxin complement(1159855..1160922) Paracoccus denitrificans PD1222 4580071 YP_914990.1 CDS Pden_1189 NC_008686.1 1160925 1162277 R PFAM: Rieske [2Fe-2S] domain protein; KEGG: sme:SMa0751 aromatic-ring hydroxylating dioxygenase, alpha-subunit; Rieske (2Fe-2S) domain-containing protein complement(1160925..1162277) Paracoccus denitrificans PD1222 4580072 YP_914991.1 CDS Pden_1190 NC_008686.1 1162292 1163167 D PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: sme:SMa0750 probable LysR-family transcriptional activator; LysR family transcriptional regulator 1162292..1163167 Paracoccus denitrificans PD1222 4580073 YP_914992.1 CDS Pden_1191 NC_008686.1 1163174 1164652 R PFAM: FAD dependent oxidoreductase; KEGG: mes:Meso_1861 FAD dependent oxidoreductase; FAD dependent oxidoreductase complement(1163174..1164652) Paracoccus denitrificans PD1222 4580074 YP_914993.1 CDS Pden_1192 NC_008686.1 1164649 1165437 R PFAM: NADP oxidoreductase, coenzyme F420-dependent; KEGG: ret:RHE_PF00409 pyrroline-5-carboxylate reductase protein; NADP oxidoreductase, coenzyme F420-dependent complement(1164649..1165437) Paracoccus denitrificans PD1222 4580075 YP_914994.1 CDS Pden_1193 NC_008686.1 1165434 1166477 R 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 complement(1165434..1166477) Paracoccus denitrificans PD1222 4580076 YP_914995.1 CDS Pden_1194 NC_008686.1 1166470 1167360 R PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: sme:SMc02379 permease protein; binding-protein-dependent transport system inner membrane protein complement(1166470..1167360) Paracoccus denitrificans PD1222 4580077 YP_914996.1 CDS Pden_1195 NC_008686.1 1167437 1168438 R 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 complement(1167437..1168438) Paracoccus denitrificans PD1222 4580078 YP_914997.1 CDS Pden_1196 NC_008686.1 1168970 1169614 R PFAM: regulatory protein, TetR; KEGG: rsp:RSP_3680 transcriptional regulator, TetR family; TetR family transcriptional regulator complement(1168970..1169614) Paracoccus denitrificans PD1222 4580079 YP_914998.1 CDS Pden_1197 NC_008686.1 1169763 1171799 D PFAM: NADH:flavin oxidoreductase/NADH oxidase; FAD-dependent pyridine nucleotide-disulphide oxidoreductase; KEGG: ppu:PP_4753 N-methylproline demethylase; NADH:flavin oxidoreductase 1169763..1171799 Paracoccus denitrificans PD1222 4580080 YP_914999.1 CDS Pden_1198 NC_008686.1 1172410 1172922 R PFAM: regulatory protein, MarR; KEGG: sil:SPO1261 transcriptional regulator, MarR family; MarR family transcriptional regulator complement(1172410..1172922) Paracoccus denitrificans PD1222 4580081 YP_915000.1 CDS Pden_1199 NC_008686.1 1173049 1174212 D KEGG: sil:SPO1214 hippurate hydrolase; TIGRFAM: amidohydrolase; PFAM: peptidase M20; peptidase dimerisation domain protein; amidohydrolase 1173049..1174212 Paracoccus denitrificans PD1222 4580082 YP_915001.1 CDS Pden_1200 NC_008686.1 1174251 1174988 D KEGG: oih:OB0951 hypothetical protein; hypothetical protein 1174251..1174988 Paracoccus denitrificans PD1222 4580083 YP_915002.1 CDS Pden_1201 NC_008686.1 1175013 1175708 D KEGG: oih:OB0952 hypothetical protein; hypothetical protein 1175013..1175708 Paracoccus denitrificans PD1222 4580084 YP_915003.1 CDS Pden_1202 NC_008686.1 1176020 1176604 R PFAM: Resolvase, N-terminal domain; KEGG: bpm:BURPS1710b_2172 recombinase; resolvase domain-containing protein complement(1176020..1176604) Paracoccus denitrificans PD1222 4578584 YP_915004.1 CDS Pden_1203 NC_008686.1 1176837 1177217 D hypothetical protein 1176837..1177217 Paracoccus denitrificans PD1222 4578585 YP_915005.1 CDS Pden_1204 NC_008686.1 1177372 1178277 R 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 complement(1177372..1178277) Paracoccus denitrificans PD1222 4578586 YP_915006.1 CDS Pden_1205 NC_008686.1 1178651 1179286 R TIGRFAM: urease accessory protein UreG; PFAM: cobalamin synthesis protein, P47K; KEGG: rsp:RSP_0302 urease accessory protein G; urease accessory protein UreG complement(1178651..1179286) Paracoccus denitrificans PD1222 4578587 YP_915007.1 CDS Pden_1206 NC_008686.1 1179283 1179930 R PFAM: Urease accessory protein UreF; KEGG: rsp:RSP_0303 urease accessory protein UreF; urease accessory protein UreF complement(1179283..1179930) Paracoccus denitrificans PD1222 4578588 YP_915008.1 CDS Pden_1207 NC_008686.1 1179911 1180375 R 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 complement(1179911..1180375) Paracoccus denitrificans PD1222 4578589 YP_915009.1 CDS ureC NC_008686.1 1180388 1182076 R 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 complement(1180388..1182076) Paracoccus denitrificans PD1222 4578590 YP_915010.1 CDS Pden_1209 NC_008686.1 1182076 1182393 R KEGG: sme:SMc01939 urease beta subunit protein; TIGRFAM: urease, beta subunit; PFAM: Urease, beta subunit; urease subunit beta complement(1182076..1182393) Paracoccus denitrificans PD1222 4578591 YP_915011.1 CDS Pden_1210 NC_008686.1 1182394 1182954 R PFAM: HupE/UreJ protein; KEGG: pst:PSPTO_4912 urease accessory protein; HupE/UreJ protein complement(1182394..1182954) Paracoccus denitrificans PD1222 4578592 YP_915012.1 CDS Pden_1211 NC_008686.1 1182955 1183266 R KEGG: rsp:RSP_0309 urease, gamma subunit; TIGRFAM: urease, gamma subunit; PFAM: Urease, gamma subunit region; urease subunit gamma complement(1182955..1183266) Paracoccus denitrificans PD1222 4578593 YP_915013.1 CDS Pden_1212 NC_008686.1 1183268 1184107 R PFAM: Urease accessory protein UreD; KEGG: rsp:RSP_0310 urease accessory protein UreD; urease accessory protein UreD complement(1183268..1184107) Paracoccus denitrificans PD1222 4578594 YP_915014.1 CDS Pden_1213 NC_008686.1 1184112 1184393 R hypothetical protein complement(1184112..1184393) Paracoccus denitrificans PD1222 4578595 YP_915015.1 CDS Pden_1214 NC_008686.1 1184520 1184873 D PFAM: regulatory protein, ArsR; KEGG: atc:AGR_L_3580 hypothetical protein; regulatory protein ArsR 1184520..1184873 Paracoccus denitrificans PD1222 4578596 YP_915016.1 CDS Pden_1215 NC_008686.1 1184870 1185346 D PFAM: Activator of Hsp90 ATPase 1 family protein; KEGG: jan:Jann_2413 hypothetical protein; activator of Hsp90 ATPase 1 family protein 1184870..1185346 Paracoccus denitrificans PD1222 4578597 YP_915017.1 CDS Pden_1216 NC_008686.1 1185343 1186215 D PFAM: Activator of Hsp90 ATPase 1 family protein; KEGG: atc:AGR_L_3582 hypothetical protein; activator of Hsp90 ATPase 1 family protein 1185343..1186215 Paracoccus denitrificans PD1222 4578598 YP_915018.1 CDS Pden_1217 NC_008686.1 1186313 1186939 D KEGG: ccr:CC1241 hypothetical protein; hypothetical protein 1186313..1186939 Paracoccus denitrificans PD1222 4578599 YP_915019.1 CDS Pden_1218 NC_008686.1 1186983 1187225 D hypothetical protein 1186983..1187225 Paracoccus denitrificans PD1222 4578600 YP_915020.1 CDS Pden_1219 NC_008686.1 1187344 1188015 R hypothetical protein complement(1187344..1188015) Paracoccus denitrificans PD1222 4578601 YP_915021.1 CDS Pden_1220 NC_008686.1 1188064 1188312 D hypothetical protein 1188064..1188312 Paracoccus denitrificans PD1222 4578602 YP_915022.1 CDS Pden_1221 NC_008686.1 1188554 1188940 R PFAM: transposase, IS4 family protein; KEGG: nmu:Nmul_A2650 transposase, IS4; transposase, IS4 family protein complement(1188554..1188940) Paracoccus denitrificans PD1222 4578603 YP_915023.1 CDS Pden_1222 NC_008686.1 1188937 1189305 R KEGG: mag:amb0408 transposase and inactivated derivative; transposase and inactivated derivative complement(1188937..1189305) Paracoccus denitrificans PD1222 4581076 YP_915024.1 CDS Pden_1223 NC_008686.1 1189396 1190604 D PFAM: phage integrase family protein; KEGG: rpc:RPC_3658 phage integrase; phage integrase family protein 1189396..1190604 Paracoccus denitrificans PD1222 4581077 YP_915025.1 CDS Pden_1224 NC_008686.1 1190595 1190783 D hypothetical protein 1190595..1190783 Paracoccus denitrificans PD1222 4581078 YP_915026.1 CDS Pden_1225 NC_008686.1 1190776 1191063 D hypothetical protein 1190776..1191063 Paracoccus denitrificans PD1222 4581079 YP_915027.1 CDS Pden_1226 NC_008686.1 1191160 1191747 D hypothetical protein 1191160..1191747 Paracoccus denitrificans PD1222 4581080 YP_915028.1 CDS Pden_1227 NC_008686.1 1191719 1192684 D KEGG: rpc:RPC_3654 hypothetical protein; hypothetical protein 1191719..1192684 Paracoccus denitrificans PD1222 4581081 YP_915029.1 CDS Pden_1228 NC_008686.1 1192946 1193203 R PFAM: helix-turn-helix domain protein; KEGG: rde:RD1_0810 DNA-binding protein; XRE family transcriptional regulator complement(1192946..1193203) Paracoccus denitrificans PD1222 4581082 YP_915030.1 CDS Pden_1229 NC_008686.1 1193452 1193832 D KEGG: ilo:IL2080 hypothetical protein; hypothetical protein 1193452..1193832 Paracoccus denitrificans PD1222 4581083 YP_915031.1 CDS Pden_1230 NC_008686.1 1193829 1194254 D hypothetical protein 1193829..1194254 Paracoccus denitrificans PD1222 4581084 YP_915032.1 CDS Pden_1231 NC_008686.1 1194291 1194746 D KEGG: ath:At4g01985 expressed protein; hypothetical protein 1194291..1194746 Paracoccus denitrificans PD1222 4581085 YP_915033.1 CDS Pden_1232 NC_008686.1 1195187 1196395 D PFAM: HI0933 family protein; FAD dependent oxidoreductase; FAD-dependent pyridine nucleotide-disulphide oxidoreductase; KEGG: ccr:CC1477 hypothetical protein; hypothetical protein 1195187..1196395 Paracoccus denitrificans PD1222 4581086 YP_915034.1 CDS Pden_1233 NC_008686.1 1196396 1197229 R 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 complement(1196396..1197229) Paracoccus denitrificans PD1222 4581087 YP_915035.1 CDS Pden_1234 NC_008686.1 1197226 1198965 R KEGG: jan:Jann_3657 capsule polysaccharide export protein-like; capsule polysaccharide export protein complement(1197226..1198965) Paracoccus denitrificans PD1222 4581088 YP_915036.1 CDS Pden_1235 NC_008686.1 1198949 1199602 R PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: jan:Jann_3656 ABC transporter related; ABC transporter complement(1198949..1199602) Paracoccus denitrificans PD1222 4581089 YP_915037.1 CDS Pden_1236 NC_008686.1 1199757 1200419 D PFAM: Uracil-DNA glycosylase superfamily; KEGG: sil:SPO0950 uracil-DNA glycosylase; uracil-DNA glycosylase 1199757..1200419 Paracoccus denitrificans PD1222 4581090 YP_915038.1 CDS Pden_1237 NC_008686.1 1200403 1201155 D KEGG: sil:SPO0951 hypothetical protein; hypothetical protein 1200403..1201155 Paracoccus denitrificans PD1222 4581091 YP_915039.1 CDS Pden_1238 NC_008686.1 1201248 1201808 R PFAM: protein of unknown function DUF882; Peptidase M15A; KEGG: rsp:RSP_2773 hypothetical protein; hypothetical protein complement(1201248..1201808) Paracoccus denitrificans PD1222 4581092 YP_915040.1 CDS Pden_1239 NC_008686.1 1201891 1202133 D hypothetical protein 1201891..1202133 Paracoccus denitrificans PD1222 4581093 YP_915041.1 CDS Pden_1240 NC_008686.1 1202142 1203749 D PFAM: Peptidoglycan-binding domain 1 protein; KEGG: rsp:RSP_2774 hypothetical protein; peptidoglycan binding domain-containing protein 1202142..1203749 Paracoccus denitrificans PD1222 4581094 YP_915042.1 CDS Pden_1241 NC_008686.1 1203776 1204870 D 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 1203776..1204870 Paracoccus denitrificans PD1222 4580007 YP_915043.1 CDS Pden_1242 NC_008686.1 1204965 1205177 D KEGG: jan:Jann_2147 phosphopantetheine-binding; phosphopantetheine-binding protein 1204965..1205177 Paracoccus denitrificans PD1222 4580008 YP_915044.1 CDS Pden_1243 NC_008686.1 1205174 1206523 D PFAM: beta-ketoacyl synthase; KEGG: rsp:RSP_2777 3-oxoacyl-(acyl-carrier-protein) synthase; beta-ketoacyl synthase 1205174..1206523 Paracoccus denitrificans PD1222 4580009 YP_915045.1 CDS Pden_1244 NC_008686.1 1206615 1207841 R PFAM: major facilitator superfamily MFS_1; KEGG: rsp:RSP_2726 multidrug/metabolite efflux pump, major facilitator superfamily (MFS); major facilitator superfamily transporter complement(1206615..1207841) Paracoccus denitrificans PD1222 4580010 YP_915046.1 CDS Pden_1245 NC_008686.1 1207849 1208487 R 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 complement(1207849..1208487) Paracoccus denitrificans PD1222 4580011 YP_915047.1 CDS Pden_1246 NC_008686.1 1208672 1209292 R KEGG: rsp:RSP_3425 hypothetical protein; hypothetical protein complement(1208672..1209292) Paracoccus denitrificans PD1222 4580012 YP_915048.1 CDS Pden_1247 NC_008686.1 1209295 1210518 R PFAM: glutathionylspermidine synthase; KEGG: rsp:RSP_3426 hypothetical protein; glutathionylspermidine synthase complement(1209295..1210518) Paracoccus denitrificans PD1222 4580013 YP_915049.1 CDS Pden_1248 NC_008686.1 1210724 1212337 D PFAM: extracellular solute-binding protein, family 5; KEGG: sit:TM1040_0038 extracellular solute-binding protein, family 5; extracellular solute-binding protein 1210724..1212337 Paracoccus denitrificans PD1222 4580014 YP_915050.1 CDS Pden_1249 NC_008686.1 1212380 1213438 D 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 1212380..1213438 Paracoccus denitrificans PD1222 4580015 YP_915051.1 CDS Pden_1250 NC_008686.1 1213435 1214340 D 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 1213435..1214340 Paracoccus denitrificans PD1222 4580016 YP_915052.1 CDS Pden_1251 NC_008686.1 1214337 1215191 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sit:TM1040_0035 ABC transporter related; ABC transporter 1214337..1215191 Paracoccus denitrificans PD1222 4580017 YP_915053.1 CDS Pden_1252 NC_008686.1 1215238 1215993 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sil:SPO1547 peptide/opine/nickel uptake family ABC transporter, ATP-binding protein; ABC transporter 1215238..1215993 Paracoccus denitrificans PD1222 4580018 YP_915054.1 CDS Pden_1253 NC_008686.1 1215990 1216697 R PFAM: protein of unknown function DUF125, transmembrane; KEGG: sit:TM1040_3365 protein of unknown function DUF125, transmembrane; hypothetical protein complement(1215990..1216697) Paracoccus denitrificans PD1222 4580019 YP_915055.1 CDS Pden_1254 NC_008686.1 1216822 1218267 D PFAM: aldehyde dehydrogenase; KEGG: bxe:Bxe_A3401 betaine-aldehyde dehydrogenase; aldehyde dehydrogenase 1216822..1218267 Paracoccus denitrificans PD1222 4580020 YP_915056.1 CDS fabG NC_008686.1 1218294 1219037 D Catalyzes the first of the two reduction steps in the elongation cycle of fatty acid synthesis; 3-ketoacyl-ACP reductase 1218294..1219037 Paracoccus denitrificans PD1222 4580021 YP_915057.1 CDS Pden_1256 NC_008686.1 1219069 1219899 R PFAM: ABC-3 protein; KEGG: rsp:RSP_0908 ABC Mn+2/Fe+2 transporter, inner membrane subunit SitD; ABC-3 protein complement(1219069..1219899) Paracoccus denitrificans PD1222 4580022 YP_915058.1 CDS Pden_1257 NC_008686.1 1219899 1220759 R PFAM: transport system permease protein; ABC-3 protein; KEGG: sme:SMc02507 iron transport system membrane ABC transporter protein; ABC-3 protein complement(1219899..1220759) Paracoccus denitrificans PD1222 4580023 YP_915059.1 CDS Pden_1258 NC_008686.1 1220756 1221625 R PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sme:SMc02508 iron transport ATP-binding ABC transporter protein; ABC transporter complement(1220756..1221625) Paracoccus denitrificans PD1222 4580024 YP_915060.1 CDS Pden_1259 NC_008686.1 1221618 1222523 R PFAM: periplasmic solute binding protein; KEGG: rsp:RSP_0904 ABC Mn+2/Fe+2 transporter, periplasmic substrate-binding protein SitA; periplasmic solute binding protein complement(1221618..1222523) Paracoccus denitrificans PD1222 4580025 YP_915061.1 CDS Pden_1260 NC_008686.1 1222629 1223051 D PFAM: ferric-uptake regulator; KEGG: sme:SMc02510 probable ferric uptake regulation protein; ferric uptake regulator family protein 1222629..1223051 Paracoccus denitrificans PD1222 4580026 YP_915062.1 CDS Pden_1261 NC_008686.1 1223048 1223422 D PFAM: protein of unknown function UPF0029; KEGG: rde:RD1_4095 hypothetical protein; hypothetical protein 1223048..1223422 Paracoccus denitrificans PD1222 4580300 YP_915063.1 CDS Pden_1262 NC_008686.1 1223419 1223793 R KEGG: sil:SPO0809 hypothetical protein; hypothetical protein complement(1223419..1223793) Paracoccus denitrificans PD1222 4580301 YP_915064.1 CDS Pden_1263 NC_008686.1 1223795 1224847 R KEGG: sme:SMc03928 hypothetical protein; hypothetical protein complement(1223795..1224847) Paracoccus denitrificans PD1222 4580302 YP_915065.1 CDS Pden_1264 NC_008686.1 1224844 1225551 R Enables the recycling of peptidyl-tRNAs produced at termination of translation; peptidyl-tRNA hydrolase complement(1224844..1225551) Paracoccus denitrificans PD1222 4580303 YP_915066.1 CDS clpP NC_008686.1 1225747 1226376 D hydrolyzes proteins to small peptides; with the ATPase subunits ClpA or ClpX, ClpP degrades specific substrates; ATP-dependent Clp protease proteolytic subunit 1225747..1226376 Paracoccus denitrificans PD1222 4580304 YP_915067.1 CDS clpX NC_008686.1 1226538 1227803 D binds and unfolds substrates as part of the ClpXP protease; ATP-dependent protease ATP-binding subunit ClpX 1226538..1227803 Paracoccus denitrificans PD1222 4580305 YP_915068.1 CDS Pden_1267 NC_008686.1 1228027 1228401 D 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 1228027..1228401 Paracoccus denitrificans PD1222 4580306 YP_915069.1 CDS Pden_1268 NC_008686.1 1228406 1228873 D PFAM: Mammalian cell entry related domain protein; KEGG: rsp:RSP_0194 possible ABC transporter, substrate-binding protein; hypothetical protein 1228406..1228873 Paracoccus denitrificans PD1222 4580307 YP_915070.1 CDS Pden_1269 NC_008686.1 1228870 1229361 D KEGG: sil:SPO1008 hypothetical protein; hypothetical protein 1228870..1229361 Paracoccus denitrificans PD1222 4580308 YP_915071.1 CDS aat NC_008686.1 1229325 1229963 R 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 complement(1229325..1229963) Paracoccus denitrificans PD1222 4580309 YP_915072.1 CDS Pden_1271 NC_008686.1 1229999 1231351 R 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 complement(1229999..1231351) Paracoccus denitrificans PD1222 4580310 YP_915073.1 CDS Pden_1272 NC_008686.1 1231359 1231880 R 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 complement(1231359..1231880) Paracoccus denitrificans PD1222 4580311 YP_915074.1 CDS Pden_1273 NC_008686.1 1231984 1232874 R PFAM: lipid A biosynthesis acyltransferase; KEGG: rsp:RSP_2219 lipid A biosynthesis lauroyl acyltransferase; lipid A biosynthesis acyltransferase complement(1231984..1232874) Paracoccus denitrificans PD1222 4580312 YP_915075.1 CDS Pden_1274 NC_008686.1 1232900 1233826 R PFAM: protein of unknown function DUF6, transmembrane; KEGG: jan:Jann_2643 protein of unknown function DUF6, transmembrane; hypothetical protein complement(1232900..1233826) Paracoccus denitrificans PD1222 4580313 YP_915076.1 CDS Pden_1275 NC_008686.1 1234011 1236029 R 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 complement(1234011..1236029) Paracoccus denitrificans PD1222 4580314 YP_915077.1 CDS Pden_1276 NC_008686.1 1236124 1238088 D hypothetical protein 1236124..1238088 Paracoccus denitrificans PD1222 4580315 YP_915078.1 CDS Pden_1277 NC_008686.1 1238179 1239669 D TIGRFAM: uracil-xanthine permease; PFAM: Xanthine/uracil/vitamin C permease; KEGG: sme:SMc02512 permease transmembrane protein; uracil-xanthine permease 1238179..1239669 Paracoccus denitrificans PD1222 4580316 YP_915079.1 CDS Pden_1278 NC_008686.1 1239663 1241015 R PFAM: CBS domain containing protein; protein of unknown function DUF21; transporter-associated region; KEGG: rsp:RSP_2814 hypothetical protein with CBS domain; hypothetical protein complement(1239663..1241015) Paracoccus denitrificans PD1222 4580317 YP_915080.1 CDS Pden_1279 NC_008686.1 1241012 1241983 R PFAM: phage integrase family protein; phage integrase domain protein SAM domain protein; KEGG: rsp:RSP_2815 probable integrase/recombinase XerD; phage integrase family protein complement(1241012..1241983) Paracoccus denitrificans PD1222 4580318 YP_915081.1 CDS Pden_1280 NC_008686.1 1241980 1243602 R KEGG: rsp:RSP_2816 hypothetical protein; hypothetical protein complement(1241980..1243602) Paracoccus denitrificans PD1222 4580899 YP_915082.1 CDS Pden_1281 NC_008686.1 1243589 1243846 R hypothetical protein complement(1243589..1243846) Paracoccus denitrificans PD1222 4580900 YP_915083.1 CDS Pden_1282 NC_008686.1 1243974 1244510 D PFAM: shikimate kinase; KEGG: rsp:RSP_2817 shikimate kinase; shikimate kinase 1243974..1244510 Paracoccus denitrificans PD1222 4580901 YP_915084.1 CDS aroB NC_008686.1 1244507 1245610 D catalyzes the formation of 3-dehydroquinate from 3-deoxy-arabino-heptulonate 7-phosphate; functions in aromatic amino acid biosynthesis; 3-dehydroquinate synthase 1244507..1245610 Paracoccus denitrificans PD1222 4580902 YP_915085.1 CDS Pden_1284 NC_008686.1 1245607 1246029 R 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 complement(1245607..1246029) Paracoccus denitrificans PD1222 4580903 YP_915086.1 CDS Pden_1285 NC_008686.1 1246026 1246307 R 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 complement(1246026..1246307) Paracoccus denitrificans PD1222 4580904 YP_915087.1 CDS Pden_1286 NC_008686.1 1246304 1246792 R PFAM: cation antiporter; KEGG: rsp:RSP_3712 hypothetical protein; cation antiporter complement(1246304..1246792) Paracoccus denitrificans PD1222 4580905 YP_915088.1 CDS Pden_1287 NC_008686.1 1246789 1248519 R 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 complement(1246789..1248519) Paracoccus denitrificans PD1222 4580906 YP_915089.1 CDS Pden_1288 NC_008686.1 1248519 1248863 R subunit C of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; monovalent cation/H+ antiporter subunit C complement(1248519..1248863) Paracoccus denitrificans PD1222 4580907 YP_915090.1 CDS Pden_1289 NC_008686.1 1248863 1251742 R 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 complement(1248863..1251742) Paracoccus denitrificans PD1222 4580908 YP_915091.1 CDS Pden_1290 NC_008686.1 1251889 1253133 R PFAM: Orn/DAP/Arg decarboxylase 2; KEGG: aeh:Mlg_0126 Orn/DAP/Arg decarboxylase 2; Orn/DAP/Arg decarboxylase 2 complement(1251889..1253133) Paracoccus denitrificans PD1222 4580909 YP_915092.1 CDS Pden_1291 NC_008686.1 1253114 1253350 R hypothetical protein complement(1253114..1253350) Paracoccus denitrificans PD1222 4580910 YP_915093.1 CDS Pden_1292 NC_008686.1 1253370 1254941 R PFAM: AMP-dependent synthetase and ligase; KEGG: nmu:Nmul_A2670 AMP-dependent synthetase and ligase; AMP-dependent synthetase/ligase complement(1253370..1254941) Paracoccus denitrificans PD1222 4580911 YP_915094.1 CDS Pden_1293 NC_008686.1 1254934 1255476 R KEGG: mca:MCA1436 serine acetyltransferase CysE; serine acetyltransferase CysE complement(1254934..1255476) Paracoccus denitrificans PD1222 4580912 YP_915095.1 CDS Pden_1294 NC_008686.1 1255559 1256623 R KEGG: pen:PSEEN2951 hypothetical protein; hypothetical protein complement(1255559..1256623) Paracoccus denitrificans PD1222 4580913 YP_915096.1 CDS Pden_1295 NC_008686.1 1256696 1257868 R KEGG: ccr:CC2454 lipase/acylhydrolase; lipase/acylhydrolase complement(1256696..1257868) Paracoccus denitrificans PD1222 4580914 YP_915097.1 CDS Pden_1296 NC_008686.1 1257917 1259086 R PFAM: DegT/DnrJ/EryC1/StrS aminotransferase; KEGG: cps:CPS_4201 polysaccharide biosynthesis protein; DegT/DnrJ/EryC1/StrS aminotransferase complement(1257917..1259086) Paracoccus denitrificans PD1222 4580915 YP_915098.1 CDS Pden_1297 NC_008686.1 1259083 1260006 R 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 complement(1259083..1260006) Paracoccus denitrificans PD1222 4580916 YP_915099.1 CDS Pden_1298 NC_008686.1 1260007 1261131 R 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 complement(1260007..1261131) Paracoccus denitrificans PD1222 4580917 YP_915100.1 CDS Pden_1299 NC_008686.1 1261338 1262690 R catalyzes the formation of prolyl-tRNA(Pro) from proline and tRNA(Pro); prolyl-tRNA synthetase complement(1261338..1262690) Paracoccus denitrificans PD1222 4580918 YP_915101.1 CDS Pden_1300 NC_008686.1 1262820 1264124 D PFAM: protein of unknown function UPF0118; KEGG: jan:Jann_1056 protein of unknown function UPF0118; hypothetical protein 1262820..1264124 Paracoccus denitrificans PD1222 4579481 YP_915102.1 CDS Pden_1301 NC_008686.1 1264128 1264817 D KEGG: rsp:RSP_0780 hypothetical protein with ATP/GTP-binding site; hypothetical protein 1264128..1264817 Paracoccus denitrificans PD1222 4579482 YP_915103.1 CDS Pden_1302 NC_008686.1 1264849 1267014 D catalyzes the reversible transfer of the terminal phosphate of ATP to form a long chain polyphosphate; polyphosphate kinase 1264849..1267014 Paracoccus denitrificans PD1222 4579483 YP_915104.1 CDS Pden_1303 NC_008686.1 1267083 1268624 D PFAM: Ppx/GppA phosphatase; KEGG: rsp:RSP_0782 Ppx/GppA phosphatase; Ppx/GppA phosphatase 1267083..1268624 Paracoccus denitrificans PD1222 4579484 YP_915105.1 CDS Pden_1304 NC_008686.1 1268835 1269884 R PFAM: peptidase M19, renal dipeptidase; KEGG: rsp:RSP_0802 dipeptidase; peptidase M19 complement(1268835..1269884) Paracoccus denitrificans PD1222 4579485 YP_915106.1 CDS Pden_1305 NC_008686.1 1270069 1270392 D PFAM: Antibiotic biosynthesis monooxygenase; KEGG: sil:SPO0462 antibiotic biosynthesis monooxygenase domain protein; antibiotic biosynthesis monooxygenase 1270069..1270392 Paracoccus denitrificans PD1222 4579486 YP_915107.1 CDS Pden_1306 NC_008686.1 1270495 1271130 D PFAM: Cobyrinic acid a,c-diamide synthase; KEGG: sil:SPO0461 ParA family protein; cobyrinic acid a,c-diamide synthase 1270495..1271130 Paracoccus denitrificans PD1222 4579487 YP_915108.1 CDS Pden_1307 NC_008686.1 1271230 1271517 D KEGG: pol:Bpro_1343 hypothetical protein; hypothetical protein 1271230..1271517 Paracoccus denitrificans PD1222 4579488 YP_915109.1 CDS Pden_1308 NC_008686.1 1271560 1273785 R 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 complement(1271560..1273785) Paracoccus denitrificans PD1222 4579489 YP_915110.1 CDS Pden_1309 NC_008686.1 1273934 1274245 D PFAM: ETC complex I subunit conserved region; KEGG: sil:SPO0482 NADH-ubiquinone oxidoreductase family protein; ETC complex I subunit region 1273934..1274245 Paracoccus denitrificans PD1222 4579490 YP_915111.1 CDS Pden_1310 NC_008686.1 1274539 1275879 R 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 complement(1274539..1275879) Paracoccus denitrificans PD1222 4579491 YP_915112.1 CDS Pden_1311 NC_008686.1 1275876 1276538 R PFAM: response regulator receiver; transcriptional regulator domain protein; KEGG: mes:Meso_0894 two component transcriptional regulator, winged helix family; two component transcriptional regulator complement(1275876..1276538) Paracoccus denitrificans PD1222 4579492 YP_915113.1 CDS Pden_1312 NC_008686.1 1276535 1276933 R hypothetical protein complement(1276535..1276933) Paracoccus denitrificans PD1222 4579493 YP_915114.1 CDS Pden_1313 NC_008686.1 1277063 1277941 D hypothetical protein 1277063..1277941 Paracoccus denitrificans PD1222 4579494 YP_915115.1 CDS mdoG NC_008686.1 1278128 1279726 D involved in the biosynthesis of osmoregulated periplasmic glucans; required for the assembly of the polyglucose structure of glucan; glucan biosynthesis protein G 1278128..1279726 Paracoccus denitrificans PD1222 4579495 YP_915116.1 CDS Pden_1315 NC_008686.1 1279723 1281897 D necessary for biosynthesis of osmoregulated periplasmic glucans possibly involved in the transfer to the periplasmic space; glucosyltransferase MdoH 1279723..1281897 Paracoccus denitrificans PD1222 4579496 YP_915117.1 CDS Pden_1316 NC_008686.1 1281894 1283027 D KEGG: rme:Rmet_4886 hypothetical protein; hypothetical protein 1281894..1283027 Paracoccus denitrificans PD1222 4579497 YP_915118.1 CDS Pden_1317 NC_008686.1 1283098 1284765 D catalyzes the formation of 10-formyltetrahydrofolate from formate and tetrahydrofolate; formate--tetrahydrofolate ligase 1283098..1284765 Paracoccus denitrificans PD1222 4579498 YP_915119.1 CDS nadD NC_008686.1 1284769 1285371 D 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 1284769..1285371 Paracoccus denitrificans PD1222 4579499 YP_915120.1 CDS Pden_1319 NC_008686.1 1285371 1286825 D 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 1285371..1286825 Paracoccus denitrificans PD1222 4579422 YP_915121.1 CDS Pden_1320 NC_008686.1 1286836 1287258 R KEGG: rsp:RSP_0583 hypothetical protein; hypothetical protein complement(1286836..1287258) Paracoccus denitrificans PD1222 4579423 YP_915122.1 CDS lysK NC_008686.1 1287350 1288942 D 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 1287350..1288942 Paracoccus denitrificans PD1222 4579424 YP_915123.1 CDS Pden_1322 NC_008686.1 1289083 1291377 D KEGG: sil:SPO0459 hypothetical protein; hypothetical protein 1289083..1291377 Paracoccus denitrificans PD1222 4579425 YP_915124.1 CDS Pden_1323 NC_008686.1 1291414 1291899 R PFAM: pyridoxamine 5'-phosphate oxidase-related, FMN-binding; KEGG: ret:RHE_CH03088 hypothetical protein; pyridoxamine 5'-phosphate oxidase-like FMN-binding protein complement(1291414..1291899) Paracoccus denitrificans PD1222 4579426 YP_915125.1 CDS Pden_1324 NC_008686.1 1291957 1292970 R 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 complement(1291957..1292970) Paracoccus denitrificans PD1222 4579427 YP_915126.1 CDS Pden_1325 NC_008686.1 1292967 1294022 R 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 complement(1292967..1294022) Paracoccus denitrificans PD1222 4579428 YP_915127.1 CDS Pden_1326 NC_008686.1 1294024 1294947 R 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 complement(1294024..1294947) Paracoccus denitrificans PD1222 4579429 YP_915128.1 CDS Pden_1327 NC_008686.1 1294951 1295868 R 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 complement(1294951..1295868) Paracoccus denitrificans PD1222 4579430 YP_915129.1 CDS Pden_1328 NC_008686.1 1295935 1297539 R PFAM: extracellular solute-binding protein, family 5; KEGG: jan:Jann_3050 extracellular solute-binding protein, family 5; extracellular solute-binding protein complement(1295935..1297539) Paracoccus denitrificans PD1222 4579431 YP_915130.1 CDS Pden_1329 NC_008686.1 1297935 1298813 D KEGG: nph:NP3544A thioredoxin reductase homolog; thioredoxin reductase 1297935..1298813 Paracoccus denitrificans PD1222 4579432 YP_915131.1 CDS Pden_1330 NC_008686.1 1298865 1299239 D KEGG: gbe:GbCGDNIH1_1136 cysteinyl-tRNA synthetase; cysteinyl-tRNA synthetase 1298865..1299239 Paracoccus denitrificans PD1222 4579433 YP_915132.1 CDS Pden_1331 NC_008686.1 1299236 1300336 D PFAM: cobalamin synthesis protein, P47K; cobalamin synthesis CobW domain protein; KEGG: atc:AGR_L_3251 hypothetical protein; cobalamin synthesis protein, P47K 1299236..1300336 Paracoccus denitrificans PD1222 4579434 YP_915133.1 CDS Pden_1332 NC_008686.1 1300377 1300775 D PFAM: helix-turn-helix- domain containing protein, AraC type; KEGG: bpm:BURPS1710b_A0955 DarR; helix-turn-helix domain-containing protein 1300377..1300775 Paracoccus denitrificans PD1222 4579435 YP_915134.1 CDS Pden_1333 NC_008686.1 1300801 1302015 R PFAM: cobalamin synthesis protein, P47K; cobalamin synthesis CobW domain protein; KEGG: eci:UTI89_C1131 hypothetical protein; cobalamin synthesis protein, P47K complement(1300801..1302015) Paracoccus denitrificans PD1222 4579436 YP_915135.1 CDS Pden_1334 NC_008686.1 1302041 1302259 R KEGG: xcb:XC_2473 hypothetical protein; hypothetical protein complement(1302041..1302259) Paracoccus denitrificans PD1222 4579437 YP_915136.1 CDS Pden_1335 NC_008686.1 1302268 1302927 R KEGG: rpc:RPC_2661 riboflavin biosynthesis protein RibD; TIGRFAM: riboflavin biosynthesis protein RibD; PFAM: CMP/dCMP deaminase, zinc-binding; riboflavin biosynthesis protein RibD complement(1302268..1302927) Paracoccus denitrificans PD1222 4579438 YP_915137.1 CDS hisI NC_008686.1 1302938 1303402 R 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 complement(1302938..1303402) Paracoccus denitrificans PD1222 4579439 YP_915138.1 CDS Pden_1337 NC_008686.1 1303421 1303873 R KEGG: ppu:PP_3321 hypothetical protein; hypothetical protein complement(1303421..1303873) Paracoccus denitrificans PD1222 4579440 YP_915139.1 CDS Pden_1338 NC_008686.1 1304019 1305242 D PFAM: cobalamin synthesis protein, P47K; cobalamin synthesis CobW domain protein; KEGG: rde:RD1_1856 cobalamin synthesis protein; cobalamin synthesis protein, P47K 1304019..1305242 Paracoccus denitrificans PD1222 4579441 YP_915140.1 CDS Pden_1339 NC_008686.1 1305333 1306001 D KEGG: jan:Jann_2253 hypothetical protein; hypothetical protein 1305333..1306001 Paracoccus denitrificans PD1222 4580593 YP_915141.1 CDS Pden_1340 NC_008686.1 1306001 1306318 D KEGG: rde:RD1_1858 hypothetical protein; hypothetical protein 1306001..1306318 Paracoccus denitrificans PD1222 4580594 YP_915142.1 CDS Pden_1341 NC_008686.1 1306419 1307921 D PFAM: extracellular solute-binding protein, family 5; KEGG: mfa:Mfla_2388 extracellular solute-binding protein, family 5; extracellular solute-binding protein 1306419..1307921 Paracoccus denitrificans PD1222 4580595 YP_915143.1 CDS Pden_1342 NC_008686.1 1307918 1308856 D 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 1307918..1308856 Paracoccus denitrificans PD1222 4580596 YP_915144.1 CDS Pden_1343 NC_008686.1 1308853 1309677 D 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 1308853..1309677 Paracoccus denitrificans PD1222 4580597 YP_915145.1 CDS Pden_1344 NC_008686.1 1309674 1311110 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: vch:VCA1101 peptide transport system ATP-binding protein; ABC transporter 1309674..1311110 Paracoccus denitrificans PD1222 4580598 YP_915146.1 CDS Pden_1346 NC_008686.1 1312023 1312937 R TIGRFAM: methylisocitrate lyase; KEGG: rpa:RPA2395 carboxyphosphonoenolpyruvate phosphonomutase; methylisocitrate lyase complement(1312023..1312937) Paracoccus denitrificans PD1222 4580599 YP_915147.1 CDS Pden_1347 NC_008686.1 1312934 1314103 R 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 complement(1312934..1314103) Paracoccus denitrificans PD1222 4580600 YP_915148.1 CDS Pden_1348 NC_008686.1 1314114 1315637 R PFAM: MmgE/PrpD family protein; KEGG: rpc:RPC_3512 2-methylcitrate dehydratase; 2-methylcitrate dehydratase complement(1314114..1315637) Paracoccus denitrificans PD1222 4580601 YP_915149.1 CDS Pden_1349 NC_008686.1 1315624 1316025 R PFAM: thioesterase superfamily protein; KEGG: rpc:RPC_3513 thioesterase superfamily; thioesterase complement(1315624..1316025) Paracoccus denitrificans PD1222 4580602 YP_915150.1 CDS Pden_1350 NC_008686.1 1316144 1317529 D PFAM: helix-turn-helix domain protein; protein of unknown function DUF955; KEGG: rru:Rru_A2316 transcriptional regulator, XRE family; hypothetical protein 1316144..1317529 Paracoccus denitrificans PD1222 4580603 YP_915151.1 CDS Pden_1351 NC_008686.1 1317508 1318200 R PFAM: LysR, substrate-binding; KEGG: atc:AGR_L_2015 transcription regulator MetR; LysR family transcriptional regulator complement(1317508..1318200) Paracoccus denitrificans PD1222 4580604 YP_915152.1 CDS Pden_1354 NC_008686.1 1320063 1321046 D KEGG: bur:Bcep18194_C7370 hypothetical protein; hypothetical protein 1320063..1321046 Paracoccus denitrificans PD1222 4580606 YP_915153.1 CDS Pden_1355 NC_008686.1 1321075 1322112 D catalyzes the formation of tetrahydropteroyl-L-glutamate and methionine from L-homocysteine and 5-methyltetrahydropteroyltri-L-glutamate; 5- methyltetrahydropteroyltriglutamate/homocysteine S-methyltransferase 1321075..1322112 Paracoccus denitrificans PD1222 4580607 YP_915154.1 CDS Pden_1357 NC_008686.1 1323389 1323796 R hypothetical protein complement(1323389..1323796) Paracoccus denitrificans PD1222 4580608 YP_915155.1 CDS Pden_1358 NC_008686.1 1323995 1324810 R 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 complement(1323995..1324810) Paracoccus denitrificans PD1222 4580609 YP_915156.1 CDS Pden_1359 NC_008686.1 1324827 1325252 R TIGRFAM: pseudoazurin; PFAM: blue (type 1) copper domain protein; KEGG: rru:Rru_A1139 blue (type 1) copper subtype; pseudoazurin complement(1324827..1325252) Paracoccus denitrificans PD1222 4580610 YP_915157.1 CDS Pden_1360 NC_008686.1 1325264 1326034 R PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sme:SMb20058 ABC transporter ATP-binding protein; ABC transporter complement(1325264..1326034) Paracoccus denitrificans PD1222 4580611 YP_915158.1 CDS Pden_1361 NC_008686.1 1326031 1327104 R PFAM: transport system permease protein; KEGG: psp:PSPPH_3007 iron ABC transporter, permease protein; transport system permease complement(1326031..1327104) Paracoccus denitrificans PD1222 4579792 YP_915159.1 CDS Pden_1362 NC_008686.1 1327101 1328108 R PFAM: periplasmic binding protein; KEGG: rru:Rru_A1136 periplasmic binding protein; periplasmic binding protein complement(1327101..1328108) Paracoccus denitrificans PD1222 4579793 YP_915160.1 CDS Pden_1363 NC_008686.1 1328565 1330172 R Catalyzes the first step in the glyoxalate cycle, which converts lipids to carbohydrates; isocitrate lyase complement(1328565..1330172) Paracoccus denitrificans PD1222 4579794 YP_915161.1 CDS Pden_1364 NC_008686.1 1330296 1331918 R 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 complement(1330296..1331918) Paracoccus denitrificans PD1222 4579795 YP_915162.1 CDS Pden_1365 NC_008686.1 1332053 1333486 D PFAM: helix-turn-helix domain protein; protein of unknown function DUF955; KEGG: hne:HNE_1237 DNA-binding protein; hypothetical protein 1332053..1333486 Paracoccus denitrificans PD1222 4579796 YP_915163.1 CDS Pden_1366 NC_008686.1 1333483 1334499 R KEGG: rru:Rru_A1617 protein of unknown function DUF1289; hypothetical protein complement(1333483..1334499) Paracoccus denitrificans PD1222 4579797 YP_915164.1 CDS Pden_1367 NC_008686.1 1334483 1335343 R PFAM: periplasmic binding protein; KEGG: rsp:RSP_2403 ABC cobalamin/Fe3+-siderophore transporter, periplasmic substrate-binding subunit; periplasmic binding protein complement(1334483..1335343) Paracoccus denitrificans PD1222 4579798 YP_915165.1 CDS Pden_1368 NC_008686.1 1335337 1337220 R PFAM: TonB-dependent receptor; TonB-dependent receptor, plug; KEGG: rru:Rru_A0488 TonB-dependent receptor; TonB-dependent receptor complement(1335337..1337220) Paracoccus denitrificans PD1222 4579799 YP_915166.1 CDS Pden_1369 NC_008686.1 1337561 1337956 R hypothetical protein complement(1337561..1337956) Paracoccus denitrificans PD1222 4579800 YP_915167.1 CDS Pden_1370 NC_008686.1 1338220 1338939 D hypothetical protein 1338220..1338939 Paracoccus denitrificans PD1222 4579801 YP_915168.1 CDS Pden_1371 NC_008686.1 1338995 1339444 D hypothetical protein 1338995..1339444 Paracoccus denitrificans PD1222 4579802 YP_915169.1 CDS Pden_1372 NC_008686.1 1339398 1340204 R KEGG: sme:SMb20398 hypothetical protein; phosphoesterase or phosphohydrolase-like protein complement(1339398..1340204) Paracoccus denitrificans PD1222 4579803 YP_915170.1 CDS Pden_1373 NC_008686.1 1340206 1341507 R KEGG: rde:RD1_4059 Lon protease; ATP-dependent Lon protease complement(1340206..1341507) Paracoccus denitrificans PD1222 4579804 YP_915171.1 CDS Pden_1374 NC_008686.1 1341954 1342742 R PFAM: metallophosphoesterase; KEGG: nha:Nham_1359 metallophosphoesterase; metallophosphoesterase complement(1341954..1342742) Paracoccus denitrificans PD1222 4579805 YP_915172.1 CDS Pden_1375 NC_008686.1 1342739 1343188 R hypothetical protein complement(1342739..1343188) Paracoccus denitrificans PD1222 4579806 YP_915173.1 CDS Pden_1376 NC_008686.1 1343653 1344600 R 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 complement(1343653..1344600) Paracoccus denitrificans PD1222 4579807 YP_915174.1 CDS Pden_1377 NC_008686.1 1344725 1345291 D PFAM: alkyl hydroperoxide reductase/ Thiol specific antioxidant/ Mal allergen; Redoxin domain protein; KEGG: rsp:RSP_2781 peroxiredoxin/glutaredoxin family protein; redoxin domain-containing protein 1344725..1345291 Paracoccus denitrificans PD1222 4579808 YP_915175.1 CDS Pden_1378 NC_008686.1 1345362 1346516 R KEGG: rsp:RSP_6073 hypothetical protein; hypothetical protein complement(1345362..1346516) Paracoccus denitrificans PD1222 4579809 YP_915176.1 CDS Pden_1379 NC_008686.1 1346729 1347061 D KEGG: rsp:RSP_6226 hypothetical protein; hypothetical protein 1346729..1347061 Paracoccus denitrificans PD1222 4579810 YP_915177.1 CDS Pden_1380 NC_008686.1 1347048 1348622 R PFAM: protein of unknown function DUF853, NPT hydrolase KEGG: sil:SPO1934 hypothetical protein; hypothetical protein complement(1347048..1348622) Paracoccus denitrificans PD1222 4579811 YP_915178.1 CDS Pden_1381 NC_008686.1 1349084 1349872 D PFAM: Invasion associated locus B family protein; KEGG: rsp:RSP_2778 hypothetical protein; invasion associated locus B family protein 1349084..1349872 Paracoccus denitrificans PD1222 4581304 YP_915179.1 CDS Pden_1382 NC_008686.1 1349947 1351491 R TIGRFAM: protease Do; PFAM: peptidase S1 and S6, chymotrypsin/Hap; PDZ/DHR/GLGF domain protein; KEGG: rsp:RSP_0355 possible serine protease; protease Do complement(1349947..1351491) Paracoccus denitrificans PD1222 4581305 YP_915180.1 CDS Pden_1383 NC_008686.1 1351705 1351956 R hypothetical protein complement(1351705..1351956) Paracoccus denitrificans PD1222 4581306 YP_915181.1 CDS Pden_1384 NC_008686.1 1352030 1355647 R Catalyzes the rate-limiting step in dNTP synthesis; ribonucleotide-diphosphate reductase subunit alpha complement(1352030..1355647) Paracoccus denitrificans PD1222 4581307 YP_915182.1 CDS Pden_1385 NC_008686.1 1356043 1356627 R PFAM: 5-formyltetrahydrofolate cyclo-ligase; KEGG: rsp:RSP_1898 5-formyltetrahydrofolate cyclo-ligase; 5-formyltetrahydrofolate cyclo-ligase complement(1356043..1356627) Paracoccus denitrificans PD1222 4581308 YP_915183.1 CDS Pden_1386 NC_008686.1 1356612 1358069 R 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 complement(1356612..1358069) Paracoccus denitrificans PD1222 4581309 YP_915184.1 CDS Pden_1387 NC_008686.1 1358090 1358905 R PFAM: inositol monophosphatase; KEGG: rde:RD1_2006 inositol monophosphatase family protein; inositol monophosphatase complement(1358090..1358905) Paracoccus denitrificans PD1222 4581310 YP_915185.1 CDS Pden_1388 NC_008686.1 1358986 1359345 R PFAM: helix-turn-helix domain protein; KEGG: rsp:RSP_1892 Cro/CI transcriptional regulator; XRE family transcriptional regulator complement(1358986..1359345) Paracoccus denitrificans PD1222 4581311 YP_915186.1 CDS Pden_1389 NC_008686.1 1359524 1360492 D PFAM: Alcohol dehydrogenase, zinc-binding domain protein; Alcohol dehydrogenase GroES domain protein; KEGG: jan:Jann_1231 alcohol dehydrogenase, zinc-binding; alcohol dehydrogenase 1359524..1360492 Paracoccus denitrificans PD1222 4581312 YP_915187.1 CDS Pden_1390 NC_008686.1 1360615 1361385 D PFAM: protein of unknown function UPF0005; KEGG: sil:SPO2963 membrane protein; hypothetical protein 1360615..1361385 Paracoccus denitrificans PD1222 4581313 YP_915188.1 CDS Pden_1391 NC_008686.1 1361653 1361895 D PFAM: BolA family protein; KEGG: rsp:RSP_2952 BolA-like protein; BolA family protein 1361653..1361895 Paracoccus denitrificans PD1222 4581314 YP_915189.1 CDS Pden_1392 NC_008686.1 1361947 1362309 D TIGRFAM: glutaredoxin-like protein; PFAM: glutaredoxin; KEGG: sil:SPO1868 glutaredoxin-related protein; glutaredoxin-like protein 1361947..1362309 Paracoccus denitrificans PD1222 4581315 YP_915190.1 CDS Pden_1393 NC_008686.1 1362397 1363092 R hypothetical protein complement(1362397..1363092) Paracoccus denitrificans PD1222 4581316 YP_915191.1 CDS Pden_1394 NC_008686.1 1363100 1363528 R PFAM: protein of unknown function DUF883, ElaB; KEGG: rha:RHA1_ro00971 hypothetical protein; hypothetical protein complement(1363100..1363528) Paracoccus denitrificans PD1222 4581317 YP_915192.1 CDS Pden_1395 NC_008686.1 1363627 1364754 R PFAM: aminotransferase, class V; KEGG: rsp:RSP_1868 serine-pyruvate aminotransferase; class V aminotransferase complement(1363627..1364754) Paracoccus denitrificans PD1222 4581318 YP_915193.1 CDS Pden_1396 NC_008686.1 1364894 1365610 D PFAM: glutamine amidotransferase class-I; KEGG: rsp:RSP_0376 glutamine amidotransferase class-I; glutamine amidotransferase 1364894..1365610 Paracoccus denitrificans PD1222 4581319 YP_915194.1 CDS Pden_1397 NC_008686.1 1365607 1366965 D PFAM: glutamine synthetase, catalytic region; KEGG: rsp:RSP_0377 probable glutamine synthetase; glutamate--ammonia ligase 1365607..1366965 Paracoccus denitrificans PD1222 4581320 YP_915195.1 CDS Pden_1398 NC_008686.1 1367038 1368348 D PFAM: FAD dependent oxidoreductase; KEGG: rsp:RSP_0378 hypothetical protein; FAD dependent oxidoreductase 1367038..1368348 Paracoccus denitrificans PD1222 4581321 YP_915196.1 CDS Pden_1399 NC_008686.1 1368345 1369001 R KEGG: rsp:RSP_1671 hypothetical protein; hypothetical protein complement(1368345..1369001) Paracoccus denitrificans PD1222 4581322 YP_915197.1 CDS Pden_1400 NC_008686.1 1369014 1371131 R 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 complement(1369014..1371131) Paracoccus denitrificans PD1222 4581265 YP_915198.1 CDS Pden_1401 NC_008686.1 1371154 1371510 R 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 complement(1371154..1371510) Paracoccus denitrificans PD1222 4581266 YP_915199.1 CDS Pden_1402 NC_008686.1 1371581 1372072 R 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 complement(1371581..1372072) Paracoccus denitrificans PD1222 4581267 YP_915200.1 CDS Pden_1403 NC_008686.1 1372187 1372738 D PFAM: protein of unknown function DUF88; KEGG: rsp:RSP_1667 hypothetical protein; hypothetical protein 1372187..1372738 Paracoccus denitrificans PD1222 4581268 YP_915201.1 CDS Pden_1404 NC_008686.1 1372781 1374172 R PFAM: OmpA/MotB domain protein; KEGG: rsp:RSP_2289 flagellar motor protein; hypothetical protein complement(1372781..1374172) Paracoccus denitrificans PD1222 4581269 YP_915202.1 CDS Pden_1405 NC_008686.1 1374162 1375871 R KEGG: rsp:RSP_2288 hypothetical protein; hypothetical protein complement(1374162..1375871) Paracoccus denitrificans PD1222 4581270 YP_915203.1 CDS Pden_1406 NC_008686.1 1375897 1376451 R PFAM: ChaC family protein; KEGG: rsp:RSP_2287 ChaC-like protein; ChaC family protein complement(1375897..1376451) Paracoccus denitrificans PD1222 4581271 YP_915204.1 CDS Pden_1407 NC_008686.1 1376502 1377551 D KEGG: rsp:RSP_2286 hypothetical protein; hypothetical protein 1376502..1377551 Paracoccus denitrificans PD1222 4581272 YP_915205.1 CDS Pden_1408 NC_008686.1 1377548 1378483 R dual function enzyme catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate and the formation of tyrosine from arogenate; cyclohexadienyl dehydrogenase complement(1377548..1378483) Paracoccus denitrificans PD1222 4581273 YP_915206.1 CDS Pden_1409 NC_008686.1 1378483 1379586 R catalyzes the formation of L-histidinol phosphate from imidazole-acetol phosphate and glutamate in histidine biosynthesis; histidinol-phosphate aminotransferase complement(1378483..1379586) Paracoccus denitrificans PD1222 4581274 YP_915207.1 CDS Pden_1410 NC_008686.1 1379784 1380302 R 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 complement(1379784..1380302) Paracoccus denitrificans PD1222 4581275 YP_915208.1 CDS Pden_1411 NC_008686.1 1380456 1381181 R 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 complement(1380456..1381181) Paracoccus denitrificans PD1222 4581276 YP_915209.1 CDS Pden_1412 NC_008686.1 1381234 1381890 R 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 complement(1381234..1381890) Paracoccus denitrificans PD1222 4581277 YP_915210.1 CDS Pden_1413 NC_008686.1 1381901 1382533 R ATP-binding protein; required for proper cytochrome c maturation; cytochrome c biogenesis protein CcmA complement(1381901..1382533) Paracoccus denitrificans PD1222 4581278 YP_915211.1 CDS Pden_1414 NC_008686.1 1382530 1382886 R PFAM: protein of unknown function DUF498; KEGG: rsp:RSP_1800 hypothetical protein; hypothetical protein complement(1382530..1382886) Paracoccus denitrificans PD1222 4581279 YP_915212.1 CDS secF NC_008686.1 1382886 1383878 R 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 complement(1382886..1383878) Paracoccus denitrificans PD1222 4581280 YP_915213.1 CDS secD NC_008686.1 1383891 1385555 R 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 complement(1383891..1385555) Paracoccus denitrificans PD1222 4581281 YP_915214.1 CDS Pden_1417 NC_008686.1 1385572 1385904 R TIGRFAM: preprotein translocase, YajC subunit; PFAM: YajC family protein; KEGG: rsp:RSP_1797 preprotein translocase subunit YajC; preprotein translocase subunit YajC complement(1385572..1385904) Paracoccus denitrificans PD1222 4581282 YP_915215.1 CDS mazG NC_008686.1 1386096 1386947 D 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 1386096..1386947 Paracoccus denitrificans PD1222 4581283 YP_915216.1 CDS Pden_1419 NC_008686.1 1386952 1387857 D hypothetical protein 1386952..1387857 Paracoccus denitrificans PD1222 4581284 YP_915217.1 CDS Pden_1420 NC_008686.1 1387841 1388830 R PFAM: dihydrouridine synthase, DuS; KEGG: sil:SPO2374 tRNA-dihydrouridine synthase A; tRNA-dihydrouridine synthase A complement(1387841..1388830) Paracoccus denitrificans PD1222 4580475 YP_915218.1 CDS Pden_1421 NC_008686.1 1388943 1389998 D PFAM: phage integrase family protein; KEGG: hne:HNE_0292 site-specific recombinase, phage integrase family; phage integrase family protein 1388943..1389998 Paracoccus denitrificans PD1222 4580476 YP_915219.1 CDS Pden_1422 NC_008686.1 1390072 1390542 R 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 complement(1390072..1390542) Paracoccus denitrificans PD1222 4580477 YP_915220.1 CDS Pden_1423 NC_008686.1 1390665 1391582 D PFAM: HI0933 family protein; FAD-dependent pyridine nucleotide-disulphide oxidoreductase; KEGG: bpm:BURPS1710b_A2517 pyridine nucleotide-disulphide oxidoreductase; FAD-dependent pyridine nucleotide-disulfide oxidoreductase 1390665..1391582 Paracoccus denitrificans PD1222 4580478 YP_915221.1 CDS Pden_1424 NC_008686.1 1391595 1392215 D PFAM: Tellurite resistance protein TehB; thiopurine S-methyltransferase; Methyltransferase type 11; Methyltransferase type 12; KEGG: mmc:Mmcs_3339 methyltransferase type 12; type 11 methyltransferase 1391595..1392215 Paracoccus denitrificans PD1222 4580479 YP_915222.1 CDS Pden_1425 NC_008686.1 1392368 1395784 R PFAM: ABC transporter, transmembrane region; SMC domain protein; ABC transporter related; SMART: AAA ATPase; KEGG: gvi:gll0322 HlyB/MsbA family ABC transporter; ABC transporter complement(1392368..1395784) Paracoccus denitrificans PD1222 4580480 YP_915223.1 CDS Pden_1426 NC_008686.1 1395781 1396800 R KEGG: mes:Meso_0337 major facilitator superfamily MFS_1; major facilitator superfamily transporter complement(1395781..1396800) Paracoccus denitrificans PD1222 4580481 YP_915224.1 CDS Pden_1427 NC_008686.1 1396961 1399102 R PFAM: TonB-dependent receptor; TonB-dependent receptor, plug; KEGG: pau:PA14_55050 possible TonB-dependent receptor; TonB-dependent receptor complement(1396961..1399102) Paracoccus denitrificans PD1222 4580482 YP_915225.1 CDS Pden_1428 NC_008686.1 1399197 1400186 R PFAM: helix-turn-helix- domain containing protein, AraC type; KEGG: pae:PA2281 probable transcriptional regulator; helix-turn-helix domain-containing protein complement(1399197..1400186) Paracoccus denitrificans PD1222 4580483 YP_915226.1 CDS Pden_1429 NC_008686.1 1400353 1400946 D PFAM: Lysine exporter protein (LYSE/YGGA); KEGG: ret:RHE_CH02787 probable amino acid efflux protein, LysE family; lysine exporter protein LysE/YggA 1400353..1400946 Paracoccus denitrificans PD1222 4580484 YP_915227.1 CDS Pden_1430 NC_008686.1 1400925 1401488 D hypothetical protein 1400925..1401488 Paracoccus denitrificans PD1222 4580485 YP_915228.1 CDS Pden_1431 NC_008686.1 1401527 1402195 D PFAM: regulatory protein GntR, HTH; GntR domain protein; KEGG: rsp:RSP_1925 transcriptional regulator, GntR family; GntR family transcriptional regulator 1401527..1402195 Paracoccus denitrificans PD1222 4580486 YP_915229.1 CDS Pden_1432 NC_008686.1 1402280 1402837 D PFAM: BioY protein; KEGG: rsp:RSP_1924 BioY family protein; BioY protein 1402280..1402837 Paracoccus denitrificans PD1222 4580487 YP_915230.1 CDS Pden_1433 NC_008686.1 1402834 1403808 D 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 1402834..1403808 Paracoccus denitrificans PD1222 4580488 YP_915231.1 CDS Pden_1434 NC_008686.1 1403811 1405253 R 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 complement(1403811..1405253) Paracoccus denitrificans PD1222 4580489 YP_915232.1 CDS Pden_1435 NC_008686.1 1405317 1406012 D PFAM: glutamine amidotransferase class-I; KEGG: rru:Rru_A3512 glutamine amidotransferase class-I; glutamine amidotransferase 1405317..1406012 Paracoccus denitrificans PD1222 4580490 YP_915233.1 CDS Pden_1436 NC_008686.1 1406009 1406689 D PFAM: 3-alpha; MOSC domain containing protein; KEGG: rsp:RSP_1921 MOSC domain protein; MOSC domain-containing protein 1406009..1406689 Paracoccus denitrificans PD1222 4580491 YP_915234.1 CDS Pden_1437 NC_008686.1 1406686 1407534 D TIGRFAM: pyridoxal kinase; PFAM: Phosphomethylpyrimidine kinase type-1; KEGG: rsp:RSP_1920 pyridoxal/pyridoxine/pyridoxamine kinase; pyridoxal kinase 1406686..1407534 Paracoccus denitrificans PD1222 4580492 YP_915235.1 CDS Pden_1438 NC_008686.1 1407734 1409686 R KEGG: bte:BTH_I2719 pathogenesis-related protein; pathogenesis-like protein complement(1407734..1409686) Paracoccus denitrificans PD1222 4580493 YP_915236.1 CDS Pden_1439 NC_008686.1 1409683 1411917 R KEGG: bte:BTH_I2720 hypothetical protein; hypothetical protein complement(1409683..1411917) Paracoccus denitrificans PD1222 4580223 YP_915237.1 CDS Pden_1440 NC_008686.1 1412139 1412408 D hypothetical protein 1412139..1412408 Paracoccus denitrificans PD1222 4580224 YP_915238.1 CDS Pden_1441 NC_008686.1 1412411 1412872 D TIGRFAM: uncharacterized domain 1; PFAM: thioesterase superfamily protein; KEGG: hne:HNE_1462 thioesterase family protein; hypothetical protein 1412411..1412872 Paracoccus denitrificans PD1222 4580225 YP_915239.1 CDS Pden_1442 NC_008686.1 1412869 1413117 R hypothetical protein complement(1412869..1413117) Paracoccus denitrificans PD1222 4580226 YP_915240.1 CDS Pden_1443 NC_008686.1 1413275 1413652 D KEGG: hne:HNE_1461 conserved hypothetical protein TIGR02246; hypothetical protein 1413275..1413652 Paracoccus denitrificans PD1222 4580227 YP_915241.1 CDS Pden_1444 NC_008686.1 1413649 1414047 D PFAM: Cupin 2, conserved barrel domain protein; KEGG: xcb:XC_1877 hypothetical protein; cupin 1413649..1414047 Paracoccus denitrificans PD1222 4580228 YP_915242.1 CDS Pden_1445 NC_008686.1 1414120 1414404 D hypothetical protein 1414120..1414404 Paracoccus denitrificans PD1222 4580229 YP_915243.1 CDS Pden_1446 NC_008686.1 1414397 1415647 D PFAM: major facilitator superfamily MFS_1; KEGG: reu:Reut_A2630 major facilitator superfamily MFS_1; major facilitator superfamily transporter 1414397..1415647 Paracoccus denitrificans PD1222 4580230 YP_915244.1 CDS Pden_1447 NC_008686.1 1415738 1416283 D PFAM: PEBP family protein; KEGG: rpa:RPA0709 hypothetical protein; PEBP family protein 1415738..1416283 Paracoccus denitrificans PD1222 4580231 YP_915245.1 CDS Pden_1448 NC_008686.1 1416302 1417177 D TIGRFAM: phenazine biosynthesis protein PhzF family; PFAM: Phenazine biosynthesis PhzC/PhzF protein; KEGG: zmo:ZMO1945 predicted epimerase; PhzF family phenazine biosynthesis protein 1416302..1417177 Paracoccus denitrificans PD1222 4580232 YP_915246.1 CDS Pden_1449 NC_008686.1 1417178 1417720 R KEGG: rsp:RSP_1919 hypothetical protein; hypothetical protein complement(1417178..1417720) Paracoccus denitrificans PD1222 4580233 YP_915247.1 CDS Pden_1450 NC_008686.1 1417876 1418190 R KEGG: rsp:RSP_1918 predicted alpha/beta hydrolase; alpha/beta hydrolase complement(1417876..1418190) Paracoccus denitrificans PD1222 4580234 YP_915248.1 CDS Pden_1452 NC_008686.1 1418685 1418975 R PFAM: protein of unknown function DUF1330; KEGG: mmc:Mmcs_0720 protein of unknown function DUF1330; hypothetical protein complement(1418685..1418975) Paracoccus denitrificans PD1222 4580235 YP_915249.1 CDS Pden_1453 NC_008686.1 1419245 1420051 D KEGG: jan:Jann_1547 DNA polymerase, beta-like; DNA polymerase, beta-like 1419245..1420051 Paracoccus denitrificans PD1222 4580236 YP_915250.1 CDS Pden_1454 NC_008686.1 1420288 1421376 D KEGG: rme:Rmet_1656 glutathione S-transferase-like protein; glutathione S-transferase-like protein 1420288..1421376 Paracoccus denitrificans PD1222 4580237 YP_915251.1 CDS Pden_1455 NC_008686.1 1421594 1422829 R PFAM: protein of unknown function DUF1228; major facilitator superfamily MFS_1; KEGG: rpe:RPE_0479 major facilitator superfamily MFS_1; major facilitator superfamily transporter complement(1421594..1422829) Paracoccus denitrificans PD1222 4580238 YP_915252.1 CDS Pden_1456 NC_008686.1 1422907 1423398 D PFAM: helix-turn-helix, HxlR type; KEGG: sit:TM1040_2008 transcriptional regulator, HxlR family; HxlR family transcriptional regulator 1422907..1423398 Paracoccus denitrificans PD1222 4580239 YP_915253.1 CDS Pden_1457 NC_008686.1 1423406 1424317 R KEGG: rsp:RSP_1918 predicted alpha/beta hydrolase; alpha/beta hydrolase complement(1423406..1424317) Paracoccus denitrificans PD1222 4580240 YP_915254.1 CDS Pden_1458 NC_008686.1 1424485 1425009 D PFAM: Cupin 2, conserved barrel domain protein; KEGG: rsp:RSP_1917 hypothetical protein; cupin 1424485..1425009 Paracoccus denitrificans PD1222 4580241 YP_915255.1 CDS Pden_1459 NC_008686.1 1425006 1425662 D PFAM: DSBA oxidoreductase; KEGG: rsp:RSP_1916 possible 2-hydroxychromene-2-carboxylate isomerase; DSBA oxidoreductase 1425006..1425662 Paracoccus denitrificans PD1222 4580242 YP_915256.1 CDS Pden_1460 NC_008686.1 1425659 1426087 D PFAM: GCN5-related N-acetyltransferase; KEGG: rsp:RSP_6026 acetyltransferase; N-acetyltransferase 1425659..1426087 Paracoccus denitrificans PD1222 4580281 YP_915257.1 CDS Pden_1461 NC_008686.1 1426069 1426521 R PFAM: GCN5-related N-acetyltransferase; KEGG: rru:Rru_A3458 GCN5-related N-acetyltransferase; N-acetyltransferase complement(1426069..1426521) Paracoccus denitrificans PD1222 4580282 YP_915258.1 CDS Pden_1462 NC_008686.1 1426766 1427152 D PFAM: GCN5-related N-acetyltransferase; KEGG: ret:RHE_CH02190 probable acetyltransferase protein; N-acetyltransferase 1426766..1427152 Paracoccus denitrificans PD1222 4580283 YP_915259.1 CDS Pden_1463 NC_008686.1 1427197 1428117 R PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: rsp:RSP_1915 transcriptional regulator, LysR family; LysR family transcriptional regulator complement(1427197..1428117) Paracoccus denitrificans PD1222 4580284 YP_915260.1 CDS Pden_1464 NC_008686.1 1428263 1429180 D PFAM: aminotransferase, class IV; KEGG: rru:Rru_A2223 branched-chain amino acid aminotransferase I; aminotransferase, class IV 1428263..1429180 Paracoccus denitrificans PD1222 4580285 YP_915261.1 CDS Pden_1465 NC_008686.1 1429171 1429911 R KEGG: atc:AGR_C_4899 hypothetical transmembrane protein; hypothetical protein complement(1429171..1429911) Paracoccus denitrificans PD1222 4580286 YP_915262.1 CDS Pden_1466 NC_008686.1 1430186 1430767 D SMART: helix-turn-helix- domain containing protein, AraC type; KEGG: cvi:CV1825 probable transcriptional regulator, AraC family; helix-turn-helix domain-containing protein 1430186..1430767 Paracoccus denitrificans PD1222 4580287 YP_915263.1 CDS Pden_1467 NC_008686.1 1430770 1431402 R PFAM: Lysine exporter protein (LYSE/YGGA); KEGG: gbe:GbCGDNIH1_1691 transporter, LysE family; lysine exporter protein LysE/YggA complement(1430770..1431402) Paracoccus denitrificans PD1222 4580288 YP_915264.1 CDS Pden_1468 NC_008686.1 1431405 1431950 R PFAM: protein of unknown function DUF1234; KEGG: bur:Bcep18194_B2508 protein of unknown function DUF1234; hypothetical protein complement(1431405..1431950) Paracoccus denitrificans PD1222 4580289 YP_915265.1 CDS Pden_1469 NC_008686.1 1432068 1432523 D PFAM: regulatory protein, AsnC/Lrp family; KEGG: bur:Bcep18194_B2509 transcriptional regulator, AsnC family; AsnC family transcriptional regulator 1432068..1432523 Paracoccus denitrificans PD1222 4580290 YP_915266.1 CDS Pden_1470 NC_008686.1 1432553 1433176 D PFAM: Lysine exporter protein (LYSE/YGGA); KEGG: jan:Jann_1597 lysine exporter protein (LysE/YggA); lysine exporter protein LysE/YggA 1432553..1433176 Paracoccus denitrificans PD1222 4580291 YP_915267.1 CDS Pden_1471 NC_008686.1 1433351 1434349 D PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: mes:Meso_3862 transcriptional regulator, LysR family; LysR family transcriptional regulator 1433351..1434349 Paracoccus denitrificans PD1222 4580292 YP_915268.1 CDS Pden_1472 NC_008686.1 1434342 1435595 D 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 1434342..1435595 Paracoccus denitrificans PD1222 4580293 YP_915269.1 CDS Pden_1473 NC_008686.1 1435611 1436129 R PFAM: MaoC domain protein dehydratase; KEGG: mag:amb1218 acyl dehydratase; dehydratase complement(1435611..1436129) Paracoccus denitrificans PD1222 4580294 YP_915270.1 CDS Pden_1474 NC_008686.1 1436263 1436496 R KEGG: gbe:GbCGDNIH1_1065 hypothetical protein; hypothetical protein complement(1436263..1436496) Paracoccus denitrificans PD1222 4580295 YP_915271.1 CDS Pden_1475 NC_008686.1 1436499 1437620 R PFAM: conjugation TrbI family protein; KEGG: mes:Meso_0500 conjugation TrbI-like protein; conjugation TrbI family protein complement(1436499..1437620) Paracoccus denitrificans PD1222 4580296 YP_915272.1 CDS Pden_1476 NC_008686.1 1437617 1438645 R PFAM: Conjugal transfer protein TrbG/VirB9/CagX; KEGG: mes:Meso_0501 conjugal transfer protein TrbG/VirB9/CagX; conjugal transfer protein TrbG/VirB9/CagX complement(1437617..1438645) Paracoccus denitrificans PD1222 4580297 YP_915273.1 CDS Pden_1477 NC_008686.1 1438642 1439331 R PFAM: Conjugal transfer protein; KEGG: mes:Meso_0502 conjugal transfer protein; conjugal transfer protein TrbF complement(1438642..1439331) Paracoccus denitrificans PD1222 4580298 YP_915274.1 CDS Pden_1478 NC_008686.1 1439328 1440680 R type IV secretion VirB6 family; conjugal transfer protein TrbL complement(1439328..1440680) Paracoccus denitrificans PD1222 4580299 YP_915275.1 CDS Pden_1479 NC_008686.1 1440684 1440971 R KEGG: mes:Meso_2319 hypothetical protein; hypothetical protein complement(1440684..1440971) Paracoccus denitrificans PD1222 4580319 YP_915276.1 CDS Pden_1480 NC_008686.1 1440989 1441771 R KEGG: mes:Meso_3855 conjugal transfer protein TrbJ; conjugal transfer protein TrbJ complement(1440989..1441771) Paracoccus denitrificans PD1222 4580320 YP_915277.1 CDS Pden_1481 NC_008686.1 1441768 1444278 R type IV secretion system VirB4 family; conjugal transfer ATPase TrbE complement(1441768..1444278) Paracoccus denitrificans PD1222 4580321 YP_915278.1 CDS Pden_1482 NC_008686.1 1444285 1444578 R KEGG: mlo:mll9611 conjugal transfer protein trbB; conjugal transfer protein trbB complement(1444285..1444578) Paracoccus denitrificans PD1222 4580322 YP_915279.1 CDS Pden_1483 NC_008686.1 1444645 1444977 R PFAM: Conjugal transfer protein TrbC; KEGG: mes:Meso_2323 conjugal transfer protein TrbC; conjugal transfer protein TrbC complement(1444645..1444977) Paracoccus denitrificans PD1222 4580323 YP_915280.1 CDS Pden_1484 NC_008686.1 1444974 1445972 R PFAM: type II secretion system protein E; KEGG: mes:Meso_2324 type II secretion system protein E; type II secretion system protein E complement(1444974..1445972) Paracoccus denitrificans PD1222 4580324 YP_915281.1 CDS Pden_1485 NC_008686.1 1446345 1447265 D PFAM: helix-turn-helix- domain containing protein, AraC type; KEGG: rru:Rru_A1456 transcriptional regulator, AraC family; helix-turn-helix domain-containing protein 1446345..1447265 Paracoccus denitrificans PD1222 4580325 YP_915282.1 CDS Pden_1486 NC_008686.1 1447354 1449435 D PFAM: TonB-dependent receptor; TonB-dependent receptor, plug; KEGG: rru:Rru_A1458 TonB-dependent receptor; TonB-dependent receptor 1447354..1449435 Paracoccus denitrificans PD1222 4580326 YP_915283.1 CDS Pden_1487 NC_008686.1 1449435 1450445 D PFAM: Methyltransferase type 11; Methyltransferase type 12; KEGG: rru:Rru_A1457 O-methyltransferase, family 2; type 12 methyltransferase 1449435..1450445 Paracoccus denitrificans PD1222 4580327 YP_915284.1 CDS Pden_1488 NC_008686.1 1450447 1451349 D KEGG: atc:AGR_L_928 sulfonate/nitrate transport system substrate-binding protein; sulfonate/nitrate transport system substrate-binding protein 1450447..1451349 Paracoccus denitrificans PD1222 4580328 YP_915285.1 CDS Pden_1489 NC_008686.1 1451349 1452080 D 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 1451349..1452080 Paracoccus denitrificans PD1222 4580329 YP_915286.1 CDS Pden_1490 NC_008686.1 1452077 1452658 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: swo:Swol_0339 sulfonate transport system ATP-binding protein; ABC transporter 1452077..1452658 Paracoccus denitrificans PD1222 4580330 YP_915287.1 CDS Pden_1491 NC_008686.1 1452668 1453366 R PFAM: regulatory protein, TetR; KEGG: nfa:nfa16940 transcriptional regulator; TetR family transcriptional regulator complement(1452668..1453366) Paracoccus denitrificans PD1222 4580331 YP_915288.1 CDS Pden_1492 NC_008686.1 1453406 1455184 R PFAM: ABC transporter, transmembrane region; ABC transporter related; SMART: AAA ATPase; KEGG: cdi:DIP2158 ABC transport protein; ABC transporter complement(1453406..1455184) Paracoccus denitrificans PD1222 4580332 YP_915289.1 CDS Pden_1493 NC_008686.1 1455181 1457001 R PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: gvi:gll0322 HlyB/MsbA family ABC transporter; ABC transporter complement(1455181..1457001) Paracoccus denitrificans PD1222 4580333 YP_915290.1 CDS Pden_1494 NC_008686.1 1457084 1458244 R PFAM: monooxygenase, FAD-binding; KEGG: sme:SMc02891 oxidoreductase transmembrane protein; FAD-binding monooxygenase complement(1457084..1458244) Paracoccus denitrificans PD1222 4580334 YP_915291.1 CDS Pden_1495 NC_008686.1 1458248 1460236 R PFAM: TonB-dependent receptor; TonB-dependent receptor, plug; KEGG: sme:SMc02890 outer membrane receptor protein; TonB-dependent receptor complement(1458248..1460236) Paracoccus denitrificans PD1222 4580335 YP_915292.1 CDS Pden_1496 NC_008686.1 1460233 1461420 R PFAM: major facilitator superfamily MFS_1; KEGG: sme:SMc02889 transport protein; major facilitator superfamily transporter complement(1460233..1461420) Paracoccus denitrificans PD1222 4580336 YP_915293.1 CDS Pden_1497 NC_008686.1 1461579 1462580 D PFAM: helix-turn-helix- domain containing protein, AraC type; KEGG: sme:SMc02888 transcription regulator protein; helix-turn-helix domain-containing protein 1461579..1462580 Paracoccus denitrificans PD1222 4580337 YP_915294.1 CDS Pden_1498 NC_008686.1 1462601 1463827 R PFAM: major facilitator superfamily MFS_1; KEGG: rru:Rru_A2336 major facilitator superfamily MFS_1; major facilitator superfamily transporter complement(1462601..1463827) Paracoccus denitrificans PD1222 4580338 YP_915295.1 CDS Pden_1499 NC_008686.1 1463830 1465779 R PFAM: TonB-dependent receptor; TonB-dependent receptor, plug; KEGG: rru:Rru_A2337 TonB-dependent receptor; TonB-dependent receptor complement(1463830..1465779) Paracoccus denitrificans PD1222 4581095 YP_915296.1 CDS Pden_1500 NC_008686.1 1466069 1467028 D PFAM: helix-turn-helix- domain containing protein, AraC type; KEGG: yps:YPTB1597 transcriptional regulator YbtA; helix-turn-helix domain-containing protein 1466069..1467028 Paracoccus denitrificans PD1222 4581096 YP_915297.1 CDS Pden_1501 NC_008686.1 1467357 1467746 R PFAM: protein of unknown function DUF454; KEGG: nha:Nham_3232 protein of unknown function DUF454; hypothetical protein complement(1467357..1467746) Paracoccus denitrificans PD1222 4581097 YP_915298.1 CDS Pden_1502 NC_008686.1 1467733 1468083 R KEGG: mxa:MXAN_7409 hypothetical protein; hypothetical protein complement(1467733..1468083) Paracoccus denitrificans PD1222 4581098 YP_915299.1 CDS Pden_1503 NC_008686.1 1468070 1469287 R PFAM: monooxygenase, FAD-binding; KEGG: nwi:Nwi_2327 hypothetical protein; hypothetical protein complement(1468070..1469287) Paracoccus denitrificans PD1222 4581099 YP_915300.1 CDS Pden_1504 NC_008686.1 1469486 1470022 R hypothetical protein complement(1469486..1470022) Paracoccus denitrificans PD1222 4581100 YP_915301.1 CDS Pden_1505 NC_008686.1 1470456 1470884 R KEGG: mlo:mlr9748 hypothetical protein; hypothetical protein complement(1470456..1470884) Paracoccus denitrificans PD1222 4581101 YP_915302.1 CDS Pden_1506 NC_008686.1 1470887 1472872 R type IV secretion VirD4 coupling protein family; conjugal transfer coupling protein TraG complement(1470887..1472872) Paracoccus denitrificans PD1222 4581102 YP_915303.1 CDS Pden_1507 NC_008686.1 1472899 1474653 R KEGG: bja:bll0044 hypothetical protein; hypothetical protein complement(1472899..1474653) Paracoccus denitrificans PD1222 4581103 YP_915304.1 CDS Pden_1508 NC_008686.1 1474897 1475661 R PFAM: Lytic transglycosylase, catalytic; KEGG: mes:Meso_2331 lytic transglycosylase, catalytic; lytic transglycosylase, catalytic complement(1474897..1475661) Paracoccus denitrificans PD1222 4581104 YP_915305.1 CDS Pden_1509 NC_008686.1 1475664 1475999 R PFAM: protein of unknown function DUF736; KEGG: mes:Meso_2332 protein of unknown function DUF736; hypothetical protein complement(1475664..1475999) Paracoccus denitrificans PD1222 4581105 YP_915306.1 CDS Pden_1510 NC_008686.1 1476066 1476608 R KEGG: mes:Meso_2333 conjugal transfer protein precursor; conjugal transfer protein precursor complement(1476066..1476608) Paracoccus denitrificans PD1222 4581106 YP_915307.1 CDS Pden_1511 NC_008686.1 1476605 1477126 R KEGG: rpc:RPC_3907 hypothetical protein; hypothetical protein complement(1476605..1477126) Paracoccus denitrificans PD1222 4581107 YP_915308.1 CDS Pden_1512 NC_008686.1 1477126 1478298 R KEGG: mlo:mlr9740 replication protein A; replication protein A complement(1477126..1478298) Paracoccus denitrificans PD1222 4581108 YP_915309.1 CDS Pden_1513 NC_008686.1 1478317 1478598 R KEGG: mlo:msr9739 hypothetical protein; hypothetical protein complement(1478317..1478598) Paracoccus denitrificans PD1222 4581109 YP_915310.1 CDS Pden_1514 NC_008686.1 1478736 1479131 R KEGG: mes:Meso_0525 hypothetical protein; hypothetical protein complement(1478736..1479131) Paracoccus denitrificans PD1222 4581110 YP_915311.1 CDS Pden_1515 NC_008686.1 1479202 1479561 R KEGG: mes:Meso_3837 hypothetical protein; hypothetical protein complement(1479202..1479561) Paracoccus denitrificans PD1222 4581111 YP_915312.1 CDS Pden_1516 NC_008686.1 1479617 1479880 R KEGG: mes:Meso_0527 hypothetical protein; hypothetical protein complement(1479617..1479880) Paracoccus denitrificans PD1222 4581112 YP_915313.1 CDS Pden_1517 NC_008686.1 1479986 1480243 R KEGG: mes:Meso_0528 transcriptional regulator, XRE family; XRE family transcriptional regulator complement(1479986..1480243) Paracoccus denitrificans PD1222 4581113 YP_915314.1 CDS Pden_1518 NC_008686.1 1480430 1480753 R PFAM: protein of unknown function DUF736; KEGG: mes:Meso_0529 protein of unknown function DUF736; hypothetical protein complement(1480430..1480753) Paracoccus denitrificans PD1222 4578976 YP_915315.1 CDS Pden_1519 NC_008686.1 1480790 1481251 D hypothetical protein 1480790..1481251 Paracoccus denitrificans PD1222 4578977 YP_915316.1 CDS Pden_1520 NC_008686.1 1481310 1481747 R KEGG: mes:Meso_2343 hypothetical protein; hypothetical protein complement(1481310..1481747) Paracoccus denitrificans PD1222 4578978 YP_915317.1 CDS Pden_1521 NC_008686.1 1481913 1482437 D KEGG: bcz:BCZK2630 2'-5' RNA ligase; hypothetical protein 1481913..1482437 Paracoccus denitrificans PD1222 4578979 YP_915318.1 CDS Pden_1522 NC_008686.1 1482485 1482733 D hypothetical protein 1482485..1482733 Paracoccus denitrificans PD1222 4578980 YP_915319.1 CDS Pden_1523 NC_008686.1 1482702 1483478 R KEGG: gox:GOX1507 restriction endonuclease; restriction endonuclease complement(1482702..1483478) Paracoccus denitrificans PD1222 4578981 YP_915320.1 CDS Pden_1524 NC_008686.1 1483478 1485439 R KEGG: gox:GOX1506 chromosome segregation SMC protein; chromosome segregation protein SMC complement(1483478..1485439) Paracoccus denitrificans PD1222 4578982 YP_915321.1 CDS Pden_1525 NC_008686.1 1485429 1489808 R KEGG: gox:GOX1505 type II DNA modification enzyme; hypothetical protein complement(1485429..1489808) Paracoccus denitrificans PD1222 4578983 YP_915322.1 CDS Pden_1526 NC_008686.1 1489811 1492582 R PFAM: SNF2-related protein; helicase domain protein; SMART: DEAD-like helicases-like; KEGG: gox:GOX1504 ATP-dependent helicase HepA; helicase complement(1489811..1492582) Paracoccus denitrificans PD1222 4578984 YP_915323.1 CDS Pden_1527 NC_008686.1 1492584 1497761 R 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 complement(1492584..1497761) Paracoccus denitrificans PD1222 4578985 YP_915324.1 CDS Pden_1528 NC_008686.1 1497762 1499684 R PFAM: protein of unknown function DUF262; KEGG: rha:RHA1_ro01680 hypothetical protein; hypothetical protein complement(1497762..1499684) Paracoccus denitrificans PD1222 4578986 YP_915325.1 CDS Pden_1529 NC_008686.1 1499748 1500635 R KEGG: nar:Saro_2176 hypothetical protein; hypothetical protein complement(1499748..1500635) Paracoccus denitrificans PD1222 4578987 YP_915326.1 CDS Pden_1530 NC_008686.1 1501056 1501295 D KEGG: rsp:RSP_3007 hypothetical protein; hypothetical protein 1501056..1501295 Paracoccus denitrificans PD1222 4578988 YP_915327.1 CDS Pden_1531 NC_008686.1 1501625 1502551 R KEGG: mes:Meso_0533 hypothetical protein; hypothetical protein complement(1501625..1502551) Paracoccus denitrificans PD1222 4578989 YP_915328.1 CDS Pden_1532 NC_008686.1 1502908 1503942 R KEGG: nwi:Nwi_2129 hypothetical protein; hypothetical protein complement(1502908..1503942) Paracoccus denitrificans PD1222 4578990 YP_915329.1 CDS Pden_1533 NC_008686.1 1503942 1508264 R KEGG: mes:Meso_3828 probably methylase/helicase; methylase/helicase complement(1503942..1508264) Paracoccus denitrificans PD1222 4578991 YP_915330.1 CDS Pden_1534 NC_008686.1 1508430 1510043 D PFAM: filamentation induced by cAMP protein Fic; KEGG: rpc:RPC_1039 filamentation induced by cAMP protein Fic; Fic family protein 1508430..1510043 Paracoccus denitrificans PD1222 4578992 YP_915331.1 CDS Pden_1535 NC_008686.1 1510055 1510699 R KEGG: mes:Meso_0536 hypothetical protein; hypothetical protein complement(1510055..1510699) Paracoccus denitrificans PD1222 4578993 YP_915332.1 CDS Pden_1536 NC_008686.1 1510692 1511108 R KEGG: mes:Meso_3827 hypothetical protein; hypothetical protein complement(1510692..1511108) Paracoccus denitrificans PD1222 4578994 YP_915333.1 CDS Pden_1537 NC_008686.1 1511174 1511731 R KEGG: net:Neut_0078 hypothetical protein; hypothetical protein complement(1511174..1511731) Paracoccus denitrificans PD1222 4578995 YP_915334.1 CDS Pden_1538 NC_008686.1 1511923 1512180 R KEGG: mlo:msr9708 hypothetical protein; hypothetical protein complement(1511923..1512180) Paracoccus denitrificans PD1222 4581285 YP_915335.1 CDS Pden_1539 NC_008686.1 1512503 1512808 R hypothetical protein complement(1512503..1512808) Paracoccus denitrificans PD1222 4581286 YP_915336.1 CDS Pden_1540 NC_008686.1 1512910 1515234 R KEGG: sil:SPO2244 hypothetical protein; hypothetical protein complement(1512910..1515234) Paracoccus denitrificans PD1222 4581287 YP_915337.1 CDS Pden_1541 NC_008686.1 1515718 1517844 R TIGRFAM: parB-like partition proteins; PFAM: ParB domain protein nuclease; KEGG: mes:Meso_0538 ParB-like partition proteins; parB-like partition proteins complement(1515718..1517844) Paracoccus denitrificans PD1222 4581288 YP_915338.1 CDS Pden_1542 NC_008686.1 1517961 1518449 R PFAM: DNA repair protein RadC; KEGG: rsp:RSP_1171 DNA repair protein; DNA repair protein RadC complement(1517961..1518449) Paracoccus denitrificans PD1222 4581289 YP_915339.1 CDS Pden_1543 NC_008686.1 1518561 1518956 R KEGG: nwi:Nwi_2122 hypothetical protein; hypothetical protein complement(1518561..1518956) Paracoccus denitrificans PD1222 4581290 YP_915340.1 CDS Pden_1544 NC_008686.1 1518953 1519915 R PFAM: domain of unknown function DUF1738; KEGG: nwi:Nwi_2121 antirestriction protein; ArdC; hypothetical protein complement(1518953..1519915) Paracoccus denitrificans PD1222 4581291 YP_915341.1 CDS Pden_1545 NC_008686.1 1520277 1520594 D 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 1520277..1520594 Paracoccus denitrificans PD1222 4581292 YP_915342.1 CDS Pden_1546 NC_008686.1 1520610 1521227 D similar to plasmid pRiA4b; PFAM: plasmid pRiA4b ORF-3 family protein; KEGG: sme:SMa0896 hypothetical protein; ORF-3 family protein 1520610..1521227 Paracoccus denitrificans PD1222 4581293 YP_915343.1 CDS Pden_1547 NC_008686.1 1521563 1521871 D PFAM: helix-turn-helix domain protein; KEGG: rpb:RPB_0688 transcriptional regulator, XRE family; XRE family transcriptional regulator 1521563..1521871 Paracoccus denitrificans PD1222 4581294 YP_915344.1 CDS Pden_1548 NC_008686.1 1521861 1523102 D PFAM: HipA domain protein; KEGG: rpb:RPB_0687 HipA-like protein; HipA domain-containing protein 1521861..1523102 Paracoccus denitrificans PD1222 4581295 YP_915345.1 CDS Pden_1549 NC_008686.1 1523662 1523889 D KEGG: rsp:RSP_6129 hypothetical protein; hypothetical protein 1523662..1523889 Paracoccus denitrificans PD1222 4581296 YP_915346.1 CDS Pden_1550 NC_008686.1 1523870 1524346 R PFAM: protein of unknown function DUF1052; KEGG: sil:SPO1766 hypothetical protein; hypothetical protein complement(1523870..1524346) Paracoccus denitrificans PD1222 4581297 YP_915347.1 CDS Pden_1551 NC_008686.1 1524673 1525593 R PFAM: protein of unknown function DUF481; KEGG: rsp:RSP_0753 salt-stress induced outer membrane protein; hypothetical protein complement(1524673..1525593) Paracoccus denitrificans PD1222 4581298 YP_915348.1 CDS Pden_1552 NC_008686.1 1526019 1526324 R KEGG: rsp:RSP_0754 hypothetical protein; hypothetical protein complement(1526019..1526324) Paracoccus denitrificans PD1222 4581299 YP_915349.1 CDS Pden_1553 NC_008686.1 1526439 1526939 R TIGRFAM: transcription antitermination factor NusB; PFAM: NusB/RsmB/TIM44; KEGG: jan:Jann_3412 NusB antitermination factor; NusB antitermination factor complement(1526439..1526939) Paracoccus denitrificans PD1222 4581300 YP_915350.1 CDS ribH NC_008686.1 1526936 1527487 R 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 complement(1526936..1527487) Paracoccus denitrificans PD1222 4581301 YP_915351.1 CDS Pden_1555 NC_008686.1 1527492 1528610 R 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 complement(1527492..1528610) Paracoccus denitrificans PD1222 4581302 YP_915352.1 CDS Pden_1556 NC_008686.1 1528600 1529178 R KEGG: sil:SPO1760 hypothetical protein; hypothetical protein complement(1528600..1529178) Paracoccus denitrificans PD1222 4581303 YP_915353.1 CDS Pden_1557 NC_008686.1 1529178 1529771 R catalyzes the formation of riboflavin from 6,7-dimethyl-8-(1-D-ribityl)lumazine; riboflavin synthase subunit alpha complement(1529178..1529771) Paracoccus denitrificans PD1222 4580859 YP_915354.1 CDS Pden_1558 NC_008686.1 1530081 1531403 D PFAM: Capsule polysaccharide biosynthesis; KEGG: sil:SPO1757 capsular polysaccharide export protein KpsS; capsule polysaccharide biosynthesis 1530081..1531403 Paracoccus denitrificans PD1222 4580860 YP_915355.1 CDS Pden_1559 NC_008686.1 1531502 1532680 D PFAM: polysaccharide export protein; KEGG: sit:TM1040_2133 polysaccharide export protein; polysaccharide export protein 1531502..1532680 Paracoccus denitrificans PD1222 4580861 YP_915356.1 CDS Pden_1560 NC_008686.1 1532685 1534676 D PFAM: Capsule polysaccharide biosynthesis; KEGG: sil:SPO1755 capsular polysaccharide export protein KpsC; capsule polysaccharide biosynthesis 1532685..1534676 Paracoccus denitrificans PD1222 4580862 YP_915357.1 CDS Pden_1561 NC_008686.1 1534673 1535650 R 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 complement(1534673..1535650) Paracoccus denitrificans PD1222 4580863 YP_915358.1 CDS nrdR NC_008686.1 1535665 1536129 R PFAM: ATP-cone domain protein; KEGG: rsp:RSP_0394 hypothetical protein; transcriptional regulator NrdR complement(1535665..1536129) Paracoccus denitrificans PD1222 4580864 YP_915359.1 CDS Pden_1563 NC_008686.1 1536368 1537492 D 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 1536368..1537492 Paracoccus denitrificans PD1222 4580865 YP_915360.1 CDS Pden_1564 NC_008686.1 1537598 1539490 R 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 complement(1537598..1539490) Paracoccus denitrificans PD1222 4580866 YP_915361.1 CDS Pden_1565 NC_008686.1 1539487 1540110 R 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 complement(1539487..1540110) Paracoccus denitrificans PD1222 4580867 YP_915362.1 CDS Pden_1566 NC_008686.1 1540248 1541015 R TIGRFAM: cobalamin 5'-phosphate synthase; PFAM: cobalamin-5-phosphate synthase CobS; KEGG: bja:bll3255 cobalamin (5'-phosphate) synthase; cobalamin 5'-phosphate synthase complement(1540248..1541015) Paracoccus denitrificans PD1222 4580868 YP_915363.1 CDS Pden_1567 NC_008686.1 1541008 1541964 R PFAM: Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase; KEGG: sil:SPO1423 nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase; nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase complement(1541008..1541964) Paracoccus denitrificans PD1222 4580869 YP_915364.1 CDS Pden_1568 NC_008686.1 1541961 1542494 R PFAM: cobalbumin biosynthesis enzyme; KEGG: bja:bll3256 cobinamide kinase / conamide phosphate guanylyltransferase; adenosylcobinamide kinase complement(1541961..1542494) Paracoccus denitrificans PD1222 4580870 YP_915365.1 CDS Pden_1569 NC_008686.1 1542634 1544238 D PFAM: extracellular solute-binding protein, family 5; KEGG: jan:Jann_3050 extracellular solute-binding protein, family 5; extracellular solute-binding protein 1542634..1544238 Paracoccus denitrificans PD1222 4580871 YP_915366.1 CDS Pden_1570 NC_008686.1 1544305 1545222 D 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 1544305..1545222 Paracoccus denitrificans PD1222 4580872 YP_915367.1 CDS Pden_1571 NC_008686.1 1545226 1546149 D 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 1545226..1546149 Paracoccus denitrificans PD1222 4580873 YP_915368.1 CDS Pden_1572 NC_008686.1 1546151 1547206 D 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 1546151..1547206 Paracoccus denitrificans PD1222 4580874 YP_915369.1 CDS Pden_1573 NC_008686.1 1547203 1548216 D 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 1547203..1548216 Paracoccus denitrificans PD1222 4580875 YP_915370.1 CDS Pden_1574 NC_008686.1 1548274 1548759 D PFAM: pyridoxamine 5'-phosphate oxidase-related, FMN-binding; KEGG: ret:RHE_CH03088 hypothetical protein; pyridoxamine 5'-phosphate oxidase-like FMN-binding protein 1548274..1548759 Paracoccus denitrificans PD1222 4580876 YP_915371.1 CDS Pden_1575 NC_008686.1 1548796 1551090 R KEGG: sil:SPO0459 hypothetical protein; hypothetical protein complement(1548796..1551090) Paracoccus denitrificans PD1222 4580877 YP_915372.1 CDS lysK NC_008686.1 1551231 1552823 R 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 complement(1551231..1552823) Paracoccus denitrificans PD1222 4580878 YP_915373.1 CDS Pden_1577 NC_008686.1 1552915 1553337 D KEGG: rsp:RSP_0583 hypothetical protein; hypothetical protein 1552915..1553337 Paracoccus denitrificans PD1222 4580840 YP_915374.1 CDS Pden_1578 NC_008686.1 1553348 1554802 R 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 complement(1553348..1554802) Paracoccus denitrificans PD1222 4580841 YP_915375.1 CDS nadD NC_008686.1 1554802 1555404 R 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 complement(1554802..1555404) Paracoccus denitrificans PD1222 4580842 YP_915376.1 CDS Pden_1580 NC_008686.1 1555408 1557075 R catalyzes the formation of 10-formyltetrahydrofolate from formate and tetrahydrofolate; formate--tetrahydrofolate ligase complement(1555408..1557075) Paracoccus denitrificans PD1222 4580843 YP_915377.1 CDS Pden_1581 NC_008686.1 1557146 1558279 R KEGG: rme:Rmet_4886 hypothetical protein; hypothetical protein complement(1557146..1558279) Paracoccus denitrificans PD1222 4580844 YP_915378.1 CDS Pden_1582 NC_008686.1 1558276 1560450 R necessary for biosynthesis of osmoregulated periplasmic glucans possibly involved in the transfer to the periplasmic space; glucosyltransferase MdoH complement(1558276..1560450) Paracoccus denitrificans PD1222 4580845 YP_915379.1 CDS mdoG NC_008686.1 1560447 1562045 R involved in the biosynthesis of osmoregulated periplasmic glucans; required for the assembly of the polyglucose structure of glucan; glucan biosynthesis protein G complement(1560447..1562045) Paracoccus denitrificans PD1222 4580846 YP_915380.1 CDS Pden_1584 NC_008686.1 1562157 1563164 D hypothetical protein 1562157..1563164 Paracoccus denitrificans PD1222 4580847 YP_915381.1 CDS Pden_1585 NC_008686.1 1563635 1564297 D PFAM: response regulator receiver; transcriptional regulator domain protein; KEGG: mes:Meso_0894 two component transcriptional regulator, winged helix family; two component transcriptional regulator 1563635..1564297 Paracoccus denitrificans PD1222 4580848 YP_915382.1 CDS Pden_1586 NC_008686.1 1564294 1565634 D 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 1564294..1565634 Paracoccus denitrificans PD1222 4580849 YP_915383.1 CDS Pden_1587 NC_008686.1 1565928 1566239 R PFAM: ETC complex I subunit conserved region; KEGG: sil:SPO0482 NADH-ubiquinone oxidoreductase family protein; ETC complex I subunit region complement(1565928..1566239) Paracoccus denitrificans PD1222 4580850 YP_915384.1 CDS Pden_1588 NC_008686.1 1566388 1568613 D 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 1566388..1568613 Paracoccus denitrificans PD1222 4580851 YP_915385.1 CDS Pden_1589 NC_008686.1 1568656 1568943 R KEGG: pol:Bpro_1343 hypothetical protein; hypothetical protein complement(1568656..1568943) Paracoccus denitrificans PD1222 4580852 YP_915386.1 CDS Pden_1590 NC_008686.1 1569043 1569678 R PFAM: Cobyrinic acid a,c-diamide synthase; KEGG: sil:SPO0461 ParA family protein; cobyrinic acid a,c-diamide synthase complement(1569043..1569678) Paracoccus denitrificans PD1222 4580853 YP_915387.1 CDS Pden_1591 NC_008686.1 1569781 1570104 R PFAM: Antibiotic biosynthesis monooxygenase; KEGG: sil:SPO0462 antibiotic biosynthesis monooxygenase domain protein; antibiotic biosynthesis monooxygenase complement(1569781..1570104) Paracoccus denitrificans PD1222 4580854 YP_915388.1 CDS Pden_1592 NC_008686.1 1570289 1571338 D PFAM: peptidase M19, renal dipeptidase; KEGG: rsp:RSP_0802 dipeptidase; peptidase M19 1570289..1571338 Paracoccus denitrificans PD1222 4580855 YP_915389.1 CDS Pden_1593 NC_008686.1 1571549 1573090 R PFAM: Ppx/GppA phosphatase; KEGG: rsp:RSP_0782 Ppx/GppA phosphatase; Ppx/GppA phosphatase complement(1571549..1573090) Paracoccus denitrificans PD1222 4580856 YP_915390.1 CDS Pden_1594 NC_008686.1 1573159 1574460 R PFAM: Polyphosphate kinase; KEGG: rde:RD1_2042 polyphosphate kinase; polyphosphate kinase complement(1573159..1574460) Paracoccus denitrificans PD1222 4580857 YP_915391.1 CDS Pden_1595 NC_008686.1 1574589 1575380 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: mlo:mll8315 ABC transporter, ATP-binding protein; ABC transporter 1574589..1575380 Paracoccus denitrificans PD1222 4580858 YP_915392.1 CDS Pden_1596 NC_008686.1 1575380 1576246 D PFAM: ABC-3 protein; KEGG: mlo:mll8314 ABC transporter, permease protein; ABC-3 protein 1575380..1576246 Paracoccus denitrificans PD1222 4580203 YP_915393.1 CDS Pden_1597 NC_008686.1 1576266 1577195 D PFAM: periplasmic solute binding protein; KEGG: atc:AGR_L_3262 adhesin, probable; periplasmic solute binding protein 1576266..1577195 Paracoccus denitrificans PD1222 4580204 YP_915394.1 CDS Pden_1598 NC_008686.1 1577267 1578493 D KEGG: mes:Meso_4007 hypothetical protein; hypothetical protein 1577267..1578493 Paracoccus denitrificans PD1222 4580205 YP_915395.1 CDS Pden_1599 NC_008686.1 1578721 1579401 R PFAM: Glutathione S-transferase, N-terminal domain; KEGG: sme:SMc00594 beta-etherase (beta-aryl ether cleaving enzyme) protein; glutathione S-transferase domain-containing protein complement(1578721..1579401) Paracoccus denitrificans PD1222 4580206 YP_915396.1 CDS Pden_1600 NC_008686.1 1579401 1580333 R PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: cvi:CV3061 probable transcriptional regulator, LysR family; LysR family transcriptional regulator complement(1579401..1580333) Paracoccus denitrificans PD1222 4580207 YP_915397.1 CDS Pden_1601 NC_008686.1 1580445 1581911 R PFAM: major facilitator superfamily MFS_1; KEGG: sme:SMc02892 transport protein; major facilitator superfamily transporter complement(1580445..1581911) Paracoccus denitrificans PD1222 4580208 YP_915398.1 CDS Pden_1602 NC_008686.1 1581989 1583947 R PFAM: TonB-dependent receptor; TonB-dependent receptor, plug; KEGG: ilo:IL0069 outer membrane protein; TonB-dependent receptor, plug complement(1581989..1583947) Paracoccus denitrificans PD1222 4580209 YP_915399.1 CDS Pden_1603 NC_008686.1 1584109 1585242 R 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 complement(1584109..1585242) Paracoccus denitrificans PD1222 4580210 YP_915400.1 CDS Pden_1604 NC_008686.1 1585243 1587324 R 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 complement(1585243..1587324) Paracoccus denitrificans PD1222 4580211 YP_915401.1 CDS Pden_1605 NC_008686.1 1587353 1587946 R PFAM: flavoprotein; KEGG: bcl:ABC3557 lantibiotic biosynthesis protein, flavoprotein; flavoprotein complement(1587353..1587946) Paracoccus denitrificans PD1222 4580212 YP_915402.1 CDS Pden_1606 NC_008686.1 1587959 1588795 R PFAM: Methyltransferase type 12; KEGG: cps:CPS_2928 hypothetical protein; type 12 methyltransferase complement(1587959..1588795) Paracoccus denitrificans PD1222 4580213 YP_915403.1 CDS Pden_1607 NC_008686.1 1588977 1590524 D PFAM: MaoC domain protein dehydratase; KEGG: nha:Nham_0934 phenylacetic acid degradation protein PaaN; dehydratase 1588977..1590524 Paracoccus denitrificans PD1222 4580214 YP_915404.1 CDS Pden_1608 NC_008686.1 1590526 1592076 D PFAM: extracellular solute-binding protein, family 5; KEGG: wsu:WS1160 oligopeptide binding protein; extracellular solute-binding protein 1590526..1592076 Paracoccus denitrificans PD1222 4580215 YP_915405.1 CDS Pden_1609 NC_008686.1 1592073 1593071 D PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: dsy:DSY3210 hypothetical protein; binding-protein-dependent transport system inner membrane protein 1592073..1593071 Paracoccus denitrificans PD1222 4580216 YP_915406.1 CDS Pden_1610 NC_008686.1 1593071 1593844 D PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: mac:MA0843 dipeptide ABC transporter, permease; binding-protein-dependent transport system inner membrane protein 1593071..1593844 Paracoccus denitrificans PD1222 4580217 YP_915407.1 CDS Pden_1611 NC_008686.1 1593841 1595223 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sma:SAV3045 ABC transporter ATP-binding protein; ABC transporter 1593841..1595223 Paracoccus denitrificans PD1222 4580218 YP_915408.1 CDS Pden_1612 NC_008686.1 1595224 1595760 R PFAM: ChaC family protein; KEGG: rsp:RSP_2287 ChaC-like protein; ChaC family protein complement(1595224..1595760) Paracoccus denitrificans PD1222 4580219 YP_915409.1 CDS Pden_1613 NC_008686.1 1595760 1596941 R PFAM: acyl-CoA dehydrogenase domain protein; Acyl-CoA dehydrogenase, type 2, C-terminal domain; KEGG: bca:BCE_5473 acyl-CoA dehydrogenase; acyl-CoA dehydrogenase complement(1595760..1596941) Paracoccus denitrificans PD1222 4580220 YP_915410.1 CDS Pden_1614 NC_008686.1 1596964 1597413 R PFAM: thioesterase superfamily protein; KEGG: sth:STH878 hypothetical protein; thioesterase complement(1596964..1597413) Paracoccus denitrificans PD1222 4580221 YP_915411.1 CDS Pden_1615 NC_008686.1 1597420 1598061 R KEGG: bld:BLi04239 YwfB; hypothetical protein complement(1597420..1598061) Paracoccus denitrificans PD1222 4580222 YP_915412.1 CDS Pden_1617 NC_008686.1 1599137 1599460 R PFAM: transposase IS3/IS911 family protein; KEGG: nwi:Nwi_2119 transposase IS3/IS911; transposase IS3/IS911 family protein complement(1599137..1599460) Paracoccus denitrificans PD1222 4580998 YP_915413.1 CDS Pden_1618 NC_008686.1 1599713 1600507 R KEGG: sil:SPO3456 flagellar protein; flagellar protein complement(1599713..1600507) Paracoccus denitrificans PD1222 4580999 YP_915414.1 CDS Pden_1619 NC_008686.1 1600823 1601188 R PFAM: flagellar FlaF family protein; KEGG: rde:RD1_0159 flagellar protein; flagellar FlaF family protein complement(1600823..1601188) Paracoccus denitrificans PD1222 4581000 YP_915415.1 CDS Pden_1620 NC_008686.1 1601253 1602107 R PFAM: flagellin domain protein; KEGG: sit:TM1040_3134 flagellin-like; flagellin domain-containing protein complement(1601253..1602107) Paracoccus denitrificans PD1222 4581001 YP_915416.1 CDS Pden_1621 NC_008686.1 1602260 1602574 R hypothetical protein complement(1602260..1602574) Paracoccus denitrificans PD1222 4581002 YP_915417.1 CDS Pden_1622 NC_008686.1 1602940 1604133 D KEGG: rde:RD1_0163 flagellar hook-length control protein; hypothetical protein 1602940..1604133 Paracoccus denitrificans PD1222 4581003 YP_915418.1 CDS flgD NC_008686.1 1604147 1604812 D 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 1604147..1604812 Paracoccus denitrificans PD1222 4581004 YP_915419.1 CDS Pden_1624 NC_008686.1 1605044 1605415 D PFAM: transposase IS3/IS911 family protein; KEGG: ret:RHE_CH03058 probable insertion sequence transposase protein; transposase IS3/IS911 family protein 1605044..1605415 Paracoccus denitrificans PD1222 4581005 YP_915420.1 CDS Pden_1626 NC_008686.1 1606371 1606682 R hypothetical protein complement(1606371..1606682) Paracoccus denitrificans PD1222 4581006 YP_915421.1 CDS Pden_1627 NC_008686.1 1606847 1608202 R KEGG: stm:STM1586 periplasmic protein; hypothetical protein complement(1606847..1608202) Paracoccus denitrificans PD1222 4581007 YP_915422.1 CDS Pden_1628 NC_008686.1 1608270 1610312 R PFAM: TonB-dependent receptor; TonB-dependent receptor, plug; KEGG: bbr:BB4761 exogenous ferric siderophore receptor; TonB-dependent receptor, plug complement(1608270..1610312) Paracoccus denitrificans PD1222 4581008 YP_915423.1 CDS Pden_1629 NC_008686.1 1610564 1611091 D 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 1610564..1611091 Paracoccus denitrificans PD1222 4581009 YP_915424.1 CDS Pden_1630 NC_008686.1 1611103 1612077 D PFAM: FecR protein; KEGG: nwi:Nwi_2882 FecR protein; FecR protein 1611103..1612077 Paracoccus denitrificans PD1222 4581010 YP_915425.1 CDS Pden_1631 NC_008686.1 1612232 1614451 D PFAM: TonB-dependent receptor; TonB-dependent receptor, plug; KEGG: csa:Csal_2678 TonB-dependent siderophore receptor; TonB-dependent receptor, plug 1612232..1614451 Paracoccus denitrificans PD1222 4581011 YP_915426.1 CDS Pden_1632 NC_008686.1 1614613 1614864 D hypothetical protein 1614613..1614864 Paracoccus denitrificans PD1222 4581012 YP_915427.1 CDS Pden_1633 NC_008686.1 1614861 1615991 D ATP-dependent carboxylate-amine ligase; carboxylate-amine ligase 1614861..1615991 Paracoccus denitrificans PD1222 4581013 YP_915428.1 CDS Pden_1634 NC_008686.1 1616089 1616586 D PFAM: superoxide dismutase, copper/zinc binding; KEGG: ret:RHE_CH01400 superoxide dismutase protein; superoxide dismutase, copper/zinc binding 1616089..1616586 Paracoccus denitrificans PD1222 4581014 YP_915429.1 CDS Pden_1635 NC_008686.1 1616616 1617704 R PFAM: HWE histidine kinase; KEGG: mes:Meso_0180 signal transduction histidine kinase; signal transduction histidine kinase complement(1616616..1617704) Paracoccus denitrificans PD1222 4581015 YP_915430.1 CDS Pden_1636 NC_008686.1 1617928 1618539 D PFAM: isochorismatase hydrolase; KEGG: mlo:mlr6855 hypothetical protein; isochorismatase hydrolase 1617928..1618539 Paracoccus denitrificans PD1222 4581016 YP_915431.1 CDS Pden_1637 NC_008686.1 1618639 1618875 D KEGG: rsp:RSP_2671 hypothetical protein; hypothetical protein 1618639..1618875 Paracoccus denitrificans PD1222 4580820 YP_915432.1 CDS Pden_1638 NC_008686.1 1619053 1619235 R KEGG: bbr:BB2396 hypothetical protein; hypothetical protein complement(1619053..1619235) Paracoccus denitrificans PD1222 4580821 YP_915433.1 CDS Pden_1640 NC_008686.1 1619984 1620940 R KEGG: rsp:RSP_4009 phosphate acetyl/butaryl transferase; TIGRFAM: phosphate acetyltransferase; PFAM: phosphate acetyl/butaryl transferase; phosphate acetyltransferase complement(1619984..1620940) Paracoccus denitrificans PD1222 4580822 YP_915434.1 CDS Pden_1641 NC_008686.1 1620953 1621969 R PFAM: conserved hypothetical protein 698; KEGG: rsp:RSP_4010 conserved hypothetical protein 698; hypothetical protein complement(1620953..1621969) Paracoccus denitrificans PD1222 4580823 YP_915435.1 CDS Pden_1642 NC_008686.1 1622243 1624024 R catalyzes the formation of acetyl phosphate and sulfite from 2-sulfoacetaldehyde; is active when grown on taurine as a sole carbon source; sulfoacetaldehyde acetyltransferase complement(1622243..1624024) Paracoccus denitrificans PD1222 4580824 YP_915436.1 CDS Pden_1643 NC_008686.1 1624037 1625428 R PFAM: FAD dependent oxidoreductase; KEGG: rsp:RSP_4012 FAD dependent oxidoreductase; FAD dependent oxidoreductase complement(1624037..1625428) Paracoccus denitrificans PD1222 4580825 YP_915437.1 CDS Pden_1644 NC_008686.1 1625437 1625856 R PFAM: protein of unknown function DUF1486; KEGG: rsp:RSP_4013 hypothetical protein; hypothetical protein complement(1625437..1625856) Paracoccus denitrificans PD1222 4580826 YP_915438.1 CDS Pden_1645 NC_008686.1 1625871 1627211 R 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 complement(1625871..1627211) Paracoccus denitrificans PD1222 4580827 YP_915439.1 CDS Pden_1646 NC_008686.1 1627208 1627768 R 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 complement(1627208..1627768) Paracoccus denitrificans PD1222 4580828 YP_915440.1 CDS Pden_1647 NC_008686.1 1627853 1628863 R 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 complement(1627853..1628863) Paracoccus denitrificans PD1222 4580829 YP_915441.1 CDS Pden_1648 NC_008686.1 1628978 1630465 D PFAM: regulatory protein GntR, HTH; aminotransferase, class I and II; KEGG: rsp:RSP_4017 transcriptional regulator, GntR family; GntR family transcriptional regulator 1628978..1630465 Paracoccus denitrificans PD1222 4580830 YP_915442.1 CDS Pden_1649 NC_008686.1 1630782 1631291 D catalyzes the dehydration of (3R)-3-hydroxydecanoyl-ACP to 2,3-decenoyl-ACP or 3,4-decenoyl-ACP; 3-hydroxydecanoyl-ACP dehydratase 1630782..1631291 Paracoccus denitrificans PD1222 4580831 YP_915443.1 CDS Pden_1650 NC_008686.1 1631313 1632542 D PFAM: beta-ketoacyl synthase; KEGG: rsp:RSP_3177 3-oxoacyl-(acyl-carrier-protein) synthase; beta-ketoacyl synthase 1631313..1632542 Paracoccus denitrificans PD1222 4580832 YP_915444.1 CDS Pden_1651 NC_008686.1 1632562 1633350 D PFAM: short-chain dehydrogenase/reductase SDR; KEGG: rsp:RSP_3176 enoyl-(acyl-carrier protein) reductase (NADH); short-chain dehydrogenase/reductase SDR 1632562..1633350 Paracoccus denitrificans PD1222 4580833 YP_915445.1 CDS Pden_1652 NC_008686.1 1633350 1634177 D KEGG: rsp:RSP_2253 predicted hydrolase or acyltransferase; hydrolase 1633350..1634177 Paracoccus denitrificans PD1222 4580834 YP_915446.1 CDS Pden_1653 NC_008686.1 1634531 1635805 R TIGRFAM: lytic murein transglycosylase; PFAM: Peptidoglycan-binding domain 1 protein; KEGG: rsp:RSP_1125 membrane bound lytic murein transglycosylase B; lytic murein transglycosylase complement(1634531..1635805) Paracoccus denitrificans PD1222 4580835 YP_915447.1 CDS Pden_1654 NC_008686.1 1635960 1637006 R PFAM: tRNA synthetase, class II (D, K and N); KEGG: rsp:RSP_0478 lysyl-tRNA synthetase; lysine--tRNA ligase complement(1635960..1637006) Paracoccus denitrificans PD1222 4580836 YP_915448.1 CDS Pden_1655 NC_008686.1 1637085 1637708 D Involved in peptide bond synthesis; alters the affinity of the ribosome for aminoacyl-tRNA; elongation factor P 1637085..1637708 Paracoccus denitrificans PD1222 4580837 YP_915449.1 CDS argC NC_008686.1 1638090 1639118 R 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 complement(1638090..1639118) Paracoccus denitrificans PD1222 4580838 YP_915450.1 CDS panB NC_008686.1 1639582 1640412 D catalyzes the formation of tetrahydrofolate and 2-dehydropantoate from 5,10-methylenetetrahydrofolate and 3-methyl-2-oxobutanoate; 3-methyl-2-oxobutanoate hydroxymethyltransferase 1639582..1640412 Paracoccus denitrificans PD1222 4580839 YP_915451.1 CDS panC NC_008686.1 1640409 1641257 D catalyzes the formation of (R)-pantothenate from pantoate and beta-alanine; pantoate--beta-alanine ligase 1640409..1641257 Paracoccus denitrificans PD1222 4579812 YP_915452.1 CDS Pden_1659 NC_008686.1 1641303 1642682 R 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 complement(1641303..1642682) Paracoccus denitrificans PD1222 4579813 YP_915453.1 CDS Pden_1660 NC_008686.1 1642679 1643362 R PFAM: response regulator receiver; transcriptional regulator domain protein; KEGG: rsp:RSP_3511 two component transcriptional regulator, winged helix family family; two component transcriptional regulator complement(1642679..1643362) Paracoccus denitrificans PD1222 4579814 YP_915454.1 CDS Pden_1661 NC_008686.1 1643362 1643676 R PFAM: Propeptide, PepSY amd peptidase M4; KEGG: rsp:RSP_3510 hypothetical protein; peptidase complement(1643362..1643676) Paracoccus denitrificans PD1222 4579815 YP_915455.1 CDS Pden_1662 NC_008686.1 1643855 1644637 D PFAM: Hemolysin-type calcium-binding region; KEGG: rsp:RSP_3509 hemolysin-type calcium-binding region, RTX; hemolysin-type calcium-binding protein 1643855..1644637 Paracoccus denitrificans PD1222 4579816 YP_915456.1 CDS Pden_1663 NC_008686.1 1644768 1645124 R PFAM: Rieske [2Fe-2S] domain protein; KEGG: gbe:GbCGDNIH1_0274 rieske (2Fe-2S) domain protein; Rieske (2Fe-2S) domain-containing protein complement(1644768..1645124) Paracoccus denitrificans PD1222 4579817 YP_915457.1 CDS Pden_1664 NC_008686.1 1645128 1646240 R KEGG: sme:SMc03211 4-hydroxyphenylpyruvate dioxygenase protein; TIGRFAM: 4-hydroxyphenylpyruvate dioxygenase; PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase; 4-hydroxyphenylpyruvate dioxygenase complement(1645128..1646240) Paracoccus denitrificans PD1222 4579818 YP_915458.1 CDS Pden_1665 NC_008686.1 1646362 1646832 D PFAM: regulatory protein, AsnC/Lrp family; KEGG: rpa:RPA0006 transcriptional regulator, AsnC family; AsnC family transcriptional regulator 1646362..1646832 Paracoccus denitrificans PD1222 4579819 YP_915459.1 CDS Pden_1666 NC_008686.1 1646854 1647954 D 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 1646854..1647954 Paracoccus denitrificans PD1222 4579820 YP_915460.1 CDS Pden_1667 NC_008686.1 1648040 1648891 R 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 complement(1648040..1648891) Paracoccus denitrificans PD1222 4579821 YP_915461.1 CDS Pden_1668 NC_008686.1 1648888 1649727 R 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 complement(1648888..1649727) Paracoccus denitrificans PD1222 4579822 YP_915462.1 CDS Pden_1669 NC_008686.1 1649731 1650633 R 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 complement(1649731..1650633) Paracoccus denitrificans PD1222 4579823 YP_915463.1 CDS Pden_1670 NC_008686.1 1650630 1651637 R 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 complement(1650630..1651637) Paracoccus denitrificans PD1222 4579824 YP_915464.1 CDS Pden_1671 NC_008686.1 1651711 1653327 R PFAM: extracellular solute-binding protein, family 5; KEGG: atc:AGR_L_1481 dipeptide transport protein; extracellular solute-binding protein complement(1651711..1653327) Paracoccus denitrificans PD1222 4579825 YP_915465.1 CDS Pden_1672 NC_008686.1 1653521 1654327 R PFAM: Myo-inositol catabolism IolB domain protein; KEGG: bmb:BruAb2_0514 IolB protein; myo-inositol catabolism IolB domain-containing protein complement(1653521..1654327) Paracoccus denitrificans PD1222 4579826 YP_915466.1 CDS Pden_1673 NC_008686.1 1654324 1654509 R KEGG: ret:RHE_CH03169 hypothetical protein; hypothetical protein complement(1654324..1654509) Paracoccus denitrificans PD1222 4579827 YP_915467.1 CDS Pden_1674 NC_008686.1 1654519 1655415 R PFAM: Xylose isomerase domain protein TIM barrel; KEGG: atc:AGR_L_177GM iolE protein; xylose isomerase domain-containing protein complement(1654519..1655415) Paracoccus denitrificans PD1222 4579828 YP_915468.1 CDS Pden_1675 NC_008686.1 1655427 1657256 R 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 complement(1655427..1657256) Paracoccus denitrificans PD1222 4579829 YP_915469.1 CDS Pden_1676 NC_008686.1 1657333 1659240 R PFAM: PfkB domain protein; KEGG: bmb:BruAb2_0517 IolC myo-catabolism protein; ribokinase-like domain-containing protein complement(1657333..1659240) Paracoccus denitrificans PD1222 4579830 YP_915470.1 CDS Pden_1677 NC_008686.1 1659244 1660044 R PFAM: Xylose isomerase domain protein TIM barrel; KEGG: atc:AGR_L_627 IolI protein; xylose isomerase domain-containing protein complement(1659244..1660044) Paracoccus denitrificans PD1222 4580085 YP_915471.1 CDS Pden_1678 NC_008686.1 1660053 1661063 R PFAM: oxidoreductase domain protein; Oxidoreductase, C-terminal domain; KEGG: atc:AGR_L_628 myo-inositol 2-dehydrogenase; inositol 2-dehydrogenase complement(1660053..1661063) Paracoccus denitrificans PD1222 4580086 YP_915472.1 CDS Pden_1679 NC_008686.1 1661066 1661968 R PFAM: Xylose isomerase domain protein TIM barrel; KEGG: atc:AGR_pAT_639 myo-inositol catabolism; xylose isomerase domain-containing protein complement(1661066..1661968) Paracoccus denitrificans PD1222 4580087 YP_915473.1 CDS Pden_1680 NC_008686.1 1661976 1663094 R PFAM: oxidoreductase domain protein; Oxidoreductase, C-terminal domain; KEGG: psb:Psyr_2455 oxidoreductase, N-terminal:oxidoreductase, C-terminal; oxidoreductase domain-containing protein complement(1661976..1663094) Paracoccus denitrificans PD1222 4580088 YP_915474.1 CDS Pden_1681 NC_008686.1 1663100 1664020 R PFAM: periplasmic binding protein/LacI transcriptional regulator; KEGG: atc:AGR_L_632 rhizopine-binding protein precursor; periplasmic binding protein/LacI transcriptional regulator complement(1663100..1664020) Paracoccus denitrificans PD1222 4580089 YP_915475.1 CDS Pden_1682 NC_008686.1 1664032 1665042 R PFAM: inner-membrane translocator; KEGG: sme:SMb20714 sugar uptake ABC transporter permease protein; inner-membrane translocator complement(1664032..1665042) Paracoccus denitrificans PD1222 4580090 YP_915476.1 CDS Pden_1683 NC_008686.1 1665055 1666566 R PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: atc:AGR_L_2903 D-galactose transport system ATP-binding protein; ABC transporter complement(1665055..1666566) Paracoccus denitrificans PD1222 4580091 YP_915477.1 CDS Pden_1684 NC_008686.1 1666620 1667561 R PFAM: periplasmic binding protein/LacI transcriptional regulator; KEGG: atc:AGR_L_634 rhizopine-binding protein precursor; periplasmic binding protein/LacI transcriptional regulator complement(1666620..1667561) Paracoccus denitrificans PD1222 4580092 YP_915478.1 CDS Pden_1685 NC_008686.1 1667791 1668795 R PFAM: regulatory protein, LacI; KEGG: atc:AGR_L_636 hypothetical protein; regulatory protein, LacI complement(1667791..1668795) Paracoccus denitrificans PD1222 4580093 YP_915479.1 CDS Pden_1686 NC_008686.1 1668901 1669575 R KEGG: bja:blr7843 hypothetical protein; hypothetical protein complement(1668901..1669575) Paracoccus denitrificans PD1222 4580094 YP_915480.1 CDS Pden_1687 NC_008686.1 1669663 1670700 R PFAM: helix-turn-helix- domain containing protein, AraC type; ThiJ/PfpI domain protein; KEGG: sil:SPO1002 transcriptional regulator, AraC family; AraC family transcriptional regulator complement(1669663..1670700) Paracoccus denitrificans PD1222 4580095 YP_915481.1 CDS Pden_1688 NC_008686.1 1670911 1671375 R KEGG: nmu:Nmul_A2076 hypothetical protein; hypothetical protein complement(1670911..1671375) Paracoccus denitrificans PD1222 4580096 YP_915482.1 CDS Pden_1689 NC_008686.1 1671389 1672597 R flavohemoprotein; catalyzes the formation of nitrate from nitric oxide; can also catalyze the reduction of dihydropteridine; nitric oxide dioxygenase complement(1671389..1672597) Paracoccus denitrificans PD1222 4580097 YP_915483.1 CDS Pden_1690 NC_008686.1 1672723 1673166 D TIGRFAM: transcriptional regulator, Rrf2 family; PFAM: protein of unknown function UPF0074; KEGG: neu:NE0928 hypothetical protein; BadM/Rrf2 family transcriptional regulator 1672723..1673166 Paracoccus denitrificans PD1222 4580098 YP_915484.1 CDS Pden_1691 NC_008686.1 1673173 1674075 R PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: atc:AGR_C_2527 hypothetical protein; LysR family transcriptional regulator complement(1673173..1674075) Paracoccus denitrificans PD1222 4580099 YP_915485.1 CDS Pden_1692 NC_008686.1 1674196 1675422 D PFAM: creatinase; peptidase M24; KEGG: rxy:Rxyl_0461 creatinase; creatinase 1674196..1675422 Paracoccus denitrificans PD1222 4580100 YP_915486.1 CDS Pden_1693 NC_008686.1 1675567 1676901 D PFAM: General substrate transporter; major facilitator superfamily MFS_1; KEGG: ppu:PP_3666 metabolite MFS transporter, MHS family; major facilitator superfamily transporter 1675567..1676901 Paracoccus denitrificans PD1222 4580101 YP_915487.1 CDS Pden_1694 NC_008686.1 1676951 1677880 R PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: rsp:RSP_1286 RuBisCO operon transcriptional regulator, CbbR; LysR family transcriptional regulator complement(1676951..1677880) Paracoccus denitrificans PD1222 4580102 YP_915488.1 CDS Pden_1695 NC_008686.1 1677976 1678968 D PFAM: Inositol phosphatase/fructose-1,6-bisphosphatase; KEGG: rsp:RSP_1285 fructose-1,6-bisphosphatase I; inositol phosphatase/fructose-1,6-bisphosphatase 1677976..1678968 Paracoccus denitrificans PD1222 4580103 YP_915489.1 CDS Pden_1696 NC_008686.1 1678991 1679863 D PFAM: phosphoribulokinase/uridine kinase; KEGG: rsp:RSP_1284 phosphoribulokinase; phosphoribulokinase 1678991..1679863 Paracoccus denitrificans PD1222 4580104 YP_915490.1 CDS Pden_1697 NC_008686.1 1679875 1681881 D 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 1679875..1681881 Paracoccus denitrificans PD1222 4581323 YP_915491.1 CDS Pden_1698 NC_008686.1 1681881 1682960 D 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 1681881..1682960 Paracoccus denitrificans PD1222 4581324 YP_915492.1 CDS rbcL NC_008686.1 1682975 1684438 D type III RuBisCO; involved in carbon fixation; ribulose bisophosphate carboxylase 1682975..1684438 Paracoccus denitrificans PD1222 4581325 YP_915493.1 CDS Pden_1700 NC_008686.1 1684450 1684839 D PFAM: ribulose bisphosphate carboxylase, small chain; KEGG: rpa:RPA1560 ribulose-bisphosphate carboxylase small chain; ribulose-bisphosphate carboxylase 1684450..1684839 Paracoccus denitrificans PD1222 4581326 YP_915494.1 CDS Pden_1701 NC_008686.1 1684912 1685838 D PFAM: AAA ATPase, central domain protein; SMART: AAA ATPase; KEGG: rsp:RSP_1280 CbbX protein; ATPase central domain-containing protein 1684912..1685838 Paracoccus denitrificans PD1222 4581327 YP_915495.1 CDS Pden_1702 NC_008686.1 1686315 1687565 R KEGG: pfl:PFL_4132 PimS2 protein; PimS2 protein complement(1686315..1687565) Paracoccus denitrificans PD1222 4581328 YP_915496.1 CDS Pden_1703 NC_008686.1 1687776 1689314 D KEGG: pfo:Pfl_2975 quinohemoprotein amine dehydrogenase, 60 kDa subunit; quinohemoprotein amine dehydrogenase, 60 kDa subunit 1687776..1689314 Paracoccus denitrificans PD1222 4581329 YP_915497.1 CDS Pden_1704 NC_008686.1 1689319 1690776 D PFAM: Radical SAM domain protein; KEGG: pfo:Pfl_2974 radical SAM; radical SAM domain-containing protein 1689319..1690776 Paracoccus denitrificans PD1222 4581330 YP_915498.1 CDS Pden_1705 NC_008686.1 1690773 1691105 D KEGG: pfo:Pfl_2973 hypothetical protein; hypothetical protein 1690773..1691105 Paracoccus denitrificans PD1222 4581331 YP_915499.1 CDS Pden_1706 NC_008686.1 1691105 1692181 D KEGG: pfo:Pfl_2972 quinohemoprotein amine dehydrogenase, subunit beta; quinohemoprotein amine dehydrogenase subunit beta 1691105..1692181 Paracoccus denitrificans PD1222 4581332 YP_915500.1 CDS Pden_1707 NC_008686.1 1692183 1692851 D KEGG: pfo:Pfl_2971 hypothetical protein; hypothetical protein 1692183..1692851 Paracoccus denitrificans PD1222 4581333 YP_915501.1 CDS Pden_1708 NC_008686.1 1692844 1694565 D PFAM: ABC transporter, transmembrane region; ABC transporter related; SMART: AAA ATPase; KEGG: pfl:PFL_4134 ABC transporter, ATP-binding protein, MsbA family; ABC transporter 1692844..1694565 Paracoccus denitrificans PD1222 4581334 YP_915502.1 CDS Pden_1709 NC_008686.1 1694469 1695449 R PFAM: helix-turn-helix- domain containing protein, AraC type; KEGG: nar:Saro_2605 transcriptional regulator, AraC family; Fis family transcriptional regulator complement(1694469..1695449) Paracoccus denitrificans PD1222 4581335 YP_915503.1 CDS Pden_1710 NC_008686.1 1695772 1697175 D PFAM: aldehyde dehydrogenase; KEGG: nar:Saro_1692 aldehyde dehydrogenase; betaine aldehyde dehydrogenase 1695772..1697175 Paracoccus denitrificans PD1222 4581336 YP_915504.1 CDS Pden_1711 NC_008686.1 1697230 1697835 R KEGG: nwi:Nwi_2052 hypothetical protein; hypothetical protein complement(1697230..1697835) Paracoccus denitrificans PD1222 4581337 YP_915505.1 CDS Pden_1712 NC_008686.1 1697832 1699442 R PFAM: glucose-methanol-choline oxidoreductase; GMC oxidoreductase; KEGG: rsp:RSP_3292 glucose-methanol-choline oxidoreductase; glucose-methanol-choline oxidoreductase complement(1697832..1699442) Paracoccus denitrificans PD1222 4581338 YP_915506.1 CDS Pden_1713 NC_008686.1 1699474 1700472 R PFAM: inner-membrane translocator; KEGG: rsp:RSP_3293 ABC branched-chain amino acid transporter, inner membrane subunit; inner-membrane translocator complement(1699474..1700472) Paracoccus denitrificans PD1222 4581339 YP_915507.1 CDS Pden_1714 NC_008686.1 1700474 1701361 R PFAM: inner-membrane translocator; KEGG: rsp:RSP_3294 ABC branched-chain amino acid transporter, inner membrane subunit; inner-membrane translocator complement(1700474..1701361) Paracoccus denitrificans PD1222 4581340 YP_915508.1 CDS Pden_1715 NC_008686.1 1701363 1702067 R PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rsp:RSP_3295 ABC branched-chain amino acid transporter, ATPase subunit; ABC transporter complement(1701363..1702067) Paracoccus denitrificans PD1222 4581341 YP_915509.1 CDS Pden_1716 NC_008686.1 1702064 1702840 R PFAM: ABC transporter related; KEGG: rsp:RSP_3296 ABC branched-chain amino acid transporter, ATPase subunit; ABC transporter complement(1702064..1702840) Paracoccus denitrificans PD1222 4580978 YP_915510.1 CDS Pden_1717 NC_008686.1 1702840 1704039 R KEGG: rsp:RSP_3297 ABC branched-chain amino acid transporter, periplasmic binding protein; branched chain amino acid ABC transporter substrate-binding protein complement(1702840..1704039) Paracoccus denitrificans PD1222 4580979 YP_915511.1 CDS Pden_1718 NC_008686.1 1704227 1705144 D PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: rsp:RSP_3298 transcriptional regulator, LysR family; LysR family transcriptional regulator 1704227..1705144 Paracoccus denitrificans PD1222 4580980 YP_915512.1 CDS Pden_1719 NC_008686.1 1705314 1706825 R catalyzes the formation of malonyl-CoA from malonate and CoA; malonyl-CoA synthase complement(1705314..1706825) Paracoccus denitrificans PD1222 4580981 YP_915513.1 CDS Pden_1720 NC_008686.1 1706842 1708212 R PFAM: Malonyl-CoA decarboxylase; KEGG: rpb:RPB_0704 malonyl-CoA decarboxylase; malonyl-CoA decarboxylase complement(1706842..1708212) Paracoccus denitrificans PD1222 4580982 YP_915514.1 CDS Pden_1721 NC_008686.1 1708247 1709629 R PFAM: Citrate transporter; Dicarboxylate carrier MatC domain protein; KEGG: rha:RHA1_ro02937 possible dicarboxylate carrier protein; dicarboxylate carrier MatC domain-containing protein complement(1708247..1709629) Paracoccus denitrificans PD1222 4580983 YP_915515.1 CDS Pden_1722 NC_008686.1 1709821 1710477 D PFAM: regulatory protein GntR, HTH; GntR domain protein; KEGG: dar:Daro_4024 regulatory protein GntR, HTH:GntR, C-terminal; GntR family transcriptional regulator 1709821..1710477 Paracoccus denitrificans PD1222 4580984 YP_915516.1 CDS Pden_1723 NC_008686.1 1710559 1711242 D KEGG: bxe:Bxe_C1278 hypothetical protein; hypothetical protein 1710559..1711242 Paracoccus denitrificans PD1222 4580985 YP_915517.1 CDS Pden_1724 NC_008686.1 1711267 1712628 D KEGG: bbr:BB1601 hypothetical protein; hypothetical protein 1711267..1712628 Paracoccus denitrificans PD1222 4580986 YP_915518.1 CDS Pden_1725 NC_008686.1 1712600 1713151 R hypothetical protein complement(1712600..1713151) Paracoccus denitrificans PD1222 4580987 YP_915519.1 CDS Pden_1726 NC_008686.1 1713148 1713696 R KEGG: sme:SMc02592 hypothetical protein; hypothetical protein complement(1713148..1713696) Paracoccus denitrificans PD1222 4580988 YP_915520.1 CDS Pden_1727 NC_008686.1 1713693 1714220 R KEGG: sme:SMc02593 hypothetical protein; hypothetical protein complement(1713693..1714220) Paracoccus denitrificans PD1222 4580989 YP_915521.1 CDS Pden_1728 NC_008686.1 1714648 1716132 D PFAM: CHAD domain containing protein; adenylate cyclase; KEGG: mlo:mll9114 hypothetical protein; CHAD domain-containing protein 1714648..1716132 Paracoccus denitrificans PD1222 4580990 YP_915522.1 CDS Pden_1729 NC_008686.1 1716154 1717272 R 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 complement(1716154..1717272) Paracoccus denitrificans PD1222 4580991 YP_915523.1 CDS Pden_1730 NC_008686.1 1717674 1718153 D hypothetical protein 1717674..1718153 Paracoccus denitrificans PD1222 4580992 YP_915524.1 CDS Pden_1731 NC_008686.1 1718248 1720026 D TIGRFAM: sulfate transporter; PFAM: Sulfate transporter/antisigma-factor antagonist STAS; sulphate transporter; KEGG: sit:TM1040_3648 sulfate permease; sulfate transporter 1718248..1720026 Paracoccus denitrificans PD1222 4580993 YP_915525.1 CDS Pden_1732 NC_008686.1 1720321 1721295 D KEGG: sil:SPO3222 glutathione S-transferase; glutathione S-transferase 1720321..1721295 Paracoccus denitrificans PD1222 4580994 YP_915526.1 CDS Pden_1733 NC_008686.1 1721402 1722316 D PFAM: iron permease FTR1; KEGG: rru:Rru_A2597 iron permease FTR1; iron permease 1721402..1722316 Paracoccus denitrificans PD1222 4580995 YP_915527.1 CDS Pden_1734 NC_008686.1 1722313 1723470 D PFAM: protein of unknown function DUF451; KEGG: rru:Rru_A2598 hypothetical protein; hypothetical protein 1722313..1723470 Paracoccus denitrificans PD1222 4580996 YP_915528.1 CDS Pden_1735 NC_008686.1 1723472 1724776 D TIGRFAM: Dyp-type peroxidase family; PFAM: Dyp-type peroxidase; KEGG: rru:Rru_A2599 Tat-translocated enzyme; Dyp-type peroxidase family protein 1723472..1724776 Paracoccus denitrificans PD1222 4580997 YP_915529.1 CDS Pden_1736 NC_008686.1 1724819 1725646 D PFAM: protein of unknown function DUF451; KEGG: rru:Rru_A2600 protein of unknown function DUF451; hypothetical protein 1724819..1725646 Paracoccus denitrificans PD1222 4581246 YP_915530.1 CDS Pden_1737 NC_008686.1 1726093 1726992 R PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: ret:RHE_CH00925 probable transcriptional regulator protein, LysR family; LysR family transcriptional regulator complement(1726093..1726992) Paracoccus denitrificans PD1222 4581247 YP_915531.1 CDS Pden_1738 NC_008686.1 1727097 1728326 D PFAM: creatinase; peptidase M24; KEGG: rxy:Rxyl_0461 creatinase; creatinase 1727097..1728326 Paracoccus denitrificans PD1222 4581248 YP_915532.1 CDS Pden_1739 NC_008686.1 1728497 1729609 D KEGG: rsp:RSP_1883 ABC polyamine/opine transporter, periplasmic substrate-binding protein; polyamine/opine ABC transporter substrate-binding protein 1728497..1729609 Paracoccus denitrificans PD1222 4581249 YP_915533.1 CDS Pden_1740 NC_008686.1 1729955 1730197 R KEGG: rde:RD1_2835 hypothetical protein; hypothetical protein complement(1729955..1730197) Paracoccus denitrificans PD1222 4581250 YP_915534.1 CDS Pden_1741 NC_008686.1 1730480 1730707 D KEGG: sit:TM1040_1503 conserved hypothetical protein; hypothetical protein 1730480..1730707 Paracoccus denitrificans PD1222 4581251 YP_915535.1 CDS Pden_1742 NC_008686.1 1730709 1731158 D 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 1730709..1731158 Paracoccus denitrificans PD1222 4581252 YP_915536.1 CDS Pden_1743 NC_008686.1 1731341 1732780 D 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 1731341..1732780 Paracoccus denitrificans PD1222 4581253 YP_915537.1 CDS Pden_1744 NC_008686.1 1732864 1733442 D catalyzes the formation of thymidine 5'-phosphate from thymidine; thymidine kinase 1732864..1733442 Paracoccus denitrificans PD1222 4581254 YP_915538.1 CDS Pden_1745 NC_008686.1 1733439 1734659 D PFAM: YceI family protein; cytochrome B561; KEGG: sit:TM1040_1049 cytochrome b561; cytochrome B561 1733439..1734659 Paracoccus denitrificans PD1222 4581255 YP_915539.1 CDS ndk NC_008686.1 1734782 1735204 R catalyzes the formation of nucleoside triphosphate from ATP and nucleoside diphosphate; nucleoside diphosphate kinase complement(1734782..1735204) Paracoccus denitrificans PD1222 4581256 YP_915540.1 CDS Pden_1747 NC_008686.1 1735334 1737181 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rsp:RSP_2895 ABC transporter, fused ATPase subunits; ABC transporter 1735334..1737181 Paracoccus denitrificans PD1222 4581257 YP_915541.1 CDS Pden_1748 NC_008686.1 1737281 1738009 D PFAM: MltA-interacting MipA family protein; KEGG: rpc:RPC_0793 MltA-interacting MipA; MltA-interacting MipA family protein 1737281..1738009 Paracoccus denitrificans PD1222 4581258 YP_915542.1 CDS Pden_1749 NC_008686.1 1738074 1738433 D PFAM: protein of unknown function DUF59; KEGG: rde:RD1_2957 hypothetical protein; hypothetical protein 1738074..1738433 Paracoccus denitrificans PD1222 4581259 YP_915543.1 CDS Pden_1750 NC_008686.1 1738430 1738978 D PFAM: transferase hexapeptide repeat containing protein; KEGG: rde:RD1_2959 maltose O-acetyltransferase; hexapaptide repeat-containing transferase 1738430..1738978 Paracoccus denitrificans PD1222 4581260 YP_915544.1 CDS Pden_1751 NC_008686.1 1738985 1739554 R PFAM: Phosphoglycerate mutase; KEGG: rde:RD1_2834 phosphoglycerate mutase; phosphoglycerate mutase complement(1738985..1739554) Paracoccus denitrificans PD1222 4581261 YP_915545.1 CDS Pden_1752 NC_008686.1 1739545 1740405 R catalyzes the conversion of the propionic acid groups of rings I and III to vinyl groups during heme synthesis; coproporphyrinogen III oxidase complement(1739545..1740405) Paracoccus denitrificans PD1222 4581262 YP_915546.1 CDS Pden_1753 NC_008686.1 1740461 1740901 D KEGG: rsp:RSP_0683 hypothetical protein; hypothetical protein 1740461..1740901 Paracoccus denitrificans PD1222 4581263 YP_915547.1 CDS Pden_1754 NC_008686.1 1740906 1741715 R PFAM: short-chain dehydrogenase/reductase SDR; KEGG: rsp:RSP_0684 possible oxidoreductase; short-chain dehydrogenase/reductase SDR; short-chain dehydrogenase/reductase SDR complement(1740906..1741715) Paracoccus denitrificans PD1222 4581264 YP_915548.1 CDS Pden_1755 NC_008686.1 1741712 1742746 R PFAM: methyltransferase small; KEGG: rsp:RSP_0685 possible ribosomal RNA small subunit methyltransferase C RsmC; methyltransferase small complement(1741712..1742746) Paracoccus denitrificans PD1222 4580919 YP_915549.1 CDS Pden_1756 NC_008686.1 1742750 1743067 R 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 complement(1742750..1743067) Paracoccus denitrificans PD1222 4580920 YP_915550.1 CDS Pden_1757 NC_008686.1 1743278 1744984 D 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 1743278..1744984 Paracoccus denitrificans PD1222 4580921 YP_915551.1 CDS Pden_1758 NC_008686.1 1745177 1745638 R PFAM: regulatory protein, AsnC/Lrp family; KEGG: rsp:RSP_1867 transcriptional regulator, AsnC family; AsnC family transcriptional regulator complement(1745177..1745638) Paracoccus denitrificans PD1222 4580922 YP_915552.1 CDS Pden_1759 NC_008686.1 1745635 1746090 R 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 complement(1745635..1746090) Paracoccus denitrificans PD1222 4580923 YP_915553.1 CDS Pden_1760 NC_008686.1 1746218 1747240 D 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 1746218..1747240 Paracoccus denitrificans PD1222 4580924 YP_915554.1 CDS Pden_1761 NC_008686.1 1747542 1748414 D PFAM: protein of unknown function DUF6, transmembrane; KEGG: rsp:RSP_1649 possible transporter, DMT superfamily; hypothetical protein 1747542..1748414 Paracoccus denitrificans PD1222 4580925 YP_915555.1 CDS dnaE NC_008686.1 1748469 1751939 R 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 complement(1748469..1751939) Paracoccus denitrificans PD1222 4580926 YP_915556.1 CDS Pden_1763 NC_008686.1 1752032 1753546 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rde:RD1_4071 sugar ABC transporter, ATP-binding protein; ABC transporter 1752032..1753546 Paracoccus denitrificans PD1222 4580927 YP_915557.1 CDS Pden_1764 NC_008686.1 1753533 1754603 D PFAM: inner-membrane translocator; KEGG: sit:TM1040_0495 inner-membrane translocator; inner-membrane translocator 1753533..1754603 Paracoccus denitrificans PD1222 4580928 YP_915558.1 CDS Pden_1765 NC_008686.1 1754600 1755490 D PFAM: inner-membrane translocator; KEGG: sil:SPO0649 sugar ABC transporter, permease protein; inner-membrane translocator 1754600..1755490 Paracoccus denitrificans PD1222 4580929 YP_915559.1 CDS Pden_1766 NC_008686.1 1755514 1756590 D PFAM: basic membrane lipoprotein; KEGG: rsp:RSP_3560 possible ABC transporter, periplasmic binding protein; basic membrane lipoprotein 1755514..1756590 Paracoccus denitrificans PD1222 4580930 YP_915560.1 CDS Pden_1767 NC_008686.1 1756646 1757119 R PFAM: Ferritin, Dps family protein; KEGG: gbe:GbCGDNIH1_0685 ferroxidase; ferritin complement(1756646..1757119) Paracoccus denitrificans PD1222 4580931 YP_915561.1 CDS acpP NC_008686.1 1757265 1757498 R carries the fatty acid chain in fatty acid biosynthesis; acyl carrier protein complement(1757265..1757498) Paracoccus denitrificans PD1222 4580932 YP_915562.1 CDS Pden_1769 NC_008686.1 1757635 1758372 R 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 complement(1757635..1758372) Paracoccus denitrificans PD1222 4580933 YP_915563.1 CDS Pden_1770 NC_008686.1 1758436 1759362 R 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 complement(1758436..1759362) Paracoccus denitrificans PD1222 4580934 YP_915564.1 CDS Pden_1771 NC_008686.1 1759435 1760772 R 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 complement(1759435..1760772) Paracoccus denitrificans PD1222 4580935 YP_915565.1 CDS Pden_1772 NC_008686.1 1760831 1761697 D PFAM: beta-lactamase domain protein; KEGG: sil:SPO2174 metallo-beta-lactamase family protein; beta-lactamase domain-containing protein 1760831..1761697 Paracoccus denitrificans PD1222 4580936 YP_915566.1 CDS Pden_1773 NC_008686.1 1762154 1763218 R PFAM: Siderophore-interacting protein; FAD-binding 9, siderophore-interacting domain protein; KEGG: mes:Meso_0336 siderophore-interacting protein; siderophore-interacting protein complement(1762154..1763218) Paracoccus denitrificans PD1222 4580937 YP_915567.1 CDS Pden_1774 NC_008686.1 1763222 1764313 R KEGG: rpc:RPC_3611 periplasmic binding protein; periplasmic binding protein complement(1763222..1764313) Paracoccus denitrificans PD1222 4580938 YP_915568.1 CDS Pden_1775 NC_008686.1 1764315 1766480 R TIGRFAM: TonB-dependent siderophore receptor; PFAM: TonB-dependent receptor; TonB-dependent receptor, plug; KEGG: neu:NE1097 TonB-dependent receptor protein; TonB-dependent siderophore receptor complement(1764315..1766480) Paracoccus denitrificans PD1222 4580959 YP_915569.1 CDS Pden_1776 NC_008686.1 1766649 1767638 D PFAM: helix-turn-helix- domain containing protein, AraC type; KEGG: bam:Bamb_1692 transcriptional regulator, AraC family; helix-turn-helix domain-containing protein 1766649..1767638 Paracoccus denitrificans PD1222 4580960 YP_915570.1 CDS Pden_1777 NC_008686.1 1767766 1769595 D PFAM: Citrate transporter; TrkA-C domain protein; TRAP C4-dicarboxylate transport system permease DctM subunit; KEGG: pau:PA14_14360 sodium/sulphate transporter; citrate transporter 1767766..1769595 Paracoccus denitrificans PD1222 4580961 YP_915571.1 CDS Pden_1778 NC_008686.1 1769921 1771135 R 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 complement(1769921..1771135) Paracoccus denitrificans PD1222 4580962 YP_915572.1 CDS Pden_1779 NC_008686.1 1771246 1771668 D PFAM: Uncharacterized conserved protein UCP032025; KEGG: rsp:RSP_3548 hypothetical protein; hypothetical protein 1771246..1771668 Paracoccus denitrificans PD1222 4580963 YP_915573.1 CDS Pden_1780 NC_008686.1 1772014 1773369 D 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 1772014..1773369 Paracoccus denitrificans PD1222 4580964 YP_915574.1 CDS Pden_1781 NC_008686.1 1773407 1775482 D 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 1773407..1775482 Paracoccus denitrificans PD1222 4580965 YP_915575.1 CDS Pden_1782 NC_008686.1 1775454 1776539 D KEGG: rsp:RSP_3318 cation/multidrug efflux pump, RND family; cation efflux transporter 1775454..1776539 Paracoccus denitrificans PD1222 4580966 YP_915576.1 CDS Pden_1783 NC_008686.1 1776681 1778087 D 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 1776681..1778087 Paracoccus denitrificans PD1222 4580967 YP_915577.1 CDS Pden_1784 NC_008686.1 1778084 1778758 D PFAM: regulatory protein, LuxR; response regulator receiver; KEGG: rpe:RPE_3142 two component transcriptional regulator, LuxR family; LuxR family transcriptional regulator 1778084..1778758 Paracoccus denitrificans PD1222 4580968 YP_915578.1 CDS Pden_1785 NC_008686.1 1778762 1780048 D PFAM: helix-turn-helix domain protein; KEGG: rsp:RSP_0172 predicted transcriptional regulators; helix-turn-helix domain-containing protein 1778762..1780048 Paracoccus denitrificans PD1222 4580969 YP_915579.1 CDS Pden_1786 NC_008686.1 1780107 1780469 D PFAM: response regulator receiver; KEGG: rde:RD1_2841 response regulator receiver domain protein; response regulator receiver protein 1780107..1780469 Paracoccus denitrificans PD1222 4580970 YP_915580.1 CDS Pden_1787 NC_008686.1 1780478 1780720 D KEGG: rsp:RSP_0170 hypothetical protein; hypothetical protein 1780478..1780720 Paracoccus denitrificans PD1222 4580971 YP_915581.1 CDS Pden_1788 NC_008686.1 1780710 1783367 D 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 1780710..1783367 Paracoccus denitrificans PD1222 4580972 YP_915582.1 CDS Pden_1789 NC_008686.1 1783427 1784605 D PFAM: surface presentation of antigens (SPOA) protein; KEGG: rsp:RSP_6099 possible flagellar switch protein FliM; surface presentation of antigens (SPOA) protein 1783427..1784605 Paracoccus denitrificans PD1222 4580973 YP_915583.1 CDS infA NC_008686.1 1784790 1785008 D stimulates the activities of the other two initiation factors, IF-2 and IF-3; translation initiation factor IF-1 1784790..1785008 Paracoccus denitrificans PD1222 4580974 YP_915584.1 CDS Pden_1791 NC_008686.1 1785037 1785678 D TIGRFAM: maf protein; PFAM: Maf family protein; KEGG: rsp:RSP_0625 Maf-like protein; maf protein 1785037..1785678 Paracoccus denitrificans PD1222 4580975 YP_915585.1 CDS Pden_1792 NC_008686.1 1785675 1786736 D KEGG: rsp:RSP_0624 ribonuclease; ribonuclease 1785675..1786736 Paracoccus denitrificans PD1222 4580976 YP_915586.1 CDS Pden_1793 NC_008686.1 1786733 1786882 D PFAM: protein of unknown function DUF329; KEGG: rpe:RPE_4479 protein of unknown function DUF329; hypothetical protein 1786733..1786882 Paracoccus denitrificans PD1222 4580977 YP_915587.1 CDS Pden_1794 NC_008686.1 1787121 1787453 R hypothetical protein complement(1787121..1787453) Paracoccus denitrificans PD1222 4580494 YP_915588.1 CDS Pden_1795 NC_008686.1 1787522 1788787 R PFAM: Allergen V5/Tpx-1 family protein; Hemolysin-type calcium-binding region; KEGG: eba:ebA7184 hypothetical protein; Allergen V5/Tpx-1 family protein complement(1787522..1788787) Paracoccus denitrificans PD1222 4580495 YP_915589.1 CDS Pden_1796 NC_008686.1 1789095 1789577 R PFAM: GCN5-related N-acetyltransferase; KEGG: rsp:RSP_2081 acetyltransferase, GNAT family; N-acetyltransferase complement(1789095..1789577) Paracoccus denitrificans PD1222 4580496 YP_915590.1 CDS Pden_1797 NC_008686.1 1789856 1790971 D 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 1789856..1790971 Paracoccus denitrificans PD1222 4580497 YP_915591.1 CDS Pden_1798 NC_008686.1 1790968 1791966 D 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 1790968..1791966 Paracoccus denitrificans PD1222 4580498 YP_915592.1 CDS Pden_1799 NC_008686.1 1791963 1792808 D 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 1791963..1792808 Paracoccus denitrificans PD1222 4580499 YP_915593.1 CDS Pden_1800 NC_008686.1 1792805 1793632 D 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 1792805..1793632 Paracoccus denitrificans PD1222 4580500 YP_915594.1 CDS Pden_1801 NC_008686.1 1793695 1794420 D PFAM: heat shock protein DnaJ domain protein; KEGG: rsp:RSP_0785 heat shock protein DnaJ; molecular chaperone DnaJ 1793695..1794420 Paracoccus denitrificans PD1222 4580501 YP_915595.1 CDS Pden_1802 NC_008686.1 1794477 1794962 D KEGG: rsp:RSP_6229 hypothetical protein; hypothetical protein 1794477..1794962 Paracoccus denitrificans PD1222 4580502 YP_915596.1 CDS Pden_1803 NC_008686.1 1794959 1796176 R PFAM: glycosyl transferase, group 1; KEGG: rsp:RSP_0700 probable glycosyltransferase; group 1 glycosyl transferase complement(1794959..1796176) Paracoccus denitrificans PD1222 4580503 YP_915597.1 CDS Pden_1804 NC_008686.1 1796176 1797789 R 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 complement(1796176..1797789) Paracoccus denitrificans PD1222 4580504 YP_915598.1 CDS Pden_1805 NC_008686.1 1797786 1798892 R 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 complement(1797786..1798892) Paracoccus denitrificans PD1222 4580505 YP_915599.1 CDS Pden_1806 NC_008686.1 1798892 1800031 R 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 complement(1798892..1800031) Paracoccus denitrificans PD1222 4580506 YP_915600.1 CDS Pden_1807 NC_008686.1 1800075 1802072 R PFAM: extracellular solute-binding protein, family 5; KEGG: rsp:RSP_0704 ABC peptide transporter, substrate binding protein; ABC transporter substrate-binding protein complement(1800075..1802072) Paracoccus denitrificans PD1222 4580507 YP_915601.1 CDS Pden_1808 NC_008686.1 1802128 1802658 R PFAM: cytochrome c, class I; KEGG: sil:SPO3538 cytochrome c552; cytochrome c, class I complement(1802128..1802658) Paracoccus denitrificans PD1222 4580508 YP_915602.1 CDS Pden_1809 NC_008686.1 1802822 1803709 D catalyzes the formation of phenylpyruvate from prephenate in phenylalanine biosynthesis; prephenate dehydratase 1802822..1803709 Paracoccus denitrificans PD1222 4580509 YP_915603.1 CDS Pden_1810 NC_008686.1 1803749 1804210 R KEGG: sit:TM1040_0171 conserved hypothetical protein; hypothetical protein complement(1803749..1804210) Paracoccus denitrificans PD1222 4580510 YP_915604.1 CDS Pden_1811 NC_008686.1 1804328 1806226 D PFAM: metallophosphoesterase; 5'-Nucleotidase domain protein; KEGG: sit:TM1040_1036 twin-arginine translocation pathway signal; 5'-nucleotidase 1804328..1806226 Paracoccus denitrificans PD1222 4580511 YP_915605.1 CDS Pden_1812 NC_008686.1 1806435 1807340 D PFAM: PfkB domain protein; KEGG: sil:SPO2060 kinase, PfkB family; ribokinase-like domain-containing protein 1806435..1807340 Paracoccus denitrificans PD1222 4580512 YP_915606.1 CDS Pden_1813 NC_008686.1 1807328 1808242 D PFAM: Indigoidine synthase A family protein; KEGG: rsp:RSP_2858 IndA involved in pigment biosynthesis; indigoidine synthase A family protein 1807328..1808242 Paracoccus denitrificans PD1222 4580513 YP_915607.1 CDS Pden_1814 NC_008686.1 1808239 1809294 R PFAM: Patatin; KEGG: jan:Jann_2313 patatin; patatin complement(1808239..1809294) Paracoccus denitrificans PD1222 4578526 YP_915608.1 CDS prfB NC_008686.1 1809473 1810681 R 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 complement(1809473..1810681) Paracoccus denitrificans PD1222 4578527 YP_915609.1 CDS Pden_1816 NC_008686.1 1810689 1813226 R 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 complement(1810689..1813226) Paracoccus denitrificans PD1222 4578528 YP_915610.1 CDS Pden_1817 NC_008686.1 1813297 1814532 R PFAM: cell wall hydrolase/autolysin; KEGG: sil:SPO2588 N-acetylmuramoyl-L-alanine amidase, family 3; N-acetylmuramoyl-L-alanine amidase complement(1813297..1814532) Paracoccus denitrificans PD1222 4578529 YP_915611.1 CDS Pden_1818 NC_008686.1 1814529 1815665 R PFAM: aminotransferase, class I and II; KEGG: rsp:RSP_2980 aspartate aminotransferase A; class I and II aminotransferase complement(1814529..1815665) Paracoccus denitrificans PD1222 4578530 YP_915612.1 CDS Pden_1819 NC_008686.1 1815801 1816553 D PFAM: DSBA oxidoreductase; KEGG: rde:RD1_2824 outer membrane protein; DSBA oxidoreductase 1815801..1816553 Paracoccus denitrificans PD1222 4578531 YP_915613.1 CDS ispG NC_008686.1 1816643 1817767 R 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 complement(1816643..1817767) Paracoccus denitrificans PD1222 4578532 YP_915614.1 CDS Pden_1821 NC_008686.1 1817894 1819114 R KEGG: rsp:RSP_2983 hypothetical protein; hypothetical protein complement(1817894..1819114) Paracoccus denitrificans PD1222 4578533 YP_915615.1 CDS Pden_1822 NC_008686.1 1819224 1820498 R catalyzes the formation of 5-aminolevulinate from succinyl-CoA and glycine; 5-aminolevulinate synthase complement(1819224..1820498) Paracoccus denitrificans PD1222 4578534 YP_915616.1 CDS Pden_1823 NC_008686.1 1820623 1822008 D PFAM: peptidase M20; peptidase dimerisation domain protein; KEGG: rsp:RSP_2986 hypothetical protein; hypothetical protein 1820623..1822008 Paracoccus denitrificans PD1222 4578535 YP_915617.1 CDS Pden_1824 NC_008686.1 1822158 1822733 D KEGG: rpa:RPA2196 hypothetical protein; hypothetical protein 1822158..1822733 Paracoccus denitrificans PD1222 4578536 YP_915618.1 CDS Pden_1825 NC_008686.1 1822871 1823380 R PFAM: transcription factor CarD; KEGG: rsp:RSP_2425 CarD-like transcriptional regulator; CarD family transcriptional regulator complement(1822871..1823380) Paracoccus denitrificans PD1222 4578537 YP_915619.1 CDS Pden_1826 NC_008686.1 1823834 1824172 R PFAM: 4Fe-4S ferredoxin, iron-sulfur binding domain protein; KEGG: sit:TM1040_0575 4Fe-4S ferredoxin, iron-sulfur binding; 4Fe-4S ferredoxin complement(1823834..1824172) Paracoccus denitrificans PD1222 4578538 YP_915620.1 CDS Pden_1827 NC_008686.1 1824335 1824604 R PFAM: RNA-binding S4 domain protein; KEGG: sil:SPO1418 S4 domain protein; RNA-binding S4 domain-containing protein complement(1824335..1824604) Paracoccus denitrificans PD1222 4578539 YP_915621.1 CDS Pden_1828 NC_008686.1 1824601 1827528 R PFAM: helicase domain protein; KEGG: rsp:RSP_2422 ATP-dependent helicase, MgpS; helicase complement(1824601..1827528) Paracoccus denitrificans PD1222 4578540 YP_915622.1 CDS Pden_1829 NC_008686.1 1827530 1828267 R PFAM: TPR repeat-containing protein; Tetratricopeptide TPR_2 repeat protein; SMART: Tetratricopeptide domain protein; KEGG: rsp:RSP_2421 hypothetical protein; hypothetical protein complement(1827530..1828267) Paracoccus denitrificans PD1222 4578541 YP_915623.1 CDS Pden_1830 NC_008686.1 1828317 1828601 D PFAM: Sterol-binding domain protein; KEGG: jan:Jann_3313 sterol-binding; sterol-binding domain-containing protein 1828317..1828601 Paracoccus denitrificans PD1222 4578542 YP_915624.1 CDS Pden_1831 NC_008686.1 1828605 1829549 D PFAM: alpha/beta hydrolase fold; KEGG: sil:SPO1414 hydrolase, alpha/beta fold family; alpha/beta hydrolase 1828605..1829549 Paracoccus denitrificans PD1222 4578543 YP_915625.1 CDS Pden_1832 NC_008686.1 1829638 1831500 D 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 1829638..1831500 Paracoccus denitrificans PD1222 4578544 YP_915626.1 CDS Pden_1833 NC_008686.1 1831685 1832866 D PFAM: peptidase M19, renal dipeptidase; KEGG: sit:TM1040_0564 peptidase M19, renal dipeptidase; peptidase M19 1831685..1832866 Paracoccus denitrificans PD1222 4581017 YP_915627.1 CDS Pden_1834 NC_008686.1 1832903 1833562 D 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 1832903..1833562 Paracoccus denitrificans PD1222 4581018 YP_915628.1 CDS Pden_1835 NC_008686.1 1833725 1834747 R PFAM: protein of unknown function DUF344; KEGG: rsp:RSP_0766 hypothetical protein; hypothetical protein complement(1833725..1834747) Paracoccus denitrificans PD1222 4581019 YP_915629.1 CDS Pden_1836 NC_008686.1 1834978 1836948 D decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling; DNA topoisomerase IV subunit B 1834978..1836948 Paracoccus denitrificans PD1222 4581020 YP_915630.1 CDS Pden_1837 NC_008686.1 1836945 1837280 D PFAM: protein of unknown function UPF0060; KEGG: mag:amb3269 hypothetical protein; hypothetical protein 1836945..1837280 Paracoccus denitrificans PD1222 4581021 YP_915631.1 CDS Pden_1838 NC_008686.1 1837363 1837866 R PFAM: phosphoesterase, PA-phosphatase related; KEGG: cch:Cag_0961 phosphoesterase, PA-phosphatase related; PA-phosphatase-like phosphoesterase complement(1837363..1837866) Paracoccus denitrificans PD1222 4581022 YP_915632.1 CDS Pden_1839 NC_008686.1 1837863 1838525 R PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rsp:RSP_0776 ABC lipoprotein efflux transporter, ATPase subunit, LolD; ABC transporter complement(1837863..1838525) Paracoccus denitrificans PD1222 4581023 YP_915633.1 CDS Pden_1840 NC_008686.1 1838518 1839819 R 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 complement(1838518..1839819) Paracoccus denitrificans PD1222 4581024 YP_915634.1 CDS Pden_1841 NC_008686.1 1839899 1840057 R 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 complement(1839899..1840057) Paracoccus denitrificans PD1222 4581025 YP_915635.1 CDS Pden_1842 NC_008686.1 1840067 1842265 R 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 complement(1840067..1842265) Paracoccus denitrificans PD1222 4581026 YP_915636.1 CDS Pden_1843 NC_008686.1 1842267 1842731 R PFAM: FixH family protein; KEGG: rsp:RSP_0691 RdxH; nitrogen fixation protein FixH complement(1842267..1842731) Paracoccus denitrificans PD1222 4581027 YP_915637.1 CDS Pden_1844 NC_008686.1 1842731 1844188 R TIGRFAM: 4Fe-4S ferredoxin, iron-sulfur binding domain protein; KEGG: rsp:RSP_0692 iron-sulfur cluster-binding protein; 4Fe-4S ferredoxin complement(1842731..1844188) Paracoccus denitrificans PD1222 4581028 YP_915638.1 CDS Pden_1845 NC_008686.1 1844464 1845513 R 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 complement(1844464..1845513) Paracoccus denitrificans PD1222 4581029 YP_915639.1 CDS Pden_1846 NC_008686.1 1845513 1845701 R PFAM: Cbb3-type cytochrome oxidase component; KEGG: sit:TM1040_2543 Cbb3-type cytochrome oxidase component; cbb3-type cytochrome oxidase subunit complement(1845513..1845701) Paracoccus denitrificans PD1222 4581030 YP_915640.1 CDS Pden_1847 NC_008686.1 1845710 1846435 R CcoO; FixO; cbb3-type cytochrome c oxidase subunit II complement(1845710..1846435) Paracoccus denitrificans PD1222 4581031 YP_915641.1 CDS Pden_1848 NC_008686.1 1846445 1848064 R CcoN; FixN; cbb3-type cytochrome c oxidase subunit I complement(1846445..1848064) Paracoccus denitrificans PD1222 4581032 YP_915642.1 CDS Pden_1849 NC_008686.1 1848315 1849148 D PFAM: UspA domain protein; KEGG: sil:SPO3527 universal stress protein family protein; UspA domain-containing protein 1848315..1849148 Paracoccus denitrificans PD1222 4581033 YP_915643.1 CDS Pden_1850 NC_008686.1 1849236 1849871 R PFAM: cyclic nucleotide-binding; regulatory protein, Crp; KEGG: rde:RD1_1268 transcriptional activator protein FnrL; Crp/Fnr family transcriptional regulator complement(1849236..1849871) Paracoccus denitrificans PD1222 4581034 YP_915644.1 CDS Pden_1851 NC_008686.1 1850034 1851389 D catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III; coproporphyrinogen III oxidase 1850034..1851389 Paracoccus denitrificans PD1222 4581035 YP_915645.1 CDS Pden_1852 NC_008686.1 1851392 1852327 R TIGRFAM: cation diffusion facilitator family transporter; PFAM: cation efflux protein; KEGG: sil:SPO1387 cation efflux system protein; cation diffusion facilitator family transporter complement(1851392..1852327) Paracoccus denitrificans PD1222 4581036 YP_915646.1 CDS Pden_1853 NC_008686.1 1852399 1855221 R 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 complement(1852399..1855221) Paracoccus denitrificans PD1222 4579112 YP_915647.1 CDS Pden_1854 NC_008686.1 1855405 1855593 R KEGG: rsp:RSP_1027 hypothetical protein; hypothetical protein complement(1855405..1855593) Paracoccus denitrificans PD1222 4579113 YP_915648.1 CDS Pden_1855 NC_008686.1 1855663 1856622 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sil:SPO3847 ABC transporter, ATP-binding protein; ABC transporter 1855663..1856622 Paracoccus denitrificans PD1222 4579114 YP_915649.1 CDS Pden_1856 NC_008686.1 1856610 1856984 R PFAM: histidine triad (HIT) protein; KEGG: rsp:RSP_1029 possible histidine triad (HIT) protein; histidine triad (HIT) protein complement(1856610..1856984) Paracoccus denitrificans PD1222 4579115 YP_915650.1 CDS Pden_1857 NC_008686.1 1856995 1858584 R PFAM: glycosyl transferase, family 14; KEGG: sil:SPO3319 EpsK domain protein; glycosyl transferase family protein complement(1856995..1858584) Paracoccus denitrificans PD1222 4579116 YP_915651.1 CDS Pden_1858 NC_008686.1 1858734 1859552 D KEGG: sit:TM1040_2487 conserved hypothetical protein; hypothetical protein 1858734..1859552 Paracoccus denitrificans PD1222 4579117 YP_915652.1 CDS rpmF NC_008686.1 1859826 1860032 D some L32 proteins have zinc finger motifs consisting of CXXC while others do not; 50S ribosomal protein L32 1859826..1860032 Paracoccus denitrificans PD1222 4579118 YP_915653.1 CDS Pden_1860 NC_008686.1 1860050 1861162 D 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 1860050..1861162 Paracoccus denitrificans PD1222 4579119 YP_915654.1 CDS Pden_1861 NC_008686.1 1861162 1862133 D 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 1861162..1862133 Paracoccus denitrificans PD1222 4579120 YP_915655.1 CDS Pden_1862 NC_008686.1 1862142 1862417 R PFAM: zinc finger, DksA/TraR C4-type; KEGG: sil:SPO1411 C4-type zinc finger protein, DksA/TraR family; hypothetical protein complement(1862142..1862417) Paracoccus denitrificans PD1222 4579121 YP_915656.1 CDS ihfA NC_008686.1 1862630 1862938 D 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 1862630..1862938 Paracoccus denitrificans PD1222 4579122 YP_915657.1 CDS Pden_1864 NC_008686.1 1862938 1863543 D PFAM: regulatory protein, MerR; KEGG: sil:SPO2496 transcriptional regulator, MerR family; MerR family transcriptional regulator 1862938..1863543 Paracoccus denitrificans PD1222 4579123 YP_915658.1 CDS Pden_1865 NC_008686.1 1863788 1864873 D Catalyzes the deamination of dCTP to form dUTP; 2'-deoxycytidine 5'-triphosphate deaminase 1863788..1864873 Paracoccus denitrificans PD1222 4579124 YP_915659.1 CDS Pden_1866 NC_008686.1 1865120 1865785 R 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 complement(1865120..1865785) Paracoccus denitrificans PD1222 4579125 YP_915660.1 CDS Pden_1867 NC_008686.1 1865782 1866636 R PFAM: chromosome segregation and condensation protein ScpA; KEGG: rde:RD1_3162 hypothetical protein; chromosome segregation and condensation protein ScpA complement(1865782..1866636) Paracoccus denitrificans PD1222 4579126 YP_915661.1 CDS Pden_1868 NC_008686.1 1866682 1867668 R PFAM: glycoside hydrolase, family 3 domain protein; KEGG: rsp:RSP_2941 glycoside hydrolase; beta-N-acetylhexosaminidase complement(1866682..1867668) Paracoccus denitrificans PD1222 4579127 YP_915662.1 CDS Pden_1869 NC_008686.1 1867678 1868847 R PFAM: Sporulation domain protein; KEGG: rde:RD1_3164 hypothetical protein; sporulation domain-containing protein complement(1867678..1868847) Paracoccus denitrificans PD1222 4579128 YP_915663.1 CDS argS NC_008686.1 1868916 1870661 R 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 complement(1868916..1870661) Paracoccus denitrificans PD1222 4579129 YP_915664.1 CDS Pden_1873 NC_008686.1 1874653 1875819 D catalyzes the formation of S-adenosylmethionine from methionine and ATP; methionine adenosyltransferase; S-adenosylmethionine synthetase 1874653..1875819 Paracoccus denitrificans PD1222 4579130 YP_915665.1 CDS Pden_1874 NC_008686.1 1875928 1876554 R PFAM: heat shock protein DnaJ domain protein; KEGG: rsp:RSP_1978 molecular chaperone, DnaJ family; molecular chaperone DnaJ complement(1875928..1876554) Paracoccus denitrificans PD1222 4580533 YP_915666.1 CDS Pden_1875 NC_008686.1 1876624 1876875 D PFAM: BolA family protein; KEGG: sil:SPO2849 BolA protein, truncation; BolA family protein 1876624..1876875 Paracoccus denitrificans PD1222 4580534 YP_915667.1 CDS glpX NC_008686.1 1876957 1877922 D type II fructose 1,6-bisphosphatae; in Escherichia coli this protein forms a dimer and binds manganese; fructose 1,6-bisphosphatase II 1876957..1877922 Paracoccus denitrificans PD1222 4580535 YP_915668.1 CDS Pden_1877 NC_008686.1 1877974 1879716 D 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 1877974..1879716 Paracoccus denitrificans PD1222 4580536 YP_915669.1 CDS Pden_1878 NC_008686.1 1880002 1880325 D hypothetical protein 1880002..1880325 Paracoccus denitrificans PD1222 4580537 YP_915670.1 CDS carB NC_008686.1 1880355 1883687 R 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 complement(1880355..1883687) Paracoccus denitrificans PD1222 4580538 YP_915671.1 CDS Pden_1880 NC_008686.1 1883878 1884402 R PFAM: Uncharacterized protein UPF0114; KEGG: ccr:CC1036 hypothetical protein; hypothetical protein complement(1883878..1884402) Paracoccus denitrificans PD1222 4580539 YP_915672.1 CDS Pden_1881 NC_008686.1 1884716 1885078 R PFAM: protein of unknown function DUF710; KEGG: rde:RD1_2980 hypothetical protein; hypothetical protein complement(1884716..1885078) Paracoccus denitrificans PD1222 4580540 YP_915673.1 CDS Pden_1882 NC_008686.1 1885082 1885717 R KEGG: rde:RD1_2981 hypothetical protein; hypothetical protein complement(1885082..1885717) Paracoccus denitrificans PD1222 4580541 YP_915674.1 CDS hisB NC_008686.1 1885895 1886482 D 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 1885895..1886482 Paracoccus denitrificans PD1222 4580542 YP_915675.1 CDS hisH NC_008686.1 1886482 1887111 D 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 1886482..1887111 Paracoccus denitrificans PD1222 4580543 YP_915676.1 CDS Pden_1885 NC_008686.1 1887211 1887597 R KEGG: rsp:RSP_2244 hypothetical protein; hypothetical protein complement(1887211..1887597) Paracoccus denitrificans PD1222 4580544 YP_915677.1 CDS Pden_1886 NC_008686.1 1887757 1888473 D 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 1887757..1888473 Paracoccus denitrificans PD1222 4580545 YP_915678.1 CDS Pden_1887 NC_008686.1 1888501 1889262 D 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 1888501..1889262 Paracoccus denitrificans PD1222 4580546 YP_915679.1 CDS hisE NC_008686.1 1889259 1889585 D catalyzes the formation of 1-(5-phosphoribosyl)-AMP from 1-(5-phosphoribolsyl)-ATP in histidine biosynthesis; phosphoribosyl-ATP pyrophosphatase 1889259..1889585 Paracoccus denitrificans PD1222 4580547 YP_915680.1 CDS Pden_1889 NC_008686.1 1889590 1890090 D PFAM: MgtC/SapB transporter; KEGG: mes:Meso_3446 MgtC/SapB transporter; MgtC/SapB transporter 1889590..1890090 Paracoccus denitrificans PD1222 4580548 YP_915681.1 CDS Pden_1890 NC_008686.1 1890087 1891292 R TIGRFAM: ribonuclease D; PFAM: HRDC domain protein; 3'-5' exonuclease; KEGG: rsp:RSP_1971 ribonuclease D; ribonuclease D complement(1890087..1891292) Paracoccus denitrificans PD1222 4580549 YP_915682.1 CDS tgt NC_008686.1 1891381 1892523 R Exchanges the guanine residue with 7-aminomethyl-7-deazaguanine in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr); queuine tRNA-ribosyltransferase complement(1891381..1892523) Paracoccus denitrificans PD1222 4580550 YP_915683.1 CDS Pden_1892 NC_008686.1 1892555 1893310 R KEGG: rsp:RSP_2618 hemolysin; hemolysin complement(1892555..1893310) Paracoccus denitrificans PD1222 4580551 YP_915684.1 CDS Pden_1893 NC_008686.1 1893409 1893801 D KEGG: sme:SMc00117 peptide methionine sulfoxide reductase; TIGRFAM: methionine-R-sulfoxide reductase; PFAM: Methionine sulfoxide reductase B; methionine-R-sulfoxide reductase 1893409..1893801 Paracoccus denitrificans PD1222 4580552 YP_915685.1 CDS Pden_1894 NC_008686.1 1893837 1894292 R KEGG: rsp:RSP_2616 hypothetical protein; hypothetical protein complement(1893837..1894292) Paracoccus denitrificans PD1222 4581114 YP_915686.1 CDS Pden_1895 NC_008686.1 1894407 1894934 D PFAM: protein of unknown function DUF177; KEGG: rsp:RSP_2615 hypothetical protein; hypothetical protein 1894407..1894934 Paracoccus denitrificans PD1222 4581115 YP_915687.1 CDS Pden_1896 NC_008686.1 1894936 1896588 R catalyzes the oxidation of choline to betaine aldehyde and betain aldehyde to glycine betaine; choline dehydrogenase complement(1894936..1896588) Paracoccus denitrificans PD1222 4581116 YP_915688.1 CDS Pden_1897 NC_008686.1 1896670 1898115 R catalyzes the formation of betaine from betaine aldehyde; betaine aldehyde dehydrogenase complement(1896670..1898115) Paracoccus denitrificans PD1222 4581117 YP_915689.1 CDS Pden_1898 NC_008686.1 1898112 1898681 R HTH-type; bet1; Repressor involved in choline regulation of the bet genes; transcriptional regulator BetI complement(1898112..1898681) Paracoccus denitrificans PD1222 4581118 YP_915690.1 CDS Pden_1899 NC_008686.1 1898812 1899765 D 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 1898812..1899765 Paracoccus denitrificans PD1222 4581119 YP_915691.1 CDS Pden_1900 NC_008686.1 1899930 1900781 D 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 1899930..1900781 Paracoccus denitrificans PD1222 4581120 YP_915692.1 CDS Pden_1901 NC_008686.1 1900774 1901832 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rsp:RSP_2179 ABC glycine betaine/L-proline tranporter, ATPase subunit, ProV; ABC transporter 1900774..1901832 Paracoccus denitrificans PD1222 4581121 YP_915693.1 CDS Pden_1902 NC_008686.1 1901854 1902780 R PFAM: protein of unknown function DUF6, transmembrane; KEGG: rsp:RSP_0654 possible transporter, DMT superfamily; hypothetical protein complement(1901854..1902780) Paracoccus denitrificans PD1222 4581122 YP_915694.1 CDS Pden_1903 NC_008686.1 1902808 1903407 R PFAM: Lysine exporter protein (LYSE/YGGA); KEGG: rru:Rru_A0657 lysine exporter protein (LysE/YggA); lysine exporter protein LysE/YggA complement(1902808..1903407) Paracoccus denitrificans PD1222 4581123 YP_915695.1 CDS Pden_1904 NC_008686.1 1903489 1904358 D 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 1903489..1904358 Paracoccus denitrificans PD1222 4581124 YP_915696.1 CDS Pden_1905 NC_008686.1 1904398 1905138 R PFAM: protein of unknown function DUF28; KEGG: rsp:RSP_0655 hypothetical protein; hypothetical protein complement(1904398..1905138) Paracoccus denitrificans PD1222 4581125 YP_915697.1 CDS Pden_1906 NC_008686.1 1905203 1905478 R KEGG: mes:Meso_1983 hypothetical protein; hypothetical protein complement(1905203..1905478) Paracoccus denitrificans PD1222 4581126 YP_915698.1 CDS Pden_1907 NC_008686.1 1905465 1905674 R KEGG: rsp:RSP_2137 hypothetical protein; hypothetical protein complement(1905465..1905674) Paracoccus denitrificans PD1222 4581127 YP_915699.1 CDS fumC NC_008686.1 1905677 1907074 R 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 complement(1905677..1907074) Paracoccus denitrificans PD1222 4581128 YP_915700.1 CDS Pden_1909 NC_008686.1 1907167 1907628 R PFAM: protein of unknown function DUF1321; KEGG: rsp:RSP_2139 hypothetical protein; hypothetical protein complement(1907167..1907628) Paracoccus denitrificans PD1222 4581129 YP_915701.1 CDS Pden_1911 NC_008686.1 1908117 1908446 R KEGG: mes:Meso_3101 PRC-barrel; hypothetical protein complement(1908117..1908446) Paracoccus denitrificans PD1222 4581130 YP_915702.1 CDS anmK NC_008686.1 1909112 1910221 R 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 complement(1909112..1910221) Paracoccus denitrificans PD1222 4581131 YP_915703.1 CDS Pden_1913 NC_008686.1 1910277 1911521 D 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 1910277..1911521 Paracoccus denitrificans PD1222 4581132 YP_915704.1 CDS Pden_1914 NC_008686.1 1911566 1912147 R KEGG: mlo:mll5005 hypothetical protein; hypothetical protein complement(1911566..1912147) Paracoccus denitrificans PD1222 4580573 YP_915705.1 CDS Pden_1915 NC_008686.1 1912182 1912637 R PFAM: protein of unknown function DUF188; KEGG: rde:RD1_0321 YaiI/YqxD family protein; hypothetical protein complement(1912182..1912637) Paracoccus denitrificans PD1222 4580574 YP_915706.1 CDS Pden_1916 NC_008686.1 1912702 1913295 R 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 complement(1912702..1913295) Paracoccus denitrificans PD1222 4580575 YP_915707.1 CDS Pden_1917 NC_008686.1 1913285 1913794 R 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 complement(1913285..1913794) Paracoccus denitrificans PD1222 4580576 YP_915708.1 CDS pgk NC_008686.1 1913972 1915168 D Converts 3-phospho-D-glycerate to 3-phospho-D-glyceroyl phosphate during the glycolysis pathway; phosphoglycerate kinase 1913972..1915168 Paracoccus denitrificans PD1222 4580577 YP_915709.1 CDS Pden_1919 NC_008686.1 1915409 1915624 R hypothetical protein complement(1915409..1915624) Paracoccus denitrificans PD1222 4580578 YP_915710.1 CDS Pden_1920 NC_008686.1 1915751 1916680 D catalyzes the formation of glycerone phosphate and D-glyceraldehyde 3-phosphate from D-fructose 1,6-bisphosphate; fructose-bisphosphate aldolase 1915751..1916680 Paracoccus denitrificans PD1222 4580579 YP_915711.1 CDS Pden_1921 NC_008686.1 1916810 1917850 D 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 1916810..1917850 Paracoccus denitrificans PD1222 4580580 YP_915712.1 CDS Pden_1922 NC_008686.1 1917907 1918275 R KEGG: rsp:RSP_2037 hypothetical protein; hypothetical protein complement(1917907..1918275) Paracoccus denitrificans PD1222 4580581 YP_915713.1 CDS hisG NC_008686.1 1918330 1919007 R 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 complement(1918330..1919007) Paracoccus denitrificans PD1222 4580582 YP_915714.1 CDS hisZ NC_008686.1 1919004 1920086 R May allow the feedback regulation of ATP phosphoribosyltransferase activity by histidine; ATP phosphoribosyltransferase complement(1919004..1920086) Paracoccus denitrificans PD1222 4580583 YP_915715.1 CDS hisS NC_008686.1 1920083 1921567 R 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 complement(1920083..1921567) Paracoccus denitrificans PD1222 4580584 YP_915716.1 CDS Pden_1926 NC_008686.1 1921616 1921831 D KEGG: rde:RD1_4066 hypothetical protein; hypothetical protein 1921616..1921831 Paracoccus denitrificans PD1222 4580585 YP_915717.1 CDS Pden_1927 NC_008686.1 1921901 1922392 R KEGG: rsp:RSP_1985 hypothetical protein; hypothetical protein complement(1921901..1922392) Paracoccus denitrificans PD1222 4580586 YP_915718.1 CDS Pden_1928 NC_008686.1 1922493 1923002 R PFAM: cell wall hydrolase, SleB; KEGG: rsp:RSP_2496 hypothetical protein; cell wall hydrolase SleB complement(1922493..1923002) Paracoccus denitrificans PD1222 4580587 YP_915719.1 CDS gatB NC_008686.1 1923126 1924640 R 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 complement(1923126..1924640) Paracoccus denitrificans PD1222 4580588 YP_915720.1 CDS Pden_1931 NC_008686.1 1925055 1928345 R KEGG: rsp:RSP_6052 hypothetical protein; hypothetical protein complement(1925055..1928345) Paracoccus denitrificans PD1222 4580589 YP_915721.1 CDS Pden_1932 NC_008686.1 1928360 1929205 D PFAM: protein of unknown function DUF541; KEGG: rsp:RSP_2430 hypothetical protein; hypothetical protein 1928360..1929205 Paracoccus denitrificans PD1222 4580590 YP_915722.1 CDS Pden_1933 NC_008686.1 1929274 1930560 R 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 complement(1929274..1930560) Paracoccus denitrificans PD1222 4580591 YP_915723.1 CDS Pden_1934 NC_008686.1 1930887 1931267 R KEGG: rsp:RSP_7183 translation initiation factor 2, gamma subunit, GTPase; translation initiation factor 2 subunit gamma, GTPase complement(1930887..1931267) Paracoccus denitrificans PD1222 4580592 YP_915724.1 CDS metH NC_008686.1 1931703 1935455 R 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 complement(1931703..1935455) Paracoccus denitrificans PD1222 4581057 YP_915725.1 CDS lipB NC_008686.1 1935600 1936256 D lipoyl-[acyl-carrier protein]-protein-N-lipoyltransferse; lipoate-protein ligase B; transfers lipoate to apolipoproteins; involved in lipoate metabolism; lipoyltransferase 1935600..1936256 Paracoccus denitrificans PD1222 4581058 YP_915726.1 CDS Pden_1937 NC_008686.1 1936399 1936866 D PFAM: cytochrome c, class I; KEGG: sil:SPO0130 cytochrome c family protein; cytochrome c, class I 1936399..1936866 Paracoccus denitrificans PD1222 4581059 YP_915727.1 CDS Pden_1938 NC_008686.1 1937038 1938714 D PFAM: cytochrome c oxidase, subunit I; KEGG: rsp:RSP_1877 cytochrome c oxidase, aa3 type, subunit I; cytochrome-c oxidase 1937038..1938714 Paracoccus denitrificans PD1222 4581060 YP_915728.1 CDS Pden_1939 NC_008686.1 1938734 1939228 D KEGG: rsp:RSP_1876 hypothetical protein; hypothetical protein 1938734..1939228 Paracoccus denitrificans PD1222 4581061 YP_915729.1 CDS Pden_1940 NC_008686.1 1939823 1942315 R 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 complement(1939823..1942315) Paracoccus denitrificans PD1222 4581062 YP_915730.1 CDS Pden_1941 NC_008686.1 1942478 1943488 R 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 complement(1942478..1943488) Paracoccus denitrificans PD1222 4581063 YP_915731.1 CDS Pden_1942 NC_008686.1 1943580 1944182 D PFAM: protein of unknown function DUF1058; KEGG: rsp:RSP_2312 hypothetical protein; hypothetical protein 1943580..1944182 Paracoccus denitrificans PD1222 4581064 YP_915732.1 CDS Pden_1943 NC_008686.1 1944200 1945057 R KEGG: syw:SYNW2410 hypothetical protein; hypothetical protein complement(1944200..1945057) Paracoccus denitrificans PD1222 4581065 YP_915733.1 CDS Pden_1944 NC_008686.1 1945211 1947247 R PFAM: peptidase M3A and M3B, thimet/oligopeptidase F; KEGG: rsp:RSP_0596 peptidyl-dipeptidase; peptidyl-dipeptidase Dcp complement(1945211..1947247) Paracoccus denitrificans PD1222 4581066 YP_915734.1 CDS Pden_1945 NC_008686.1 1947281 1948333 R 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 complement(1947281..1948333) Paracoccus denitrificans PD1222 4581067 YP_915735.1 CDS Pden_1946 NC_008686.1 1948338 1948799 R KEGG: sil:SPO0409 deoxyuridine 5'-triphosphate nucleotidohydrolase; TIGRFAM: deoxyuridine 5'-triphosphate nucleotidohydrolase Dut; PFAM: deoxyUTP pyrophosphatase; deoxyuridine 5'-triphosphate nucleotidohydrolase Dut complement(1948338..1948799) Paracoccus denitrificans PD1222 4581068 YP_915736.1 CDS Pden_1948 NC_008686.1 1950168 1951043 D KEGG: sit:TM1040_0184 conserved hypothetical protein; hypothetical protein 1950168..1951043 Paracoccus denitrificans PD1222 4581069 YP_915737.1 CDS Pden_1949 NC_008686.1 1951059 1952348 R KEGG: rsp:RSP_3072 L-sorbosone dehydrogenase; L-sorbosone dehydrogenase complement(1951059..1952348) Paracoccus denitrificans PD1222 4581070 YP_915738.1 CDS pgi NC_008686.1 1952489 1954090 R 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 complement(1952489..1954090) Paracoccus denitrificans PD1222 4581071 YP_915739.1 CDS Pden_1951 NC_008686.1 1954092 1954766 R TIGRFAM: 6-phosphogluconolactonase; KEGG: rsp:RSP_2735 6-phosphogluconolactonase; 6-phosphogluconolactonase complement(1954092..1954766) Paracoccus denitrificans PD1222 4581072 YP_915740.1 CDS Pden_1952 NC_008686.1 1954763 1956265 R catalyzes the formation of D-glucono-1,5-lactone 6-phosphate from D-glucose 6-phosphate; glucose-6-phosphate 1-dehydrogenase complement(1954763..1956265) Paracoccus denitrificans PD1222 4581073 YP_915741.1 CDS Pden_1953 NC_008686.1 1956291 1956884 R KEGG: jan:Jann_2688 hypothetical protein; hypothetical protein complement(1956291..1956884) Paracoccus denitrificans PD1222 4581074 YP_915742.1 CDS Pden_1954 NC_008686.1 1956881 1958077 R KEGG: rsp:RSP_2647 predicted SAM-dependent methyltransferase; SAM-dependent methyltransferase complement(1956881..1958077) Paracoccus denitrificans PD1222 4581075 YP_915743.1 CDS Pden_1955 NC_008686.1 1958193 1959995 D catalyzes the formation of 2-dehydro-3-deoxy-6-phospho-D-gluconate from 6-phospho-D-gluconate; phosphogluconate dehydratase 1958193..1959995 Paracoccus denitrificans PD1222 4578721 YP_915744.1 CDS Pden_1956 NC_008686.1 1960034 1960564 R TIGRFAM: PAS sensor protein; PFAM: PAS fold domain protein; KEGG: mca:MCA2070 sensory box protein; PAS/PAC sensor protein complement(1960034..1960564) Paracoccus denitrificans PD1222 4578722 YP_915745.1 CDS Pden_1957 NC_008686.1 1960643 1961101 R PFAM: low molecular weight phosphotyrosine protein phosphatase; KEGG: rsp:RSP_0630 hypothetical protein; protein tyrosine phosphatase complement(1960643..1961101) Paracoccus denitrificans PD1222 4578723 YP_915746.1 CDS Pden_1958 NC_008686.1 1961105 1961593 R PFAM: Uncharacterized conserved protein UCP032146; KEGG: rde:RD1_1069 hypothetical protein; hypothetical protein complement(1961105..1961593) Paracoccus denitrificans PD1222 4578724 YP_915747.1 CDS hisD NC_008686.1 1961590 1962900 R catalyzes the oxidation of L-histidinol to L-histidinaldehyde and then to L-histidine in histidine biosynthesis; functions as a dimer; histidinol dehydrogenase complement(1961590..1962900) Paracoccus denitrificans PD1222 4578725 YP_915748.1 CDS Pden_1960 NC_008686.1 1963111 1963590 R KEGG: sit:TM1040_3566 conserved hypothetical protein; hypothetical protein complement(1963111..1963590) Paracoccus denitrificans PD1222 4578726 YP_915749.1 CDS Pden_1961 NC_008686.1 1963583 1964863 R 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 complement(1963583..1964863) Paracoccus denitrificans PD1222 4578727 YP_915750.1 CDS Pden_1962 NC_008686.1 1965483 1965734 D KEGG: mca:MCA2639 hypothetical protein; hypothetical protein 1965483..1965734 Paracoccus denitrificans PD1222 4578728 YP_915751.1 CDS Pden_1963 NC_008686.1 1965805 1966104 R 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 complement(1965805..1966104) Paracoccus denitrificans PD1222 4578729 YP_915752.1 CDS Pden_1964 NC_008686.1 1966566 1967483 R KEGG: shm:Shewmr7_0348 hypothetical protein; hypothetical protein complement(1966566..1967483) Paracoccus denitrificans PD1222 4578730 YP_915753.1 CDS Pden_1965 NC_008686.1 1967473 1968294 R KEGG: mes:Meso_4610 hypothetical protein; hypothetical protein complement(1967473..1968294) Paracoccus denitrificans PD1222 4578731 YP_915754.1 CDS Pden_1966 NC_008686.1 1968478 1968774 R hypothetical protein complement(1968478..1968774) Paracoccus denitrificans PD1222 4578732 YP_915755.1 CDS Pden_1967 NC_008686.1 1968801 1969079 D hypothetical protein 1968801..1969079 Paracoccus denitrificans PD1222 4578733 YP_915756.1 CDS Pden_1968 NC_008686.1 1969222 1969740 R hypothetical protein complement(1969222..1969740) Paracoccus denitrificans PD1222 4578734 YP_915757.1 CDS Pden_1969 NC_008686.1 1969844 1970968 R KEGG: bxe:Bxe_A0083 hypothetical protein; hypothetical protein complement(1969844..1970968) Paracoccus denitrificans PD1222 4578735 YP_915758.1 CDS Pden_1970 NC_008686.1 1970958 1971539 R KEGG: psp:PSPPH_0608 pancortin-3; pancortin-3 complement(1970958..1971539) Paracoccus denitrificans PD1222 4578736 YP_915759.1 CDS Pden_1971 NC_008686.1 1971910 1972491 D KEGG: bja:blr1827 transposase; hypothetical protein 1971910..1972491 Paracoccus denitrificans PD1222 4578737 YP_915760.1 CDS Pden_1972 NC_008686.1 1972763 1974499 D PFAM: Resolvase, N-terminal domain; Recombinase; KEGG: nha:Nham_3864 recombinase; recombinase 1972763..1974499 Paracoccus denitrificans PD1222 4578738 YP_915761.1 CDS Pden_1973 NC_008686.1 1979926 1980246 D KEGG: rsp:RSP_3837 hypothetical protein; hypothetical protein 1979926..1980246 Paracoccus denitrificans PD1222 4578739 YP_915762.1 CDS Pden_1974 NC_008686.1 1980668 1980853 D KEGG: mag:amb1768 Mu-like prophage major head subunit gpT; Mu-like prophage major head subunit gpT 1980668..1980853 Paracoccus denitrificans PD1222 4578740 YP_915763.1 CDS Pden_1975 NC_008686.1 1980891 1981145 R hypothetical protein complement(1980891..1981145) Paracoccus denitrificans PD1222 4581133 YP_915764.1 CDS Pden_1976 NC_008686.1 1981241 1981540 D hypothetical protein 1981241..1981540 Paracoccus denitrificans PD1222 4581134 YP_915765.1 CDS Pden_1977 NC_008686.1 1981544 1981885 D hypothetical protein 1981544..1981885 Paracoccus denitrificans PD1222 4581135 YP_915766.1 CDS Pden_1978 NC_008686.1 1982268 1983287 D PFAM: regulatory protein, LacI; periplasmic binding protein/LacI transcriptional regulator; KEGG: rsp:RSP_1663 transcriptional regulator, LacI family; periplasmic binding protein/LacI transcriptional regulator 1982268..1983287 Paracoccus denitrificans PD1222 4581136 YP_915767.1 CDS Pden_1979 NC_008686.1 1983453 1984283 R TIGRFAM: methionine aminopeptidase, type I; PFAM: peptidase M24; KEGG: rsp:RSP_0923 methionine aminopeptidase, subfamily 1; methionine aminopeptidase complement(1983453..1984283) Paracoccus denitrificans PD1222 4581137 YP_915768.1 CDS Pden_1980 NC_008686.1 1984370 1985110 D PFAM: molybdopterin binding domain; KEGG: sit:TM1040_2467 molybdopterin binding domain; molybdopterin binding domain-containing protein 1984370..1985110 Paracoccus denitrificans PD1222 4581138 YP_915769.1 CDS Pden_1981 NC_008686.1 1985107 1985826 D PFAM: GCN5-related N-acetyltransferase; KEGG: rsp:RSP_0925 acetyl transferase; N-acetyltransferase 1985107..1985826 Paracoccus denitrificans PD1222 4581139 YP_915770.1 CDS Pden_1982 NC_008686.1 1985841 1986227 R KEGG: sit:TM1040_2681 conserved hypothetical protein; hypothetical protein complement(1985841..1986227) Paracoccus denitrificans PD1222 4581140 YP_915771.1 CDS Pden_1983 NC_008686.1 1986242 1987042 R KEGG: sil:SPO3814 hypothetical protein; hypothetical protein complement(1986242..1987042) Paracoccus denitrificans PD1222 4581141 YP_915772.1 CDS Pden_1984 NC_008686.1 1987039 1988772 R catalyzes the dehydration of 2,3-dihydroxy-3-methylbutanoate to 3-methyl-2-oxobutanoate in valine and isoleucine biosynthesis; dihydroxy-acid dehydratase complement(1987039..1988772) Paracoccus denitrificans PD1222 4581142 YP_915773.1 CDS Pden_1985 NC_008686.1 1988851 1989174 R PFAM: transcriptional coactivator/pterin dehydratase; KEGG: mca:MCA0497 pterin-4-alpha-carbinolamine dehydratase; transcriptional coactivator/pterin dehydratase complement(1988851..1989174) Paracoccus denitrificans PD1222 4581143 YP_915774.1 CDS Pden_1986 NC_008686.1 1989186 1990613 R PFAM: phospholipase D/Transphosphatidylase; KEGG: rba:RB9533 cardiolipin synthase; phospholipase D/transphosphatidylase complement(1989186..1990613) Paracoccus denitrificans PD1222 4581144 YP_915775.1 CDS Pden_1987 NC_008686.1 1990702 1991643 D 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 1990702..1991643 Paracoccus denitrificans PD1222 4581145 YP_915776.1 CDS Pden_1988 NC_008686.1 1991660 1992928 D KEGG: rsp:RSP_0930 folylpolyglutamate synthetase; TIGRFAM: FolC bifunctional protein; PFAM: Mur ligase, middle domain protein; bifunctional folylpolyglutamate synthase/dihydrofolate synthase 1991660..1992928 Paracoccus denitrificans PD1222 4581146 YP_915777.1 CDS Pden_1989 NC_008686.1 1992946 1994052 R PFAM: AFG1-family ATPase; KEGG: rsp:RSP_1349 hypothetical protein; AFG1 family ATPase complement(1992946..1994052) Paracoccus denitrificans PD1222 4581147 YP_915778.1 CDS Pden_1990 NC_008686.1 1994137 1994742 R KEGG: jan:Jann_2690 hypothetical protein; hypothetical protein complement(1994137..1994742) Paracoccus denitrificans PD1222 4581148 YP_915779.1 CDS Pden_1991 NC_008686.1 1994943 1996325 D PFAM: aldehyde dehydrogenase; KEGG: rme:Rmet_0158 aldehyde dehydrogenase; aldehyde dehydrogenase 1994943..1996325 Paracoccus denitrificans PD1222 4581149 YP_915780.1 CDS Pden_1992 NC_008686.1 1996322 1997632 R PFAM: General substrate transporter; major facilitator superfamily MFS_1; KEGG: atc:AGR_C_4107 hypothetical protein; major facilitator superfamily transporter complement(1996322..1997632) Paracoccus denitrificans PD1222 4581150 YP_915781.1 CDS Pden_1993 NC_008686.1 1997908 1999521 D KEGG: ade:Adeh_0560 hypothetical protein; hypothetical protein 1997908..1999521 Paracoccus denitrificans PD1222 4581151 YP_915782.1 CDS Pden_1994 NC_008686.1 1999629 2000324 R KEGG: hsa:729099 hypothetical protein LOC729099; hypothetical protein complement(1999629..2000324) Paracoccus denitrificans PD1222 4578663 YP_915783.1 CDS Pden_1995 NC_008686.1 2000815 2002605 R PFAM: HemY domain protein; KEGG: rsp:RSP_1508 uncharacterized HemY-like membrane protein; HemY domain-containing protein complement(2000815..2002605) Paracoccus denitrificans PD1222 4578664 YP_915784.1 CDS Pden_1996 NC_008686.1 2002568 2004139 R KEGG: jan:Jann_4082 hypothetical protein; hypothetical protein complement(2002568..2004139) Paracoccus denitrificans PD1222 4578665 YP_915785.1 CDS Pden_1997 NC_008686.1 2004193 2004867 R KEGG: rsp:RSP_6208 uroporphyrinogen-III synthase; uroporphyrinogen-III synthase complement(2004193..2004867) Paracoccus denitrificans PD1222 4578666 YP_915786.1 CDS Pden_1998 NC_008686.1 2004932 2006002 D 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 2004932..2006002 Paracoccus denitrificans PD1222 4578667 YP_915787.1 CDS gpsA NC_008686.1 2005999 2006943 D catalyzes the NAD(P)H-dependent reduction of glycerol 3-phosphate to glycerone phosphate; NAD(P)H-dependent glycerol-3-phosphate dehydrogenase 2005999..2006943 Paracoccus denitrificans PD1222 4578668 YP_915788.1 CDS Pden_2000 NC_008686.1 2006940 2007215 D PFAM: YCII-related; KEGG: rsp:RSP_1511 hypothetical protein; hypothetical protein 2006940..2007215 Paracoccus denitrificans PD1222 4578669 YP_915789.1 CDS Pden_2001 NC_008686.1 2007215 2007640 D PFAM: protein of unknown function DUF55; KEGG: rsp:RSP_1512 hypothetical protein; hypothetical protein 2007215..2007640 Paracoccus denitrificans PD1222 4578670 YP_915790.1 CDS Pden_2002 NC_008686.1 2007683 2009476 D 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 2007683..2009476 Paracoccus denitrificans PD1222 4578671 YP_915791.1 CDS Pden_2003 NC_008686.1 2009604 2010026 R PFAM: Allergen V5/Tpx-1 family protein; KEGG: fra:Francci3_3457 allergen V5/TPX-1 related; Allergen V5/Tpx-1 family protein complement(2009604..2010026) Paracoccus denitrificans PD1222 4578672 YP_915792.1 CDS Pden_2004 NC_008686.1 2010277 2010762 D PFAM: Peptidoglycan-binding LysM; transport-associated; KEGG: sil:SPO3004 LysM/phospholipid-binding domain protein; LysM domain/BON superfamily protein 2010277..2010762 Paracoccus denitrificans PD1222 4578673 YP_915793.1 CDS Pden_2005 NC_008686.1 2010891 2012780 D activates fatty acids by binding to coenzyme A; AMP-binding protein 2010891..2012780 Paracoccus denitrificans PD1222 4578674 YP_915794.1 CDS Pden_2006 NC_008686.1 2012982 2014001 D KEGG: sit:TM1040_2837 conserved hypothetical protein; hypothetical protein 2012982..2014001 Paracoccus denitrificans PD1222 4578675 YP_915795.1 CDS Pden_2007 NC_008686.1 2014058 2015065 D KEGG: sil:SPO3503 hypothetical protein; hypothetical protein 2014058..2015065 Paracoccus denitrificans PD1222 4578676 YP_915796.1 CDS Pden_2008 NC_008686.1 2015124 2016779 R ChvD; in Agrobacterium tumefaciens, mutations in both Walker boxes were found to affect virulence; ABC transporter ATP-binding protein complement(2015124..2016779) Paracoccus denitrificans PD1222 4578677 YP_915797.1 CDS Pden_2009 NC_008686.1 2016852 2017709 R PFAM: sulfotransferase; KEGG: syg:sync_0226 hypothetical protein; sulfotransferase complement(2016852..2017709) Paracoccus denitrificans PD1222 4578678 YP_915798.1 CDS rimO NC_008686.1 2017786 2019177 R catalyzes the methylthiolation of an aspartic acid residue of the S12 protein of the 30S ribosomal subunit; 30S ribosomal protein S12 methylthiotransferase complement(2017786..2019177) Paracoccus denitrificans PD1222 4578679 YP_915799.1 CDS Pden_2011 NC_008686.1 2019275 2019745 D hypothetical protein 2019275..2019745 Paracoccus denitrificans PD1222 4578680 YP_915800.1 CDS Pden_2012 NC_008686.1 2019730 2020119 D hypothetical protein 2019730..2020119 Paracoccus denitrificans PD1222 4578681 YP_915801.1 CDS Pden_2013 NC_008686.1 2020124 2020885 R PFAM: ABC-2 type transporter; KEGG: sit:TM1040_2524 ABC-2 type transporter; ABC transporter complement(2020124..2020885) Paracoccus denitrificans PD1222 4578682 YP_915802.1 CDS Pden_2014 NC_008686.1 2020882 2021811 R PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: jan:Jann_0746 ABC transporter related; ABC transporter complement(2020882..2021811) Paracoccus denitrificans PD1222 4580398 YP_915803.1 CDS Pden_2015 NC_008686.1 2021929 2022711 R PFAM: phospholipid/glycerol acyltransferase; KEGG: rde:RD1_1601 acyltransferase; phospholipid/glycerol acyltransferase complement(2021929..2022711) Paracoccus denitrificans PD1222 4580399 YP_915804.1 CDS Pden_2016 NC_008686.1 2022711 2023640 R PFAM: protein of unknown function DUF214; KEGG: rsp:RSP_0734 cell division protein FtsX; hypothetical protein complement(2022711..2023640) Paracoccus denitrificans PD1222 4580400 YP_915805.1 CDS Pden_2017 NC_008686.1 2023637 2024311 R PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sil:SPO0337 cell division ATP-binding protein FtsE; ABC transporter complement(2023637..2024311) Paracoccus denitrificans PD1222 4580401 YP_915806.1 CDS Pden_2018 NC_008686.1 2024436 2025395 D TIGRFAM: MJ0042 family finger-like protein; KEGG: rsp:RSP_0732 hypothetical protein; Zinc finger-domain-containing protein 2024436..2025395 Paracoccus denitrificans PD1222 4580402 YP_915807.1 CDS Pden_2019 NC_008686.1 2025475 2027979 R KEGG: rsp:RSP_0730 hypothetical protein; hypothetical protein complement(2025475..2027979) Paracoccus denitrificans PD1222 4580403 YP_915808.1 CDS Pden_2020 NC_008686.1 2028070 2029335 R TIGRFAM: diaminopimelate decarboxylase; PFAM: Orn/DAP/Arg decarboxylase 2; KEGG: rsp:RSP_0729 Orn/DAP/Arg decarboxylase, family 2; diaminopimelate decarboxylase complement(2028070..2029335) Paracoccus denitrificans PD1222 4580404 YP_915809.1 CDS Pden_2021 NC_008686.1 2029335 2029610 R KEGG: rsp:RSP_0728 hypothetical protein; hypothetical protein complement(2029335..2029610) Paracoccus denitrificans PD1222 4580405 YP_915810.1 CDS Pden_2022 NC_008686.1 2029755 2031164 R catalyzes the formation of arginine from (N-L-arginino)succinate; argininosuccinate lyase complement(2029755..2031164) Paracoccus denitrificans PD1222 4580406 YP_915811.1 CDS Pden_2023 NC_008686.1 2031256 2031741 D PFAM: Redoxin domain protein; Thioredoxin domain; KEGG: rsp:RSP_0725 thioredoxin, thioldisulfide interchange protein; redoxin domain-containing protein 2031256..2031741 Paracoccus denitrificans PD1222 4580407 YP_915812.1 CDS Pden_2024 NC_008686.1 2031719 2032303 R KEGG: rsp:RSP_0744 DNA-3-methyladenine glycosylase I; TIGRFAM: DNA-3-methyladenine glycosylase I; PFAM: methyladenine glycosylase; DNA-3-methyladenine glycosylase I complement(2031719..2032303) Paracoccus denitrificans PD1222 4580408 YP_915813.1 CDS Pden_2025 NC_008686.1 2032396 2033223 D PFAM: EAL domain protein; KEGG: jan:Jann_0494 diguanylate phosphodiesterase; diguanylate phosphodiesterase 2032396..2033223 Paracoccus denitrificans PD1222 4580409 YP_915814.1 CDS Pden_2026 NC_008686.1 2033477 2034652 D 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 2033477..2034652 Paracoccus denitrificans PD1222 4580410 YP_915815.1 CDS Pden_2027 NC_008686.1 2034739 2035464 D TIGRFAM: acetoacetyl-CoA reductase; PFAM: short-chain dehydrogenase/reductase SDR; KR; KEGG: rsp:RSP_0747 short-chain dehydrogenase/reductase; acetoacetyl-CoA reductase 2034739..2035464 Paracoccus denitrificans PD1222 4580411 YP_915816.1 CDS Pden_2028 NC_008686.1 2035563 2035781 R PFAM: protein of unknown function DUF465; KEGG: rde:RD1_3398 hypothetical protein; hypothetical protein complement(2035563..2035781) Paracoccus denitrificans PD1222 4580412 YP_915817.1 CDS Pden_2029 NC_008686.1 2035786 2036544 R PFAM: methyltransferase small; Methyltransferase type 11; KEGG: rsp:RSP_0748 N-6 adenine-specific DNA methylase; methyltransferase small complement(2035786..2036544) Paracoccus denitrificans PD1222 4580413 YP_915818.1 CDS Pden_2030 NC_008686.1 2036537 2036749 R KEGG: rsp:RSP_0749 hypothetical protein; hypothetical protein complement(2036537..2036749) Paracoccus denitrificans PD1222 4580414 YP_915819.1 CDS Pden_2031 NC_008686.1 2036825 2037826 D PFAM: Polyprenyl synthetase; KEGG: sit:TM1040_3742 farnesyltranstransferase; trans-hexaprenyltranstransferase 2036825..2037826 Paracoccus denitrificans PD1222 4580415 YP_915820.1 CDS Pden_2032 NC_008686.1 2037929 2039377 R TIGRFAM: ammonium transporter; PFAM: Rh family protein/ammonium transporter; KEGG: mca:MCA2136 ammonium transporter; ammonium transporter complement(2037929..2039377) Paracoccus denitrificans PD1222 4580416 YP_915821.1 CDS Pden_2033 NC_008686.1 2039634 2041964 D 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 2039634..2041964 Paracoccus denitrificans PD1222 4580417 YP_915822.1 CDS Pden_2034 NC_008686.1 2042017 2042622 R PFAM: toluene tolerance family protein; KEGG: rsp:RSP_0890 possible protein YrbC precursor; toluene tolerance family protein complement(2042017..2042622) Paracoccus denitrificans PD1222 4580418 YP_915823.1 CDS Pden_2035 NC_008686.1 2042603 2043328 R PFAM: VacJ family lipoprotein; KEGG: sil:SPO3727 VacJ lipoprotein; VacJ family lipoprotein complement(2042603..2043328) Paracoccus denitrificans PD1222 4580419 YP_915824.1 CDS Pden_2036 NC_008686.1 2043489 2045231 D 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 2043489..2045231 Paracoccus denitrificans PD1222 4580420 YP_915825.1 CDS Pden_2037 NC_008686.1 2045228 2046661 D 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 2045228..2046661 Paracoccus denitrificans PD1222 4580421 YP_915826.1 CDS Pden_2038 NC_008686.1 2046692 2046952 D hypothetical protein 2046692..2046952 Paracoccus denitrificans PD1222 4580422 YP_915827.1 CDS Pden_2039 NC_008686.1 2047060 2047986 R catalyzes the formation of L-citrulline from carbamoyl phosphate and L-ornithine in arginine biosynthesis and degradation; ornithine carbamoyltransferase complement(2047060..2047986) Paracoccus denitrificans PD1222 4580423 YP_915828.1 CDS Pden_2040 NC_008686.1 2048084 2048560 R PFAM: GCN5-related N-acetyltransferase; KEGG: mlo:mll5006 aminoglycoside 6'-N-acetyltransferase; N-acetyltransferase complement(2048084..2048560) Paracoccus denitrificans PD1222 4580424 YP_915829.1 CDS argD NC_008686.1 2048553 2049725 R 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 complement(2048553..2049725) Paracoccus denitrificans PD1222 4580425 YP_915830.1 CDS Pden_2042 NC_008686.1 2049899 2050720 R PFAM: ABC-2 type transporter; KEGG: sil:SPO0957 ABC transporter, permease protein; ABC transporter complement(2049899..2050720) Paracoccus denitrificans PD1222 4580426 YP_915831.1 CDS Pden_2043 NC_008686.1 2050852 2051457 D PFAM: GcrA cell cycle regulator; KEGG: rsp:RSP_2007 conservd hypothetical protein; GcrA cell cycle regulator 2050852..2051457 Paracoccus denitrificans PD1222 4580427 YP_915832.1 CDS Pden_2044 NC_008686.1 2051458 2051901 D PFAM: NUDIX hydrolase; KEGG: sit:TM1040_3067 NUDIX hydrolase; NUDIX hydrolase 2051458..2051901 Paracoccus denitrificans PD1222 4580428 YP_915833.1 CDS Pden_2045 NC_008686.1 2052010 2053728 D 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 2052010..2053728 Paracoccus denitrificans PD1222 4580429 YP_915834.1 CDS Pden_2046 NC_008686.1 2053922 2056063 D PFAM: TonB-dependent receptor; TonB-dependent receptor, plug; KEGG: atc:AGR_L_1858 outer membrane protein irgA precursor; TonB-dependent receptor 2053922..2056063 Paracoccus denitrificans PD1222 4580430 YP_915835.1 CDS Pden_2047 NC_008686.1 2056156 2057076 D TIGRFAM: arginase; PFAM: Arginase/agmatinase/formiminoglutamase; KEGG: rsp:RSP_2632 arginase; arginase 2056156..2057076 Paracoccus denitrificans PD1222 4580431 YP_915836.1 CDS Pden_2048 NC_008686.1 2057392 2057754 R hypothetical protein complement(2057392..2057754) Paracoccus denitrificans PD1222 4580432 YP_915837.1 CDS Pden_2049 NC_008686.1 2057841 2058308 R hypothetical protein complement(2057841..2058308) Paracoccus denitrificans PD1222 4580433 YP_915838.1 CDS Pden_2050 NC_008686.1 2059246 2059770 R hypothetical protein complement(2059246..2059770) Paracoccus denitrificans PD1222 4580434 YP_915839.1 CDS Pden_2051 NC_008686.1 2059763 2060041 R hypothetical protein complement(2059763..2060041) Paracoccus denitrificans PD1222 4580435 YP_915840.1 CDS Pden_2052 NC_008686.1 2060592 2060891 D hypothetical protein 2060592..2060891 Paracoccus denitrificans PD1222 4580436 YP_915841.1 CDS Pden_2053 NC_008686.1 2060891 2061109 D hypothetical protein 2060891..2061109 Paracoccus denitrificans PD1222 4578917 YP_915842.1 CDS Pden_2054 NC_008686.1 2061405 2062328 D KEGG: nha:Nham_2360 hypothetical protein; hypothetical protein 2061405..2062328 Paracoccus denitrificans PD1222 4578918 YP_915843.1 CDS Pden_2055 NC_008686.1 2063243 2063758 D hypothetical protein 2063243..2063758 Paracoccus denitrificans PD1222 4578919 YP_915844.1 CDS Pden_2056 NC_008686.1 2063766 2065175 R KEGG: xft:PD1844 hypothetical protein; hypothetical protein complement(2063766..2065175) Paracoccus denitrificans PD1222 4578920 YP_915845.1 CDS Pden_2057 NC_008686.1 2065343 2065744 D hypothetical protein 2065343..2065744 Paracoccus denitrificans PD1222 4578921 YP_915846.1 CDS Pden_2058 NC_008686.1 2065737 2066510 R KEGG: jan:Jann_0233 hypothetical protein; hypothetical protein complement(2065737..2066510) Paracoccus denitrificans PD1222 4578922 YP_915847.1 CDS Pden_2059 NC_008686.1 2066523 2066894 R KEGG: nar:Saro_2759 transposase orfA IS5 family element; IS5 family transposase OrfA complement(2066523..2066894) Paracoccus denitrificans PD1222 4578923 YP_915848.1 CDS Pden_2060 NC_008686.1 2067123 2067452 D PFAM: HNH endonuclease; SMART: HNH nuclease; KEGG: reu:Reut_A0008 HNH endonuclease; HNH endonuclease 2067123..2067452 Paracoccus denitrificans PD1222 4578924 YP_915849.1 CDS Pden_2061 NC_008686.1 2067435 2068970 R TIGRFAM: DNA-cytosine methyltransferase; PFAM: C-5 cytosine-specific DNA methylase; KEGG: jan:Jann_2858 DNA-cytosine methyltransferase; DNA-cytosine methyltransferase complement(2067435..2068970) Paracoccus denitrificans PD1222 4578925 YP_915850.1 CDS Pden_2062 NC_008686.1 2069038 2069502 D PFAM: DNA mismatch endonuclease vsr; KEGG: dvu:DVU2843 DNA mismatch endonuclease Vsr; DNA mismatch endonuclease vsr 2069038..2069502 Paracoccus denitrificans PD1222 4578926 YP_915851.1 CDS Pden_2063 NC_008686.1 2069678 2070169 R KEGG: son:SO2967 hypothetical phage terminase large subunit; phage terminase large subunit complement(2069678..2070169) Paracoccus denitrificans PD1222 4578927 YP_915852.1 CDS Pden_2064 NC_008686.1 2070153 2070623 R 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 complement(2070153..2070623) Paracoccus denitrificans PD1222 4578928 YP_915853.1 CDS Pden_2065 NC_008686.1 2070830 2071036 D 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 2070830..2071036 Paracoccus denitrificans PD1222 4578929 YP_915854.1 CDS Pden_2066 NC_008686.1 2071116 2071421 D KEGG: rsp:RSP_3622 hypothetical protein; hypothetical protein 2071116..2071421 Paracoccus denitrificans PD1222 4578930 YP_915855.1 CDS Pden_2067 NC_008686.1 2071691 2071915 R KEGG: mag:amb1162 hypothetical protein; hypothetical protein complement(2071691..2071915) Paracoccus denitrificans PD1222 4578931 YP_915856.1 CDS Pden_2068 NC_008686.1 2071912 2073303 R PFAM: DNA methylase N-4/N-6 domain protein; ParB domain protein nuclease; KEGG: mag:amb0363 modification methylase DpnIIB; nuclease complement(2071912..2073303) Paracoccus denitrificans PD1222 4578932 YP_915857.1 CDS Pden_2069 NC_008686.1 2073402 2073797 R PFAM: HNH endonuclease; SMART: HNH nuclease; KEGG: rso:RSc1680 probable phage PHI-105 holin-like protein; HNH endonuclease complement(2073402..2073797) Paracoccus denitrificans PD1222 4578933 YP_915858.1 CDS Pden_2070 NC_008686.1 2073885 2074262 R KEGG: hch:HCH_05683 hypothetical protein; hypothetical protein complement(2073885..2074262) Paracoccus denitrificans PD1222 4578934 YP_915859.1 CDS Pden_2071 NC_008686.1 2074255 2074743 R KEGG: mag:amb0360 hypothetical protein; hypothetical protein complement(2074255..2074743) Paracoccus denitrificans PD1222 4578935 YP_915860.1 CDS Pden_2072 NC_008686.1 2074747 2076405 R KEGG: ade:Adeh_1681 PE-PGRS family protein; hypothetical protein complement(2074747..2076405) Paracoccus denitrificans PD1222 4578936 YP_915861.1 CDS Pden_2073 NC_008686.1 2076402 2076602 R hypothetical protein complement(2076402..2076602) Paracoccus denitrificans PD1222 4578937 YP_915862.1 CDS Pden_2074 NC_008686.1 2076726 2076965 D KEGG: bbr:BB2472 plasmid stability protein; plasmid stability protein 2076726..2076965 Paracoccus denitrificans PD1222 4578938 YP_915863.1 CDS Pden_2075 NC_008686.1 2076962 2077396 D PFAM: PilT protein domain protein; KEGG: gox:GOX2696 plasmid stabilization protein; twitching motility protein PilT 2076962..2077396 Paracoccus denitrificans PD1222 4578939 YP_915864.1 CDS Pden_2076 NC_008686.1 2077384 2078100 R KEGG: mxa:MXAN_1879 hypothetical protein; ECF subfamily RNA polymerase sigma-24 factor complement(2077384..2078100) Paracoccus denitrificans PD1222 4578940 YP_915865.1 CDS Pden_2077 NC_008686.1 2078198 2078431 R hypothetical protein complement(2078198..2078431) Paracoccus denitrificans PD1222 4578941 YP_915866.1 CDS Pden_2078 NC_008686.1 2078525 2080687 R KEGG: rso:RSc3240 hypothetical protein; hypothetical protein complement(2078525..2080687) Paracoccus denitrificans PD1222 4578942 YP_915867.1 CDS Pden_2079 NC_008686.1 2080770 2081024 D hypothetical protein 2080770..2081024 Paracoccus denitrificans PD1222 4578943 YP_915868.1 CDS Pden_2080 NC_008686.1 2081021 2081476 D KEGG: nwi:Nwi_1952 hypothetical protein; hypothetical protein 2081021..2081476 Paracoccus denitrificans PD1222 4578944 YP_915869.1 CDS Pden_2081 NC_008686.1 2081476 2082801 D PFAM: Resolvase, N-terminal domain; Recombinase; KEGG: nwi:Nwi_1951 resolvase; recombinase 2081476..2082801 Paracoccus denitrificans PD1222 4578945 YP_915870.1 CDS Pden_2082 NC_008686.1 2082798 2083181 D KEGG: nwi:Nwi_2834 hypothetical protein; hypothetical protein 2082798..2083181 Paracoccus denitrificans PD1222 4578946 YP_915871.1 CDS Pden_2083 NC_008686.1 2083185 2084021 R KEGG: rsp:RSP_3808 hypothetical protein; hypothetical protein complement(2083185..2084021) Paracoccus denitrificans PD1222 4578947 YP_915872.1 CDS Pden_2084 NC_008686.1 2084031 2084288 R hypothetical protein complement(2084031..2084288) Paracoccus denitrificans PD1222 4578948 YP_915873.1 CDS Pden_2085 NC_008686.1 2084523 2085431 D KEGG: nar:Saro_2176 hypothetical protein; hypothetical protein 2084523..2085431 Paracoccus denitrificans PD1222 4578949 YP_915874.1 CDS Pden_2086 NC_008686.1 2085415 2087601 D 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 2085415..2087601 Paracoccus denitrificans PD1222 4578950 YP_915875.1 CDS Pden_2087 NC_008686.1 2087606 2089108 D KEGG: rfr:Rfer_3071 hypothetical protein; hypothetical protein 2087606..2089108 Paracoccus denitrificans PD1222 4578951 YP_915876.1 CDS Pden_2088 NC_008686.1 2089105 2091972 D KEGG: rfr:Rfer_3072 endonuclease; endonuclease 2089105..2091972 Paracoccus denitrificans PD1222 4578952 YP_915877.1 CDS Pden_2089 NC_008686.1 2091956 2092960 D KEGG: rfr:Rfer_3073 hypothetical protein; hypothetical protein 2091956..2092960 Paracoccus denitrificans PD1222 4578953 YP_915878.1 CDS Pden_2090 NC_008686.1 2092962 2094764 D KEGG: rfr:Rfer_3074 hypothetical protein; hypothetical protein 2092962..2094764 Paracoccus denitrificans PD1222 4578954 YP_915879.1 CDS Pden_2091 NC_008686.1 2094772 2095239 D hypothetical protein 2094772..2095239 Paracoccus denitrificans PD1222 4578955 YP_915880.1 CDS Pden_2092 NC_008686.1 2095223 2095783 R PFAM: transposase, IS4 family protein; KEGG: sil:SPOA0134 ISSpo7, transposase; transposase, IS4 family protein complement(2095223..2095783) Paracoccus denitrificans PD1222 4579889 YP_915881.1 CDS Pden_2093 NC_008686.1 2096063 2097922 D KEGG: rsp:RSP_1461 3-deoxy-D-manno-octulosonic-acid transferase; 3-deoxy-D-manno-octulosonic-acid transferase 2096063..2097922 Paracoccus denitrificans PD1222 4579890 YP_915882.1 CDS lpxK NC_008686.1 2097919 2098908 D 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 2097919..2098908 Paracoccus denitrificans PD1222 4579891 YP_915883.1 CDS Pden_2095 NC_008686.1 2098948 2099619 R PFAM: DSBA oxidoreductase; KEGG: sit:TM1040_2643 thiol:disulfide interchange protein, DsbA family; DSBA oxidoreductase complement(2098948..2099619) Paracoccus denitrificans PD1222 4579892 YP_915884.1 CDS Pden_2096 NC_008686.1 2099616 2100158 R PFAM: protein of unknown function DUF1159; KEGG: rsp:RSP_1465 hypothetical protein; hypothetical protein complement(2099616..2100158) Paracoccus denitrificans PD1222 4579893 YP_915885.1 CDS Pden_2097 NC_008686.1 2100310 2101296 D 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 2100310..2101296 Paracoccus denitrificans PD1222 4579894 YP_915886.1 CDS Pden_2098 NC_008686.1 2101374 2102516 D PFAM: fatty acid desaturase; KEGG: sit:TM1040_2646 alkane-1 monooxygenase; alkane 1-monooxygenase 2101374..2102516 Paracoccus denitrificans PD1222 4579895 YP_915887.1 CDS Pden_2099 NC_008686.1 2102511 2103296 R hypothetical protein complement(2102511..2103296) Paracoccus denitrificans PD1222 4579896 YP_915888.1 CDS Pden_2100 NC_008686.1 2103293 2104414 R KEGG: jan:Jann_1007 hypothetical protein; hypothetical protein complement(2103293..2104414) Paracoccus denitrificans PD1222 4579897 YP_915889.1 CDS Pden_2101 NC_008686.1 2104472 2105602 R 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 complement(2104472..2105602) Paracoccus denitrificans PD1222 4579898 YP_915890.1 CDS rnhB NC_008686.1 2105691 2106323 R RNH2; RNase HII; binds manganese; endonuclease which specifically degrades the RNA of RNA-DNA hybrids; ribonuclease HII complement(2105691..2106323) Paracoccus denitrificans PD1222 4579899 YP_915891.1 CDS Pden_2103 NC_008686.1 2106320 2106799 R PFAM: Ureidoglycolate hydrolase; KEGG: sit:TM1040_3474 ureidoglycolate hydrolase; ureidoglycolate hydrolase complement(2106320..2106799) Paracoccus denitrificans PD1222 4579900 YP_915892.1 CDS Pden_2104 NC_008686.1 2106857 2108032 R PFAM: major facilitator superfamily MFS_1; KEGG: mlo:mlr2687 probable fosmidomycin resistance protein; major facilitator superfamily transporter complement(2106857..2108032) Paracoccus denitrificans PD1222 4579901 YP_915893.1 CDS Pden_2105 NC_008686.1 2108324 2109073 D 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 2108324..2109073 Paracoccus denitrificans PD1222 4579902 YP_915894.1 CDS Pden_2106 NC_008686.1 2109183 2110664 D PFAM: Peptidoglycan-binding domain 1 protein; ErfK/YbiS/YcfS/YnhG family protein; KEGG: ret:RHE_CH01741 hypothetical protein; ErfK/YbiS/YcfS/YnhG family protein 2109183..2110664 Paracoccus denitrificans PD1222 4579903 YP_915895.1 CDS Pden_2107 NC_008686.1 2110666 2111502 D PFAM: Extensin family protein; KEGG: sme:SMc02727 hypothetical protein; extensin family protein 2110666..2111502 Paracoccus denitrificans PD1222 4579904 YP_915896.1 CDS Pden_2108 NC_008686.1 2111506 2112237 R PFAM: cyclic nucleotide-binding; regulatory protein, Crp; KEGG: mlo:mll3135 transcriptional regulator, Fnr-type; Crp/Fnr family transcriptional regulator complement(2111506..2112237) Paracoccus denitrificans PD1222 4579905 YP_915897.1 CDS Pden_2109 NC_008686.1 2112344 2113678 R 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 complement(2112344..2113678) Paracoccus denitrificans PD1222 4579906 YP_915898.1 CDS flgB NC_008686.1 2113787 2114176 D with FlgF and C makes up the proximal portion of the flagellar basal body rod; flagellar basal-body rod protein FlgB 2113787..2114176 Paracoccus denitrificans PD1222 4579907 YP_915899.1 CDS flgC NC_008686.1 2114188 2114580 D with FlgF and B makes up the proximal portion of the flagellar basal body rod; flagellar basal body rod protein FlgC 2114188..2114580 Paracoccus denitrificans PD1222 4579908 YP_915900.1 CDS Pden_2112 NC_008686.1 2114592 2114870 D 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 2114592..2114870 Paracoccus denitrificans PD1222 4579909 YP_915901.1 CDS Pden_2113 NC_008686.1 2114881 2115147 D PFAM: export protein FliQ, family 3; KEGG: rsp:RSP_1328 flagellar biosynthetic protein FliQ; export protein FliQ 2114881..2115147 Paracoccus denitrificans PD1222 4579910 YP_915902.1 CDS flgF NC_008686.1 2115151 2115867 D 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 2115151..2115867 Paracoccus denitrificans PD1222 4579911 YP_915903.1 CDS flgG NC_008686.1 2115879 2116664 D 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 2115879..2116664 Paracoccus denitrificans PD1222 4579912 YP_915904.1 CDS flgA NC_008686.1 2116664 2117080 D required for the assembly of the flagellar basal body P-ring; flagellar basal body P-ring biosynthesis protein FlgA 2116664..2117080 Paracoccus denitrificans PD1222 4579913 YP_915905.1 CDS flgH NC_008686.1 2117091 2117843 D 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 2117091..2117843 Paracoccus denitrificans PD1222 4579914 YP_915906.1 CDS Pden_2118 NC_008686.1 2117857 2118390 D KEGG: jan:Jann_4190 hypothetical protein; hypothetical protein 2117857..2118390 Paracoccus denitrificans PD1222 4579915 YP_915907.1 CDS Pden_2119 NC_008686.1 2119104 2120006 R TIGRFAM: glucose-1-phosphate thymidylyltransferase; PFAM: Nucleotidyl transferase; KEGG: sit:TM1040_3859 glucose-1-phosphate thymidylyltransferase; glucose-1-phosphate thymidylyltransferase complement(2119104..2120006) Paracoccus denitrificans PD1222 4579916 YP_915908.1 CDS Pden_2120 NC_008686.1 2120003 2120854 R 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 complement(2120003..2120854) Paracoccus denitrificans PD1222 4579917 YP_915909.1 CDS Pden_2121 NC_008686.1 2120851 2121888 R 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 complement(2120851..2121888) Paracoccus denitrificans PD1222 4579918 YP_915910.1 CDS Pden_2122 NC_008686.1 2121885 2122466 R 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 complement(2121885..2122466) Paracoccus denitrificans PD1222 4579919 YP_915911.1 CDS Pden_2123 NC_008686.1 2122642 2123313 D hypothetical protein 2122642..2123313 Paracoccus denitrificans PD1222 4579920 YP_915912.1 CDS Pden_2124 NC_008686.1 2123332 2126172 D PFAM: Hemolysin-type calcium-binding region; KEGG: ter:Tery_2034 RTX toxins and related Ca2+-binding protein; hemolysin-type calcium-binding protein 2123332..2126172 Paracoccus denitrificans PD1222 4579921 YP_915913.1 CDS Pden_2125 NC_008686.1 2126169 2126921 R PFAM: ABC-2 type transporter; KEGG: sme:SMb20833 cell surface polysaccharide export ABC-2 transporter permease protein, close relative of Y20822wzm2; ABC transporter complement(2126169..2126921) Paracoccus denitrificans PD1222 4579922 YP_915914.1 CDS Pden_2126 NC_008686.1 2127145 2129103 D KEGG: mes:Meso_2756 capsule polysaccharide export protein-like; capsule polysaccharide export protein 2127145..2129103 Paracoccus denitrificans PD1222 4579923 YP_915915.1 CDS Pden_2127 NC_008686.1 2129108 2129785 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sme:SMb20832 cell surface polysaccharide export ABC-2 transporter ATP-binding protein; ABC transporter 2129108..2129785 Paracoccus denitrificans PD1222 4579924 YP_915916.1 CDS Pden_2128 NC_008686.1 2129883 2130284 D PFAM: protein of unknown function DUF1486; KEGG: rsp:RSP_0629 hypothetical protein; hypothetical protein 2129883..2130284 Paracoccus denitrificans PD1222 4579925 YP_915917.1 CDS Pden_2129 NC_008686.1 2130281 2130862 D KEGG: rsp:RSP_0628 hypothetical protein; hypothetical protein 2130281..2130862 Paracoccus denitrificans PD1222 4579926 YP_915918.1 CDS Pden_2130 NC_008686.1 2130871 2131728 D PFAM: Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase; KEGG: rsp:RSP_0627 amidohydrolase; nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase 2130871..2131728 Paracoccus denitrificans PD1222 4579927 YP_915919.1 CDS Pden_2131 NC_008686.1 2131809 2132297 R PFAM: GCN5-related N-acetyltransferase; KEGG: bbr:BB0980 GnaT-family acetyltransferase; N-acetyltransferase complement(2131809..2132297) Paracoccus denitrificans PD1222 4579948 YP_915920.1 CDS Pden_2132 NC_008686.1 2132432 2133934 R with component II, the glutamine amidotransferase, catalyzes the formation of anthranilate from chorismate and glutamine; anthranilate synthase component I complement(2132432..2133934) Paracoccus denitrificans PD1222 4579949 YP_915921.1 CDS Pden_2133 NC_008686.1 2133934 2135892 R KEGG: rsp:RSP_2005 possible peptidyl-prolyl cis-trans isomerse; peptidyl-prolyl cis-trans isomerse complement(2133934..2135892) Paracoccus denitrificans PD1222 4579950 YP_915922.1 CDS Pden_2134 NC_008686.1 2136018 2137193 R PFAM: aminotransferase, class V; aminotransferase, class I and II; KEGG: rsp:RSP_2341 hypothetical protein; hypothetical protein complement(2136018..2137193) Paracoccus denitrificans PD1222 4579951 YP_915923.1 CDS Pden_2135 NC_008686.1 2137203 2137916 R KEGG: cel:ZK84.1 Hypothetical protein ZK84.1; hypothetical protein complement(2137203..2137916) Paracoccus denitrificans PD1222 4579952 YP_915924.1 CDS Pden_2136 NC_008686.1 2138071 2138661 D TIGRFAM: glutamine amidotransferase of anthranilate synthase; PFAM: glutamine amidotransferase class-I; KEGG: rsp:RSP_2002 anthranilate synthase component II; glutamine amidotransferase of anthranilate synthase 2138071..2138661 Paracoccus denitrificans PD1222 4579953 YP_915925.1 CDS trpD NC_008686.1 2138658 2139695 D Catalyzes the conversion of N-(5-phospho-D-ribosyl)-anthranilate and diphosphate to anthranilate and 5-phospho-alpha-D-ribose 1-diphosphate; anthranilate phosphoribosyltransferase 2138658..2139695 Paracoccus denitrificans PD1222 4579954 YP_915926.1 CDS Pden_2138 NC_008686.1 2139688 2140356 D TIGRFAM: uracil-DNA glycosylase; PFAM: Uracil-DNA glycosylase superfamily; KEGG: sit:TM1040_1139 uracil-DNA glycosylase; uracil-DNA glycosylase 2139688..2140356 Paracoccus denitrificans PD1222 4579955 YP_915927.1 CDS Pden_2139 NC_008686.1 2140366 2141157 D PFAM: Indole-3-glycerol phosphate synthase; KEGG: sil:SPO2151 indole-3-glycerol phosphate synthase; indole-3-glycerol phosphate synthase 2140366..2141157 Paracoccus denitrificans PD1222 4579956 YP_915928.1 CDS Pden_2140 NC_008686.1 2141154 2141627 D 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 2141154..2141627 Paracoccus denitrificans PD1222 4579957 YP_915929.1 CDS Pden_2141 NC_008686.1 2141638 2142810 D 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 2141638..2142810 Paracoccus denitrificans PD1222 4579958 YP_915930.1 CDS Pden_2142 NC_008686.1 2142920 2143618 D Represses a number of genes involved in the response to DNA damage; LexA repressor 2142920..2143618 Paracoccus denitrificans PD1222 4579959 YP_915931.1 CDS Pden_2143 NC_008686.1 2143743 2144900 D 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 2143743..2144900 Paracoccus denitrificans PD1222 4579960 YP_915932.1 CDS Pden_2144 NC_008686.1 2144912 2145511 D PFAM: thymidylate kinase; KEGG: sil:SPO2740 thymidylate kinase; dTMP kinase 2144912..2145511 Paracoccus denitrificans PD1222 4579961 YP_915933.1 CDS Pden_2145 NC_008686.1 2145508 2146605 D 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' 2145508..2146605 Paracoccus denitrificans PD1222 4579962 YP_915934.1 CDS Pden_2146 NC_008686.1 2146618 2147415 D TIGRFAM: hydrolase, TatD family; PFAM: TatD-related deoxyribonuclease; amidohydrolase 2; KEGG: rsp:RSP_0675 TatD-related deoxyribonuclease; TatD family hydrolase 2146618..2147415 Paracoccus denitrificans PD1222 4579963 YP_915935.1 CDS Pden_2147 NC_008686.1 2147412 2148212 D PFAM: beta-lactamase domain protein; KEGG: rsp:RSP_0676 PhnP-like protein; beta-lactamase domain-containing protein 2147412..2148212 Paracoccus denitrificans PD1222 4579964 YP_915936.1 CDS Pden_2148 NC_008686.1 2148209 2149153 D PFAM: Auxin Efflux Carrier; KEGG: rsp:RSP_0677 malonate transporter, MdcF, AEC family; auxin efflux carrier 2148209..2149153 Paracoccus denitrificans PD1222 4579965 YP_915937.1 CDS Pden_2149 NC_008686.1 2149189 2150142 R 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 complement(2149189..2150142) Paracoccus denitrificans PD1222 4579966 YP_915938.1 CDS Pden_2150 NC_008686.1 2150148 2151449 R 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 complement(2150148..2151449) Paracoccus denitrificans PD1222 4579967 YP_915939.1 CDS Pden_2151 NC_008686.1 2151524 2152603 R KEGG: sil:SPO3473 polyamine ABC trasnporter, periplasmic polyamine-binding protein; polyamine ABC transporter periplasmic substrate-binding protein complement(2151524..2152603) Paracoccus denitrificans PD1222 4579968 YP_915940.1 CDS Pden_2152 NC_008686.1 2152702 2153784 R PFAM: extracellular solute-binding protein, family 1; KEGG: rsp:RSP_0161 spermidine/putrescine-binding periplasmic protein; extracellular solute-binding protein complement(2152702..2153784) Paracoccus denitrificans PD1222 4579969 YP_915941.1 CDS Pden_2153 NC_008686.1 2153814 2154917 R 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 complement(2153814..2154917) Paracoccus denitrificans PD1222 4579970 YP_915942.1 CDS Pden_2154 NC_008686.1 2155122 2155688 R PFAM: protein of unknown function DUF421; KEGG: rsp:RSP_1130 hypothetical membrane protein; hypothetical protein complement(2155122..2155688) Paracoccus denitrificans PD1222 4579971 YP_915943.1 CDS Pden_2155 NC_008686.1 2155791 2156528 R PFAM: short-chain dehydrogenase/reductase SDR; KR; KEGG: atc:AGR_L_1073 short chain dehydrogenase; short chain dehydrogenase complement(2155791..2156528) Paracoccus denitrificans PD1222 4579972 YP_915944.1 CDS Pden_2156 NC_008686.1 2156531 2158153 R TIGRFAM: FGGY-family pentulose kinase; PFAM: carbohydrate kinase, FGGY; KEGG: atc:AGR_L_1075 D-ribulokinase; FGGY-family pentulose kinase complement(2156531..2158153) Paracoccus denitrificans PD1222 4579973 YP_915945.1 CDS Pden_2157 NC_008686.1 2158182 2158913 R PFAM: short-chain dehydrogenase/reductase SDR; KEGG: atc:AGR_L_1076 ribitol 2-dehydrogenase; short-chain dehydrogenase/reductase SDR complement(2158182..2158913) Paracoccus denitrificans PD1222 4579974 YP_915946.1 CDS Pden_2158 NC_008686.1 2158950 2159927 R PFAM: inner-membrane translocator; KEGG: atc:AGR_L_1078 ribose ABC transporter (permease); inner-membrane translocator complement(2158950..2159927) Paracoccus denitrificans PD1222 4579975 YP_915947.1 CDS Pden_2159 NC_008686.1 2159917 2161419 R PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: atu:Atu4321 ABC transporter, nucleotide binding/ATPase protein [ribose]; ABC transporter complement(2159917..2161419) Paracoccus denitrificans PD1222 4579976 YP_915948.1 CDS Pden_2160 NC_008686.1 2161490 2162395 R 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 complement(2161490..2162395) Paracoccus denitrificans PD1222 4579977 YP_915949.1 CDS Pden_2161 NC_008686.1 2162495 2163379 R PFAM: helix-turn-helix- domain containing protein, AraC type; KEGG: atc:AGR_L_1086 hypothetical protein; helix-turn-helix domain-containing protein complement(2162495..2163379) Paracoccus denitrificans PD1222 4579978 YP_915950.1 CDS Pden_2162 NC_008686.1 2163630 2165087 R TIGRFAM: xylulokinase; PFAM: carbohydrate kinase, FGGY; KEGG: mlo:mlr5033 xylulokinase; xylulokinase complement(2163630..2165087) Paracoccus denitrificans PD1222 4579979 YP_915951.1 CDS Pden_2163 NC_008686.1 2165092 2166129 R PFAM: Alcohol dehydrogenase, zinc-binding domain protein; Alcohol dehydrogenase GroES domain protein; KEGG: atc:AGR_L_1091 xylitol dehydrogenase; alcohol dehydrogenase complement(2165092..2166129) Paracoccus denitrificans PD1222 4579980 YP_915952.1 CDS Pden_2164 NC_008686.1 2166333 2166797 R PFAM: GatB/Yqey domain protein; KEGG: rsp:RSP_1875 hypothetical protein; GatB/Yqey domain-containing protein complement(2166333..2166797) Paracoccus denitrificans PD1222 4579981 YP_915953.1 CDS Pden_2165 NC_008686.1 2166966 2168114 D 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 2166966..2168114 Paracoccus denitrificans PD1222 4579982 YP_915954.1 CDS Pden_2166 NC_008686.1 2168202 2170298 D 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 2168202..2170298 Paracoccus denitrificans PD1222 4579983 YP_915955.1 CDS Pden_2167 NC_008686.1 2170435 2173236 R PFAM: glutamate-ammonia ligase adenylyltransferase; KEGG: rsp:RSP_2643 glutamate-ammonia-ligase adenylyltransferase; (glutamate--ammonia-ligase) adenylyltransferase complement(2170435..2173236) Paracoccus denitrificans PD1222 4579984 YP_915956.1 CDS Pden_2168 NC_008686.1 2173462 2174307 D Conjugates Arg from its aminoacyl-tRNA to the N-termini of proteins containing an N-terminal aspartate or glutamate; arginyl-tRNA-protein transferase 2173462..2174307 Paracoccus denitrificans PD1222 4579985 YP_915957.1 CDS Pden_2169 NC_008686.1 2174500 2176227 D 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 2174500..2176227 Paracoccus denitrificans PD1222 4579986 YP_915958.1 CDS ilvH NC_008686.1 2176242 2176802 D 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 2176242..2176802 Paracoccus denitrificans PD1222 4579146 YP_915959.1 CDS Pden_2171 NC_008686.1 2176808 2177149 R KEGG: rde:RD1_2814 hypothetical protein; hypothetical protein complement(2176808..2177149) Paracoccus denitrificans PD1222 4579147 YP_915960.1 CDS Pden_2172 NC_008686.1 2177401 2178204 R PFAM: peptidase M48, Ste24p; KEGG: rde:RD1_1656 peptidase, M48 family; peptidase M48, Ste24p complement(2177401..2178204) Paracoccus denitrificans PD1222 4579148 YP_915961.1 CDS Pden_2173 NC_008686.1 2178277 2178528 D KEGG: rsp:RSP_6045 hypothetical protein; hypothetical protein 2178277..2178528 Paracoccus denitrificans PD1222 4579149 YP_915962.1 CDS Pden_2174 NC_008686.1 2178525 2178773 R PFAM: protein of unknown function DUF167; KEGG: sil:SPO0937 hypothetical protein; hypothetical protein complement(2178525..2178773) Paracoccus denitrificans PD1222 4579150 YP_915963.1 CDS Pden_2175 NC_008686.1 2178879 2179445 D PFAM: nitroreductase; KEGG: jan:Jann_3161 nitroreductase; nitroreductase 2178879..2179445 Paracoccus denitrificans PD1222 4579151 YP_915964.1 CDS Pden_2176 NC_008686.1 2179445 2180137 D KEGG: rsp:RSP_0810 hypothetical protein; hypothetical protein 2179445..2180137 Paracoccus denitrificans PD1222 4579152 YP_915965.1 CDS Pden_2177 NC_008686.1 2180103 2180363 R PFAM: protein of unknown function DUF1467; KEGG: rsp:RSP_0811 hypothetical protein; hypothetical protein complement(2180103..2180363) Paracoccus denitrificans PD1222 4579153 YP_915966.1 CDS Pden_2178 NC_008686.1 2180363 2180767 R PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase; KEGG: sit:TM1040_0637 glyoxalase/bleomycin resistance protein/dioxygenase; glyoxalase/bleomycin resistance protein/dioxygenase complement(2180363..2180767) Paracoccus denitrificans PD1222 4579154 YP_915967.1 CDS Pden_2179 NC_008686.1 2180904 2181632 D PFAM: response regulator receiver; KEGG: sil:SPO0931 response regulator; response regulator receiver protein 2180904..2181632 Paracoccus denitrificans PD1222 4579155 YP_915968.1 CDS Pden_2180 NC_008686.1 2181637 2182377 R PFAM: GCN5-related N-acetyltransferase; KEGG: rsp:RSP_0814 acetyltransferase; N-acetyltransferase complement(2181637..2182377) Paracoccus denitrificans PD1222 4579156 YP_915969.1 CDS Pden_2181 NC_008686.1 2182398 2183579 R PFAM: protein of unknown function DUF1501; KEGG: ret:RHE_CH02550 hypothetical protein; hypothetical protein complement(2182398..2183579) Paracoccus denitrificans PD1222 4579157 YP_915970.1 CDS Pden_2182 NC_008686.1 2183589 2184956 R KEGG: ret:RHE_CH02551 hypothetical protein; hypothetical protein complement(2183589..2184956) Paracoccus denitrificans PD1222 4579158 YP_915971.1 CDS aspS NC_008686.1 2185083 2186858 R 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 complement(2185083..2186858) Paracoccus denitrificans PD1222 4579159 YP_915972.1 CDS Pden_2184 NC_008686.1 2186919 2187575 R PFAM: Abortive infection protein; KEGG: pat:Patl_3840 abortive infection protein; abortive infection protein complement(2186919..2187575) Paracoccus denitrificans PD1222 4579160 YP_915973.1 CDS Pden_2185 NC_008686.1 2187551 2188333 R PFAM: glycoside hydrolase, family 25; KEGG: sil:SPO3258 glycosyl hydrolase, family 25; glycoside hydrolase complement(2187551..2188333) Paracoccus denitrificans PD1222 4579161 YP_915974.1 CDS Pden_2186 NC_008686.1 2188538 2188897 D hypothetical protein 2188538..2188897 Paracoccus denitrificans PD1222 4579162 YP_915975.1 CDS Pden_2187 NC_008686.1 2188967 2190346 R PFAM: FAD linked oxidase domain protein; KEGG: rsp:RSP_2120 D-lactate dehydrogenase (cytochrome), FAD/FMN-containing oxidoreductase; D-lactate dehydrogenase complement(2188967..2190346) Paracoccus denitrificans PD1222 4579163 YP_915976.1 CDS Pden_2188 NC_008686.1 2190412 2191380 R PFAM: protein of unknown function DUF808; KEGG: jan:Jann_1699 protein of unknown function DUF808; hypothetical protein complement(2190412..2191380) Paracoccus denitrificans PD1222 4579164 YP_915977.1 CDS Pden_2189 NC_008686.1 2191536 2192510 D 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 2191536..2192510 Paracoccus denitrificans PD1222 4579165 YP_915978.1 CDS Pden_2190 NC_008686.1 2192507 2192944 D hypothetical protein 2192507..2192944 Paracoccus denitrificans PD1222 4579166 YP_915979.1 CDS Pden_2191 NC_008686.1 2193033 2194895 D 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 2193033..2194895 Paracoccus denitrificans PD1222 4579167 YP_915980.1 CDS Pden_2192 NC_008686.1 2194934 2196247 D PFAM: glycosyl transferase, group 1; KEGG: mxa:MXAN_7445 glycosyl transferase, group 1 family protein; group 1 glycosyl transferase 2194934..2196247 Paracoccus denitrificans PD1222 4579168 YP_915981.1 CDS Pden_2193 NC_008686.1 2196275 2198092 D PFAM: peptidase M24; KEGG: rsp:RSP_1975 aminopeptidase P; peptidase M24 2196275..2198092 Paracoccus denitrificans PD1222 4579169 YP_915982.1 CDS Pden_2194 NC_008686.1 2198283 2199329 R PFAM: protein of unknown function DUF475; KEGG: rsp:RSP_0459 hypothetical protein; hypothetical protein complement(2198283..2199329) Paracoccus denitrificans PD1222 4579170 YP_915983.1 CDS Pden_2195 NC_008686.1 2199445 2200671 R PFAM: MOFRL domain protein; KEGG: sit:TM1040_3471 hydroxypyruvate reductase; hydroxypyruvate reductase complement(2199445..2200671) Paracoccus denitrificans PD1222 4579171 YP_915984.1 CDS Pden_2196 NC_008686.1 2200671 2201621 R 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 complement(2200671..2201621) Paracoccus denitrificans PD1222 4579172 YP_915985.1 CDS Pden_2197 NC_008686.1 2201621 2201962 R TIGRFAM: export-related chaperone CsaA; PFAM: t-RNA-binding domain protein; KEGG: rsp:RSP_3365 protein secretion chaperonine; export-related chaperone CsaA complement(2201621..2201962) Paracoccus denitrificans PD1222 4579173 YP_915986.1 CDS Pden_2198 NC_008686.1 2201959 2202762 R catalyzes the formation of L-proline from pyrroline-5-carboxylate; pyrroline-5-carboxylate reductase complement(2201959..2202762) Paracoccus denitrificans PD1222 4579174 YP_915987.1 CDS Pden_2199 NC_008686.1 2202801 2203301 R KEGG: jan:Jann_3330 hypothetical protein; hypothetical protein complement(2202801..2203301) Paracoccus denitrificans PD1222 4579175 YP_915988.1 CDS Pden_2200 NC_008686.1 2203527 2204489 D PFAM: aminotransferase, class I and II; KEGG: rsp:RSP_0789 aminotransferase, class-I; class I and II aminotransferase 2203527..2204489 Paracoccus denitrificans PD1222 4579176 YP_915989.1 CDS Pden_2201 NC_008686.1 2204473 2205516 R With PurE catalyzes the conversion of aminoimidazole ribonucleotide to carboxyaminoimidazole ribonucleotide in the de novo purine nucleotide biosynthetic pathway; phosphoribosylaminoimidazole carboxylase ATPase subunit complement(2204473..2205516) Paracoccus denitrificans PD1222 4579177 YP_915990.1 CDS Pden_2202 NC_008686.1 2205509 2206006 R 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 complement(2205509..2206006) Paracoccus denitrificans PD1222 4579178 YP_915991.1 CDS Pden_2203 NC_008686.1 2206059 2206277 R PFAM: protein of unknown function DUF465; KEGG: jan:Jann_3351 protein of unknown function DUF465; hypothetical protein complement(2206059..2206277) Paracoccus denitrificans PD1222 4579179 YP_915992.1 CDS Pden_2204 NC_008686.1 2206440 2207036 D KEGG: jan:Jann_2350 hypothetical protein; hypothetical protein 2206440..2207036 Paracoccus denitrificans PD1222 4579180 YP_915993.1 CDS Pden_2205 NC_008686.1 2207159 2207569 D PFAM: heat shock protein Hsp20; KEGG: jan:Jann_3350 heat shock protein HSP20; heat shock protein Hsp20 2207159..2207569 Paracoccus denitrificans PD1222 4579181 YP_915994.1 CDS Pden_2206 NC_008686.1 2207583 2207810 D PFAM: protein of unknown function DUF1150; KEGG: rsp:RSP_1573 hypothetical protein; hypothetical protein 2207583..2207810 Paracoccus denitrificans PD1222 4579182 YP_915995.1 CDS Pden_2207 NC_008686.1 2207975 2208787 R KEGG: rsp:RSP_1575 binfunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; binfunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein complement(2207975..2208787) Paracoccus denitrificans PD1222 4579183 YP_915996.1 CDS Pden_2208 NC_008686.1 2208807 2209823 R TIGRFAM: thioredoxin reductase; PFAM: FAD-dependent pyridine nucleotide-disulphide oxidoreductase; glucose-inhibited division protein A; KEGG: rsp:RSP_1576 thioredoxin reductase; thioredoxin reductase complement(2208807..2209823) Paracoccus denitrificans PD1222 4579184 YP_915997.1 CDS Pden_2209 NC_008686.1 2209988 2210488 D PFAM: regulatory protein, AsnC/Lrp family; KEGG: rsp:RSP_1577 proline dehydrogenase transcriptional activator; AsnC family transcriptional regulator 2209988..2210488 Paracoccus denitrificans PD1222 4579185 YP_915998.1 CDS Pden_2210 NC_008686.1 2210569 2211006 D hypothetical protein 2210569..2211006 Paracoccus denitrificans PD1222 4579186 YP_915999.1 CDS Pden_2211 NC_008686.1 2211103 2211867 R PFAM: protein of unknown function DUF152; KEGG: rde:RD1_3503 hypothetical protein; hypothetical protein complement(2211103..2211867) Paracoccus denitrificans PD1222 4579187 YP_916000.1 CDS Pden_2212 NC_008686.1 2211851 2212918 R PFAM: protein of unknown function DUF185; KEGG: sil:SPO0907 hypothetical protein; hypothetical protein complement(2211851..2212918) Paracoccus denitrificans PD1222 4579188 YP_916001.1 CDS Pden_2213 NC_008686.1 2212915 2213805 R transfers the N-acyl diglyceride moiety to the prospective N-terminal cysteine in prolipoprotein; prolipoprotein diacylglyceryl transferase complement(2212915..2213805) Paracoccus denitrificans PD1222 4579189 YP_916002.1 CDS Pden_2214 NC_008686.1 2213932 2214186 D PFAM: protein of unknown function DUF526; KEGG: sit:TM1040_0621 protein of unknown function DUF526; hypothetical protein 2213932..2214186 Paracoccus denitrificans PD1222 4579190 YP_916003.1 CDS Pden_2215 NC_008686.1 2214481 2215506 D TIGRFAM: pseudouridine synthase, RluA family; PFAM: pseudouridine synthase; KEGG: rsp:RSP_2409 pseudouridine synthase, Rlu; RluA family pseudouridine synthase 2214481..2215506 Paracoccus denitrificans PD1222 4579191 YP_916004.1 CDS Pden_2216 NC_008686.1 2215573 2216478 D 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 2215573..2216478 Paracoccus denitrificans PD1222 4579192 YP_916005.1 CDS Pden_2217 NC_008686.1 2216845 2217864 D KEGG: rsp:RSP_6009 hypothetical protein; hypothetical protein 2216845..2217864 Paracoccus denitrificans PD1222 4579193 YP_916006.1 CDS Pden_2218 NC_008686.1 2217872 2218921 R PFAM: Sporulation domain protein; KEGG: rsp:RSP_6008 hypothetical protein; sporulation domain-containing protein complement(2217872..2218921) Paracoccus denitrificans PD1222 4579194 YP_916007.1 CDS upp NC_008686.1 2218991 2219626 R Catalyzes the formation of uracil and 5-phospho-alpha-D-ribosy 1-diphosphate from UMP and diphosphate; uracil phosphoribosyltransferase complement(2218991..2219626) Paracoccus denitrificans PD1222 4579195 YP_916008.1 CDS Pden_2220 NC_008686.1 2219623 2220591 R catalyzes the formation of inosine from adenosine; adenosine deaminase complement(2219623..2220591) Paracoccus denitrificans PD1222 4579196 YP_916009.1 CDS Pden_2221 NC_008686.1 2220588 2221772 R catalyzes the transfer of phosphate between the C1 and C5 carbons of pentose; phosphopentomutase complement(2220588..2221772) Paracoccus denitrificans PD1222 4579197 YP_916010.1 CDS deoA NC_008686.1 2221769 2223061 R Catalyzes the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate; thymidine phosphorylase complement(2221769..2223061) Paracoccus denitrificans PD1222 4579198 YP_916011.1 CDS Pden_2223 NC_008686.1 2223058 2223453 R TIGRFAM: cytidine deaminase; PFAM: CMP/dCMP deaminase, zinc-binding; KEGG: sil:SPO2930 cytidine deaminase; cytidine deaminase complement(2223058..2223453) Paracoccus denitrificans PD1222 4579199 YP_916012.1 CDS Pden_2224 NC_008686.1 2223617 2225896 D NAD-dependent; catalyzes the oxidative decarboxylation of malate to form pyruvate; does not decarboxylate oxaloacetate; malic enzyme 2223617..2225896 Paracoccus denitrificans PD1222 4579200 YP_916013.1 CDS Pden_2225 NC_008686.1 2226148 2228052 D PFAM: AMP-dependent synthetase and ligase; KEGG: rsp:RSP_1592 possible acyl-CoA sythetase; AMP-dependent synthetase/ligase 2226148..2228052 Paracoccus denitrificans PD1222 4579201 YP_916014.1 CDS Pden_2226 NC_008686.1 2228138 2229469 R catalyzes the formation of 5-O-(1-carboxyvinyl)-3-phosphoshikimate from phosphoenolpyruvate and 3-phosphoshikimate in tryptophan biosynthesis; 3-phosphoshikimate 1-carboxyvinyltransferase complement(2228138..2229469) Paracoccus denitrificans PD1222 4579202 YP_916015.1 CDS trmB NC_008686.1 2229547 2230248 R 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 complement(2229547..2230248) Paracoccus denitrificans PD1222 4579203 YP_916016.1 CDS Pden_2228 NC_008686.1 2230270 2231946 R 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 complement(2230270..2231946) Paracoccus denitrificans PD1222 4579282 YP_916017.1 CDS Pden_2229 NC_008686.1 2231939 2232718 R 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 complement(2231939..2232718) Paracoccus denitrificans PD1222 4579283 YP_916018.1 CDS Pden_2230 NC_008686.1 2232722 2233480 R 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 complement(2232722..2233480) Paracoccus denitrificans PD1222 4579284 YP_916019.1 CDS Pden_2231 NC_008686.1 2233473 2234972 R Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit N complement(2233473..2234972) Paracoccus denitrificans PD1222 4579285 YP_916020.1 CDS Pden_2232 NC_008686.1 2234982 2236523 R Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit M complement(2234982..2236523) Paracoccus denitrificans PD1222 4579286 YP_916021.1 CDS Pden_2233 NC_008686.1 2236525 2238636 R Catalyzes the transfer of electrons from NADH to ubiquinone; NADH dehydrogenase subunit L complement(2236525..2238636) Paracoccus denitrificans PD1222 4579287 YP_916022.1 CDS Pden_2234 NC_008686.1 2238643 2238948 R PFAM: NADH-ubiquinone oxidoreductase, chain 4L; KEGG: sit:TM1040_0757 NADH-ubiquinone oxidoreductase, chain 4L; NADH-ubiquinone oxidoreductase, chain 4L complement(2238643..2238948) Paracoccus denitrificans PD1222 4579288 YP_916023.1 CDS Pden_2235 NC_008686.1 2239048 2239647 R Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit J complement(2239048..2239647) Paracoccus denitrificans PD1222 4579289 YP_916024.1 CDS Pden_2236 NC_008686.1 2239647 2240051 R PFAM: Carboxymuconolactone decarboxylase; KEGG: rsp:RSP_2524 possible carboxymuconolactone decarboxylase family protein; carboxymuconolactone decarboxylase complement(2239647..2240051) Paracoccus denitrificans PD1222 4579290 YP_916025.1 CDS Pden_2237 NC_008686.1 2240048 2240440 R PFAM: Carboxymuconolactone decarboxylase; KEGG: jan:Jann_1188 carboxymuconolactone decarboxylase; carboxymuconolactone decarboxylase complement(2240048..2240440) Paracoccus denitrificans PD1222 4579291 YP_916026.1 CDS Pden_2238 NC_008686.1 2240437 2240928 R Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit I complement(2240437..2240928) Paracoccus denitrificans PD1222 4579292 YP_916027.1 CDS Pden_2239 NC_008686.1 2241114 2242151 R Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit H complement(2241114..2242151) Paracoccus denitrificans PD1222 4579293 YP_916028.1 CDS Pden_2240 NC_008686.1 2242170 2242937 R KEGG: jan:Jann_1184 lipoprotein; hypothetical protein complement(2242170..2242937) Paracoccus denitrificans PD1222 4579294 YP_916029.1 CDS Pden_2241 NC_008686.1 2242943 2244967 R Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit G complement(2242943..2244967) Paracoccus denitrificans PD1222 4579295 YP_916030.1 CDS Pden_2242 NC_008686.1 2245247 2245813 R KEGG: sil:SPO2775 hypothetical protein; hypothetical protein complement(2245247..2245813) Paracoccus denitrificans PD1222 4579296 YP_916031.1 CDS Pden_2243 NC_008686.1 2245820 2247115 R 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 complement(2245820..2247115) Paracoccus denitrificans PD1222 4579297 YP_916032.1 CDS Pden_2244 NC_008686.1 2247120 2247383 R KEGG: jan:Jann_1178 hypothetical protein; hypothetical protein complement(2247120..2247383) Paracoccus denitrificans PD1222 4579298 YP_916033.1 CDS Pden_2245 NC_008686.1 2247383 2248027 R KEGG: jan:Jann_1177 hypothetical protein; hypothetical protein complement(2247383..2248027) Paracoccus denitrificans PD1222 4579299 YP_916034.1 CDS Pden_2246 NC_008686.1 2248052 2248771 R Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit E complement(2248052..2248771) Paracoccus denitrificans PD1222 4579300 YP_916035.1 CDS Pden_2247 NC_008686.1 2248771 2250009 R Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit D complement(2248771..2250009) Paracoccus denitrificans PD1222 4579301 YP_916036.1 CDS Pden_2248 NC_008686.1 2250063 2250689 R Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit C complement(2250063..2250689) Paracoccus denitrificans PD1222 4579302 YP_916037.1 CDS Pden_2249 NC_008686.1 2250693 2251220 R 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 complement(2250693..2251220) Paracoccus denitrificans PD1222 4579303 YP_916038.1 CDS Pden_2250 NC_008686.1 2251217 2251582 R Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit A complement(2251217..2251582) Paracoccus denitrificans PD1222 4579304 YP_916039.1 CDS Pden_2251 NC_008686.1 2251761 2252132 R KEGG: sit:TM1040_0660 conserved hypothetical protein; hypothetical protein complement(2251761..2252132) Paracoccus denitrificans PD1222 4579305 YP_916040.1 CDS uvrA NC_008686.1 2252129 2255008 R 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 complement(2252129..2255008) Paracoccus denitrificans PD1222 4579306 YP_916041.1 CDS Pden_2253 NC_008686.1 2255154 2255507 D PFAM: glutathione-dependent formaldehyde-activating, GFA; KEGG: atc:AGR_C_4363 hypothetical protein; glutathione-dependent formaldehyde-activating protein 2255154..2255507 Paracoccus denitrificans PD1222 4579307 YP_916042.1 CDS moaA NC_008686.1 2255504 2256538 R together with moaC, is involved in the conversion of a guanosine derivative (GXP) into molybdopterin precursor Z; molybdenum cofactor biosynthesis protein A complement(2255504..2256538) Paracoccus denitrificans PD1222 4579308 YP_916043.1 CDS Pden_2255 NC_008686.1 2256663 2257166 D KEGG: rsp:RSP_6106 hypothetical protein; hypothetical protein 2256663..2257166 Paracoccus denitrificans PD1222 4579309 YP_916044.1 CDS Pden_2256 NC_008686.1 2257154 2257858 R KEGG: sil:SPO2798 hypothetical protein; hypothetical protein complement(2257154..2257858) Paracoccus denitrificans PD1222 4579310 YP_916045.1 CDS Pden_2257 NC_008686.1 2258143 2259615 D KEGG: rsp:RSP_1012 succinate-semialdehyde dehdyrogenase; TIGRFAM: succinic semialdehyde dehydrogenase; PFAM: aldehyde dehydrogenase; succinate-semialdehyde dehydrogenase 2258143..2259615 Paracoccus denitrificans PD1222 4579311 YP_916046.1 CDS Pden_2258 NC_008686.1 2259661 2260407 R PFAM: protein of unknown function DUF1013; KEGG: rsp:RSP_0714 hypothetical protein; hypothetical protein complement(2259661..2260407) Paracoccus denitrificans PD1222 4579312 YP_916047.1 CDS Pden_2259 NC_008686.1 2260568 2261188 D PFAM: ribonuclease T2; KEGG: sit:TM1040_2631 ribonuclease T2; ribonuclease T2 2260568..2261188 Paracoccus denitrificans PD1222 4579313 YP_916048.1 CDS Pden_2260 NC_008686.1 2261370 2261852 D hypothetical protein 2261370..2261852 Paracoccus denitrificans PD1222 4579314 YP_916049.1 CDS Pden_2261 NC_008686.1 2261861 2262172 R PFAM: TM2 domain containing protein+B7201; KEGG: pau:PA14_53630 hypothetical protein; TM2 domain-containing protein complement(2261861..2262172) Paracoccus denitrificans PD1222 4579315 YP_916050.1 CDS pheT NC_008686.1 2262355 2264742 D 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 2262355..2264742 Paracoccus denitrificans PD1222 4579316 YP_916051.1 CDS Pden_2263 NC_008686.1 2264921 2265478 D hypothetical protein 2264921..2265478 Paracoccus denitrificans PD1222 4579317 YP_916052.1 CDS Pden_2264 NC_008686.1 2265660 2266376 R PFAM: Glutathione S-transferase, N-terminal domain; KEGG: bxe:Bxe_A3350 glutathione S-transferase; glutathione S-transferase domain-containing protein complement(2265660..2266376) Paracoccus denitrificans PD1222 4579318 YP_916053.1 CDS Pden_2265 NC_008686.1 2266459 2266896 D TIGRFAM: large conductance mechanosensitive channel protein; PFAM: large-conductance mechanosensitive channel; KEGG: sil:SPO3495 large conductance mechanosensitive channel protein; large conductance mechanosensitive channel protein 2266459..2266896 Paracoccus denitrificans PD1222 4579319 YP_916054.1 CDS Pden_2266 NC_008686.1 2267048 2267509 D PFAM: regulatory protein, AsnC/Lrp family; KEGG: rsp:RSP_0722 transcriptional regulator, AsnC family; AsnC family transcriptional regulator 2267048..2267509 Paracoccus denitrificans PD1222 4579320 YP_916055.1 CDS rpsU NC_008686.1 2267563 2267769 R 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 complement(2267563..2267769) Paracoccus denitrificans PD1222 4579321 YP_916056.1 CDS Pden_2268 NC_008686.1 2267894 2268580 D TIGRFAM: rpsU-divergently transcribed protein; PFAM: COQ9 domain protein; KEGG: sil:SPO0230 hypothetical protein; rpsU-divergently transcribed protein 2267894..2268580 Paracoccus denitrificans PD1222 4579322 YP_916057.1 CDS Pden_2269 NC_008686.1 2268592 2269569 D 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 2268592..2269569 Paracoccus denitrificans PD1222 4579323 YP_916058.1 CDS pheS NC_008686.1 2269677 2270759 R 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 complement(2269677..2270759) Paracoccus denitrificans PD1222 4579324 YP_916059.1 CDS Pden_2271 NC_008686.1 2270818 2271162 R TIGRFAM: arsenate reductase; PFAM: arsenate reductase and related; KEGG: hne:HNE_0991 arsenate reductase; arsenate reductase complement(2270818..2271162) Paracoccus denitrificans PD1222 4579325 YP_916060.1 CDS Pden_2272 NC_008686.1 2271194 2272555 R PFAM: cytochrome P450; KEGG: rde:RD1_1394 cytochrome P450; cytochrome P450 complement(2271194..2272555) Paracoccus denitrificans PD1222 4579326 YP_916061.1 CDS rplT NC_008686.1 2272794 2273153 R binds directly to 23S ribosomal RNA prior to in vitro assembly of the 50S ribosomal subunit; 50S ribosomal protein L20 complement(2272794..2273153) Paracoccus denitrificans PD1222 4579327 YP_916062.1 CDS rpmI NC_008686.1 2273166 2273366 R PFAM: ribosomal protein L35; KEGG: rsp:RSP_1765 50S ribosomal protein L35; 50S ribosomal protein L35 complement(2273166..2273366) Paracoccus denitrificans PD1222 4579328 YP_916063.1 CDS Pden_2275 NC_008686.1 2273475 2273864 R hypothetical protein complement(2273475..2273864) Paracoccus denitrificans PD1222 4579329 YP_916064.1 CDS Pden_2276 NC_008686.1 2273905 2275350 R PFAM: pyruvate kinase; KEGG: sil:SPO3600 pyruvate kinase; pyruvate kinase complement(2273905..2275350) Paracoccus denitrificans PD1222 4579330 YP_916065.1 CDS Pden_2277 NC_008686.1 2275471 2276211 D PFAM: N-formylglutamate amidohydrolase; KEGG: rsp:RSP_1767 possible N-formylglutamate amidohydrolase; N-formylglutamate amidohydrolase 2275471..2276211 Paracoccus denitrificans PD1222 4579331 YP_916066.1 CDS Pden_2278 NC_008686.1 2276961 2277200 R hypothetical protein complement(2276961..2277200) Paracoccus denitrificans PD1222 4579332 YP_916067.1 CDS Pden_2279 NC_008686.1 2277297 2277767 R hypothetical protein complement(2277297..2277767) Paracoccus denitrificans PD1222 4579333 YP_916068.1 CDS Pden_2280 NC_008686.1 2277814 2278233 D hypothetical protein 2277814..2278233 Paracoccus denitrificans PD1222 4579334 YP_916069.1 CDS Pden_2281 NC_008686.1 2278522 2279088 D PFAM: Arc domain protein DNA binding domain protein; Arc domain-containing protein 2278522..2279088 Paracoccus denitrificans PD1222 4579335 YP_916070.1 CDS Pden_2282 NC_008686.1 2279485 2280549 R PFAM: TPR repeat-containing protein; Tetratricopeptide TPR_2 repeat protein; SMART: Tetratricopeptide domain protein; KEGG: mca:MCA1751 hypothetical protein; hypothetical protein complement(2279485..2280549) Paracoccus denitrificans PD1222 4579336 YP_916071.1 CDS Pden_2283 NC_008686.1 2280660 2281010 R hypothetical protein complement(2280660..2281010) Paracoccus denitrificans PD1222 4579337 YP_916072.1 CDS Pden_2285 NC_008686.1 2281578 2282513 D 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 2281578..2282513 Paracoccus denitrificans PD1222 4579338 YP_916073.1 CDS Pden_2286 NC_008686.1 2282514 2284010 D PFAM: sulfatase; KEGG: rsp:RSP_0594 choline sulfatase; sulfatase 2282514..2284010 Paracoccus denitrificans PD1222 4579339 YP_916074.1 CDS Pden_2287 NC_008686.1 2284145 2284726 D PFAM: membrane protein of uknown function UCP014873; KEGG: gvi:gll1598 hypothetical protein; hypothetical protein 2284145..2284726 Paracoccus denitrificans PD1222 4579340 YP_916075.1 CDS Pden_2288 NC_008686.1 2284766 2285524 D TIGRFAM: monofunctional biosynthetic peptidoglycan transglycosylase; PFAM: glycosyl transferase, family 51; KEGG: sil:SPO3766 monofunctional biosynthetic peptidoglycan transglycosylase; monofunctional biosynthetic peptidoglycan transglycosylase 2284766..2285524 Paracoccus denitrificans PD1222 4579341 YP_916076.1 CDS Pden_2289 NC_008686.1 2285541 2286299 D PFAM: Glutathione S-transferase, N-terminal domain; KEGG: jan:Jann_0275 glutathione S-transferase-like; glutathione S-transferase domain-containing protein 2285541..2286299 Paracoccus denitrificans PD1222 4579342 YP_916077.1 CDS Pden_2290 NC_008686.1 2286280 2287323 D 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 2286280..2287323 Paracoccus denitrificans PD1222 4579343 YP_916078.1 CDS Pden_2291 NC_008686.1 2287320 2288261 D PFAM: protein of unknown function DUF6, transmembrane; KEGG: rsp:RSP_0987 transporter, RarD family, DMT superfamily; hypothetical protein 2287320..2288261 Paracoccus denitrificans PD1222 4579344 YP_916079.1 CDS Pden_2292 NC_008686.1 2288274 2289668 R KEGG: sit:TM1040_0020 conserved hypothetical protein; hypothetical protein complement(2288274..2289668) Paracoccus denitrificans PD1222 4579345 YP_916080.1 CDS Pden_2293 NC_008686.1 2289665 2291365 R PFAM: glycosyl transferase, family 14; KEGG: sit:TM1040_0019 glycosyl transferase, family 14; glycosyl transferase family protein complement(2289665..2291365) Paracoccus denitrificans PD1222 4579346 YP_916081.1 CDS Pden_2294 NC_008686.1 2291362 2292387 R KEGG: jan:Jann_0220 hypothetical protein; hypothetical protein complement(2291362..2292387) Paracoccus denitrificans PD1222 4579347 YP_916082.1 CDS Pden_2295 NC_008686.1 2292415 2293653 R PFAM: glycosyl transferase, group 1; KEGG: jan:Jann_0219 glycosyl transferase, group 1; group 1 glycosyl transferase complement(2292415..2293653) Paracoccus denitrificans PD1222 4579348 YP_916083.1 CDS Pden_2296 NC_008686.1 2293643 2294641 R 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 complement(2293643..2294641) Paracoccus denitrificans PD1222 4579349 YP_916084.1 CDS Pden_2297 NC_008686.1 2294647 2295537 R PFAM: Nucleotidyl transferase; KEGG: rsp:RSP_1159 UDP-glucose pyrophosphate; nucleotidyl transferase complement(2294647..2295537) Paracoccus denitrificans PD1222 4579350 YP_916085.1 CDS Pden_2298 NC_008686.1 2295684 2296892 R PFAM: glycosyl transferase, family 2; KEGG: jan:Jann_0217 glycosyl transferase, family 2; glycosyl transferase family protein complement(2295684..2296892) Paracoccus denitrificans PD1222 4579351 YP_916086.1 CDS Pden_2299 NC_008686.1 2296892 2297692 R 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 complement(2296892..2297692) Paracoccus denitrificans PD1222 4579352 YP_916087.1 CDS Pden_2300 NC_008686.1 2297697 2298494 R TIGRFAM: 3'(2'),5'-bisphosphate nucleotidase; PFAM: inositol monophosphatase; KEGG: rsp:RSP_1161 3'-phosphadenosine 5'-phosphosulfate 3'-phosphatase; 3'(2'),5'-bisphosphate nucleotidase complement(2297697..2298494) Paracoccus denitrificans PD1222 4579353 YP_916088.1 CDS Pden_2301 NC_008686.1 2298636 2299457 D PFAM: ABC-2 type transporter; KEGG: sil:SPO0040 ABC transporter, permease protein; ABC transporter 2298636..2299457 Paracoccus denitrificans PD1222 4579354 YP_916089.1 CDS dnaK NC_008686.1 2299715 2301631 D 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 2299715..2301631 Paracoccus denitrificans PD1222 4579355 YP_916090.1 CDS Pden_2303 NC_008686.1 2301713 2302867 D 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 2301713..2302867 Paracoccus denitrificans PD1222 4579356 YP_916091.1 CDS radC NC_008686.1 2302913 2303704 D 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 2302913..2303704 Paracoccus denitrificans PD1222 4579357 YP_916092.1 CDS Pden_2305 NC_008686.1 2303887 2304474 D 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 2303887..2304474 Paracoccus denitrificans PD1222 4579358 YP_916093.1 CDS Pden_2306 NC_008686.1 2304485 2305807 D 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 2304485..2305807 Paracoccus denitrificans PD1222 4579359 YP_916094.1 CDS Pden_2307 NC_008686.1 2305820 2307172 D PFAM: cytochrome c1; KEGG: rde:RD1_0565 cytochrome c1; cytochrome c1 2305820..2307172 Paracoccus denitrificans PD1222 4579360 YP_916095.1 CDS Pden_2308 NC_008686.1 2307311 2308180 D PFAM: PfkB domain protein; KEGG: rsp:RSP_1216 RbsK, carbohydrate kinase, ribokinase family; ribokinase 2307311..2308180 Paracoccus denitrificans PD1222 4579361 YP_916096.1 CDS Pden_2309 NC_008686.1 2308220 2309023 D PFAM: peptidase S49; KEGG: sil:SPO3640 peptidase, family S49; peptidase S49 2308220..2309023 Paracoccus denitrificans PD1222 4579362 YP_916097.1 CDS Pden_2310 NC_008686.1 2309020 2309130 D hypothetical protein 2309020..2309130 Paracoccus denitrificans PD1222 4579363 YP_916098.1 CDS Pden_2311 NC_008686.1 2309127 2309897 D PFAM: short-chain dehydrogenase/reductase SDR; KR; KEGG: jan:Jann_3920 short-chain dehydrogenase/reductase SDR; short chain dehydrogenase 2309127..2309897 Paracoccus denitrificans PD1222 4579364 YP_916099.1 CDS uvrC NC_008686.1 2310199 2312070 D 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 2310199..2312070 Paracoccus denitrificans PD1222 4579365 YP_916100.1 CDS Pden_2313 NC_008686.1 2312083 2312514 D KEGG: atc:AGR_C_2408 hypothetical protein; hypothetical protein 2312083..2312514 Paracoccus denitrificans PD1222 4579366 YP_916101.1 CDS Pden_2314 NC_008686.1 2312521 2313147 R KEGG: rsp:RSP_2812 hypothetical protein; hypothetical protein complement(2312521..2313147) Paracoccus denitrificans PD1222 4579367 YP_916102.1 CDS Pden_2315 NC_008686.1 2313159 2314460 R PFAM: Mammalian cell entry related domain protein; KEGG: rsp:RSP_2811 ABC transporter, periplasmic substrate-binding protein; hypothetical protein complement(2313159..2314460) Paracoccus denitrificans PD1222 4579368 YP_916103.1 CDS Pden_2316 NC_008686.1 2314465 2315241 R PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rsp:RSP_2810 ABC transporter, ATPase subunit; ABC transporter complement(2314465..2315241) Paracoccus denitrificans PD1222 4579369 YP_916104.1 CDS Pden_2317 NC_008686.1 2315238 2316332 R PFAM: protein of unknown function DUF140; KEGG: rsp:RSP_2809 ABC transporter, inner membrane subunit; hypothetical protein complement(2315238..2316332) Paracoccus denitrificans PD1222 4579370 YP_916105.1 CDS Pden_2318 NC_008686.1 2316776 2317693 R PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: jan:Jann_1027 transcriptional regulator, LysR family; LysR family transcriptional regulator complement(2316776..2317693) Paracoccus denitrificans PD1222 4579371 YP_916106.1 CDS Pden_2319 NC_008686.1 2317784 2318647 D TIGRFAM: 5,10-methylenetetrahydrofolate reductase; PFAM: methylenetetrahydrofolate reductase; KEGG: rsp:RSP_2172 5,10-methylenetetrahydrofolate reductase; 5,10-methylenetetrahydrofolate reductase 2317784..2318647 Paracoccus denitrificans PD1222 4579372 YP_916107.1 CDS Pden_2320 NC_008686.1 2318675 2319826 R KEGG: sil:SPO3018 hypothetical protein; hypothetical protein complement(2318675..2319826) Paracoccus denitrificans PD1222 4579373 YP_916108.1 CDS Pden_2321 NC_008686.1 2319868 2321031 R PFAM: Orn/DAP/Arg decarboxylase 2; KEGG: rsp:RSP_1991 ornithine decarboxylase; Orn/DAP/Arg decarboxylase 2 complement(2319868..2321031) Paracoccus denitrificans PD1222 4579374 YP_916109.1 CDS Pden_2322 NC_008686.1 2321165 2321596 D PFAM: regulatory protein, AsnC/Lrp family; KEGG: rsp:RSP_1990 transcriptional regulator, AsnC family; AsnC family transcriptional regulator 2321165..2321596 Paracoccus denitrificans PD1222 4579375 YP_916110.1 CDS Pden_2323 NC_008686.1 2321563 2322159 R TIGRFAM: methyltransferase; PFAM: conserved hypothetical protein 95; KEGG: rsp:RSP_0901 N-6 adenine-specific DNA methylase; methyltransferase complement(2321563..2322159) Paracoccus denitrificans PD1222 4579376 YP_916111.1 CDS Pden_2324 NC_008686.1 2322156 2323352 R PFAM: FAD-dependent pyridine nucleotide-disulphide oxidoreductase; KEGG: rsp:RSP_0900 FAD-dependent pyridine nucleotide-disulphide oxidoreductase; FAD-dependent pyridine nucleotide-disulfide oxidoreductase complement(2322156..2323352) Paracoccus denitrificans PD1222 4579377 YP_916112.1 CDS Pden_2325 NC_008686.1 2323408 2323914 D PFAM: Redoxin domain protein; KEGG: sit:TM1040_2472 redoxin; redoxin domain-containing protein 2323408..2323914 Paracoccus denitrificans PD1222 4579378 YP_916113.1 CDS Pden_2326 NC_008686.1 2323848 2324561 R PFAM: helix-turn-helix, HxlR type; KEGG: bpa:BPP3401 transcriptional regulator; HxlR family transcriptional regulator complement(2323848..2324561) Paracoccus denitrificans PD1222 4579379 YP_916114.1 CDS Pden_2327 NC_008686.1 2324650 2325006 D PFAM: protein of unknown function DUF1428; KEGG: hne:HNE_1019 hypothetical protein; hypothetical protein 2324650..2325006 Paracoccus denitrificans PD1222 4579380 YP_916115.1 CDS Pden_2328 NC_008686.1 2325203 2325805 D PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase; KEGG: sme:SMc04054 hypothetical protein; glyoxalase/bleomycin resistance protein/dioxygenase 2325203..2325805 Paracoccus denitrificans PD1222 4579381 YP_916116.1 CDS Pden_2329 NC_008686.1 2325802 2326437 D PFAM: YceI family protein; KEGG: bma:BMAA0007 YceI like family protein; hypothetical protein 2325802..2326437 Paracoccus denitrificans PD1222 4579382 YP_916117.1 CDS Pden_2330 NC_008686.1 2326441 2327073 D 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 2326441..2327073 Paracoccus denitrificans PD1222 4579383 YP_916118.1 CDS valS NC_008686.1 2327364 2330456 D 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 2327364..2330456 Paracoccus denitrificans PD1222 4579384 YP_916119.1 CDS Pden_2332 NC_008686.1 2330519 2331211 R PFAM: cobalamin (vitamin B12) biosynthesis CbiX protein; KEGG: sil:SPO2745 hypothetical protein; cobalamin (vitamin B12) biosynthesis CbiX protein complement(2330519..2331211) Paracoccus denitrificans PD1222 4579385 YP_916120.1 CDS Pden_2333 NC_008686.1 2331204 2331767 R KEGG: sil:SPOA0324 hypothetical protein; hypothetical protein complement(2331204..2331767) Paracoccus denitrificans PD1222 4579386 YP_916121.1 CDS Pden_2334 NC_008686.1 2331856 2332365 D PFAM: NnrUfamily protein; KEGG: rpe:RPE_1287 NnrU family protein; NnrU family protein 2331856..2332365 Paracoccus denitrificans PD1222 4579387 YP_916122.1 CDS Pden_2335 NC_008686.1 2332349 2333365 R PFAM: FAD dependent oxidoreductase; KEGG: jan:Jann_0139 FAD dependent oxidoreductase; FAD dependent oxidoreductase complement(2332349..2333365) Paracoccus denitrificans PD1222 4579388 YP_916123.1 CDS Pden_2336 NC_008686.1 2333413 2334069 D PFAM: protein of unknown function DUF752; KEGG: sil:SPO3553 hypothetical protein; hypothetical protein 2333413..2334069 Paracoccus denitrificans PD1222 4579389 YP_916124.1 CDS Pden_2337 NC_008686.1 2334066 2334782 R PFAM: Rhomboid family protein; KEGG: jan:Jann_3255 rhomboid-like protein; rhomboid family protein complement(2334066..2334782) Paracoccus denitrificans PD1222 4579390 YP_916125.1 CDS Pden_2338 NC_008686.1 2334887 2336155 D catalyzes the formation of succinate semialdehyde and glutamate from 4-aminobutanoate and 2-oxoglutarate; 4-aminobutyrate aminotransferase 2334887..2336155 Paracoccus denitrificans PD1222 4579391 YP_916126.1 CDS Pden_2339 NC_008686.1 2336443 2337399 R 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 complement(2336443..2337399) Paracoccus denitrificans PD1222 4579392 YP_916127.1 CDS Pden_2340 NC_008686.1 2337468 2337908 R PFAM: molybdopterin biosynthesis MoaE; KEGG: sit:TM1040_3633 molybdopterin biosynthesis MoaE; molybdopterin biosynthesis MoaE complement(2337468..2337908) Paracoccus denitrificans PD1222 4579393 YP_916128.1 CDS Pden_2341 NC_008686.1 2337910 2338161 R TIGRFAM: molybdopterin converting factor, subunit 1; PFAM: thiamineS protein; KEGG: sit:TM1040_3632 molybdopterin converting factor, subunit 1; molybdopterin converting factor subunit 1 complement(2337910..2338161) Paracoccus denitrificans PD1222 4579394 YP_916129.1 CDS Pden_2342 NC_008686.1 2338151 2338780 R 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 complement(2338151..2338780) Paracoccus denitrificans PD1222 4579395 YP_916130.1 CDS Pden_2343 NC_008686.1 2338840 2339280 R PFAM: regulatory protein, MerR; KEGG: rsp:RSP_1790 probable transcriptional regulator; MerR family transcriptional regulator complement(2338840..2339280) Paracoccus denitrificans PD1222 4579396 YP_916131.1 CDS Pden_2344 NC_008686.1 2339369 2341567 D 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 2339369..2341567 Paracoccus denitrificans PD1222 4579397 YP_916132.1 CDS Pden_2346 NC_008686.1 2341915 2344743 R acts in conjunction with GvcH to form H-protein-S-aminomethyldihydrolipoyllysine from glycine; glycine dehydrogenase complement(2341915..2344743) Paracoccus denitrificans PD1222 4579398 YP_916133.1 CDS Pden_2347 NC_008686.1 2344903 2345259 R 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 complement(2344903..2345259) Paracoccus denitrificans PD1222 4579204 YP_916134.1 CDS Pden_2348 NC_008686.1 2345270 2346382 R 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 complement(2345270..2346382) Paracoccus denitrificans PD1222 4579205 YP_916135.1 CDS Pden_2349 NC_008686.1 2346659 2347441 R PFAM: short-chain dehydrogenase/reductase SDR; KEGG: sil:SPO2692 oxidoreductase, short chain dehydrogenase/reductase family; short-chain dehydrogenase/reductase SDR complement(2346659..2347441) Paracoccus denitrificans PD1222 4579206 YP_916136.1 CDS Pden_2350 NC_008686.1 2347500 2347838 R KEGG: rde:RD1_0883 hypothetical protein; hypothetical protein complement(2347500..2347838) Paracoccus denitrificans PD1222 4579207 YP_916137.1 CDS Pden_2351 NC_008686.1 2347835 2348449 R KEGG: rsp:RSP_2594 hypothetical protein; hypothetical protein complement(2347835..2348449) Paracoccus denitrificans PD1222 4579208 YP_916138.1 CDS Pden_2352 NC_008686.1 2348533 2349858 R 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 complement(2348533..2349858) Paracoccus denitrificans PD1222 4579209 YP_916139.1 CDS Pden_2353 NC_008686.1 2349862 2351043 R PFAM: domain of unknown function DUF1745; KEGG: rsp:RSP_2592 hypothetical protein; hypothetical protein complement(2349862..2351043) Paracoccus denitrificans PD1222 4579210 YP_916140.1 CDS Pden_2354 NC_008686.1 2351040 2351750 R 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 complement(2351040..2351750) Paracoccus denitrificans PD1222 4579211 YP_916141.1 CDS Pden_2355 NC_008686.1 2351939 2352928 D KEGG: sme:SMb20181 ABC transporter periplasmic solute-binding protein; ABC transporter periplasmic solute-binding protein 2351939..2352928 Paracoccus denitrificans PD1222 4579212 YP_916142.1 CDS Pden_2356 NC_008686.1 2352936 2353718 D PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: sme:SMb20182 ABC transporter protein; binding-protein-dependent transport system inner membrane protein 2352936..2353718 Paracoccus denitrificans PD1222 4579213 YP_916143.1 CDS Pden_2357 NC_008686.1 2353708 2354298 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rde:RD1_0904 ABC transporter; ABC transporter 2353708..2354298 Paracoccus denitrificans PD1222 4579214 YP_916144.1 CDS Pden_2358 NC_008686.1 2354286 2355056 R KEGG: rsp:RSP_2590 hypothetical protein; hypothetical protein complement(2354286..2355056) Paracoccus denitrificans PD1222 4579215 YP_916145.1 CDS Pden_2359 NC_008686.1 2355053 2356189 R 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 complement(2355053..2356189) Paracoccus denitrificans PD1222 4579216 YP_916146.1 CDS Pden_2360 NC_008686.1 2356186 2356494 R PFAM: coenzyme PQQ synthesis D; KEGG: rde:RD1_1151 coenzyme PQQ synthesis protein D; coenzyme PQQ biosynthesis protein PqqD complement(2356186..2356494) Paracoccus denitrificans PD1222 4579217 YP_916147.1 CDS Pden_2361 NC_008686.1 2356491 2357285 R Required in the synthesis of PPQ, but its exact function is unknown; pyrroloquinoline quinone biosynthesis protein PqqC complement(2356491..2357285) Paracoccus denitrificans PD1222 4579218 YP_916148.1 CDS Pden_2362 NC_008686.1 2357282 2358172 R possibly involved in transport of pyrroloquinoline quinone transport; pyrroloquinoline quinone biosynthesis protein PqqB complement(2357282..2358172) Paracoccus denitrificans PD1222 4579219 YP_916149.1 CDS Pden_2363 NC_008686.1 2358471 2359526 D PFAM: beta-lactamase domain protein; KEGG: rsp:RSP_2589 hypothetical protein; beta-lactamase domain-containing protein 2358471..2359526 Paracoccus denitrificans PD1222 4579220 YP_916150.1 CDS Pden_2364 NC_008686.1 2359584 2365085 D 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 2359584..2365085 Paracoccus denitrificans PD1222 4579221 YP_916151.1 CDS Pden_2365 NC_008686.1 2365153 2366238 D PFAM: helix-turn-helix, Fis-type; GAF domain protein; KEGG: sit:TM1040_3622 GAF sensor protein; Fis family transcriptional regulator 2365153..2366238 Paracoccus denitrificans PD1222 4579222 YP_916152.1 CDS Pden_2366 NC_008686.1 2366345 2367871 D PFAM: aldehyde dehydrogenase; KEGG: sme:SMc02689 probable aldehyde dehydrogenase protein; aldehyde dehydrogenase 2366345..2367871 Paracoccus denitrificans PD1222 4579223 YP_916153.1 CDS Pden_2367 NC_008686.1 2367955 2368989 D PFAM: Alcohol dehydrogenase, zinc-binding domain protein; Alcohol dehydrogenase GroES domain protein; KEGG: bmb:BruAb1_0198 alcohol dehydrogenase, zinc-containing; alcohol dehydrogenase 2367955..2368989 Paracoccus denitrificans PD1222 4579224 YP_916154.1 CDS Pden_2368 NC_008686.1 2368992 2369348 D PFAM: protein of unknown function DUF779; KEGG: mlo:mll6637 hypothetical protein; hypothetical protein 2368992..2369348 Paracoccus denitrificans PD1222 4579225 YP_916155.1 CDS Pden_2369 NC_008686.1 2369402 2369593 R PFAM: protein of unknown function DUF343; KEGG: sit:TM1040_0056 protein of unknown function DUF343; hypothetical protein complement(2369402..2369593) Paracoccus denitrificans PD1222 4579226 YP_916156.1 CDS Pden_2370 NC_008686.1 2369590 2370228 R PFAM: peptidase S16, lon domain protein; KEGG: sit:TM1040_0055 peptidase S16, lon-like; peptidase S16, lon domain-containing protein complement(2369590..2370228) Paracoccus denitrificans PD1222 4579227 YP_916157.1 CDS Pden_2371 NC_008686.1 2370230 2371141 R PFAM: Thioredoxin domain; KEGG: rsp:RSP_1489 protein containing thioredoxin domain; thioredoxin complement(2370230..2371141) Paracoccus denitrificans PD1222 4579228 YP_916158.1 CDS Pden_2372 NC_008686.1 2371232 2372017 R TIGRFAM: exodeoxyribonuclease III Xth; PFAM: Endonuclease/exonuclease/phosphatase; KEGG: sit:TM1040_0053 exodeoxyribonuclease III; exodeoxyribonuclease III complement(2371232..2372017) Paracoccus denitrificans PD1222 4579229 YP_916159.1 CDS Pden_2373 NC_008686.1 2372110 2372355 D hypothetical protein 2372110..2372355 Paracoccus denitrificans PD1222 4579230 YP_916160.1 CDS Pden_2374 NC_008686.1 2372321 2373007 R PFAM: response regulator receiver; transcriptional regulator domain protein; KEGG: jan:Jann_0417 two component transcriptional regulator, winged helix family; two component transcriptional regulator complement(2372321..2373007) Paracoccus denitrificans PD1222 4579231 YP_916161.1 CDS Pden_2375 NC_008686.1 2373141 2374202 D PFAM: GTP cyclohydrolase II; KEGG: jan:Jann_0416 GTP cyclohydrolase II; GTP cyclohydrolase II 2373141..2374202 Paracoccus denitrificans PD1222 4579232 YP_916162.1 CDS Pden_2376 NC_008686.1 2374211 2374735 D KEGG: sil:SPO3428 hypothetical protein; hypothetical protein 2374211..2374735 Paracoccus denitrificans PD1222 4579233 YP_916163.1 CDS Pden_2377 NC_008686.1 2374740 2375489 R PFAM: short-chain dehydrogenase/reductase SDR; KR; KEGG: mes:Meso_2224 short-chain dehydrogenase/reductase SDR; short-chain dehydrogenase/reductase SDR complement(2374740..2375489) Paracoccus denitrificans PD1222 4579234 YP_916164.1 CDS Pden_2378 NC_008686.1 2375591 2376790 R PFAM: RNA methylase; KEGG: sit:TM1040_2415 RNA methylase; RNA methylase complement(2375591..2376790) Paracoccus denitrificans PD1222 4579235 YP_916165.1 CDS Pden_2379 NC_008686.1 2376954 2377748 D PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase; KEGG: mes:Meso_1284 glyoxalase/bleomycin resistance protein/dioxygenase; glyoxalase/bleomycin resistance protein/dioxygenase 2376954..2377748 Paracoccus denitrificans PD1222 4579236 YP_916166.1 CDS Pden_2380 NC_008686.1 2377750 2378538 R PFAM: metallophosphoesterase; KEGG: rsp:RSP_0337 possible phospodiesterase; metallophosphoesterase complement(2377750..2378538) Paracoccus denitrificans PD1222 4579237 YP_916167.1 CDS Pden_2381 NC_008686.1 2378535 2379515 R PFAM: diacylglycerol kinase, catalytic region; KEGG: rsp:RSP_0338 hypothetical protein; diacylglycerol kinase catalytic subunit complement(2378535..2379515) Paracoccus denitrificans PD1222 4579238 YP_916168.1 CDS Pden_2382 NC_008686.1 2379864 2381087 D TIGRFAM: isochorismate synthases; PFAM: Anthranilate synthase component I and chorismate binding protein; KEGG: tfu:Tfu_1872 isochorismate synthase; isochorismate synthase 2379864..2381087 Paracoccus denitrificans PD1222 4579239 YP_916169.1 CDS Pden_2383 NC_008686.1 2381087 2381743 D PFAM: isochorismatase hydrolase; KEGG: bsu:BG11241 isochorismatase (2,3 dihydro-2,3 dihydroxybenzoate synthase); isochorismatase 2381087..2381743 Paracoccus denitrificans PD1222 4579240 YP_916170.1 CDS Pden_2384 NC_008686.1 2381734 2382504 D 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 2381734..2382504 Paracoccus denitrificans PD1222 4579241 YP_916171.1 CDS entE NC_008686.1 2382798 2384420 R 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 complement(2382798..2384420) Paracoccus denitrificans PD1222 4579242 YP_916172.1 CDS Pden_2387 NC_008686.1 2384608 2385957 D PFAM: condensation domain protein; KEGG: bmb:BruAb2_0017 hypothetical enterobactin synthetase, component F; condensation domain-containing protein 2384608..2385957 Paracoccus denitrificans PD1222 4579243 YP_916173.1 CDS Pden_2388 NC_008686.1 2386014 2386469 D PFAM: GCN5-related N-acetyltransferase; KEGG: pfl:PFL_4020 acetyltransferase, GNAT family; N-acetyltransferase 2386014..2386469 Paracoccus denitrificans PD1222 4579244 YP_916174.1 CDS Pden_2389 NC_008686.1 2386466 2386900 R KEGG: hne:HNE_2962 hypothetical protein; hypothetical protein complement(2386466..2386900) Paracoccus denitrificans PD1222 4579245 YP_916175.1 CDS Pden_2390 NC_008686.1 2386893 2387513 R KEGG: hne:HNE_2963 hypothetical protein; hypothetical protein complement(2386893..2387513) Paracoccus denitrificans PD1222 4579246 YP_916176.1 CDS Pden_2392 NC_008686.1 2388052 2389314 D 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 2388052..2389314 Paracoccus denitrificans PD1222 4579247 YP_916177.1 CDS Pden_2393 NC_008686.1 2389473 2390873 D catalyzes the formation of D-ribulose 5-phosphate from 6-phospho-D-gluconate; 6-phosphogluconate dehydrogenase 2389473..2390873 Paracoccus denitrificans PD1222 4579248 YP_916178.1 CDS Pden_2394 NC_008686.1 2391447 2392544 D KEGG: ret:RHE_PB00165 plasmid replication protein RepCb; hypothetical protein 2391447..2392544 Paracoccus denitrificans PD1222 4579249 YP_916179.1 CDS Pden_2395 NC_008686.1 2392537 2393898 D hypothetical protein 2392537..2393898 Paracoccus denitrificans PD1222 4579250 YP_916180.1 CDS Pden_2396 NC_008686.1 2394003 2394248 D TIGRFAM: addiction module antidote protein, CC2985 family; PFAM: protein of unknown function UPF0156; KEGG: xfa:XF2071 conserved hypothetical protein; CopG family transcriptional regulator 2394003..2394248 Paracoccus denitrificans PD1222 4579251 YP_916181.1 CDS Pden_2397 NC_008686.1 2394370 2394717 D hypothetical protein 2394370..2394717 Paracoccus denitrificans PD1222 4579252 YP_916182.1 CDS Pden_2398 NC_008686.1 2394938 2396110 R KEGG: mlo:mlr9349 hypothetical protein; hypothetical protein complement(2394938..2396110) Paracoccus denitrificans PD1222 4579253 YP_916183.1 CDS Pden_2399 NC_008686.1 2396435 2396644 R hypothetical protein complement(2396435..2396644) Paracoccus denitrificans PD1222 4579254 YP_916184.1 CDS Pden_2400 NC_008686.1 2396780 2397058 R hypothetical protein complement(2396780..2397058) Paracoccus denitrificans PD1222 4579255 YP_916185.1 CDS Pden_2401 NC_008686.1 2397055 2397564 R hypothetical protein complement(2397055..2397564) Paracoccus denitrificans PD1222 4579256 YP_916186.1 CDS Pden_2402 NC_008686.1 2397740 2398063 R hypothetical protein complement(2397740..2398063) Paracoccus denitrificans PD1222 4579257 YP_916187.1 CDS Pden_2403 NC_008686.1 2398139 2398366 D PFAM: helix-turn-helix domain protein; KEGG: ngo:NGO0797 transcriptional regulator; XRE family transcriptional regulator 2398139..2398366 Paracoccus denitrificans PD1222 4579258 YP_916188.1 CDS Pden_2404 NC_008686.1 2398439 2399194 D KEGG: ccr:CC1796 hypothetical protein; hypothetical protein 2398439..2399194 Paracoccus denitrificans PD1222 4579259 YP_916189.1 CDS Pden_2405 NC_008686.1 2399178 2399603 D KEGG: ccr:CC1796 hypothetical protein; hypothetical protein 2399178..2399603 Paracoccus denitrificans PD1222 4579260 YP_916190.1 CDS Pden_2406 NC_008686.1 2399885 2400790 D 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 2399885..2400790 Paracoccus denitrificans PD1222 4579261 YP_916191.1 CDS Pden_2407 NC_008686.1 2400950 2404012 R 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 complement(2400950..2404012) Paracoccus denitrificans PD1222 4579262 YP_916192.1 CDS Pden_2408 NC_008686.1 2404009 2405817 R hypothetical protein complement(2404009..2405817) Paracoccus denitrificans PD1222 4580742 YP_916193.1 CDS Pden_2409 NC_008686.1 2405814 2406701 R hypothetical protein complement(2405814..2406701) Paracoccus denitrificans PD1222 4580743 YP_916194.1 CDS Pden_2410 NC_008686.1 2406704 2408428 R KEGG: bcl:ABC0984 hypothetical protein; hypothetical protein complement(2406704..2408428) Paracoccus denitrificans PD1222 4580744 YP_916195.1 CDS Pden_2411 NC_008686.1 2408431 2409807 R PFAM: outer membrane efflux protein; KEGG: spt:SPA2549 type I secretion protein; outer membrane efflux protein complement(2408431..2409807) Paracoccus denitrificans PD1222 4580745 YP_916196.1 CDS Pden_2412 NC_008686.1 2409815 2411014 R 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 complement(2409815..2411014) Paracoccus denitrificans PD1222 4580746 YP_916197.1 CDS Pden_2413 NC_008686.1 2411014 2413311 R PFAM: ABC transporter, transmembrane region; ABC transporter related; SMART: AAA ATPase; KEGG: aeh:Mlg_2167 ABC transporter related; ABC transporter complement(2411014..2413311) Paracoccus denitrificans PD1222 4580747 YP_916198.1 CDS Pden_2414 NC_008686.1 2419791 2420072 D hypothetical protein 2419791..2420072 Paracoccus denitrificans PD1222 4580748 YP_916199.1 CDS Pden_2415 NC_008686.1 2420089 2420415 R PFAM: helix-turn-helix domain protein; KEGG: hne:HNE_0388 DNA-binding protein; XRE family transcriptional regulator complement(2420089..2420415) Paracoccus denitrificans PD1222 4580749 YP_916200.1 CDS Pden_2416 NC_008686.1 2421784 2421978 R KEGG: sme:SMa2171 hypothetical protein; hypothetical protein complement(2421784..2421978) Paracoccus denitrificans PD1222 4580750 YP_916201.1 CDS Pden_2417 NC_008686.1 2422041 2422346 R PFAM: IS66 Orf2 family protein; KEGG: sme:SMa1613 hypothetical protein; IS66 Orf2 family protein complement(2422041..2422346) Paracoccus denitrificans PD1222 4580751 YP_916202.1 CDS Pden_2418 NC_008686.1 2422453 2423145 D PFAM: phage integrase family protein; KEGG: sit:TM1040_1328 phage integrase; phage integrase family protein 2422453..2423145 Paracoccus denitrificans PD1222 4580752 YP_916203.1 CDS Pden_2419 NC_008686.1 2423384 2424307 R PFAM: phage integrase family protein; KEGG: sit:TM1040_1328 phage integrase; phage integrase family protein complement(2423384..2424307) Paracoccus denitrificans PD1222 4580753 YP_916204.1 CDS Pden_2420 NC_008686.1 2424334 2424609 R hypothetical protein complement(2424334..2424609) Paracoccus denitrificans PD1222 4580754 YP_916205.1 CDS Pden_2421 NC_008686.1 2424703 2425491 D PFAM: helix-turn-helix domain protein; XRE family transcriptional regulator 2424703..2425491 Paracoccus denitrificans PD1222 4580755 YP_916206.1 CDS Pden_2423 NC_008686.1 2426535 2427872 R hypothetical protein complement(2426535..2427872) Paracoccus denitrificans PD1222 4580756 YP_916207.1 CDS Pden_2424 NC_008686.1 2428012 2428923 D TIGRFAM: RarD protein, DMT superfamily transporter; PFAM: protein of unknown function DUF6, transmembrane; KEGG: sil:SPO2338 RarD; transporter DMT superfamily protein 2428012..2428923 Paracoccus denitrificans PD1222 4580757 YP_916208.1 CDS Pden_2425 NC_008686.1 2428920 2429660 D KEGG: sil:SPO2330 hypothetical protein; hypothetical protein 2428920..2429660 Paracoccus denitrificans PD1222 4580758 YP_916209.1 CDS Pden_2426 NC_008686.1 2429742 2431064 D PFAM: Pyrrolo-quinoline quinone; KEGG: rsp:RSP_2698 quinoprotein; Pyrrolo-quinoline quinone 2429742..2431064 Paracoccus denitrificans PD1222 4580759 YP_916210.1 CDS engA NC_008686.1 2431061 2432530 D 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 2431061..2432530 Paracoccus denitrificans PD1222 4580760 YP_916211.1 CDS Pden_2428 NC_008686.1 2432540 2433400 R KEGG: sil:SPO1487 hypothetical protein; hypothetical protein complement(2432540..2433400) Paracoccus denitrificans PD1222 4580761 YP_916212.1 CDS Pden_2429 NC_008686.1 2433457 2434749 R 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 complement(2433457..2434749) Paracoccus denitrificans PD1222 4580762 YP_916213.1 CDS Pden_2430 NC_008686.1 2434831 2435190 R KEGG: rde:RD1_1508 SoxS; SoxS protein complement(2434831..2435190) Paracoccus denitrificans PD1222 4580763 YP_916214.1 CDS Pden_2431 NC_008686.1 2435333 2436346 D 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 2435333..2436346 Paracoccus denitrificans PD1222 4580764 YP_916215.1 CDS Pden_2432 NC_008686.1 2436330 2436920 D TIGRFAM: methylated-DNA--protein-cysteine methyltransferase; PFAM: methylated-DNA-[protein]-cysteine S-methyltransferase; KEGG: sil:SPO3311 ADA regulatory protein; methylated-DNA--protein-cysteine methyltransferase 2436330..2436920 Paracoccus denitrificans PD1222 4580765 YP_916216.1 CDS rpmB NC_008686.1 2437076 2437351 D required for 70S ribosome assembly; 50S ribosomal protein L28 2437076..2437351 Paracoccus denitrificans PD1222 4580766 YP_916217.1 CDS Pden_2434 NC_008686.1 2437625 2438041 D KEGG: mlo:mll2356 hypothetical protein; hypothetical protein 2437625..2438041 Paracoccus denitrificans PD1222 4580767 YP_916218.1 CDS Pden_2435 NC_008686.1 2438041 2438394 D KEGG: mlo:mll2355 hypothetical protein; hypothetical protein 2438041..2438394 Paracoccus denitrificans PD1222 4580768 YP_916219.1 CDS Pden_2436 NC_008686.1 2438382 2439323 R hypothetical protein complement(2438382..2439323) Paracoccus denitrificans PD1222 4580769 YP_916220.1 CDS Pden_2437 NC_008686.1 2439316 2440302 R KEGG: mlo:mlr2353 hypothetical protein; hypothetical protein complement(2439316..2440302) Paracoccus denitrificans PD1222 4580770 YP_916221.1 CDS Pden_2438 NC_008686.1 2440299 2441363 R catalyzes a condensation reaction in fatty acid biosynthesis: addition of an acyl acceptor of two carbons from malonyl-ACP; 3-oxoacyl-ACP synthase complement(2440299..2441363) Paracoccus denitrificans PD1222 4580771 YP_916222.1 CDS Pden_2439 NC_008686.1 2441360 2442460 R KEGG: mlo:mlr2351 hypothetical protein; hypothetical protein complement(2441360..2442460) Paracoccus denitrificans PD1222 4580772 YP_916223.1 CDS Pden_2440 NC_008686.1 2442469 2445216 R 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 complement(2442469..2445216) Paracoccus denitrificans PD1222 4580773 YP_916224.1 CDS Pden_2441 NC_008686.1 2445389 2447494 D PFAM: protein kinase; SMART: tyrosine protein kinase; serine/threonine protein kinase; KEGG: rsp:RSP_3475 serine/threonine protein kinase; protein kinase 2445389..2447494 Paracoccus denitrificans PD1222 4580774 YP_916225.1 CDS Pden_2442 NC_008686.1 2447625 2448755 D PFAM: ImpA domain protein; KEGG: rsp:RSP_3476 hypothetical protein; ImpA domain-containing protein 2447625..2448755 Paracoccus denitrificans PD1222 4580775 YP_916226.1 CDS Pden_2443 NC_008686.1 2448813 2449355 D PFAM: Uncharacterized conserved protein UCP028301; KEGG: rsp:RSP_3477 hypothetical protein; hypothetical protein 2448813..2449355 Paracoccus denitrificans PD1222 4580776 YP_916227.1 CDS Pden_2444 NC_008686.1 2449359 2450873 D PFAM: protein of unknown function DUF877; KEGG: rsp:RSP_3478 hypothetical protein; hypothetical protein 2449359..2450873 Paracoccus denitrificans PD1222 4580777 YP_916228.1 CDS Pden_2445 NC_008686.1 2451018 2451506 D PFAM: protein of unknown function DUF796; KEGG: rsp:RSP_3479 hypothetical protein; hypothetical protein 2451018..2451506 Paracoccus denitrificans PD1222 4580778 YP_916229.1 CDS Pden_2446 NC_008686.1 2451532 2452278 D PFAM: protein of unknown function DUF1316; KEGG: rsp:RSP_3480 hypothetical protein; hypothetical protein 2451532..2452278 Paracoccus denitrificans PD1222 4580779 YP_916230.1 CDS Pden_2447 NC_008686.1 2452278 2454140 D PFAM: protein of unknown function DUF879; KEGG: rsp:RSP_3481 hypothetical protein; hypothetical protein 2452278..2454140 Paracoccus denitrificans PD1222 4580780 YP_916231.1 CDS Pden_2448 NC_008686.1 2454104 2455141 D PFAM: protein of unknown function DUF1305; KEGG: mlo:mlr2343 hypothetical protein; hypothetical protein 2454104..2455141 Paracoccus denitrificans PD1222 4580781 YP_916232.1 CDS Pden_2449 NC_008686.1 2455141 2456376 D PFAM: Forkhead-associated protein; KEGG: rsp:RSP_3483 FHA domain-containing protein; FHA domain-containing protein 2455141..2456376 Paracoccus denitrificans PD1222 4580782 YP_916233.1 CDS Pden_2450 NC_008686.1 2456373 2456846 D KEGG: rsp:RSP_3484 hypothetical protein; hypothetical protein 2456373..2456846 Paracoccus denitrificans PD1222 4580783 YP_916234.1 CDS Pden_2451 NC_008686.1 2456858 2458192 D PFAM: protein of unknown function DUF876; KEGG: rsp:RSP_3485 hypothetical protein; hypothetical protein 2456858..2458192 Paracoccus denitrificans PD1222 4580784 YP_916235.1 CDS Pden_2452 NC_008686.1 2458202 2459593 D PFAM: OmpA/MotB domain protein; KEGG: rsp:RSP_3486 possible outer membrane protein, OmpA family; OmpA/MotB domain-containing protein 2458202..2459593 Paracoccus denitrificans PD1222 4580785 YP_916236.1 CDS Pden_2453 NC_008686.1 2459594 2463124 D PFAM: ImcF domain protein; protein of unknown function DUF1215; KEGG: rsp:RSP_3487 hypothetical protein; ImcF domain-containing protein 2459594..2463124 Paracoccus denitrificans PD1222 4580786 YP_916237.1 CDS Pden_2454 NC_008686.1 2463106 2463621 D KEGG: rsp:RSP_3488 hypothetical protein; hypothetical protein 2463106..2463621 Paracoccus denitrificans PD1222 4580787 YP_916238.1 CDS Pden_2455 NC_008686.1 2463608 2465959 R PFAM: Rhs element Vgr protein; Gp5 domain protein; KEGG: rsp:RSP_3489 hypothetical protein; Rhs element Vgr protein complement(2463608..2465959) Paracoccus denitrificans PD1222 4580788 YP_916239.1 CDS Pden_2456 NC_008686.1 2466042 2468447 R PFAM: protein of unknown function DUF1215; KEGG: rsp:RSP_3490 hypothetical protein; hypothetical protein complement(2466042..2468447) Paracoccus denitrificans PD1222 4580789 YP_916240.1 CDS Pden_2457 NC_008686.1 2468423 2469370 R KEGG: rsp:RSP_3491 hypothetical protein; hypothetical protein complement(2468423..2469370) Paracoccus denitrificans PD1222 4580790 YP_916241.1 CDS Pden_2458 NC_008686.1 2469372 2470148 R PFAM: protein phosphatase 2C domain protein; Stage II sporulation E family protein; KEGG: rsp:RSP_3492 protein phosphatase 2C-like; protein phosphatase 2C complement(2469372..2470148) Paracoccus denitrificans PD1222 4580791 YP_916242.1 CDS Pden_2459 NC_008686.1 2470233 2470826 D PFAM: OmpA/MotB domain protein; KEGG: rsp:RSP_3494 OmpA/MotB domain protein; OmpA/MotB domain-containing protein 2470233..2470826 Paracoccus denitrificans PD1222 4580792 YP_916243.1 CDS Pden_2460 NC_008686.1 2470943 2472706 D PFAM: Polypeptide-transport-associated domain protein, ShlB-type; KEGG: pau:PA14_61190 hemolysin activation/secretion protein; polypeptide-transport-associated domain-containing protein 2470943..2472706 Paracoccus denitrificans PD1222 4580793 YP_916244.1 CDS Pden_2461 NC_008686.1 2472753 2477666 D TIGRFAM: filamentous haemagglutinin family outer membrane protein; PFAM: filamentous haemagglutinin domain protein; GLUG domain protein; KEGG: pau:PA14_61200 hypothetical protein; filamentous hemagglutinin 2472753..2477666 Paracoccus denitrificans PD1222 4580794 YP_916245.1 CDS Pden_2462 NC_008686.1 2477635 2479584 D 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 2477635..2479584 Paracoccus denitrificans PD1222 4580795 YP_916246.1 CDS Pden_2463 NC_008686.1 2479845 2480135 R hypothetical protein complement(2479845..2480135) Paracoccus denitrificans PD1222 4580796 YP_916247.1 CDS Pden_2464 NC_008686.1 2480226 2480945 R KEGG: bms:BRA0423 outer membrane protein, 31 kDa; hypothetical protein complement(2480226..2480945) Paracoccus denitrificans PD1222 4580797 YP_916248.1 CDS Pden_2465 NC_008686.1 2480963 2482648 R PFAM: Hemolysin-type calcium-binding region; KEGG: sil:SPO1617 type I secretion target repeat protein; hemolysin-type calcium-binding protein complement(2480963..2482648) Paracoccus denitrificans PD1222 4580798 YP_916249.1 CDS Pden_2466 NC_008686.1 2482759 2483106 R hypothetical protein complement(2482759..2483106) Paracoccus denitrificans PD1222 4580799 YP_916250.1 CDS Pden_2467 NC_008686.1 2483174 2484091 R PFAM: LytTr DNA-binding region; KEGG: sil:SPO1616 transcriptional regulator; response regulator receiver protein complement(2483174..2484091) Paracoccus denitrificans PD1222 4580105 YP_916251.1 CDS Pden_2468 NC_008686.1 2484647 2485534 D TIGRFAM: cation diffusion facilitator family transporter; PFAM: cation efflux protein; KEGG: rsp:RSP_0463 cation efflux transporter, CDF family; cation diffusion facilitator family transporter 2484647..2485534 Paracoccus denitrificans PD1222 4580106 YP_916252.1 CDS Pden_2469 NC_008686.1 2485531 2486523 R PFAM: ABC transporter related; Transport-associated OB domain protein; SMART: AAA ATPase; KEGG: sme:SMc02869 ATP-binding ABC transporter protein; ABC transporter complement(2485531..2486523) Paracoccus denitrificans PD1222 4580107 YP_916253.1 CDS Pden_2470 NC_008686.1 2486561 2487400 R 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 complement(2486561..2487400) Paracoccus denitrificans PD1222 4580108 YP_916254.1 CDS Pden_2471 NC_008686.1 2487410 2488327 R 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 complement(2487410..2488327) Paracoccus denitrificans PD1222 4580109 YP_916255.1 CDS Pden_2472 NC_008686.1 2488422 2489681 R PFAM: extracellular solute-binding protein, family 1; KEGG: mes:Meso_2706 extracellular solute-binding protein, family 1; extracellular solute-binding protein complement(2488422..2489681) Paracoccus denitrificans PD1222 4580110 YP_916256.1 CDS murQ NC_008686.1 2489730 2490608 R 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 complement(2489730..2490608) Paracoccus denitrificans PD1222 4580111 YP_916257.1 CDS Pden_2474 NC_008686.1 2490761 2491594 D PFAM: ATPase, BadF/BadG/BcrA/BcrD type; KEGG: mes:Meso_2705 ATPase, BadF/BadG/BcrA/BcrD type; BadF/BadG/BcrA/BcrD type ATPase 2490761..2491594 Paracoccus denitrificans PD1222 4580112 YP_916258.1 CDS Pden_2475 NC_008686.1 2491594 2492361 D 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 2491594..2492361 Paracoccus denitrificans PD1222 4580113 YP_916259.1 CDS Pden_2476 NC_008686.1 2492361 2493386 D PFAM: sugar isomerase (SIS); KEGG: mlo:mll4767 glucosamine-fructose-6-phosphate aminotransferase; glutamine--fructose-6-phosphate transaminase (isomerizing) 2492361..2493386 Paracoccus denitrificans PD1222 4580114 YP_916260.1 CDS Pden_2477 NC_008686.1 2493386 2494507 D KEGG: rsp:RSP_1296 N-acetylglucosamine-6-phosphate deacetylase; TIGRFAM: N-acetylglucosamine-6-phosphate deacetylase; PFAM: amidohydrolase; N-acetylglucosamine-6-phosphate deacetylase 2493386..2494507 Paracoccus denitrificans PD1222 4580115 YP_916261.1 CDS Pden_2478 NC_008686.1 2494525 2495274 D PFAM: cyclic nucleotide-binding; SMART: regulatory protein, Crp; KEGG: sil:SPOA0323 cyclic nucleotide-binding protein; Crp/Fnr family transcriptional regulator 2494525..2495274 Paracoccus denitrificans PD1222 4580116 YP_916262.1 CDS Pden_2479 NC_008686.1 2495469 2495702 R hypothetical protein complement(2495469..2495702) Paracoccus denitrificans PD1222 4580117 YP_916263.1 CDS Pden_2480 NC_008686.1 2495706 2496242 R PFAM: cytochrome c oxidase, subunit III; KEGG: sil:SPOA0213 nitric oxide reductase E protein; cytochrome c oxidase subunit III complement(2495706..2496242) Paracoccus denitrificans PD1222 4580118 YP_916264.1 CDS Pden_2481 NC_008686.1 2496242 2498158 R PFAM: von Willebrand factor, type A; KEGG: sil:SPOA0214 nitric oxide reductase D protein; von Willebrand factor A complement(2496242..2498158) Paracoccus denitrificans PD1222 4580119 YP_916265.1 CDS Pden_2482 NC_008686.1 2498170 2498982 R 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 complement(2498170..2498982) Paracoccus denitrificans PD1222 4580120 YP_916266.1 CDS Pden_2483 NC_008686.1 2498986 2500374 R PFAM: cytochrome c oxidase, subunit I; KEGG: sil:SPOA0216 nitric oxide reductase, large subunit; cytochrome c oxidase subunit I complement(2498986..2500374) Paracoccus denitrificans PD1222 4580121 YP_916267.1 CDS Pden_2484 NC_008686.1 2500388 2500840 R KEGG: sil:SPOA0217 nitric oxide reductase, small subunit; nitric-oxide reductase complement(2500388..2500840) Paracoccus denitrificans PD1222 4580122 YP_916268.1 CDS Pden_2485 NC_008686.1 2500915 2501829 R PFAM: ApbE family lipoprotein; KEGG: rde:RD1_1552 nitrous-oxide reductase protein NosX; ApbE family lipoprotein complement(2500915..2501829) Paracoccus denitrificans PD1222 4580123 YP_916269.1 CDS Pden_2486 NC_008686.1 2501826 2503871 R PFAM: FMN-binding domain protein; KEGG: rde:RD1_1564 nitrous oxide reductase regulatory protein NosR; FMN-binding domain-containing protein complement(2501826..2503871) Paracoccus denitrificans PD1222 4580124 YP_916270.1 CDS Pden_2487 NC_008686.1 2503999 2505789 D PFAM: cytochrome c, class I; cytochrome d1, heme region; KEGG: sil:SPOA0220 cytochrome cd1 nitrite reductase; hydroxylamine reductase 2503999..2505789 Paracoccus denitrificans PD1222 4580125 YP_916271.1 CDS Pden_2488 NC_008686.1 2505861 2506724 D 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 2505861..2506724 Paracoccus denitrificans PD1222 4580126 YP_916272.1 CDS Pden_2489 NC_008686.1 2506717 2507028 D KEGG: rde:RD1_1567 cytochrome c (c55X); cytochrome c (c55X) 2506717..2507028 Paracoccus denitrificans PD1222 4580127 YP_916273.1 CDS Pden_2490 NC_008686.1 2507025 2508179 D PFAM: cytochrome d1, heme region; KEGG: sil:SPOA0223 cytochrome cd1 nitrite reductase; cytochrome d1, heme region 2507025..2508179 Paracoccus denitrificans PD1222 4580128 YP_916274.1 CDS Pden_2491 NC_008686.1 2508182 2509153 D KEGG: sil:SPOA0224 nitrite reductase heme biosynthesis D/L protein; AsnC family transcriptional regulator 2508182..2509153 Paracoccus denitrificans PD1222 4580129 YP_916275.1 CDS Pden_2492 NC_008686.1 2509150 2509623 D KEGG: rde:RD1_1570 nitrite reductase heme biosynthesis G; AsnC family transcriptional regulator 2509150..2509623 Paracoccus denitrificans PD1222 4580130 YP_916276.1 CDS Pden_2493 NC_008686.1 2509620 2510102 D KEGG: sil:SPOA0226 nitrite reductase heme biosynthesis H protein; AsnC family transcriptional regulator 2509620..2510102 Paracoccus denitrificans PD1222 4580131 YP_916277.1 CDS Pden_2494 NC_008686.1 2510116 2511339 D 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 2510116..2511339 Paracoccus denitrificans PD1222 4580132 YP_916278.1 CDS Pden_2495 NC_008686.1 2511314 2512768 D PFAM: cytochrome d1, heme region; KEGG: sil:SPOA0228 nitrite reductase protein N; cytochrome d1, heme region 2511314..2512768 Paracoccus denitrificans PD1222 4580133 YP_916279.1 CDS Pden_2496 NC_008686.1 2512725 2512991 D KEGG: rde:RD1_1575 hypothetical protein; hypothetical protein 2512725..2512991 Paracoccus denitrificans PD1222 4580134 YP_916280.1 CDS Pden_2497 NC_008686.1 2513247 2515424 D KEGG: atc:AGR_L_481 catalase; TIGRFAM: catalase/peroxidase HPI; PFAM: Haem peroxidase; catalase/peroxidase HPI 2513247..2515424 Paracoccus denitrificans PD1222 4580135 YP_916281.1 CDS Pden_2498 NC_008686.1 2515560 2517761 R binding of PriA to forked DNA starts the assembly of the primosome, also possesses 3'-5' helicase activity; primosome assembly protein PriA complement(2515560..2517761) Paracoccus denitrificans PD1222 4580136 YP_916282.1 CDS Pden_2499 NC_008686.1 2518051 2518704 D similar to novel fructose-6-phosphate aldolase from Escherichia coli; enzyme from Methanocaldococcus janaschii shows transaldolase activity; translaldolase 2518051..2518704 Paracoccus denitrificans PD1222 4580137 YP_916283.1 CDS Pden_2500 NC_008686.1 2518704 2519414 D KEGG: rsp:RSP_0562 hypothetical protein; hypothetical protein 2518704..2519414 Paracoccus denitrificans PD1222 4580138 YP_916284.1 CDS xerC NC_008686.1 2519411 2520349 D 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 2519411..2520349 Paracoccus denitrificans PD1222 4580139 YP_916285.1 CDS Pden_2502 NC_008686.1 2520515 2521273 D PFAM: protein of unknown function DUF81; KEGG: sit:TM1040_3018 protein of unknown function DUF81; hypothetical protein 2520515..2521273 Paracoccus denitrificans PD1222 4580140 YP_916286.1 CDS Pden_2503 NC_008686.1 2521311 2522297 R PFAM: L-asparaginase II; KEGG: rsp:RSP_1384 hypothetical protein; L-asparaginase II complement(2521311..2522297) Paracoccus denitrificans PD1222 4580141 YP_916287.1 CDS Pden_2504 NC_008686.1 2522449 2522976 D KEGG: rsp:RSP_1383 hypothetical protein; hypothetical protein 2522449..2522976 Paracoccus denitrificans PD1222 4580142 YP_916288.1 CDS Pden_2505 NC_008686.1 2523082 2524257 D TIGRFAM: radical SAM enzyme, Cfr family; PFAM: Radical SAM domain protein; KEGG: rsp:RSP_1382 radical SAM superfamily protein; radical SAM protein 2523082..2524257 Paracoccus denitrificans PD1222 4580143 YP_916289.1 CDS Pden_2506 NC_008686.1 2524476 2525999 D catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate; phosphoglyceromutase 2524476..2525999 Paracoccus denitrificans PD1222 4580144 YP_916290.1 CDS Pden_2507 NC_008686.1 2525996 2527231 D PFAM: peptidase M23B; KEGG: rsp:RSP_0933 hypothetical protein; peptidase M23B 2525996..2527231 Paracoccus denitrificans PD1222 4580145 YP_916291.1 CDS Pden_2508 NC_008686.1 2527228 2528643 D KEGG: sil:SPO3812 carboxyl-terminal protease family protein; TIGRFAM: carboxyl-terminal protease; PFAM: PDZ/DHR/GLGF domain protein; peptidase S41; carboxyl-terminal protease 2527228..2528643 Paracoccus denitrificans PD1222 4580146 YP_916292.1 CDS Pden_2509 NC_008686.1 2528640 2529131 D hydrolyzes diadenosine polyphosphate; dinucleoside polyphosphate hydrolase 2528640..2529131 Paracoccus denitrificans PD1222 4580147 YP_916293.1 CDS Pden_2510 NC_008686.1 2529222 2530475 R TIGRFAM: lytic murein transglycosylase; PFAM: Peptidoglycan-binding domain 1 protein; KEGG: rsp:RSP_1125 membrane bound lytic murein transglycosylase B; lytic murein transglycosylase complement(2529222..2530475) Paracoccus denitrificans PD1222 4580148 YP_916294.1 CDS Pden_2511 NC_008686.1 2530564 2530881 R KEGG: sil:SPO3336 hypothetical protein; hypothetical protein complement(2530564..2530881) Paracoccus denitrificans PD1222 4580149 YP_916295.1 CDS Pden_2512 NC_008686.1 2530938 2531408 D PFAM: YbaK/prolyl-tRNA synthetase associated region; KEGG: jan:Jann_2447 YbaK/prolyl-tRNA synthetase associated protein; prolyl-tRNA synthetase 2530938..2531408 Paracoccus denitrificans PD1222 4580150 YP_916296.1 CDS Pden_2513 NC_008686.1 2531453 2531704 R PFAM: Transglycosylase-associated protein; KEGG: jan:Jann_0350 transglycosylase-associated protein; transglycosylase-associated protein complement(2531453..2531704) Paracoccus denitrificans PD1222 4580151 YP_916297.1 CDS dapD NC_008686.1 2531809 2532633 R 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 complement(2531809..2532633) Paracoccus denitrificans PD1222 4580152 YP_916298.1 CDS Pden_2515 NC_008686.1 2532699 2533553 D PFAM: conserved hypothetical protein 730; KEGG: rsp:RSP_1132 hypothetical protein; hypothetical protein 2532699..2533553 Paracoccus denitrificans PD1222 4580153 YP_916299.1 CDS Pden_2516 NC_008686.1 2533772 2534299 R hypothetical protein complement(2533772..2534299) Paracoccus denitrificans PD1222 4580154 YP_916300.1 CDS Pden_2517 NC_008686.1 2534412 2534879 R 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 complement(2534412..2534879) Paracoccus denitrificans PD1222 4580155 YP_916301.1 CDS Pden_2518 NC_008686.1 2534883 2535215 R TIGRFAM: iojap-like protein; PFAM: Iojap-related protein; KEGG: rsp:RSP_0865 hypothetical protein; iojap family protein complement(2534883..2535215) Paracoccus denitrificans PD1222 4580156 YP_916302.1 CDS Pden_2519 NC_008686.1 2535414 2535647 R hypothetical protein complement(2535414..2535647) Paracoccus denitrificans PD1222 4580157 YP_916303.1 CDS Pden_2520 NC_008686.1 2535943 2537379 D dehydratase component, catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; isopropylmalate isomerase large subunit 2535943..2537379 Paracoccus denitrificans PD1222 4580158 YP_916304.1 CDS Pden_2521 NC_008686.1 2537397 2537981 R hypothetical protein complement(2537397..2537981) Paracoccus denitrificans PD1222 4580159 YP_916305.1 CDS leuD NC_008686.1 2538074 2538679 D catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate in leucine biosynthesis; forms a heterodimer of LeuC/D; isopropylmalate isomerase small subunit 2538074..2538679 Paracoccus denitrificans PD1222 4580160 YP_916306.1 CDS Pden_2523 NC_008686.1 2538670 2539722 D KEGG: sil:SPO0213 hypothetical protein; hypothetical protein 2538670..2539722 Paracoccus denitrificans PD1222 4580161 YP_916307.1 CDS Pden_2524 NC_008686.1 2540009 2540185 D KEGG: sil:SPO2875 hypothetical protein; hypothetical protein 2540009..2540185 Paracoccus denitrificans PD1222 4580162 YP_916308.1 CDS Pden_2525 NC_008686.1 2540187 2540885 D TIGRFAM: cobalt transporter, subunit CbtA; KEGG: sit:TM1040_2222 cobalt transporter subunit CbtA; cobalt transporter subunit CbtA 2540187..2540885 Paracoccus denitrificans PD1222 4580163 YP_916309.1 CDS Pden_2526 NC_008686.1 2540955 2541488 D KEGG: sit:TM1040_2223 conserved hypothetical protein; hypothetical protein 2540955..2541488 Paracoccus denitrificans PD1222 4579831 YP_916310.1 CDS Pden_2527 NC_008686.1 2541488 2542111 D 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 2541488..2542111 Paracoccus denitrificans PD1222 4579832 YP_916311.1 CDS Pden_2528 NC_008686.1 2542115 2542531 R KEGG: bbr:BB2359 hypothetical protein; hypothetical protein complement(2542115..2542531) Paracoccus denitrificans PD1222 4579833 YP_916312.1 CDS Pden_2529 NC_008686.1 2542536 2543147 R 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 complement(2542536..2543147) Paracoccus denitrificans PD1222 4579834 YP_916313.1 CDS Pden_2530 NC_008686.1 2543463 2543816 D PFAM: protein of unknown function DUF1636; KEGG: rsp:RSP_2829 hypothetical protein; hypothetical protein 2543463..2543816 Paracoccus denitrificans PD1222 4579835 YP_916314.1 CDS Pden_2531 NC_008686.1 2543820 2544854 D 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 2543820..2544854 Paracoccus denitrificans PD1222 4579836 YP_916315.1 CDS cobN NC_008686.1 2544858 2548028 D 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 2544858..2548028 Paracoccus denitrificans PD1222 4579837 YP_916316.1 CDS Pden_2533 NC_008686.1 2548025 2549188 D TIGRFAM: precorrin-3B synthase; PFAM: nitrite/sulfite reductase, hemoprotein beta-component, ferrodoxin domain protein; KEGG: sit:TM1040_2211 precorrin-3B synthase; precorrin-3B synthase 2548025..2549188 Paracoccus denitrificans PD1222 4579838 YP_916317.1 CDS cobH NC_008686.1 2549232 2549861 D catalyzes the interconversion of precorrin-8X and hydrogenobyrinate; precorrin-8X methylmutase 2549232..2549861 Paracoccus denitrificans PD1222 4579839 YP_916318.1 CDS Pden_2535 NC_008686.1 2549864 2550625 D 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 2549864..2550625 Paracoccus denitrificans PD1222 4579840 YP_916319.1 CDS Pden_2536 NC_008686.1 2550622 2551350 D 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 2550622..2551350 Paracoccus denitrificans PD1222 4579841 YP_916320.1 CDS Pden_2537 NC_008686.1 2551326 2552018 R PFAM: Precorrin-6x reductase CbiJ/CobK; KEGG: rsp:RSP_2825 precorrin-6x reductase; precorrin-6A reductase complement(2551326..2552018) Paracoccus denitrificans PD1222 4579842 YP_916321.1 CDS Pden_2538 NC_008686.1 2552062 2553234 D 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 2552062..2553234 Paracoccus denitrificans PD1222 4579843 YP_916322.1 CDS Pden_2539 NC_008686.1 2553231 2553581 D KEGG: bja:blr3270 precorrin methylase; precorrin methylase 2553231..2553581 Paracoccus denitrificans PD1222 4579844 YP_916323.1 CDS Pden_2540 NC_008686.1 2553578 2554351 D 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 2553578..2554351 Paracoccus denitrificans PD1222 4579845 YP_916324.1 CDS Pden_2541 NC_008686.1 2554348 2555637 D responsible for the amidation of carboxylic groups at position A and C of cobyrinic acid or hydrogenobrynic acid; cobyrinic acid a,c-diamide synthase 2554348..2555637 Paracoccus denitrificans PD1222 4579846 YP_916325.1 CDS Pden_2542 NC_008686.1 2555634 2556383 D catalyzes the formation of precorrin 6x from precorrin 5; precorrin 6A synthase 2555634..2556383 Paracoccus denitrificans PD1222 4579847 YP_916326.1 CDS Pden_2543 NC_008686.1 2556368 2556676 D KEGG: sil:SPO2878 hypothetical protein; hypothetical protein 2556368..2556676 Paracoccus denitrificans PD1222 4579848 YP_916327.1 CDS Pden_2544 NC_008686.1 2557025 2557504 D PFAM: cytochrome c, class II; KEGG: rsp:RSP_0474 cytochrome c'; cytochrome c, class II 2557025..2557504 Paracoccus denitrificans PD1222 4579849 YP_916328.1 CDS Pden_2545 NC_008686.1 2557504 2558085 D PFAM: cytochrome B561; KEGG: rsp:RSP_0475 cytochrome b; cytochrome B561 2557504..2558085 Paracoccus denitrificans PD1222 4579850 YP_916329.1 CDS Pden_2546 NC_008686.1 2558375 2560618 R decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling; DNA topoisomerase IV subunit A complement(2558375..2560618) Paracoccus denitrificans PD1222 4579851 YP_916330.1 CDS Pden_2547 NC_008686.1 2560721 2561539 D PFAM: short-chain dehydrogenase/reductase SDR; KR; KEGG: rsp:RSP_1694 probable short-chain dehydrogenase/reductase; short-chain dehydrogenase/reductase SDR 2560721..2561539 Paracoccus denitrificans PD1222 4579852 YP_916331.1 CDS Pden_2548 NC_008686.1 2561564 2561764 D KEGG: rsp:RSP_6016 hypothetical protein; hypothetical protein 2561564..2561764 Paracoccus denitrificans PD1222 4579853 YP_916332.1 CDS Pden_2549 NC_008686.1 2561764 2562336 D TIGRFAM: ATP--cobalamin adenosyltransferase; PFAM: cobalamin adenosyltransferase; KEGG: jan:Jann_0549 cobalamin adenosyltransferase; ATP--cobalamin adenosyltransferase 2561764..2562336 Paracoccus denitrificans PD1222 4579854 YP_916333.1 CDS Pden_2550 NC_008686.1 2562457 2563215 D PFAM: electron transfer flavoprotein beta-subunit; KEGG: sit:TM1040_2427 electron transfer flavoprotein beta-subunit; electron transfer flavoprotein subunit beta 2562457..2563215 Paracoccus denitrificans PD1222 4579855 YP_916334.1 CDS Pden_2551 NC_008686.1 2563215 2564141 D 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 2563215..2564141 Paracoccus denitrificans PD1222 4579856 YP_916335.1 CDS Pden_2552 NC_008686.1 2564340 2565215 D converts (S)-3-hydroxybutanoyl-CoA to 3-acetoacetyl-CoA; 3-hydroxybutyryl-CoA dehydrogenase 2564340..2565215 Paracoccus denitrificans PD1222 4579857 YP_916336.1 CDS Pden_2553 NC_008686.1 2565291 2565875 R PFAM: protein of unknown function DUF205; KEGG: rsp:RSP_1004 hypothetical protein; hypothetical protein complement(2565291..2565875) Paracoccus denitrificans PD1222 4579858 YP_916337.1 CDS Pden_2554 NC_008686.1 2565872 2567143 R TIGRFAM: dihydroorotase, multifunctional complex type; PFAM: amidohydrolase; KEGG: rsp:RSP_1003 dihydroorotase and related cyclic amidohydrolase; dihydroorotase, multifunctional complex type complement(2565872..2567143) Paracoccus denitrificans PD1222 4579859 YP_916338.1 CDS pyrB NC_008686.1 2567140 2568099 R catalyzes the transfer of the carbamoyl moiety from carbamoyl phosphate to L- aspartate in pyrimidine biosynthesis; aspartate carbamoyltransferase complement(2567140..2568099) Paracoccus denitrificans PD1222 4579860 YP_916339.1 CDS Pden_2556 NC_008686.1 2568202 2568936 D 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 2568202..2568936 Paracoccus denitrificans PD1222 4579861 YP_916340.1 CDS Pden_2557 NC_008686.1 2569020 2569535 D KEGG: sil:SPO1135 hypothetical protein; hypothetical protein 2569020..2569535 Paracoccus denitrificans PD1222 4579862 YP_916341.1 CDS Pden_2558 NC_008686.1 2569538 2569780 D PFAM: SirA family protein; KEGG: sil:SPO1895 SirA family protein; SirA family protein 2569538..2569780 Paracoccus denitrificans PD1222 4579863 YP_916342.1 CDS Pden_2559 NC_008686.1 2569780 2570709 D PFAM: Auxin Efflux Carrier; KEGG: rsp:RSP_0851 transporter, AEC family; auxin efflux carrier 2569780..2570709 Paracoccus denitrificans PD1222 4579864 YP_916343.1 CDS Pden_2560 NC_008686.1 2570713 2571519 D Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA; enoyl-CoA hydratase 2570713..2571519 Paracoccus denitrificans PD1222 4579865 YP_916344.1 CDS Pden_2561 NC_008686.1 2571625 2572569 D PFAM: protein of unknown function DUF6, transmembrane; KEGG: atc:AGR_C_3767 hypothetical protein; hypothetical protein 2571625..2572569 Paracoccus denitrificans PD1222 4579866 YP_916345.1 CDS Pden_2562 NC_008686.1 2572609 2572944 R KEGG: sit:TM1040_3453 conserved hypothetical protein; hypothetical protein complement(2572609..2572944) Paracoccus denitrificans PD1222 4579867 YP_916346.1 CDS Pden_2563 NC_008686.1 2573003 2573602 R PFAM: cytochrome B561; KEGG: rde:RD1_3654 cytochrome b561; cytochrome B561 complement(2573003..2573602) Paracoccus denitrificans PD1222 4579868 YP_916347.1 CDS entF NC_008686.1 2573716 2577630 D 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 2573716..2577630 Paracoccus denitrificans PD1222 4579869 YP_916348.1 CDS Pden_2565 NC_008686.1 2577850 2578683 R PFAM: esterase; KEGG: ppu:PP_0532 hypothetical protein; esterase complement(2577850..2578683) Paracoccus denitrificans PD1222 4579870 YP_916349.1 CDS Pden_2566 NC_008686.1 2578835 2580241 D KEGG: tac:Ta1322 surface antigen genes (Methanosarcina mazei) related protein; hypothetical protein 2578835..2580241 Paracoccus denitrificans PD1222 4579871 YP_916350.1 CDS Pden_2567 NC_008686.1 2580301 2581398 D PFAM: periplasmic binding protein; KEGG: rpb:RPB_2696 periplasmic binding protein; periplasmic binding protein 2580301..2581398 Paracoccus denitrificans PD1222 4579872 YP_916351.1 CDS Pden_2568 NC_008686.1 2581395 2582429 D PFAM: transport system permease protein; KEGG: pfl:PFL_3501 heme/hemin ABC transporter, permease protein; transport system permease 2581395..2582429 Paracoccus denitrificans PD1222 4579873 YP_916352.1 CDS Pden_2569 NC_008686.1 2582429 2583205 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rpb:RPB_2698 ABC transporter related; ABC transporter 2582429..2583205 Paracoccus denitrificans PD1222 4579874 YP_916353.1 CDS Pden_2570 NC_008686.1 2583236 2583655 R PFAM: protein of unknown function DUF1178; KEGG: rsp:RSP_2387 hypothetical protein; hypothetical protein complement(2583236..2583655) Paracoccus denitrificans PD1222 4579875 YP_916354.1 CDS Pden_2571 NC_008686.1 2583696 2584895 R 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 complement(2583696..2584895) Paracoccus denitrificans PD1222 4579876 YP_916355.1 CDS Pden_2572 NC_008686.1 2584892 2585626 R PFAM: ribulose-phosphate 3-epimerase; KEGG: rsp:RSP_2864 pentose-5-phosphate-3-epimerase; ribulose-phosphate 3-epimerase complement(2584892..2585626) Paracoccus denitrificans PD1222 4579877 YP_916356.1 CDS Pden_2573 NC_008686.1 2585807 2586832 D PFAM: Hsp33 protein; KEGG: sil:SPO0024 chaperonin, 33 kDa; heat shock protein 33 2585807..2586832 Paracoccus denitrificans PD1222 4579878 YP_916357.1 CDS Pden_2574 NC_008686.1 2586829 2587416 D PFAM: NUDIX hydrolase; KEGG: rde:RD1_0410 hydrolase; NUDIX hydrolase 2586829..2587416 Paracoccus denitrificans PD1222 4579879 YP_916358.1 CDS Pden_2575 NC_008686.1 2587413 2588579 D PFAM: Polynucleotide adenylyltransferase region; KEGG: rsp:RSP_1205 poly A polymerase family protein; polynucleotide adenylyltransferase 2587413..2588579 Paracoccus denitrificans PD1222 4579880 YP_916359.1 CDS Pden_2576 NC_008686.1 2588579 2590441 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rsp:RSP_1203 ABC multidrug efflux pump, fused ATPase and inner membrane subunits; ABC transporter 2588579..2590441 Paracoccus denitrificans PD1222 4579881 YP_916360.1 CDS Pden_2577 NC_008686.1 2590438 2591658 D PFAM: (Uracil-5)-methyltransferase; KEGG: sil:SPO0029 23S rRNA (uracil-5-)-methyltransferase RumA; (uracil-5)-methyltransferase 2590438..2591658 Paracoccus denitrificans PD1222 4579882 YP_916361.1 CDS Pden_2578 NC_008686.1 2591724 2592239 D KEGG: rsp:RSP_1201 hypothetical protein; hypothetical protein 2591724..2592239 Paracoccus denitrificans PD1222 4579883 YP_916362.1 CDS Pden_2579 NC_008686.1 2592340 2592993 R PFAM: Glutathione S-transferase, N-terminal domain; KEGG: bja:blr5350 glutathione S-transferase; glutathione S-transferase domain-containing protein complement(2592340..2592993) Paracoccus denitrificans PD1222 4579884 YP_916363.1 CDS Pden_2580 NC_008686.1 2593137 2593736 R PFAM: Allergen V5/Tpx-1 family protein; KEGG: rsp:RSP_1200 hypothetical protein; Allergen V5/Tpx-1 family protein complement(2593137..2593736) Paracoccus denitrificans PD1222 4579885 YP_916364.1 CDS Pden_2581 NC_008686.1 2593932 2594585 D 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 2593932..2594585 Paracoccus denitrificans PD1222 4579886 YP_916365.1 CDS Pden_2582 NC_008686.1 2594774 2595289 D hypothetical protein 2594774..2595289 Paracoccus denitrificans PD1222 4579887 YP_916366.1 CDS hemH NC_008686.1 2595317 2596348 R 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 complement(2595317..2596348) Paracoccus denitrificans PD1222 4579888 YP_916367.1 CDS Pden_2584 NC_008686.1 2596345 2597184 R KEGG: rsp:RSP_1196 SAM-dependent methyltransferase; SAM-dependent methyltransferase complement(2596345..2597184) Paracoccus denitrificans PD1222 4580683 YP_916368.1 CDS Pden_2585 NC_008686.1 2597216 2597953 D KEGG: rsp:RSP_1195 competence protein F; competence protein F 2597216..2597953 Paracoccus denitrificans PD1222 4580684 YP_916369.1 CDS Pden_2586 NC_008686.1 2597986 2598252 D TIGRFAM: glutaredoxin 3; PFAM: glutaredoxin; glutaredoxin 2; KEGG: rsp:RSP_1194 glutaredoxin; glutaredoxin 3 2597986..2598252 Paracoccus denitrificans PD1222 4580685 YP_916370.1 CDS Pden_2587 NC_008686.1 2598249 2599100 D PFAM: Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase; KEGG: sil:SPO0069 hydrolase, carbon-nitrogen family; nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase 2598249..2599100 Paracoccus denitrificans PD1222 4580686 YP_916371.1 CDS Pden_2588 NC_008686.1 2599097 2599606 D PFAM: regulatory protein, MarR; KEGG: rsp:RSP_1191 transcriptional regulator, MarR family; MarR family transcriptional regulator 2599097..2599606 Paracoccus denitrificans PD1222 4580687 YP_916372.1 CDS Pden_2589 NC_008686.1 2599691 2600479 R Involved in ubiquinone biosynthesis; 3-demethylubiquinone-9 3-methyltransferase complement(2599691..2600479) Paracoccus denitrificans PD1222 4580688 YP_916373.1 CDS Pden_2590 NC_008686.1 2600516 2601502 D KEGG: rsp:RSP_1174 prolyl aminopeptidase; TIGRFAM: proline iminopeptidase; PFAM: alpha/beta hydrolase fold; proline iminopeptidase 2600516..2601502 Paracoccus denitrificans PD1222 4580689 YP_916374.1 CDS Pden_2591 NC_008686.1 2601698 2602318 D 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 2601698..2602318 Paracoccus denitrificans PD1222 4580690 YP_916375.1 CDS nusA NC_008686.1 2602322 2604001 D modifies transcription through interactions with RNA polymerase affecting elongation, readthrough, termination, and antitermination; transcription elongation factor NusA 2602322..2604001 Paracoccus denitrificans PD1222 4580691 YP_916376.1 CDS Pden_2593 NC_008686.1 2604017 2604637 D PFAM: protein of unknown function DUF448; KEGG: jan:Jann_0039 protein of unknown function DUF448; hypothetical protein 2604017..2604637 Paracoccus denitrificans PD1222 4580692 YP_916377.1 CDS infB NC_008686.1 2604645 2607191 D 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 2604645..2607191 Paracoccus denitrificans PD1222 4580693 YP_916378.1 CDS Pden_2595 NC_008686.1 2607332 2607460 R hypothetical protein complement(2607332..2607460) Paracoccus denitrificans PD1222 4580694 YP_916379.1 CDS Pden_2596 NC_008686.1 2607579 2607977 R TIGRFAM: mutator MutT protein; PFAM: NUDIX hydrolase; KEGG: sil:SPO0060 mutator MutT protein; mutator MutT protein complement(2607579..2607977) Paracoccus denitrificans PD1222 4580695 YP_916380.1 CDS argJ NC_008686.1 2607974 2609371 R 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 complement(2607974..2609371) Paracoccus denitrificans PD1222 4580696 YP_916381.1 CDS Pden_2598 NC_008686.1 2609375 2610214 R 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 complement(2609375..2610214) Paracoccus denitrificans PD1222 4580697 YP_916382.2 CDS Pden_2599 NC_008686.1 2610423 2613128 D 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 2610423..2613128 Paracoccus denitrificans PD1222 4580698 YP_916383.1 CDS Pden_2600 NC_008686.1 2613274 2613993 R PFAM: response regulator receiver; transcriptional regulator domain protein; KEGG: rsp:RSP_1138 two component transcriptional regulator, winged helix family; two component transcriptional regulator complement(2613274..2613993) Paracoccus denitrificans PD1222 4580699 YP_916384.1 CDS Pden_2601 NC_008686.1 2613990 2614508 R PFAM: regulatory protein, MarR; KEGG: rsp:RSP_1139 transcriptional regulator, MarR family; MarR family transcriptional regulator complement(2613990..2614508) Paracoccus denitrificans PD1222 4580700 YP_916385.1 CDS Pden_2602 NC_008686.1 2614661 2615530 D catalyzes the transamination of the branched-chain amino acids to their respective alpha-keto acids; branched-chain amino acid aminotransferase 2614661..2615530 Paracoccus denitrificans PD1222 4580701 YP_916386.1 CDS Pden_2603 NC_008686.1 2615882 2616346 R 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 complement(2615882..2616346) Paracoccus denitrificans PD1222 4580702 YP_916387.1 CDS Pden_2604 NC_008686.1 2616429 2617007 R 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 complement(2616429..2617007) Paracoccus denitrificans PD1222 4580703 YP_916388.1 CDS Pden_2605 NC_008686.1 2617172 2617906 R PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rsp:RSP_1156 ABC transporter, ATPase subunit; ABC transporter complement(2617172..2617906) Paracoccus denitrificans PD1222 4580704 YP_916389.1 CDS Pden_2606 NC_008686.1 2617911 2618396 R PFAM: OstA family protein; KEGG: sil:SPO0080 hypothetical protein; OstA family protein complement(2617911..2618396) Paracoccus denitrificans PD1222 4580705 YP_916390.1 CDS Pden_2607 NC_008686.1 2618449 2619030 R KEGG: rsp:RSP_1154 hypothetical protein; hypothetical protein complement(2618449..2619030) Paracoccus denitrificans PD1222 4580706 YP_916391.1 CDS Pden_2608 NC_008686.1 2619033 2619980 R KEGG: rsp:RSP_1153 sugar phosphate isomerase; TIGRFAM: KpsF/GutQ family protein; PFAM: CBS domain containing protein; sugar isomerase (SIS); KpsF/GutQ family protein complement(2619033..2619980) Paracoccus denitrificans PD1222 4580707 YP_916392.1 CDS Pden_2609 NC_008686.1 2619991 2620605 R PFAM: 3'-5' exonuclease; KEGG: rsp:RSP_1152 ribonuclease D; 3'-5' exonuclease complement(2619991..2620605) Paracoccus denitrificans PD1222 4580708 YP_916393.1 CDS Pden_2610 NC_008686.1 2620850 2622847 D PFAM: TonB-dependent receptor; TonB-dependent receptor, plug; KEGG: bmb:BruAb2_1126 TonB dependent receptor domain protein; TonB-dependent receptor 2620850..2622847 Paracoccus denitrificans PD1222 4580709 YP_916394.1 CDS Pden_2611 NC_008686.1 2622995 2623249 D KEGG: mes:Meso_2258 transcriptional regulator, XRE family; XRE family transcriptional regulator 2622995..2623249 Paracoccus denitrificans PD1222 4580710 YP_916395.1 CDS Pden_2612 NC_008686.1 2623316 2624983 D PFAM: Sulfate transporter/antisigma-factor antagonist STAS; Xanthine/uracil/vitamin C permease; sulphate transporter; KEGG: mes:Meso_2257 sulphate transporter; sulfate transporter 2623316..2624983 Paracoccus denitrificans PD1222 4580711 YP_916396.1 CDS purU NC_008686.1 2625098 2625982 R 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 complement(2625098..2625982) Paracoccus denitrificans PD1222 4580712 YP_916397.1 CDS Pden_2614 NC_008686.1 2626054 2626950 R 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 complement(2626054..2626950) Paracoccus denitrificans PD1222 4580713 YP_916398.1 CDS Pden_2615 NC_008686.1 2627184 2629964 R PFAM: Patatin; KEGG: sus:Acid_5056 patatin; patatin complement(2627184..2629964) Paracoccus denitrificans PD1222 4580714 YP_916399.1 CDS Pden_2616 NC_008686.1 2630065 2631792 R KEGG: atc:AGR_L_695 hypothetical protein; hypothetical protein complement(2630065..2631792) Paracoccus denitrificans PD1222 4580715 YP_916400.1 CDS Pden_2617 NC_008686.1 2631792 2632925 R PFAM: iron-containing alcohol dehydrogenase; KEGG: rsp:RSP_2661 iron-containing alcohol dehydrogenase; iron-containing alcohol dehydrogenase complement(2631792..2632925) Paracoccus denitrificans PD1222 4580716 YP_916401.1 CDS Pden_2618 NC_008686.1 2632922 2634409 R TIGRFAM: glycerol kinase; PFAM: carbohydrate kinase, FGGY; KEGG: rsp:RSP_2662 glycerol kinase; glycerol kinase complement(2632922..2634409) Paracoccus denitrificans PD1222 4580717 YP_916402.1 CDS Pden_2619 NC_008686.1 2634599 2635369 D 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 2634599..2635369 Paracoccus denitrificans PD1222 4580718 YP_916403.1 CDS Pden_2620 NC_008686.1 2635379 2636623 R TIGRFAM: kynureninase; PFAM: aminotransferase, class V; KEGG: mlo:mll0621 probable kynureninase (kyurenine hydrolase); kynureninase complement(2635379..2636623) Paracoccus denitrificans PD1222 4580719 YP_916404.1 CDS Pden_2621 NC_008686.1 2636641 2637669 R 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 complement(2636641..2637669) Paracoccus denitrificans PD1222 4580720 YP_916405.1 CDS Pden_2622 NC_008686.1 2637985 2638272 R KEGG: rsp:RSP_6001 hypothetical protein; hypothetical protein complement(2637985..2638272) Paracoccus denitrificans PD1222 4580721 YP_916406.1 CDS Pden_2623 NC_008686.1 2638276 2638668 R hypothetical protein complement(2638276..2638668) Paracoccus denitrificans PD1222 4580722 YP_916407.1 CDS Pden_2624 NC_008686.1 2638735 2639379 R PFAM: regulatory protein, TetR; KEGG: rsp:RSP_6137 transcriptional regulator, TetR family; TetR family transcriptional regulator complement(2638735..2639379) Paracoccus denitrificans PD1222 4580723 YP_916408.1 CDS Pden_2625 NC_008686.1 2639404 2639751 R hypothetical protein complement(2639404..2639751) Paracoccus denitrificans PD1222 4580724 YP_916409.1 CDS flhB NC_008686.1 2640280 2641386 R membrane protein responsible for substrate specificity switching from rod/hook-type export to filament-type export; flagellar biosynthesis protein FlhB complement(2640280..2641386) Paracoccus denitrificans PD1222 4580725 YP_916410.1 CDS Pden_2627 NC_008686.1 2641383 2642141 R KEGG: sil:SPO0171 flagellar biosynthetic protein FliR; flagellar biosynthetic protein FliR complement(2641383..2642141) Paracoccus denitrificans PD1222 4580726 YP_916411.1 CDS flhA NC_008686.1 2642138 2644222 R membrane protein involved in the flagellar export apparatus; flagellar biosynthesis protein FlhA complement(2642138..2644222) Paracoccus denitrificans PD1222 4580727 YP_916412.1 CDS Pden_2629 NC_008686.1 2644219 2644488 R hypothetical protein complement(2644219..2644488) Paracoccus denitrificans PD1222 4580728 YP_916413.1 CDS Pden_2630 NC_008686.1 2644485 2644985 R KEGG: rsp:RSP_1316 flagellar motor protein; flagellar motor protein complement(2644485..2644985) Paracoccus denitrificans PD1222 4580729 YP_916414.1 CDS Pden_2631 NC_008686.1 2645365 2645898 D KEGG: rpa:RPA1896 homologue of rhodobacter capsulatus gene transfer agent (GTA) orfg6 (21% identity); hypothetical protein 2645365..2645898 Paracoccus denitrificans PD1222 4580730 YP_916415.1 CDS Pden_2632 NC_008686.1 2645895 2646161 D hypothetical protein 2645895..2646161 Paracoccus denitrificans PD1222 4580731 YP_916416.1 CDS Pden_2633 NC_008686.1 2646726 2648360 D PFAM: phage Terminase; KEGG: rsp:RSP_0213 phage terminase-like protein large subunit; phage terminase 2646726..2648360 Paracoccus denitrificans PD1222 4580732 YP_916417.1 CDS Pden_2634 NC_008686.1 2648357 2648689 D PFAM: HNH endonuclease; SMART: HNH nuclease; KEGG: rsp:RSP_0212 HNH nuclease; HNH endonuclease 2648357..2648689 Paracoccus denitrificans PD1222 4580733 YP_916418.1 CDS Pden_2635 NC_008686.1 2648698 2649933 D KEGG: rsp:RSP_0211 hypothetical protein; hypothetical protein 2648698..2649933 Paracoccus denitrificans PD1222 4580734 YP_916419.1 CDS Pden_2636 NC_008686.1 2649933 2650484 D 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 2649933..2650484 Paracoccus denitrificans PD1222 4580735 YP_916420.1 CDS Pden_2637 NC_008686.1 2650486 2651547 D KEGG: rsp:RSP_0208 hypothetical protein; hypothetical protein 2650486..2651547 Paracoccus denitrificans PD1222 4580736 YP_916421.1 CDS Pden_2638 NC_008686.1 2651547 2652053 D KEGG: rsp:RSP_0207 hypothetical protein; hypothetical protein 2651547..2652053 Paracoccus denitrificans PD1222 4580737 YP_916422.1 CDS Pden_2639 NC_008686.1 2652029 2652595 D KEGG: rsp:RSP_0206 hypothetical protein; hypothetical protein 2652029..2652595 Paracoccus denitrificans PD1222 4580738 YP_916423.1 CDS Pden_2640 NC_008686.1 2652588 2652845 D hypothetical protein 2652588..2652845 Paracoccus denitrificans PD1222 4580739 YP_916424.1 CDS Pden_2641 NC_008686.1 2652854 2653138 D hypothetical protein 2652854..2653138 Paracoccus denitrificans PD1222 4580740 YP_916425.1 CDS Pden_2642 NC_008686.1 2653148 2653450 D hypothetical protein 2653148..2653450 Paracoccus denitrificans PD1222 4580741 YP_916426.1 CDS Pden_2643 NC_008686.1 2653740 2653967 D hypothetical protein 2653740..2653967 Paracoccus denitrificans PD1222 4581188 YP_916427.1 CDS Pden_2644 NC_008686.1 2654388 2655395 D PFAM: phage integrase family protein; KEGG: rsp:RSP_2080 tyrosine recombinase; phage integrase family protein 2654388..2655395 Paracoccus denitrificans PD1222 4581189 YP_916428.1 CDS Pden_2645 NC_008686.1 2655460 2655906 R KEGG: sit:TM1040_2951 chemotaxis protein MotA; chemotaxis protein MotA complement(2655460..2655906) Paracoccus denitrificans PD1222 4581190 YP_916429.1 CDS Pden_2646 NC_008686.1 2655915 2656457 R KEGG: rsp:RSP_1315 hypothetical protein; hypothetical protein complement(2655915..2656457) Paracoccus denitrificans PD1222 4581191 YP_916430.1 CDS Pden_2647 NC_008686.1 2656450 2656797 R KEGG: sit:TM1040_2949 conserved hypothetical protein; hypothetical protein complement(2656450..2656797) Paracoccus denitrificans PD1222 4581192 YP_916431.1 CDS Pden_2648 NC_008686.1 2656794 2657276 R PFAM: flagellar basal body-associated protein FliL; KEGG: rsp:RSP_1313 possible flagellar synthesis protein; flagellar basal body protein FliL complement(2656794..2657276) Paracoccus denitrificans PD1222 4581193 YP_916432.1 CDS fliF NC_008686.1 2657379 2658959 D 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 2657379..2658959 Paracoccus denitrificans PD1222 4581194 YP_916433.1 CDS Pden_2650 NC_008686.1 2658956 2659516 D hypothetical protein 2658956..2659516 Paracoccus denitrificans PD1222 4581195 YP_916434.1 CDS Pden_2651 NC_008686.1 2659519 2659776 D PFAM: surface presentation of antigens (SPOA) protein; KEGG: rsp:RSP_1310 flagellar motor switch protein FliN/FliY; surface presentation of antigens (SPOA) protein 2659519..2659776 Paracoccus denitrificans PD1222 4581196 YP_916435.1 CDS fliP NC_008686.1 2659773 2660498 D FliP, with proteins FliQ and FliR, forms the core of the central channel in the flagella export apparatus; flagellar biosynthesis protein FliP 2659773..2660498 Paracoccus denitrificans PD1222 4581197 YP_916436.1 CDS Pden_2653 NC_008686.1 2660610 2661785 D 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 2660610..2661785 Paracoccus denitrificans PD1222 4581198 YP_916437.1 CDS Pden_2654 NC_008686.1 2661782 2662882 D 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 2661782..2662882 Paracoccus denitrificans PD1222 4581199 YP_916438.1 CDS Pden_2655 NC_008686.1 2662879 2665974 D PFAM: acriflavin resistance protein; KEGG: ret:RHE_PF00284 probable efflux transporter protein, acriflavin resistance protein family; acriflavin resistance protein 2662879..2665974 Paracoccus denitrificans PD1222 4581200 YP_916439.1 CDS Pden_2656 NC_008686.1 2666082 2668454 R 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 complement(2666082..2668454) Paracoccus denitrificans PD1222 4581201 YP_916440.1 CDS Pden_2657 NC_008686.1 2668554 2669126 D KEGG: sit:TM1040_2661 conserved hypothetical protein; hypothetical protein 2668554..2669126 Paracoccus denitrificans PD1222 4581202 YP_916441.1 CDS Pden_2658 NC_008686.1 2669142 2670551 D PFAM: major facilitator superfamily MFS_1; KEGG: rsp:RSP_1362 major facilitator superfamily (MFS) transporter; major facilitator superfamily transporter 2669142..2670551 Paracoccus denitrificans PD1222 4581203 YP_916442.1 CDS mepA NC_008686.1 2670548 2671420 D D-alanyl-D-alanine endopeptidase; functions in hydrolyzing cell wall peptidoglycan; similar to LAS metallopeptidases; forms a dimer in periplasm; penicillin-insensitive murein endopeptidase 2670548..2671420 Paracoccus denitrificans PD1222 4581204 YP_916443.1 CDS Pden_2660 NC_008686.1 2671393 2672361 D KEGG: rsp:RSP_1364 hypothetical protein; hypothetical protein 2671393..2672361 Paracoccus denitrificans PD1222 4581205 YP_916444.1 CDS Pden_2661 NC_008686.1 2672358 2673491 D PFAM: beta-lactamase; KEGG: bte:BTH_II1108 beta-lactamase; beta-lactamase 2672358..2673491 Paracoccus denitrificans PD1222 4581206 YP_916445.1 CDS Pden_2662 NC_008686.1 2673590 2674204 D TIGRFAM: conserved hypothetical integral membrane protein; PFAM: protein of unknown function DUF165; KEGG: rde:RD1_0365 hypothetical protein; hypothetical protein 2673590..2674204 Paracoccus denitrificans PD1222 4581207 YP_916446.1 CDS Pden_2663 NC_008686.1 2674609 2675790 R catalyzes the formation of beta-ketovaleryl-CoA from acetyl-CoA and propionyl-CoA; beta-ketothiolase complement(2674609..2675790) Paracoccus denitrificans PD1222 4581208 YP_916447.1 CDS Pden_2664 NC_008686.1 2675895 2676251 D PFAM: regulatory protein, LysR; KEGG: nha:Nham_2952 transcriptional regulator, ModE family; ModE family transcriptional regulator 2675895..2676251 Paracoccus denitrificans PD1222 4581209 YP_916448.1 CDS Pden_2665 NC_008686.1 2676318 2677058 D 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 2676318..2677058 Paracoccus denitrificans PD1222 4581210 YP_916449.1 CDS Pden_2666 NC_008686.1 2677055 2677759 D 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 2677055..2677759 Paracoccus denitrificans PD1222 4581211 YP_916450.1 CDS Pden_2667 NC_008686.1 2677759 2678814 D 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 2677759..2678814 Paracoccus denitrificans PD1222 4581212 YP_916451.1 CDS Pden_2668 NC_008686.1 2678889 2679467 D KEGG: rsp:RSP_1496 hypothetical protein; hypothetical protein 2678889..2679467 Paracoccus denitrificans PD1222 4581213 YP_916452.1 CDS Pden_2669 NC_008686.1 2679482 2680078 R PFAM: outer membrane lipoprotein carrier protein LolA; KEGG: rsp:RSP_1497 outer membrane lipoprotein carrier protein; outer membrane lipoprotein carrier protein LolA complement(2679482..2680078) Paracoccus denitrificans PD1222 4581214 YP_916453.1 CDS Pden_2670 NC_008686.1 2680168 2681427 R 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 complement(2680168..2681427) Paracoccus denitrificans PD1222 4581215 YP_916454.1 CDS Pden_2671 NC_008686.1 2681521 2682846 D PFAM: Amidase; KEGG: rsp:RSP_1493 amidase; amidase 2681521..2682846 Paracoccus denitrificans PD1222 4581216 YP_916455.1 CDS Pden_2672 NC_008686.1 2682975 2684168 D PFAM: aminotransferase, class I and II; KEGG: rsp:RSP_1494 aspartate aminotransferase; class I and II aminotransferase 2682975..2684168 Paracoccus denitrificans PD1222 4581217 YP_916456.1 CDS Pden_2673 NC_008686.1 2684172 2686856 D PFAM: cell divisionFtsK/SpoIIIE; SMART: AAA ATPase; KEGG: sil:SPO3416 FtsK/SpoIIIE family protein; DNA translocase FtsK 2684172..2686856 Paracoccus denitrificans PD1222 4581218 YP_916457.1 CDS Pden_2674 NC_008686.1 2686926 2687822 R KEGG: ppu:PP_0532 hypothetical protein; hypothetical protein complement(2686926..2687822) Paracoccus denitrificans PD1222 4581219 YP_916458.1 CDS Pden_2675 NC_008686.1 2687928 2689010 R PFAM: secretion protein HlyD family protein; KEGG: rru:Rru_A3484 secretion protein HlyD; secretion protein HlyD family protein complement(2687928..2689010) Paracoccus denitrificans PD1222 4581220 YP_916459.1 CDS Pden_2676 NC_008686.1 2689007 2690668 R KEGG: sme:SMc00563 transport protein transmembrane; transporter complement(2689007..2690668) Paracoccus denitrificans PD1222 4581221 YP_916460.1 CDS Pden_2677 NC_008686.1 2690665 2691126 R PFAM: regulatory protein, MarR; KEGG: sme:SMc00562 transcription regulator protein; MarR family transcriptional regulator complement(2690665..2691126) Paracoccus denitrificans PD1222 4581222 YP_916461.1 CDS Pden_2678 NC_008686.1 2691217 2695722 R PFAM: protein of unknown function DUF490; KEGG: rsp:RSP_1183 hypothetical protein; hypothetical protein complement(2691217..2695722) Paracoccus denitrificans PD1222 4581223 YP_916462.1 CDS Pden_2679 NC_008686.1 2695722 2697605 R PFAM: surface antigen (D15); KEGG: rsp:RSP_1182 outer membrane protein; surface antigen (D15) complement(2695722..2697605) Paracoccus denitrificans PD1222 4581224 YP_916463.1 CDS Pden_2680 NC_008686.1 2697697 2698620 R PFAM: Glucokinase; KEGG: sil:SPO0864 glucokinase; glucokinase complement(2697697..2698620) Paracoccus denitrificans PD1222 4581225 YP_916464.1 CDS Pden_2681 NC_008686.1 2698786 2699229 D hypothetical protein 2698786..2699229 Paracoccus denitrificans PD1222 4581226 YP_916465.1 CDS Pden_2682 NC_008686.1 2699299 2700690 D catalyzes the formation of L-homocysteine from S-adenosyl-L-homocysteine; S-adenosyl-L-homocysteine hydrolase 2699299..2700690 Paracoccus denitrificans PD1222 4581227 YP_916466.1 CDS Pden_2683 NC_008686.1 2700753 2701202 D PFAM: histidine triad (HIT) protein; KEGG: bbr:BB0059 histidine triad protein; histidine triad (HIT) protein 2700753..2701202 Paracoccus denitrificans PD1222 4581228 YP_916467.1 CDS Pden_2684 NC_008686.1 2701280 2701621 D KEGG: sit:TM1040_2834 conserved hypothetical protein; hypothetical protein 2701280..2701621 Paracoccus denitrificans PD1222 4581229 YP_916468.1 CDS Pden_2685 NC_008686.1 2701707 2702327 R PFAM: Enoyl-CoA hydratase/isomerase; KEGG: rsp:RSP_0913 enoyl-CoA hydratase/isomerase; enoyl-CoA hydratase complement(2701707..2702327) Paracoccus denitrificans PD1222 4581230 YP_916469.1 CDS Pden_2686 NC_008686.1 2702411 2703961 D KEGG: sil:SPO3441 hypothetical protein; hypothetical protein 2702411..2703961 Paracoccus denitrificans PD1222 4581231 YP_916470.1 CDS Pden_2687 NC_008686.1 2704057 2705409 D PFAM: peptidase U62, modulator of DNA gyrase; KEGG: jan:Jann_0403 peptidase U62, modulator of DNA gyrase; C69 family peptidase 2704057..2705409 Paracoccus denitrificans PD1222 4581232 YP_916471.1 CDS Pden_2688 NC_008686.1 2705396 2706217 D PFAM: inositol monophosphatase; KEGG: rsp:RSP_0917 inositol monophosphatase; inositol monophosphatase 2705396..2706217 Paracoccus denitrificans PD1222 4581233 YP_916472.1 CDS Pden_2689 NC_008686.1 2706278 2706823 D PFAM: flavin reductase domain protein, FMN-binding; KEGG: atc:AGR_L_3083 hypothetical protein; flavin reductase domain-containing protein 2706278..2706823 Paracoccus denitrificans PD1222 4581234 YP_916473.1 CDS Pden_2690 NC_008686.1 2706830 2707306 R KEGG: ppu:PP_4887 hypothetical protein; hypothetical protein complement(2706830..2707306) Paracoccus denitrificans PD1222 4581235 YP_916474.1 CDS Pden_2691 NC_008686.1 2707385 2708035 R PFAM: protein of unknown function DUF330; KEGG: sit:TM1040_3329 protein of unknown function DUF330; hypothetical protein complement(2707385..2708035) Paracoccus denitrificans PD1222 4581236 YP_916475.1 CDS Pden_2692 NC_008686.1 2708037 2710103 R PFAM: Mammalian cell entry related domain protein; KEGG: sit:TM1040_3328 mammalian cell entry related; hypothetical protein complement(2708037..2710103) Paracoccus denitrificans PD1222 4581237 YP_916476.1 CDS Pden_2693 NC_008686.1 2710100 2710759 R PFAM: Paraquat-inducible protein A; KEGG: sit:TM1040_3327 paraquat-inducible protein A; paraquat-inducible protein A complement(2710100..2710759) Paracoccus denitrificans PD1222 4581238 YP_916477.1 CDS Pden_2694 NC_008686.1 2710756 2711436 R PFAM: Paraquat-inducible protein A; KEGG: sit:TM1040_3326 paraquat-inducible protein A; paraquat-inducible protein A complement(2710756..2711436) Paracoccus denitrificans PD1222 4581239 YP_916478.1 CDS Pden_2695 NC_008686.1 2711699 2712499 D KEGG: rsp:RSP_1302 chemotaxis MotB protein; chemotaxis protein MotB 2711699..2712499 Paracoccus denitrificans PD1222 4581240 YP_916479.1 CDS Pden_2696 NC_008686.1 2712587 2713927 D PFAM: flagellar basal body rod protein; protein of unknown function DUF1078 domain protein; KEGG: rsp:RSP_1303 flagellar hook protein; hypothetical protein 2712587..2713927 Paracoccus denitrificans PD1222 4581241 YP_916480.1 CDS flgK NC_008686.1 2713983 2715443 D with FlgL acts as a hook filament junction protein to join the flagellar filament to the hook; flagellar hook-associated protein FlgK 2713983..2715443 Paracoccus denitrificans PD1222 4581242 YP_916481.1 CDS Pden_2698 NC_008686.1 2715440 2716459 D KEGG: rsp:RSP_1305 flagellar hook-associated protein; flagellar hook-associated protein 2715440..2716459 Paracoccus denitrificans PD1222 4581243 YP_916482.1 CDS flgI NC_008686.1 2716456 2717556 D 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 2716456..2717556 Paracoccus denitrificans PD1222 4581244 YP_916483.1 CDS Pden_2703 NC_008686.1 2719808 2720194 R PFAM: transposase, IS4 family protein; KEGG: nmu:Nmul_A2650 transposase, IS4; transposase, IS4 family protein complement(2719808..2720194) Paracoccus denitrificans PD1222 4581245 YP_916484.1 CDS Pden_2704 NC_008686.1 2720191 2720559 R KEGG: mag:amb0408 transposase and inactivated derivative; transposase and inactivated derivative complement(2720191..2720559) Paracoccus denitrificans PD1222 4580339 YP_916485.1 CDS Pden_2705 NC_008686.1 2720874 2721524 R PFAM: carbonic anhydrase; KEGG: rsp:RSP_1377 carbonic anhydrase; carbonate dehydratase complement(2720874..2721524) Paracoccus denitrificans PD1222 4580340 YP_916486.1 CDS Pden_2706 NC_008686.1 2721656 2722045 D KEGG: rde:RD1_0313 hypothetical protein; hypothetical protein 2721656..2722045 Paracoccus denitrificans PD1222 4580341 YP_916487.1 CDS Pden_2707 NC_008686.1 2722118 2723521 D PFAM: peptidase M17, leucyl aminopeptidase domain protein; KEGG: sit:TM1040_3455 leucyl aminopeptidase; leucyl aminopeptidase 2722118..2723521 Paracoccus denitrificans PD1222 4580342 YP_916488.1 CDS Pden_2708 NC_008686.1 2723518 2724366 D PFAM: NLP/P60 protein; KEGG: rsp:RSP_1380 hypothetical protein; NLP/P60 protein 2723518..2724366 Paracoccus denitrificans PD1222 4580343 YP_916489.1 CDS Pden_2709 NC_008686.1 2724389 2725444 D PFAM: alanine dehydrogenase/PNT domain protein; KEGG: sil:SPO3307 saccharopine dehydrogenase; NAD(P) transhydrogenase subunit alpha 2724389..2725444 Paracoccus denitrificans PD1222 4580344 YP_916490.1 CDS Pden_2710 NC_008686.1 2725508 2726692 D PFAM: glucose sorbosone dehydrogenase; KEGG: neu:NE1997 glucose dehydrogenase B; glucose sorbosone dehydrogenase 2725508..2726692 Paracoccus denitrificans PD1222 4580345 YP_916491.1 CDS Pden_2711 NC_008686.1 2726876 2727247 R KEGG: sil:SPO3310 hypothetical protein; hypothetical protein complement(2726876..2727247) Paracoccus denitrificans PD1222 4580346 YP_916492.1 CDS Pden_2712 NC_008686.1 2727297 2727944 R KEGG: rsp:RSP_3367 hypothetical protein; hypothetical protein complement(2727297..2727944) Paracoccus denitrificans PD1222 4580347 YP_916493.1 CDS mutL NC_008686.1 2727941 2729761 R 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 complement(2727941..2729761) Paracoccus denitrificans PD1222 4580348 YP_916494.1 CDS Pden_2714 NC_008686.1 2729805 2731118 R PFAM: peptidase M16 domain protein; KEGG: rde:RD1_0659 peptidase, M16 family; peptidase M16 domain-containing protein complement(2729805..2731118) Paracoccus denitrificans PD1222 4580349 YP_916495.1 CDS Pden_2715 NC_008686.1 2731115 2732533 R PFAM: peptidase M16 domain protein; KEGG: rsp:RSP_1097 zinc protease; peptidase M16 domain-containing protein complement(2731115..2732533) Paracoccus denitrificans PD1222 4580350 YP_916496.1 CDS Pden_2716 NC_008686.1 2732634 2733206 R KEGG: rsp:RSP_1098 hypothetical protein; hypothetical protein complement(2732634..2733206) Paracoccus denitrificans PD1222 4580351 YP_916497.1 CDS Pden_2717 NC_008686.1 2733238 2733921 R TIGRFAM: lipoprotein signal peptidase; PFAM: peptidase A8, signal peptidase II; KEGG: rsp:RSP_1099 signal peptidase II; lipoprotein signal peptidase complement(2733238..2733921) Paracoccus denitrificans PD1222 4580352 YP_916498.1 CDS purH NC_008686.1 2733921 2735510 R involved in de novo purine biosynthesis; bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase complement(2733921..2735510) Paracoccus denitrificans PD1222 4580353 YP_916499.1 CDS Pden_2719 NC_008686.1 2735550 2737199 R PFAM: Heparinase II/III family protein; KEGG: sil:SPO3375 hypothetical protein; heparinase II/III family protein complement(2735550..2737199) Paracoccus denitrificans PD1222 4580354 YP_916500.1 CDS Pden_2720 NC_008686.1 2737230 2738837 R PFAM: Fmu (Sun) domain protein; NusB/RsmB/TIM44; methyltransferase small; KEGG: sil:SPO3376 ribosomal RNA small subunit methyltransferase B; Fmu (Sun) domain-containing protein complement(2737230..2738837) Paracoccus denitrificans PD1222 4580355 YP_916501.1 CDS Pden_2721 NC_008686.1 2738891 2740060 D 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 2738891..2740060 Paracoccus denitrificans PD1222 4580356 YP_916502.1 CDS Pden_2722 NC_008686.1 2740064 2743162 D 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 2740064..2743162 Paracoccus denitrificans PD1222 4580357 YP_916503.1 CDS Pden_2723 NC_008686.1 2743159 2744202 D catalyzes the formation of selenophosphate from selenide and ATP; selenophosphate synthetase 2743159..2744202 Paracoccus denitrificans PD1222 4580358 YP_916504.1 CDS Pden_2724 NC_008686.1 2744297 2744662 D KEGG: sme:SMa0026 hypothetical protein; hypothetical protein 2744297..2744662 Paracoccus denitrificans PD1222 4580359 YP_916505.1 CDS Pden_2725 NC_008686.1 2744730 2745149 D TIGRFAM: uncharacterized domain 1; PFAM: thioesterase superfamily protein; KEGG: rpe:RPE_2404 uncharacterized domain 1; hypothetical protein 2744730..2745149 Paracoccus denitrificans PD1222 4580360 YP_916506.1 CDS Pden_2726 NC_008686.1 2745472 2746125 D 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 2745472..2746125 Paracoccus denitrificans PD1222 4580361 YP_916507.1 CDS Pden_2727 NC_008686.1 2746148 2747542 D 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 2746148..2747542 Paracoccus denitrificans PD1222 4580362 YP_916508.1 CDS Pden_2728 NC_008686.1 2747569 2748357 D KEGG: rsp:RSP_0250 hypothetical protein; hypothetical protein 2747569..2748357 Paracoccus denitrificans PD1222 4580363 YP_916509.1 CDS Pden_2729 NC_008686.1 2748435 2749604 R PFAM: Peptidoglycan-binding LysM; peptidase M23B; KEGG: rsp:RSP_2543 peptidoglycan-binding LysM (possible peptidase); peptidase M23B complement(2748435..2749604) Paracoccus denitrificans PD1222 4580364 YP_916510.1 CDS Pden_2730 NC_008686.1 2749636 2750286 R 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 complement(2749636..2750286) Paracoccus denitrificans PD1222 4580365 YP_916511.1 CDS Pden_2731 NC_008686.1 2750295 2751089 R catalyzes the conversion of a phosphate monoester to an alcohol and a phosphate; stationary phase survival protein SurE complement(2750295..2751089) Paracoccus denitrificans PD1222 4580366 YP_916512.1 CDS Pden_2732 NC_008686.1 2751281 2752204 D PFAM: protein of unknown function DUF81; KEGG: rsp:RSP_2206 hypothetical protein; hypothetical protein 2751281..2752204 Paracoccus denitrificans PD1222 4580367 YP_916513.1 CDS Pden_2733 NC_008686.1 2752201 2752998 D KEGG: rde:RD1_1641 hypothetical protein; hypothetical protein 2752201..2752998 Paracoccus denitrificans PD1222 4580368 YP_916514.1 CDS Pden_2734 NC_008686.1 2752985 2754142 R PFAM: protein of unknown function DUF482; KEGG: sil:SPO3732 hypothetical protein; hypothetical protein complement(2752985..2754142) Paracoccus denitrificans PD1222 4580369 YP_916515.1 CDS Pden_2735 NC_008686.1 2754163 2754918 R PFAM: glycerophosphoryl diester phosphodiesterase; KEGG: jan:Jann_0436 glycerophosphoryl diester phosphodiesterase; glycerophosphoryl diester phosphodiesterase complement(2754163..2754918) Paracoccus denitrificans PD1222 4580370 YP_916516.1 CDS Pden_2736 NC_008686.1 2754918 2755358 R PFAM: Endoribonuclease L-PSP; KEGG: rsp:RSP_0894 hypothetical protein; endoribonuclease L-PSP complement(2754918..2755358) Paracoccus denitrificans PD1222 4580371 YP_916517.1 CDS Pden_2737 NC_008686.1 2755368 2755820 R KEGG: sal:Sala_1312 hypothetical protein; hypothetical protein complement(2755368..2755820) Paracoccus denitrificans PD1222 4580372 YP_916518.1 CDS Pden_2738 NC_008686.1 2755866 2759369 R 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 complement(2755866..2759369) Paracoccus denitrificans PD1222 4580373 YP_916519.1 CDS Pden_2739 NC_008686.1 2759463 2759816 D PFAM: LrgA family protein; KEGG: bcn:Bcen_5769 LrgA; LrgA family protein 2759463..2759816 Paracoccus denitrificans PD1222 4580374 YP_916520.1 CDS Pden_2740 NC_008686.1 2759813 2760529 D PFAM: LrgB family protein; KEGG: rsp:RSP_3332 transmembrane protein; LrgB family protein 2759813..2760529 Paracoccus denitrificans PD1222 4580375 YP_916521.1 CDS Pden_2741 NC_008686.1 2760542 2761012 R hypothetical protein complement(2760542..2761012) Paracoccus denitrificans PD1222 4580376 YP_916522.1 CDS Pden_2742 NC_008686.1 2761122 2761448 R KEGG: rsp:RSP_6107 hypothetical protein; hypothetical protein complement(2761122..2761448) Paracoccus denitrificans PD1222 4580377 YP_916523.1 CDS Pden_2743 NC_008686.1 2761790 2762353 D Involved in peptide bond synthesis; alters the affinity of the ribosome for aminoacyl-tRNA; elongation factor P 2761790..2762353 Paracoccus denitrificans PD1222 4580378 YP_916524.1 CDS Pden_2744 NC_008686.1 2762441 2763574 D KEGG: jan:Jann_1003 hypothetical protein; acetyltransferase 2762441..2763574 Paracoccus denitrificans PD1222 4580379 YP_916525.1 CDS Pden_2745 NC_008686.1 2763832 2764896 D KEGG: mes:Meso_0838 sugar uptake ABC transporter periplasmic solute-binding protein precursor; sugar uptake ABC transporter periplasmic solute-binding protein 2763832..2764896 Paracoccus denitrificans PD1222 4580380 YP_916526.1 CDS Pden_2746 NC_008686.1 2764956 2766530 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: mes:Meso_0839 ABC transporter related; ABC transporter 2764956..2766530 Paracoccus denitrificans PD1222 4580381 YP_916527.1 CDS Pden_2747 NC_008686.1 2766523 2767707 D PFAM: inner-membrane translocator; KEGG: mes:Meso_0840 inner-membrane translocator; inner-membrane translocator 2766523..2767707 Paracoccus denitrificans PD1222 4580382 YP_916528.1 CDS Pden_2748 NC_008686.1 2767704 2768606 D PFAM: 2-keto-3-deoxy-galactonokinase; KEGG: rsp:RSP_1371 2-dehydro-3-deoxygalactonokinase; 2-keto-3-deoxy-galactonokinase 2767704..2768606 Paracoccus denitrificans PD1222 4580383 YP_916529.1 CDS Pden_2749 NC_008686.1 2768603 2769205 D 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 2768603..2769205 Paracoccus denitrificans PD1222 4580384 YP_916530.1 CDS Pden_2750 NC_008686.1 2769202 2770044 D PFAM: SMP-30/Gluconolaconase/LRE domain protein; KEGG: jan:Jann_3831 senescence marker protein-30 (SMP-30); SMP-30/gluconolaconase/LRE domain-containing protein 2769202..2770044 Paracoccus denitrificans PD1222 4580385 YP_916531.1 CDS Pden_2751 NC_008686.1 2770041 2771051 D PFAM: Aldose 1-epimerase; KEGG: sme:SMc03798 probable aldose 1-epimerase protein; aldose 1-epimerase 2770041..2771051 Paracoccus denitrificans PD1222 4580386 YP_916532.1 CDS Pden_2752 NC_008686.1 2771095 2771817 D PFAM: regulatory protein GntR, HTH; GntR domain protein; KEGG: sil:SPO1722 transcriptional regulator, GntR family; GntR family transcriptional regulator 2771095..2771817 Paracoccus denitrificans PD1222 4580387 YP_916533.1 CDS Pden_2753 NC_008686.1 2771858 2772703 R PFAM: fumarylacetoacetate (FAA) hydrolase; KEGG: bcn:Bcen_5340 5-carboxymethyl-2-hydroxymuconate delta-isomerase; 5-carboxymethyl-2-hydroxymuconate delta-isomerase complement(2771858..2772703) Paracoccus denitrificans PD1222 4580388 YP_916534.1 CDS Pden_2754 NC_008686.1 2772733 2773470 R 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 complement(2772733..2773470) Paracoccus denitrificans PD1222 4580389 YP_916535.1 CDS Pden_2755 NC_008686.1 2773558 2775009 R PFAM: aldehyde dehydrogenase; KEGG: rsp:RSP_1507 aldehyde dehydrogenase; aldehyde dehydrogenase complement(2773558..2775009) Paracoccus denitrificans PD1222 4580390 YP_916536.1 CDS Pden_2756 NC_008686.1 2775171 2775827 D PFAM: alkyl hydroperoxide reductase/ Thiol specific antioxidant/ Mal allergen; Redoxin domain protein; KEGG: sil:SPO3383 thiol-specific antioxidant protein; peroxidase 2775171..2775827 Paracoccus denitrificans PD1222 4580391 YP_916537.1 CDS Pden_2757 NC_008686.1 2775867 2776655 R PFAM: glycosyl transferase, family 25; KEGG: sfr:Sfri_3927 glycosyl transferase, family 25; glycosyl transferase family protein complement(2775867..2776655) Paracoccus denitrificans PD1222 4580392 YP_916538.1 CDS Pden_2758 NC_008686.1 2776652 2777455 R hypothetical protein complement(2776652..2777455) Paracoccus denitrificans PD1222 4580393 YP_916539.1 CDS Pden_2759 NC_008686.1 2777503 2779713 R 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 complement(2777503..2779713) Paracoccus denitrificans PD1222 4580394 YP_916540.1 CDS rpsO NC_008686.1 2780143 2780412 R 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 complement(2780143..2780412) Paracoccus denitrificans PD1222 4580395 YP_916541.1 CDS Pden_2761 NC_008686.1 2780558 2781487 R KEGG: sil:SPO2352 type I secretion target repeat protein; type I secretion target repeat-containing protein complement(2780558..2781487) Paracoccus denitrificans PD1222 4580396 YP_916542.1 CDS Pden_2762 NC_008686.1 2781594 2782247 R PFAM: alanine racemase domain protein; KEGG: rsp:RSP_0844 hypothetical protein; alanine racemase complement(2781594..2782247) Paracoccus denitrificans PD1222 4580397 YP_916543.1 CDS Pden_2763 NC_008686.1 2782317 2783438 R KEGG: sil:SPO3430 outer membrane porin; porin complement(2782317..2783438) Paracoccus denitrificans PD1222 4581342 YP_916544.1 CDS Pden_2764 NC_008686.1 2783615 2784124 D KEGG: sil:SPO3431 hypothetical protein; hypothetical protein 2783615..2784124 Paracoccus denitrificans PD1222 4581343 YP_916545.1 CDS leuS NC_008686.1 2784200 2786734 D 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 2784200..2786734 Paracoccus denitrificans PD1222 4581344 YP_916546.1 CDS Pden_2766 NC_008686.1 2786721 2787206 D KEGG: rsp:RSP_0839 predicted secreted periplasmic protein; secreted periplasmic protein 2786721..2787206 Paracoccus denitrificans PD1222 4581345 YP_916547.1 CDS Pden_2767 NC_008686.1 2787203 2788231 D TIGRFAM: DNA polymerase III, delta subunit; PFAM: DNA polymerase III, delta; KEGG: sil:SPO3434 DNA polymerase III delta subunit; DNA polymerase III subunit delta 2787203..2788231 Paracoccus denitrificans PD1222 4581346 YP_916548.1 CDS Pden_2768 NC_008686.1 2788228 2789433 D PFAM: HI0933 family protein; KEGG: rsp:RSP_0836 flavoprotein; hypothetical protein 2788228..2789433 Paracoccus denitrificans PD1222 4581347 YP_916549.1 CDS Pden_2769 NC_008686.1 2789409 2789996 R PFAM: Glutathione S-transferase, N-terminal domain; KEGG: rde:RD1_0053 glutathione S-transferase family protein; glutathione S-transferase domain-containing protein complement(2789409..2789996) Paracoccus denitrificans PD1222 4581348 YP_916550.1 CDS Pden_2770 NC_008686.1 2790118 2791362 D PFAM: major facilitator superfamily MFS_1; KEGG: rsp:RSP_1372 major facilitator superfamily (MFS) transporter; major facilitator superfamily transporter 2790118..2791362 Paracoccus denitrificans PD1222 4581349 YP_916551.1 CDS Pden_2771 NC_008686.1 2791452 2792228 D TIGRFAM: 5'-nucleotidase, lipoprotein e(P4) family; PFAM: acid phosphatase (Class B); KEGG: hpy:HP1285 conserved hypothetical secreted protein; 5'-nucleotidase 2791452..2792228 Paracoccus denitrificans PD1222 4581350 YP_916552.1 CDS Pden_2772 NC_008686.1 2792380 2793573 D PFAM: major facilitator superfamily MFS_1; KEGG: rsp:RSP_1373 major facilitator superfamily (MFS) transporter; major facilitator superfamily transporter 2792380..2793573 Paracoccus denitrificans PD1222 4581351 YP_916553.1 CDS Pden_2773 NC_008686.1 2793566 2794612 D PFAM: glycosyl transferase, group 1; KEGG: rsp:RSP_1374 lipopolysaccharide core biosynthesis mannosyltransferase protein; group 1 glycosyl transferase 2793566..2794612 Paracoccus denitrificans PD1222 4581352 YP_916554.1 CDS Pden_2774 NC_008686.1 2794609 2795223 D KEGG: rsp:RSP_1375 hypothetical protein; hypothetical protein 2794609..2795223 Paracoccus denitrificans PD1222 4581353 YP_916555.1 CDS Pden_2775 NC_008686.1 2795325 2796347 D catalyzes the formation of 4-aspartyl phosphate from aspartate 4-semialdehyde; aspartate-semialdehyde dehydrogenase 2795325..2796347 Paracoccus denitrificans PD1222 4581354 YP_916556.1 CDS Pden_2776 NC_008686.1 2796442 2798079 D KEGG: sit:TM1040_3460 conserved hypothetical protein; hypothetical protein 2796442..2798079 Paracoccus denitrificans PD1222 4581355 YP_916557.1 CDS Pden_2777 NC_008686.1 2798267 2798905 R Enables the cleavage of the glycosidic bond in both 5'-methylthioadenosine and S-adenosylhomocysteine; 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase complement(2798267..2798905) Paracoccus denitrificans PD1222 4581356 YP_916558.1 CDS Pden_2778 NC_008686.1 2799011 2800606 R SMART: PAS domain containing protein; KEGG: rsp:RSP_1521 hypothetical protein; PAS/PAC sensor protein complement(2799011..2800606) Paracoccus denitrificans PD1222 4581357 YP_916559.1 CDS Pden_2779 NC_008686.1 2800682 2802070 R 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 complement(2800682..2802070) Paracoccus denitrificans PD1222 4581358 YP_916560.1 CDS Pden_2780 NC_008686.1 2802107 2802757 D PFAM: electron transport protein SCO1/SenC; KEGG: rde:RD1_0460 SenC protein; electron transport protein SCO1/SenC 2802107..2802757 Paracoccus denitrificans PD1222 4581359 YP_916561.1 CDS Pden_2781 NC_008686.1 2802810 2803358 D PFAM: response regulator receiver; KEGG: sit:TM1040_2838 response regulator receiver protein; Fis family transcriptional regulator 2802810..2803358 Paracoccus denitrificans PD1222 4581360 YP_916562.1 CDS Pden_2782 NC_008686.1 2803442 2803750 D 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 2803442..2803750 Paracoccus denitrificans PD1222 4581361 YP_916563.1 CDS Pden_2783 NC_008686.1 2803796 2804404 R PFAM: metal-dependent phosphohydrolase, HD sub domain; KEGG: rsp:RSP_1516 S-adenosyl L-homocystein hydrolase; metal dependent phosphohydrolase complement(2803796..2804404) Paracoccus denitrificans PD1222 4581362 YP_916564.1 CDS Pden_2784 NC_008686.1 2804552 2805085 R 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 complement(2804552..2805085) Paracoccus denitrificans PD1222 4581363 YP_916565.1 CDS Pden_2785 NC_008686.1 2805135 2805713 R PFAM: FxsA cytoplasmic membrane protein; KEGG: ppr:PBPRA3390 FxsA protein; FxsA cytoplasmic membrane protein complement(2805135..2805713) Paracoccus denitrificans PD1222 4581364 YP_916566.1 CDS Pden_2786 NC_008686.1 2805825 2806481 D PFAM: import inner membrane translocase, subunit Tim44; KEGG: jan:Jann_0191 import inner membrane translocase, subunit Tim44; import inner membrane translocase subunit Tim44 2805825..2806481 Paracoccus denitrificans PD1222 4581365 YP_916567.1 CDS Pden_2787 NC_008686.1 2806485 2807093 D PFAM: Smr protein/MutS2; KEGG: rsp:RSP_1241 Smr protein/MutS2; Smr protein/MutS2 2806485..2807093 Paracoccus denitrificans PD1222 4581366 YP_916568.1 CDS Pden_2788 NC_008686.1 2807090 2808163 R PFAM: protein of unknown function DUF900, hydrolase family protein; KEGG: sil:SPO3883 lipoprotein; hypothetical protein complement(2807090..2808163) Paracoccus denitrificans PD1222 4581367 YP_916569.1 CDS Pden_2789 NC_008686.1 2808226 2808402 R KEGG: rpb:RPB_1461 hypothetical protein; hypothetical protein complement(2808226..2808402) Paracoccus denitrificans PD1222 4581368 YP_916570.1 CDS hslU NC_008686.1 2808460 2809767 R heat shock protein involved in degradation of misfolded proteins; ATP-dependent protease ATP-binding subunit HslU complement(2808460..2809767) Paracoccus denitrificans PD1222 4581369 YP_916571.1 CDS Pden_2791 NC_008686.1 2809962 2810516 R heat shock protein involved in degradation of misfolded proteins; ATP-dependent protease peptidase subunit complement(2809962..2810516) Paracoccus denitrificans PD1222 4581370 YP_916572.1 CDS Pden_2792 NC_008686.1 2810620 2811540 D KEGG: rsp:RSP_1530 hypothetical protein; hypothetical protein 2810620..2811540 Paracoccus denitrificans PD1222 4581371 YP_916573.1 CDS Pden_2793 NC_008686.1 2811544 2811867 R TIGRFAM: thioredoxin; PFAM: glutaredoxin; Thioredoxin domain; KEGG: jan:Jann_4067 thioredoxin; thioredoxin complement(2811544..2811867) Paracoccus denitrificans PD1222 4581372 YP_916574.1 CDS Pden_2794 NC_008686.1 2811921 2815295 R 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 complement(2811921..2815295) Paracoccus denitrificans PD1222 4581373 YP_916575.1 CDS Pden_2795 NC_008686.1 2815285 2818227 R KEGG: rsp:RSP_1525 helicase/exonuclease; helicase/exonuclease complement(2815285..2818227) Paracoccus denitrificans PD1222 4581374 YP_916576.1 CDS Pden_2796 NC_008686.1 2818220 2818891 R PFAM: Nucleotidyl transferase; KEGG: rsp:RSP_1524 nucleotidyltransferase family protein; nucleotidyl transferase complement(2818220..2818891) Paracoccus denitrificans PD1222 4581375 YP_916577.1 CDS Pden_2797 NC_008686.1 2818888 2820306 R PFAM: aminoglycoside phosphotransferase; protein of unknown function UPF0079; KEGG: rpb:RPB_0625 hypothetical protein; hypothetical protein complement(2818888..2820306) Paracoccus denitrificans PD1222 4581376 YP_916578.1 CDS Pden_2798 NC_008686.1 2820352 2821158 R catalyzes the reduction of 2,3-dihydrodipicolinate to 2,3,4,5-tetrahydrodipicolinate in lysine and diaminopimelate biosynthesis; dihydrodipicolinate reductase complement(2820352..2821158) Paracoccus denitrificans PD1222 4581377 YP_916579.1 CDS rbfA NC_008686.1 2821228 2821644 D 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 2821228..2821644 Paracoccus denitrificans PD1222 4581378 YP_916580.1 CDS Pden_2800 NC_008686.1 2821634 2822389 D KEGG: rsp:RSP_1107 hypothetical protein; hypothetical protein 2821634..2822389 Paracoccus denitrificans PD1222 4581379 YP_916581.1 CDS truB NC_008686.1 2822391 2823287 D catalyzes isomerization of specific uridines in RNA to pseudouridine; responsible for residues in T loops of many tRNAs; tRNA pseudouridine synthase B 2822391..2823287 Paracoccus denitrificans PD1222 4581380 YP_916582.1 CDS Pden_2802 NC_008686.1 2823284 2824120 R KEGG: sme:SMc02687 hypothetical protein; hypothetical protein complement(2823284..2824120) Paracoccus denitrificans PD1222 4581381 YP_916583.1 CDS Pden_2803 NC_008686.1 2824229 2825167 R PFAM: beta-lactamase domain protein; KEGG: rsp:RSP_0799 hypothetical protein; beta-lactamase domain-containing protein complement(2824229..2825167) Paracoccus denitrificans PD1222 4581382 YP_916584.1 CDS Pden_2804 NC_008686.1 2825242 2825889 R PFAM: pseudouridine synthase; KEGG: rsp:RSP_1506 pseudouridine synthase, Rlu; pseudouridylate synthase complement(2825242..2825889) Paracoccus denitrificans PD1222 4581383 YP_916585.1 CDS Pden_2805 NC_008686.1 2825886 2826512 R PFAM: Lysine exporter protein (LYSE/YGGA); KEGG: rru:Rru_A3172 lysine exporter protein (LysE/YggA); lysine exporter protein LysE/YggA complement(2825886..2826512) Paracoccus denitrificans PD1222 4581384 YP_916586.1 CDS Pden_2806 NC_008686.1 2826562 2826957 R PFAM: glutathione-dependent formaldehyde-activating, GFA; KEGG: sit:TM1040_0070 glutathione-dependent formaldehyde-activating, GFA; glutathione-dependent formaldehyde-activating protein complement(2826562..2826957) Paracoccus denitrificans PD1222 4581385 YP_916587.1 CDS Pden_2807 NC_008686.1 2826935 2827387 R KEGG: rde:RD1_0024 hypothetical protein; hypothetical protein complement(2826935..2827387) Paracoccus denitrificans PD1222 4581386 YP_916588.1 CDS Pden_2808 NC_008686.1 2827435 2827812 R hypothetical protein complement(2827435..2827812) Paracoccus denitrificans PD1222 4581387 YP_916589.1 CDS Pden_2809 NC_008686.1 2827915 2828736 R 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 complement(2827915..2828736) Paracoccus denitrificans PD1222 4581388 YP_916590.1 CDS Pden_2810 NC_008686.1 2828733 2829587 R PFAM: glycosyl transferase, family 8; KEGG: rsp:RSP_2568 glycosyl transferase (sulfolipid biosynthesis) protein; glycosyl transferase family protein complement(2828733..2829587) Paracoccus denitrificans PD1222 4581389 YP_916591.1 CDS Pden_2811 NC_008686.1 2829584 2830804 R PFAM: NAD-dependent epimerase/dehydratase; KEGG: rsp:RSP_2569 sulfolipid (UDP-sulfoquinovose) biosynthesis protein; NAD-dependent epimerase/dehydratase complement(2829584..2830804) Paracoccus denitrificans PD1222 4581390 YP_916592.1 CDS Pden_2812 NC_008686.1 2830922 2831401 D 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 2830922..2831401 Paracoccus denitrificans PD1222 4581391 YP_916593.1 CDS aroE NC_008686.1 2831555 2832403 D AroE; catalyzes the conversion of shikimate to 3-dehydroshikimate; shikimate 5-dehydrogenase 2831555..2832403 Paracoccus denitrificans PD1222 4581392 YP_916594.1 CDS Pden_2814 NC_008686.1 2832400 2832996 D KEGG: rsp:RSP_1235 dephospho-CoA kinase; TIGRFAM: dephospho-CoA kinase; PFAM: Dephospho-CoA kinase; dephospho-CoA kinase 2832400..2832996 Paracoccus denitrificans PD1222 4581393 YP_916595.1 CDS Pden_2815 NC_008686.1 2832989 2833708 D 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 2832989..2833708 Paracoccus denitrificans PD1222 4581394 YP_916596.1 CDS Pden_2816 NC_008686.1 2833781 2834662 D TIGRFAM: ribonuclease BN; PFAM: ribonuclease BN; KEGG: rde:RD1_0088 ribonuclease BN; ribonuclease BN 2833781..2834662 Paracoccus denitrificans PD1222 4581395 YP_916597.1 CDS Pden_2817 NC_008686.1 2834698 2835090 D PFAM: glutathione-dependent formaldehyde-activating, GFA; KEGG: pae:PA2722 hypothetical protein; glutathione-dependent formaldehyde-activating protein 2834698..2835090 Paracoccus denitrificans PD1222 4581396 YP_916598.1 CDS Pden_2818 NC_008686.1 2835095 2835727 R PFAM: Lysine exporter protein (LYSE/YGGA); KEGG: pen:PSEEN2025 transporter, LysE family; lysine exporter protein LysE/YggA complement(2835095..2835727) Paracoccus denitrificans PD1222 4581397 YP_916599.1 CDS Pden_2819 NC_008686.1 2835831 2837624 R 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 complement(2835831..2837624) Paracoccus denitrificans PD1222 4581398 YP_916600.1 CDS Pden_2820 NC_008686.1 2837634 2838227 R 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 complement(2837634..2838227) Paracoccus denitrificans PD1222 4581399 YP_916601.1 CDS Pden_2821 NC_008686.1 2838233 2838379 R KEGG: rsp:RSP_1273 hypothetical protein; hypothetical protein complement(2838233..2838379) Paracoccus denitrificans PD1222 4581152 YP_916602.1 CDS Pden_2822 NC_008686.1 2838473 2839276 D in Caulobacter crescentus, CC3477 is differentially expressed in minimal salts media with glucose as compared to complex media; two-component response regulator 2838473..2839276 Paracoccus denitrificans PD1222 4581153 YP_916603.1 CDS Pden_2823 NC_008686.1 2839399 2840286 R PFAM: 2-nitropropane dioxygenase, NPD; KEGG: jan:Jann_2812 2-nitropropane dioxygenase, NPD; 2-nitropropane dioxygenase complement(2839399..2840286) Paracoccus denitrificans PD1222 4581154 YP_916604.1 CDS Pden_2824 NC_008686.1 2840283 2841512 R PFAM: aldo/keto reductase; KEGG: sil:SPO1433 oxidoreductase, aldo/keto reductase family; aldo/keto reductase complement(2840283..2841512) Paracoccus denitrificans PD1222 4581155 YP_916605.1 CDS Pden_2825 NC_008686.1 2841629 2843560 R 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 complement(2841629..2843560) Paracoccus denitrificans PD1222 4581156 YP_916606.1 CDS Pden_2826 NC_008686.1 2843580 2844488 R TIGRFAM: formate dehydrogenase accessory protein FdhE; PFAM: formate dehydrogenase accessory protein; KEGG: sme:SMa0009 probable FdhE formate formation; formate dehydrogenase accessory protein FdhE complement(2843580..2844488) Paracoccus denitrificans PD1222 4581157 YP_916607.1 CDS Pden_2827 NC_008686.1 2844513 2845199 R TIGRFAM: formate dehydrogenase, gamma subunit; KEGG: sme:SMa0007 probable FdoI formate dehydrogenase-O,gamma subunit; formate dehydrogenase subunit gamma complement(2844513..2845199) Paracoccus denitrificans PD1222 4581158 YP_916608.1 CDS Pden_2828 NC_008686.1 2845199 2846197 R 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 complement(2845199..2846197) Paracoccus denitrificans PD1222 4581159 YP_916609.1 CDS Pden_2829 NC_008686.1 2846194 2848656 R 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 complement(2846194..2848656) Paracoccus denitrificans PD1222 4581160 YP_916610.1 CDS Pden_2830 NC_008686.1 2848678 2849277 R PFAM: molybdopterin oxidoreductase Fe4S4 region; KEGG: sme:SMa0002 probable FdoG formate dehydrogenase-O alpha subunit; molybdopterin oxidoreductase Fe4S4 region complement(2848678..2849277) Paracoccus denitrificans PD1222 4581161 YP_916611.1 CDS Pden_2831 NC_008686.1 2849430 2850506 R PFAM: ferredoxin; oxidoreductase FAD/NAD(P)-binding domain protein; Oxidoreductase FAD-binding domain protein; KEGG: rsp:RSP_3979 ferredoxin; ferredoxin complement(2849430..2850506) Paracoccus denitrificans PD1222 4581162 YP_916612.1 CDS Pden_2832 NC_008686.1 2850506 2851744 R PFAM: Rieske [2Fe-2S] domain protein; KEGG: sit:TM1040_3219 Rieske (2Fe-2S) region; Rieske (2Fe-2S) domain-containing protein complement(2850506..2851744) Paracoccus denitrificans PD1222 4581163 YP_916613.1 CDS dnaA NC_008687.1 405 1751 D 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 405..1751 Paracoccus denitrificans PD1222 4581400 YP_916614.1 CDS Pden_2834 NC_008687.1 1843 2961 D binds the polymerase to DNA and acts as a sliding clamp; DNA polymerase III subunit beta 1843..2961 Paracoccus denitrificans PD1222 4581401 YP_916615.1 CDS recF NC_008687.1 2958 4034 D Required for DNA replication; binds preferentially to single-stranded, linear DNA; recombination protein F 2958..4034 Paracoccus denitrificans PD1222 4581402 YP_916616.1 CDS Pden_2836 NC_008687.1 4068 5861 R KEGG: sit:TM1040_2799 adenine deaminase; TIGRFAM: adenine deaminase; PFAM: amidohydrolase; adenine deaminase complement(4068..5861) Paracoccus denitrificans PD1222 4581403 YP_916617.1 CDS recO NC_008687.1 5907 6635 D 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 5907..6635 Paracoccus denitrificans PD1222 4581404 YP_916618.1 CDS Pden_2838 NC_008687.1 6604 6987 R PFAM: protein of unknown function DUF306, Meta and HslJ; KEGG: sil:SPO3197 hypothetical protein; hypothetical protein complement(6604..6987) Paracoccus denitrificans PD1222 4581425 YP_916619.1 CDS Pden_2839 NC_008687.1 7020 7439 R PFAM: protein of unknown function DUF306, Meta and HslJ; hypothetical protein complement(7020..7439) Paracoccus denitrificans PD1222 4581426 YP_916620.1 CDS Pden_2840 NC_008687.1 7517 9172 R PFAM: acyl-CoA dehydrogenase domain protein; Acyl-CoA dehydrogenase, type 2, C-terminal domain; KEGG: rsp:RSP_1679 acyl-CoA dehydrogenase; acyl-CoA dehydrogenase complement(7517..9172) Paracoccus denitrificans PD1222 4581427 YP_916621.1 CDS Pden_2841 NC_008687.1 9330 10103 D PFAM: protein of unknown function DUF81; KEGG: sit:TM1040_2445 protein of unknown function DUF81; hypothetical protein 9330..10103 Paracoccus denitrificans PD1222 4581428 YP_916622.1 CDS Pden_2842 NC_008687.1 10132 11280 D 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 10132..11280 Paracoccus denitrificans PD1222 4581429 YP_916623.1 CDS Pden_2843 NC_008687.1 11277 11696 D PFAM: GCN5-related N-acetyltransferase; KEGG: rsp:RSP_1127 acetyltransferase, GNAT family; N-acetyltransferase GCN5 11277..11696 Paracoccus denitrificans PD1222 4581430 YP_916624.1 CDS Pden_2844 NC_008687.1 11693 12208 D KEGG: rsp:RSP_1006 hypothetical protein; hypothetical protein 11693..12208 Paracoccus denitrificans PD1222 4581431 YP_916625.1 CDS Pden_2845 NC_008687.1 12258 13637 D TIGRFAM: glutamate--cysteine ligase; PFAM: glutamate--cysteine ligase, GCS2; KEGG: sil:SPO3626 glutamate--cysteine ligase; glutamate--cysteine ligase 12258..13637 Paracoccus denitrificans PD1222 4581432 YP_916626.1 CDS Pden_2846 NC_008687.1 13690 14103 R KEGG: jan:Jann_1905 hypothetical protein; hypothetical protein complement(13690..14103) Paracoccus denitrificans PD1222 4581433 YP_916627.1 CDS Pden_2847 NC_008687.1 14216 14827 R PFAM: regulatory protein, TetR; KEGG: rsp:RSP_0014 transcriptional regulator, TetR family; TetR family transcriptional regulator complement(14216..14827) Paracoccus denitrificans PD1222 4581434 YP_916628.1 CDS Pden_2848 NC_008687.1 14837 15127 R TIGRFAM: phosphocarrier, HPr family; PFAM: phosphocarrier HPr protein; KEGG: rsp:RSP_1686 phosphocarrier HPr protein; phosphotransferase system, phosphocarrier protein HPr complement(14837..15127) Paracoccus denitrificans PD1222 4581435 YP_916629.1 CDS Pden_2849 NC_008687.1 15124 15549 R PFAM: PTS system fructose subfamily IIA component; KEGG: sil:SPO0714 PTS system IIA component, Man family; PTS system fructose subfamily transporter subunit IIA complement(15124..15549) Paracoccus denitrificans PD1222 4581436 YP_916630.1 CDS Pden_2850 NC_008687.1 15574 16533 R PFAM: Uncharacterized P-loop ATPase UPF0042; KEGG: rsp:RSP_1684 hypothetical protein; hypothetical protein complement(15574..16533) Paracoccus denitrificans PD1222 4581437 YP_916631.1 CDS Pden_2851 NC_008687.1 16542 16970 R KEGG: sil:SPO0712 HPr serine kinase/phosphatase domain protein; HPr kinase complement(16542..16970) Paracoccus denitrificans PD1222 4581438 YP_916632.1 CDS Pden_2852 NC_008687.1 17197 18795 D PEP carboxykinase; PEP carboxylase; PEPCK; catalyzes the phosphorylation and decarboxylation of oxaloacetate to form phosphoenolpyruvate using ATP; phosphoenolpyruvate carboxykinase 17197..18795 Paracoccus denitrificans PD1222 4581439 YP_916633.1 CDS Pden_2853 NC_008687.1 18955 21219 R 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 complement(18955..21219) Paracoccus denitrificans PD1222 4581440 YP_916634.1 CDS Pden_2854 NC_008687.1 21264 21485 R KEGG: sme:SMc03086 NAD-dependent formate dehydrogenase delta subunit protein; NAD-dependent formate dehydrogenase delta subunit protein complement(21264..21485) Paracoccus denitrificans PD1222 4581441 YP_916635.1 CDS Pden_2855 NC_008687.1 21492 22313 R 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 complement(21492..22313) Paracoccus denitrificans PD1222 4581442 YP_916636.1 CDS Pden_2856 NC_008687.1 22318 25197 R 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 complement(22318..25197) Paracoccus denitrificans PD1222 4581443 YP_916637.1 CDS Pden_2857 NC_008687.1 25194 26735 R PFAM: Respiratory-chain NADH dehydrogenase domain, 51 kDa subunit; KEGG: rsp:RSP_1079 NAD dependent formate dehydrogenase, beta subunit (51 kDa); NADH dehydrogenase (quinone) complement(25194..26735) Paracoccus denitrificans PD1222 4581444 YP_916638.1 CDS Pden_2858 NC_008687.1 26732 27211 R PFAM: NADH dehydrogenase (ubiquinone), 24 kDa subunit; KEGG: gbe:GbCGDNIH1_1932 NAD-dependent formate dehydrogenase gamma subunit (FdsG); NADH dehydrogenase (ubiquinone), 24 kDa subunit complement(26732..27211) Paracoccus denitrificans PD1222 4581445 YP_916639.1 CDS Pden_2859 NC_008687.1 27287 28159 R PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: rsp:RSP_1077 transcriptional regulator, LysR family; LysR family transcriptional regulator complement(27287..28159) Paracoccus denitrificans PD1222 4581446 YP_916640.1 CDS Pden_2860 NC_008687.1 28248 28487 R TIGRFAM: phosphoribosylformylglycinamidine synthase, purS; PFAM: phosphoribosylformylglycinamidine synthetase PurS; KEGG: rsp:RSP_2127 component of phosphoribosylformylglycinamidine (FGAM) synthetase; phosphoribosylformylglycinamidine synthase PurS complement(28248..28487) Paracoccus denitrificans PD1222 4581447 YP_916641.1 CDS Pden_2861 NC_008687.1 28499 29263 R 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 complement(28499..29263) Paracoccus denitrificans PD1222 4581448 YP_916642.1 CDS Pden_2862 NC_008687.1 29411 29725 D PFAM: protein of unknown function DUF1476; KEGG: sil:SPO1886 hypothetical protein; hypothetical protein 29411..29725 Paracoccus denitrificans PD1222 4581449 YP_916643.1 CDS Pden_2863 NC_008687.1 29772 31109 R TIGRFAM: MATE efflux family protein; PFAM: multi antimicrobial extrusion protein MatE; KEGG: rsp:RSP_2204 multidrug efflux pump, MATE family; MATE efflux family protein complement(29772..31109) Paracoccus denitrificans PD1222 4581450 YP_916644.1 CDS Pden_2864 NC_008687.1 31102 31605 R PFAM: thioesterase superfamily protein; KEGG: rsp:RSP_2203 hypothetical protein; thioesterase superfamily protein complement(31102..31605) Paracoccus denitrificans PD1222 4581451 YP_916645.1 CDS Pden_2865 NC_008687.1 31607 32110 R TIGRFAM: uncharacterized domain 1; PFAM: thioesterase superfamily protein; KEGG: sil:SPO2911 thioesterase family protein; hypothetical protein complement(31607..32110) Paracoccus denitrificans PD1222 4581452 YP_916646.1 CDS Pden_2866 NC_008687.1 32188 32604 D PFAM: regulatory protein, MerR; KEGG: rsp:RSP_2201 transcriptional regulator, MerR family; MerR family transcriptional regulator 32188..32604 Paracoccus denitrificans PD1222 4581453 YP_916647.1 CDS Pden_2867 NC_008687.1 32576 33085 D PFAM: regulatory protein, MerR; KEGG: sit:TM1040_1556 transcriptional regulator, MerR family; MerR family transcriptional regulator 32576..33085 Paracoccus denitrificans PD1222 4581454 YP_916648.1 CDS Pden_2868 NC_008687.1 33110 34888 D PFAM: acyl-CoA dehydrogenase domain protein; KEGG: rsp:RSP_2199 acyl-CoA dehydrogenase; acyl-CoA dehydrogenase 33110..34888 Paracoccus denitrificans PD1222 4581455 YP_916649.1 CDS Pden_2869 NC_008687.1 35165 35806 D 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 35165..35806 Paracoccus denitrificans PD1222 4581456 YP_916650.1 CDS Pden_2870 NC_008687.1 35803 37014 D 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 35803..37014 Paracoccus denitrificans PD1222 4581457 YP_916651.1 CDS Pden_2871 NC_008687.1 37026 39209 D 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 37026..39209 Paracoccus denitrificans PD1222 4581458 YP_916652.1 CDS Pden_2872 NC_008687.1 39349 40356 R PFAM: PfkB domain protein; KEGG: jan:Jann_1671 PfkB; ribokinase-like domain-containing protein complement(39349..40356) Paracoccus denitrificans PD1222 4581459 YP_916653.1 CDS Pden_2873 NC_008687.1 40353 41021 R 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 complement(40353..41021) Paracoccus denitrificans PD1222 4581460 YP_916654.1 CDS Pden_2874 NC_008687.1 41122 41718 D 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 41122..41718 Paracoccus denitrificans PD1222 4581461 YP_916655.1 CDS Pden_2875 NC_008687.1 41880 42527 D PFAM: OmpA/MotB domain protein; KEGG: rde:RD1_0967 OmpA family domain protein; OmpA/MotB domain-containing protein 41880..42527 Paracoccus denitrificans PD1222 4581462 YP_916656.1 CDS Pden_2876 NC_008687.1 42697 43251 R 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 complement(42697..43251) Paracoccus denitrificans PD1222 4581463 YP_916657.1 CDS Pden_2877 NC_008687.1 43248 43895 R 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' complement(43248..43895) Paracoccus denitrificans PD1222 4581405 YP_916658.1 CDS Pden_2878 NC_008687.1 43975 44208 R 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 complement(43975..44208) Paracoccus denitrificans PD1222 4581406 YP_916659.1 CDS Pden_2879 NC_008687.1 44268 45014 R 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 complement(44268..45014) Paracoccus denitrificans PD1222 4581407 YP_916660.1 CDS Pden_2880 NC_008687.1 45017 45358 R KEGG: sit:TM1040_2595 ATP synthase F0, subunit I; hypothetical protein complement(45017..45358) Paracoccus denitrificans PD1222 4581408 YP_916661.1 CDS Pden_2881 NC_008687.1 45545 45901 D PFAM: regulatory protein, ArsR; KEGG: sil:SPO3238 transcriptional regulator, ArsR family; regulatory protein ArsR 45545..45901 Paracoccus denitrificans PD1222 4581409 YP_916662.1 CDS Pden_2882 NC_008687.1 45967 47568 R PFAM: metallophosphoesterase; 5'-Nucleotidase domain protein; KEGG: sit:TM1040_1548 5'-nucleotidase-like; 5'-nucleotidase domain-containing protein complement(45967..47568) Paracoccus denitrificans PD1222 4581410 YP_916663.1 CDS Pden_2883 NC_008687.1 47660 48034 D PFAM: protein of unknown function DUF952; KEGG: rsp:RSP_0956 hypothetical protein; hypothetical protein 47660..48034 Paracoccus denitrificans PD1222 4581411 YP_916664.1 CDS Pden_2884 NC_008687.1 48031 49089 D 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 48031..49089 Paracoccus denitrificans PD1222 4581412 YP_916665.1 CDS Pden_2885 NC_008687.1 49086 49925 R KEGG: rsp:RSP_2481 serine acetyltransferase; TIGRFAM: serine O-acetyltransferase; PFAM: transferase hexapeptide repeat containing protein; serine acetyltransferase domain protein; serine O-acetyltransferase complement(49086..49925) Paracoccus denitrificans PD1222 4581413 YP_916666.1 CDS Pden_2886 NC_008687.1 49990 50712 R KEGG: jan:Jann_1647 hypothetical protein; hypothetical protein complement(49990..50712) Paracoccus denitrificans PD1222 4581414 YP_916667.1 CDS Pden_2887 NC_008687.1 50705 54595 R KEGG: rsp:RSP_2479 phage host specificity protein; phage host specificity protein complement(50705..54595) Paracoccus denitrificans PD1222 4581415 YP_916668.1 CDS Pden_2888 NC_008687.1 54614 55039 R 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 complement(54614..55039) Paracoccus denitrificans PD1222 4581416 YP_916669.1 CDS Pden_2889 NC_008687.1 55036 55854 R KEGG: sit:TM1040_1070 phage conserved hypothetical protein BR0599; phage protein complement(55036..55854) Paracoccus denitrificans PD1222 4581417 YP_916670.1 CDS Pden_2890 NC_008687.1 55851 56492 R KEGG: sit:TM1040_1069 conserved hypothetical protein; hypothetical protein complement(55851..56492) Paracoccus denitrificans PD1222 4581418 YP_916671.1 CDS Pden_2891 NC_008687.1 56485 57156 R KEGG: jan:Jann_1642 phage-related minor tail protein-like; phage-related minor tail protein-like complement(56485..57156) Paracoccus denitrificans PD1222 4581419 YP_916672.1 CDS Pden_2892 NC_008687.1 57181 57393 R KEGG: sit:TM1040_1067 conserved hypothetical protein; hypothetical protein complement(57181..57393) Paracoccus denitrificans PD1222 4581420 YP_916673.1 CDS Pden_2893 NC_008687.1 57390 57707 R KEGG: sil:SPO2256 hypothetical protein; hypothetical protein complement(57390..57707) Paracoccus denitrificans PD1222 4581421 YP_916674.1 CDS Pden_2894 NC_008687.1 57709 58122 R 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 complement(57709..58122) Paracoccus denitrificans PD1222 4581422 YP_916675.1 CDS Pden_2895 NC_008687.1 58135 58554 R KEGG: jan:Jann_1638 hypothetical protein; hypothetical protein complement(58135..58554) Paracoccus denitrificans PD1222 4581423 YP_916676.1 CDS Pden_2896 NC_008687.1 58551 58901 R KEGG: sil:SPO2259 head-tail adaptor; head-tail adaptor complement(58551..58901) Paracoccus denitrificans PD1222 4581424 YP_916677.1 CDS Pden_2897 NC_008687.1 58898 59515 R KEGG: rsp:RSP_2472 hypothetical protein; hypothetical protein complement(58898..59515) Paracoccus denitrificans PD1222 4581464 YP_916678.1 CDS Pden_2898 NC_008687.1 59644 60810 R 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 complement(59644..60810) Paracoccus denitrificans PD1222 4581465 YP_916679.1 CDS Pden_2899 NC_008687.1 60834 61391 R TIGRFAM: phage prohead protease, HK97 family; PFAM: peptidase U35, phage prohead HK97; KEGG: rsp:RSP_2470 prohead protease; HK97 family phage prohead protease complement(60834..61391) Paracoccus denitrificans PD1222 4581466 YP_916680.1 CDS Pden_2900 NC_008687.1 61372 61605 R KEGG: rde:RD1_3031 hypothetical protein; hypothetical protein complement(61372..61605) Paracoccus denitrificans PD1222 4581467 YP_916681.1 CDS Pden_2901 NC_008687.1 61607 62809 R TIGRFAM: phage portal protein, HK97 family; PFAM: phage portal protein; KEGG: rde:RD1_3033 phage portal protein; HK97 family phage portal protein complement(61607..62809) Paracoccus denitrificans PD1222 4581468 YP_916682.1 CDS Pden_2902 NC_008687.1 62958 64349 R PFAM: protein of unknown function DUF264; KEGG: rde:RD1_3034 hypothetical protein; hypothetical protein complement(62958..64349) Paracoccus denitrificans PD1222 4581469 YP_916683.1 CDS Pden_2903 NC_008687.1 64871 66049 R PFAM: aminodeoxychorismate lyase; KEGG: rsp:RSP_2465 hypothetical protein; aminodeoxychorismate lyase complement(64871..66049) Paracoccus denitrificans PD1222 4581470 YP_916684.1 CDS Pden_2904 NC_008687.1 66046 67308 R 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 complement(66046..67308) Paracoccus denitrificans PD1222 4581471 YP_916685.1 CDS Pden_2905 NC_008687.1 67429 68199 R PFAM: Enoyl-CoA hydratase/isomerase; KEGG: mmc:Mmcs_4156 enoyl-CoA hydratase/isomerase; enoyl-CoA hydratase/isomerase complement(67429..68199) Paracoccus denitrificans PD1222 4581472 YP_916686.1 CDS Pden_2906 NC_008687.1 68209 69336 R PFAM: acyl-CoA dehydrogenase domain protein; Acyl-CoA dehydrogenase, type 2, C-terminal domain; KEGG: bms:BRA0447 acyl-CoA dehydrogenase; acyl-CoA dehydrogenase complement(68209..69336) Paracoccus denitrificans PD1222 4581473 YP_916687.1 CDS Pden_2907 NC_008687.1 69333 70514 R KEGG: bms:BRA0448 acetyl-CoA acetyltransferase; TIGRFAM: acetyl-CoA acetyltransferases; PFAM: Thiolase; acetyl-CoA acetyltransferase complement(69333..70514) Paracoccus denitrificans PD1222 4581474 YP_916688.1 CDS Pden_2908 NC_008687.1 70527 71294 R PFAM: short-chain dehydrogenase/reductase SDR; KR; KEGG: bms:BRA0449 3-hydroxyacyl-CoA dehydrogenase; short-chain dehydrogenase/reductase SDR complement(70527..71294) Paracoccus denitrificans PD1222 4581475 YP_916689.1 CDS Pden_2909 NC_008687.1 71302 72993 R PFAM: AMP-dependent synthetase and ligase; KEGG: bms:BRA0450 acetyl-CoA synthetase; AMP-dependent synthetase/ligase complement(71302..72993) Paracoccus denitrificans PD1222 4581476 YP_916690.1 CDS Pden_2910 NC_008687.1 73096 74118 D PFAM: helix-turn-helix- domain containing protein, AraC type; KEGG: bms:BRA0451 transcriptional regulator, AraC family; helix-turn-helix domain-containing protein 73096..74118 Paracoccus denitrificans PD1222 4581477 YP_916691.1 CDS Pden_2911 NC_008687.1 74075 75058 R KEGG: rsp:RSP_1308 hypothetical protein; hypothetical protein complement(74075..75058) Paracoccus denitrificans PD1222 4581478 YP_916692.1 CDS Pden_2912 NC_008687.1 75215 76324 R KEGG: sil:SPOA0303 replication protein; replication protein complement(75215..76324) Paracoccus denitrificans PD1222 4581479 YP_916693.1 CDS Pden_2913 NC_008687.1 76321 77625 R PFAM: Cobyrinic acid a,c-diamide synthase; KEGG: sil:SPOA0304 replication protein; cobyrinic acid a,c-diamide synthase complement(76321..77625) Paracoccus denitrificans PD1222 4581480 YP_916694.1 CDS Pden_2914 NC_008687.1 78109 78783 D KEGG: sil:SPOA0305 hypothetical protein; hypothetical protein 78109..78783 Paracoccus denitrificans PD1222 4581481 YP_916695.1 CDS Pden_2915 NC_008687.1 78876 79133 D KEGG: rsp:RSP_7166 hypothetical protein; hypothetical protein 78876..79133 Paracoccus denitrificans PD1222 4581482 YP_916696.1 CDS Pden_2916 NC_008687.1 79269 80231 D 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 79269..80231 Paracoccus denitrificans PD1222 4581483 YP_916697.1 CDS Pden_2917 NC_008687.1 80228 81343 D catalyzes the formation of 8-amino-7-oxononanoate from 6-carboxyhexanoyl-CoA and L-alanine; 8-amino-7-oxononanoate synthase 80228..81343 Paracoccus denitrificans PD1222 4581484 YP_916698.1 CDS bioD NC_008687.1 81340 81948 D DTB synthetase; dethiobiotin synthase; involved in production of dethiobiotin from ATP and 7,8-diaminononanoate and carbon dioxide; contains magnesium; dithiobiotin synthetase 81340..81948 Paracoccus denitrificans PD1222 4581485 YP_916699.1 CDS Pden_2919 NC_008687.1 81948 83231 D 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 81948..83231 Paracoccus denitrificans PD1222 4581486 YP_916700.1 CDS Pden_2920 NC_008687.1 83228 83836 D PFAM: protein of unknown function DUF452; KEGG: nme:NMB0473 hypothetical protein; hypothetical protein 83228..83836 Paracoccus denitrificans PD1222 4581487 YP_916701.1 CDS Pden_2921 NC_008687.1 83833 84576 D PFAM: Methyltransferase type 11; Methyltransferase type 12; KEGG: cte:CT0049 biotin synthesis protein; methyltransferase type 11 83833..84576 Paracoccus denitrificans PD1222 4581488 YP_916702.1 CDS Pden_2922 NC_008687.1 84573 85238 R PFAM: regulatory protein GntR, HTH; GntR domain protein; KEGG: mlo:mlr7428 transcription regulator; GntR family transcriptional regulator complement(84573..85238) Paracoccus denitrificans PD1222 4581489 YP_916703.1 CDS Pden_2923 NC_008687.1 85282 85866 R PFAM: 2',5' RNA ligase; KEGG: bxe:Bxe_A1918 ligase; 2'-5' RNA ligase complement(85282..85866) Paracoccus denitrificans PD1222 4581490 YP_916704.1 CDS Pden_2924 NC_008687.1 85916 86572 R PFAM: protein of unknown function DUF162; KEGG: rde:RD1_0071 hypothetical protein; hypothetical protein complement(85916..86572) Paracoccus denitrificans PD1222 4581491 YP_916705.1 CDS Pden_2925 NC_008687.1 86569 87984 R 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 complement(86569..87984) Paracoccus denitrificans PD1222 4581492 YP_916706.1 CDS Pden_2926 NC_008687.1 87981 88751 R PFAM: protein of unknown function DUF224, cysteine-rich region domain protein; KEGG: rde:RD1_0073 hypothetical protein; hypothetical protein complement(87981..88751) Paracoccus denitrificans PD1222 4581493 YP_916707.1 CDS Pden_2927 NC_008687.1 88761 90527 R TIGRFAM: L-lactate transport; PFAM: L-lactate permease; KEGG: par:Psyc_1653 glycolate/L-lactate:H+ symporter; L-lactate transport complement(88761..90527) Paracoccus denitrificans PD1222 4581494 YP_916708.1 CDS Pden_2928 NC_008687.1 90605 92314 R component of the membrane-bound D-lactate oxidase, FAD-binding, NADH independent; D-lactate dehydrogenase complement(90605..92314) Paracoccus denitrificans PD1222 4581495 YP_916709.1 CDS Pden_2929 NC_008687.1 92529 93302 D PFAM: regulatory protein GntR, HTH; GntR domain protein; Helix-turn-helix, type 11 domain protein; KEGG: mag:amb0238 transcriptional regulator; GntR family transcriptional regulator 92529..93302 Paracoccus denitrificans PD1222 4581496 YP_916710.1 CDS Pden_2930 NC_008687.1 93367 93633 D KEGG: rsp:RSP_2678 hypothetical protein; hypothetical protein 93367..93633 Paracoccus denitrificans PD1222 4581497 YP_916711.1 CDS Pden_2931 NC_008687.1 93763 95139 D TIGRFAM: gluconate transporter; PFAM: Gluconate transporter; Citrate transporter; KEGG: eca:ECA4158 gluconate permease; gluconate transporter 93763..95139 Paracoccus denitrificans PD1222 4581498 YP_916712.1 CDS Pden_2932 NC_008687.1 95148 95651 D KEGG: tfu:Tfu_2114 carbohydrate kinase, thermoresistant glucokinase; TIGRFAM: carbohydrate kinase, thermoresistant glucokinase family; PFAM: shikimate kinase; carbohydrate kinase 95148..95651 Paracoccus denitrificans PD1222 4581499 YP_916713.1 CDS Pden_2933 NC_008687.1 95810 97648 R catalyzes the dehydration of 2,3-dihydroxy-3-methylbutanoate to 3-methyl-2-oxobutanoate in valine and isoleucine biosynthesis; dihydroxy-acid dehydratase complement(95810..97648) Paracoccus denitrificans PD1222 4581500 YP_916714.1 CDS Pden_2934 NC_008687.1 97755 98402 R PFAM: CDP-alcohol phosphatidyltransferase; KEGG: sme:SMc02159 hypothetical protein; CDP-alcohol phosphatidyltransferase complement(97755..98402) Paracoccus denitrificans PD1222 4581501 YP_916715.1 CDS Pden_2935 NC_008687.1 98399 99337 R PFAM: phosphatidate cytidylyltransferase; KEGG: xcv:XCV0555 phosphatidate cytidiltransferase; phosphatidate cytidylyltransferase complement(98399..99337) Paracoccus denitrificans PD1222 4581502 YP_916716.1 CDS Pden_2936 NC_008687.1 99341 99973 R PFAM: phospholipid/glycerol acyltransferase; KEGG: reu:Reut_B4015 phospholipid/glycerol acyltransferase; phospholipid/glycerol acyltransferase complement(99341..99973) Paracoccus denitrificans PD1222 4581503 YP_916717.1 CDS Pden_2937 NC_008687.1 100393 102399 R PFAM: ABC transporter related; protein of unknown function DUF214; SMART: AAA ATPase; KEGG: rpb:RPB_2235 hypothetical protein; ABC transporter complement(100393..102399) Paracoccus denitrificans PD1222 4581504 YP_916718.1 CDS Pden_2938 NC_008687.1 102392 103726 R 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 complement(102392..103726) Paracoccus denitrificans PD1222 4581505 YP_916719.1 CDS Pden_2939 NC_008687.1 104045 104569 D hypothetical protein 104045..104569 Paracoccus denitrificans PD1222 4581506 YP_916720.1 CDS Pden_2940 NC_008687.1 104685 105251 D PFAM: regulatory protein, TetR; KEGG: rru:Rru_A1116 transcriptional regulator, TetR family; TetR family transcriptional regulator 104685..105251 Paracoccus denitrificans PD1222 4581507 YP_916721.1 CDS Pden_2941 NC_008687.1 105290 106483 D 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 105290..106483 Paracoccus denitrificans PD1222 4581508 YP_916722.1 CDS Pden_2942 NC_008687.1 106488 109613 D 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 106488..109613 Paracoccus denitrificans PD1222 4581509 YP_916723.1 CDS Pden_2943 NC_008687.1 109715 111163 D 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 109715..111163 Paracoccus denitrificans PD1222 4581510 YP_916724.1 CDS Pden_2944 NC_008687.1 111383 113182 D required for the synthesis of the hydromethylpyrimidine moiety of thiamine; thiamine biosynthesis protein ThiC 111383..113182 Paracoccus denitrificans PD1222 4581511 YP_916725.1 CDS Pden_2945 NC_008687.1 113238 113993 R PFAM: Exopolysaccharide synthesis, ExoD; KEGG: mes:Meso_1827 exopolysaccharide synthesis, ExoD; exopolysaccharide synthesis, ExoD complement(113238..113993) Paracoccus denitrificans PD1222 4581512 YP_916726.1 CDS Pden_2946 NC_008687.1 114101 115021 R PFAM: PfkB domain protein; KEGG: rsp:RSP_2257 fructokinase; ribokinase-like domain-containing protein complement(114101..115021) Paracoccus denitrificans PD1222 4581513 YP_916727.1 CDS Pden_2947 NC_008687.1 115042 116349 R KEGG: rsp:RSP_2260 hypothetical protein; hypothetical protein complement(115042..116349) Paracoccus denitrificans PD1222 4581514 YP_916728.1 CDS Pden_2948 NC_008687.1 116359 117489 R KEGG: rsp:RSP_2261 antifreeze protein, type I; antifreeze protein, type I complement(116359..117489) Paracoccus denitrificans PD1222 4581515 YP_916729.1 CDS Pden_2949 NC_008687.1 117505 118170 R hypothetical protein complement(117505..118170) Paracoccus denitrificans PD1222 4581516 YP_916730.1 CDS Pden_2950 NC_008687.1 118177 119208 R KEGG: rsp:RSP_2263 hypothetical protein; hypothetical protein complement(118177..119208) Paracoccus denitrificans PD1222 4581517 YP_916731.1 CDS Pden_2951 NC_008687.1 119205 120398 R PFAM: toxic anion resistance family protein; KEGG: sil:SPO2986 tellurite resistance protein; toxic anion resistance family protein complement(119205..120398) Paracoccus denitrificans PD1222 4581518 YP_916732.1 CDS Pden_2952 NC_008687.1 120579 121031 R hypothetical protein complement(120579..121031) Paracoccus denitrificans PD1222 4581519 YP_916733.1 CDS Pden_2953 NC_008687.1 121116 122165 R PFAM: helix-turn-helix- domain containing protein, AraC type; KEGG: mes:Meso_0590 transcriptional regulator, AraC family; helix-turn-helix domain-containing protein complement(121116..122165) Paracoccus denitrificans PD1222 4581520 YP_916734.1 CDS Pden_2954 NC_008687.1 122201 123535 R PFAM: protein of unknown function UPF0118; KEGG: jan:Jann_2214 protein of unknown function UPF0118; hypothetical protein complement(122201..123535) Paracoccus denitrificans PD1222 4581521 YP_916735.1 CDS Pden_2955 NC_008687.1 123627 124850 R PFAM: Saccharopine dehydrogenase; KEGG: rsp:RSP_1475 saccharopine dehydrogenase family; saccharopine dehydrogenase complement(123627..124850) Paracoccus denitrificans PD1222 4581522 YP_916736.1 CDS Pden_2956 NC_008687.1 124897 126003 R TIGRFAM: carboxynorspermidine decarboxylase; PFAM: Orn/DAP/Arg decarboxylase 2; KEGG: sme:SMb21631 carboxynorspermidine decarboxylase; carboxynorspermidine decarboxylase complement(124897..126003) Paracoccus denitrificans PD1222 4581523 YP_916737.1 CDS Pden_2957 NC_008687.1 126127 127152 R PFAM: oxidoreductase domain protein; homoserine dehydrogenase, NAD-binding; KEGG: mes:Meso_2709 oxidoreductase-like; oxidoreductase domain-containing protein complement(126127..127152) Paracoccus denitrificans PD1222 4581524 YP_916738.1 CDS Pden_2958 NC_008687.1 127156 127614 R TIGRFAM: transcriptional regulator, Rrf2 family; PFAM: protein of unknown function UPF0074; KEGG: rsp:RSP_0443 Rrf2 family transcriptional regulator; BadM/Rrf2 family transcriptional regulator complement(127156..127614) Paracoccus denitrificans PD1222 4581525 YP_916739.1 CDS Pden_2959 NC_008687.1 127780 128439 D KEGG: jan:Jann_2367 hypothetical protein; hypothetical protein 127780..128439 Paracoccus denitrificans PD1222 4581526 YP_916740.1 CDS Pden_2960 NC_008687.1 128477 129601 D PFAM: metal-dependent phosphohydrolase, HD sub domain; SMART: metal-dependent phosphohydrolase, HD region; KEGG: sil:SPO2028 HD domain protein; metal dependent phosphohydrolase 128477..129601 Paracoccus denitrificans PD1222 4581527 YP_916741.1 CDS Pden_2961 NC_008687.1 129721 130935 D Converts isocitrate to alpha ketoglutarate; isocitrate dehydrogenase 129721..130935 Paracoccus denitrificans PD1222 4581528 YP_916742.1 CDS Pden_2962 NC_008687.1 131180 131848 D TIGRFAM: phosphoribosylformylglycinamidine synthase I; PFAM: CobB/CobQ domain protein glutamine amidotransferase; KEGG: rsp:RSP_2128 phosphoribosylformylglycinamidine synthase I (FGAM) synthase; phosphoribosylformylglycinamidine synthase I 131180..131848 Paracoccus denitrificans PD1222 4581529 YP_916743.1 CDS Pden_2963 NC_008687.1 131915 133708 D 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 131915..133708 Paracoccus denitrificans PD1222 4581530 YP_916744.1 CDS Pden_2964 NC_008687.1 133728 135053 D 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 133728..135053 Paracoccus denitrificans PD1222 4581531 YP_916745.1 CDS Pden_2965 NC_008687.1 135504 138113 D TIGRFAM: ribonuclease, Rne/Rng family; PFAM: RNA binding S1 domain protein; KEGG: sil:SPO1893 ribonuclease, Rne/Rng family; ribonuclease 135504..138113 Paracoccus denitrificans PD1222 4581532 YP_916746.1 CDS Pden_2966 NC_008687.1 138190 138933 D PFAM: cytochrome c biogenesis protein, transmembrane region; KEGG: rde:RD1_2269 cytochrome c-type biogenesis protein CcdA; cytochrome c biogenesis protein, transmembrane region 138190..138933 Paracoccus denitrificans PD1222 4581533 YP_916747.1 CDS Pden_2967 NC_008687.1 138930 139730 R PFAM: Enoyl-CoA hydratase/isomerase; KEGG: rsp:RSP_3833 enoyl-CoA hydratase; enoyl-CoA hydratase/isomerase complement(138930..139730) Paracoccus denitrificans PD1222 4581534 YP_916748.1 CDS Pden_2968 NC_008687.1 139815 140237 D TIGRFAM: uncharacterized domain 1; PFAM: thioesterase superfamily protein; KEGG: sit:TM1040_1390 phenylacetic acid degradation-related protein; hypothetical protein 139815..140237 Paracoccus denitrificans PD1222 4581535 YP_916749.1 CDS rplM NC_008687.1 140388 140852 D in Escherichia coli this protein is one of the earliest assembly proteins in the large subunit; 50S ribosomal protein L13 140388..140852 Paracoccus denitrificans PD1222 4581536 YP_916750.1 CDS rpsI NC_008687.1 140856 141335 D forms a direct contact with the tRNA during translation; 30S ribosomal protein S9 140856..141335 Paracoccus denitrificans PD1222 4581537 YP_916751.1 CDS Pden_2971 NC_008687.1 141439 141723 D hypothetical protein 141439..141723 Paracoccus denitrificans PD1222 4581538 YP_916752.1 CDS Pden_2972 NC_008687.1 147370 148221 R KEGG: lbl:LBL_1989 transposase, ISLbp9; hypothetical protein complement(147370..148221) Paracoccus denitrificans PD1222 4581539 YP_916753.1 CDS Pden_2974 NC_008687.1 148499 150403 R PFAM: helicase domain protein; KEGG: rpe:RPE_2164 helicase domain protein; helicase complement(148499..150403) Paracoccus denitrificans PD1222 4581540 YP_916754.1 CDS Pden_2975 NC_008687.1 150397 150711 R KEGG: pat:Patl_4096 DNA-cytosine methyltransferase; hypothetical protein complement(150397..150711) Paracoccus denitrificans PD1222 4581541 YP_916755.1 CDS Pden_2976 NC_008687.1 150708 151268 R PFAM: transposase, IS4 family protein; KEGG: sil:SPOA0134 ISSpo7, transposase; transposase, IS4 family protein complement(150708..151268) Paracoccus denitrificans PD1222 4581542 YP_916756.1 CDS Pden_2977 NC_008687.1 151529 153085 R 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 complement(151529..153085) Paracoccus denitrificans PD1222 4581543 YP_916757.1 CDS Pden_2978 NC_008687.1 153212 154198 R PFAM: FecR protein; KEGG: nwi:Nwi_2050 probable FecR, iron siderophore sensor protein; FecR protein complement(153212..154198) Paracoccus denitrificans PD1222 4581544 YP_916758.1 CDS Pden_2979 NC_008687.1 154267 154779 R 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 complement(154267..154779) Paracoccus denitrificans PD1222 4581545 YP_916759.1 CDS Pden_2980 NC_008687.1 155557 156567 D PFAM: periplasmic binding protein; KEGG: ppu:PP_2418 iron ABC transporter, periplasmic iron-binding protein; periplasmic binding protein 155557..156567 Paracoccus denitrificans PD1222 4581546 YP_916760.1 CDS Pden_2981 NC_008687.1 156564 157625 D PFAM: transport system permease; KEGG: bmb:BruAb2_0477 iron compound ABC transporter, permease; transport system permease 156564..157625 Paracoccus denitrificans PD1222 4581547 YP_916761.1 CDS Pden_2982 NC_008687.1 157622 158386 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rsp:RSP_3390 ABC Fe3+-siderophores transporter, ATPase subunit; ABC transporter 157622..158386 Paracoccus denitrificans PD1222 4581548 YP_916762.1 CDS Pden_2983 NC_008687.1 158387 158818 D TIGRFAM: pseudoazurin; PFAM: blue (type 1) copper domain protein; KEGG: rru:Rru_A1139 blue (type 1) copper subtype; pseudoazurin 158387..158818 Paracoccus denitrificans PD1222 4581549 YP_916763.1 CDS Pden_2984 NC_008687.1 158815 159498 D PFAM: UbiE/COQ5 methyltransferase; Methyltransferase type 11; Methyltransferase type 12; KEGG: mba:Mbar_A0646 UbiE/COQ5 methyltransferase; methyltransferase type 11 158815..159498 Paracoccus denitrificans PD1222 4581550 YP_916764.1 CDS Pden_2985 NC_008687.1 159505 159954 R KEGG: hne:HNE_1237 DNA-binding protein; DNA-binding protein complement(159505..159954) Paracoccus denitrificans PD1222 4581551 YP_916765.1 CDS Pden_2986 NC_008687.1 159971 160462 D KEGG: rpa:RPA2395 carboxyphosphonoenolpyruvate phosphonomutase; PEP phosphonomutase 159971..160462 Paracoccus denitrificans PD1222 4581552 YP_916766.1 CDS Pden_2987 NC_008687.1 160576 161202 R 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 complement(160576..161202) Paracoccus denitrificans PD1222 4581553 YP_916767.1 CDS Pden_2988 NC_008687.1 161195 161377 R KEGG: rpc:RPC_3516 hypothetical protein; hypothetical protein complement(161195..161377) Paracoccus denitrificans PD1222 4581554 YP_916768.1 CDS Pden_2989 NC_008687.1 161392 163137 R Catalyzes the reduction of nucleoside 5'-triphosphates to 2'-deoxynucleoside 5'-triphosphates; anaerobic ribonucleoside triphosphate reductase complement(161392..163137) Paracoccus denitrificans PD1222 4581555 YP_916769.1 CDS Pden_2990 NC_008687.1 163940 164611 R PFAM: regulatory protein, LuxR; response regulator receiver; KEGG: rpe:RPE_3142 two component transcriptional regulator, LuxR family; two component LuxR family transcriptional regulator complement(163940..164611) Paracoccus denitrificans PD1222 4581556 YP_916770.1 CDS Pden_2991 NC_008687.1 164596 166023 R 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 complement(164596..166023) Paracoccus denitrificans PD1222 4581557 YP_916771.1 CDS Pden_2992 NC_008687.1 166020 166484 R hypothetical protein complement(166020..166484) Paracoccus denitrificans PD1222 4581558 YP_916772.1 CDS Pden_2993 NC_008687.1 166833 168731 D PFAM: Pyrrolo-quinoline quinone; KEGG: rpe:RPE_3139 pyrrolo-quinoline quinone; Pyrrolo-quinoline quinone 166833..168731 Paracoccus denitrificans PD1222 4581559 YP_916773.1 CDS Pden_2994 NC_008687.1 168805 169635 D SMART: extracellular solute-binding protein, family 3; KEGG: rpc:RPC_1908 extracellular solute-binding protein, family 3; extracellular solute-binding protein 168805..169635 Paracoccus denitrificans PD1222 4581560 YP_916774.1 CDS Pden_2995 NC_008687.1 169646 170179 D PFAM: cytochrome c, class I; KEGG: rpc:RPC_1909 cytochrome c, class I; cytochrome c, class I 169646..170179 Paracoccus denitrificans PD1222 4581561 YP_916775.1 CDS Pden_2996 NC_008687.1 170234 170545 D PFAM: methanol dehydrogenase, beta subunit; KEGG: rpe:RPE_3136 methanol dehydrogenase, beta subunit; methanol dehydrogenase, beta subunit 170234..170545 Paracoccus denitrificans PD1222 4581562 YP_916776.1 CDS Pden_2997 NC_008687.1 170607 171626 D 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 170607..171626 Paracoccus denitrificans PD1222 4581563 YP_916777.1 CDS Pden_2998 NC_008687.1 171623 172477 D KEGG: rpc:RPC_1912 hypothetical protein; hypothetical protein 171623..172477 Paracoccus denitrificans PD1222 4581564 YP_916778.1 CDS Pden_2999 NC_008687.1 172474 173277 D KEGG: rpc:RPC_1913 MxaA protein; MxaA protein 172474..173277 Paracoccus denitrificans PD1222 4581565 YP_916779.1 CDS Pden_3000 NC_008687.1 173274 174281 D PFAM: von Willebrand factor, type A; KEGG: rpe:RPE_3132 von Willebrand factor, type A; von Willebrand factor A 173274..174281 Paracoccus denitrificans PD1222 4581566 YP_916780.1 CDS Pden_3001 NC_008687.1 174278 174829 D KEGG: rpe:RPE_3131 hypothetical protein; hypothetical protein 174278..174829 Paracoccus denitrificans PD1222 4581567 YP_916781.1 CDS Pden_3002 NC_008687.1 174955 175758 D KEGG: rpe:RPE_3130 von Willebrand factor, type A; von Willebrand factor A 174955..175758 Paracoccus denitrificans PD1222 4581568 YP_916782.1 CDS Pden_3003 NC_008687.1 175755 176288 D KEGG: rpe:RPE_3129 MxaD protein; MxaD protein 175755..176288 Paracoccus denitrificans PD1222 4581569 YP_916783.1 CDS Pden_3004 NC_008687.1 176306 177154 R PFAM: peptidase S15; dienelactone hydrolase; KEGG: tte:TTE1809 hydrolases of the alpha/beta superfamily; peptidase S15 complement(176306..177154) Paracoccus denitrificans PD1222 4581570 YP_916784.1 CDS Pden_3005 NC_008687.1 177218 177655 R hypothetical protein complement(177218..177655) Paracoccus denitrificans PD1222 4581571 YP_916785.1 CDS Pden_3006 NC_008687.1 177706 178218 R hypothetical protein complement(177706..178218) Paracoccus denitrificans PD1222 4581572 YP_916786.1 CDS Pden_3007 NC_008687.1 178458 180536 R TIGRFAM: TonB-dependent siderophore receptor; PFAM: TonB-dependent receptor; TonB-dependent receptor, plug; KEGG: rru:Rru_A2312 TonB-dependent receptor; TonB-dependent siderophore receptor complement(178458..180536) Paracoccus denitrificans PD1222 4581573 YP_916787.1 CDS Pden_3008 NC_008687.1 180896 182563 D PFAM: AMP-dependent synthetase and ligase; KEGG: bur:Bcep18194_B0670 AMP-dependent synthetase and ligase; AMP-dependent synthetase/ligase 180896..182563 Paracoccus denitrificans PD1222 4581574 YP_916788.1 CDS Pden_3009 NC_008687.1 182560 183015 D TIGRFAM: chorismate mutase related enzymes; PFAM: Chorismate mutase; KEGG: pfl:PFL_3489 isochorismate pyruvate-lyase; chorismate mutase related enzymes 182560..183015 Paracoccus denitrificans PD1222 4581575 YP_916789.1 CDS Pden_3010 NC_008687.1 182950 183927 R PFAM: periplasmic binding protein; KEGG: ecs:ECs3913 ferrichrome-binding protein; periplasmic binding protein complement(182950..183927) Paracoccus denitrificans PD1222 4581576 YP_916790.1 CDS Pden_3011 NC_008687.1 183941 184975 R PFAM: transport system permease; KEGG: hch:HCH_03457 ABC-type enterobactin transport system, permease component; transport system permease complement(183941..184975) Paracoccus denitrificans PD1222 4581577 YP_916791.1 CDS Pden_3012 NC_008687.1 184972 185970 R PFAM: transport system permease; KEGG: pfl:PFL_3624 ferric vibriobactin ABC transporter, permease VC0777; transport system permease complement(184972..185970) Paracoccus denitrificans PD1222 4581578 YP_916792.1 CDS Pden_3013 NC_008687.1 185967 186746 R PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: bur:Bcep18194_A4781 ABC cobalamin/Fe3+-siderophore transporter, ATPase subunit; ABC transporter complement(185967..186746) Paracoccus denitrificans PD1222 4581579 YP_916793.1 CDS Pden_3014 NC_008687.1 186830 188014 D KEGG: pfl:PFL_3619 monooxygenase, NtaA/SnaA/SoxA family; NtaA/SnaA/SoxA family monooxygenase 186830..188014 Paracoccus denitrificans PD1222 4581580 YP_916794.1 CDS Pden_3015 NC_008687.1 187954 193665 R 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 complement(187954..193665) Paracoccus denitrificans PD1222 4581581 YP_916795.1 CDS Pden_3016 NC_008687.1 193771 194019 D PFAM: phosphopantetheine-binding; KEGG: pen:PSEEN2505 2,3-dihydroxybenzoate-AMP ligase; phosphopantetheine-binding protein 193771..194019 Paracoccus denitrificans PD1222 4581582 YP_916796.1 CDS Pden_3017 NC_008687.1 194271 196073 D PFAM: ABC transporter, transmembrane region; ABC transporter related; SMART: AAA ATPase; KEGG: eci:UTI89_C2181 inner membrane ABC-transporter; ABC transporter 194271..196073 Paracoccus denitrificans PD1222 4581583 YP_916797.1 CDS Pden_3018 NC_008687.1 196070 197857 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: yps:YPTB1599 inner membrane ABC-transporter YbtQ; ABC transporter 196070..197857 Paracoccus denitrificans PD1222 4581584 YP_916798.1 CDS Pden_3019 NC_008687.1 198236 198676 R PFAM: CBS domain containing protein; KEGG: lpf:lpl2035 hypothetical protein; signal-transduction protein complement(198236..198676) Paracoccus denitrificans PD1222 4581585 YP_916799.1 CDS Pden_3020 NC_008687.1 198689 199072 R PFAM: succinate dehydrogenase, cytochrome b subunit; KEGG: mca:MCA1549 succinate dehydrogenase, hydrophobic membrane anchor protein; succinate dehydrogenase, cytochrome b subunit complement(198689..199072) Paracoccus denitrificans PD1222 4581586 YP_916800.1 CDS Pden_3021 NC_008687.1 199069 199446 R PFAM: succinate dehydrogenase, cytochrome b subunit; KEGG: aeh:Mlg_1332 succinate dehydrogenase, cytochrome b subunit; succinate dehydrogenase, cytochrome b subunit complement(199069..199446) Paracoccus denitrificans PD1222 4581587 YP_916801.1 CDS Pden_3022 NC_008687.1 199462 199830 R KEGG: rru:Rru_A1205 succinate dehydrogenase/fumarate reductase iron-sulfur protein; succinate dehydrogenase (ubiquinone) complement(199462..199830) Paracoccus denitrificans PD1222 4581588 YP_916802.1 CDS Pden_3023 NC_008687.1 199948 200400 R KEGG: rde:RD1_1693 hypothetical protein; hypothetical protein complement(199948..200400) Paracoccus denitrificans PD1222 4581589 YP_916803.1 CDS Pden_3024 NC_008687.1 200422 200859 R TIGRFAM: transcriptional regulator, Rrf2 family; PFAM: protein of unknown function UPF0074; KEGG: hne:HNE_1541 transcriptional regulator; BadM/Rrf2 family transcriptional regulator complement(200422..200859) Paracoccus denitrificans PD1222 4581590 YP_916804.1 CDS Pden_3025 NC_008687.1 201003 201674 D PFAM: protein of unknown function DUF542, ScdA domain protein; Hemerythrin HHE cation binding domain protein; KEGG: rso:RS02289 hypothetical protein; hypothetical protein 201003..201674 Paracoccus denitrificans PD1222 4581591 YP_916805.1 CDS Pden_3026 NC_008687.1 201788 202111 D KEGG: sil:SPOA0172 hypothetical protein; hypothetical protein 201788..202111 Paracoccus denitrificans PD1222 4581592 YP_916806.1 CDS Pden_3027 NC_008687.1 202131 202469 D TIGRFAM: alkylhydroperoxidase like protein, AhpD family; PFAM: Carboxymuconolactone decarboxylase; KEGG: nha:Nham_4301 alkylhydroperoxidase AhpD core; alkylhydroperoxidase 202131..202469 Paracoccus denitrificans PD1222 4581593 YP_916807.1 CDS Pden_3028 NC_008687.1 202683 204353 D PFAM: cytochrome c oxidase, subunit I; KEGG: rsp:RSP_1877 cytochrome c oxidase, aa3 type, subunit I; cytochrome-c oxidase 202683..204353 Paracoccus denitrificans PD1222 4581594 YP_916808.1 CDS Pden_3029 NC_008687.1 204776 206932 D 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 204776..206932 Paracoccus denitrificans PD1222 4581595 YP_916809.1 CDS Pden_3030 NC_008687.1 206944 207768 D PFAM: Methyltransferase type 12; KEGG: dps:DP0853 hypothetical protein; methyltransferase type 12 206944..207768 Paracoccus denitrificans PD1222 4581596 YP_916810.1 CDS Pden_3031 NC_008687.1 207773 208786 D PFAM: transport system permease; KEGG: nha:Nham_0954 transport system permease; transport system permease 207773..208786 Paracoccus denitrificans PD1222 4581597 YP_916811.1 CDS Pden_3032 NC_008687.1 208783 209553 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: nwi:Nwi_2074 ABC transporter, ATPase subunit; ABC transporter 208783..209553 Paracoccus denitrificans PD1222 4581598 YP_916812.1 CDS Pden_3033 NC_008687.1 209564 210601 D PFAM: periplasmic binding protein; KEGG: eca:ECA3564 iron-chelating periplasmic-binding protein; periplasmic binding protein 209564..210601 Paracoccus denitrificans PD1222 4581599 YP_916813.1 CDS Pden_3034 NC_008687.1 210616 210993 D hypothetical protein 210616..210993 Paracoccus denitrificans PD1222 4581600 YP_916814.1 CDS Pden_3035 NC_008687.1 211066 211221 R KEGG: rru:Rru_A1382 butyrate-acetoacetate CoA-transferase; butyrate-acetoacetate CoA-transferase complement(211066..211221) Paracoccus denitrificans PD1222 4581601 YP_916815.1 CDS Pden_3036 NC_008687.1 211416 212906 D PFAM: Sulfate transporter/antisigma-factor antagonist STAS; Xanthine/uracil/vitamin C permease; sulphate transporter; KEGG: rsp:RSP_4197 antisigma-factor antagonist, STAS; sulfate transporter 211416..212906 Paracoccus denitrificans PD1222 4581602 YP_916816.1 CDS Pden_3037 NC_008687.1 213391 214716 R PFAM: Cl- channel, voltage-gated family protein; KEGG: mes:Meso_1046 Cl-channel, voltage gated; Cl- channel, voltage-gated family protein complement(213391..214716) Paracoccus denitrificans PD1222 4581603 YP_916817.1 CDS Pden_3038 NC_008687.1 214845 216509 R TIGRFAM: choline/carnitine/betaine transporter; PFAM: BCCT transporter; KEGG: rsp:RSP_3080 choline/carnitine/betaine transporter, BCCT family; choline/carnitine/betaine transporter complement(214845..216509) Paracoccus denitrificans PD1222 4581604 YP_916818.1 CDS Pden_3039 NC_008687.1 216885 218168 D KEGG: pol:Bpro_5072 hypothetical protein; hypothetical protein 216885..218168 Paracoccus denitrificans PD1222 4581605 YP_916819.1 CDS Pden_3040 NC_008687.1 218003 218413 R KEGG: sil:SPOA0122 ISSpo9, transposase; ISSpo9, transposase complement(218003..218413) Paracoccus denitrificans PD1222 4581606 YP_916820.1 CDS Pden_3041 NC_008687.1 218479 218688 R KEGG: bja:blr1867 hypothetical protein; hypothetical protein complement(218479..218688) Paracoccus denitrificans PD1222 4581607 YP_916821.1 CDS Pden_3044 NC_008687.1 221466 222683 R PFAM: major facilitator superfamily MFS_1; KEGG: bja:bll3850 multidrug resistance protein; major facilitator transporter complement(221466..222683) Paracoccus denitrificans PD1222 4581608 YP_916822.1 CDS Pden_3045 NC_008687.1 222708 223940 R PFAM: major facilitator superfamily MFS_1; KEGG: stm:STM1545 multidrug efflux protein; major facilitator transporter complement(222708..223940) Paracoccus denitrificans PD1222 4581609 YP_916823.1 CDS Pden_3046 NC_008687.1 224252 225097 D PFAM: Alcohol dehydrogenase, zinc-binding domain protein; KEGG: rpc:RPC_4092 alcohol dehydrogenase, zinc-binding; alcohol dehydrogenase 224252..225097 Paracoccus denitrificans PD1222 4581610 YP_916824.1 CDS Pden_3047 NC_008687.1 225122 225607 R PFAM: regulatory protein, MarR; KEGG: ret:RHE_CH02035 probable transcriptional regulator protein, MarR family; MarR family transcriptional regulator complement(225122..225607) Paracoccus denitrificans PD1222 4581611 YP_916825.1 CDS Pden_3048 NC_008687.1 225654 227174 D PFAM: monooxygenase, FAD-binding; FAD dependent oxidoreductase; KEGG: ret:RHE_CH02034 probable monooxygenase; hypothetical protein 225654..227174 Paracoccus denitrificans PD1222 4581612 YP_916826.1 CDS Pden_3049 NC_008687.1 228088 229941 D PFAM: dehydrogenase, E1 component; Transketolase, central region; Transketolase domain protein; KEGG: aeh:Mlg_2596 dehydrogenase, E1 component; transketolase, central region 228088..229941 Paracoccus denitrificans PD1222 4581613 YP_916827.1 CDS Pden_3050 NC_008687.1 229941 230696 D PFAM: regulatory proteins, IclR; KEGG: rha:RHA1_ro08622 probable transcriptional regulator, IclR family; regulatory proteins, IclR 229941..230696 Paracoccus denitrificans PD1222 4581614 YP_916828.1 CDS Pden_3051 NC_008687.1 230709 231107 D PFAM: Endoribonuclease L-PSP; KEGG: mlo:mlr1297 hypothetical protein; endoribonuclease L-PSP 230709..231107 Paracoccus denitrificans PD1222 4581615 YP_916829.1 CDS Pden_3052 NC_008687.1 231104 232495 D PFAM: aminotransferase class-III; KEGG: pol:Bpro_0421 aminotransferase class-III; class III aminotransferase 231104..232495 Paracoccus denitrificans PD1222 4581616 YP_916830.1 CDS Pden_3053 NC_008687.1 232485 233912 D PFAM: Amidase; KEGG: mxa:MXAN_2852 amidase family protein; amidase 232485..233912 Paracoccus denitrificans PD1222 4581617 YP_916831.1 CDS Pden_3054 NC_008687.1 233971 235251 D KEGG: sil:SPO2534 branched-chain amino acid ABC transporter, periplasmic branched-chain amino acid-binding protein; branched-chain amino acid ABC transporter 233971..235251 Paracoccus denitrificans PD1222 4581618 YP_916832.1 CDS Pden_3055 NC_008687.1 235254 236066 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sil:SPO2533 branched-chain amino acid ABC transporter, ATP-binding protein; ABC transporter 235254..236066 Paracoccus denitrificans PD1222 4581619 YP_916833.1 CDS Pden_3056 NC_008687.1 236056 236769 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sil:SPO2532 branched-chain amino acid ABC transporter, ATP-binding protein; ABC transporter 236056..236769 Paracoccus denitrificans PD1222 4581620 YP_916834.1 CDS Pden_3057 NC_008687.1 236773 237651 D PFAM: inner-membrane translocator; KEGG: sil:SPO2531 branched-chain amino acid ABC transporter, permease; inner-membrane translocator 236773..237651 Paracoccus denitrificans PD1222 4581621 YP_916835.1 CDS Pden_3058 NC_008687.1 237648 238664 D PFAM: inner-membrane translocator; KEGG: sil:SPO2530 branched-chain amino acid ABC transporter, permease; inner-membrane translocator 237648..238664 Paracoccus denitrificans PD1222 4581622 YP_916836.1 CDS Pden_3059 NC_008687.1 238652 240073 D PFAM: Amidase; KEGG: bxe:Bxe_B1011 indole acetamide hydrolase; amidase 238652..240073 Paracoccus denitrificans PD1222 4581623 YP_916837.1 CDS Pden_3060 NC_008687.1 240368 240727 R KEGG: gox:GOX2722 truncated transposase; hypothetical protein complement(240368..240727) Paracoccus denitrificans PD1222 4581624 YP_916838.1 CDS Pden_3061 NC_008687.1 240832 242865 D TIGRFAM: outer membrane autotransporter barrel domain; PFAM: Autotransporter beta- domain protein; KEGG: bbr:BB0916 autotransporter; outer membrane autotransporter 240832..242865 Paracoccus denitrificans PD1222 4581625 YP_916839.1 CDS Pden_3062 NC_008687.1 242895 243410 D KEGG: mlo:mlr4672 hypothetical protein; hypothetical protein 242895..243410 Paracoccus denitrificans PD1222 4581626 YP_916840.1 CDS Pden_3063 NC_008687.1 243469 243720 R hypothetical protein complement(243469..243720) Paracoccus denitrificans PD1222 4581627 YP_916841.1 CDS Pden_3064 NC_008687.1 243789 245771 D KEGG: zmo:ZMO0213 autotransporter; hypothetical protein 243789..245771 Paracoccus denitrificans PD1222 4581628 YP_916842.1 CDS Pden_3065 NC_008687.1 246211 246522 R PFAM: plasmid stabilization system; KEGG: rsp:RSP_3809 hypothetical protein; plasmid stabilization system protein complement(246211..246522) Paracoccus denitrificans PD1222 4581629 YP_916843.1 CDS Pden_3066 NC_008687.1 246527 246793 R KEGG: rsp:RSP_3810 hypothetical protein; hypothetical protein complement(246527..246793) Paracoccus denitrificans PD1222 4581630 YP_916844.1 CDS Pden_3067 NC_008687.1 247092 247268 D KEGG: mes:Meso_0525 hypothetical protein; hypothetical protein 247092..247268 Paracoccus denitrificans PD1222 4581631 YP_916845.1 CDS Pden_3068 NC_008687.1 247372 248271 D PFAM: protein of unknown function DUF6, transmembrane; KEGG: sit:TM1040_2078 protein of unknown function DUF6, transmembrane; hypothetical protein 247372..248271 Paracoccus denitrificans PD1222 4581632 YP_916846.1 CDS Pden_3069 NC_008687.1 248442 248864 D KEGG: bmb:BruAb1_1812 transcriptional regulator, LysR family; LysR family transcriptional regulator 248442..248864 Paracoccus denitrificans PD1222 4581633 YP_916847.1 CDS Pden_3070 NC_008687.1 248809 249432 R hypothetical protein complement(248809..249432) Paracoccus denitrificans PD1222 4581634 YP_916848.1 CDS acnA NC_008687.1 249529 252093 R catalyzes the conversion of citrate to isocitrate; aconitate hydratase complement(249529..252093) Paracoccus denitrificans PD1222 4581635 YP_916849.1 CDS Pden_3072 NC_008687.1 252149 253021 R 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 complement(252149..253021) Paracoccus denitrificans PD1222 4581636 YP_916850.1 CDS Pden_3073 NC_008687.1 253108 254607 R PFAM: protein of unknown function DUF112, transmembrane; KEGG: bja:blr3163 hypothetical protein; hypothetical protein complement(253108..254607) Paracoccus denitrificans PD1222 4581637 YP_916851.1 CDS Pden_3074 NC_008687.1 254618 255088 R KEGG: bja:blr3162 tricarboxylic transport membrane protein; tricarboxylic transport membrane protein complement(254618..255088) Paracoccus denitrificans PD1222 4581638 YP_916852.1 CDS Pden_3075 NC_008687.1 255140 256111 R PFAM: Uncharacterized protein UPF0065; KEGG: bja:blr3161 tricarboxylic transport membrane protein; hypothetical protein complement(255140..256111) Paracoccus denitrificans PD1222 4581639 YP_916853.1 CDS Pden_3076 NC_008687.1 256282 256695 D KEGG: gme:Gmet_0306 CoA-binding protein; hypothetical protein 256282..256695 Paracoccus denitrificans PD1222 4581640 YP_916854.1 CDS Pden_3077 NC_008687.1 256692 259682 D KEGG: nwi:Nwi_0792 gene transfer agent (GTA) like protein; gene transfer agent (GTA) like protein 256692..259682 Paracoccus denitrificans PD1222 4581641 YP_916855.1 CDS Pden_3078 NC_008687.1 259693 260769 D KEGG: rde:RD1_0477 hypothetical protein; hypothetical protein 259693..260769 Paracoccus denitrificans PD1222 4581642 YP_916856.1 CDS Pden_3079 NC_008687.1 261211 261627 D PFAM: transposase IS200-family protein; KEGG: dra:DR1927 transposase; transposase IS200-family protein 261211..261627 Paracoccus denitrificans PD1222 4581643 YP_916857.1 CDS Pden_3080 NC_008687.1 261632 262105 R KEGG: sil:SPO2736 hypothetical protein; hypothetical protein complement(261632..262105) Paracoccus denitrificans PD1222 4581644 YP_916858.1 CDS Pden_3081 NC_008687.1 262396 263058 R hypothetical protein complement(262396..263058) Paracoccus denitrificans PD1222 4581645 YP_916859.1 CDS Pden_3082 NC_008687.1 263530 267024 R TIGRFAM: outer membrane autotransporter barrel domain; PFAM: Autotransporter beta- domain protein; KEGG: zmo:ZMO0213 autotransporter; outer membrane autotransporter complement(263530..267024) Paracoccus denitrificans PD1222 4581646 YP_916860.1 CDS Pden_3083 NC_008687.1 267354 267965 D KEGG: rsp:RSP_2718 possible outer membrane protein; outer membrane protein 267354..267965 Paracoccus denitrificans PD1222 4581647 YP_916861.1 CDS Pden_3084 NC_008687.1 268005 268373 D KEGG: nwi:Nwi_1490 lipoprotein; lipoprotein 268005..268373 Paracoccus denitrificans PD1222 4581648 YP_916862.1 CDS Pden_3085 NC_008687.1 268564 268971 D PFAM: protein of unknown function DUF1311; KEGG: pfo:Pfl_3894 protein of unknown function DUF1311; hypothetical protein 268564..268971 Paracoccus denitrificans PD1222 4581649 YP_916863.1 CDS Pden_3086 NC_008687.1 268991 269851 D KEGG: sme:SMb21025 hypothetical protein; hypothetical protein 268991..269851 Paracoccus denitrificans PD1222 4581650 YP_916864.1 CDS Pden_3087 NC_008687.1 270066 271148 D PFAM: extracellular solute-binding protein, family 3; SMART: ionotropic glutamate receptor; KEGG: gbe:GbCGDNIH1_1769 glutamate-gated potassium channel; extracellular solute-binding protein 270066..271148 Paracoccus denitrificans PD1222 4581651 YP_916865.1 CDS Pden_3088 NC_008687.1 271163 271765 R KEGG: mlo:mll4938 hypothetical protein; hypothetical protein complement(271163..271765) Paracoccus denitrificans PD1222 4581652 YP_916866.1 CDS Pden_3089 NC_008687.1 271811 272704 R PFAM: helix-turn-helix- domain containing protein, AraC type; KEGG: mes:Meso_3689 transcriptional regulator, AraC family; helix-turn-helix domain-containing protein complement(271811..272704) Paracoccus denitrificans PD1222 4581653 YP_916867.1 CDS Pden_3090 NC_008687.1 273007 273519 R hypothetical protein complement(273007..273519) Paracoccus denitrificans PD1222 4581654 YP_916868.1 CDS Pden_3091 NC_008687.1 273579 274733 R PFAM: phage integrase family protein; KEGG: sit:TM1040_3585 phage integrase; phage integrase family protein complement(273579..274733) Paracoccus denitrificans PD1222 4581655 YP_916869.1 CDS Pden_3092 NC_008687.1 274853 276391 D KEGG: rpe:RPE_2955 hypothetical protein; hypothetical protein 274853..276391 Paracoccus denitrificans PD1222 4581656 YP_916870.1 CDS Pden_3093 NC_008687.1 276953 278287 D 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 276953..278287 Paracoccus denitrificans PD1222 4581657 YP_916871.1 CDS Pden_3094 NC_008687.1 278284 279273 D PFAM: NADH ubiquinone oxidoreductase, 20 kDa subunit; KEGG: rsp:RSP_0492 hydrogenase small subunit; NADH ubiquinone oxidoreductase, 20 kDa subunit 278284..279273 Paracoccus denitrificans PD1222 4581658 YP_916872.1 CDS Pden_3095 NC_008687.1 279291 280724 D PFAM: nickel-dependent hydrogenase, large subunit; KEGG: rsp:RSP_0493 hydrogenase large subunit; nickel-dependent hydrogenase, large subunit 279291..280724 Paracoccus denitrificans PD1222 4581659 YP_916873.1 CDS Pden_3096 NC_008687.1 280745 282994 D 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 280745..282994 Paracoccus denitrificans PD1222 4581660 YP_916874.1 CDS Pden_3097 NC_008687.1 283197 284282 D 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 283197..284282 Paracoccus denitrificans PD1222 4581661 YP_916875.1 CDS Pden_3098 NC_008687.1 284286 286079 D PFAM: nickel-dependent hydrogenase, large subunit; KEGG: rsp:RSP_0496 hydrogenase large subunit; nickel-dependent hydrogenase, large subunit 284286..286079 Paracoccus denitrificans PD1222 4581662 YP_916876.1 CDS Pden_3099 NC_008687.1 286095 286679 D PFAM: HupE/UreJ protein; KEGG: rsp:RSP_0497 HupE/UreJ accessory protein; HupE/UreJ protein 286095..286679 Paracoccus denitrificans PD1222 4581663 YP_916877.1 CDS Pden_3100 NC_008687.1 286684 287430 D 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 286684..287430 Paracoccus denitrificans PD1222 4581664 YP_916878.1 CDS Pden_3101 NC_008687.1 287636 288304 D 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 287636..288304 Paracoccus denitrificans PD1222 4581665 YP_916879.1 CDS Pden_3102 NC_008687.1 288304 288615 D PFAM: hydrogenase expression/formation protein (HUPF/HYPC); KEGG: rsp:RSP_0500 HupF/HypC hydrogenase; hydrogenase expression/formation protein HupF/HypC 288304..288615 Paracoccus denitrificans PD1222 4581666 YP_916880.1 CDS Pden_3103 NC_008687.1 288619 289038 D PFAM: hydrogenase-1 expression HyaE; KEGG: rsp:RSP_0501 HupG hydrogenase expression/formation protein; hydrogenase-1 expression HyaE 288619..289038 Paracoccus denitrificans PD1222 4581667 YP_916881.1 CDS Pden_3104 NC_008687.1 289051 289884 D PFAM: HupH hydrogenase expression protein; KEGG: rsp:RSP_0502 HupH hydrogenase expression/formation protein; HupH hydrogenase expression protein 289051..289884 Paracoccus denitrificans PD1222 4581668 YP_916882.1 CDS Pden_3105 NC_008687.1 289881 290732 D PFAM: Rubredoxin-type Fe(Cys)4 protein; KEGG: rsp:RSP_0503 HupJ, contains rubredoxin domain; rubredoxin-type Fe(Cys)4 protein 289881..290732 Paracoccus denitrificans PD1222 4581669 YP_916883.1 CDS Pden_3106 NC_008687.1 290729 291631 D KEGG: rsp:RSP_0504 HupK; HupK protein 290729..291631 Paracoccus denitrificans PD1222 4581670 YP_916884.1 CDS Pden_3107 NC_008687.1 291624 291965 D 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 291624..291965 Paracoccus denitrificans PD1222 4581671 YP_916885.1 CDS Pden_3108 NC_008687.1 291965 292885 D TIGRFAM: hydrogenase accessory protein HypB; PFAM: cobalamin synthesis protein, P47K; KEGG: rsp:RSP_0506 NI2+-binding GTPase HypB; hydrogenase nickel incorporation protein HypB 291965..292885 Paracoccus denitrificans PD1222 4581672 YP_916886.1 CDS Pden_3109 NC_008687.1 292889 294370 D 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 292889..294370 Paracoccus denitrificans PD1222 4581673 YP_916887.1 CDS Pden_3110 NC_008687.1 294373 294657 D 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 294373..294657 Paracoccus denitrificans PD1222 4581674 YP_916888.1 CDS Pden_3111 NC_008687.1 294654 295790 D 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 294654..295790 Paracoccus denitrificans PD1222 4581675 YP_916889.1 CDS Pden_3112 NC_008687.1 295803 296858 D 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 295803..296858 Paracoccus denitrificans PD1222 4581676 YP_916890.1 CDS Pden_3113 NC_008687.1 297085 297600 D hypothetical protein 297085..297600 Paracoccus denitrificans PD1222 4581677 YP_916891.1 CDS Pden_3114 NC_008687.1 297507 298544 R PFAM: CBS domain containing protein; protein of unknown function DUF21; KEGG: rha:RHA1_ro03326 possible CBS domain-containing protein; hypothetical protein complement(297507..298544) Paracoccus denitrificans PD1222 4581678 YP_916892.1 CDS Pden_3115 NC_008687.1 298541 299911 R PFAM: CBS domain containing protein; protein of unknown function DUF21; transporter-associated region; KEGG: nfa:nfa28250 hypothetical protein; hypothetical protein complement(298541..299911) Paracoccus denitrificans PD1222 4581679 YP_916893.1 CDS Pden_3116 NC_008687.1 300689 301594 R PFAM: helix-turn-helix- domain containing protein, AraC type; KEGG: bxe:Bxe_C1385 transcriptional regulator, AraC family; helix-turn-helix domain-containing protein complement(300689..301594) Paracoccus denitrificans PD1222 4581680 YP_916894.1 CDS Pden_3117 NC_008687.1 301647 302417 D PFAM: short-chain dehydrogenase/reductase SDR; KEGG: mmc:Mmcs_1038 short-chain dehydrogenase/reductase SDR; short-chain dehydrogenase/reductase SDR 301647..302417 Paracoccus denitrificans PD1222 4581681 YP_916895.1 CDS Pden_3118 NC_008687.1 302450 303199 R 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 complement(302450..303199) Paracoccus denitrificans PD1222 4581682 YP_916896.1 CDS Pden_3119 NC_008687.1 303258 303755 D 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 303258..303755 Paracoccus denitrificans PD1222 4581683 YP_916897.1 CDS Pden_3120 NC_008687.1 303759 304643 D PFAM: FAD-dependent pyridine nucleotide-disulphide oxidoreductase; KEGG: rpb:RPB_3951 FAD-dependent pyridine nucleotide-disulphide oxidoreductase; FAD-dependent pyridine nucleotide-disulfide oxidoreductase 303759..304643 Paracoccus denitrificans PD1222 4581684 YP_916898.1 CDS Pden_3121 NC_008687.1 304640 305311 D PFAM: Methyltransferase type 11; Methyltransferase type 12; KEGG: rpb:RPB_3655 SAM binding protein; methyltransferase type 12 304640..305311 Paracoccus denitrificans PD1222 4581685 YP_916899.1 CDS Pden_3122 NC_008687.1 305322 306503 R PFAM: phage integrase family protein; KEGG: sit:TM1040_3585 phage integrase; phage integrase family protein complement(305322..306503) Paracoccus denitrificans PD1222 4581686 YP_916900.1 CDS Pden_3123 NC_008687.1 306693 308351 R PFAM: Resolvase, N-terminal domain; Recombinase; KEGG: nha:Nham_3864 recombinase; recombinase complement(306693..308351) Paracoccus denitrificans PD1222 4581687 YP_916901.1 CDS Pden_3124 NC_008687.1 308371 308598 R hypothetical protein complement(308371..308598) Paracoccus denitrificans PD1222 4581688 YP_916902.1 CDS Pden_3125 NC_008687.1 308737 309381 R KEGG: rde:RD1_1995 hypothetical protein; hypothetical protein complement(308737..309381) Paracoccus denitrificans PD1222 4581689 YP_916903.1 CDS Pden_3126 NC_008687.1 309663 310022 R hypothetical protein complement(309663..310022) Paracoccus denitrificans PD1222 4581690 YP_916904.1 CDS Pden_3127 NC_008687.1 310237 310989 R PFAM: Peptidase C24, Calicivirus polyprotein ORF 1; KEGG: rpd:RPD_2286 hypothetical protein; peptidase C24 complement(310237..310989) Paracoccus denitrificans PD1222 4581691 YP_916905.1 CDS Pden_3128 NC_008687.1 311064 312305 R KEGG: nar:Saro_2202 hypothetical protein; hypothetical protein complement(311064..312305) Paracoccus denitrificans PD1222 4581692 YP_916906.1 CDS Pden_3129 NC_008687.1 312313 313308 R PFAM: SMF family protein; KEGG: nar:Saro_2201 smf protein; SMF family protein complement(312313..313308) Paracoccus denitrificans PD1222 4581693 YP_916907.1 CDS Pden_3130 NC_008687.1 313398 313784 D KEGG: nwi:Nwi_0831 phage integrase; phage integrase 313398..313784 Paracoccus denitrificans PD1222 4581694 YP_916908.1 CDS Pden_3131 NC_008687.1 314148 315512 R TIGRFAM: chromate transporter, chromate ion transporter (CHR) family; PFAM: Chromate transporter; KEGG: sme:SMc00808 chromate transport protein; chromate transporter complement(314148..315512) Paracoccus denitrificans PD1222 4581695 YP_916909.1 CDS Pden_3132 NC_008687.1 315509 316354 R SMART: Rhodanese domain protein; KEGG: mlo:mlr5406 hypothetical protein; rhodanese domain-containing protein complement(315509..316354) Paracoccus denitrificans PD1222 4581696 YP_916910.1 CDS Pden_3133 NC_008687.1 316569 317276 R PFAM: NADPH-dependent FMN reductase; KEGG: rsp:RSP_2731 arsenical resistance protein, ArsH; NADPH-dependent FMN reductase complement(316569..317276) Paracoccus denitrificans PD1222 4581697 YP_916911.1 CDS Pden_3134 NC_008687.1 317273 318346 R TIGRFAM: arsenical-resistance protein; PFAM: Bile acid:sodium symporter; KEGG: sal:Sala_2405 arsenical-resistance protein; arsenical-resistance protein complement(317273..318346) Paracoccus denitrificans PD1222 4581698 YP_916912.1 CDS Pden_3135 NC_008687.1 318359 318784 R TIGRFAM: arsenate reductase; PFAM: arsenate reductase and related; KEGG: sal:Sala_2539 arsenate reductase; arsenate reductase complement(318359..318784) Paracoccus denitrificans PD1222 4581699 YP_916913.1 CDS Pden_3136 NC_008687.1 318787 319146 R PFAM: regulatory protein, ArsR; KEGG: nwi:Nwi_3123 transcriptional regulatory protein, ArsR family; regulatory protein ArsR complement(318787..319146) Paracoccus denitrificans PD1222 4581700 YP_916914.1 CDS Pden_3137 NC_008687.1 319199 319678 R hypothetical protein complement(319199..319678) Paracoccus denitrificans PD1222 4581701 YP_916915.1 CDS Pden_3138 NC_008687.1 320014 320844 R hypothetical protein complement(320014..320844) Paracoccus denitrificans PD1222 4581702 YP_916916.1 CDS Pden_3139 NC_008687.1 320864 321223 D hypothetical protein 320864..321223 Paracoccus denitrificans PD1222 4581703 YP_916917.1 CDS Pden_3140 NC_008687.1 321481 321687 D 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 321481..321687 Paracoccus denitrificans PD1222 4581704 YP_916918.1 CDS Pden_3141 NC_008687.1 321760 322095 D KEGG: rsp:RSP_3622 hypothetical protein; hypothetical protein 321760..322095 Paracoccus denitrificans PD1222 4581705 YP_916919.1 CDS Pden_3142 NC_008687.1 322388 322627 R hypothetical protein complement(322388..322627) Paracoccus denitrificans PD1222 4581706 YP_916920.1 CDS Pden_3143 NC_008687.1 322642 322848 D PFAM: Cold-shock protein, DNA-binding; SMART: Cold shock protein; KEGG: sil:SPO3625 cold shock protein CspA; cold-shock DNA-binding domain-containing protein 322642..322848 Paracoccus denitrificans PD1222 4581707 YP_916921.1 CDS Pden_3144 NC_008687.1 322903 323103 D hypothetical protein 322903..323103 Paracoccus denitrificans PD1222 4581708 YP_916922.1 CDS Pden_3145 NC_008687.1 323419 323967 D PFAM: heat shock protein Hsp20; KEGG: ret:RHE_CH01244 probable molecular chaperone small heat shock protein, HSP20 family; heat shock protein Hsp20 323419..323967 Paracoccus denitrificans PD1222 4581709 YP_916923.1 CDS Pden_3146 NC_008687.1 324049 324552 D PFAM: heat shock protein Hsp20; KEGG: ret:RHE_CH01245 probable molecular chaperone small heat shock protein, HSP20 family; heat shock protein Hsp20 324049..324552 Paracoccus denitrificans PD1222 4581710 YP_916924.1 CDS Pden_3147 NC_008687.1 324652 325017 D KEGG: ret:RHE_CH01246 hypothetical protein; hypothetical protein 324652..325017 Paracoccus denitrificans PD1222 4581711 YP_916925.1 CDS Pden_3148 NC_008687.1 325116 326492 D TIGRFAM: protease Do; PFAM: peptidase S1 and S6, chymotrypsin/Hap; PDZ/DHR/GLGF domain protein; KEGG: nmu:Nmul_A0510 peptidase S1C, Do; protease Do 325116..326492 Paracoccus denitrificans PD1222 4581712 YP_916926.1 CDS Pden_3149 NC_008687.1 326590 327381 R PFAM: Phytanoyl-CoA dioxygenase; KEGG: mxa:MXAN_4531 hypothetical protein; phytanoyl-CoA dioxygenase complement(326590..327381) Paracoccus denitrificans PD1222 4581713 YP_916927.1 CDS Pden_3150 NC_008687.1 327688 328374 R PFAM: protein of unknown function DUF899, thioredoxin family protein; KEGG: pfo:Pfl_1441 protein of unknown function DUF899, thioredoxin-like; hypothetical protein complement(327688..328374) Paracoccus denitrificans PD1222 4581714 YP_916928.1 CDS Pden_3151 NC_008687.1 328642 329901 D PFAM: Tetratricopeptide TPR_4; KEGG: mes:Meso_0992 tetratricopeptide TPR_4; hypothetical protein 328642..329901 Paracoccus denitrificans PD1222 4581715 YP_916929.1 CDS Pden_3152 NC_008687.1 329911 330552 D KEGG: mes:Meso_0991 hypothetical protein; hypothetical protein 329911..330552 Paracoccus denitrificans PD1222 4581716 YP_916930.1 CDS Pden_3153 NC_008687.1 330661 331068 D PFAM: Cupin 2, conserved barrel domain protein; KEGG: pol:Bpro_3707 cupin 2, conserved barrel; cupin 330661..331068 Paracoccus denitrificans PD1222 4581717 YP_916931.1 CDS Pden_3154 NC_008687.1 331073 331906 D PFAM: aminoglycoside 3-N-acetyltransferase; KEGG: gvi:gll0484 aminoglycoside N3'-acetyltransferase; aminoglycoside N(3')-acetyltransferase 331073..331906 Paracoccus denitrificans PD1222 4581718 YP_916932.1 CDS Pden_3155 NC_008687.1 331919 332353 D PFAM: Methyltransferase type 11; Methyltransferase type 12; KEGG: gvi:glr1626 hypothetical protein; methyltransferase type 12 331919..332353 Paracoccus denitrificans PD1222 4581719 YP_916933.1 CDS Pden_3156 NC_008687.1 332449 332766 D 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 332449..332766 Paracoccus denitrificans PD1222 4581720 YP_916934.1 CDS Pden_3157 NC_008687.1 332782 333399 D PFAM: plasmid pRiA4b ORF-3 family protein; KEGG: sme:SMa0896 hypothetical protein; plasmid pRiA4b ORF-3 family protein 332782..333399 Paracoccus denitrificans PD1222 4581721 YP_916935.1 CDS Pden_3158 NC_008687.1 333475 333834 D hypothetical protein 333475..333834 Paracoccus denitrificans PD1222 4581722 YP_916936.1 CDS Pden_3159 NC_008687.1 333864 334322 D PFAM: GCN5-related N-acetyltransferase; KEGG: sal:Sala_0626 gentamicin 3'-N-acetyltransferase; gentamicin 3'-N-acetyltransferase 333864..334322 Paracoccus denitrificans PD1222 4581723 YP_916937.1 CDS Pden_3160 NC_008687.1 334803 335831 R 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 complement(334803..335831) Paracoccus denitrificans PD1222 4581724 YP_916938.1 CDS Pden_3161 NC_008687.1 335940 336263 D PFAM: transposase IS3/IS911 family protein; KEGG: nwi:Nwi_2119 transposase IS3/IS911; transposase IS3/IS911 family protein 335940..336263 Paracoccus denitrificans PD1222 4581725 YP_916939.1 CDS Pden_3162 NC_008687.1 336263 337168 D PFAM: Integrase, catalytic region; KEGG: nwi:Nwi_2120 integrase, catalytic region; integrase catalytic subunit 336263..337168 Paracoccus denitrificans PD1222 4581726 YP_916940.1 CDS Pden_3163 NC_008687.1 337267 337683 D KEGG: mes:Meso_3831 hypothetical protein; hypothetical protein 337267..337683 Paracoccus denitrificans PD1222 4581727 YP_916941.1 CDS Pden_3164 NC_008687.1 338133 338810 D 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 338133..338810 Paracoccus denitrificans PD1222 4581728 YP_916942.1 CDS Pden_3165 NC_008687.1 338882 339184 D hypothetical protein 338882..339184 Paracoccus denitrificans PD1222 4581729 YP_916943.1 CDS Pden_3166 NC_008687.1 339330 340253 D PFAM: protein of unknown function DUF81; KEGG: rsp:RSP_1646 possible transmembrane protein; hypothetical protein 339330..340253 Paracoccus denitrificans PD1222 4581730 YP_916944.1 CDS Pden_3167 NC_008687.1 341031 341438 D 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 341031..341438 Paracoccus denitrificans PD1222 4581731 YP_916945.1 CDS Pden_3168 NC_008687.1 341929 342132 D hypothetical protein 341929..342132 Paracoccus denitrificans PD1222 4581732 YP_916946.1 CDS Pden_3169 NC_008687.1 342234 342449 D hypothetical protein 342234..342449 Paracoccus denitrificans PD1222 4581733 YP_916947.1 CDS Pden_3170 NC_008687.1 342529 342795 D hypothetical protein 342529..342795 Paracoccus denitrificans PD1222 4581734 YP_916948.1 CDS Pden_3171 NC_008687.1 342906 343163 R PFAM: helix-turn-helix domain protein; KEGG: ret:RHE_PA00165 transcriptional regulator protein; XRE family transcriptional regulator complement(342906..343163) Paracoccus denitrificans PD1222 4581735 YP_916949.1 CDS Pden_3172 NC_008687.1 343217 343663 D KEGG: mes:Meso_0527 hypothetical protein; hypothetical protein 343217..343663 Paracoccus denitrificans PD1222 4581736 YP_916950.1 CDS Pden_3173 NC_008687.1 343788 344096 D KEGG: mes:Meso_0526 hypothetical protein; hypothetical protein 343788..344096 Paracoccus denitrificans PD1222 4581737 YP_916951.1 CDS Pden_3174 NC_008687.1 344116 344568 D KEGG: mes:Meso_0525 hypothetical protein; hypothetical protein 344116..344568 Paracoccus denitrificans PD1222 4581738 YP_916952.1 CDS Pden_3175 NC_008687.1 344690 345589 D PFAM: protein of unknown function DUF6, transmembrane; KEGG: sit:TM1040_2078 protein of unknown function DUF6, transmembrane; hypothetical protein 344690..345589 Paracoccus denitrificans PD1222 4581739 YP_916953.1 CDS Pden_3176 NC_008687.1 345773 346171 R KEGG: sme:SMc01177 hypothetical protein; hypothetical protein complement(345773..346171) Paracoccus denitrificans PD1222 4581740 YP_916954.1 CDS Pden_3177 NC_008687.1 346168 346452 R TIGRFAM: transcriptional regulator, AbrB family; PFAM: SpoVT/AbrB domain protein; KEGG: sme:SMc01176 hypothetical protein; AbrB family transcriptional regulator complement(346168..346452) Paracoccus denitrificans PD1222 4581741 YP_916955.1 CDS Pden_3178 NC_008687.1 346610 346891 D KEGG: mes:Meso_3841 transcriptional regulator; transcriptional regulator 346610..346891 Paracoccus denitrificans PD1222 4581742 YP_916956.1 CDS Pden_3179 NC_008687.1 346902 348014 D KEGG: mes:Meso_3842 replication protein A; replication protein A 346902..348014 Paracoccus denitrificans PD1222 4581743 YP_916957.1 CDS Pden_3180 NC_008687.1 348011 348313 D hypothetical protein 348011..348313 Paracoccus denitrificans PD1222 4581744 YP_916958.1 CDS Pden_3181 NC_008687.1 348310 348798 D KEGG: mes:Meso_2334 hypothetical protein; hypothetical protein 348310..348798 Paracoccus denitrificans PD1222 4581745 YP_916959.1 CDS Pden_3182 NC_008687.1 348795 350282 D PFAM: C-5 cytosine-specific DNA methylase; KEGG: ngo:NGO1894 5-methylcytosine methyltransferase; C-5 cytosine-specific DNA methylase 348795..350282 Paracoccus denitrificans PD1222 4581746 YP_916960.1 CDS Pden_3183 NC_008687.1 350279 350881 D KEGG: mes:Meso_3845 conjugal transfer protein precursor; conjugal transfer protein precursor 350279..350881 Paracoccus denitrificans PD1222 4581747 YP_916961.1 CDS Pden_3184 NC_008687.1 350878 351216 D PFAM: protein of unknown function DUF736; KEGG: mes:Meso_2332 protein of unknown function DUF736; hypothetical protein 350878..351216 Paracoccus denitrificans PD1222 4581748 YP_916962.1 CDS Pden_3185 NC_008687.1 351220 352026 D PFAM: Lytic transglycosylase, catalytic; KEGG: mes:Meso_0517 lytic transglycosylase, catalytic; lytic transglycosylase, catalytic 351220..352026 Paracoccus denitrificans PD1222 4581749 YP_916963.1 CDS Pden_3186 NC_008687.1 352076 352657 D hypothetical protein 352076..352657 Paracoccus denitrificans PD1222 4581750 YP_916964.1 CDS Pden_3187 NC_008687.1 352908 354701 D KEGG: mes:Meso_3848 hypothetical protein; hypothetical protein 352908..354701 Paracoccus denitrificans PD1222 4581751 YP_916965.1 CDS Pden_3188 NC_008687.1 354719 356728 D type IV secretion VirD4 coupling protein family; conjugal transfer coupling protein TraG 354719..356728 Paracoccus denitrificans PD1222 4581752 YP_916966.1 CDS Pden_3189 NC_008687.1 356759 357280 D KEGG: mes:Meso_0514 helix-turn-helix protein, CopG; hypothetical protein 356759..357280 Paracoccus denitrificans PD1222 4581753 YP_916967.1 CDS Pden_3190 NC_008687.1 357306 357827 R KEGG: mxa:MXAN_3433 hypothetical protein; hypothetical protein complement(357306..357827) Paracoccus denitrificans PD1222 4581754 YP_916968.1 CDS Pden_3191 NC_008687.1 357824 358063 R hypothetical protein complement(357824..358063) Paracoccus denitrificans PD1222 4581755 YP_916969.1 CDS Pden_3192 NC_008687.1 358045 358470 R PFAM: PilT protein domain protein; KEGG: plu:plu3057 hypothetical protein; twitching motility protein PilT complement(358045..358470) Paracoccus denitrificans PD1222 4581756 YP_916970.1 CDS Pden_3193 NC_008687.1 358467 358730 R KEGG: ret:RHE_PE00297 plasmid stabilization protein; plasmid stabilization protein complement(358467..358730) Paracoccus denitrificans PD1222 4581757 YP_916971.1 CDS Pden_3194 NC_008687.1 359010 360014 D PFAM: type II secretion system protein E; KEGG: mes:Meso_2324 type II secretion system protein E; type II secretion system protein E 359010..360014 Paracoccus denitrificans PD1222 4581758 YP_916972.1 CDS Pden_3195 NC_008687.1 360011 360343 D PFAM: Conjugal transfer protein TrbC; KEGG: mes:Meso_0508 conjugal transfer protein TrbC; conjugal transfer protein TrbC 360011..360343 Paracoccus denitrificans PD1222 4581759 YP_916973.1 CDS Pden_3196 NC_008687.1 360343 360624 D KEGG: mes:Meso_2322 conjugal transfer protein TrbB; conjugal transfer protein TrbB 360343..360624 Paracoccus denitrificans PD1222 4581760 YP_916974.1 CDS Pden_3197 NC_008687.1 360637 363270 D type IV secretion system VirB4 family; conjugal transfer ATPase TrbE 360637..363270 Paracoccus denitrificans PD1222 4581761 YP_916975.1 CDS Pden_3198 NC_008687.1 363267 364064 D KEGG: mes:Meso_3855 conjugal transfer protein TrbJ; conjugal transfer protein TrbJ 363267..364064 Paracoccus denitrificans PD1222 4581762 YP_916976.1 CDS Pden_3199 NC_008687.1 364085 364372 D KEGG: mes:Meso_2319 hypothetical protein; hypothetical protein 364085..364372 Paracoccus denitrificans PD1222 4581763 YP_916977.1 CDS Pden_3200 NC_008687.1 364380 365702 D type IV secretion VirB6 family; conjugal transfer protein TrbL 364380..365702 Paracoccus denitrificans PD1222 4581764 YP_916978.1 CDS Pden_3201 NC_008687.1 365699 366388 D PFAM: Conjugal transfer protein; KEGG: mes:Meso_0502 conjugal transfer protein; conjugal transfer protein TrbF 365699..366388 Paracoccus denitrificans PD1222 4581765 YP_916979.1 CDS Pden_3202 NC_008687.1 366385 367428 D PFAM: Conjugal transfer protein TrbG/VirB9/CagX; KEGG: mes:Meso_0501 conjugal transfer protein TrbG/VirB9/CagX; conjugal transfer protein TrbG/VirB9/CagX 366385..367428 Paracoccus denitrificans PD1222 4581766 YP_916980.1 CDS Pden_3203 NC_008687.1 367428 368594 D PFAM: conjugation TrbI family protein; KEGG: mes:Meso_0500 conjugation TrbI-like protein; conjugation TrbI family protein 367428..368594 Paracoccus denitrificans PD1222 4581767 YP_916981.1 CDS Pden_3204 NC_008687.1 368591 368845 D KEGG: rpc:RPC_3531 hypothetical protein; hypothetical protein 368591..368845 Paracoccus denitrificans PD1222 4581768 YP_916982.1 CDS Pden_3205 NC_008687.1 368847 369791 R PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: mes:Meso_3862 transcriptional regulator, LysR family; LysR family transcriptional regulator complement(368847..369791) Paracoccus denitrificans PD1222 4581769 YP_916983.1 CDS Pden_3206 NC_008687.1 369824 370534 R 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 complement(369824..370534) Paracoccus denitrificans PD1222 4581770 YP_916984.1 CDS Pden_3207 NC_008687.1 370806 372089 R 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 complement(370806..372089) Paracoccus denitrificans PD1222 4581771 YP_916985.1 CDS Pden_3208 NC_008687.1 372102 372653 R KEGG: rpd:RPD_0610 tripartite ATP-independent periplasmic transporter, DctQ component; hypothetical protein complement(372102..372653) Paracoccus denitrificans PD1222 4581772 YP_916986.1 CDS Pden_3209 NC_008687.1 372650 373663 R PFAM: TRAP dicarboxylate transporter- DctP subunit; KEGG: bja:bll6794 hypothetical protein; TRAP dicarboxylate transporter- DctP subunit complement(372650..373663) Paracoccus denitrificans PD1222 4581773 YP_916987.1 CDS Pden_3210 NC_008687.1 374073 375254 D PFAM: iron-containing alcohol dehydrogenase; KEGG: bbr:BB0636 iron-containing alcohol dehydrogenase; iron-containing alcohol dehydrogenase 374073..375254 Paracoccus denitrificans PD1222 4581774 YP_916988.1 CDS Pden_3211 NC_008687.1 375275 376708 D PFAM: aldehyde dehydrogenase; KEGG: rme:Rmet_1577 aldehyde dehydrogenase; aldehyde dehydrogenase 375275..376708 Paracoccus denitrificans PD1222 4581775 YP_916989.1 CDS Pden_3212 NC_008687.1 376719 377762 D PFAM: Alcohol dehydrogenase, zinc-binding domain protein; Alcohol dehydrogenase GroES domain protein; KEGG: sma:SAV3314 NADP-dependent alcohol dehydrogenase; alcohol dehydrogenase 376719..377762 Paracoccus denitrificans PD1222 4581776 YP_916990.1 CDS Pden_3213 NC_008687.1 377773 378576 D PFAM: Enoyl-CoA hydratase/isomerase; KEGG: bxe:Bxe_C0603 enoyl-CoA hydratase/isomerase; enoyl-CoA hydratase/isomerase 377773..378576 Paracoccus denitrificans PD1222 4581777 YP_916991.1 CDS Pden_3214 NC_008687.1 378583 378828 D hypothetical protein 378583..378828 Paracoccus denitrificans PD1222 4581778 YP_916992.1 CDS Pden_3215 NC_008687.1 378959 379333 R PFAM: Carboxymuconolactone decarboxylase; KEGG: sai:Saci_1814 carboxymuconolactone decarboxylase; carboxymuconolactone decarboxylase complement(378959..379333) Paracoccus denitrificans PD1222 4581779 YP_916993.1 CDS Pden_3216 NC_008687.1 379406 380335 R PFAM: NADP oxidoreductase, coenzyme F420-dependent; 6-phosphogluconate dehydrogenase, NAD-binding; KEGG: dar:Daro_3339 6-phosphogluconate dehydrogenase, NAD-binding; 3-hydroxyisobutyrate dehydrogenase complement(379406..380335) Paracoccus denitrificans PD1222 4581780 YP_916994.1 CDS Pden_3217 NC_008687.1 380455 380880 R PFAM: Cupin 2, conserved barrel domain protein; KEGG: sme:SMc01911 hypothetical protein; cupin complement(380455..380880) Paracoccus denitrificans PD1222 4581781 YP_916995.1 CDS Pden_3218 NC_008687.1 380901 381794 R PFAM: beta-lactamase domain protein; KEGG: bja:bll0351 hypothetical protein; beta-lactamase domain-containing protein complement(380901..381794) Paracoccus denitrificans PD1222 4581782 YP_916996.1 CDS Pden_3219 NC_008687.1 381847 382848 R PFAM: TRAP dicarboxylate transporter- DctP subunit; KEGG: bja:bll6794 hypothetical protein; TRAP dicarboxylate transporter- DctP subunit complement(381847..382848) Paracoccus denitrificans PD1222 4581783 YP_916997.1 CDS Pden_3220 NC_008687.1 382965 383393 R PFAM: thioesterase superfamily protein; KEGG: rha:RHA1_ro00319 possible thioesterase; thioesterase superfamily protein complement(382965..383393) Paracoccus denitrificans PD1222 4581784 YP_916998.1 CDS Pden_3221 NC_008687.1 383452 384405 R PFAM: Uncharacterized protein UPF0065; KEGG: bbr:BB3965 hypothetical protein; hypothetical protein complement(383452..384405) Paracoccus denitrificans PD1222 4581785 YP_916999.1 CDS Pden_3222 NC_008687.1 384445 385959 R PFAM: protein of unknown function DUF112, transmembrane; KEGG: mes:Meso_2918 protein of unknown function DUF112, transmembrane; hypothetical protein complement(384445..385959) Paracoccus denitrificans PD1222 4581786 YP_917000.1 CDS Pden_3223 NC_008687.1 385965 386414 R PFAM: protein of unknown function DUF1468; KEGG: bpa:BPP0373 hypothetical protein; hypothetical protein complement(385965..386414) Paracoccus denitrificans PD1222 4581787 YP_917001.1 CDS Pden_3224 NC_008687.1 386490 388244 R PFAM: acyl-CoA dehydrogenase domain protein; KEGG: abo:ABO_2098 acyl-CoA dehydrogenase; acyl-CoA dehydrogenase complement(386490..388244) Paracoccus denitrificans PD1222 4581788 YP_917002.1 CDS Pden_3225 NC_008687.1 388262 390559 R 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 complement(388262..390559) Paracoccus denitrificans PD1222 4581789 YP_917003.1 CDS Pden_3226 NC_008687.1 390556 391677 R KEGG: rru:Rru_A1310 acetyl-CoA C-acyltransferase; TIGRFAM: acetyl-CoA acetyltransferases; PFAM: Thiolase; acetyl-CoA acetyltransferase complement(390556..391677) Paracoccus denitrificans PD1222 4581790 YP_917004.1 CDS Pden_3227 NC_008687.1 391797 393029 R 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 complement(391797..393029) Paracoccus denitrificans PD1222 4581791 YP_917005.1 CDS Pden_3228 NC_008687.1 393111 394610 R PFAM: aldehyde dehydrogenase; KEGG: bur:Bcep18194_C7342 aldehyde dehydrogenase; aldehyde dehydrogenase complement(393111..394610) Paracoccus denitrificans PD1222 4581792 YP_917006.1 CDS Pden_3229 NC_008687.1 394918 396066 D KEGG: fal:FRAAL2833 hypothetical protein; hypothetical protein 394918..396066 Paracoccus denitrificans PD1222 4581793 YP_917007.1 CDS Pden_3230 NC_008687.1 396188 397768 D PFAM: AMP-dependent synthetase and ligase; KEGG: mmc:Mmcs_3946 AMP-dependent synthetase and ligase; AMP-dependent synthetase/ligase 396188..397768 Paracoccus denitrificans PD1222 4581794 YP_917008.1 CDS Pden_3231 NC_008687.1 397808 398662 D KEGG: rha:RHA1_ro03060 probable transciptional regulator, IclR family; IclR family transciptional regulator 397808..398662 Paracoccus denitrificans PD1222 4581795 YP_917009.1 CDS Pden_3232 NC_008687.1 398991 399803 R 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 complement(398991..399803) Paracoccus denitrificans PD1222 4581796 YP_917010.1 CDS Pden_3233 NC_008687.1 400008 400685 R PFAM: transposase IS116/IS110/IS902 family protein; KEGG: nha:Nham_3955 transposase IS116/IS110/IS902; transposase IS116/IS110/IS902 family protein complement(400008..400685) Paracoccus denitrificans PD1222 4581797 YP_917011.1 CDS Pden_3234 NC_008687.1 400725 401084 R KEGG: yps:YPTB1994 hypothetical protein; hypothetical protein complement(400725..401084) Paracoccus denitrificans PD1222 4581798 YP_917012.1 CDS Pden_3235 NC_008687.1 401247 402308 D KEGG: mes:Meso_3912 hypothetical protein; hypothetical protein 401247..402308 Paracoccus denitrificans PD1222 4581799 YP_917013.1 CDS Pden_3236 NC_008687.1 402410 403183 D PFAM: NAD-dependent epimerase/dehydratase; dTDP-4-dehydrorhamnose reductase; NmrA family protein; KEGG: mes:Meso_3897 NmrA-like; NmrA family protein 402410..403183 Paracoccus denitrificans PD1222 4581800 YP_917014.1 CDS Pden_3237 NC_008687.1 403185 404078 R PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: mes:Meso_3905 transcriptional regulator, LysR family; LysR family transcriptional regulator complement(403185..404078) Paracoccus denitrificans PD1222 4581801 YP_917015.1 CDS Pden_3238 NC_008687.1 404224 404697 D KEGG: mes:Meso_3908 hypothetical protein; hypothetical protein 404224..404697 Paracoccus denitrificans PD1222 4581802 YP_917016.1 CDS Pden_3239 NC_008687.1 404744 405418 D KEGG: mes:Meso_3907 hypothetical protein; hypothetical protein 404744..405418 Paracoccus denitrificans PD1222 4581803 YP_917017.1 CDS Pden_3240 NC_008687.1 405618 406619 D KEGG: ade:Adeh_3220 hypothetical protein; hypothetical protein 405618..406619 Paracoccus denitrificans PD1222 4581804 YP_917018.1 CDS Pden_3241 NC_008687.1 406649 407218 D KEGG: mes:Meso_3899 twin-arginine translocation pathway signal; twin-arginine translocation pathway signal 406649..407218 Paracoccus denitrificans PD1222 4581805 YP_917019.1 CDS Pden_3242 NC_008687.1 407264 408247 D PFAM: aldo/keto reductase; KEGG: bur:Bcep18194_B2855 aldo/keto reductase; aldo/keto reductase 407264..408247 Paracoccus denitrificans PD1222 4581806 YP_917020.1 CDS Pden_3243 NC_008687.1 408296 409462 D PFAM: aldo/keto reductase; KEGG: mes:Meso_3904 twin-arginine translocation pathway signal; aldo/keto reductase 408296..409462 Paracoccus denitrificans PD1222 4581807 YP_917021.1 CDS Pden_3244 NC_008687.1 409473 410462 D PFAM: aldo/keto reductase; KEGG: bxe:Bxe_B1949 aldo/keto reductase; aldo/keto reductase 409473..410462 Paracoccus denitrificans PD1222 4581808 YP_917022.1 CDS Pden_3245 NC_008687.1 410491 411477 D KEGG: mes:Meso_3911 hypothetical protein; hypothetical protein 410491..411477 Paracoccus denitrificans PD1222 4581809 YP_917023.1 CDS Pden_3246 NC_008687.1 411556 411753 D KEGG: nha:Nham_3076 transposase; hypothetical protein 411556..411753 Paracoccus denitrificans PD1222 4581810 YP_917024.1 CDS Pden_3247 NC_008687.1 411867 412448 D KEGG: mag:amb0411 transposase; transposase 411867..412448 Paracoccus denitrificans PD1222 4581811 YP_917025.1 CDS Pden_3248 NC_008687.1 412476 413243 R PFAM: regulatory proteins, IclR; KEGG: rha:RHA1_ro06686 probable transciptional regulator, IclR family; regulatory proteins, IclR complement(412476..413243) Paracoccus denitrificans PD1222 4581812 YP_917026.1 CDS Pden_3250 NC_008687.1 414038 414535 R PFAM: protein of unknown function DUF1468; KEGG: bpa:BPP0373 hypothetical protein; hypothetical protein complement(414038..414535) Paracoccus denitrificans PD1222 4581813 YP_917027.1 CDS Pden_3251 NC_008687.1 414737 415615 D PFAM: alpha/beta hydrolase fold; PGAP1 family protein; KEGG: dar:Daro_3230 alpha/beta hydrolase fold; alpha/beta hydrolase 414737..415615 Paracoccus denitrificans PD1222 4581814 YP_917028.1 CDS Pden_3252 NC_008687.1 415612 415989 D SMART: regulatory protein, MerR; KEGG: rsp:RSP_2201 transcriptional regulator, MerR family; MerR family transcriptional regulator 415612..415989 Paracoccus denitrificans PD1222 4581815 YP_917029.1 CDS Pden_3253 NC_008687.1 416027 417628 D PFAM: protein of unknown function DUF894, DitE; major facilitator superfamily MFS_1; KEGG: rsp:RSP_0945 major facilitator superfamily (MFS) transporter; hypothetical protein 416027..417628 Paracoccus denitrificans PD1222 4581816 YP_917030.1 CDS Pden_3255 NC_008687.1 418832 419227 D PFAM: Cupin 2, conserved barrel domain protein; KEGG: mes:Meso_2098 cupin 2, conserved barrel; cupin 418832..419227 Paracoccus denitrificans PD1222 4581817 YP_917031.1 CDS Pden_3256 NC_008687.1 419378 420307 D PFAM: 6-phosphogluconate dehydrogenase, NAD-binding; KEGG: sth:STH938 3-hydroxyisobutyrate dehydrogenase; 3-hydroxyisobutyrate dehydrogenase 419378..420307 Paracoccus denitrificans PD1222 4581818 YP_917032.1 CDS Pden_3257 NC_008687.1 420270 420716 D PFAM: Carboxymuconolactone decarboxylase; KEGG: pst:PSPTO_4478 4-carboxymuconolactone decarboxylase; carboxymuconolactone decarboxylase 420270..420716 Paracoccus denitrificans PD1222 4581819 YP_917033.1 CDS Pden_3258 NC_008687.1 420838 421839 D PFAM: TRAP dicarboxylate transporter- DctP subunit; KEGG: rpd:RPD_0609 TRAP dicarboxylate transporter-DctP subunit; TRAP dicarboxylate transporter- DctP subunit 420838..421839 Paracoccus denitrificans PD1222 4581820 YP_917034.1 CDS Pden_3259 NC_008687.1 422255 422542 D KEGG: sme:SMa2189 integrase/recombinase; integrase/recombinase 422255..422542 Paracoccus denitrificans PD1222 4581821 YP_917035.1 CDS Pden_3260 NC_008687.1 422920 424332 D PFAM: aldehyde dehydrogenase; KEGG: dra:DRA0126 aldehyde dehydrogenase; aldehyde dehydrogenase 422920..424332 Paracoccus denitrificans PD1222 4581822 YP_917036.1 CDS Pden_3262 NC_008687.1 425326 426882 D PFAM: transposase, IS204/IS1001/IS1096/IS1165 family protein; KEGG: atu:Atu5094 ISL3 family transposase; transposase, IS204/IS1001/IS1096/IS1165 family protein 425326..426882 Paracoccus denitrificans PD1222 4581823 YP_917037.1 CDS Pden_3263 NC_008687.1 426907 427194 R hypothetical protein complement(426907..427194) Paracoccus denitrificans PD1222 4581824 YP_917038.1 CDS Pden_3264 NC_008687.1 427531 429057 R PFAM: aldehyde dehydrogenase; KEGG: sme:SMb20262 semialdehyde dehydrogenase; aldehyde dehydrogenase complement(427531..429057) Paracoccus denitrificans PD1222 4581825 YP_917039.1 CDS Pden_3265 NC_008687.1 429142 430152 R KEGG: mes:Meso_2079 ABC transporter, periplasmic substrate-binding protein; ABC-type nitrate/sulfonate/bicarbonate transport systems periplasmic components-like complement(429142..430152) Paracoccus denitrificans PD1222 4581826 YP_917040.1 CDS Pden_3266 NC_008687.1 430569 431600 D PFAM: Uncharacterized protein UPF0065; KEGG: dsy:DSY0976 hypothetical protein; hypothetical protein 430569..431600 Paracoccus denitrificans PD1222 4581827 YP_917041.1 CDS Pden_3267 NC_008687.1 431624 432613 D PFAM: amidohydrolase 2; KEGG: reu:Reut_B5784 amidohydrolase 2; amidohydrolase 431624..432613 Paracoccus denitrificans PD1222 4581828 YP_917042.1 CDS Pden_3268 NC_008687.1 432650 434680 D PFAM: protein of unknown function DUF112, transmembrane; KEGG: bcl:ABC0625 hypothetical protein; hypothetical protein 432650..434680 Paracoccus denitrificans PD1222 4581829 YP_917043.1 CDS Pden_3269 NC_008687.1 434713 435375 D KEGG: bja:bll1020 hypothetical protein; hypothetical protein 434713..435375 Paracoccus denitrificans PD1222 4581830 YP_917044.1 CDS Pden_3270 NC_008687.1 435394 436701 R PFAM: protein of unknown function DUF894, DitE; major facilitator superfamily MFS_1; KEGG: hne:HNE_1254 major facilitator family protein; major facilitator transporter complement(435394..436701) Paracoccus denitrificans PD1222 4581831 YP_917045.1 CDS Pden_3271 NC_008687.1 436878 438143 D PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: csa:Csal_0331 transcriptional regulator, LysR family; LysR family transcriptional regulator 436878..438143 Paracoccus denitrificans PD1222 4581832 YP_917046.1 CDS Pden_3272 NC_008687.1 438194 439045 R PFAM: HpcH/HpaI aldolase; KEGG: sus:Acid_0199 HpcH/HpaI aldolase; HpcH/HpaI aldolase complement(438194..439045) Paracoccus denitrificans PD1222 4581833 YP_917047.1 CDS Pden_3273 NC_008687.1 439072 440046 R KEGG: bja:blr3843 hypothetical protein; hypothetical protein complement(439072..440046) Paracoccus denitrificans PD1222 4581834 YP_917048.1 CDS Pden_3274 NC_008687.1 440299 441330 D PFAM: amidohydrolase 2; KEGG: rme:Rmet_3705 amidohydrolase 2; amidohydrolase 440299..441330 Paracoccus denitrificans PD1222 4581835 YP_917049.1 CDS Pden_3275 NC_008687.1 441327 443006 D 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 441327..443006 Paracoccus denitrificans PD1222 4581836 YP_917050.1 CDS Pden_3276 NC_008687.1 443021 443260 D hypothetical protein 443021..443260 Paracoccus denitrificans PD1222 4581837 YP_917051.1 CDS Pden_3277 NC_008687.1 443257 444138 D PFAM: amidohydrolase 2; KEGG: reu:Reut_B5784 amidohydrolase 2; amidohydrolase 443257..444138 Paracoccus denitrificans PD1222 4581838 YP_917052.1 CDS Pden_3278 NC_008687.1 444135 445052 D KEGG: bja:blr3843 hypothetical protein; hypothetical protein 444135..445052 Paracoccus denitrificans PD1222 4581839 YP_917053.1 CDS Pden_3279 NC_008687.1 445296 446237 D KEGG: sil:SPO3430 outer membrane porin; hypothetical protein 445296..446237 Paracoccus denitrificans PD1222 4581840 YP_917054.1 CDS Pden_3280 NC_008687.1 446254 447207 R PFAM: Integrase, catalytic region; KEGG: rsp:RSP_3937 probable transposase, Y4bF; integrase catalytic subunit complement(446254..447207) Paracoccus denitrificans PD1222 4581841 YP_917055.1 CDS Pden_3281 NC_008687.1 447565 449121 D PFAM: transposase, IS204/IS1001/IS1096/IS1165 family protein; KEGG: atu:Atu5094 ISL3 family transposase; transposase, IS204/IS1001/IS1096/IS1165 family protein 447565..449121 Paracoccus denitrificans PD1222 4581842 YP_917056.1 CDS Pden_3282 NC_008687.1 449183 449533 R hypothetical protein complement(449183..449533) Paracoccus denitrificans PD1222 4581843 YP_917057.1 CDS Pden_3283 NC_008687.1 449813 451183 R 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 complement(449813..451183) Paracoccus denitrificans PD1222 4581844 YP_917058.1 CDS Pden_3284 NC_008687.1 451180 451839 R PFAM: response regulator receiver; transcriptional regulator domain protein; KEGG: bmb:BruAb2_0224 two component response regulator; two component transcriptional regulator complement(451180..451839) Paracoccus denitrificans PD1222 4581845 YP_917059.1 CDS Pden_3285 NC_008687.1 451981 452295 D KEGG: rsp:RSP_7166 hypothetical protein; hypothetical protein 451981..452295 Paracoccus denitrificans PD1222 4581846 YP_917060.1 CDS Pden_3286 NC_008687.1 452288 452920 D PFAM: cytochrome B561; KEGG: rsp:RSP_2807 cytochrome b; cytochrome B561 452288..452920 Paracoccus denitrificans PD1222 4581847 YP_917061.1 CDS Pden_3287 NC_008687.1 453110 453412 D KEGG: bmb:BruAb1_1622 hypothetical protein; hypothetical protein 453110..453412 Paracoccus denitrificans PD1222 4581848 YP_917062.1 CDS Pden_3288 NC_008687.1 453524 453904 D KEGG: bma:BMAA0783 hypothetical protein; hypothetical protein 453524..453904 Paracoccus denitrificans PD1222 4581849 YP_917063.1 CDS Pden_3289 NC_008687.1 453931 454401 D KEGG: bmb:BruAb2_0227 hypothetical protein; hypothetical protein 453931..454401 Paracoccus denitrificans PD1222 4581850 YP_917064.1 CDS Pden_3290 NC_008687.1 454411 456618 D 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 454411..456618 Paracoccus denitrificans PD1222 4581851 YP_917065.1 CDS Pden_3291 NC_008687.1 456599 457591 D PFAM: ApbE family lipoprotein; KEGG: bmb:BruAb2_0229 ApbE family protein; ApbE family lipoprotein 456599..457591 Paracoccus denitrificans PD1222 4581852 YP_917066.1 CDS Pden_3292 NC_008687.1 457734 458207 D KEGG: dar:Daro_1035 hypothetical protein; hypothetical protein 457734..458207 Paracoccus denitrificans PD1222 4581853 YP_917067.1 CDS Pden_3293 NC_008687.1 458241 459146 R PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: rsp:RSP_3052 transcriptional regulator, LysR family; LysR family transcriptional regulator complement(458241..459146) Paracoccus denitrificans PD1222 4581854 YP_917068.1 CDS Pden_3294 NC_008687.1 459255 459473 D PFAM: Heavy metal transport/detoxification protein; KEGG: rxy:Rxyl_1802 heavy metal transport/detoxification protein; heavy metal transport/detoxification protein 459255..459473 Paracoccus denitrificans PD1222 4581855 YP_917069.1 CDS Pden_3295 NC_008687.1 459535 461454 D 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 459535..461454 Paracoccus denitrificans PD1222 4581856 YP_917070.1 CDS Pden_3296 NC_008687.1 461511 462173 D PFAM: protein of unknown function DUF924; KEGG: gvi:glr1115 hypothetical protein; hypothetical protein 461511..462173 Paracoccus denitrificans PD1222 4581857 YP_917071.1 CDS Pden_3297 NC_008687.1 462189 464129 R 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 complement(462189..464129) Paracoccus denitrificans PD1222 4581858 YP_917072.1 CDS Pden_3298 NC_008687.1 464191 464571 R KEGG: sat:SYN_02345 hypothetical membrane protein; hypothetical protein complement(464191..464571) Paracoccus denitrificans PD1222 4581859 YP_917073.1 CDS Pden_3299 NC_008687.1 464586 465278 R PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: mag:amb2540 ABC-type antimicrobial peptide transport system, ATPase component; ABC transporter complement(464586..465278) Paracoccus denitrificans PD1222 4581860 YP_917074.1 CDS Pden_3300 NC_008687.1 465284 466417 R PFAM: protein of unknown function DUF214; KEGG: mag:amb2541 ABC-type antimicrobial peptide transport system, permease component; hypothetical protein complement(465284..466417) Paracoccus denitrificans PD1222 4581861 YP_917075.1 CDS Pden_3301 NC_008687.1 466414 467559 R 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 complement(466414..467559) Paracoccus denitrificans PD1222 4581862 YP_917076.1 CDS Pden_3302 NC_008687.1 467563 468210 R PFAM: regulatory protein, TetR; KEGG: eba:ebA6247 transcriptional regulator, TetR family; TetR family transcriptional regulator complement(467563..468210) Paracoccus denitrificans PD1222 4581863 YP_917077.1 CDS Pden_3305 NC_008687.1 470021 471202 D PFAM: filamentation induced by cAMP protein Fic; KEGG: atc:AGR_pAT_51 hypothetical protein; filamentation induced by cAMP protein fic 470021..471202 Paracoccus denitrificans PD1222 4581864 YP_917078.1 CDS Pden_3306 NC_008687.1 471348 471779 R KEGG: bja:blr1867 hypothetical protein; hypothetical protein complement(471348..471779) Paracoccus denitrificans PD1222 4581865 YP_917079.1 CDS Pden_3307 NC_008687.1 471872 472897 R PFAM: transposase IS66; KEGG: bja:blr1700 transposase; transposase IS66 complement(471872..472897) Paracoccus denitrificans PD1222 4581866 YP_917080.1 CDS Pden_3308 NC_008687.1 472952 473305 R PFAM: IS66 Orf2 family protein; KEGG: bja:bll2160 transposase; IS66 Orf2 family protein complement(472952..473305) Paracoccus denitrificans PD1222 4581867 YP_917081.1 CDS Pden_3309 NC_008687.1 473299 473631 R PFAM: transposase IS3/IS911 family protein; KEGG: atc:AGR_pTi_30 hypothetical protein; transposase IS3/IS911 family protein complement(473299..473631) Paracoccus denitrificans PD1222 4581868 YP_917082.1 CDS Pden_3310 NC_008687.1 473734 474063 D KEGG: sme:SMb21085 hypothetical protein encoded by ORF3 of ISRm14, IS66 family; hypothetical protein 473734..474063 Paracoccus denitrificans PD1222 4581869 YP_917083.1 CDS Pden_3311 NC_008687.1 474208 475173 R PFAM: regulatory protein, LuxR; response regulator receiver; KEGG: rpd:RPD_3866 response regulator receiver; response regulator receiver protein complement(474208..475173) Paracoccus denitrificans PD1222 4581870 YP_917084.1 CDS Pden_3312 NC_008687.1 475170 476507 R 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 complement(475170..476507) Paracoccus denitrificans PD1222 4581871 YP_917085.1 CDS Pden_3313 NC_008687.1 476504 476986 R KEGG: rde:RD1_3578 hypothetical protein; hypothetical protein complement(476504..476986) Paracoccus denitrificans PD1222 4581872 YP_917086.1 CDS Pden_3314 NC_008687.1 477123 477602 D hypothetical protein 477123..477602 Paracoccus denitrificans PD1222 4581873 YP_917087.1 CDS Pden_3315 NC_008687.1 477604 478176 D hypothetical protein 477604..478176 Paracoccus denitrificans PD1222 4581874 YP_917088.1 CDS Pden_3316 NC_008687.1 478185 478664 D hypothetical protein 478185..478664 Paracoccus denitrificans PD1222 4581875 YP_917089.1 CDS Pden_3317 NC_008687.1 478661 479188 D hypothetical protein 478661..479188 Paracoccus denitrificans PD1222 4581876 YP_917090.1 CDS Pden_3318 NC_008687.1 479185 479709 D hypothetical protein 479185..479709 Paracoccus denitrificans PD1222 4581877 YP_917091.1 CDS Pden_3319 NC_008687.1 479733 480704 D KEGG: mlo:mlr7467 hypothetical protein; hypothetical protein 479733..480704 Paracoccus denitrificans PD1222 4581878 YP_917092.1 CDS Pden_3320 NC_008687.1 480701 483268 D PFAM: von Willebrand factor, type A; KEGG: jan:Jann_1721 von Willebrand factor, type A; von Willebrand factor, type A 480701..483268 Paracoccus denitrificans PD1222 4581879 YP_917093.1 CDS Pden_3321 NC_008687.1 483265 483801 D hypothetical protein 483265..483801 Paracoccus denitrificans PD1222 4581880 YP_917094.1 CDS Pden_3322 NC_008687.1 483798 484283 D hypothetical protein 483798..484283 Paracoccus denitrificans PD1222 4581881 YP_917095.1 CDS Pden_3323 NC_008687.1 484311 484901 D hypothetical protein 484311..484901 Paracoccus denitrificans PD1222 4581882 YP_917096.1 CDS Pden_3324 NC_008687.1 484910 485728 D KEGG: rpe:RPE_0562 type III restriction enzyme, res subunit; type III restriction enzyme, res subunit 484910..485728 Paracoccus denitrificans PD1222 4581883 YP_917097.1 CDS Pden_3325 NC_008687.1 485821 488112 D KEGG: rfr:Rfer_4292 hypothetical protein; hypothetical protein 485821..488112 Paracoccus denitrificans PD1222 4581884 YP_917098.1 CDS Pden_3326 NC_008687.1 488297 490102 R PFAM: Resolvase, N-terminal domain; Recombinase; KEGG: nha:Nham_3864 recombinase; recombinase complement(488297..490102) Paracoccus denitrificans PD1222 4581885 YP_917099.1 CDS Pden_3327 NC_008687.1 490103 490552 D hypothetical protein 490103..490552 Paracoccus denitrificans PD1222 4581886 YP_917100.1 CDS Pden_3330 NC_008687.1 492010 492963 D 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 492010..492963 Paracoccus denitrificans PD1222 4581888 YP_917101.1 CDS Pden_3331 NC_008687.1 493215 493538 D hypothetical protein 493215..493538 Paracoccus denitrificans PD1222 4581889 YP_917102.1 CDS Pden_3332 NC_008687.1 493535 494413 D KEGG: bxe:Bxe_A0212 hypothetical protein; XRE family transcriptional regulator 493535..494413 Paracoccus denitrificans PD1222 4581890 YP_917103.1 CDS Pden_3333 NC_008687.1 494397 494957 R PFAM: transposase, IS4 family protein; KEGG: sil:SPOA0134 ISSpo7, transposase; transposase, IS4 family protein complement(494397..494957) Paracoccus denitrificans PD1222 4581891 YP_917104.1 CDS Pden_3334 NC_008687.1 495252 495524 D hypothetical protein 495252..495524 Paracoccus denitrificans PD1222 4581892 YP_917105.1 CDS Pden_3335 NC_008687.1 495620 495898 R PFAM: SH3, type 3 domain protein; KEGG: rsp:RSP_6161 hypothetical protein; SH3 type 3 domain-containing protein complement(495620..495898) Paracoccus denitrificans PD1222 4581893 YP_917106.1 CDS Pden_3336 NC_008687.1 495960 496316 D hypothetical protein 495960..496316 Paracoccus denitrificans PD1222 4581894 YP_917107.1 CDS Pden_3337 NC_008687.1 496474 497838 R TIGRFAM: chromate transporter, chromate ion transporter (CHR) family; PFAM: Chromate transporter; KEGG: sme:SMc00808 chromate transport protein; chromate transporter complement(496474..497838) Paracoccus denitrificans PD1222 4581895 YP_917108.1 CDS Pden_3338 NC_008687.1 497835 498680 R SMART: Rhodanese domain protein; KEGG: mlo:mlr5406 hypothetical protein; rhodanese domain-containing protein complement(497835..498680) Paracoccus denitrificans PD1222 4581896 YP_917109.1 CDS Pden_3339 NC_008687.1 498895 499602 R PFAM: NADPH-dependent FMN reductase; KEGG: rsp:RSP_2731 arsenical resistance protein, ArsH; NADPH-dependent FMN reductase complement(498895..499602) Paracoccus denitrificans PD1222 4581897 YP_917110.1 CDS Pden_3340 NC_008687.1 499599 500675 R TIGRFAM: arsenical-resistance protein; PFAM: Bile acid:sodium symporter; KEGG: sal:Sala_2405 arsenical-resistance protein; arsenical-resistance protein complement(499599..500675) Paracoccus denitrificans PD1222 4581898 YP_917111.1 CDS Pden_3341 NC_008687.1 500685 501638 R 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 complement(500685..501638) Paracoccus denitrificans PD1222 4581899 YP_917112.1 CDS Pden_3342 NC_008687.1 501631 501993 R PFAM: regulatory protein, ArsR; KEGG: nwi:Nwi_3123 transcriptional regulatory protein, ArsR family; regulatory protein ArsR complement(501631..501993) Paracoccus denitrificans PD1222 4581900 YP_917113.1 CDS Pden_3344 NC_008687.1 502687 504177 R PFAM: Sulfate transporter/antisigma-factor antagonist STAS; Xanthine/uracil/vitamin C permease; sulphate transporter; KEGG: rsp:RSP_4197 antisigma-factor antagonist, STAS; sulfate transporter complement(502687..504177) Paracoccus denitrificans PD1222 4581901 YP_917114.1 CDS Pden_3345 NC_008687.1 504673 504870 D PFAM: protein of unknown function DUF1127; KEGG: rde:RD1_2086 hypothetical protein; hypothetical protein 504673..504870 Paracoccus denitrificans PD1222 4581902 YP_917115.1 CDS Pden_3346 NC_008687.1 505006 505248 D hypothetical protein 505006..505248 Paracoccus denitrificans PD1222 4581903 YP_917116.1 CDS Pden_3347 NC_008687.1 505270 505680 D PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase; KEGG: mlo:mlr1197 hypothetical protein; glyoxalase/bleomycin resistance protein/dioxygenase 505270..505680 Paracoccus denitrificans PD1222 4581904 YP_917117.1 CDS Pden_3348 NC_008687.1 505686 506120 D PFAM: Methyltransferase type 11; Methyltransferase type 12; KEGG: gvi:glr1626 hypothetical protein; methyltransferase type 12 505686..506120 Paracoccus denitrificans PD1222 4581905 YP_917118.1 CDS Pden_3349 NC_008687.1 506216 506533 D 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 506216..506533 Paracoccus denitrificans PD1222 4581906 YP_917119.1 CDS Pden_3350 NC_008687.1 506549 507166 D PFAM: plasmid pRiA4b ORF-3 family protein; KEGG: sme:SMa0896 hypothetical protein; plasmid pRiA4b ORF-3 family protein 506549..507166 Paracoccus denitrificans PD1222 4581907 YP_917120.1 CDS Pden_3351 NC_008687.1 507323 508096 R PFAM: Methyltransferase type 11; Methyltransferase type 12; KEGG: bja:blr0060 hypothetical protein; methyltransferase type 11 complement(507323..508096) Paracoccus denitrificans PD1222 4581908 YP_917121.1 CDS Pden_3352 NC_008687.1 508181 508453 D PFAM: protein of unknown function DUF156; KEGG: atc:AGR_C_1623 hypothetical protein; hypothetical protein 508181..508453 Paracoccus denitrificans PD1222 4581909 YP_917122.1 CDS Pden_3353 NC_008687.1 508469 509425 D TIGRFAM: cation diffusion facilitator family transporter; PFAM: cation efflux protein; KEGG: sme:SMc04167 histidine-rich transporter transmembrane protein; cation diffusion facilitator family transporter 508469..509425 Paracoccus denitrificans PD1222 4581910 YP_917123.1 CDS Pden_3354 NC_008687.1 509433 509882 D hypothetical protein 509433..509882 Paracoccus denitrificans PD1222 4581911 YP_917124.1 CDS Pden_3355 NC_008687.1 509912 510370 D PFAM: GCN5-related N-acetyltransferase; KEGG: sal:Sala_0626 gentamicin 3'-N-acetyltransferase; gentamicin 3'-N-acetyltransferase 509912..510370 Paracoccus denitrificans PD1222 4581912 YP_917125.1 CDS Pden_3356 NC_008687.1 510604 511020 D KEGG: mes:Meso_3831 hypothetical protein; hypothetical protein 510604..511020 Paracoccus denitrificans PD1222 4581913 YP_917126.1 CDS Pden_3357 NC_008687.1 511449 512126 D 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 511449..512126 Paracoccus denitrificans PD1222 4581914 YP_917127.1 CDS Pden_3358 NC_008687.1 512201 512491 D hypothetical protein 512201..512491 Paracoccus denitrificans PD1222 4581915 YP_917128.1 CDS Pden_3359 NC_008687.1 512788 513231 D PFAM: GCN5-related N-acetyltransferase; KEGG: atc:AGR_L_1711 acetyltransferase; hypothetical protein 512788..513231 Paracoccus denitrificans PD1222 4581916 YP_917129.1 CDS Pden_3360 NC_008687.1 513239 513475 R hypothetical protein complement(513239..513475) Paracoccus denitrificans PD1222 4581917 YP_917130.1 CDS Pden_3361 NC_008687.1 513986 514396 D 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 513986..514396 Paracoccus denitrificans PD1222 4581918 YP_917131.1 CDS Pden_3362 NC_008687.1 514440 514847 D hypothetical protein 514440..514847 Paracoccus denitrificans PD1222 4581919 YP_917132.1 CDS Pden_3363 NC_008687.1 514954 515157 D hypothetical protein 514954..515157 Paracoccus denitrificans PD1222 4581920 YP_917133.1 CDS Pden_3364 NC_008687.1 515762 515974 D hypothetical protein 515762..515974 Paracoccus denitrificans PD1222 4581921 YP_917134.1 CDS Pden_3365 NC_008687.1 515995 516369 R KEGG: mes:Meso_3838 hypothetical protein; hypothetical protein complement(515995..516369) Paracoccus denitrificans PD1222 4581922 YP_917135.1 CDS Pden_3366 NC_008687.1 516539 516805 R hypothetical protein complement(516539..516805) Paracoccus denitrificans PD1222 4581923 YP_917136.1 CDS Pden_3367 NC_008687.1 516952 517215 R KEGG: nwi:Nwi_0844 hypothetical protein; hypothetical protein complement(516952..517215) Paracoccus denitrificans PD1222 4581924 YP_917137.1 CDS Pden_3368 NC_008687.1 517401 517637 R PFAM: helix-turn-helix domain protein; KEGG: mlo:msr6108 transcriptional regulator; XRE family transcriptional regulator complement(517401..517637) Paracoccus denitrificans PD1222 4581925 YP_917138.1 CDS Pden_3369 NC_008687.1 517829 518098 D KEGG: nwi:Nwi_0845 hypothetical protein; hypothetical protein 517829..518098 Paracoccus denitrificans PD1222 4581926 YP_917139.1 CDS Pden_3370 NC_008687.1 518095 518964 D KEGG: nwi:Nwi_0846 possible replication protein A; replication protein A 518095..518964 Paracoccus denitrificans PD1222 4581927 YP_917140.1 CDS Pden_3371 NC_008687.1 519220 519720 D KEGG: mes:Meso_2334 hypothetical protein; hypothetical protein 519220..519720 Paracoccus denitrificans PD1222 4581928 YP_917141.1 CDS Pden_3372 NC_008687.1 519717 521225 D PFAM: C-5 cytosine-specific DNA methylase; KEGG: ngo:NGO1894 5-methylcytosine methyltransferase; C-5 cytosine-specific DNA methylase 519717..521225 Paracoccus denitrificans PD1222 4581929 YP_917142.1 CDS Pden_3373 NC_008687.1 521222 521788 D KEGG: mes:Meso_2333 conjugal transfer protein precursor; conjugal transfer protein precursor 521222..521788 Paracoccus denitrificans PD1222 4581930 YP_917143.1 CDS Pden_3374 NC_008687.1 521824 522159 D PFAM: protein of unknown function DUF736; KEGG: mes:Meso_2332 protein of unknown function DUF736; hypothetical protein 521824..522159 Paracoccus denitrificans PD1222 4581931 YP_917144.1 CDS Pden_3375 NC_008687.1 522163 522981 D PFAM: Lytic transglycosylase, catalytic; KEGG: mes:Meso_0517 lytic transglycosylase, catalytic; lytic transglycosylase, catalytic 522163..522981 Paracoccus denitrificans PD1222 4581932 YP_917145.1 CDS Pden_3376 NC_008687.1 523031 523612 D hypothetical protein 523031..523612 Paracoccus denitrificans PD1222 4581933 YP_917146.1 CDS Pden_3377 NC_008687.1 523854 525593 D KEGG: bja:bll0044 hypothetical protein; hypothetical protein 523854..525593 Paracoccus denitrificans PD1222 4581934 YP_917147.1 CDS Pden_3378 NC_008687.1 525662 525913 D 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 525662..525913 Paracoccus denitrificans PD1222 4581935 YP_917148.1 CDS Pden_3379 NC_008687.1 525917 526351 D PFAM: PilT protein domain protein; KEGG: rru:Rru_A0091 PilT protein-like; twitching motility protein PilT 525917..526351 Paracoccus denitrificans PD1222 4581936 YP_917149.1 CDS Pden_3380 NC_008687.1 526562 526813 R KEGG: nmu:Nmul_A0143 ATP-dependent endonuclease of the OLD family-like; hypothetical protein complement(526562..526813) Paracoccus denitrificans PD1222 4581937 YP_917150.1 CDS Pden_3381 NC_008687.1 526818 527030 D PFAM: helix-turn-helix- domain containing protein, AraC type; KEGG: rsp:RSP_3202 transcriptional regulator, AraC family; helix-turn-helix domain-containing protein 526818..527030 Paracoccus denitrificans PD1222 4581938 YP_917151.1 CDS Pden_3382 NC_008687.1 527269 527922 R PFAM: class II aldolase/adducin family protein; KEGG: bja:bll2927 hypothetical protein; class II aldolase/adducin family protein complement(527269..527922) Paracoccus denitrificans PD1222 4581939 YP_917152.1 CDS Pden_3383 NC_008687.1 527919 529178 R PFAM: type III effector Hrp-dependent outers; KEGG: reu:Reut_A1426 type III effector Hrp-dependent outers; Hrp-dependent type III effector protein complement(527919..529178) Paracoccus denitrificans PD1222 4581940 YP_917153.1 CDS Pden_3384 NC_008687.1 529196 530473 R TIGRFAM: TRAP dicarboxylate transporter, DctM subunit; PFAM: TRAP C4-dicarboxylate transport system permease DctM subunit; KEGG: gka:GK1972 transporter; TRAP dicarboxylate transporter, DctM subunit complement(529196..530473) Paracoccus denitrificans PD1222 4581941 YP_917154.1 CDS Pden_3385 NC_008687.1 530470 531030 R PFAM: Tripartite ATP-independent periplasmic transporter, DctQ component; KEGG: msu:MS0052 hypothetical protein; tripartite ATP-independent periplasmic transporter DctQ complement(530470..531030) Paracoccus denitrificans PD1222 4581942 YP_917155.1 CDS Pden_3386 NC_008687.1 531027 531698 R PFAM: cyclase family protein; KEGG: pmu:PM1641 hypothetical Synechocystis sp.; cyclase family protein complement(531027..531698) Paracoccus denitrificans PD1222 4581943 YP_917156.1 CDS Pden_3387 NC_008687.1 531715 532722 R 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 complement(531715..532722) Paracoccus denitrificans PD1222 4581944 YP_917157.1 CDS Pden_3388 NC_008687.1 532760 534163 R PFAM: SAF domain; KEGG: rru:Rru_A3141 homoserine dehydrogenase, NAD-binding; SAF domain-containing protein complement(532760..534163) Paracoccus denitrificans PD1222 4581945 YP_917158.1 CDS Pden_3389 NC_008687.1 534444 535115 D PFAM: regulatory protein GntR, HTH; GntR domain protein; KEGG: sme:SMb20773 transcriptional regulator, GntR family protein; GntR family transcriptional regulator 534444..535115 Paracoccus denitrificans PD1222 4581946 YP_917159.1 CDS Pden_3390 NC_008687.1 535370 538231 R KEGG: ade:Adeh_3797 hypothetical protein; hypothetical protein complement(535370..538231) Paracoccus denitrificans PD1222 4581947 YP_917160.1 CDS Pden_3391 NC_008687.1 538268 539467 R hypothetical protein complement(538268..539467) Paracoccus denitrificans PD1222 4581948 YP_917161.1 CDS Pden_3392 NC_008687.1 539614 539919 R hypothetical protein complement(539614..539919) Paracoccus denitrificans PD1222 4581949 YP_917162.1 CDS Pden_3395 NC_008687.1 540885 541514 D KEGG: sal:Sala_0067 transposase; transposase 540885..541514 Paracoccus denitrificans PD1222 4581951 YP_917163.1 CDS Pden_3396 NC_008687.1 541860 542732 R PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: abo:ABO_1099 transcriptional regulator, LysR family; LysR family transcriptional regulator complement(541860..542732) Paracoccus denitrificans PD1222 4581952 YP_917164.1 CDS Pden_3397 NC_008687.1 542800 543111 D hypothetical protein 542800..543111 Paracoccus denitrificans PD1222 4581953 YP_917165.1 CDS Pden_3398 NC_008687.1 543498 543977 D KEGG: rpb:RPB_3880 twin-arginine translocation pathway signal; twin-arginine translocation pathway signal 543498..543977 Paracoccus denitrificans PD1222 4581954 YP_917166.1 CDS Pden_3399 NC_008687.1 543983 544609 D PFAM: Ferric reductase domain protein transmembrane component, N-terminal domain; KEGG: rde:RD1_1724 hypothetical protein; ferric reductase domain-containing protein 543983..544609 Paracoccus denitrificans PD1222 4581955 YP_917167.1 CDS Pden_3400 NC_008687.1 544753 545640 R 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 complement(544753..545640) Paracoccus denitrificans PD1222 4581956 YP_917168.1 CDS Pden_3401 NC_008687.1 545967 546131 D KEGG: nwi:Nwi_2919 transposase, IS4; transposase, IS4 545967..546131 Paracoccus denitrificans PD1222 4581957 YP_917169.1 CDS Pden_3402 NC_008687.1 546172 547575 R 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 complement(546172..547575) Paracoccus denitrificans PD1222 4581958 YP_917170.1 CDS Pden_3403 NC_008687.1 547568 548272 R PFAM: response regulator receiver; transcriptional regulator domain protein; KEGG: rfr:Rfer_3646 two component transcriptional regulator, winged helix family; two component transcriptional regulator complement(547568..548272) Paracoccus denitrificans PD1222 4581959 YP_917171.1 CDS Pden_3404 NC_008687.1 548443 549684 D PFAM: extracellular solute-binding protein, family 1; KEGG: pub:SAR11_0769 probable binding protein component of ABC sugar transporter; extracellular solute-binding protein 548443..549684 Paracoccus denitrificans PD1222 4581960 YP_917172.1 CDS Pden_3405 NC_008687.1 549751 550623 D 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 549751..550623 Paracoccus denitrificans PD1222 4581961 YP_917173.1 CDS Pden_3406 NC_008687.1 550613 551482 D 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 550613..551482 Paracoccus denitrificans PD1222 4581962 YP_917174.1 CDS Pden_3407 NC_008687.1 551486 552592 D PFAM: ABC transporter related; Transport-associated OB domain protein; SMART: AAA ATPase; KEGG: sme:SMc04393 ATP-binding ABC transporter protein; ABC transporter 551486..552592 Paracoccus denitrificans PD1222 4581963 YP_917175.1 CDS Pden_3408 NC_008687.1 552977 553237 D hypothetical protein 552977..553237 Paracoccus denitrificans PD1222 4581964 YP_917176.1 CDS Pden_3409 NC_008687.1 553476 554615 D PFAM: creatinase; peptidase M24; KEGG: ppu:PP_3667 creatinase; creatinase 553476..554615 Paracoccus denitrificans PD1222 4581965 YP_917177.1 CDS Pden_3410 NC_008687.1 554677 555207 R KEGG: rxy:Rxyl_0459 creatininase; hypothetical protein complement(554677..555207) Paracoccus denitrificans PD1222 4581966 YP_917178.1 CDS Pden_3411 NC_008687.1 555233 556117 R KEGG: ccr:CC1457 flagellin modification protein FlmG; hypothetical protein complement(555233..556117) Paracoccus denitrificans PD1222 4581967 YP_917179.1 CDS Pden_3412 NC_008687.1 556142 557041 R hypothetical protein complement(556142..557041) Paracoccus denitrificans PD1222 4581968 YP_917180.1 CDS Pden_3413 NC_008687.1 557134 557493 R hypothetical protein complement(557134..557493) Paracoccus denitrificans PD1222 4581969 YP_917181.1 CDS Pden_3414 NC_008687.1 558039 558896 R KEGG: rpa:RPA2826 hypothetical protein; hypothetical protein complement(558039..558896) Paracoccus denitrificans PD1222 4581970 YP_917182.1 CDS Pden_3415 NC_008687.1 559011 560171 D PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: atc:AGR_pAT_469 hypothetical protein; LysR family transcriptional regulator 559011..560171 Paracoccus denitrificans PD1222 4581971 YP_917183.1 CDS Pden_3416 NC_008687.1 560290 561237 R PFAM: Acetamidase/Formamidase; KEGG: rsp:RSP_3443 acetamidase/formamidase; acetamidase/formamidase complement(560290..561237) Paracoccus denitrificans PD1222 4581972 YP_917184.1 CDS Pden_3417 NC_008687.1 561264 561575 R hypothetical protein complement(561264..561575) Paracoccus denitrificans PD1222 4581973 YP_917185.1 CDS Pden_3418 NC_008687.1 561585 562298 R PFAM: Dimethylmenaquinone methyltransferase; KEGG: rsp:RSP_3441 hypothetical protein; hypothetical protein complement(561585..562298) Paracoccus denitrificans PD1222 4581974 YP_917186.1 CDS Pden_3419 NC_008687.1 562313 563098 R PFAM: short-chain dehydrogenase/reductase SDR; KEGG: rsp:RSP_3440 short chain dehydrogenase; short-chain dehydrogenase/reductase SDR complement(562313..563098) Paracoccus denitrificans PD1222 4581975 YP_917187.1 CDS Pden_3420 NC_008687.1 563140 564366 R PFAM: aminotransferase, class I and II; KEGG: rsp:RSP_3439 aspartate aminotransferase; class I and II aminotransferase complement(563140..564366) Paracoccus denitrificans PD1222 4581976 YP_917188.1 CDS Pden_3421 NC_008687.1 564392 564814 R PFAM: Endoribonuclease L-PSP; KEGG: rsp:RSP_3438 translation initiation inhibitor; endoribonuclease L-PSP complement(564392..564814) Paracoccus denitrificans PD1222 4581977 YP_917189.1 CDS Pden_3422 NC_008687.1 564811 566043 R catalyzes the formation of oxalozcetate and L-glutamate from L-aspartate and 2-oxoglutarate; aspartate aminotransferase complement(564811..566043) Paracoccus denitrificans PD1222 4581978 YP_917190.1 CDS Pden_3423 NC_008687.1 566180 567067 D PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: rsp:RSP_3436 transcriptional regulator, LysR-family; LysR family transcriptional regulator 566180..567067 Paracoccus denitrificans PD1222 4581979 YP_917191.1 CDS Pden_3424 NC_008687.1 567071 567997 R PFAM: dihydrodipicolinate synthetase; KEGG: rsp:RSP_3456 dihydrodipicolinate synthase; dihydrodipicolinate synthetase complement(567071..567997) Paracoccus denitrificans PD1222 4581980 YP_917192.1 CDS Pden_3425 NC_008687.1 568008 568865 R PFAM: aminotransferase, class IV; KEGG: rsp:RSP_3455 D-alanine aminotransferase; aminotransferase, class IV complement(568008..568865) Paracoccus denitrificans PD1222 4581981 YP_917193.1 CDS Pden_3426 NC_008687.1 568877 569647 R PFAM: LamB/YcsF family protein; KEGG: rsp:RSP_3454 hypothetical protein; LamB/YcsF family protein complement(568877..569647) Paracoccus denitrificans PD1222 4581982 YP_917194.1 CDS Pden_3427 NC_008687.1 569820 570806 D PFAM: TRAP dicarboxylate transporter- DctP subunit; KEGG: rsp:RSP_3453 TRAP-T family transporter, periplasmic binding protein; TRAP dicarboxylate transporter- DctP subunit 569820..570806 Paracoccus denitrificans PD1222 4581983 YP_917195.1 CDS Pden_3428 NC_008687.1 570897 571439 D 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 570897..571439 Paracoccus denitrificans PD1222 4581984 YP_917196.1 CDS Pden_3429 NC_008687.1 571452 572753 D 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 571452..572753 Paracoccus denitrificans PD1222 4581985 YP_917197.1 CDS Pden_3430 NC_008687.1 572761 573534 D PFAM: Allophanate hydrolase subunit 1; KEGG: rsp:RSP_3450 hypothetical protein; allophanate hydrolase subunit 1 572761..573534 Paracoccus denitrificans PD1222 4581986 YP_917198.1 CDS Pden_3431 NC_008687.1 573531 574595 D TIGRFAM: urea amidolyase related protein; PFAM: Allophanate hydrolase subunit 2; KEGG: rsp:RSP_3449 allophanate hydrolase subunit 2; urea amidolyase 573531..574595 Paracoccus denitrificans PD1222 4581987 YP_917199.1 CDS Pden_3432 NC_008687.1 574592 575242 D PFAM: regulatory protein GntR, HTH; GntR domain protein; KEGG: rsp:RSP_3448 transcriptional regulator, GntR-family; GntR family transcriptional regulator 574592..575242 Paracoccus denitrificans PD1222 4581988 YP_917200.1 CDS Pden_3433 NC_008687.1 575239 576189 D 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 575239..576189 Paracoccus denitrificans PD1222 4581989 YP_917201.1 CDS Pden_3434 NC_008687.1 576186 577457 D 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 576186..577457 Paracoccus denitrificans PD1222 4581990 YP_917202.1 CDS Pden_3435 NC_008687.1 577454 578089 D PFAM: regulatory protein GntR, HTH; GntR domain protein; KEGG: rsp:RSP_3445 transcriptional regulator, GntR family; GntR family transcriptional regulator 577454..578089 Paracoccus denitrificans PD1222 4581991 YP_917203.1 CDS Pden_3436 NC_008687.1 578094 579287 D PFAM: peptidase M24; KEGG: rsp:RSP_3444 Xaa-Pro aminopeptidase; peptidase M24 578094..579287 Paracoccus denitrificans PD1222 4581992 YP_917204.1 CDS Pden_3437 NC_008687.1 579311 579997 D PFAM: fumarylacetoacetate (FAA) hydrolase; KEGG: jan:Jann_2909 5-carboxymethyl-2-hydroxymuconate delta-isomerase; fumarylacetoacetate (FAA) hydrolase 579311..579997 Paracoccus denitrificans PD1222 4581993 YP_917205.1 CDS Pden_3438 NC_008687.1 580165 581424 R 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 complement(580165..581424) Paracoccus denitrificans PD1222 4581994 YP_917206.1 CDS Pden_3439 NC_008687.1 581421 582140 R PFAM: response regulator receiver; transcriptional regulator domain protein; KEGG: rpc:RPC_3029 two component transcriptional regulator, winged helix family; two component transcriptional regulator complement(581421..582140) Paracoccus denitrificans PD1222 4581995 YP_917207.1 CDS Pden_3440 NC_008687.1 582349 582957 D hypothetical protein 582349..582957 Paracoccus denitrificans PD1222 4581996 YP_917208.1 CDS Pden_3441 NC_008687.1 583029 583505 D hypothetical protein 583029..583505 Paracoccus denitrificans PD1222 4581997 YP_917209.1 CDS Pden_3442 NC_008687.1 583517 583921 D hypothetical protein 583517..583921 Paracoccus denitrificans PD1222 4581998 YP_917210.1 CDS Pden_3443 NC_008687.1 583981 584262 R hypothetical protein complement(583981..584262) Paracoccus denitrificans PD1222 4581999 YP_917211.1 CDS Pden_3444 NC_008687.1 584310 586316 R PFAM: ABC transporter related; protein of unknown function DUF214; SMART: AAA ATPase; KEGG: rpb:RPB_2235 hypothetical protein; ABC transporter complement(584310..586316) Paracoccus denitrificans PD1222 4582000 YP_917212.1 CDS Pden_3445 NC_008687.1 586309 587514 R 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 complement(586309..587514) Paracoccus denitrificans PD1222 4582001 YP_917213.1 CDS Pden_3446 NC_008687.1 587614 588063 D hypothetical protein 587614..588063 Paracoccus denitrificans PD1222 4582002 YP_917214.1 CDS Pden_3447 NC_008687.1 588344 589516 D 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 588344..589516 Paracoccus denitrificans PD1222 4582003 YP_917215.1 CDS Pden_3448 NC_008687.1 589521 592625 D 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 589521..592625 Paracoccus denitrificans PD1222 4582004 YP_917216.1 CDS Pden_3449 NC_008687.1 592622 593998 D 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 592622..593998 Paracoccus denitrificans PD1222 4582005 YP_917217.1 CDS ampC NC_008687.1 594069 595274 R PFAM: beta-lactamase; KEGG: rsp:RSP_3749 beta-lactamase precursor; beta-lactamase complement(594069..595274) Paracoccus denitrificans PD1222 4582006 YP_917218.1 CDS Pden_3451 NC_008687.1 595356 596231 D PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: sme:SMa2293 probable beta lactamase transcriptional activator; LysR family transcriptional regulator 595356..596231 Paracoccus denitrificans PD1222 4582007 YP_917219.1 CDS Pden_3452 NC_008687.1 596329 596745 D hypothetical protein 596329..596745 Paracoccus denitrificans PD1222 4582008 YP_917220.1 CDS Pden_3453 NC_008687.1 596845 597135 D hypothetical protein 596845..597135 Paracoccus denitrificans PD1222 4582009 YP_917221.1 CDS Pden_3454 NC_008687.1 597192 598448 R PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: rde:RD1_4140 transcriptional regulator, LysR family; LysR family transcriptional regulator complement(597192..598448) Paracoccus denitrificans PD1222 4582010 YP_917222.1 CDS Pden_3455 NC_008687.1 598445 599119 R PFAM: protein of unknown function DUF1028; KEGG: rde:RD1_4139 hypothetical protein; hypothetical protein complement(598445..599119) Paracoccus denitrificans PD1222 4582011 YP_917223.1 CDS Pden_3456 NC_008687.1 599124 599540 R PFAM: Endoribonuclease L-PSP; KEGG: rde:RD1_4138 endoribonuclease L-PSP family protein; endoribonuclease L-PSP complement(599124..599540) Paracoccus denitrificans PD1222 4582012 YP_917224.1 CDS Pden_3457 NC_008687.1 599599 600870 R PFAM: FAD dependent oxidoreductase; KEGG: pau:PA14_71210 monooxygenase; FAD dependent oxidoreductase complement(599599..600870) Paracoccus denitrificans PD1222 4582013 YP_917225.1 CDS Pden_3458 NC_008687.1 601117 602274 D catalyzes the formation of L-ornithine from N(2)-acetyl-L-ornithine; acetylornithine deacetylase 601117..602274 Paracoccus denitrificans PD1222 4582014 YP_917226.1 CDS Pden_3459 NC_008687.1 602523 603659 D 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 602523..603659 Paracoccus denitrificans PD1222 4582015 YP_917227.1 CDS Pden_3460 NC_008687.1 603742 604812 D KEGG: rsp:RSP_1883 ABC polyamine/opine transporter, periplasmic substrate-binding protein; ABC polyamine/opine transporter, periplasmic substrate-binding protein 603742..604812 Paracoccus denitrificans PD1222 4582016 YP_917228.1 CDS Pden_3461 NC_008687.1 604937 606229 D 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 604937..606229 Paracoccus denitrificans PD1222 4582017 YP_917229.1 CDS Pden_3462 NC_008687.1 606235 607188 D 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 606235..607188 Paracoccus denitrificans PD1222 4582018 YP_917230.1 CDS Pden_3463 NC_008687.1 607236 608441 D PFAM: FAD-dependent pyridine nucleotide-disulphide oxidoreductase; KEGG: sil:SPO3737 pyridine nucleotide-disulphide oxidoreductase family protein; FAD-dependent pyridine nucleotide-disulfide oxidoreductase 607236..608441 Paracoccus denitrificans PD1222 4582019 YP_917231.1 CDS Pden_3464 NC_008687.1 608674 609030 R PFAM: ferredoxin; KEGG: sil:SPO0766 iron-sulfur cluster-binding protein; ferredoxin complement(608674..609030) Paracoccus denitrificans PD1222 4582020 YP_917232.1 CDS Pden_3465 NC_008687.1 609104 610258 R PFAM: Rieske [2Fe-2S] domain protein; KEGG: bxe:Bxe_A3468 iron-sulphur rieske protein; Rieske (2Fe-2S) domain-containing protein complement(609104..610258) Paracoccus denitrificans PD1222 4582021 YP_917233.1 CDS Pden_3466 NC_008687.1 610387 611307 D PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: csa:Csal_2385 transcriptional regulator, LysR family; LysR family transcriptional regulator 610387..611307 Paracoccus denitrificans PD1222 4582022 YP_917234.1 CDS Pden_3467 NC_008687.1 611548 612549 R PFAM: proline racemase; KEGG: atc:AGR_L_1800 hypothetical protein; hydroxyproline-2-epimerase complement(611548..612549) Paracoccus denitrificans PD1222 4582023 YP_917235.1 CDS Pden_3468 NC_008687.1 612943 613653 R PFAM: cyclic nucleotide-binding; regulatory protein, Crp; KEGG: sil:SPOA0206 transcriptional regulator, Crp/Fnr family; CRP/FNR family transcriptional regulator complement(612943..613653) Paracoccus denitrificans PD1222 4582024 YP_917236.1 CDS Pden_3469 NC_008687.1 613765 614847 D KEGG: ade:Adeh_2705 response regulator receiver; hypothetical protein 613765..614847 Paracoccus denitrificans PD1222 4582025 YP_917237.1 CDS Pden_3470 NC_008687.1 615004 615549 R KEGG: ret:RHE_PC00193 hypothetical protein; hypothetical protein complement(615004..615549) Paracoccus denitrificans PD1222 4582026 YP_917238.1 CDS Pden_3471 NC_008687.1 615599 616954 R PFAM: TfuA domain protein, core; KEGG: mxa:MXAN_2398 hypothetical protein; TfuA domain-containing protein complement(615599..616954) Paracoccus denitrificans PD1222 4582027 YP_917239.1 CDS Pden_3472 NC_008687.1 616951 618120 R TIGRFAM: uncharacterized domain; PFAM: protein of unknown function DUF181; KEGG: ret:RHE_PE00437 hypothetical protein; hypothetical protein complement(616951..618120) Paracoccus denitrificans PD1222 4582028 YP_917240.1 CDS Pden_3473 NC_008687.1 618747 620537 D 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 618747..620537 Paracoccus denitrificans PD1222 4582029 YP_917241.1 CDS Pden_3474 NC_008687.1 620705 622696 D PFAM: protein of unknown function DUF839; KEGG: rsp:RSP_3051 phosphatase; hypothetical protein 620705..622696 Paracoccus denitrificans PD1222 4582030 YP_917242.1 CDS Pden_3475 NC_008687.1 622786 623484 R PFAM: ThiJ/PfpI domain protein; KEGG: bms:BRA0227 ThiJ/PfpI family protein; ThiJ/PfpI domain-containing protein complement(622786..623484) Paracoccus denitrificans PD1222 4582031 YP_917243.1 CDS Pden_3476 NC_008687.1 623489 624766 R PFAM: NADH:flavin oxidoreductase/NADH oxidase; KEGG: ccr:CC3083 FMN oxidoreductase; NADH:flavin oxidoreductase complement(623489..624766) Paracoccus denitrificans PD1222 4582032 YP_917244.1 CDS Pden_3477 NC_008687.1 624840 625202 D PFAM: regulatory protein, MerR; KEGG: ccr:CC3082 transcriptional regulator, MerR family; MerR family transcriptional regulator 624840..625202 Paracoccus denitrificans PD1222 4582033 YP_917245.1 CDS Pden_3479 NC_008687.1 625891 626646 R PFAM: regulatory proteins, IclR; KEGG: rpc:RPC_0118 transcriptional regulator, IclR family; regulatory proteins, IclR complement(625891..626646) Paracoccus denitrificans PD1222 4582034 YP_917246.1 CDS Pden_3480 NC_008687.1 626754 627746 D 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 626754..627746 Paracoccus denitrificans PD1222 4582035 YP_917247.1 CDS Pden_3481 NC_008687.1 627805 628311 D PFAM: Tripartite ATP-independent periplasmic transporter, DctQ component; KEGG: dvu:DVU0010 TRAP transporter, DctQ subunit; tripartite ATP-independent periplasmic transporter DctQ 627805..628311 Paracoccus denitrificans PD1222 4582036 YP_917248.1 CDS Pden_3482 NC_008687.1 628308 629591 D 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 628308..629591 Paracoccus denitrificans PD1222 4582037 YP_917249.1 CDS Pden_3483 NC_008687.1 629588 630667 D PFAM: dihydroorotate dehydrogenase; KEGG: tac:Ta0404 dihydroorotate oxidase; dihydroorotate dehydrogenase 629588..630667 Paracoccus denitrificans PD1222 4582038 YP_917250.1 CDS Pden_3484 NC_008687.1 630664 631563 D KEGG: pol:Bpro_3857 hypothetical protein; hypothetical protein 630664..631563 Paracoccus denitrificans PD1222 4582039 YP_917251.1 CDS Pden_3485 NC_008687.1 631560 632309 D PFAM: HpcH/HpaI aldolase; KEGG: bxe:Bxe_C0507 HpcH/HpaI aldolase; HpcH/HpaI aldolase 631560..632309 Paracoccus denitrificans PD1222 4582040 YP_917252.1 CDS Pden_3486 NC_008687.1 632340 633242 D KEGG: rpc:RPC_0116 hypothetical protein; hypothetical protein 632340..633242 Paracoccus denitrificans PD1222 4582041 YP_917253.1 CDS Pden_3487 NC_008687.1 633436 634008 R PFAM: regulatory protein, MarR; KEGG: bja:bll4221 transcriptional regulatory protein; MarR family transcriptional regulator complement(633436..634008) Paracoccus denitrificans PD1222 4582042 YP_917254.1 CDS Pden_3488 NC_008687.1 634065 635972 D catalyzes the formation of catechol from phenol; phenol 2-monooxygenase 634065..635972 Paracoccus denitrificans PD1222 4582043 YP_917255.1 CDS Pden_3489 NC_008687.1 635969 636961 R 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 complement(635969..636961) Paracoccus denitrificans PD1222 4582044 YP_917256.1 CDS Pden_3490 NC_008687.1 637053 638222 D catalyzes the formation of protocatechuate from 4-hydroxybenzoate; 4-hydroxybenzoate 3-monooxygenase 637053..638222 Paracoccus denitrificans PD1222 4582045 YP_917257.1 CDS Pden_3491 NC_008687.1 638222 639010 D TIGRFAM: 3-oxoadipate enol-lactonase; PFAM: alpha/beta hydrolase fold; KEGG: jan:Jann_1663 3-oxoadipate enol-lactonase; 3-oxoadipate enol-lactonase 638222..639010 Paracoccus denitrificans PD1222 4582046 YP_917258.1 CDS Pden_3492 NC_008687.1 639003 639434 D TIGRFAM: 4-carboxymuconolactone decarboxylase; PFAM: Carboxymuconolactone decarboxylase; KEGG: sit:TM1040_0559 4-carboxymuconolactone decarboxylase; 4-carboxymuconolactone decarboxylase 639003..639434 Paracoccus denitrificans PD1222 4582047 YP_917259.1 CDS Pden_3493 NC_008687.1 639431 640153 D 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 639431..640153 Paracoccus denitrificans PD1222 4582048 YP_917260.1 CDS Pden_3494 NC_008687.1 640153 640863 D 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 640153..640863 Paracoccus denitrificans PD1222 4582049 YP_917261.1 CDS Pden_3495 NC_008687.1 640856 641701 D PFAM: protein of unknown function DUF849; KEGG: sil:SPOA0042 hypothetical protein; hypothetical protein 640856..641701 Paracoccus denitrificans PD1222 4582050 YP_917262.1 CDS Pden_3496 NC_008687.1 641701 643002 D PFAM: fumarate lyase; KEGG: sil:SPOA0432 3-carboxy-cis,cis-muconate cycloisomerase; fumarate lyase 641701..643002 Paracoccus denitrificans PD1222 4582051 YP_917263.1 CDS Pden_3497 NC_008687.1 643024 644049 D PFAM: TRAP dicarboxylate transporter- DctP subunit; KEGG: eba:ebA5362 predicted TRAP dicarboxylate transporter, DctP subunit; TRAP dicarboxylate transporter- DctP subunit 643024..644049 Paracoccus denitrificans PD1222 4582052 YP_917264.1 CDS Pden_3498 NC_008687.1 644067 644588 D KEGG: eba:ebB188 hypothetical protein; hypothetical protein 644067..644588 Paracoccus denitrificans PD1222 4582053 YP_917265.1 CDS Pden_3499 NC_008687.1 644585 645904 D 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 644585..645904 Paracoccus denitrificans PD1222 4582054 YP_917266.1 CDS Pden_3500 NC_008687.1 645946 646842 R PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: atc:AGR_L_1754 hypothetical protein; LysR family transcriptional regulator complement(645946..646842) Paracoccus denitrificans PD1222 4582055 YP_917267.1 CDS Pden_3501 NC_008687.1 646964 647896 D PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase; KEGG: atc:AGR_L_1752 hypothetical protein; glyoxalase/bleomycin resistance protein/dioxygenase 646964..647896 Paracoccus denitrificans PD1222 4582056 YP_917268.1 CDS Pden_3502 NC_008687.1 647954 648583 D KEGG: rde:RD1_A0097 RC150; hypothetical protein 647954..648583 Paracoccus denitrificans PD1222 4582057 YP_917269.1 CDS Pden_3503 NC_008687.1 648580 648828 D PFAM: protein of unknown function DUF1427; KEGG: rde:RD1_A0096 hypothetical protein; hypothetical protein 648580..648828 Paracoccus denitrificans PD1222 4582058 YP_917270.1 CDS Pden_3504 NC_008687.1 648874 649563 D PFAM: isochorismatase hydrolase; KEGG: rde:RD1_A0094 hydrolase; isochorismatase hydrolase 648874..649563 Paracoccus denitrificans PD1222 4582059 YP_917271.1 CDS Pden_3505 NC_008687.1 649884 650186 D KEGG: rde:RD1_A0090 hypothetical protein; hypothetical protein 649884..650186 Paracoccus denitrificans PD1222 4582060 YP_917272.1 CDS Pden_3506 NC_008687.1 650236 650454 D KEGG: reu:Reut_B4847 DoxX; DoxX 650236..650454 Paracoccus denitrificans PD1222 4582061 YP_917273.1 CDS Pden_3507 NC_008687.1 650698 652557 D PFAM: Amidohydrolase 3; KEGG: reu:Reut_B4849 conserved hypothetical protein PA2699; amidohydrolase 650698..652557 Paracoccus denitrificans PD1222 4582062 YP_917274.1 CDS Pden_3508 NC_008687.1 652649 654229 D PFAM: protein of unknown function DUF894, DitE; major facilitator superfamily MFS_1; KEGG: tbd:Tbd_1578 probable MFS transporter; hypothetical protein 652649..654229 Paracoccus denitrificans PD1222 4582063 YP_917275.1 CDS Pden_3509 NC_008687.1 654270 654662 D PFAM: DoxX family protein; KEGG: mes:Meso_0934 DoxX; DoxX family protein 654270..654662 Paracoccus denitrificans PD1222 4582064 YP_917276.1 CDS Pden_3510 NC_008687.1 654707 655651 D PFAM: Pirin domain protein domain protein; Pirin domain protein; KEGG: sit:TM1040_1889 pirin-like; pirin 654707..655651 Paracoccus denitrificans PD1222 4582065 YP_917277.1 CDS Pden_3511 NC_008687.1 655815 656942 R KEGG: bbr:BB2355 hypothetical protein; hypothetical protein complement(655815..656942) Paracoccus denitrificans PD1222 4582066 YP_917278.1 CDS Pden_3512 NC_008687.1 656939 657409 R PFAM: regulatory protein, MarR; KEGG: gme:Gmet_0359 transcriptional regulator, MarR family; MarR family transcriptional regulator complement(656939..657409) Paracoccus denitrificans PD1222 4582067 YP_917279.1 CDS Pden_3513 NC_008687.1 657528 658811 D PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: mes:Meso_2630 transcriptional regulator, LysR family; LysR family transcriptional regulator 657528..658811 Paracoccus denitrificans PD1222 4582068 YP_917280.1 CDS Pden_3514 NC_008687.1 658965 660347 D PFAM: amidohydrolase; KEGG: mes:Meso_2641 amidohydrolase; allantoinase 658965..660347 Paracoccus denitrificans PD1222 4582069 YP_917281.1 CDS Pden_3515 NC_008687.1 660347 661585 D 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 660347..661585 Paracoccus denitrificans PD1222 4582070 YP_917282.1 CDS Pden_3516 NC_008687.1 661587 662678 D PFAM: protein of unknown function DUF917; KEGG: mes:Meso_2639 protein of unknown function DUF917; hypothetical protein 661587..662678 Paracoccus denitrificans PD1222 4582071 YP_917283.1 CDS Pden_3517 NC_008687.1 662681 664339 D catalyzes the formation of 4-imidazolone-5-propanoate from urocanate during histidine metabolism; urocanate hydratase 662681..664339 Paracoccus denitrificans PD1222 4582072 YP_917284.1 CDS Pden_3518 NC_008687.1 664452 665795 D PFAM: General substrate transporter; major facilitator superfamily MFS_1; KEGG: bur:Bcep18194_B3017 major facilitator superfamily (MFS_1) transporter; major facilitator transporter 664452..665795 Paracoccus denitrificans PD1222 4582073 YP_917285.1 CDS Pden_3519 NC_008687.1 665822 667486 D PFAM: phenylalanine/histidine ammonia-lyase; KEGG: son:SO3057 Pal/histidase family protein; phenylalanine/histidine ammonia-lyase 665822..667486 Paracoccus denitrificans PD1222 4582074 YP_917286.1 CDS Pden_3520 NC_008687.1 667754 668722 D PFAM: helix-turn-helix- domain containing protein, AraC type; KEGG: sme:SMa1749 transcriptional regulator; helix-turn-helix domain-containing protein 667754..668722 Paracoccus denitrificans PD1222 4582075 YP_917287.1 CDS Pden_3521 NC_008687.1 668767 670866 R TIGRFAM: TonB-dependent siderophore receptor; PFAM: TonB-dependent receptor; TonB-dependent receptor, plug; KEGG: sme:SMa1747 ferrichrome-iron receptor; TonB-dependent siderophore receptor complement(668767..670866) Paracoccus denitrificans PD1222 4582076 YP_917288.1 CDS Pden_3522 NC_008687.1 671140 672141 D PFAM: periplasmic binding protein; KEGG: rsp:RSP_3416 ABC Fe+3-siderophore transporter, periplasmic binding protein; periplasmic binding protein 671140..672141 Paracoccus denitrificans PD1222 4582077 YP_917289.1 CDS Pden_3523 NC_008687.1 672138 673163 D PFAM: transport system permease; KEGG: sme:SMa1745 iron uptake protein; transport system permease 672138..673163 Paracoccus denitrificans PD1222 4582078 YP_917290.1 CDS Pden_3524 NC_008687.1 673166 674206 D PFAM: transport system permease; KEGG: sme:SMa1742 iron uptake protein; transport system permease 673166..674206 Paracoccus denitrificans PD1222 4582079 YP_917291.1 CDS Pden_3525 NC_008687.1 674203 675066 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rsp:RSP_3413 ABC Fe+3-siderophore transporter, ATPase subunit; ABC transporter 674203..675066 Paracoccus denitrificans PD1222 4582080 YP_917292.1 CDS Pden_3526 NC_008687.1 675279 676580 R KEGG: pae:PA4155 hypothetical protein; hypothetical protein complement(675279..676580) Paracoccus denitrificans PD1222 4582081 YP_917293.1 CDS Pden_3527 NC_008687.1 676659 678743 R PFAM: TonB-dependent receptor; TonB-dependent receptor, plug; KEGG: rpb:RPB_2695 TonB-dependent receptor; TonB-dependent receptor complement(676659..678743) Paracoccus denitrificans PD1222 4582082 YP_917294.1 CDS Pden_3528 NC_008687.1 678951 679748 D PFAM: regulatory proteins, IclR; KEGG: pfl:PFL_3621 transcriptional regulator, IclR family; regulatory proteins, IclR 678951..679748 Paracoccus denitrificans PD1222 4582083 YP_917295.1 CDS Pden_3529 NC_008687.1 679749 680531 R PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: pau:PA14_10180 ferric enterobactin transport protein FepC; ABC transporter complement(679749..680531) Paracoccus denitrificans PD1222 4582084 YP_917296.1 CDS Pden_3530 NC_008687.1 680760 681563 D PFAM: Siderophore-interacting protein; FAD-binding 9, siderophore-interacting domain protein; KEGG: cgb:cg0054 iron-chelator utilization protein; siderophore-interacting protein 680760..681563 Paracoccus denitrificans PD1222 4582085 YP_917297.1 CDS Pden_3531 NC_008687.1 681573 682511 D with FepCDG is involved in the transport of ferric enterobactin; iron-enterobactin transporter periplasmic binding protein 681573..682511 Paracoccus denitrificans PD1222 4582086 YP_917298.1 CDS Pden_3532 NC_008687.1 682508 683215 D PFAM: transport system permease; KEGG: pfl:PFL_3624 ferric vibriobactin ABC transporter, permease VC0777; transport system permease 682508..683215 Paracoccus denitrificans PD1222 4582087 YP_917299.1 CDS Pden_3533 NC_008687.1 683199 683549 D PFAM: transport system permease; KEGG: pfl:PFL_3624 ferric vibriobactin ABC transporter, permease VC0777; transport system permease 683199..683549 Paracoccus denitrificans PD1222 4582088 YP_917300.1 CDS Pden_3534 NC_008687.1 683546 684598 D PFAM: transport system permease; KEGG: pfl:PFL_3625 ferric vibriobactin ABC transporter, permease VC0778; transport system permease 683546..684598 Paracoccus denitrificans PD1222 4582089 YP_917301.1 CDS Pden_3535 NC_008687.1 684676 685290 R PFAM: Glutathione S-transferase, N-terminal domain; KEGG: sil:SPO0270 glutathione S-transferase family protein; glutathione S-transferase domain-containing protein complement(684676..685290) Paracoccus denitrificans PD1222 4582090 YP_917302.1 CDS Pden_3536 NC_008687.1 685290 686033 R PFAM: regulatory protein GntR, HTH; GntR domain protein; KEGG: pau:PA14_64820 transcriptional regulator; GntR family transcriptional regulator complement(685290..686033) Paracoccus denitrificans PD1222 4582091 YP_917303.1 CDS Pden_3537 NC_008687.1 686155 686913 D 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 686155..686913 Paracoccus denitrificans PD1222 4582092 YP_917304.1 CDS Pden_3538 NC_008687.1 686930 687436 D KEGG: rsp:RSP_0635 TRAP-T family transporter, DctQ (4 TMs) subunit; TRAP dicarboxylate family transporter subunit DctQ 686930..687436 Paracoccus denitrificans PD1222 4582093 YP_917305.1 CDS Pden_3539 NC_008687.1 687446 688756 D 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 687446..688756 Paracoccus denitrificans PD1222 4582094 YP_917306.1 CDS Pden_3540 NC_008687.1 688822 689940 D PFAM: TRAP dicarboxylate transporter- DctP subunit; KEGG: rsp:RSP_0636 TRAP-T family transporter, DctP (periplasmic binding) subunit; TRAP dicarboxylate transporter- DctP subunit 688822..689940 Paracoccus denitrificans PD1222 4582095 YP_917307.1 CDS Pden_3541 NC_008687.1 690013 690750 D PFAM: short-chain dehydrogenase/reductase SDR; KR; KEGG: bxe:Bxe_A1074 3-oxoacyl-(acyl-carrier-protein) reductase; short-chain dehydrogenase/reductase SDR 690013..690750 Paracoccus denitrificans PD1222 4582096 YP_917308.1 CDS Pden_3542 NC_008687.1 690766 691551 D 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 690766..691551 Paracoccus denitrificans PD1222 4582097 YP_917309.1 CDS Pden_3543 NC_008687.1 691538 693247 D PFAM: fumarate reductase/succinate dehydrogenase flavoprotein domain protein; FAD dependent oxidoreductase; KEGG: bja:blr6805 dehydrogenase; fumarate reductase/succinate dehydrogenase flavoprotein domain-containing protein 691538..693247 Paracoccus denitrificans PD1222 4582098 YP_917310.1 CDS Pden_3544 NC_008687.1 693244 693693 D hypothetical protein 693244..693693 Paracoccus denitrificans PD1222 4582099 YP_917311.1 CDS Pden_3545 NC_008687.1 693902 694393 D PFAM: regulatory protein, MarR; KEGG: mlo:mll8302 transcriptional regulator; MarR family transcriptional regulator 693902..694393 Paracoccus denitrificans PD1222 4582100 YP_917312.1 CDS Pden_3546 NC_008687.1 694390 694821 R PFAM: regulatory protein, MarR; KEGG: rde:RD1_3650 transcriptional regulator MarR/EmrR family; MarR family transcriptional regulator complement(694390..694821) Paracoccus denitrificans PD1222 4582101 YP_917313.1 CDS Pden_3547 NC_008687.1 694964 696325 D 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 694964..696325 Paracoccus denitrificans PD1222 4582102 YP_917314.1 CDS Pden_3548 NC_008687.1 696400 697605 D KEGG: sit:TM1040_2622 fumarylacetoacetase; TIGRFAM: fumarylacetoacetase; PFAM: fumarylacetoacetate (FAA) hydrolase; fumarylacetoacetase 696400..697605 Paracoccus denitrificans PD1222 4582103 YP_917315.1 CDS Pden_3549 NC_008687.1 697602 698237 D TIGRFAM: maleylacetoacetate isomerase; PFAM: Glutathione S-transferase, N-terminal domain; KEGG: sme:SMc03206 maleylacetoacetate isomerase (glutathione transferase ZETA 1) protein; maleylacetoacetate isomerase 697602..698237 Paracoccus denitrificans PD1222 4582104 YP_917316.1 CDS Pden_3550 NC_008687.1 698668 699378 D PFAM: acylneuraminate cytidylyltransferase; KEGG: aeh:Mlg_2324 acylneuraminate cytidylyltransferase; acylneuraminate cytidylyltransferase 698668..699378 Paracoccus denitrificans PD1222 4582105 YP_917317.1 CDS Pden_3551 NC_008687.1 699375 700421 D KEGG: ccr:CC2854 flagellin modification protein FlmD; flagellin modification protein FlmD 699375..700421 Paracoccus denitrificans PD1222 4582106 YP_917318.1 CDS Pden_3552 NC_008687.1 700418 701539 D 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 700418..701539 Paracoccus denitrificans PD1222 4582107 YP_917319.1 CDS Pden_3553 NC_008687.1 701536 702444 D 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 701536..702444 Paracoccus denitrificans PD1222 4582108 YP_917320.1 CDS Pden_3554 NC_008687.1 702466 704322 R hypothetical protein complement(702466..704322) Paracoccus denitrificans PD1222 4582109 YP_917321.1 CDS Pden_3555 NC_008687.1 704351 707368 R hypothetical protein complement(704351..707368) Paracoccus denitrificans PD1222 4582110 YP_917322.1 CDS Pden_3556 NC_008687.1 707372 708448 R PFAM: N-acetylneuraminic acid synthase, N-terminal domain; SAF domain; KEGG: mhu:Mhun_3098 N-acylneuraminate-9-phosphate synthase; N-acylneuraminate-9-phosphate synthase complement(707372..708448) Paracoccus denitrificans PD1222 4582111 YP_917323.1 CDS Pden_3557 NC_008687.1 708579 709733 R PFAM: DegT/DnrJ/EryC1/StrS aminotransferase; KEGG: aeh:Mlg_2323 DegT/DnrJ/EryC1/StrS aminotransferase; DegT/DnrJ/EryC1/StrS aminotransferase complement(708579..709733) Paracoccus denitrificans PD1222 4582112 YP_917324.1 CDS Pden_3558 NC_008687.1 709730 710731 R 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 complement(709730..710731) Paracoccus denitrificans PD1222 4582113 YP_917325.1 CDS Pden_3560 NC_008687.1 711428 711823 D KEGG: rso:RS01910 probable transport transmembrane protein; transport transmembrane protein 711428..711823 Paracoccus denitrificans PD1222 4582114 YP_917326.1 CDS Pden_3561 NC_008687.1 712270 713298 R 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 complement(712270..713298) Paracoccus denitrificans PD1222 4582115 YP_917327.1 CDS Pden_3562 NC_008687.1 713407 713730 D PFAM: transposase IS3/IS911 family protein; KEGG: nwi:Nwi_2119 transposase IS3/IS911; transposase IS3/IS911 family protein 713407..713730 Paracoccus denitrificans PD1222 4582116 YP_917328.1 CDS Pden_3564 NC_008687.1 714938 715459 D hypothetical protein 714938..715459 Paracoccus denitrificans PD1222 4582117 YP_917329.1 CDS Pden_3565 NC_008687.1 715570 715953 D KEGG: rsp:RSP_0396 hypothetical protein; hypothetical protein 715570..715953 Paracoccus denitrificans PD1222 4582118 YP_917330.1 CDS Pden_3566 NC_008687.1 716125 716892 D PFAM: response regulator receiver; transcriptional regulator domain protein; KEGG: bja:blr6651 two-component response regulator; two component transcriptional regulator 716125..716892 Paracoccus denitrificans PD1222 4582119 YP_917331.1 CDS Pden_3567 NC_008687.1 716868 717983 R 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 complement(716868..717983) Paracoccus denitrificans PD1222 4582120 YP_917332.1 CDS Pden_3568 NC_008687.1 717980 720604 R 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 complement(717980..720604) Paracoccus denitrificans PD1222 4582121 YP_917333.1 CDS Pden_3569 NC_008687.1 720832 722058 D PFAM: Acetamidase/Formamidase; KEGG: bbr:BB1405 formamidase; formamidase 720832..722058 Paracoccus denitrificans PD1222 4582122 YP_917334.1 CDS Pden_3570 NC_008687.1 722119 722631 D PFAM: AmiS/UreI transporter; KEGG: bpa:BPP1188 transporter protein; AmiS/UreI transporter 722119..722631 Paracoccus denitrificans PD1222 4582123 YP_917335.1 CDS Pden_3571 NC_008687.1 722641 722937 D KEGG: abo:ABO_1977 hypothetical protein; hypothetical protein 722641..722937 Paracoccus denitrificans PD1222 4582124 YP_917336.1 CDS Pden_3572 NC_008687.1 723093 723860 R PFAM: short-chain dehydrogenase/reductase SDR; KR; KEGG: bcn:Bcen_4032 short-chain dehydrogenase/reductase SDR; short-chain dehydrogenase/reductase SDR complement(723093..723860) Paracoccus denitrificans PD1222 4582125 YP_917337.1 CDS Pden_3573 NC_008687.1 723857 724570 R PFAM: regulatory protein GntR, HTH; GntR domain protein; KEGG: reu:Reut_C6220 regulatory protein GntR, HTH:GntR, C-terminal; GntR family transcriptional regulator complement(723857..724570) Paracoccus denitrificans PD1222 4582126 YP_917338.1 CDS Pden_3574 NC_008687.1 724667 725908 D KEGG: rso:RS05343 hypothetical protein; hypothetical protein 724667..725908 Paracoccus denitrificans PD1222 4582127 YP_917339.1 CDS Pden_3575 NC_008687.1 725984 726859 D PFAM: inner-membrane translocator; KEGG: bja:bll3662 ABC transporter permease; inner-membrane translocator 725984..726859 Paracoccus denitrificans PD1222 4582128 YP_917340.1 CDS Pden_3576 NC_008687.1 726867 729383 D PFAM: inner-membrane translocator; ABC transporter related; SMART: AAA ATPase; KEGG: bja:bll3661 ABC transporter ATP-binding/permease; ABC transporter related 726867..729383 Paracoccus denitrificans PD1222 4582129 YP_917341.1 CDS Pden_3577 NC_008687.1 729392 730327 D 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 729392..730327 Paracoccus denitrificans PD1222 4582130 YP_917342.1 CDS Pden_3578 NC_008687.1 730346 731278 D PFAM: protein of unknown function DUF849; KEGG: rde:RD1_4158 hypothetical protein; hypothetical protein 730346..731278 Paracoccus denitrificans PD1222 4582131 YP_917343.1 CDS Pden_3579 NC_008687.1 731289 732599 D catalyzes the oxidation of L-histidinol to L-histidinaldehyde and then to L-histidine in histidine biosynthesis; functions as a dimer; histidinol dehydrogenase 731289..732599 Paracoccus denitrificans PD1222 4582132 YP_917344.1 CDS Pden_3580 NC_008687.1 732596 733354 D PFAM: short-chain dehydrogenase/reductase SDR; KR; KEGG: bxe:Bxe_C0308 short-chain dehydrogenase/reductase; short-chain dehydrogenase/reductase SDR 732596..733354 Paracoccus denitrificans PD1222 4582133 YP_917345.1 CDS Pden_3581 NC_008687.1 733447 733827 R hypothetical protein complement(733447..733827) Paracoccus denitrificans PD1222 4582134 YP_917346.1 CDS Pden_3582 NC_008687.1 733985 734776 R PFAM: regulatory protein, LuxR; Sigma-70, region 4 type 2; KEGG: sme:SMc01630 transcription regulator protein; response regulator receiver protein complement(733985..734776) Paracoccus denitrificans PD1222 4582135 YP_917347.1 CDS Pden_3583 NC_008687.1 734835 735674 D PFAM: short-chain dehydrogenase/reductase SDR; KR; KEGG: sme:SMc00778 oxidoreductase; short-chain dehydrogenase/reductase SDR 734835..735674 Paracoccus denitrificans PD1222 4582136 YP_917348.1 CDS Pden_3584 NC_008687.1 735702 736973 D TIGRFAM: FAD-linked oxidoreductase; PFAM: FAD linked oxidase domain protein; KEGG: sme:SMc00779 FAD-dependent oxidoreductase; FAD-linked oxidoreductase 735702..736973 Paracoccus denitrificans PD1222 4582137 YP_917349.1 CDS Pden_3585 NC_008687.1 737038 738234 D PFAM: Ethanolamine utilisation protein, EutH; KEGG: pfl:PFL_5470 ethanolamine utilization protein EutH; ethanolamine utilisation protein, EutH 737038..738234 Paracoccus denitrificans PD1222 4582138 YP_917350.1 CDS Pden_3586 NC_008687.1 738420 739511 R PFAM: transglutaminase domain protein; KEGG: eba:ebA3478 predicted transglutaminase-like enzyme, cysteine protease; transglutaminase domain-containing protein complement(738420..739511) Paracoccus denitrificans PD1222 4582139 YP_917351.1 CDS Pden_3587 NC_008687.1 739698 740423 R KEGG: atc:AGR_L_572 hypothetical protein; hypothetical protein complement(739698..740423) Paracoccus denitrificans PD1222 4582140 YP_917352.1 CDS Pden_3588 NC_008687.1 740435 741883 R PFAM: amidohydrolase; KEGG: sus:Acid_5787 amidohydrolase; amidohydrolase complement(740435..741883) Paracoccus denitrificans PD1222 4582141 YP_917353.1 CDS Pden_3589 NC_008687.1 741907 742203 R hypothetical protein complement(741907..742203) Paracoccus denitrificans PD1222 4582142 YP_917354.1 CDS Pden_3590 NC_008687.1 742380 742631 R hypothetical protein complement(742380..742631) Paracoccus denitrificans PD1222 4582143 YP_917355.1 CDS Pden_3591 NC_008687.1 742686 742979 D TIGRFAM: addiction module antitoxin, RelB/DinJ family; PFAM: RelB antitoxin; KEGG: sme:SMa0471 DNA-damage-inducibile protein; addiction module antitoxin 742686..742979 Paracoccus denitrificans PD1222 4582144 YP_917356.1 CDS Pden_3592 NC_008687.1 742972 743247 D TIGRFAM: addiction module toxin, RelE/StbE family; PFAM: plasmid stabilization system; KEGG: plu:plu2210 hypothetical protein; addiction module antitoxin 742972..743247 Paracoccus denitrificans PD1222 4582145 YP_917357.1 CDS Pden_3593 NC_008687.1 743455 744669 R PFAM: transposase IS66; KEGG: mag:amb3320 transposase and inactivated derivative; transposase IS66 complement(743455..744669) Paracoccus denitrificans PD1222 4582146 YP_917358.1 CDS Pden_3595 NC_008687.1 745050 745397 R PFAM: IS66 Orf2 family protein; KEGG: pol:Bpro_5536 IS66 Orf2 like; IS66 Orf2 family protein complement(745050..745397) Paracoccus denitrificans PD1222 4582147 YP_917359.1 CDS Pden_3596 NC_008687.1 745691 747589 D TIGRFAM: phage tape measure protein; KEGG: nwi:Nwi_1471 hypothetical protein; phage tape measure protein 745691..747589 Paracoccus denitrificans PD1222 4582148 YP_917360.1 CDS Pden_3597 NC_008687.1 747589 748251 D hypothetical protein 747589..748251 Paracoccus denitrificans PD1222 4582149 YP_917361.1 CDS Pden_3598 NC_008687.1 748251 748835 D hypothetical protein 748251..748835 Paracoccus denitrificans PD1222 4582150 YP_917362.1 CDS Pden_3599 NC_008687.1 748845 749105 R hypothetical protein complement(748845..749105) Paracoccus denitrificans PD1222 4582151 YP_917363.1 CDS Pden_3600 NC_008687.1 749213 749608 D hypothetical protein 749213..749608 Paracoccus denitrificans PD1222 4582152 YP_917364.1 CDS Pden_3601 NC_008687.1 749608 751692 D PFAM: Fibronectin, type III domain protein; KEGG: mlo:mlr8544 hypothetical protein; fibronectin, type III domain-containing protein 749608..751692 Paracoccus denitrificans PD1222 4582153 YP_917365.1 CDS Pden_3602 NC_008687.1 751752 753809 D KEGG: mlo:mlr8029 hypothetical protein; hypothetical protein 751752..753809 Paracoccus denitrificans PD1222 4582154 YP_917366.1 CDS Pden_3603 NC_008687.1 753875 754198 D hypothetical protein 753875..754198 Paracoccus denitrificans PD1222 4582155 YP_917367.1 CDS Pden_3604 NC_008687.1 754198 757080 D hypothetical protein 754198..757080 Paracoccus denitrificans PD1222 4582156 YP_917368.1 CDS Pden_3605 NC_008687.1 757105 757386 D hypothetical protein 757105..757386 Paracoccus denitrificans PD1222 4582157 YP_917369.1 CDS Pden_3606 NC_008687.1 757589 758383 D PFAM: glycoside hydrolase, family 19; Peptidoglycan-binding domain 1 protein; KEGG: sme:SMb20518 hypothetical protein; peptidoglycan binding domain-containing protein 757589..758383 Paracoccus denitrificans PD1222 4582158 YP_917370.1 CDS Pden_3607 NC_008687.1 759034 759303 R hypothetical protein complement(759034..759303) Paracoccus denitrificans PD1222 4582159 YP_917371.1 CDS Pden_3608 NC_008687.1 759414 759689 R hypothetical protein complement(759414..759689) Paracoccus denitrificans PD1222 4582160 YP_917372.1 CDS Pden_3609 NC_008687.1 760497 762914 R 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 complement(760497..762914) Paracoccus denitrificans PD1222 4582161 YP_917373.1 CDS Pden_3610 NC_008687.1 763116 763316 R PFAM: CsbD family protein; KEGG: rpb:RPB_1394 CsbD-like; CsbD family protein complement(763116..763316) Paracoccus denitrificans PD1222 4582162 YP_917374.1 CDS Pden_3611 NC_008687.1 764201 765376 D KEGG: sit:TM1040_0586 conserved hypothetical protein; hypothetical protein 764201..765376 Paracoccus denitrificans PD1222 4582163 YP_917375.1 CDS ileS NC_008687.1 765426 768389 R 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 complement(765426..768389) Paracoccus denitrificans PD1222 4582164 YP_917376.1 CDS Pden_3613 NC_008687.1 768541 769713 D PFAM: monooxygenase, FAD-binding; FAD dependent oxidoreductase; KEGG: jan:Jann_3466 monooxygenase, FAD-binding; monooxygenase, FAD-binding 768541..769713 Paracoccus denitrificans PD1222 4582165 YP_917377.1 CDS Pden_3614 NC_008687.1 769733 770155 D KEGG: sil:SPO3139 hypothetical protein; hypothetical protein 769733..770155 Paracoccus denitrificans PD1222 4582166 YP_917378.1 CDS Pden_3615 NC_008687.1 770204 770527 D PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase; KEGG: jan:Jann_0570 glyoxalase/bleomycin resistance protein/dioxygenase; glyoxalase/bleomycin resistance protein/dioxygenase 770204..770527 Paracoccus denitrificans PD1222 4582167 YP_917379.1 CDS Pden_3616 NC_008687.1 770524 771156 R PFAM: protein of unknown function UPF0126; KEGG: sil:SPO3213 hypothetical protein; hypothetical protein complement(770524..771156) Paracoccus denitrificans PD1222 4582168 YP_917380.1 CDS rnhA NC_008687.1 771153 771620 R An endonuclease that specifically degrades the RNA strand of RNA-DNA hybrids; ribonuclease H complement(771153..771620) Paracoccus denitrificans PD1222 4582169 YP_917381.1 CDS Pden_3618 NC_008687.1 771617 772222 R 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 complement(771617..772222) Paracoccus denitrificans PD1222 4582170 YP_917382.1 CDS ispH NC_008687.1 772316 773266 R 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 complement(772316..773266) Paracoccus denitrificans PD1222 4582171 YP_917383.1 CDS Pden_3620 NC_008687.1 773306 773869 R catalyzes a salvage reaction resulting in the formation of AMP which is metabolically less costly than a de novo synthesis; adenine phosphoribosyltransferase complement(773306..773869) Paracoccus denitrificans PD1222 4582172 YP_917384.1 CDS Pden_3621 NC_008687.1 773869 774531 R KEGG: sit:TM1040_2319 conserved hypothetical protein; hypothetical protein complement(773869..774531) Paracoccus denitrificans PD1222 4582173 YP_917385.1 CDS Pden_3622 NC_008687.1 774687 775247 D PFAM: GCN5-related N-acetyltransferase; KEGG: sil:SPO3055 acetyltransferase, GNAT family; N-acetyltransferase GCN5 774687..775247 Paracoccus denitrificans PD1222 4582174 YP_917386.1 CDS Pden_3623 NC_008687.1 775235 775804 R inactivates vertebrate C-type lysozyme; C-lysozyme inhibitor complement(775235..775804) Paracoccus denitrificans PD1222 4582175 YP_917387.1 CDS Pden_3624 NC_008687.1 775896 776762 D KEGG: rde:RD1_2154 hypothetical protein; hypothetical protein 775896..776762 Paracoccus denitrificans PD1222 4582176 YP_917388.1 CDS Pden_3625 NC_008687.1 776774 778309 R SMART: AAA ATPase; KEGG: jan:Jann_0847 ATPase; ATPase AAA complement(776774..778309) Paracoccus denitrificans PD1222 4582177 YP_917389.1 CDS Pden_3626 NC_008687.1 778453 778971 R PFAM: regulatory protein, AsnC/Lrp family; KEGG: rde:RD1_1000 transcriptional regulator, AsnC family; AsnC family transcriptional regulator complement(778453..778971) Paracoccus denitrificans PD1222 4582178 YP_917390.1 CDS Pden_3627 NC_008687.1 778997 779587 D PFAM: Lysine exporter protein (LYSE/YGGA); KEGG: sal:Sala_1362 lysine exporter protein (LysE/YggA); lysine exporter protein LysE/YggA 778997..779587 Paracoccus denitrificans PD1222 4582179 YP_917391.1 CDS Pden_3628 NC_008687.1 779574 780452 R PFAM: protein of unknown function DUF6, transmembrane; KEGG: rpe:RPE_0156 protein of unknown function DUF6, transmembrane; hypothetical protein complement(779574..780452) Paracoccus denitrificans PD1222 4582180 YP_917392.1 CDS hemE NC_008687.1 780469 781497 R catalyzes the formation of coproporphyrinogen from uroporphyrinogen III; uroporphyrinogen decarboxylase complement(780469..781497) Paracoccus denitrificans PD1222 4582181 YP_917393.1 CDS hemC NC_008687.1 781573 782514 D transformation of porphobilinogen to hydroxymethylbilane in porphyrin biosynthesis; porphobilinogen deaminase 781573..782514 Paracoccus denitrificans PD1222 4582182 YP_917394.1 CDS Pden_3631 NC_008687.1 782511 783443 R TIGRFAM: cobalamin biosynthesis protein CobD; PFAM: cobalamin biosynthesis protein CbiB; KEGG: rsp:RSP_0430 cobalamin biosynthesis protein CobD; cobalamin biosynthesis protein CobD complement(782511..783443) Paracoccus denitrificans PD1222 4582183 YP_917395.1 CDS Pden_3632 NC_008687.1 783440 784039 R PFAM: Phosphoglycerate mutase; KEGG: rpa:RPA0993 possible alpha-ribazole-5'-phosphate phosphatase CobC (vit B12 synthesis); phosphoglycerate mutase complement(783440..784039) Paracoccus denitrificans PD1222 4582184 YP_917396.1 CDS Pden_3633 NC_008687.1 784178 785338 D PFAM: acyl-CoA dehydrogenase domain protein; Acyl-CoA dehydrogenase, type 2, C-terminal domain; KEGG: sil:SPO2793 isovaleryl-CoA dehydrogenase; acyl-CoA dehydrogenase 784178..785338 Paracoccus denitrificans PD1222 4582185 YP_917397.1 CDS Pden_3634 NC_008687.1 785338 785877 D PFAM: protein of unknown function DUF1311; KEGG: mmr:Mmar10_1738 protein of unknown function DUF1311; hypothetical protein 785338..785877 Paracoccus denitrificans PD1222 4582186 YP_917398.1 CDS Pden_3635 NC_008687.1 785895 786359 D PFAM: protein of unknown function DUF1311; hypothetical protein 785895..786359 Paracoccus denitrificans PD1222 4582187 YP_917399.1 CDS Pden_3636 NC_008687.1 786419 787054 R PFAM: OmpW family protein; KEGG: xcb:XC_0970 outer membrane protein; OmpW family protein complement(786419..787054) Paracoccus denitrificans PD1222 4582188 YP_917400.1 CDS Pden_3637 NC_008687.1 787177 788781 D PFAM: carboxyl transferase; KEGG: sit:TM1040_0737 propionyl-CoA carboxylase; propionyl-CoA carboxylase 787177..788781 Paracoccus denitrificans PD1222 4582189 YP_917401.1 CDS Pden_3638 NC_008687.1 788787 789287 D PFAM: Appr-1-p processing domain protein; KEGG: cvi:CV3563 hypothetical protein; appr-1-p processing domain-containing protein 788787..789287 Paracoccus denitrificans PD1222 4582190 YP_917402.1 CDS Pden_3639 NC_008687.1 789367 791295 D 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 789367..791295 Paracoccus denitrificans PD1222 4582191 YP_917403.1 CDS Pden_3640 NC_008687.1 791292 791945 D PFAM: Glutathione S-transferase, N-terminal domain; KEGG: jan:Jann_1148 glutathione S-transferase-like; glutathione S-transferase domain-containing protein 791292..791945 Paracoccus denitrificans PD1222 4582192 YP_917404.1 CDS Pden_3641 NC_008687.1 791932 792801 D catalyzes the formation of acetoacetate and acetyl-CoA from 3-hydroxy-3-methylglutaryl-CoA; hydroxymethylglutaryl-CoA lyase 791932..792801 Paracoccus denitrificans PD1222 4582193 YP_917405.1 CDS Pden_3642 NC_008687.1 792801 793583 D Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA; enoyl-CoA hydratase 792801..793583 Paracoccus denitrificans PD1222 4582194 YP_917406.1 CDS Pden_3643 NC_008687.1 793859 795055 D PFAM: major facilitator superfamily MFS_1; KEGG: bja:blr4870 MFS permease; major facilitator transporter 793859..795055 Paracoccus denitrificans PD1222 4582195 YP_917407.1 CDS Pden_3644 NC_008687.1 794966 795748 R KEGG: rde:RD1_0624 hypothetical protein; hypothetical protein complement(794966..795748) Paracoccus denitrificans PD1222 4582196 YP_917408.1 CDS Pden_3645 NC_008687.1 795841 796083 D PFAM: protein of unknown function DUF465; KEGG: bms:BRA0175 hypothetical protein; hypothetical protein 795841..796083 Paracoccus denitrificans PD1222 4582197 YP_917409.1 CDS Pden_3646 NC_008687.1 796319 796765 D PFAM: heat shock protein Hsp20; KEGG: sil:SPO3484 heat shock protein, Hsp20 family; heat shock protein Hsp20 796319..796765 Paracoccus denitrificans PD1222 4582198 YP_917410.1 CDS recR NC_008687.1 796871 797470 R involved in a recombinational process of DNA repair, independent of the recBC complex; recombination protein RecR complement(796871..797470) Paracoccus denitrificans PD1222 4582199 YP_917411.1 CDS Pden_3648 NC_008687.1 797471 797812 R PFAM: conserved hypothetical protein 103; KEGG: jan:Jann_3877 conserved hypothetical protein 103; hypothetical protein complement(797471..797812) Paracoccus denitrificans PD1222 4582200 YP_917412.1 CDS Pden_3649 NC_008687.1 797816 799594 R 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 complement(797816..799594) Paracoccus denitrificans PD1222 4582201 YP_917413.1 CDS Pden_3650 NC_008687.1 799654 799950 R KEGG: bmb:BruAb1_1279 hypothetical protein; hypothetical protein complement(799654..799950) Paracoccus denitrificans PD1222 4582202 YP_917414.1 CDS Pden_3651 NC_008687.1 800145 800831 R porin involved in osmoregulation allowing water to move into and out of the cell in response to osmotic pressure; aquaporin Z complement(800145..800831) Paracoccus denitrificans PD1222 4582203 YP_917415.1 CDS Pden_3652 NC_008687.1 800979 802793 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rsp:RSP_2717 UUP ATPase; ABC transporter 800979..802793 Paracoccus denitrificans PD1222 4582204 YP_917416.1 CDS Pden_3653 NC_008687.1 802948 803190 D 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 802948..803190 Paracoccus denitrificans PD1222 4582205 YP_917417.1 CDS groEL NC_008687.1 804012 805649 R 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 complement(804012..805649) Paracoccus denitrificans PD1222 4582206 YP_917418.1 CDS Pden_3655 NC_008687.1 806209 807537 D PFAM: glycosyl transferase, group 1; KEGG: jan:Jann_4272 glycosyl transferase, group 1; group 1 glycosyl transferase 806209..807537 Paracoccus denitrificans PD1222 4582207 YP_917419.1 CDS Pden_3656 NC_008687.1 807534 808592 D PFAM: GumN family protein; KEGG: rsp:RSP_2309 hypothetical protein; GumN family protein 807534..808592 Paracoccus denitrificans PD1222 4582208 YP_917420.1 CDS Pden_3657 NC_008687.1 808582 808917 D KEGG: sme:SMc01433 hypothetical protein; hypothetical protein 808582..808917 Paracoccus denitrificans PD1222 4582209 YP_917421.1 CDS Pden_3658 NC_008687.1 808917 809558 D PFAM: protein of unknown function DUF1345; KEGG: sme:SMc01272 hypothetical protein; hypothetical protein 808917..809558 Paracoccus denitrificans PD1222 4582210 YP_917422.1 CDS Pden_3659 NC_008687.1 809625 810545 D catalyzes the hydrolysis of pyrophosphate to phosphate; manganese-dependent inorganic pyrophosphatase 809625..810545 Paracoccus denitrificans PD1222 4582211 YP_917423.1 CDS Pden_3660 NC_008687.1 810561 811430 D 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 810561..811430 Paracoccus denitrificans PD1222 4582212 YP_917424.1 CDS Pden_3661 NC_008687.1 811536 811982 D PFAM: MaoC domain protein dehydratase; KEGG: rsp:RSP_2305 MaoC family protein; dehydratase 811536..811982 Paracoccus denitrificans PD1222 4582213 YP_917425.1 CDS Pden_3662 NC_008687.1 812015 812944 D 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 812015..812944 Paracoccus denitrificans PD1222 4582214 YP_917426.1 CDS Pden_3663 NC_008687.1 812944 813384 D PFAM: protein of unknown function UPF0153; KEGG: sil:SPO3155 hypothetical protein; hypothetical protein 812944..813384 Paracoccus denitrificans PD1222 4582215 YP_917427.1 CDS Pden_3664 NC_008687.1 813381 814424 D PFAM: aromatic amino acid beta-eliminating lyase/threonine aldolase; KEGG: rsp:RSP_2302 low specificity L-threonine aldolase; threonine aldolase 813381..814424 Paracoccus denitrificans PD1222 4582216 YP_917428.1 CDS Pden_3665 NC_008687.1 814421 814840 R PFAM: CinA domain protein; KEGG: rde:RD1_2769 competence/damage-inducible protein CinA; CinA domain-containing protein complement(814421..814840) Paracoccus denitrificans PD1222 4582217 YP_917429.1 CDS Pden_3666 NC_008687.1 814885 815385 R PFAM: phosphatidylglycerophosphatase A; KEGG: rde:RD1_2768 phosphatidylglycerophosphatase A; phosphatidylglycerophosphatase A complement(814885..815385) Paracoccus denitrificans PD1222 4582218 YP_917430.1 CDS Pden_3667 NC_008687.1 815398 816633 R 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 complement(815398..816633) Paracoccus denitrificans PD1222 4582219 YP_917431.1 CDS Pden_3668 NC_008687.1 816691 817416 D KEGG: rsp:RSP_0359 ribose-5-phosphate isomerase; TIGRFAM: ribose 5-phosphate isomerase; PFAM: Ribose 5-phosphate isomerase; ribose 5-phosphate isomerase 816691..817416 Paracoccus denitrificans PD1222 4582220 YP_917432.1 CDS Pden_3669 NC_008687.1 817413 818813 D 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 817413..818813 Paracoccus denitrificans PD1222 4582221 YP_917433.1 CDS Pden_3670 NC_008687.1 818872 820071 D TIGRFAM: HflK protein; PFAM: band 7 protein; KEGG: rsp:RSP_0357 probable HflK protein; HflK protein 818872..820071 Paracoccus denitrificans PD1222 4582222 YP_917434.1 CDS Pden_3671 NC_008687.1 820071 821180 D TIGRFAM: HflC protein; PFAM: band 7 protein; KEGG: rsp:RSP_0356 probable HflC protein; HflC protein 820071..821180 Paracoccus denitrificans PD1222 4582223 YP_917435.1 CDS Pden_3672 NC_008687.1 821309 822499 R PFAM: protein of unknown function UPF0118; KEGG: rsp:RSP_1564 transmembrane transport protein; hypothetical protein complement(821309..822499) Paracoccus denitrificans PD1222 4582224 YP_917436.1 CDS Pden_3673 NC_008687.1 822864 823505 D PFAM: TENA/THI-4 domain protein; KEGG: ppu:PP_3185 pet18 protein; TenA family transcription regulator 822864..823505 Paracoccus denitrificans PD1222 4582225 YP_917437.1 CDS Pden_3674 NC_008687.1 823509 823982 R PFAM: NUDIX hydrolase; KEGG: sco:SCO5600 hypothetical protein; NUDIX hydrolase complement(823509..823982) Paracoccus denitrificans PD1222 4582226 YP_917438.1 CDS Pden_3675 NC_008687.1 824056 824379 R KEGG: sit:TM1040_0507 conserved hypothetical protein; hypothetical protein complement(824056..824379) Paracoccus denitrificans PD1222 4582227 YP_917439.1 CDS Pden_3676 NC_008687.1 824528 825211 D PFAM: protein of unknown function DUF45; KEGG: rsp:RSP_0982 zinc metallopeptidase-like protein; hypothetical protein 824528..825211 Paracoccus denitrificans PD1222 4582228 YP_917440.1 CDS Pden_3677 NC_008687.1 825257 825901 D PFAM: regulatory protein GntR, HTH; GntR domain protein; KEGG: rsp:RSP_0981 transcriptional regulator, GntR family; GntR family transcriptional regulator 825257..825901 Paracoccus denitrificans PD1222 4582229 YP_917441.1 CDS Pden_3678 NC_008687.1 825984 827300 R catalyzes the formation of L-aspartate 4-semialdehyde from L-homoserine; homoserine dehydrogenase complement(825984..827300) Paracoccus denitrificans PD1222 4582230 YP_917442.1 CDS Pden_3679 NC_008687.1 827368 827901 R KEGG: syf:Synpcc7942_1655 hypothetical protein; hypothetical protein complement(827368..827901) Paracoccus denitrificans PD1222 4582231 YP_917443.1 CDS Pden_3680 NC_008687.1 828021 828509 R PFAM: GCN5-related N-acetyltransferase; KEGG: rsp:RSP_0784 acetyltransferase, GNAT family; N-acetyltransferase GCN5 complement(828021..828509) Paracoccus denitrificans PD1222 4582232 YP_917444.1 CDS Pden_3681 NC_008687.1 828616 830760 R MDM; functions in conversion of succinate to propionate; methylmalonyl-CoA mutase complement(828616..830760) Paracoccus denitrificans PD1222 4582233 YP_917445.1 CDS Pden_3682 NC_008687.1 830818 831345 D KEGG: sil:SPO1103 hypothetical protein; hypothetical protein 830818..831345 Paracoccus denitrificans PD1222 4582234 YP_917446.1 CDS Pden_3683 NC_008687.1 831593 832252 R hypothetical protein complement(831593..832252) Paracoccus denitrificans PD1222 4582235 YP_917447.1 CDS Pden_3684 NC_008687.1 832302 834359 R 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 complement(832302..834359) Paracoccus denitrificans PD1222 4582236 YP_917448.1 CDS Pden_3685 NC_008687.1 834756 835001 R hypothetical protein complement(834756..835001) Paracoccus denitrificans PD1222 4582237 YP_917449.1 CDS Pden_3686 NC_008687.1 835147 835560 R KEGG: rsp:RSP_2190 hypothetical protein; hypothetical protein complement(835147..835560) Paracoccus denitrificans PD1222 4582238 YP_917450.1 CDS Pden_3687 NC_008687.1 835970 836623 R KEGG: rsp:RSP_6040 hypothetical protein; hypothetical protein complement(835970..836623) Paracoccus denitrificans PD1222 4582239 YP_917451.1 CDS Pden_3688 NC_008687.1 836649 838181 R PFAM: carboxyl transferase; KEGG: rsp:RSP_2189 propionyl-CoA carboxylase beta chain; carboxyl transferase complement(836649..838181) Paracoccus denitrificans PD1222 4582240 YP_917452.1 CDS Pden_3689 NC_008687.1 838262 839359 D KEGG: sil:SPO2670 alanine racemase; TIGRFAM: alanine racemase; PFAM: alanine racemase domain protein; alanine racemase 838262..839359 Paracoccus denitrificans PD1222 4582241 YP_917453.1 CDS Pden_3690 NC_008687.1 839356 840114 D PFAM: protein of unknown function DUF140; KEGG: rsp:RSP_2459 ABC transporter, inner membrane subunit; hypothetical protein 839356..840114 Paracoccus denitrificans PD1222 4582242 YP_917454.1 CDS Pden_3691 NC_008687.1 840114 840851 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rsp:RSP_2458 ABC transporter, ATPase subunit; ABC transporter 840114..840851 Paracoccus denitrificans PD1222 4582243 YP_917455.1 CDS Pden_3692 NC_008687.1 840967 842094 D PFAM: PhoH family protein; KEGG: rsp:RSP_3599 hypothetical protein; PhoH family protein 840967..842094 Paracoccus denitrificans PD1222 4582244 YP_917456.1 CDS Pden_3693 NC_008687.1 842087 842611 D PFAM: protein of unknown function UPF0054; KEGG: rsp:RSP_3598 hypothetical protein; hypothetical protein 842087..842611 Paracoccus denitrificans PD1222 4582245 YP_917457.1 CDS Pden_3694 NC_008687.1 842608 843540 D PFAM: CBS domain containing protein; transporter-associated region; KEGG: rsp:RSP_3597 CorC/HlyC family protein with CBS domains; hypothetical protein 842608..843540 Paracoccus denitrificans PD1222 4582246 YP_917458.1 CDS Pden_3695 NC_008687.1 843547 844356 R PFAM: GCN5-related N-acetyltransferase; Antibiotic biosynthesis monooxygenase; KEGG: aba:Acid345_3954 GCN5-related N-acetyltransferase; N-acetyltransferase GCN5 complement(843547..844356) Paracoccus denitrificans PD1222 4582247 YP_917459.1 CDS guaA NC_008687.1 844552 846111 R contains glutamine-hydrolyzing domain and glutamine amidotransferase; GMP-binding domain; functions to produce GMP from XMP in the IMP pathway; GMP synthase complement(844552..846111) Paracoccus denitrificans PD1222 4582248 YP_917460.1 CDS Pden_3697 NC_008687.1 846293 846904 R PFAM: thiamine monophosphate synthase; KEGG: rsp:RSP_3828 thiamine-phosphate pyrophosphorylase; thiamine monophosphate synthase complement(846293..846904) Paracoccus denitrificans PD1222 4582249 YP_917461.1 CDS Pden_3698 NC_008687.1 846979 847719 D TIGRFAM: RNA methyltransferase, TrmH family, group 1; PFAM: tRNA/rRNA methyltransferase (SpoU); KEGG: rsp:RSP_3829 tRNA/rRNA methyltransferase (SpoU); RNA methyltransferase 846979..847719 Paracoccus denitrificans PD1222 4582250 YP_917462.1 CDS Pden_3699 NC_008687.1 847745 848920 D PFAM: cytochrome oxidase assembly; KEGG: sit:TM1040_1335 cytochrome oxidase assembly; cytochrome oxidase assembly 847745..848920 Paracoccus denitrificans PD1222 4582251 YP_917463.1 CDS Pden_3700 NC_008687.1 848917 850389 D PFAM: peptidase M32, carboxypeptidase Taq metallopeptidase; KEGG: rsp:RSP_3832 thermostable carboxypeptidase 1; carboxypeptidase Taq 848917..850389 Paracoccus denitrificans PD1222 4582252 YP_917464.1 CDS Pden_3701 NC_008687.1 850505 851842 D 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 850505..851842 Paracoccus denitrificans PD1222 4582253 YP_917465.1 CDS Pden_3702 NC_008687.1 851875 853206 R PFAM: glutamine synthetase, catalytic region; KEGG: rsp:RSP_0375 probable glutamine synthetase; glutamate--ammonia ligase complement(851875..853206) Paracoccus denitrificans PD1222 4582254 YP_917466.1 CDS Pden_3703 NC_008687.1 853210 854037 R 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 complement(853210..854037) Paracoccus denitrificans PD1222 4582255 YP_917467.1 CDS Pden_3704 NC_008687.1 854034 854915 R 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 complement(854034..854915) Paracoccus denitrificans PD1222 4582256 YP_917468.1 CDS Pden_3705 NC_008687.1 854964 855686 R 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 complement(854964..855686) Paracoccus denitrificans PD1222 4582257 YP_917469.1 CDS Pden_3706 NC_008687.1 855711 856532 R PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rsp:RSP_0371 ABC basic amino acid transporter, ATPase subunit; ABC transporter complement(855711..856532) Paracoccus denitrificans PD1222 4582258 YP_917470.1 CDS Pden_3707 NC_008687.1 856657 857118 R PFAM: protein of unknown function DUF1332; KEGG: sil:SPO1309 hypothetical protein; hypothetical protein complement(856657..857118) Paracoccus denitrificans PD1222 4582259 YP_917471.1 CDS Pden_3708 NC_008687.1 857171 857467 R PFAM: protein of unknown function DUF1330; KEGG: sit:TM1040_1707 protein of unknown function DUF1330; hypothetical protein complement(857171..857467) Paracoccus denitrificans PD1222 4582260 YP_917472.1 CDS Pden_3709 NC_008687.1 857539 858447 R PFAM: protein of unknown function DUF344; KEGG: sme:SMa0172 hypothetical protein; hypothetical protein complement(857539..858447) Paracoccus denitrificans PD1222 4582261 YP_917473.1 CDS Pden_3710 NC_008687.1 858511 858966 R hypothetical protein complement(858511..858966) Paracoccus denitrificans PD1222 4582262 YP_917474.1 CDS pyrG NC_008687.1 859014 860657 R 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 complement(859014..860657) Paracoccus denitrificans PD1222 4582263 YP_917475.1 CDS secG NC_008687.1 860806 861336 R TIGRFAM: preprotein translocase, SecG subunit; PFAM: Preprotein translocase SecG subunit; KEGG: rsp:RSP_0367 preprotein translocase SecG subunit; preprotein translocase subunit SecG complement(860806..861336) Paracoccus denitrificans PD1222 4582264 YP_917476.1 CDS Pden_3713 NC_008687.1 861405 862838 D 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 861405..862838 Paracoccus denitrificans PD1222 4582265 YP_917477.1 CDS Pden_3714 NC_008687.1 862835 863545 R PFAM: short-chain dehydrogenase/reductase SDR; KEGG: rsp:RSP_2453 oxidoreductase (NAD/NADP dependent); short-chain dehydrogenase/reductase SDR complement(862835..863545) Paracoccus denitrificans PD1222 4582266 YP_917478.1 CDS Pden_3715 NC_008687.1 863640 864020 R PFAM: protein of unknown function DUF1284; KEGG: wol:WD1205 hypothetical protein; hypothetical protein complement(863640..864020) Paracoccus denitrificans PD1222 4582267 YP_917479.1 CDS Pden_3716 NC_008687.1 864089 865381 R KEGG: sit:TM1040_1132 citrate synthase I; TIGRFAM: citrate synthase I; PFAM: Citrate synthase; citrate synthase I complement(864089..865381) Paracoccus denitrificans PD1222 4582268 YP_917480.1 CDS gltX NC_008687.1 865436 866842 R Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation; glutamyl-tRNA synthetase complement(865436..866842) Paracoccus denitrificans PD1222 4582269 YP_917481.1 CDS Pden_3718 NC_008687.1 866992 869145 D PFAM: ComEC/Rec2-related protein; KEGG: sil:SPO2155 competence protein; ComEC/Rec2-like protein 866992..869145 Paracoccus denitrificans PD1222 4582270 YP_917482.1 CDS Pden_3719 NC_008687.1 869183 869752 D PFAM: Heme NO binding domain protein; KEGG: rsp:RSP_6114 hypothetical protein; heme NO binding domain-containing protein 869183..869752 Paracoccus denitrificans PD1222 4582271 YP_917483.1 CDS Pden_3720 NC_008687.1 869749 870711 D TIGRFAM: diguanylate cyclase; PFAM: GGDEF domain containing protein; KEGG: rsp:RSP_0410 sensor diguanylate cyclase (GGDEF); diguanylate cyclase 869749..870711 Paracoccus denitrificans PD1222 4582272 YP_917484.1 CDS Pden_3721 NC_008687.1 870984 871859 D KEGG: sit:TM1040_0587 conserved hypothetical protein; hypothetical protein 870984..871859 Paracoccus denitrificans PD1222 4582273 YP_917485.1 CDS Pden_3722 NC_008687.1 871922 872185 D hypothetical protein 871922..872185 Paracoccus denitrificans PD1222 4582274 YP_917486.1 CDS Pden_3723 NC_008687.1 872182 872424 D hypothetical protein 872182..872424 Paracoccus denitrificans PD1222 4582275 YP_917487.1 CDS Pden_3724 NC_008687.1 872490 873362 D 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 872490..873362 Paracoccus denitrificans PD1222 4582276 YP_917488.1 CDS tsf NC_008687.1 873445 874335 R 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 complement(873445..874335) Paracoccus denitrificans PD1222 4582277 YP_917489.1 CDS rpsB NC_008687.1 874433 875218 R 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 complement(874433..875218) Paracoccus denitrificans PD1222 4582278 YP_917490.1 CDS Pden_3727 NC_008687.1 875753 875902 D hypothetical protein 875753..875902 Paracoccus denitrificans PD1222 4582279 YP_917491.1 CDS Pden_3728 NC_008687.1 876103 877131 R PFAM: phage integrase family protein; KEGG: sit:TM1040_1692 phage integrase; phage integrase family protein complement(876103..877131) Paracoccus denitrificans PD1222 4582280 YP_917492.1 CDS Pden_3729 NC_008687.1 877128 877334 R hypothetical protein complement(877128..877334) Paracoccus denitrificans PD1222 4582281 YP_917493.1 CDS Pden_3730 NC_008687.1 877335 877580 R hypothetical protein complement(877335..877580) Paracoccus denitrificans PD1222 4582282 YP_917494.1 CDS Pden_3731 NC_008687.1 877561 878016 R PFAM: HNH endonuclease; SMART: HNH nuclease; KEGG: sty:HCM1.27c hypothetical protein; HNH endonuclease complement(877561..878016) Paracoccus denitrificans PD1222 4582283 YP_917495.1 CDS Pden_3732 NC_008687.1 878016 878258 R hypothetical protein complement(878016..878258) Paracoccus denitrificans PD1222 4582284 YP_917496.1 CDS Pden_3733 NC_008687.1 878356 878757 R hypothetical protein complement(878356..878757) Paracoccus denitrificans PD1222 4582285 YP_917497.1 CDS Pden_3734 NC_008687.1 878995 879273 R hypothetical protein complement(878995..879273) Paracoccus denitrificans PD1222 4582286 YP_917498.1 CDS Pden_3735 NC_008687.1 879266 879910 R hypothetical protein complement(879266..879910) Paracoccus denitrificans PD1222 4582287 YP_917499.1 CDS Pden_3736 NC_008687.1 879900 880430 R hypothetical protein complement(879900..880430) Paracoccus denitrificans PD1222 4582288 YP_917500.1 CDS Pden_3737 NC_008687.1 880555 880806 R KEGG: rde:RD1_2835 hypothetical protein; hypothetical protein complement(880555..880806) Paracoccus denitrificans PD1222 4582289 YP_917501.1 CDS Pden_3738 NC_008687.1 880905 881876 R KEGG: gox:GOX2477 hypothetical protein; Fis family transcriptional regulator complement(880905..881876) Paracoccus denitrificans PD1222 4582290 YP_917502.1 CDS Pden_3739 NC_008687.1 881888 882856 R KEGG: par:Psyc_0982 probable phage-related protein; hypothetical protein complement(881888..882856) Paracoccus denitrificans PD1222 4582291 YP_917503.1 CDS Pden_3740 NC_008687.1 882959 883261 R hypothetical protein complement(882959..883261) Paracoccus denitrificans PD1222 4582292 YP_917504.1 CDS Pden_3741 NC_008687.1 883261 883566 R hypothetical protein complement(883261..883566) Paracoccus denitrificans PD1222 4582293 YP_917505.1 CDS Pden_3742 NC_008687.1 883566 883850 R hypothetical protein complement(883566..883850) Paracoccus denitrificans PD1222 4582294 YP_917506.1 CDS Pden_3743 NC_008687.1 883987 884574 R hypothetical protein complement(883987..884574) Paracoccus denitrificans PD1222 4582295 YP_917507.1 CDS Pden_3744 NC_008687.1 884562 884804 R hypothetical protein complement(884562..884804) Paracoccus denitrificans PD1222 4582296 YP_917508.1 CDS Pden_3745 NC_008687.1 884798 885220 R hypothetical protein complement(884798..885220) Paracoccus denitrificans PD1222 4582297 YP_917509.1 CDS Pden_3746 NC_008687.1 885407 885880 R XRE family transcriptional regulator complement(885407..885880) Paracoccus denitrificans PD1222 4582298 YP_917510.1 CDS Pden_3747 NC_008687.1 886094 886435 D hypothetical protein 886094..886435 Paracoccus denitrificans PD1222 4582299 YP_917511.1 CDS Pden_3748 NC_008687.1 886553 886882 D hypothetical protein 886553..886882 Paracoccus denitrificans PD1222 4582300 YP_917512.1 CDS Pden_3749 NC_008687.1 886882 887592 D KEGG: rsp:RSP_3792 hypothetical protein; hypothetical protein 886882..887592 Paracoccus denitrificans PD1222 4582301 YP_917513.1 CDS Pden_3750 NC_008687.1 887626 888087 D hypothetical protein 887626..888087 Paracoccus denitrificans PD1222 4582302 YP_917514.1 CDS Pden_3751 NC_008687.1 888087 888629 D KEGG: sit:TM1040_0792 hypothetical protein; hypothetical protein 888087..888629 Paracoccus denitrificans PD1222 4582303 YP_917515.1 CDS Pden_3752 NC_008687.1 888626 888994 D KEGG: xfa:XF1666 hypothetical protein; hypothetical protein 888626..888994 Paracoccus denitrificans PD1222 4582304 YP_917516.1 CDS Pden_3754 NC_008687.1 890380 890703 D hypothetical protein 890380..890703 Paracoccus denitrificans PD1222 4582305 YP_917517.1 CDS Pden_3755 NC_008687.1 890706 891107 D KEGG: ngo:NGO0494 hypothetical protein, phage associated protein; hypothetical protein 890706..891107 Paracoccus denitrificans PD1222 4582306 YP_917518.1 CDS Pden_3756 NC_008687.1 891208 892533 D TIGRFAM: phage terminase, large subunit, PBSX family; KEGG: zmo:ZMO0379 terminase; PBSX family phage terminase large subunit 891208..892533 Paracoccus denitrificans PD1222 4582307 YP_917519.1 CDS Pden_3757 NC_008687.1 892594 892848 D hypothetical protein 892594..892848 Paracoccus denitrificans PD1222 4582308 YP_917520.1 CDS Pden_3758 NC_008687.1 892848 896072 D KEGG: ppu:PP_1573 major tail protein; hypothetical protein 892848..896072 Paracoccus denitrificans PD1222 4582309 YP_917521.1 CDS Pden_3759 NC_008687.1 896330 898006 D KEGG: ppr:PBPRB0567 head-tail connector protein; head-tail connector protein 896330..898006 Paracoccus denitrificans PD1222 4582310 YP_917522.1 CDS Pden_3760 NC_008687.1 898003 898332 D hypothetical protein 898003..898332 Paracoccus denitrificans PD1222 4582311 YP_917523.1 CDS Pden_3761 NC_008687.1 898325 898981 D KEGG: ppr:PBPRB0569 endoprotease; hypothetical protein 898325..898981 Paracoccus denitrificans PD1222 4582312 YP_917524.1 CDS Pden_3762 NC_008687.1 898985 900016 D KEGG: ppr:PBPRB0570 hypothetical protein; hypothetical protein 898985..900016 Paracoccus denitrificans PD1222 4582313 YP_917525.1 CDS Pden_3763 NC_008687.1 900074 900502 D KEGG: ppr:PBPRB0571 hypothetical protein; hypothetical protein 900074..900502 Paracoccus denitrificans PD1222 4582314 YP_917526.1 CDS Pden_3764 NC_008687.1 900495 900818 D hypothetical protein 900495..900818 Paracoccus denitrificans PD1222 4582315 YP_917527.1 CDS Pden_3765 NC_008687.1 900876 901178 D KEGG: pol:Bpro_3742 hypothetical protein; hypothetical protein 900876..901178 Paracoccus denitrificans PD1222 4582316 YP_917528.1 CDS Pden_3766 NC_008687.1 901229 901837 D KEGG: dde:Dde_2546 hypothetical protein; hypothetical protein 901229..901837 Paracoccus denitrificans PD1222 4582317 YP_917529.1 CDS Pden_3767 NC_008687.1 901837 903876 D KEGG: dvu:DVU1714 hypothetical protein; hypothetical protein 901837..903876 Paracoccus denitrificans PD1222 4582318 YP_917530.1 CDS Pden_3768 NC_008687.1 903878 904345 D KEGG: ppr:PBPRB_2036 hypothetical protein; hypothetical protein 903878..904345 Paracoccus denitrificans PD1222 4582319 YP_917531.1 CDS Pden_3769 NC_008687.1 904345 904896 D KEGG: sgl:SG1192 hypothetical protein; hypothetical protein 904345..904896 Paracoccus denitrificans PD1222 4582320 YP_917532.1 CDS Pden_3770 NC_008687.1 904896 907511 D KEGG: mlo:mlr2365 hypothetical protein; hypothetical protein 904896..907511 Paracoccus denitrificans PD1222 4582321 YP_917533.1 CDS Pden_3771 NC_008687.1 907529 910828 D KEGG: mag:amb3639 hypothetical protein; hypothetical protein 907529..910828 Paracoccus denitrificans PD1222 4582322 YP_917534.1 CDS Pden_3772 NC_008687.1 910818 911285 R hypothetical protein complement(910818..911285) Paracoccus denitrificans PD1222 4582323 YP_917535.1 CDS Pden_3773 NC_008687.1 911496 911693 R KEGG: jan:Jann_1865 hypothetical protein; hypothetical protein complement(911496..911693) Paracoccus denitrificans PD1222 4582324 YP_917536.1 CDS Pden_3774 NC_008687.1 911697 911996 R PFAM: Arc domain protein DNA binding domain protein; KEGG: ypn:YPN_1596 phage regulatory protein; Arc domain-containing protein complement(911697..911996) Paracoccus denitrificans PD1222 4582325 YP_917537.1 CDS Pden_3775 NC_008687.1 912308 913123 D KEGG: nha:Nham_2408 uncharacterized phage-encoded protein-like; hypothetical protein 912308..913123 Paracoccus denitrificans PD1222 4582326 YP_917538.1 CDS Pden_3776 NC_008687.1 913120 913377 D hypothetical protein 913120..913377 Paracoccus denitrificans PD1222 4582327 YP_917539.1 CDS Pden_3777 NC_008687.1 913374 913730 D hypothetical protein 913374..913730 Paracoccus denitrificans PD1222 4582328 YP_917540.1 CDS Pden_3778 NC_008687.1 914005 916314 D PFAM: metallophosphoesterase; metallophosphoesterase 914005..916314 Paracoccus denitrificans PD1222 4582329 YP_917541.1 CDS Pden_3779 NC_008687.1 916324 916611 D hypothetical protein 916324..916611 Paracoccus denitrificans PD1222 4582330 YP_917542.1 CDS Pden_3780 NC_008687.1 916814 917608 D PFAM: Peptidoglycan-binding domain 1 protein; KEGG: sme:SMb20518 hypothetical protein; peptidoglycan binding domain-containing protein 916814..917608 Paracoccus denitrificans PD1222 4582331 YP_917543.1 CDS Pden_3781 NC_008687.1 917805 918059 D hypothetical protein 917805..918059 Paracoccus denitrificans PD1222 4582332 YP_917544.1 CDS Pden_3782 NC_008687.1 918515 918847 R hypothetical protein complement(918515..918847) Paracoccus denitrificans PD1222 4582333 YP_917545.1 CDS Pden_3783 NC_008687.1 919205 919489 R hypothetical protein complement(919205..919489) Paracoccus denitrificans PD1222 4582334 YP_917546.1 CDS cmk NC_008687.1 920022 920606 D Catalyzes the formation of (d)CDP from ATP and (d)CMP; cytidylate kinase 920022..920606 Paracoccus denitrificans PD1222 4582335 YP_917547.1 CDS Pden_3785 NC_008687.1 920603 921682 D PFAM: dihydroorotate dehydrogenase; 2-nitropropane dioxygenase, NPD; KEGG: reu:Reut_B5128 2-nitropropane dioxygenase, NPD; 2-nitropropane dioxygenase 920603..921682 Paracoccus denitrificans PD1222 4582336 YP_917548.1 CDS rpsA NC_008687.1 921809 923524 D 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 921809..923524 Paracoccus denitrificans PD1222 4582337 YP_917549.1 CDS ihfB NC_008687.1 923722 924009 D 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 923722..924009 Paracoccus denitrificans PD1222 4582338 YP_917550.1 CDS Pden_3788 NC_008687.1 924048 924449 D KEGG: sil:SPO0805 hypothetical protein; hypothetical protein 924048..924449 Paracoccus denitrificans PD1222 4582339 YP_917551.1 CDS Pden_3789 NC_008687.1 924454 925101 D PFAM: N-(5'phosphoribosyl)anthranilate isomerase (PRAI); KEGG: sil:SPO0806 N-(5'-phosphoribosyl)anthranilate isomerase; phosphoribosylanthranilate isomerase 924454..925101 Paracoccus denitrificans PD1222 4582340 YP_917552.1 CDS Pden_3790 NC_008687.1 925113 925565 D PFAM: GCN5-related N-acetyltransferase; KEGG: rsp:RSP_3586 aromatic pathway regulator; N-acetyltransferase GCN5 925113..925565 Paracoccus denitrificans PD1222 4582341 YP_917553.1 CDS Pden_3791 NC_008687.1 925618 926850 D catalyzes the formation of L-tryptophan from L-serine and 1-(indol-3-yl)glycerol 3-phosphate; tryptophan synthase subunit beta 925618..926850 Paracoccus denitrificans PD1222 4582342 YP_917554.1 CDS Pden_3792 NC_008687.1 926867 927484 R PFAM: DSBA oxidoreductase; KEGG: sil:SPOA0362 27kDa outer membrane protein; DSBA oxidoreductase complement(926867..927484) Paracoccus denitrificans PD1222 4582343 YP_917555.1 CDS Pden_3793 NC_008687.1 927552 928208 D PFAM: 2OG-Fe(II) oxygenase; KEGG: bmb:BruAb2_0689 AlkB, alkylated DNA repair protein; 2OG-Fe(II) oxygenase 927552..928208 Paracoccus denitrificans PD1222 4582344 YP_917556.1 CDS Pden_3794 NC_008687.1 928302 929129 R 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 complement(928302..929129) Paracoccus denitrificans PD1222 4582345 YP_917557.1 CDS Pden_3795 NC_008687.1 929216 930628 R PFAM: polysaccharide deacetylase; KEGG: sil:SPO0872 polysaccharide deacetylase family protein; polysaccharide deacetylase complement(929216..930628) Paracoccus denitrificans PD1222 4582346 YP_917558.1 CDS Pden_3796 NC_008687.1 930848 932212 D PFAM: Xanthine/uracil/vitamin C permease; KEGG: bms:BRA0661 uracil-xanthine permease; xanthine/uracil/vitamin C permease 930848..932212 Paracoccus denitrificans PD1222 4582347 YP_917559.1 CDS Pden_3797 NC_008687.1 932343 933260 R PFAM: helix-turn-helix protein RpiR; sugar isomerase (SIS); KEGG: sme:SMb20276 transcriptional regulator protein; RpiR family transcriptional regulator complement(932343..933260) Paracoccus denitrificans PD1222 4582348 YP_917560.1 CDS Pden_3798 NC_008687.1 933412 934737 D PFAM: aminotransferase class-III; KEGG: sme:SMb20277 hypothetical protein; hypothetical protein 933412..934737 Paracoccus denitrificans PD1222 4582349 YP_917561.1 CDS Pden_3799 NC_008687.1 934745 936244 D PFAM: MlrC domain protein; KEGG: rpd:RPD_1322 MlrC-like; MlrC domain-containing protein 934745..936244 Paracoccus denitrificans PD1222 4582350 YP_917562.1 CDS Pden_3800 NC_008687.1 936241 937833 D PFAM: extracellular solute-binding protein, family 5; KEGG: rpc:RPC_1200 extracellular solute-binding protein, family 5; extracellular solute-binding protein 936241..937833 Paracoccus denitrificans PD1222 4582351 YP_917563.1 CDS Pden_3801 NC_008687.1 937889 938833 D 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 937889..938833 Paracoccus denitrificans PD1222 4582352 YP_917564.1 CDS Pden_3802 NC_008687.1 938830 939693 D 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 938830..939693 Paracoccus denitrificans PD1222 4582353 YP_917565.1 CDS Pden_3803 NC_008687.1 939693 941363 D 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 939693..941363 Paracoccus denitrificans PD1222 4582354 YP_917566.1 CDS Pden_3804 NC_008687.1 941360 942220 D PFAM: Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase; KEGG: bxe:Bxe_C1311 carbon-nitrogen hydrolase; nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase 941360..942220 Paracoccus denitrificans PD1222 4582355 YP_917567.1 CDS Pden_3805 NC_008687.1 942233 942772 D PFAM: Carboxymuconolactone decarboxylase; KEGG: jan:Jann_2958 carboxymuconolactone decarboxylase; carboxymuconolactone decarboxylase 942233..942772 Paracoccus denitrificans PD1222 4582356 YP_917568.1 CDS Pden_3806 NC_008687.1 942769 943281 R 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 complement(942769..943281) Paracoccus denitrificans PD1222 4582357 YP_917569.1 CDS Pden_3807 NC_008687.1 943514 944161 D PFAM: Lytic transglycosylase, catalytic; KEGG: rsp:RSP_1794 lytic transglycosylase; lytic transglycosylase, catalytic 943514..944161 Paracoccus denitrificans PD1222 4582358 YP_917570.1 CDS Pden_3808 NC_008687.1 944224 944796 R KEGG: rsp:RSP_2847 hypothetical protein; hypothetical protein complement(944224..944796) Paracoccus denitrificans PD1222 4582359 YP_917571.1 CDS Pden_3809 NC_008687.1 944867 945787 R catalyzes the formation of porphobilinogen from 5-aminolevulinate; delta-aminolevulinic acid dehydratase complement(944867..945787) Paracoccus denitrificans PD1222 4582360 YP_917572.1 CDS Pden_3810 NC_008687.1 945864 946583 D KEGG: rde:RD1_2747 hypothetical protein; hypothetical protein 945864..946583 Paracoccus denitrificans PD1222 4582361 YP_917573.1 CDS Pden_3811 NC_008687.1 946626 950090 D 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 946626..950090 Paracoccus denitrificans PD1222 4582362 YP_917574.1 CDS Pden_3812 NC_008687.1 950384 952702 R 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 complement(950384..952702) Paracoccus denitrificans PD1222 4582363 YP_917575.1 CDS Pden_3813 NC_008687.1 952964 953710 R PFAM: beta-lactamase domain protein; KEGG: sil:SPO3168 hydroxyacylglutathione hydrolase; hydroxyacylglutathione hydrolase complement(952964..953710) Paracoccus denitrificans PD1222 4582364 YP_917576.1 CDS Pden_3814 NC_008687.1 953762 954544 D PFAM: Methyltransferase type 11; KEGG: rsp:RSP_2295 hypothetical protein; methyltransferase type 11 953762..954544 Paracoccus denitrificans PD1222 4582365 YP_917577.1 CDS Pden_3815 NC_008687.1 954784 955419 D 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 954784..955419 Paracoccus denitrificans PD1222 4582366 YP_917578.1 CDS Pden_3816 NC_008687.1 955419 956954 D 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 955419..956954 Paracoccus denitrificans PD1222 4582367 YP_917579.1 CDS Pden_3817 NC_008687.1 956967 957839 D 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 956967..957839 Paracoccus denitrificans PD1222 4582368 YP_917580.1 CDS Pden_3818 NC_008687.1 957857 959281 D 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 957857..959281 Paracoccus denitrificans PD1222 4582369 YP_917581.1 CDS Pden_3819 NC_008687.1 959291 959737 D 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 959291..959737 Paracoccus denitrificans PD1222 4582370 YP_917582.1 CDS Pden_3820 NC_008687.1 959832 960182 D KEGG: sil:SPO3160 hypothetical protein; hypothetical protein 959832..960182 Paracoccus denitrificans PD1222 4582371 YP_917583.1 CDS Pden_3821 NC_008687.1 960188 960958 R PFAM: alpha/beta hydrolase fold; KEGG: sil:SPO3157 hydrolase, alpha/beta fold family; alpha/beta hydrolase complement(960188..960958) Paracoccus denitrificans PD1222 4582372 YP_917584.1 CDS Pden_3822 NC_008687.1 960955 961554 R PFAM: DSBA oxidoreductase; KEGG: sil:SPO3158 2-hydroxychromene-2-carboxylate isomerase; DSBA oxidoreductase complement(960955..961554) Paracoccus denitrificans PD1222 4582373 YP_917585.1 CDS Pden_3823 NC_008687.1 961636 962655 D KEGG: rsp:RSP_2301 phosphoribosyl pyrophosphate synthetase; TIGRFAM: ribose-phosphate pyrophosphokinase; PFAM: phosphoribosyltransferase; ribose-phosphate pyrophosphokinase 961636..962655 Paracoccus denitrificans PD1222 4582374 YP_917586.1 CDS Pden_3824 NC_008687.1 962723 963175 R PFAM: CoA-binding domain protein; KEGG: rsp:RSP_2240 hypothetical protein; CoA-binding domain-containing protein complement(962723..963175) Paracoccus denitrificans PD1222 4582375 YP_917587.1 CDS Pden_3825 NC_008687.1 963359 963772 R KEGG: sit:TM1040_2051 hypothetical protein; hypothetical protein complement(963359..963772) Paracoccus denitrificans PD1222 4582376 YP_917588.1 CDS Pden_3826 NC_008687.1 963873 964670 R 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 complement(963873..964670) Paracoccus denitrificans PD1222 4582377 YP_917589.1 CDS Pden_3827 NC_008687.1 964815 965072 R hypothetical protein complement(964815..965072) Paracoccus denitrificans PD1222 4582378 YP_917590.1 CDS Pden_3828 NC_008687.1 965152 966009 D hypothetical protein 965152..966009 Paracoccus denitrificans PD1222 4582379 YP_917591.1 CDS Pden_3829 NC_008687.1 966002 967363 D hypothetical protein 966002..967363 Paracoccus denitrificans PD1222 4582380 YP_917592.1 CDS Pden_3830 NC_008687.1 967468 967713 D 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 967468..967713 Paracoccus denitrificans PD1222 4582381 YP_917593.1 CDS Pden_3831 NC_008687.1 967710 967997 D PFAM: plasmid stabilization system; KEGG: sme:SMb20063 hypothetical protein; plasmid stabilization system protein 967710..967997 Paracoccus denitrificans PD1222 4582382 YP_917594.1 CDS Pden_3832 NC_008687.1 968083 968589 D hypothetical protein 968083..968589 Paracoccus denitrificans PD1222 4582383 YP_917595.1 CDS Pden_3833 NC_008687.1 968814 969986 R KEGG: mlo:mlr9349 hypothetical protein; hypothetical protein complement(968814..969986) Paracoccus denitrificans PD1222 4582384 YP_917596.1 CDS Pden_3834 NC_008687.1 970254 970937 D hypothetical protein 970254..970937 Paracoccus denitrificans PD1222 4582385 YP_917597.1 CDS Pden_3835 NC_008687.1 970940 971449 R hypothetical protein complement(970940..971449) Paracoccus denitrificans PD1222 4582386 YP_917598.1 CDS Pden_3836 NC_008687.1 971625 971948 R hypothetical protein complement(971625..971948) Paracoccus denitrificans PD1222 4582387 YP_917599.1 CDS Pden_3837 NC_008687.1 972058 972303 D PFAM: helix-turn-helix domain protein; KEGG: nha:Nham_0800 transcriptional regulator, XRE family; helix-turn-helix domain-containing protein 972058..972303 Paracoccus denitrificans PD1222 4582388 YP_917600.1 CDS Pden_3838 NC_008687.1 972636 973571 D 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 972636..973571 Paracoccus denitrificans PD1222 4582389 YP_917601.1 CDS Pden_3839 NC_008687.1 973574 974044 D hypothetical protein 973574..974044 Paracoccus denitrificans PD1222 4582390 YP_917602.1 CDS Pden_3840 NC_008687.1 974059 975390 D hypothetical protein 974059..975390 Paracoccus denitrificans PD1222 4582391 YP_917603.1 CDS Pden_3841 NC_008687.1 975397 977307 D PFAM: helicase domain protein; SMART: DEAD-like helicases-like; KEGG: ppe:PEPE_0535 superfamily II DNA/RNA helicase, SNF2 family; helicase 975397..977307 Paracoccus denitrificans PD1222 4582392 YP_917604.1 CDS Pden_3842 NC_008687.1 977304 978140 D hypothetical protein 977304..978140 Paracoccus denitrificans PD1222 4582393 YP_917605.1 CDS Pden_3843 NC_008687.1 978209 978457 D hypothetical protein 978209..978457 Paracoccus denitrificans PD1222 4582394 YP_917606.1 CDS Pden_3844 NC_008687.1 978675 979703 R 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 complement(978675..979703) Paracoccus denitrificans PD1222 4582395 YP_917607.1 CDS Pden_3845 NC_008687.1 979812 980135 D PFAM: transposase IS3/IS911 family protein; KEGG: nwi:Nwi_2119 transposase IS3/IS911; transposase IS3/IS911 family protein 979812..980135 Paracoccus denitrificans PD1222 4582396 YP_917608.1 CDS Pden_3846 NC_008687.1 980135 981040 D PFAM: Integrase, catalytic region; KEGG: nwi:Nwi_2120 integrase, catalytic region; integrase catalytic subunit 980135..981040 Paracoccus denitrificans PD1222 4582397 YP_917609.1 CDS Pden_3847 NC_008687.1 981103 981894 R PFAM: helix-turn-helix domain protein; XRE family transcriptional regulator complement(981103..981894) Paracoccus denitrificans PD1222 4582398 YP_917610.1 CDS Pden_3848 NC_008687.1 981969 982262 D hypothetical protein 981969..982262 Paracoccus denitrificans PD1222 4582399 YP_917611.1 CDS Pden_3849 NC_008687.1 982462 983535 D PFAM: phage integrase family protein; KEGG: rsp:RSP_1968 possible integrase/recombinase; phage integrase family protein 982462..983535 Paracoccus denitrificans PD1222 4582400 YP_917612.1 CDS Pden_3850 NC_008687.1 983791 984180 D hypothetical protein 983791..984180 Paracoccus denitrificans PD1222 4582401 YP_917613.1 CDS Pden_3851 NC_008687.1 984185 986230 R hypothetical protein complement(984185..986230) Paracoccus denitrificans PD1222 4582402 YP_917614.1 CDS Pden_3852 NC_008687.1 986350 987189 R hypothetical protein complement(986350..987189) Paracoccus denitrificans PD1222 4582403 YP_917615.1 CDS Pden_3853 NC_008687.1 987193 987768 R hypothetical protein complement(987193..987768) Paracoccus denitrificans PD1222 4582404 YP_917616.1 CDS Pden_3854 NC_008687.1 988104 988364 D hypothetical protein 988104..988364 Paracoccus denitrificans PD1222 4582405 YP_917617.1 CDS Pden_3855 NC_008687.1 988330 988797 R hypothetical protein complement(988330..988797) Paracoccus denitrificans PD1222 4582406 YP_917618.1 CDS Pden_3856 NC_008687.1 988892 989887 D 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 988892..989887 Paracoccus denitrificans PD1222 4582407 YP_917619.1 CDS Pden_3857 NC_008687.1 989964 990845 D PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: sme:SMc02379 permease; binding-protein-dependent transport system inner membrane protein 989964..990845 Paracoccus denitrificans PD1222 4582408 YP_917620.1 CDS Pden_3858 NC_008687.1 990842 991888 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rsp:RSP_3057 ABC proline/glycine betaine transporter, ATPase subunit; ABC transporter 990842..991888 Paracoccus denitrificans PD1222 4582409 YP_917621.1 CDS Pden_3859 NC_008687.1 991961 992359 D hypothetical protein 991961..992359 Paracoccus denitrificans PD1222 4582410 YP_917622.1 CDS Pden_3860 NC_008687.1 992416 993522 D PFAM: NUDIX hydrolase; KEGG: rsp:RSP_2146 tellurite resistance protein; NUDIX hydrolase 992416..993522 Paracoccus denitrificans PD1222 4582411 YP_917623.1 CDS Pden_3861 NC_008687.1 993557 994588 D CysK; forms a complex with serine acetyltransferase CysE; functions in cysteine biosynthesis; cysteine synthase A 993557..994588 Paracoccus denitrificans PD1222 4582412 YP_917624.1 CDS Pden_3862 NC_008687.1 994597 997089 D PFAM: MscS Mechanosensitive ion channel; KEGG: rsp:RSP_2148 small conductance mechanosensitive ion channel; MscS mechanosensitive ion channel 994597..997089 Paracoccus denitrificans PD1222 4582413 YP_917625.1 CDS Pden_3863 NC_008687.1 997086 997472 D KEGG: atc:AGR_C_4132 hypothetical protein; hypothetical protein 997086..997472 Paracoccus denitrificans PD1222 4582414 YP_917626.1 CDS Pden_3864 NC_008687.1 997469 998539 R PFAM: protein of unknown function UPF0118; KEGG: rsp:RSP_3345 hypothetical protein; hypothetical protein complement(997469..998539) Paracoccus denitrificans PD1222 4582415 YP_917627.1 CDS Pden_3865 NC_008687.1 998605 1001346 R negatively supercoils closed circular double-stranded DNA; DNA gyrase subunit A complement(998605..1001346) Paracoccus denitrificans PD1222 4582416 YP_917628.1 CDS Pden_3866 NC_008687.1 1001441 1001935 R PFAM: Disulphide bond formation protein DsbB; KEGG: sil:SPO2117 disulfide bond formation protein, DsbB family; disulfide bond formation protein DsbB complement(1001441..1001935) Paracoccus denitrificans PD1222 4582417 YP_917629.1 CDS Pden_3867 NC_008687.1 1001988 1002584 R KEGG: rpd:RPD_2135 DedA family protein; DedA family protein complement(1001988..1002584) Paracoccus denitrificans PD1222 4582418 YP_917630.1 CDS Pden_3868 NC_008687.1 1002716 1003567 D PFAM: protein of unknown function, zinc metallopeptidase KEGG: sil:SPO3546 zinc metallopeptidase; zinc metallopeptidase 1002716..1003567 Paracoccus denitrificans PD1222 4582419 YP_917631.1 CDS Pden_3869 NC_008687.1 1003738 1003926 R hypothetical protein complement(1003738..1003926) Paracoccus denitrificans PD1222 4582420 YP_917632.1 CDS Pden_3870 NC_008687.1 1003986 1004438 D PFAM: cyclase/dehydrase; KEGG: rsp:RSP_2787 hypothetical protein; cyclase/dehydrase 1003986..1004438 Paracoccus denitrificans PD1222 4582421 YP_917633.1 CDS Pden_3871 NC_008687.1 1004426 1005031 R KEGG: jan:Jann_1985 hypothetical protein; hypothetical protein complement(1004426..1005031) Paracoccus denitrificans PD1222 4582422 YP_917634.1 CDS Pden_3872 NC_008687.1 1005125 1006486 R 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 complement(1005125..1006486) Paracoccus denitrificans PD1222 4582423 YP_917635.1 CDS Pden_3873 NC_008687.1 1006744 1008033 R 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 complement(1006744..1008033) Paracoccus denitrificans PD1222 4582424 YP_917636.1 CDS Pden_3874 NC_008687.1 1008225 1009139 R KEGG: fal:FRAAL4242 hypothetical protein; hypothetical protein complement(1008225..1009139) Paracoccus denitrificans PD1222 4582425 YP_917637.1 CDS Pden_3875 NC_008687.1 1009234 1011300 D 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 1009234..1011300 Paracoccus denitrificans PD1222 4582426 YP_917638.1 CDS Pden_3876 NC_008687.1 1011399 1012304 R PFAM: protein of unknown function DUF6, transmembrane; KEGG: sil:SPO3239 integral membrane protein; hypothetical protein complement(1011399..1012304) Paracoccus denitrificans PD1222 4582427 YP_917639.1 CDS Pden_3877 NC_008687.1 1012304 1012906 R TIGRFAM: alkylhydroperoxidase like protein, AhpD family; uncharacterized peroxidase-related enzyme; PFAM: Carboxymuconolactone decarboxylase; KEGG: rpe:RPE_2026 uncharacterized peroxidase-related enzyme; peroxidase-like protein complement(1012304..1012906) Paracoccus denitrificans PD1222 4582428 YP_917640.1 CDS Pden_3878 NC_008687.1 1013103 1014599 D 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 1013103..1014599 Paracoccus denitrificans PD1222 4582429 YP_917641.1 CDS Pden_3879 NC_008687.1 1014604 1015134 D PFAM: GCN5-related N-acetyltransferase; KEGG: rsp:RSP_1051 hypothetical protein; N-acetyltransferase GCN5 1014604..1015134 Paracoccus denitrificans PD1222 4582430 YP_917642.1 CDS Pden_3880 NC_008687.1 1015131 1015481 D catalyzes the interconversion of chorismate to prephenate; chorismate mutase 1015131..1015481 Paracoccus denitrificans PD1222 4582431 YP_917643.1 CDS rpsP NC_008687.1 1015531 1015905 D 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 1015531..1015905 Paracoccus denitrificans PD1222 4582432 YP_917644.1 CDS rimM NC_008687.1 1015905 1016408 D Essential for efficient processing of 16S rRNA; 16S rRNA-processing protein RimM 1015905..1016408 Paracoccus denitrificans PD1222 4582433 YP_917645.1 CDS Pden_3883 NC_008687.1 1016405 1017274 D KEGG: rsp:RSP_1045 tRNA (guanine-N1-)-methyltransferase; TIGRFAM: tRNA (guanine-N1)-methyltransferase; PFAM: tRNA (guanine-N1-)-methyltransferase; tRNA (guanine-N1)-methyltransferase 1016405..1017274 Paracoccus denitrificans PD1222 4582434 YP_917646.1 CDS rplS NC_008687.1 1017271 1017651 D 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 1017271..1017651 Paracoccus denitrificans PD1222 4582435 YP_917647.1 CDS Pden_3885 NC_008687.1 1017663 1017884 D PFAM: ribosomal protein L31; KEGG: rde:RD1_1304 ribosomal protein L31; 50S ribosomal protein L31 1017663..1017884 Paracoccus denitrificans PD1222 4582436 YP_917648.1 CDS Pden_3886 NC_008687.1 1018209 1018454 R hypothetical protein complement(1018209..1018454) Paracoccus denitrificans PD1222 4582437 YP_917649.1 CDS Pden_3887 NC_008687.1 1018726 1019508 D KEGG: rsp:RSP_1042 chromosome partitioning protein; chromosome partitioning protein 1018726..1019508 Paracoccus denitrificans PD1222 4582438 YP_917650.1 CDS Pden_3888 NC_008687.1 1019578 1020747 D 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 1019578..1020747 Paracoccus denitrificans PD1222 4582439 YP_917651.1 CDS Pden_3889 NC_008687.1 1020744 1023800 D PFAM: acriflavin resistance protein; KEGG: rpa:RPA4680 efflux transporter; acriflavin resistance protein 1020744..1023800 Paracoccus denitrificans PD1222 4582440 YP_917652.1 CDS Pden_3890 NC_008687.1 1023906 1025210 R 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 complement(1023906..1025210) Paracoccus denitrificans PD1222 4582441 YP_917653.1 CDS Pden_3891 NC_008687.1 1025223 1026593 R 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 complement(1025223..1026593) Paracoccus denitrificans PD1222 4582442 YP_917654.1 CDS Pden_3892 NC_008687.1 1026606 1027637 R PFAM: dehydrogenase, E1 component; KEGG: sit:TM1040_1079 pyruvate dehydrogenase (lipoamide); pyruvate dehydrogenase (acetyl-transferring) complement(1026606..1027637) Paracoccus denitrificans PD1222 4582443 YP_917655.1 CDS Pden_3893 NC_008687.1 1027872 1028165 R PFAM: Septum formation initiator; KEGG: sit:TM1040_1081 septum formation initiator; septum formation initiator complement(1027872..1028165) Paracoccus denitrificans PD1222 4582444 YP_917656.1 CDS Pden_3894 NC_008687.1 1028190 1029491 R 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 complement(1028190..1029491) Paracoccus denitrificans PD1222 4582445 YP_917657.1 CDS Pden_3895 NC_008687.1 1029595 1029876 D KEGG: rde:RD1_0930 hypothetical protein; hypothetical protein 1029595..1029876 Paracoccus denitrificans PD1222 4582446 YP_917658.1 CDS Pden_3896 NC_008687.1 1029887 1030546 D PFAM: protein of unknown function DUF1523; KEGG: rsp:RSP_1760 hypothetical protein; hypothetical protein 1029887..1030546 Paracoccus denitrificans PD1222 4582447 YP_917659.1 CDS Pden_3897 NC_008687.1 1030550 1031494 D KEGG: rsp:RSP_3739 deoxyribose phosphate aldolase; TIGRFAM: deoxyribose-phosphate aldolase; PFAM: deoxyribose-phosphate aldolase/phospho-2-dehydro-3-deoxyheptonate aldolase; deoxyribose-phosphate aldolase 1030550..1031494 Paracoccus denitrificans PD1222 4582448 YP_917660.1 CDS Pden_3898 NC_008687.1 1031497 1033827 D PFAM: aldehyde dehydrogenase; KEGG: mes:Meso_0313 aldehyde dehydrogenase; aldehyde dehydrogenase 1031497..1033827 Paracoccus denitrificans PD1222 4582449 YP_917661.1 CDS Pden_3899 NC_008687.1 1033911 1034666 R PFAM: Xylose isomerase domain protein TIM barrel; KEGG: sit:TM1040_2765 hydroxypyruvate isomerase; hydroxypyruvate isomerase complement(1033911..1034666) Paracoccus denitrificans PD1222 4582450 YP_917662.1 CDS Pden_3900 NC_008687.1 1034669 1035214 R PFAM: protein of unknown function DUF1285; KEGG: jan:Jann_0682 protein of unknown function DUF1285; hypothetical protein complement(1034669..1035214) Paracoccus denitrificans PD1222 4582451 YP_917663.1 CDS Pden_3901 NC_008687.1 1035276 1036277 D 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 1035276..1036277 Paracoccus denitrificans PD1222 4582452 YP_917664.1 CDS Pden_3902 NC_008687.1 1036274 1037143 D KEGG: jan:Jann_0684 hypothetical protein; hypothetical protein 1036274..1037143 Paracoccus denitrificans PD1222 4582453 YP_917665.1 CDS Pden_3903 NC_008687.1 1037143 1039062 D TIGRFAM: conserved hypothetical membrane protein; KEGG: rsp:RSP_1022 conserved hypothetical protein (possibly transmembrane); hypothetical protein 1037143..1039062 Paracoccus denitrificans PD1222 4582454 YP_917666.1 CDS Pden_3904 NC_008687.1 1039059 1039898 D KEGG: rde:RD1_0355 N-terminal double-transmembrane domain protein; hypothetical protein 1039059..1039898 Paracoccus denitrificans PD1222 4582455 YP_917667.1 CDS Pden_3905 NC_008687.1 1039895 1041997 D KEGG: rde:RD1_0356 hypothetical protein; hypothetical protein 1039895..1041997 Paracoccus denitrificans PD1222 4582456 YP_917668.1 CDS Pden_3906 NC_008687.1 1042009 1042554 D 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 1042009..1042554 Paracoccus denitrificans PD1222 4582457 YP_917669.1 CDS Pden_3907 NC_008687.1 1042547 1043332 D catalyzes the addition of (R)-3-hydroxytetradecanoyl to the glucosamine disaccharide in lipid A biosynthesis; UDP-N-acetylglucosamine acyltransferase 1042547..1043332 Paracoccus denitrificans PD1222 4582458 YP_917670.1 CDS Pden_3908 NC_008687.1 1043329 1044126 D PFAM: protein of unknown function DUF1009; KEGG: rsp:RSP_2715 hypothetical protein; hypothetical protein 1043329..1044126 Paracoccus denitrificans PD1222 4582459 YP_917671.1 CDS Pden_3909 NC_008687.1 1044291 1045454 D KEGG: rsp:RSP_2716 lipid-A-disaccharide synthase; TIGRFAM: lipid-A-disaccharide synthase; PFAM: glycosyl transferase, family 19; lipid-A-disaccharide synthase 1044291..1045454 Paracoccus denitrificans PD1222 4582460 YP_917672.1 CDS Pden_3910 NC_008687.1 1045429 1045779 R PFAM: Endoribonuclease L-PSP; KEGG: bms:BRA1019 hypothetical protein; endoribonuclease L-PSP complement(1045429..1045779) Paracoccus denitrificans PD1222 4582461 YP_917673.1 CDS Pden_3911 NC_008687.1 1045807 1046553 R PFAM: protein of unknown function DUF81; KEGG: ade:Adeh_2178 protein of unknown function DUF81; hypothetical protein complement(1045807..1046553) Paracoccus denitrificans PD1222 4582462 YP_917674.1 CDS Pden_3912 NC_008687.1 1046946 1047236 D hypothetical protein 1046946..1047236 Paracoccus denitrificans PD1222 4582463 YP_917675.1 CDS Pden_3913 NC_008687.1 1047397 1048095 R PFAM: NodS family protein; Methyltransferase type 11; Methyltransferase type 12; KEGG: bja:bll5506 hypothetical protein; methyltransferase type 11 complement(1047397..1048095) Paracoccus denitrificans PD1222 4582464 YP_917676.1 CDS Pden_3914 NC_008687.1 1048159 1049406 R PFAM: protein of unknown function DUF989; KEGG: sil:SPO0869 hypothetical protein; hypothetical protein complement(1048159..1049406) Paracoccus denitrificans PD1222 4582465 YP_917677.1 CDS Pden_3915 NC_008687.1 1049608 1049958 R PFAM: Transthyretin; KEGG: rde:RD1_4150 hypothetical protein; transthyretin complement(1049608..1049958) Paracoccus denitrificans PD1222 4582466 YP_917678.1 CDS Pden_3916 NC_008687.1 1049975 1051318 R catalyzes the transformation of hydroxyatrazine to N-isopropylammelide and ethylamine in the atrazine degradation pathway.; hydroxydechloroatrazine ethylaminohydrolase complement(1049975..1051318) Paracoccus denitrificans PD1222 4582467 YP_917679.1 CDS Pden_3917 NC_008687.1 1051318 1052799 R TIGRFAM: uracil-xanthine permease; PFAM: Xanthine/uracil/vitamin C permease; KEGG: sme:SMc02512 permease transmembrane protein; uracil-xanthine permease complement(1051318..1052799) Paracoccus denitrificans PD1222 4582468 YP_917680.1 CDS Pden_3918 NC_008687.1 1052841 1053803 R PFAM: ornithine cyclodeaminase/mu-crystallin; Shikimate/quinate 5-dehydrogenase; KEGG: mes:Meso_4368 ornithine cyclodeaminase/mu-crystallin; ornithine cyclodeaminase complement(1052841..1053803) Paracoccus denitrificans PD1222 4582469 YP_917681.1 CDS Pden_3919 NC_008687.1 1053803 1054966 R PFAM: alanine racemase domain protein; KEGG: mes:Meso_4367 alanine racemase-like; alanine racemase complement(1053803..1054966) Paracoccus denitrificans PD1222 4582470 YP_917682.1 CDS Pden_3920 NC_008687.1 1054988 1055935 R PFAM: Pyridoxal-5'-phosphate-dependent enzyme, beta subunit; KEGG: sil:SPOA0145 pyridoxal-phosphate dependent enzyme; pyridoxal-5'-phosphate-dependent protein subunit beta complement(1054988..1055935) Paracoccus denitrificans PD1222 4582471 YP_917683.1 CDS Pden_3921 NC_008687.1 1055950 1057140 R PFAM: aminotransferase, class V; KEGG: mes:Meso_3308 aminotransferase, class V; serine--glyoxylate transaminase complement(1055950..1057140) Paracoccus denitrificans PD1222 4582472 YP_917684.1 CDS Pden_3922 NC_008687.1 1057325 1058164 D PFAM: regulatory protein, DeoR; regulatory proteins, IclR; KEGG: sil:SPOA0143 transcriptional regulator, IclR family; regulatory proteins, IclR 1057325..1058164 Paracoccus denitrificans PD1222 4582473 YP_917685.1 CDS Pden_3923 NC_008687.1 1058292 1060046 D hypothetical protein 1058292..1060046 Paracoccus denitrificans PD1222 4582474 YP_917686.1 CDS Pden_3924 NC_008687.1 1060135 1060851 D PFAM: pentapeptide repeat protein; KEGG: cyb:CYB_1243 pentapeptide repeat family protein; pentapeptide repeat-containing protein 1060135..1060851 Paracoccus denitrificans PD1222 4582475 YP_917687.1 CDS Pden_3925 NC_008687.1 1060864 1062450 R KEGG: jan:Jann_1578 transcriptional regulator, SARP family; SARP family transcriptional regulator complement(1060864..1062450) Paracoccus denitrificans PD1222 4582476 YP_917688.1 CDS Pden_3926 NC_008687.1 1062638 1063684 D catalyzes the formation of 1-(5-phosphoribosyl)-5-aminoimidazole from 2-(formamido)-N1-(5-phosphoribosyl)acetamidine and ATP in purine biosynthesis; phosphoribosylaminoimidazole synthetase 1062638..1063684 Paracoccus denitrificans PD1222 4582477 YP_917689.1 CDS Pden_3927 NC_008687.1 1063681 1064277 D TIGRFAM: phosphoribosylglycinamide formyltransferase; PFAM: formyl transferase domain protein; KEGG: rsp:RSP_1970 phosphoribosylglycinamide formyltransferase; phosphoribosylglycinamide formyltransferase 1063681..1064277 Paracoccus denitrificans PD1222 4582478 YP_917690.1 CDS Pden_3928 NC_008687.1 1064359 1065699 R PFAM: inner-membrane translocator; KEGG: sil:SPO1935 branched-chain amino acid ABC transporter, permease; inner-membrane translocator complement(1064359..1065699) Paracoccus denitrificans PD1222 4582479 YP_917691.1 CDS Pden_3929 NC_008687.1 1065715 1066716 R PFAM: inner-membrane translocator; KEGG: rsp:RSP_2926 ABC branched-chain amino acid transporter family, inner membrane subunit; inner-membrane translocator complement(1065715..1066716) Paracoccus denitrificans PD1222 4582480 YP_917692.1 CDS Pden_3930 NC_008687.1 1066719 1067429 R PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rsp:RSP_2925 ABC branched-chain amino acid transporter family, ATPase subunit; ABC transporter complement(1066719..1067429) Paracoccus denitrificans PD1222 4582481 YP_917693.1 CDS Pden_3931 NC_008687.1 1067429 1068334 R PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rde:RD1_2630 branched-chain amino acid ABC transporter, ATP-binding protein; ABC transporter complement(1067429..1068334) Paracoccus denitrificans PD1222 4582482 YP_917694.1 CDS Pden_3932 NC_008687.1 1068413 1069597 R PFAM: Extracellular ligand-binding receptor; KEGG: rsp:RSP_2923 ABC branched amino acid transporter family, periplasmic substrate-binding protein; extracellular ligand-binding receptor complement(1068413..1069597) Paracoccus denitrificans PD1222 4582483 YP_917695.1 CDS Pden_3933 NC_008687.1 1069721 1070734 R 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 complement(1069721..1070734) Paracoccus denitrificans PD1222 4582484 YP_917696.1 CDS Pden_3934 NC_008687.1 1070820 1072262 D 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 1070820..1072262 Paracoccus denitrificans PD1222 4582485 YP_917697.1 CDS Pden_3935 NC_008687.1 1072372 1073130 R KEGG: rde:RD1_2636 hypothetical protein; hypothetical protein complement(1072372..1073130) Paracoccus denitrificans PD1222 4582486 YP_917698.1 CDS gmk NC_008687.1 1073313 1073951 D Essential for recycling GMP and indirectly, cGMP; guanylate kinase 1073313..1073951 Paracoccus denitrificans PD1222 4582487 YP_917699.1 CDS Pden_3937 NC_008687.1 1073948 1074475 D KEGG: jan:Jann_2439 transferase hexapeptide protein; transferase 1073948..1074475 Paracoccus denitrificans PD1222 4582488 YP_917700.1 CDS Pden_3938 NC_008687.1 1074472 1075524 D 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 1074472..1075524 Paracoccus denitrificans PD1222 4582489 YP_917701.1 CDS Pden_3939 NC_008687.1 1075615 1077114 R Catalyzes first step of the de novo purine nucleotide biosynthetic pathway; amidophosphoribosyltransferase complement(1075615..1077114) Paracoccus denitrificans PD1222 4582490 YP_917702.1 CDS Pden_3940 NC_008687.1 1077245 1077856 R PFAM: Colicin V production protein; KEGG: rsp:RSP_2455 colicin V production protein, DedE; colicin V production protein complement(1077245..1077856) Paracoccus denitrificans PD1222 4582491 YP_917703.1 CDS Pden_3941 NC_008687.1 1077900 1079264 R 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 complement(1077900..1079264) Paracoccus denitrificans PD1222 4582492 YP_917704.1 CDS Pden_3942 NC_008687.1 1079413 1080603 R 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 complement(1079413..1080603) Paracoccus denitrificans PD1222 4582493 YP_917705.1 CDS Pden_3943 NC_008687.1 1080857 1081543 R 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 complement(1080857..1081543) Paracoccus denitrificans PD1222 4582494 YP_917706.1 CDS Pden_3944 NC_008687.1 1081609 1082244 D PFAM: regulatory protein GntR, HTH; GntR domain protein; KEGG: rsp:RSP_1871 transcriptional regulator, GntR family; GntR family transcriptional regulator 1081609..1082244 Paracoccus denitrificans PD1222 4582495 YP_917707.1 CDS Pden_3945 NC_008687.1 1082244 1082867 D PFAM: HhH-GPD family protein; KEGG: sil:SPO2127 DNA-3-methyladenine glycosylase II; HhH-GPD family protein 1082244..1082867 Paracoccus denitrificans PD1222 4582496 YP_917708.1 CDS Pden_3946 NC_008687.1 1082878 1083537 D PFAM: dienelactone hydrolase; phospholipase/Carboxylesterase; KEGG: rsp:RSP_2728 phospholipase/carboxylesterase; phospholipase/carboxylesterase 1082878..1083537 Paracoccus denitrificans PD1222 4582497 YP_917709.1 CDS Pden_3947 NC_008687.1 1083740 1084216 R PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase; KEGG: mlo:mlr4624 lactoylglutathione lyase; glyoxalase/bleomycin resistance protein/dioxygenase complement(1083740..1084216) Paracoccus denitrificans PD1222 4582498 YP_917710.1 CDS Pden_3948 NC_008687.1 1084256 1084576 D PFAM: small multidrug resistance protein; KEGG: pau:PA14_40170 transporter; small multidrug resistance protein 1084256..1084576 Paracoccus denitrificans PD1222 4582499 YP_917711.1 CDS Pden_3949 NC_008687.1 1084712 1085308 D PFAM: HNH endonuclease; SMART: HNH nuclease; KEGG: sil:SPO2123 HNH endonuclease family protein; HNH endonuclease 1084712..1085308 Paracoccus denitrificans PD1222 4582500 YP_917712.1 CDS Pden_3950 NC_008687.1 1085439 1085807 D hypothetical protein 1085439..1085807 Paracoccus denitrificans PD1222 4582501 YP_917713.1 CDS Pden_3951 NC_008687.1 1086199 1087281 D PFAM: Radical SAM domain protein; SMART: Elongator protein 3/MiaB/NifB; KEGG: sil:SPO2159 radical SAM domain protein; radical SAM domain-containing protein 1086199..1087281 Paracoccus denitrificans PD1222 4582502 YP_917714.1 CDS Pden_3952 NC_008687.1 1087282 1088241 R catalyzes the formation of methionine from L-homocysteine and S-adenosyl-L-methionine; methionine synthase I complement(1087282..1088241) Paracoccus denitrificans PD1222 4582503 YP_917715.1 CDS Pden_3953 NC_008687.1 1088330 1089349 R 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 complement(1088330..1089349) Paracoccus denitrificans PD1222 4582504 YP_917716.1 CDS Pden_3954 NC_008687.1 1089460 1090173 D PFAM: Rhomboid family protein; KEGG: sit:TM1040_0444 rhomboid-like protein; rhomboid family protein 1089460..1090173 Paracoccus denitrificans PD1222 4582505 YP_917717.1 CDS Pden_3955 NC_008687.1 1090164 1091708 R 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 complement(1090164..1091708) Paracoccus denitrificans PD1222 4582506 YP_917718.1 CDS Pden_3956 NC_008687.1 1091719 1094529 R catalyzes the uridylylation or deuridylylation of the PII nitrogen regulatory protein; PII uridylyl-transferase complement(1091719..1094529) Paracoccus denitrificans PD1222 4582507 YP_917719.1 CDS Pden_3957 NC_008687.1 1094532 1095734 R KEGG: rsp:RSP_1812 hypothetical protein; hypothetical protein complement(1094532..1095734) Paracoccus denitrificans PD1222 4582508 YP_917720.1 CDS Pden_3958 NC_008687.1 1095839 1096747 D PFAM: Uroporphyrin-III C/tetrapyrrole (Corrin/Porphyrin) methyltransferase; KEGG: rsp:RSP_1813 hypothetical protein; uroporphyrin-III C/tetrapyrrole methyltransferase 1095839..1096747 Paracoccus denitrificans PD1222 4582509 YP_917721.1 CDS Pden_3959 NC_008687.1 1096744 1097157 D PFAM: protein of unknown function UPF0102; KEGG: sil:SPO0400 endonuclease; hypothetical protein 1096744..1097157 Paracoccus denitrificans PD1222 4582510 YP_917722.1 CDS Pden_3960 NC_008687.1 1097346 1098296 D catalyzes the second step in the glutathione biosynthesis pathway, where it synthesizes ATP + gamma-L-glutamyl-L-cysteine + glycine = ADP + phosphate + glutathione; glutathione synthetase 1097346..1098296 Paracoccus denitrificans PD1222 4582511 YP_917723.1 CDS Pden_3961 NC_008687.1 1098421 1099953 R KEGG: sil:SPO0402 competence protein ComM; TIGRFAM: Mg chelatase, subunit ChlI; PFAM: magnesium chelatase, ChlI subunit; SMART: AAA ATPase; Mg chelatase subunit ChlI complement(1098421..1099953) Paracoccus denitrificans PD1222 4582512 YP_917724.1 CDS Pden_3962 NC_008687.1 1100033 1101343 D 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 1100033..1101343 Paracoccus denitrificans PD1222 4582513 YP_917725.1 CDS Pden_3963 NC_008687.1 1101340 1102407 D PFAM: aminotransferase, class V; KEGG: rsp:RSP_0442 aminotransferase; cysteine desulfurase 1101340..1102407 Paracoccus denitrificans PD1222 4582514 YP_917726.1 CDS Pden_3964 NC_008687.1 1102409 1103935 D with SufCD activates cysteine desulfurase SufS; cysteine desulfurase activator complex subunit SufB 1102409..1103935 Paracoccus denitrificans PD1222 4582515 YP_917727.1 CDS Pden_3965 NC_008687.1 1103932 1104243 D PFAM: protein of unknown function DUF74; KEGG: rsp:RSP_0439 hypothetical protein; hypothetical protein 1103932..1104243 Paracoccus denitrificans PD1222 4582516 YP_917728.1 CDS Pden_3966 NC_008687.1 1104253 1105008 D KEGG: sil:SPO2018 FeS assembly ATPase SufC; TIGRFAM: FeS assembly ATPase SufC; PFAM: ABC transporter related; SMART: AAA ATPase; FeS assembly ATPase SufC 1104253..1105008 Paracoccus denitrificans PD1222 4582517 YP_917729.1 CDS Pden_3967 NC_008687.1 1105008 1106354 D PFAM: SufBD protein; KEGG: rde:RD1_2692 FeS assembly protein SufD; SufBD protein 1105008..1106354 Paracoccus denitrificans PD1222 4582518 YP_917730.1 CDS Pden_3968 NC_008687.1 1106351 1106839 D KEGG: rsp:RSP_0433 hypothetical protein; hypothetical protein 1106351..1106839 Paracoccus denitrificans PD1222 4582519 YP_917731.1 CDS Pden_3969 NC_008687.1 1106836 1107423 D KEGG: rsp:RSP_0432 hypothetical protein; hypothetical protein 1106836..1107423 Paracoccus denitrificans PD1222 4582520 YP_917732.1 CDS Pden_3970 NC_008687.1 1107420 1108631 D 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 1107420..1108631 Paracoccus denitrificans PD1222 4582521 YP_917733.1 CDS Pden_3971 NC_008687.1 1109057 1111228 R 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 complement(1109057..1111228) Paracoccus denitrificans PD1222 4582522 YP_917734.1 CDS Pden_3972 NC_008687.1 1111534 1112475 R PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: rsp:RSP_2950 transcriptional regulator, LysR family; LysR family transcriptional regulator complement(1111534..1112475) Paracoccus denitrificans PD1222 4582523 YP_917735.1 CDS Pden_3973 NC_008687.1 1112959 1113771 D KEGG: rsp:RSP_2947 glutamate racemase; TIGRFAM: glutamate racemase; PFAM: Asp/Glu racemase; glutamate racemase 1112959..1113771 Paracoccus denitrificans PD1222 4582524 YP_917736.1 CDS Pden_3974 NC_008687.1 1113790 1114233 D 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 1113790..1114233 Paracoccus denitrificans PD1222 4582525 YP_917737.1 CDS Pden_3975 NC_008687.1 1114309 1114920 D PFAM: protein of unknown function DUF847; KEGG: rsp:RSP_2944 hypothetical protein; hypothetical protein 1114309..1114920 Paracoccus denitrificans PD1222 4582526 YP_917738.1 CDS Pden_3976 NC_008687.1 1114911 1115441 D KEGG: rsp:RSP_6081 hypothetical protein; hypothetical protein 1114911..1115441 Paracoccus denitrificans PD1222 4582527 YP_917739.1 CDS Pden_3977 NC_008687.1 1115530 1117491 D 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 1115530..1117491 Paracoccus denitrificans PD1222 4582528 YP_917740.1 CDS Pden_3978 NC_008687.1 1117495 1117947 D PFAM: cytochrome C biogenesis protein; KEGG: sil:SPO1881 cytochrome c biogenesis family protein; cytochrome C biogenesis protein 1117495..1117947 Paracoccus denitrificans PD1222 4582529 YP_917741.1 CDS Pden_3979 NC_008687.1 1118017 1118787 D PFAM: Enoyl-CoA hydratase/isomerase; KEGG: jan:Jann_2154 enoyl-CoA hydratase/isomerase; enoyl-CoA hydratase/isomerase 1118017..1118787 Paracoccus denitrificans PD1222 4582530 YP_917742.1 CDS Pden_3980 NC_008687.1 1118822 1119541 R PFAM: NUDIX hydrolase; KEGG: rsp:RSP_0419 hypothetical protein; NUDIX hydrolase complement(1118822..1119541) Paracoccus denitrificans PD1222 4582531 YP_917743.1 CDS Pden_3981 NC_008687.1 1119544 1119963 R PFAM: protein of unknown function DUF983; KEGG: rsp:RSP_0418 hypothetical protein; hypothetical protein complement(1119544..1119963) Paracoccus denitrificans PD1222 4582532 YP_917744.1 CDS Pden_3982 NC_008687.1 1120068 1121462 R TIGRFAM: diguanylate cyclase; PFAM: GGDEF domain containing protein; response regulator receiver; KEGG: jan:Jann_3131 diguanylate cyclase; response regulator receiver modulated diguanylate cyclase complement(1120068..1121462) Paracoccus denitrificans PD1222 4582533 YP_917745.1 CDS Pden_3983 NC_008687.1 1121571 1121840 D KEGG: rru:Rru_A1259 hypothetical protein; hypothetical protein 1121571..1121840 Paracoccus denitrificans PD1222 4582534 YP_917746.1 CDS Pden_3984 NC_008687.1 1121859 1123220 R PFAM: aminotransferase class-III; KEGG: rsp:RSP_0379 aminotransferase; class III aminotransferase complement(1121859..1123220) Paracoccus denitrificans PD1222 4582535 YP_917747.1 CDS Pden_3985 NC_008687.1 1123458 1124807 R PFAM: cytochrome P450; KEGG: sil:SPO1898 cytochrome P450 family protein; cytochrome P450 complement(1123458..1124807) Paracoccus denitrificans PD1222 4582536 YP_917748.1 CDS Pden_3986 NC_008687.1 1124804 1126003 R KEGG: sil:SPO1897 hypothetical protein; hypothetical protein complement(1124804..1126003) Paracoccus denitrificans PD1222 4582537 YP_917749.1 CDS Pden_3987 NC_008687.1 1126057 1126743 R PFAM: peptidase M48, Ste24p; KEGG: jan:Jann_2687 peptidase M48, Ste24p; peptidase M48, Ste24p complement(1126057..1126743) Paracoccus denitrificans PD1222 4582538 YP_917750.1 CDS Pden_3988 NC_008687.1 1126771 1127952 R PFAM: VWA containing CoxE family protein; KEGG: rsp:RSP_2650 hypothetical protein; von Willebrand factor A complement(1126771..1127952) Paracoccus denitrificans PD1222 4582539 YP_917751.1 CDS Pden_3989 NC_008687.1 1128237 1129361 D PFAM: Ppx/GppA phosphatase; KEGG: rsp:RSP_2771 exopolyphosphatase; Ppx/GppA phosphatase 1128237..1129361 Paracoccus denitrificans PD1222 4582540 YP_917752.1 CDS Pden_3990 NC_008687.1 1129363 1130133 D PFAM: ribosomal RNA methyltransferase RrmJ/FtsJ; KEGG: rsp:RSP_2772 23S rRNA methylase; ribosomal RNA methyltransferase RrmJ/FtsJ 1129363..1130133 Paracoccus denitrificans PD1222 4582541 YP_917753.1 CDS Pden_3991 NC_008687.1 1130270 1131376 R PFAM: helix-turn-helix- domain containing protein, AraC type; KEGG: jan:Jann_2462 transcriptional regulator, AraC family; helix-turn-helix domain-containing protein complement(1130270..1131376) Paracoccus denitrificans PD1222 4582542 YP_917754.1 CDS miaA NC_008687.1 1131504 1132412 R 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 complement(1131504..1132412) Paracoccus denitrificans PD1222 4582543 YP_917755.1 CDS pyrH NC_008687.1 1132498 1133232 D Catalyzes the phosphorylation of UMP to UDP; uridylate kinase 1132498..1133232 Paracoccus denitrificans PD1222 4582544 YP_917756.1 CDS frr NC_008687.1 1133313 1133876 D 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 1133313..1133876 Paracoccus denitrificans PD1222 4582545 YP_917757.1 CDS Pden_3995 NC_008687.1 1133880 1134614 D KEGG: rsp:RSP_2707 UDP pyrophosphate synthase; TIGRFAM: UDP diphosphate synthase; PFAM: Di-trans-poly-cis-decaprenylcistransferase; UDP diphosphate synthase 1133880..1134614 Paracoccus denitrificans PD1222 4582546 YP_917758.1 CDS Pden_3996 NC_008687.1 1134611 1135465 D PFAM: phosphatidate cytidylyltransferase; KEGG: rsp:RSP_2708 phosphatidate cytidylyltransferase; phosphatidate cytidylyltransferase 1134611..1135465 Paracoccus denitrificans PD1222 4582547 YP_917759.1 CDS Pden_3997 NC_008687.1 1135470 1136642 D 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 1135470..1136642 Paracoccus denitrificans PD1222 4582548 YP_917760.1 CDS Pden_3998 NC_008687.1 1136639 1137964 D TIGRFAM: membrane-associated zinc metalloprotease; PFAM: PDZ/DHR/GLGF domain protein; peptidase M50; KEGG: sil:SPO1668 membrane-associated zinc metalloprotease; membrane-associated zinc metalloprotease 1136639..1137964 Paracoccus denitrificans PD1222 4582549 YP_917761.1 CDS Pden_3999 NC_008687.1 1138068 1140416 D PFAM: surface antigen (D15); surface antigen variable number repeat protein; KEGG: rsp:RSP_2711 outer membrane protein; surface antigen (D15) 1138068..1140416 Paracoccus denitrificans PD1222 4582550 YP_917762.1 CDS Pden_4000 NC_008687.1 1140416 1141195 D PFAM: outer membrane chaperone Skp (OmpH); KEGG: rde:RD1_2594 hypothetical protein; outer membrane chaperone Skp (OmpH) 1140416..1141195 Paracoccus denitrificans PD1222 4582551 YP_917763.1 CDS Pden_4001 NC_008687.1 1141217 1142164 R PFAM: Inosine/uridine-preferring nucleoside hydrolase; KEGG: rsp:RSP_2914 nucleoside hydrolase; purine nucleosidase complement(1141217..1142164) Paracoccus denitrificans PD1222 4582552 YP_917764.1 CDS Pden_4002 NC_008687.1 1142225 1144681 R PFAM: peptidase S45, penicillin amidase; KEGG: rsp:RSP_2845 penicillin acylase (penicillin amidase); penicillin amidase complement(1142225..1144681) Paracoccus denitrificans PD1222 4582553 YP_917765.1 CDS Pden_4003 NC_008687.1 1144811 1145677 D PFAM: NADP oxidoreductase, coenzyme F420-dependent; 6-phosphogluconate dehydrogenase, NAD-binding; KEGG: rsp:RSP_2846 3-hydroxyisobutyrate dehydrogenase; 3-hydroxyisobutyrate dehydrogenase 1144811..1145677 Paracoccus denitrificans PD1222 4582554 YP_917766.1 CDS Pden_4004 NC_008687.1 1145983 1146531 R PFAM: protein of unknown function DUF1130; KEGG: bbr:BB2477 hypothetical protein; hypothetical protein complement(1145983..1146531) Paracoccus denitrificans PD1222 4582555 YP_917767.1 CDS Pden_4005 NC_008687.1 1146544 1146753 R KEGG: nha:Nham_2097 hypothetical protein; hypothetical protein complement(1146544..1146753) Paracoccus denitrificans PD1222 4582556 YP_917768.1 CDS Pden_4006 NC_008687.1 1147245 1148897 D PFAM: major facilitator superfamily MFS_1; KEGG: atc:AGR_L_343 hypothetical protein; major facilitator transporter 1147245..1148897 Paracoccus denitrificans PD1222 4582557 YP_917769.1 CDS Pden_4007 NC_008687.1 1148956 1150926 R 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 complement(1148956..1150926) Paracoccus denitrificans PD1222 4582558 YP_917770.1 CDS Pden_4008 NC_008687.1 1150919 1152289 R 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 complement(1150919..1152289) Paracoccus denitrificans PD1222 4582559 YP_917771.1 CDS Pden_4009 NC_008687.1 1152491 1154755 D KEGG: sal:Sala_0186 oxidoreductase alpha (molybdopterin) subunit; TIGRFAM: oxidoreductase alpha (molybdopterin) subunit; PFAM: molybdopterin oxidoreductase; molydopterin dinucleotide-binding region; oxidoreductase alpha (molybdopterin) subunit 1152491..1154755 Paracoccus denitrificans PD1222 4582560 YP_917772.1 CDS Pden_4010 NC_008687.1 1154774 1156177 D PFAM: cytochrome bd ubiquinol oxidase, subunit I; KEGG: nar:Saro_1025 cytochrome bd ubiquinol oxidase, subunit I; cytochrome bd ubiquinol oxidase, subunit I 1154774..1156177 Paracoccus denitrificans PD1222 4582561 YP_917773.1 CDS Pden_4011 NC_008687.1 1156179 1157183 D 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 1156179..1157183 Paracoccus denitrificans PD1222 4582562 YP_917774.1 CDS Pden_4012 NC_008687.1 1157362 1160223 D 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 1157362..1160223 Paracoccus denitrificans PD1222 4582563 YP_917775.1 CDS Pden_4013 NC_008687.1 1160292 1160924 D PFAM: multiple antibiotic resistance (MarC)-related proteins; KEGG: bur:Bcep18194_C7011 multiple antibiotic resistance (MarC)-related proteins; multiple antibiotic resistance (MarC)-like proteins 1160292..1160924 Paracoccus denitrificans PD1222 4582564 YP_917776.1 CDS Pden_4014 NC_008687.1 1160987 1162009 D TIGRFAM: Dyp-type peroxidase family; PFAM: Dyp-type peroxidase; KEGG: bam:Bamb_5665 Dyp-type peroxidase family; Dyp-type peroxidase family protein 1160987..1162009 Paracoccus denitrificans PD1222 4582565 YP_917777.1 CDS Pden_4015 NC_008687.1 1162011 1162808 D PFAM: Linocin_M18 bacteriocin protein; KEGG: bbr:BB2479 bacteriocin; Linocin_M18 bacteriocin protein 1162011..1162808 Paracoccus denitrificans PD1222 4582566 YP_917778.1 CDS Pden_4016 NC_008687.1 1162815 1163705 D PFAM: protein of unknown function UPF0187; KEGG: pen:PSEEN4044 hypothetical protein; hypothetical protein 1162815..1163705 Paracoccus denitrificans PD1222 4582567 YP_917779.1 CDS Pden_4017 NC_008687.1 1164011 1165297 D KEGG: rsp:RSP_0301 ABC branched chain amino acid transporter, substrate binding protein; ABC branched chain amino acid transporter, substrate binding protein 1164011..1165297 Paracoccus denitrificans PD1222 4582568 YP_917780.1 CDS Pden_4018 NC_008687.1 1165346 1167265 D PFAM: inner-membrane translocator; KEGG: rsp:RSP_0300 ABC branched chain amino acid transporter, inner membrane subunit; inner-membrane translocator 1165346..1167265 Paracoccus denitrificans PD1222 4582569 YP_917781.1 CDS Pden_4019 NC_008687.1 1167267 1168502 D PFAM: inner-membrane translocator; KEGG: rsp:RSP_0299 ABC branched chain amino acid transporter, inner membrane subunit; inner-membrane translocator 1167267..1168502 Paracoccus denitrificans PD1222 4582570 YP_917782.1 CDS Pden_4020 NC_008687.1 1168499 1169239 D PFAM: ABC transporter related; KEGG: rsp:RSP_0298 ABC branched chain amino acid transporter, ATPase subunit; ABC transporter 1168499..1169239 Paracoccus denitrificans PD1222 4582571 YP_917783.1 CDS Pden_4021 NC_008687.1 1169243 1169950 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rsp:RSP_0297 ABC branched chain amino acid transporter, ATPase subunit; ABC transporter 1169243..1169950 Paracoccus denitrificans PD1222 4582572 YP_917784.1 CDS Pden_4022 NC_008687.1 1170462 1171013 D PFAM: Redoxin domain protein; KEGG: dar:Daro_3587 hypothetical protein; redoxin domain-containing protein 1170462..1171013 Paracoccus denitrificans PD1222 4582573 YP_917785.1 CDS Pden_4023 NC_008687.1 1171014 1171697 D catalyzes the dephosphorylation of 2-phosphoglycolate to form glycolate and phosphate; phosphoglycolate phosphatase 1171014..1171697 Paracoccus denitrificans PD1222 4582574 YP_917786.1 CDS Pden_4024 NC_008687.1 1171756 1172226 D PFAM: protein of unknown function DUF442; KEGG: rsp:RSP_0167 hypothetical protein; hypothetical protein 1171756..1172226 Paracoccus denitrificans PD1222 4582575 YP_917787.1 CDS Pden_4025 NC_008687.1 1172479 1174299 D 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 1172479..1174299 Paracoccus denitrificans PD1222 4582576 YP_917788.1 CDS Pden_4026 NC_008687.1 1174385 1175020 D hypothetical protein 1174385..1175020 Paracoccus denitrificans PD1222 4582577 YP_917789.1 CDS Pden_4027 NC_008687.1 1175033 1175356 R PFAM: ferredoxin; KEGG: sit:TM1040_1949 ferredoxin; ferredoxin complement(1175033..1175356) Paracoccus denitrificans PD1222 4582578 YP_917790.1 CDS xseA NC_008687.1 1175481 1177040 R bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides; exodeoxyribonuclease VII large subunit complement(1175481..1177040) Paracoccus denitrificans PD1222 4582579 YP_917791.1 CDS Pden_4029 NC_008687.1 1177155 1178417 D catalyzes the formation of N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-D-ribosylamine and glycine in purine biosynthesis; phosphoribosylamine--glycine ligase 1177155..1178417 Paracoccus denitrificans PD1222 4582580 YP_917792.1 CDS Pden_4030 NC_008687.1 1178755 1180317 D catalyzes the formation of 2-isopropylmalate from acetyl-CoA and 2-oxoisovalerate in leucine biosynthesis; 2-isopropylmalate synthase 1178755..1180317 Paracoccus denitrificans PD1222 4582581 YP_917793.1 CDS Pden_4031 NC_008687.1 1180350 1181189 R KEGG: jan:Jann_0572 hypothetical protein; hypothetical protein complement(1180350..1181189) Paracoccus denitrificans PD1222 4582582 YP_917794.1 CDS Pden_4032 NC_008687.1 1181383 1182483 D functions in MreBCD complex in some organisms; rod shape-determining protein MreB 1181383..1182483 Paracoccus denitrificans PD1222 4582583 YP_917795.1 CDS Pden_4033 NC_008687.1 1182497 1183429 D 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 1182497..1183429 Paracoccus denitrificans PD1222 4582584 YP_917796.1 CDS Pden_4034 NC_008687.1 1183422 1183952 D KEGG: rsp:RSP_2327 rod shape-determining protein MreD; rod shape-determining protein MreD 1183422..1183952 Paracoccus denitrificans PD1222 4582585 YP_917797.1 CDS Pden_4035 NC_008687.1 1183956 1185899 D PFAM: penicillin-binding protein, transpeptidase; Penicillin-binding protein, dimerisation domain; KEGG: rsp:RSP_2326 cell division protein FtsI; peptidoglycan glycosyltransferase 1183956..1185899 Paracoccus denitrificans PD1222 4582586 YP_917798.1 CDS Pden_4036 NC_008687.1 1185903 1187045 D 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 1185903..1187045 Paracoccus denitrificans PD1222 4582587 YP_917799.1 CDS Pden_4037 NC_008687.1 1187055 1187975 D 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 1187055..1187975 Paracoccus denitrificans PD1222 4582588 YP_917800.1 CDS Pden_4038 NC_008687.1 1188106 1189533 D 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 1188106..1189533 Paracoccus denitrificans PD1222 4582589 YP_917801.1 CDS Pden_4039 NC_008687.1 1189606 1190637 D KEGG: rsp:RSP_0179 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components TauA; ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components TauA 1189606..1190637 Paracoccus denitrificans PD1222 4582590 YP_917802.1 CDS Pden_4040 NC_008687.1 1190693 1191298 D PFAM: protein of unknown function DUF161; KEGG: rsp:RSP_0447 hypothetical protein; hypothetical protein 1190693..1191298 Paracoccus denitrificans PD1222 4582591 YP_917803.1 CDS Pden_4041 NC_008687.1 1191308 1191634 R PFAM: arsenate reductase and related; KEGG: rsp:RSP_0387 hypothetical protein; arsenate reductase complement(1191308..1191634) Paracoccus denitrificans PD1222 4582592 YP_917804.1 CDS Pden_4042 NC_008687.1 1191781 1193100 R KEGG: rsp:RSP_0238 hypothetical protein; hypothetical protein complement(1191781..1193100) Paracoccus denitrificans PD1222 4582593 YP_917805.1 CDS Pden_4043 NC_008687.1 1193259 1193768 D PFAM: ErfK/YbiS/YcfS/YnhG family protein; KEGG: rsp:RSP_1201 hypothetical protein; ErfK/YbiS/YcfS/YnhG family protein 1193259..1193768 Paracoccus denitrificans PD1222 4582594 YP_917806.1 CDS Pden_4044 NC_008687.1 1193832 1195346 D PFAM: NnrS family protein; KEGG: sme:SMa1194 hypothetical protein; NnrS family protein 1193832..1195346 Paracoccus denitrificans PD1222 4582595 YP_917807.1 CDS Pden_4045 NC_008687.1 1195503 1196720 D TIGRFAM: chromate transporter, chromate ion transporter (CHR) family; PFAM: Chromate transporter; KEGG: atc:AGR_L_3461 probable transporter PA4289; chromate transporter 1195503..1196720 Paracoccus denitrificans PD1222 4582596 YP_917808.1 CDS Pden_4046 NC_008687.1 1196881 1197174 D hypothetical protein 1196881..1197174 Paracoccus denitrificans PD1222 4582597 YP_917809.1 CDS Pden_4047 NC_008687.1 1197245 1198684 R PFAM: NAD(P) transhydrogenase, beta subunit; KEGG: sil:SPO2819 NAD(P)+ transhydrogenase, beta subunit; NAD(P) transhydrogenase subunit beta complement(1197245..1198684) Paracoccus denitrificans PD1222 4582598 YP_917810.1 CDS pntA NC_008687.1 1198698 1200272 R 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 complement(1198698..1200272) Paracoccus denitrificans PD1222 4582599 YP_917811.1 CDS Pden_4049 NC_008687.1 1200368 1201048 R KEGG: jan:Jann_3303 protein of unknown function DUF1498; hypothetical protein complement(1200368..1201048) Paracoccus denitrificans PD1222 4582600 YP_917812.1 CDS Pden_4050 NC_008687.1 1201059 1201466 R PFAM: Isoprenylcysteine carboxyl methyltransferase; KEGG: rsp:RSP_0241 protein-S-isoprenylcysteine methyltransferase; isoprenylcysteine carboxyl methyltransferase complement(1201059..1201466) Paracoccus denitrificans PD1222 4582601 YP_917813.1 CDS Pden_4051 NC_008687.1 1201502 1203649 R catalyzes the formation of malate from glyoxylate and acetyl-CoA; malate synthase G complement(1201502..1203649) Paracoccus denitrificans PD1222 4582602 YP_917814.1 CDS Pden_4052 NC_008687.1 1203819 1204523 R KEGG: jan:Jann_1769 mucin-associated surface protein; mucin-associated surface protein complement(1203819..1204523) Paracoccus denitrificans PD1222 4582603 YP_917815.1 CDS pepN NC_008687.1 1204691 1207234 D TIGRFAM: aminopeptidase N; PFAM: peptidase M1, membrane alanine aminopeptidase; KEGG: rsp:RSP_1982 aminopeptidase N; aminopeptidase 1204691..1207234 Paracoccus denitrificans PD1222 4582604 YP_917816.1 CDS Pden_4054 NC_008687.1 1207252 1208193 D PFAM: phospholipid/glycerol acyltransferase; KEGG: rsp:RSP_1983 phospholipid/glycerol acyltransferase; phospholipid/glycerol acyltransferase 1207252..1208193 Paracoccus denitrificans PD1222 4582605 YP_917817.1 CDS Pden_4055 NC_008687.1 1208346 1209458 R catalyzes the formation of glutamate 5-phosphate from glutamate in proline biosynthesis; gamma-glutamyl kinase complement(1208346..1209458) Paracoccus denitrificans PD1222 4582606 YP_917818.1 CDS obgE NC_008687.1 1209446 1210477 R essential GTPase; exhibits high exchange rate for GTP/GDP; associates with 50S ribosomal subunit; involved in regulation of chromosomal replication; GTPase ObgE complement(1209446..1210477) Paracoccus denitrificans PD1222 4582607 YP_917819.1 CDS Pden_4057 NC_008687.1 1210622 1210960 D PFAM: small multidrug resistance protein; KEGG: hch:HCH_07085 membrane transporters of cations and cationic drugs; small multidrug resistance protein 1210622..1210960 Paracoccus denitrificans PD1222 4582608 YP_917820.1 CDS Pden_4058 NC_008687.1 1211023 1212438 D PFAM: protein of unknown function UPF0061; KEGG: sil:SPO2480 hypothetical protein; hypothetical protein 1211023..1212438 Paracoccus denitrificans PD1222 4582609 YP_917821.1 CDS Pden_4059 NC_008687.1 1212457 1213239 D PFAM: Endonuclease/exonuclease/phosphatase; KEGG: bme:BMEII0240 dioxygenase; endonuclease/exonuclease/phosphatase 1212457..1213239 Paracoccus denitrificans PD1222 4582610 YP_917822.1 CDS eno NC_008687.1 1213306 1214583 D enolase; catalyzes the formation of phosphoenolpyruvate from 2-phospho-D-glycerate in glycolysis; phosphopyruvate hydratase 1213306..1214583 Paracoccus denitrificans PD1222 4582611 YP_917823.1 CDS Pden_4061 NC_008687.1 1214632 1215447 R KEGG: sil:SPO2129 hypothetical protein; hypothetical protein complement(1214632..1215447) Paracoccus denitrificans PD1222 4582612 YP_917824.1 CDS Pden_4062 NC_008687.1 1215444 1217066 R 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 complement(1215444..1217066) Paracoccus denitrificans PD1222 4582613 YP_917825.1 CDS Pden_4063 NC_008687.1 1217099 1218487 R KEGG: sit:TM1040_1153 cysteinyl-tRNA synthetase; TIGRFAM: cysteinyl-tRNA synthetase; PFAM: cysteinyl-tRNA synthetase, class Ia; cysteinyl-tRNA synthetase complement(1217099..1218487) Paracoccus denitrificans PD1222 4582614 YP_917826.1 CDS Pden_4064 NC_008687.1 1218643 1218984 D KEGG: rsp:RSP_2721 hypothetical protein; hypothetical protein 1218643..1218984 Paracoccus denitrificans PD1222 4582615 YP_917827.1 CDS Pden_4065 NC_008687.1 1219068 1219508 R KEGG: gbe:GbCGDNIH1_2282 hypothetical secreted protein; hypothetical protein complement(1219068..1219508) Paracoccus denitrificans PD1222 4582616 YP_917828.1 CDS Pden_4066 NC_008687.1 1219607 1220746 R PFAM: ABC transporter related; Transport-associated OB domain protein; SMART: AAA ATPase; KEGG: rsp:RSP_0015 ABC spermidine/putrescine transporter, ATPase subunit; ABC transporter complement(1219607..1220746) Paracoccus denitrificans PD1222 4582617 YP_917829.1 CDS Pden_4067 NC_008687.1 1220743 1221549 R 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 complement(1220743..1221549) Paracoccus denitrificans PD1222 4582618 YP_917830.1 CDS Pden_4068 NC_008687.1 1221546 1222415 R 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 complement(1221546..1222415) Paracoccus denitrificans PD1222 4582619 YP_917831.1 CDS Pden_4069 NC_008687.1 1222509 1222934 R PFAM: protein of unknown function UPF0047; KEGG: rde:RD1_1797 hypothetical protein; hypothetical protein complement(1222509..1222934) Paracoccus denitrificans PD1222 4582620 YP_917832.1 CDS Pden_4070 NC_008687.1 1222931 1224445 R PFAM: protein of unknown function DUF195; KEGG: mmr:Mmar10_0441 protein of unknown function DUF195; hypothetical protein complement(1222931..1224445) Paracoccus denitrificans PD1222 4582621 YP_917833.1 CDS Pden_4071 NC_008687.1 1224537 1225085 D PFAM: NADPH-dependent FMN reductase; KEGG: bte:BTH_II2367 NADPH-dependent FMN reductase domain protein; NADPH-dependent FMN reductase 1224537..1225085 Paracoccus denitrificans PD1222 4582622 YP_917834.1 CDS Pden_4072 NC_008687.1 1225149 1227143 R 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 complement(1225149..1227143) Paracoccus denitrificans PD1222 4582623 YP_917835.1 CDS dnaG NC_008687.1 1227285 1229225 R synthesizes RNA primers at the replication forks; DNA primase complement(1227285..1229225) Paracoccus denitrificans PD1222 4582624 YP_917836.1 CDS Pden_4074 NC_008687.1 1229265 1229849 R PFAM: regulatory protein, TetR; KEGG: sil:SPO1736 transcriptional regulator, TetR family; TetR family transcriptional regulator complement(1229265..1229849) Paracoccus denitrificans PD1222 4582625 YP_917837.1 CDS Pden_4075 NC_008687.1 1230311 1231474 D PFAM: FMN-dependent alpha-hydroxy acid dehydrogenase; KEGG: rsp:RSP_0829 lactate dehydrogenase; L-lactate dehydrogenase (cytochrome) 1230311..1231474 Paracoccus denitrificans PD1222 4582626 YP_917838.1 CDS Pden_4076 NC_008687.1 1231504 1232571 R KEGG: pfl:PFL_4227 acyltransferase family protein; acyltransferase complement(1231504..1232571) Paracoccus denitrificans PD1222 4582627 YP_917839.1 CDS Pden_4077 NC_008687.1 1232663 1233289 D 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 1232663..1233289 Paracoccus denitrificans PD1222 4582628 YP_917840.1 CDS Pden_4078 NC_008687.1 1233405 1234745 D 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 1233405..1234745 Paracoccus denitrificans PD1222 4582629 YP_917841.1 CDS Pden_4079 NC_008687.1 1234742 1235587 D PFAM: glutamyl-tRNA synthetase, class Ic; KEGG: rsp:RSP_2628 glutamyl-/glutaminyl-tRNA synthetase; glutamyl-tRNA synthetase, class Ic 1234742..1235587 Paracoccus denitrificans PD1222 4582630 YP_917842.1 CDS Pden_4080 NC_008687.1 1235569 1235934 R PFAM: phosphoribosyl-AMP cyclohydrolase; KEGG: rsp:RSP_2627 phosphoribosyl-AMP cyclohydrolase; phosphoribosyl-AMP cyclohydrolase complement(1235569..1235934) Paracoccus denitrificans PD1222 4582631 YP_917843.1 CDS Pden_4081 NC_008687.1 1235995 1236432 D KEGG: rsp:RSP_2625 NifU-related protein involved in Fe-S cluster formation; NifU-related protein involved in Fe-S cluster formation 1235995..1236432 Paracoccus denitrificans PD1222 4582632 YP_917844.1 CDS Pden_4082 NC_008687.1 1236788 1238881 R catalyzes branch migration in Holliday junction intermediates; ATP-dependent DNA helicase RecG complement(1236788..1238881) Paracoccus denitrificans PD1222 4582633 YP_917845.1 CDS Pden_4083 NC_008687.1 1238878 1241175 R 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 complement(1238878..1241175) Paracoccus denitrificans PD1222 4582634 YP_917846.1 CDS Pden_4084 NC_008687.1 1241333 1241506 R KEGG: mmr:Mmar10_0669 two component transcriptional regulator, winged helix family; response regulator receiver protein complement(1241333..1241506) Paracoccus denitrificans PD1222 4582635 YP_917847.1 CDS Pden_4085 NC_008687.1 1241524 1241892 R hypothetical protein complement(1241524..1241892) Paracoccus denitrificans PD1222 4582636 YP_917848.1 CDS Pden_4086 NC_008687.1 1241928 1242326 D hypothetical protein 1241928..1242326 Paracoccus denitrificans PD1222 4582637 YP_917849.1 CDS Pden_4087 NC_008687.1 1242832 1243461 R PFAM: protein of unknown function DUF847; KEGG: bmb:BruAb1_0990 secretion activator protein, hypothetical; hypothetical protein complement(1242832..1243461) Paracoccus denitrificans PD1222 4582638 YP_917850.1 CDS Pden_4088 NC_008687.1 1243464 1243733 R hypothetical protein complement(1243464..1243733) Paracoccus denitrificans PD1222 4582639 YP_917851.1 CDS Pden_4089 NC_008687.1 1243733 1245883 R PFAM: metallophosphoesterase; KEGG: nha:Nham_3850 complement C1q protein; metallophosphoesterase complement(1243733..1245883) Paracoccus denitrificans PD1222 4582640 YP_917852.1 CDS Pden_4090 NC_008687.1 1245880 1246230 R hypothetical protein complement(1245880..1246230) Paracoccus denitrificans PD1222 4582641 YP_917853.1 CDS Pden_4091 NC_008687.1 1246230 1247267 R KEGG: sat:SYN_02283 hypothetical cytosolic protein; hypothetical protein complement(1246230..1247267) Paracoccus denitrificans PD1222 4582642 YP_917854.1 CDS Pden_4092 NC_008687.1 1247347 1247706 D KEGG: mlo:mll5675 hypothetical protein; hypothetical protein 1247347..1247706 Paracoccus denitrificans PD1222 4582643 YP_917855.1 CDS Pden_4093 NC_008687.1 1247883 1249376 R KEGG: jan:Jann_0236 hypothetical protein; hypothetical protein complement(1247883..1249376) Paracoccus denitrificans PD1222 4582644 YP_917856.1 CDS Pden_4094 NC_008687.1 1249366 1250628 R hypothetical protein complement(1249366..1250628) Paracoccus denitrificans PD1222 4582645 YP_917857.1 CDS Pden_4095 NC_008687.1 1250937 1251944 D PFAM: phage integrase family protein; KEGG: mag:amb2709 integrase; phage integrase family protein 1250937..1251944 Paracoccus denitrificans PD1222 4582646 YP_917858.1 CDS Pden_4096 NC_008687.1 1251970 1252524 R PFAM: response regulator receiver; KEGG: sil:SPO1679 DNA-binding response regulator CtrA; two component transcriptional regulator complement(1251970..1252524) Paracoccus denitrificans PD1222 4582647 YP_917859.1 CDS Pden_4097 NC_008687.1 1252581 1252892 R PFAM: protein of unknown function DUF1153; KEGG: rsp:RSP_2620 hypothetical protein; hypothetical protein complement(1252581..1252892) Paracoccus denitrificans PD1222 4582648 YP_917860.1 CDS mnmA NC_008687.1 1253056 1254225 D catalyzes a sulfuration reaction to synthesize 2-thiouridine at the U34 position of tRNAs; tRNA-specific 2-thiouridylase MnmA 1253056..1254225 Paracoccus denitrificans PD1222 4582649 YP_917861.1 CDS Pden_4099 NC_008687.1 1254239 1254646 R PFAM: Fe-S metabolism associated SufE; KEGG: jan:Jann_1840 Fe-S metabolism associated SufE; Fe-S metabolism associated SufE complement(1254239..1254646) Paracoccus denitrificans PD1222 4582650 YP_917862.1 CDS Pden_4100 NC_008687.1 1254775 1255284 D KEGG: rsp:RSP_1972 hypothetical protein; hypothetical protein 1254775..1255284 Paracoccus denitrificans PD1222 4582651 YP_917863.1 CDS Pden_4101 NC_008687.1 1255587 1256132 R PFAM: GCN5-related N-acetyltransferase; KEGG: rsp:RSP_3821 acetyltransferase; N-acetyltransferase GCN5 complement(1255587..1256132) Paracoccus denitrificans PD1222 4582652 YP_917864.1 CDS rpmA NC_008687.1 1256245 1256517 R involved in the peptidyltransferase reaction during translation; 50S ribosomal protein L27 complement(1256245..1256517) Paracoccus denitrificans PD1222 4582653 YP_917865.1 CDS rplU NC_008687.1 1256537 1256959 R PFAM: ribosomal protein L21; KEGG: sil:SPO1990 ribosomal protein L21; 50S ribosomal protein L21 complement(1256537..1256959) Paracoccus denitrificans PD1222 4582654 YP_917866.1 CDS Pden_4104 NC_008687.1 1257151 1258212 R PFAM: L-carnitine dehydratase/bile acid-inducible protein F; KEGG: sco:SCO6730 racemase; L-carnitine dehydratase/bile acid-inducible protein F complement(1257151..1258212) Paracoccus denitrificans PD1222 4582655 YP_917867.1 CDS Pden_4105 NC_008687.1 1258639 1258827 R KEGG: sil:SPO2944 hypothetical protein; hypothetical protein complement(1258639..1258827) Paracoccus denitrificans PD1222 4582656 YP_917868.1 CDS Pden_4106 NC_008687.1 1258997 1260334 R KEGG: rha:RHA1_ro05532 nitrilotriacetate monooxygenase; nitrilotriacetate monooxygenase complement(1258997..1260334) Paracoccus denitrificans PD1222 4582657 YP_917869.1 CDS Pden_4107 NC_008687.1 1260347 1261075 R PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: mlo:mll9179 ABC transporter ATP-binding subunit; ABC transporter complement(1260347..1261075) Paracoccus denitrificans PD1222 4582658 YP_917870.1 CDS Pden_4108 NC_008687.1 1261072 1261923 R PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: nfa:nfa18270 transporter; binding-protein-dependent transport system inner membrane protein complement(1261072..1261923) Paracoccus denitrificans PD1222 4582659 YP_917871.1 CDS Pden_4109 NC_008687.1 1261944 1263161 R KEGG: nfa:nfa18260 sulfonate/nitrate transport system substrate-binding protein; sulfonate/nitrate transport system substrate-binding protein complement(1261944..1263161) Paracoccus denitrificans PD1222 4582660 YP_917872.1 CDS Pden_4110 NC_008687.1 1263193 1263993 R PFAM: HpcH/HpaI aldolase; KEGG: bmb:BruAb2_0163 hypothetical citrate lyase, beta subunit; HpcH/HpaI aldolase complement(1263193..1263993) Paracoccus denitrificans PD1222 4582661 YP_917873.1 CDS Pden_4111 NC_008687.1 1263987 1264820 R KEGG: bmb:BruAb2_0162 hypothetical protein; hypothetical protein complement(1263987..1264820) Paracoccus denitrificans PD1222 4582662 YP_917874.1 CDS Pden_4112 NC_008687.1 1264817 1265923 R PFAM: L-carnitine dehydratase/bile acid-inducible protein F; KEGG: rpa:RPA1611 dehydratase; L-carnitine dehydratase/bile acid-inducible protein F complement(1264817..1265923) Paracoccus denitrificans PD1222 4582663 YP_917875.1 CDS Pden_4115 NC_008687.1 1267193 1267576 R PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase; KEGG: pfl:PFL_3598 glyoxalase family protein; glyoxalase/bleomycin resistance protein/dioxygenase complement(1267193..1267576) Paracoccus denitrificans PD1222 4582665 YP_917876.1 CDS Pden_4116 NC_008687.1 1267591 1269003 R KEGG: rru:Rru_A2561 hypothetical protein; hypothetical protein complement(1267591..1269003) Paracoccus denitrificans PD1222 4582666 YP_917877.1 CDS Pden_4117 NC_008687.1 1269315 1270067 D 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 1269315..1270067 Paracoccus denitrificans PD1222 4582667 YP_917878.1 CDS Pden_4118 NC_008687.1 1270064 1271038 D PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: mag:amb3232 transcriptional regulator; LysR family transcriptional regulator 1270064..1271038 Paracoccus denitrificans PD1222 4582668 YP_917879.1 CDS Pden_4119 NC_008687.1 1271048 1272553 D 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 1271048..1272553 Paracoccus denitrificans PD1222 4582669 YP_917880.1 CDS Pden_4120 NC_008687.1 1272599 1273921 R 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 complement(1272599..1273921) Paracoccus denitrificans PD1222 4582670 YP_917881.1 CDS Pden_4121 NC_008687.1 1273918 1274550 R 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 complement(1273918..1274550) Paracoccus denitrificans PD1222 4582671 YP_917882.1 CDS Pden_4122 NC_008687.1 1274606 1275613 R 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 complement(1274606..1275613) Paracoccus denitrificans PD1222 4582672 YP_917883.1 CDS Pden_4123 NC_008687.1 1276073 1277380 R TIGRFAM: small GTP-binding protein; PFAM: GTP-binding protein, HSR1-related; KEGG: rsp:RSP_2844 GTP-binding protein; small GTP-binding protein complement(1276073..1277380) Paracoccus denitrificans PD1222 4582673 YP_917884.1 CDS hfq NC_008687.1 1277381 1277614 R Stimulates the elongation of poly(A) tails; RNA-binding protein Hfq complement(1277381..1277614) Paracoccus denitrificans PD1222 4582674 YP_917885.1 CDS Pden_4125 NC_008687.1 1277695 1279317 R PFAM: cation transporter; KEGG: rsp:RSP_2842 potassium uptake transporter, transmembrane subunit, TrkH; cation transporter complement(1277695..1279317) Paracoccus denitrificans PD1222 4582675 YP_917886.1 CDS trkA NC_008687.1 1279326 1280702 R 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 complement(1279326..1280702) Paracoccus denitrificans PD1222 4582676 YP_917887.1 CDS Pden_4127 NC_008687.1 1281036 1282424 R 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 complement(1281036..1282424) Paracoccus denitrificans PD1222 4582677 YP_917888.1 CDS Pden_4128 NC_008687.1 1282421 1284679 R 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 complement(1282421..1284679) Paracoccus denitrificans PD1222 4582678 YP_917889.1 CDS Pden_4129 NC_008687.1 1284765 1286222 R 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 complement(1284765..1286222) Paracoccus denitrificans PD1222 4582679 YP_917890.1 CDS Pden_4130 NC_008687.1 1286231 1287388 R 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 complement(1286231..1287388) Paracoccus denitrificans PD1222 4582680 YP_917891.1 CDS Pden_4131 NC_008687.1 1287385 1288434 R 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 complement(1287385..1288434) Paracoccus denitrificans PD1222 4582681 YP_917892.1 CDS Pden_4132 NC_008687.1 1288663 1290045 D 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 1288663..1290045 Paracoccus denitrificans PD1222 4582682 YP_917893.1 CDS Pden_4133 NC_008687.1 1290172 1291083 D KEGG: cal:orf19.4334 hypothetical protein; FHA domain-containing protein 1290172..1291083 Paracoccus denitrificans PD1222 4582683 YP_917894.1 CDS Pden_4134 NC_008687.1 1291171 1293366 D PFAM: protein of unknown function DUF940, membrane lipoprotein KEGG: rsp:RSP_1187 hypothetical protein; membrane lipoprotein 1291171..1293366 Paracoccus denitrificans PD1222 4582684 YP_917895.1 CDS Pden_4135 NC_008687.1 1293363 1294031 D KEGG: rsp:RSP_1186 hypothetical protein; hypothetical protein 1293363..1294031 Paracoccus denitrificans PD1222 4582685 YP_917896.1 CDS Pden_4136 NC_008687.1 1294204 1294596 R hypothetical protein complement(1294204..1294596) Paracoccus denitrificans PD1222 4582686 YP_917897.1 CDS Pden_4137 NC_008687.1 1294622 1295404 R PFAM: ABC-3 protein; KEGG: rsp:RSP_3567 ABC zinc tranporter, inner membrane subunit ZnuB; ABC-3 protein complement(1294622..1295404) Paracoccus denitrificans PD1222 4582687 YP_917898.1 CDS Pden_4138 NC_008687.1 1295411 1296175 R PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rsp:RSP_3568 ABC zinc transporter, ATPase subunit ZnuC; ABC transporter complement(1295411..1296175) Paracoccus denitrificans PD1222 4582688 YP_917899.1 CDS Pden_4139 NC_008687.1 1296172 1296666 R KEGG: rsp:RSP_3569 zinc-uptake regulator, Zur; ferric uptake regulator family protein complement(1296172..1296666) Paracoccus denitrificans PD1222 4582689 YP_917900.1 CDS Pden_4140 NC_008687.1 1296748 1297728 D PFAM: periplasmic solute binding protein; KEGG: rsp:RSP_3571 ABC zinc transporter, periplasmic binding protein ZnuA; periplasmic solute binding protein 1296748..1297728 Paracoccus denitrificans PD1222 4582690 YP_917901.1 CDS Pden_4141 NC_008687.1 1297911 1298087 D KEGG: sil:SPO0789 hypothetical protein; hypothetical protein 1297911..1298087 Paracoccus denitrificans PD1222 4582691 YP_917902.1 CDS Pden_4142 NC_008687.1 1298113 1299486 R PFAM: RNA-binding S4 domain protein; pseudouridine synthase; KEGG: rsp:RSP_2266 pseudouridine synthase, (predicted); RNA-binding S4 domain-containing protein complement(1298113..1299486) Paracoccus denitrificans PD1222 4582692 YP_917903.1 CDS Pden_4143 NC_008687.1 1299595 1300044 D PFAM: CMP/dCMP deaminase, zinc-binding; KEGG: rde:RD1_1993 cytidine and deoxycytidylate deaminase family protein; zinc-binding CMP/dCMP deaminase 1299595..1300044 Paracoccus denitrificans PD1222 4582693 YP_917904.1 CDS Pden_4144 NC_008687.1 1300140 1303574 D biotin-containing enzyme that catalyzes a two step carboxylation of pyruvate to oxaloacetate; pyruvate carboxylase 1300140..1303574 Paracoccus denitrificans PD1222 4582694 YP_917905.1 CDS Pden_4145 NC_008687.1 1303951 1305000 R PFAM: protein of unknown function DUF395, YeeE/YedE; KEGG: sil:SPO0988 YeeE/YedE family protein; hypothetical protein complement(1303951..1305000) Paracoccus denitrificans PD1222 4582695 YP_917906.1 CDS Pden_4146 NC_008687.1 1305071 1305412 R PFAM: regulatory protein, ArsR; KEGG: rsp:RSP_2606 ArsR family arsenical resistance operon repressor; regulatory protein ArsR complement(1305071..1305412) Paracoccus denitrificans PD1222 4582696 YP_917907.1 CDS Pden_4147 NC_008687.1 1305520 1305903 R KEGG: rde:RD1_1508 SoxS; SoxS complement(1305520..1305903) Paracoccus denitrificans PD1222 4582697 YP_917908.1 CDS Pden_4148 NC_008687.1 1305975 1306712 D PFAM: cytochrome c biogenesis protein, transmembrane region; KEGG: sil:SPO0991 sulfur oxidation V protein; cytochrome c biogenesis protein, transmembrane region 1305975..1306712 Paracoccus denitrificans PD1222 4582698 YP_917909.1 CDS Pden_4149 NC_008687.1 1306726 1307286 D KEGG: sil:SPO0992 thioredoxin SoxW; thioredoxin SoxW 1306726..1307286 Paracoccus denitrificans PD1222 4582699 YP_917910.1 CDS Pden_4150 NC_008687.1 1307402 1307875 D PFAM: cytochrome c, class I; KEGG: sil:SPO0993 monoheme cytochrome c SoxX; cytochrome c, class I 1307402..1307875 Paracoccus denitrificans PD1222 4582700 YP_917911.1 CDS Pden_4151 NC_008687.1 1307915 1308337 D with SoxZ catalyzes the oxidation of sulfur compounds; sulfur oxidation protein SoxY 1307915..1308337 Paracoccus denitrificans PD1222 4582701 YP_917912.1 CDS Pden_4152 NC_008687.1 1308359 1308688 D KEGG: rde:RD1_1513 sulfur oxidation Z protein; sulfur oxidation Z protein 1308359..1308688 Paracoccus denitrificans PD1222 4582702 YP_917913.1 CDS Pden_4153 NC_008687.1 1308725 1309597 D KEGG: sil:SPO0996 diheme cytochrome c SoxA; diheme cytochrome c SoxA 1308725..1309597 Paracoccus denitrificans PD1222 4582703 YP_917914.1 CDS Pden_4154 NC_008687.1 1309716 1311410 D PFAM: metallophosphoesterase; 5'-Nucleotidase domain protein; KEGG: sil:SPO0997 sulfur oxidation B protein; 5'-nucleotidase domain-containing protein 1309716..1311410 Paracoccus denitrificans PD1222 4582704 YP_917915.1 CDS Pden_4155 NC_008687.1 1311433 1312725 D PFAM: oxidoreductase, molybdopterin binding; Mo-co oxidoreductase dimerisation domain; KEGG: rde:RD1_1516 sulfite dehydrogenase SoxC protein; oxidoreductase, molybdopterin binding 1311433..1312725 Paracoccus denitrificans PD1222 4582705 YP_917916.1 CDS Pden_4156 NC_008687.1 1312709 1313857 D PFAM: cytochrome c, class I; KEGG: sil:SPO0999 diheme cytochrome c SoxD; cytochrome c, class I 1312709..1313857 Paracoccus denitrificans PD1222 4582706 YP_917917.1 CDS Pden_4157 NC_008687.1 1313861 1314571 D PFAM: cytochrome c, class I; KEGG: rde:RD1_1518 cytochrome c2; cytochrome c, class I 1313861..1314571 Paracoccus denitrificans PD1222 4582707 YP_917918.1 CDS Pden_4158 NC_008687.1 1314627 1315889 D PFAM: FAD-dependent pyridine nucleotide-disulphide oxidoreductase; KEGG: sil:SPO1001 sulfur oxidation F protein; FAD-dependent pyridine nucleotide-disulfide oxidoreductase 1314627..1315889 Paracoccus denitrificans PD1222 4582708 YP_917919.1 CDS Pden_4159 NC_008687.1 1315907 1316818 D PFAM: beta-lactamase domain protein; KEGG: sil:SPO0788 metallo-beta-lactamase family protein; beta-lactamase domain-containing protein 1315907..1316818 Paracoccus denitrificans PD1222 4582709 YP_917920.1 CDS Pden_4160 NC_008687.1 1316818 1317756 D KEGG: sil:SPO2822 SoxH protein, homolog; SoxH protein-like 1316818..1317756 Paracoccus denitrificans PD1222 4582710 YP_917921.1 CDS Pden_4161 NC_008687.1 1317760 1318842 R PFAM: protein of unknown function DUF395, YeeE/YedE; KEGG: sil:SPO3123 YeeE/YedE family protein; hypothetical protein complement(1317760..1318842) Paracoccus denitrificans PD1222 4582711 YP_917922.1 CDS Pden_4162 NC_008687.1 1319216 1320298 D KEGG: ana:all1980 unknown protein; hypothetical protein 1319216..1320298 Paracoccus denitrificans PD1222 4582712 YP_917923.1 CDS Pden_4163 NC_008687.1 1320373 1321368 D KEGG: sit:TM1040_2280 hypothetical protein; hypothetical protein 1320373..1321368 Paracoccus denitrificans PD1222 4582713 YP_917924.1 CDS Pden_4164 NC_008687.1 1321384 1321752 R PFAM: helix-turn-helix, HxlR type; KEGG: bja:bll5105 transcriptional regulatory protein; HxlR family transcriptional regulator complement(1321384..1321752) Paracoccus denitrificans PD1222 4582714 YP_917925.1 CDS Pden_4165 NC_008687.1 1321888 1322436 D PFAM: NAD(P)H dehydrogenase (quinone); NADPH-dependent FMN reductase; KEGG: bja:blr5106 acyl-carrier-protein phosphodiesterase; ACP phosphodiesterase 1321888..1322436 Paracoccus denitrificans PD1222 4582715 YP_917926.1 CDS Pden_4166 NC_008687.1 1322456 1323625 R PFAM: NnrS family protein; KEGG: atc:AGR_L_924 hypothetical protein; NnrS family protein complement(1322456..1323625) Paracoccus denitrificans PD1222 4582716 YP_917927.1 CDS Pden_4167 NC_008687.1 1323622 1324371 R PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: atc:AGR_L_926 probable ATP-binding component of ABC taurine transporter; ABC transporter complement(1323622..1324371) Paracoccus denitrificans PD1222 4582717 YP_917928.1 CDS Pden_4168 NC_008687.1 1324368 1325186 R 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 complement(1324368..1325186) Paracoccus denitrificans PD1222 4582718 YP_917929.1 CDS Pden_4169 NC_008687.1 1325183 1326178 R KEGG: atc:AGR_L_928 sulfonate/nitrate transport system substrate-binding protein; sulfonate/nitrate transport system substrate-binding protein complement(1325183..1326178) Paracoccus denitrificans PD1222 4582719 YP_917930.1 CDS Pden_4170 NC_008687.1 1326284 1326589 R KEGG: nha:Nham_2539 hypothetical protein; hypothetical protein complement(1326284..1326589) Paracoccus denitrificans PD1222 4582720 YP_917931.1 CDS Pden_4171 NC_008687.1 1326586 1327206 R KEGG: net:Neut_2232 conserved hypothetical protein; hypothetical protein complement(1326586..1327206) Paracoccus denitrificans PD1222 4582721 YP_917932.1 CDS Pden_4172 NC_008687.1 1327210 1327758 R 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 complement(1327210..1327758) Paracoccus denitrificans PD1222 4582722 YP_917933.1 CDS Pden_4173 NC_008687.1 1327758 1329977 R PFAM: TonB-dependent receptor; TonB-dependent receptor, plug; KEGG: rpd:RPD_3065 TonB-dependent receptor; TonB-dependent receptor complement(1327758..1329977) Paracoccus denitrificans PD1222 4582723 YP_917934.1 CDS Pden_4174 NC_008687.1 1330301 1331233 D PFAM: sugar-binding domain protein; KEGG: mes:Meso_3776 transcriptional regulator, DeoR family; DeoR family transcriptional regulator 1330301..1331233 Paracoccus denitrificans PD1222 4582724 YP_917935.1 CDS Pden_4175 NC_008687.1 1331237 1332679 R PFAM: carbohydrate kinase, FGGY; KEGG: mes:Meso_3784 FGGY-family pentulose kinase; carbohydrate kinase complement(1331237..1332679) Paracoccus denitrificans PD1222 4582725 YP_917936.1 CDS Pden_4176 NC_008687.1 1332694 1333350 R TIGRFAM: HAD-superfamily hydrolase, subfamily IA, variant 3; PFAM: Haloacid dehalogenase domain protein hydrolase; KEGG: atc:AGR_L_828 hypothetical protein; HAD family hydrolase complement(1332694..1333350) Paracoccus denitrificans PD1222 4582726 YP_917937.1 CDS Pden_4177 NC_008687.1 1333354 1334817 R PFAM: Mannitol dehydrogenase, C-terminal domain; Mannitol dehydrogenase rossman, N-terminal domain; KEGG: mlo:mll4920 mannitol dehydrogenase; mannitol dehydrogenase complement(1333354..1334817) Paracoccus denitrificans PD1222 4582727 YP_917938.1 CDS Pden_4178 NC_008687.1 1334887 1335885 R PFAM: ABC transporter related; TOBE domain protein; Transport-associated OB domain protein; SMART: AAA ATPase; KEGG: sit:TM1040_0428 ABC transporter related; ABC transporter complement(1334887..1335885) Paracoccus denitrificans PD1222 4582728 YP_917939.1 CDS Pden_4179 NC_008687.1 1335897 1336727 R 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 complement(1335897..1336727) Paracoccus denitrificans PD1222 4582729 YP_917940.1 CDS Pden_4180 NC_008687.1 1336733 1337602 R 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 complement(1336733..1337602) Paracoccus denitrificans PD1222 4582730 YP_917941.1 CDS Pden_4181 NC_008687.1 1337701 1339008 R PFAM: extracellular solute-binding protein, family 1; KEGG: sme:SMc01496 probable sorbitol-binding periplasmic protein; extracellular solute-binding protein complement(1337701..1339008) Paracoccus denitrificans PD1222 4582731 YP_917942.1 CDS Pden_4182 NC_008687.1 1339157 1339621 R NADPH-dependent; catalyzes the reduction of 7-cyano-7-deazaguanine to 7-aminomethyl-7-deazaguanine in queuosine biosynthesis; 7-cyano-7-deazaguanine reductase complement(1339157..1339621) Paracoccus denitrificans PD1222 4582732 YP_917943.1 CDS Pden_4183 NC_008687.1 1339637 1340344 R PFAM: Radical SAM domain protein; KEGG: sit:TM1040_2045 radical SAM; radical SAM domain-containing protein complement(1339637..1340344) Paracoccus denitrificans PD1222 4582733 YP_917944.1 CDS Pden_4184 NC_008687.1 1340341 1340694 R PFAM: 6-pyruvoyl tetrahydropterin synthase and hypothetical protein; KEGG: sit:TM1040_2046 6-pyruvoyl tetrahydropterin synthase and hypothetical protein; 6-pyruvoyl tetrahydrobiopterin synthase complement(1340341..1340694) Paracoccus denitrificans PD1222 4582734 YP_917945.1 CDS Pden_4185 NC_008687.1 1340694 1341395 R TIGRFAM: exsB protein; PFAM: ExsB family protein; KEGG: sit:TM1040_2047 ExsB; exsB protein complement(1340694..1341395) Paracoccus denitrificans PD1222 4582735 YP_917946.1 CDS Pden_4186 NC_008687.1 1341593 1342585 D KEGG: mes:Meso_1301 hypothetical protein; hypothetical protein 1341593..1342585 Paracoccus denitrificans PD1222 4582736 YP_917947.1 CDS ugpC NC_008687.1 1342595 1343656 R part of the UgpABCE glycerol-3-phosphate uptake system; glycerol-3-phosphate transporter ATP-binding subunit complement(1342595..1343656) Paracoccus denitrificans PD1222 4582737 YP_917948.1 CDS Pden_4188 NC_008687.1 1343657 1344520 R 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 complement(1343657..1344520) Paracoccus denitrificans PD1222 4582738 YP_917949.1 CDS Pden_4189 NC_008687.1 1344513 1345394 R 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 complement(1344513..1345394) Paracoccus denitrificans PD1222 4582739 YP_917950.1 CDS Pden_4190 NC_008687.1 1345444 1346739 R PFAM: extracellular solute-binding protein, family 1; KEGG: rsp:RSP_3290 ABC glycerol-3-phosphate transporter, periplasmic binding protein, UgpB; extracellular solute-binding protein complement(1345444..1346739) Paracoccus denitrificans PD1222 4582740 YP_917951.1 CDS Pden_4191 NC_008687.1 1346993 1348057 D hypothetical protein 1346993..1348057 Paracoccus denitrificans PD1222 4582741 YP_917952.1 CDS Pden_4192 NC_008687.1 1348066 1349481 D KEGG: gvi:glr3599 hypothetical protein; hypothetical protein 1348066..1349481 Paracoccus denitrificans PD1222 4582742 YP_917953.1 CDS Pden_4193 NC_008687.1 1349495 1350223 D hypothetical protein 1349495..1350223 Paracoccus denitrificans PD1222 4582743 YP_917954.1 CDS Pden_4194 NC_008687.1 1350220 1352109 R PFAM: transcriptional activator domain; Tetratricopeptide TPR_2 repeat protein; KEGG: mlo:mlr7075 similar to trifolitoxin synthesis, TfuA; SARP family transcriptional regulator complement(1350220..1352109) Paracoccus denitrificans PD1222 4582744 YP_917955.1 CDS Pden_4195 NC_008687.1 1352237 1353016 R PFAM: nitroreductase; KEGG: tko:TK0839 NAD(P)H-flavin oxidoreductase; nitroreductase complement(1352237..1353016) Paracoccus denitrificans PD1222 4582745 YP_917956.1 CDS Pden_4196 NC_008687.1 1353021 1354331 R TIGRFAM: uncharacterized domain; PFAM: protein of unknown function DUF181; KEGG: bcn:Bcen_5136 protein of unknown function DUF181; hypothetical protein complement(1353021..1354331) Paracoccus denitrificans PD1222 4582746 YP_917957.1 CDS Pden_4197 NC_008687.1 1354328 1355443 R PFAM: UBA/THIF-type NAD/FAD binding protein; KEGG: ccr:CC3726 molybdopterin biosynthesis protein MoeB; UBA/THIF-type NAD/FAD binding protein complement(1354328..1355443) Paracoccus denitrificans PD1222 4582747 YP_917958.1 CDS Pden_4198 NC_008687.1 1355415 1357277 R PFAM: Radical SAM domain protein; SMART: Elongator protein 3/MiaB/NifB; KEGG: sus:Acid_0877 radical SAM domain protein; radical SAM domain-containing protein complement(1355415..1357277) Paracoccus denitrificans PD1222 4582748 YP_917959.1 CDS Pden_4199 NC_008687.1 1357309 1357701 R hypothetical protein complement(1357309..1357701) Paracoccus denitrificans PD1222 4582749 YP_917960.1 CDS Pden_4200 NC_008687.1 1358307 1360007 D 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 1358307..1360007 Paracoccus denitrificans PD1222 4582750 YP_917961.1 CDS Pden_4201 NC_008687.1 1360113 1362173 R 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 complement(1360113..1362173) Paracoccus denitrificans PD1222 4582751 YP_917962.1 CDS Pden_4202 NC_008687.1 1362333 1363373 D PFAM: Haemin-degrading family protein; KEGG: jan:Jann_2133 haemin-degrading; hemin-degrading family protein 1362333..1363373 Paracoccus denitrificans PD1222 4582752 YP_917963.1 CDS Pden_4203 NC_008687.1 1363370 1364245 D PFAM: periplasmic binding protein; KEGG: rde:RD1_4189 hemin ABC transporter, periplasmic hemin-binding protein; periplasmic binding protein 1363370..1364245 Paracoccus denitrificans PD1222 4582753 YP_917964.1 CDS Pden_4204 NC_008687.1 1364245 1365321 D PFAM: transport system permease; KEGG: jan:Jann_2135 transport system permease; transport system permease 1364245..1365321 Paracoccus denitrificans PD1222 4582754 YP_917965.1 CDS hmuV NC_008687.1 1365318 1366091 D with HmuTU is involved in the transport of hemin; hemin importer ATP-binding subunit 1365318..1366091 Paracoccus denitrificans PD1222 4582755 YP_917966.1 CDS Pden_4206 NC_008687.1 1366192 1367175 D PFAM: Alcohol dehydrogenase GroES domain protein; KEGG: bja:blr6070 alcohol dehydrogenase; alcohol dehydrogenase 1366192..1367175 Paracoccus denitrificans PD1222 4582756 YP_917967.1 CDS Pden_4207 NC_008687.1 1367233 1369002 D 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 1367233..1369002 Paracoccus denitrificans PD1222 4582757 YP_917968.1 CDS Pden_4208 NC_008687.1 1368999 1370102 R TIGRFAM: acetate kinase; PFAM: acetate and butyrate kinase; KEGG: lpn:lpg2262 acetate kinase; acetate kinase complement(1368999..1370102) Paracoccus denitrificans PD1222 4582758 YP_917969.1 CDS Pden_4209 NC_008687.1 1370099 1371025 R PFAM: phosphate acetyl/butaryl transferase; KEGG: lpp:lpp2215 phosphate acetyltransferase; phosphate butyryltransferase complement(1370099..1371025) Paracoccus denitrificans PD1222 4582759 YP_917970.1 CDS Pden_4210 NC_008687.1 1371199 1371570 R PFAM: response regulator receiver; KEGG: rsp:RSP_0573 response regulator receiver protein; response regulator receiver protein complement(1371199..1371570) Paracoccus denitrificans PD1222 4582760 YP_917971.1 CDS actP NC_008687.1 1371664 1373379 R member of the sodium:solute symporter family; cotranscribed with the acs gene which encodes acetyl coenzyme A synthase; mutations affect acetate uptake; acetate permease complement(1371664..1373379) Paracoccus denitrificans PD1222 4582761 YP_917972.1 CDS Pden_4212 NC_008687.1 1373376 1373684 R PFAM: protein of unknown function DUF485; KEGG: rsp:RSP_3141 hypothetical protein; hypothetical protein complement(1373376..1373684) Paracoccus denitrificans PD1222 4582762 YP_917973.1 CDS Pden_4213 NC_008687.1 1373891 1375846 R TIGRFAM: acetate--CoA ligase; PFAM: AMP-dependent synthetase and ligase; KEGG: rsp:RSP_0579 acetyl-coenzyme A synthetase; acetate--CoA ligase complement(1373891..1375846) Paracoccus denitrificans PD1222 4582763 YP_917974.1 CDS Pden_4214 NC_008687.1 1376134 1377048 R PFAM: ApbE family lipoprotein; KEGG: rpc:RPC_0433 twin-arginine translocation pathway signal; ApbE family lipoprotein complement(1376134..1377048) Paracoccus denitrificans PD1222 4582764 YP_917975.1 CDS Pden_4215 NC_008687.1 1377045 1377620 R PFAM: NosL family protein; KEGG: sil:SPOA0054 nitrous oxide reductase accessory protein; NosL family protein complement(1377045..1377620) Paracoccus denitrificans PD1222 4582765 YP_917976.1 CDS Pden_4216 NC_008687.1 1377617 1378441 R KEGG: sil:SPOA0053 nitrous oxide maturation protein NosY; nitrous oxide maturation protein NosY complement(1377617..1378441) Paracoccus denitrificans PD1222 4582766 YP_917977.1 CDS Pden_4217 NC_008687.1 1378438 1379337 R PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sil:SPOA0052 ABC transporter, ATP-binding protein NosF; ABC transporter complement(1378438..1379337) Paracoccus denitrificans PD1222 4582767 YP_917978.1 CDS Pden_4218 NC_008687.1 1379303 1380634 R 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 complement(1379303..1380634) Paracoccus denitrificans PD1222 4582768 YP_917979.1 CDS Pden_4219 NC_008687.1 1380640 1382598 R reduces nitrous oxide to nitrogen; nitrous-oxide reductase complement(1380640..1382598) Paracoccus denitrificans PD1222 4582769 YP_917980.1 CDS Pden_4220 NC_008687.1 1382616 1384796 R PFAM: FMN-binding domain protein; KEGG: sil:SPOA0049 nitrous-oxide reductase transcriptional activator NosR; FMN-binding domain-containing protein complement(1382616..1384796) Paracoccus denitrificans PD1222 4582770 YP_917981.1 CDS Pden_4221 NC_008687.1 1384793 1385203 R hypothetical protein complement(1384793..1385203) Paracoccus denitrificans PD1222 4582771 YP_917982.1 CDS Pden_4222 NC_008687.1 1385540 1385983 D TIGRFAM: pseudoazurin; PFAM: blue (type 1) copper domain protein; KEGG: sme:SMa1243 Azu1 pseudoazurin (blue copper protein); pseudoazurin 1385540..1385983 Paracoccus denitrificans PD1222 4582772 YP_917983.1 CDS Pden_4223 NC_008687.1 1386142 1386414 D KEGG: rde:RD1_1693 hypothetical protein; hypothetical protein 1386142..1386414 Paracoccus denitrificans PD1222 4582773 YP_917984.1 CDS Pden_4224 NC_008687.1 1386481 1387161 R PFAM: protein of unknown function DUF542, ScdA domain protein; Hemerythrin HHE cation binding domain protein; KEGG: sme:SMa1195 hypothetical protein; hypothetical protein complement(1386481..1387161) Paracoccus denitrificans PD1222 4582774 YP_917985.1 CDS Pden_4225 NC_008687.1 1387139 1387732 R 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 complement(1387139..1387732) Paracoccus denitrificans PD1222 4582775 YP_917986.1 CDS Pden_4226 NC_008687.1 1387729 1389198 R TIGRFAM: UbiD family decarboxylases; PFAM: Carboxylyase-related protein; KEGG: rsp:RSP_0467 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; UbiD family decarboxylase complement(1387729..1389198) Paracoccus denitrificans PD1222 4582776 YP_917987.1 CDS Pden_4227 NC_008687.1 1389319 1389852 D KEGG: rsp:RSP_0466 hypothetical protein; hypothetical protein 1389319..1389852 Paracoccus denitrificans PD1222 4582777 YP_917988.1 CDS Pden_4228 NC_008687.1 1389849 1390844 D PFAM: peptidase U32; KEGG: rsp:RSP_0465 protease; peptidase U32 1389849..1390844 Paracoccus denitrificans PD1222 4582778 YP_917989.1 CDS Pden_4229 NC_008687.1 1390847 1391737 D PFAM: peptidase U32; KEGG: rsp:RSP_0464 protease; peptidase U32 1390847..1391737 Paracoccus denitrificans PD1222 4582779 YP_917990.1 CDS Pden_4230 NC_008687.1 1391761 1392975 D PFAM: NnrS family protein; KEGG: rde:RD1_1694 NnrS protein; NnrS family protein 1391761..1392975 Paracoccus denitrificans PD1222 4582780 YP_917991.1 CDS Pden_4231 NC_008687.1 1393035 1393547 R KEGG: sil:SPO1135 hypothetical protein; hypothetical protein complement(1393035..1393547) Paracoccus denitrificans PD1222 4582781 YP_917992.1 CDS Pden_4232 NC_008687.1 1393547 1394350 R PFAM: PpiC-type peptidyl-prolyl cis-trans isomerase; KEGG: rde:RD1_2446 peptidyl-prolyl cis-trans isomerase; PpiC-type peptidyl-prolyl cis-trans isomerase complement(1393547..1394350) Paracoccus denitrificans PD1222 4582782 YP_917993.1 CDS Pden_4233 NC_008687.1 1394356 1395057 R 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 complement(1394356..1395057) Paracoccus denitrificans PD1222 4582783 YP_917994.1 CDS Pden_4234 NC_008687.1 1395072 1395761 R 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 complement(1395072..1395761) Paracoccus denitrificans PD1222 4582784 YP_917995.1 CDS Pden_4235 NC_008687.1 1395758 1397275 R 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 complement(1395758..1397275) Paracoccus denitrificans PD1222 4582785 YP_917996.1 CDS Pden_4236 NC_008687.1 1397272 1401036 R TIGRFAM: nitrate reductase, alpha subunit; PFAM: molybdopterin oxidoreductase; molydopterin dinucleotide-binding region; KEGG: rde:RD1_2442 nitrate reductase, alpha subunit; nitrate reductase subunit alpha complement(1397272..1401036) Paracoccus denitrificans PD1222 4582786 YP_917997.1 CDS Pden_4237 NC_008687.1 1401051 1403768 R TIGRFAM: nitrite transporter; PFAM: major facilitator superfamily MFS_1; KEGG: bms:BRA0300 nitrite extrusion protein; nitrite transporter complement(1401051..1403768) Paracoccus denitrificans PD1222 4582787 YP_917998.1 CDS ftrB NC_008687.1 1404042 1404746 D upregulated by FixLJ/FixK under oxygen limitation; involved in regulation of genes involved in carbon and amino acid metabolism; transcriptional activator FtrB 1404042..1404746 Paracoccus denitrificans PD1222 4582788 YP_917999.1 CDS Pden_4239 NC_008687.1 1404840 1405901 D 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 1404840..1405901 Paracoccus denitrificans PD1222 4582789 YP_918000.1 CDS Pden_4240 NC_008687.1 1405972 1406949 D 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 1405972..1406949 Paracoccus denitrificans PD1222 4582790 YP_918001.1 CDS Pden_4241 NC_008687.1 1406954 1408144 R 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 complement(1406954..1408144) Paracoccus denitrificans PD1222 4582791 YP_918002.1 CDS Pden_4242 NC_008687.1 1408491 1408673 D KEGG: atc:AGR_L_2076 hypothetical protein; hypothetical protein 1408491..1408673 Paracoccus denitrificans PD1222 4582792 YP_918003.1 CDS Pden_4243 NC_008687.1 1408704 1409231 D PFAM: GntR domain protein; KEGG: atc:AGR_L_2076 hypothetical protein; GntR family transcriptional regulator 1408704..1409231 Paracoccus denitrificans PD1222 4582793 YP_918004.1 CDS Pden_4244 NC_008687.1 1409413 1410396 D PFAM: Asparaginase/glutaminase; KEGG: atc:AGR_L_2084 L-asparaginase; asparaginase/glutaminase 1409413..1410396 Paracoccus denitrificans PD1222 4582794 YP_918005.1 CDS Pden_4245 NC_008687.1 1410436 1411347 R PFAM: oxidoreductase domain protein; KEGG: mes:Meso_0843 oxidoreductase-like; galactose 1-dehydrogenase complement(1410436..1411347) Paracoccus denitrificans PD1222 4582795 YP_918006.1 CDS Pden_4246 NC_008687.1 1411347 1413095 R catalyzes the formation of 3-methyl-2-oxobutanoate from 2,3,-dihydroxy-3-methylbutanoate; dihydroxy-acid dehydratase complement(1411347..1413095) Paracoccus denitrificans PD1222 4582796 YP_918007.1 CDS Pden_4247 NC_008687.1 1413095 1414078 R PFAM: protein of unknown function DUF1238; KEGG: mlo:mll5655 hypothetical protein; hypothetical protein complement(1413095..1414078) Paracoccus denitrificans PD1222 4582797 YP_918008.1 CDS Pden_4248 NC_008687.1 1414230 1415183 D PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: mes:Meso_0837 transcriptional regulator, LysR family; LysR family transcriptional regulator 1414230..1415183 Paracoccus denitrificans PD1222 4582798 YP_918009.1 CDS Pden_4249 NC_008687.1 1415269 1416657 R PFAM: sodium:dicarboxylate symporter; KEGG: yps:YPTB2365 DAACS family Na/dicarboxylate symporter; sodium:dicarboxylate symporter complement(1415269..1416657) Paracoccus denitrificans PD1222 4582799 YP_918010.1 CDS Pden_4250 NC_008687.1 1416909 1417622 D PFAM: Ankyrin; KEGG: bur:Bcep18194_B0071 ankyrin repeat protein; ankyrin 1416909..1417622 Paracoccus denitrificans PD1222 4582800 YP_918011.1 CDS Pden_4251 NC_008687.1 1417634 1418107 D PFAM: CMP/dCMP deaminase, zinc-binding; KEGG: rme:Rmet_3722 CMP/dCMP deaminase, zinc-binding; zinc-binding CMP/dCMP deaminase 1417634..1418107 Paracoccus denitrificans PD1222 4582801 YP_918012.1 CDS Pden_4252 NC_008687.1 1418104 1419321 D PFAM: major facilitator superfamily MFS_1; KEGG: reu:Reut_B5382 major facilitator superfamily MFS_1; major facilitator transporter 1418104..1419321 Paracoccus denitrificans PD1222 4582802 YP_918013.1 CDS Pden_4253 NC_008687.1 1419350 1419775 D PFAM: protein of unknown function DUF336; KEGG: cps:CPS_4893 GlcG protein; hypothetical protein 1419350..1419775 Paracoccus denitrificans PD1222 4582803 YP_918014.1 CDS Pden_4254 NC_008687.1 1419940 1420677 D PFAM: protein of unknown function DUF81; KEGG: rpa:RPA0111 DUF81; hypothetical protein 1419940..1420677 Paracoccus denitrificans PD1222 4582804 YP_918015.1 CDS Pden_4255 NC_008687.1 1420741 1421979 D KEGG: rsp:RSP_3200 molecular chaperone, DnaK; molecular chaperone DnaK 1420741..1421979 Paracoccus denitrificans PD1222 4582805 YP_918016.1 CDS Pden_4256 NC_008687.1 1422043 1422939 R PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: sit:TM1040_2703 transcriptional regulator, LysR family; LysR family transcriptional regulator complement(1422043..1422939) Paracoccus denitrificans PD1222 4582806 YP_918017.1 CDS Pden_4257 NC_008687.1 1423057 1424502 D 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 1423057..1424502 Paracoccus denitrificans PD1222 4582807 YP_918018.1 CDS Pden_4258 NC_008687.1 1424499 1426811 D PFAM: aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead; aldehyde oxidase and xanthine dehydrogenase, molybdopterin binding; KEGG: sit:TM1040_2705 xanthine dehydrogenase; aldehyde oxidase 1424499..1426811 Paracoccus denitrificans PD1222 4582808 YP_918019.1 CDS Pden_4259 NC_008687.1 1426808 1427551 D PFAM: protein of unknown function DUF182; KEGG: mlo:mlr5136 xanthine dehydrogenase accessory factor; hypothetical protein 1426808..1427551 Paracoccus denitrificans PD1222 4582809 YP_918020.1 CDS Pden_4260 NC_008687.1 1427539 1428816 D Catalyzes the deamination of guanine; guanine deaminase 1427539..1428816 Paracoccus denitrificans PD1222 4582810 YP_918021.1 CDS Pden_4261 NC_008687.1 1429004 1429504 R KEGG: rpc:RPC_3603 acetone carboxylase gamma subunit; acetone carboxylase subunit gamma complement(1429004..1429504) Paracoccus denitrificans PD1222 4582811 YP_918022.1 CDS Pden_4262 NC_008687.1 1429569 1431884 R PFAM: Hydantoinase B/oxoprolinase; KEGG: rpc:RPC_3604 hydantoinase B/oxoprolinase; hydantoinase B/oxoprolinase complement(1429569..1431884) Paracoccus denitrificans PD1222 4582812 YP_918023.1 CDS Pden_4263 NC_008687.1 1431909 1434080 R PFAM: Hydantoinase/oxoprolinase; Hydantoinaseoxoprolinase domain protein; KEGG: rpc:RPC_3605 hydantoinase/oxoprolinase; hydantoinase/oxoprolinase complement(1431909..1434080) Paracoccus denitrificans PD1222 4582813 YP_918024.1 CDS Pden_4264 NC_008687.1 1434201 1436009 R 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 complement(1434201..1436009) Paracoccus denitrificans PD1222 4582814 YP_918025.1 CDS Pden_4265 NC_008687.1 1436146 1436916 R PFAM: regulatory protein GntR, HTH; GntR domain protein; KEGG: pfl:PFL_3673 transcriptional regulator, GntR family; GntR family transcriptional regulator complement(1436146..1436916) Paracoccus denitrificans PD1222 4582815 YP_918026.1 CDS Pden_4266 NC_008687.1 1436925 1438409 R PFAM: Uncharacterized conserved protein UCP012702; MlrC domain protein; KEGG: bam:Bamb_6097 MlrC domain protein; MlrC domain-containing protein complement(1436925..1438409) Paracoccus denitrificans PD1222 4582816 YP_918027.1 CDS Pden_4267 NC_008687.1 1438406 1439680 R KEGG: sil:SPO1781 amidase, hydantoinase/carbamoylase family; TIGRFAM: amidase, hydantoinase/carbamoylase family; PFAM: peptidase M20; peptidase dimerisation domain protein; amidase complement(1438406..1439680) Paracoccus denitrificans PD1222 4582817 YP_918028.1 CDS Pden_4268 NC_008687.1 1439677 1440381 R PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rme:Rmet_4479 ABC transporter related; ABC transporter complement(1439677..1440381) Paracoccus denitrificans PD1222 4582818 YP_918029.1 CDS Pden_4269 NC_008687.1 1440378 1441145 R PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rme:Rmet_4478 ABC transporter related; ABC transporter complement(1440378..1441145) Paracoccus denitrificans PD1222 4582819 YP_918030.1 CDS Pden_4270 NC_008687.1 1441147 1442124 R PFAM: inner-membrane translocator; KEGG: bxe:Bxe_B2564 ABC branched chain amino acid family transporter, inner membrane subunit; inner-membrane translocator complement(1441147..1442124) Paracoccus denitrificans PD1222 4582820 YP_918031.1 CDS Pden_4271 NC_008687.1 1442121 1443065 R PFAM: inner-membrane translocator; KEGG: rme:Rmet_4476 inner-membrane translocator; inner-membrane translocator complement(1442121..1443065) Paracoccus denitrificans PD1222 4582821 YP_918032.1 CDS Pden_4272 NC_008687.1 1443040 1444251 R 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 complement(1443040..1444251) Paracoccus denitrificans PD1222 4582822 YP_918033.1 CDS Pden_4273 NC_008687.1 1444586 1445965 D PFAM: aminotransferase class-III; KEGG: rsp:RSP_0943 probable adenosylmethionine-8-amino-7-oxononanoate aminotransferase; class III aminotransferase 1444586..1445965 Paracoccus denitrificans PD1222 4582823 YP_918034.1 CDS Pden_4274 NC_008687.1 1446028 1447527 D PFAM: regulatory protein GntR, HTH; aminotransferase, class I and II; KEGG: rde:RD1_0978 transcriptional regulator, GntR family; GntR family transcriptional regulator 1446028..1447527 Paracoccus denitrificans PD1222 4582824 YP_918035.1 CDS Pden_4275 NC_008687.1 1447511 1448467 R KEGG: rsp:RSP_4009 phosphate acetyl/butaryl transferase; TIGRFAM: phosphate acetyltransferase; PFAM: phosphate acetyl/butaryl transferase; phosphate acetyltransferase complement(1447511..1448467) Paracoccus denitrificans PD1222 4582825 YP_918036.1 CDS Pden_4276 NC_008687.1 1448480 1449496 R PFAM: conserved hypothetical protein 698; KEGG: rsp:RSP_4010 conserved hypothetical protein 698; hypothetical protein complement(1448480..1449496) Paracoccus denitrificans PD1222 4582826 YP_918037.1 CDS Pden_4277 NC_008687.1 1449770 1451551 R catalyzes the formation of acetyl phosphate and sulfite from 2-sulfoacetaldehyde; is active when grown on taurine as a sole carbon source; sulfoacetaldehyde acetyltransferase complement(1449770..1451551) Paracoccus denitrificans PD1222 4582827 YP_918038.1 CDS Pden_4278 NC_008687.1 1451564 1453204 R PFAM: glucose-methanol-choline oxidoreductase; FAD dependent oxidoreductase; GMC oxidoreductase; KEGG: sil:SPO2359 oxidoreductase, GMC family; glucose-methanol-choline oxidoreductase complement(1451564..1453204) Paracoccus denitrificans PD1222 4582828 YP_918039.1 CDS Pden_4279 NC_008687.1 1453293 1454600 R PFAM: General substrate transporter; major facilitator superfamily MFS_1; KEGG: bxe:Bxe_B0699 major facilitator superfamily (MFS)metabolite/H+ symporter; major facilitator transporter complement(1453293..1454600) Paracoccus denitrificans PD1222 4582829 YP_918040.1 CDS Pden_4280 NC_008687.1 1454824 1455588 D PFAM: regulatory proteins, IclR; KEGG: sil:SPO2355 transcriptional regulator, IclR family; regulatory proteins, IclR 1454824..1455588 Paracoccus denitrificans PD1222 4582830 YP_918041.1 CDS Pden_4281 NC_008687.1 1455734 1456684 R 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 complement(1455734..1456684) Paracoccus denitrificans PD1222 4582831 YP_918042.1 CDS Pden_4282 NC_008687.1 1456681 1457673 R 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 complement(1456681..1457673) Paracoccus denitrificans PD1222 4582832 YP_918043.1 CDS Pden_4283 NC_008687.1 1457677 1458555 R PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: rpa:RPA0100 ABC transporter permease; binding-protein-dependent transport system inner membrane protein complement(1457677..1458555) Paracoccus denitrificans PD1222 4582833 YP_918044.1 CDS Pden_4284 NC_008687.1 1458559 1459530 R PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: sil:SPO0661 peptide ABC transporter, permease; binding-protein-dependent transport systems inner membrane component complement(1458559..1459530) Paracoccus denitrificans PD1222 4582834 YP_918045.1 CDS Pden_4285 NC_008687.1 1459549 1461141 R PFAM: extracellular solute-binding protein, family 5; KEGG: rpa:RPA0102 ABC transporter oligopeptide-binding protein; extracellular solute-binding protein complement(1459549..1461141) Paracoccus denitrificans PD1222 4582835 YP_918046.1 CDS Pden_4286 NC_008687.1 1461247 1462191 R PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: sil:SPO0659 transcriptional regulator, LysR family; LysR family transcriptional regulator complement(1461247..1462191) Paracoccus denitrificans PD1222 4582836 YP_918047.1 CDS Pden_4287 NC_008687.1 1462297 1463931 D PFAM: amidohydrolase; Amidohydrolase 3; KEGG: jan:Jann_3250 amidohydrolase 3; amidohydrolase 1462297..1463931 Paracoccus denitrificans PD1222 4582837 YP_918048.1 CDS Pden_4288 NC_008687.1 1463935 1464846 D PFAM: cobalamin synthesis protein, P47K; cobalamin synthesis CobW domain protein; KEGG: jan:Jann_3251 cobalamin synthesis protein, P47K; cobalamin synthesis protein, P47K 1463935..1464846 Paracoccus denitrificans PD1222 4582838 YP_918049.1 CDS Pden_4289 NC_008687.1 1465112 1465765 D KEGG: jan:Jann_1560 hypothetical protein; hypothetical protein 1465112..1465765 Paracoccus denitrificans PD1222 4582839 YP_918050.1 CDS Pden_4290 NC_008687.1 1465671 1467191 D KEGG: jan:Jann_1559 hypothetical protein; hypothetical protein 1465671..1467191 Paracoccus denitrificans PD1222 4582840 YP_918051.1 CDS Pden_4291 NC_008687.1 1467191 1470424 D 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 1467191..1470424 Paracoccus denitrificans PD1222 4582841 YP_918052.1 CDS rpmG NC_008687.1 1470491 1470658 R 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 complement(1470491..1470658) Paracoccus denitrificans PD1222 4582842 YP_918053.1 CDS Pden_4293 NC_008687.1 1471303 1471668 R PFAM: helix-turn-helix, HxlR type; KEGG: ccr:CC3368 hypothetical protein; HxlR family transcriptional regulator complement(1471303..1471668) Paracoccus denitrificans PD1222 4582843 YP_918054.1 CDS Pden_4294 NC_008687.1 1471754 1472596 D PFAM: 3-beta hydroxysteroid dehydrogenase/isomerase; NmrA family protein; KEGG: stm:STM4401 reductase; NmrA family protein 1471754..1472596 Paracoccus denitrificans PD1222 4582844 YP_918055.1 CDS Pden_4295 NC_008687.1 1472593 1474992 R PFAM: UvrD/REP helicase; KEGG: rsp:RSP_2092 UvrD/DNA helicase II; UvrD/REP helicase complement(1472593..1474992) Paracoccus denitrificans PD1222 4582845 YP_918056.1 CDS Pden_4296 NC_008687.1 1475039 1475350 R hypothetical protein complement(1475039..1475350) Paracoccus denitrificans PD1222 4582846 YP_918057.1 CDS Pden_4297 NC_008687.1 1475351 1476316 R 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 complement(1475351..1476316) Paracoccus denitrificans PD1222 4582847 YP_918058.1 CDS Pden_4298 NC_008687.1 1476404 1477600 R 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 complement(1476404..1477600) Paracoccus denitrificans PD1222 4582848 YP_918059.1 CDS Pden_4299 NC_008687.1 1477671 1478360 R PFAM: Intracellular septation protein A; KEGG: rsp:RSP_1841 probable intracellular septation protein; intracellular septation protein A complement(1477671..1478360) Paracoccus denitrificans PD1222 4582849 YP_918060.1 CDS Pden_4300 NC_008687.1 1478374 1479465 R PFAM: protein of unknown function DUF1223; KEGG: sil:SPO2311 hypothetical protein; hypothetical protein complement(1478374..1479465) Paracoccus denitrificans PD1222 4582850 YP_918061.1 CDS Pden_4301 NC_008687.1 1479732 1482491 D Catalyzes the conversion of citrate to isocitrate; aconitate hydratase 1479732..1482491 Paracoccus denitrificans PD1222 4582851 YP_918062.1 CDS Pden_4302 NC_008687.1 1482658 1483326 R KEGG: rsp:RSP_0681 hypothetical protein; hypothetical protein complement(1482658..1483326) Paracoccus denitrificans PD1222 4582852 YP_918063.1 CDS rpsD NC_008687.1 1483465 1484085 R 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 complement(1483465..1484085) Paracoccus denitrificans PD1222 4582853 YP_918064.1 CDS Pden_4304 NC_008687.1 1484284 1484655 D 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 1484284..1484655 Paracoccus denitrificans PD1222 4582854 YP_918065.1 CDS Pden_4305 NC_008687.1 1484756 1485499 D PFAM: triosephosphate isomerase; KEGG: rsp:RSP_1947 triosephosphate isomerase; Triose-phosphate isomerase 1484756..1485499 Paracoccus denitrificans PD1222 4582855 YP_918066.1 CDS Pden_4306 NC_008687.1 1485545 1486678 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rsp:RSP_0129 ABC D-methionine uptake transporter, ATPase subunit; ABC transporter 1485545..1486678 Paracoccus denitrificans PD1222 4582856 YP_918067.1 CDS Pden_4307 NC_008687.1 1486668 1487342 D 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 1486668..1487342 Paracoccus denitrificans PD1222 4582857 YP_918068.1 CDS Pden_4308 NC_008687.1 1487359 1488153 D TIGRFAM: lipoprotein, YaeC family; PFAM: NLPA lipoprotein; KEGG: rsp:RSP_0132 ABC D-methionine uptake transporter, substrate-binding protein; YaeC family lipoprotein 1487359..1488153 Paracoccus denitrificans PD1222 4582858 YP_918069.1 CDS Pden_4309 NC_008687.1 1488263 1489765 R PFAM: acetyl-CoA hydrolase/transferase; KEGG: rsp:RSP_0029 acetyl-CoA hydrolase/transferase family protein; Acetyl-CoA hydrolase complement(1488263..1489765) Paracoccus denitrificans PD1222 4582859 YP_918070.1 CDS Pden_4310 NC_008687.1 1489904 1490347 R PFAM: DoxX family protein; KEGG: bja:bll6552 hypothetical protein; DoxX family protein complement(1489904..1490347) Paracoccus denitrificans PD1222 4582860 YP_918071.1 CDS Pden_4311 NC_008687.1 1490452 1491363 D PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: rru:Rru_A1041 transcriptional regulator, LysR family; LysR family transcriptional regulator 1490452..1491363 Paracoccus denitrificans PD1222 4582861 YP_918072.1 CDS Pden_4312 NC_008687.1 1491326 1492726 R PFAM: FAD linked oxidase domain protein; KEGG: rsp:RSP_1835 FAD dependent oxidoreductase; FAD linked oxidase domain-containing protein complement(1491326..1492726) Paracoccus denitrificans PD1222 4582862 YP_918073.1 CDS Pden_4313 NC_008687.1 1492726 1493307 R PFAM: GCN5-related N-acetyltransferase; KEGG: jan:Jann_3147 GCN5-related N-acetyltransferase; N-acetyltransferase GCN5 complement(1492726..1493307) Paracoccus denitrificans PD1222 4582863 YP_918074.1 CDS Pden_4314 NC_008687.1 1493307 1494572 R PFAM: peptidase M16 domain protein; KEGG: rsp:RSP_1832 peptidase, M16 family; peptidase M16 domain-containing protein complement(1493307..1494572) Paracoccus denitrificans PD1222 4582864 YP_918075.1 CDS Pden_4315 NC_008687.1 1494569 1495957 R catalyzes the formation of L-threonine from O-phospho-L-homoserine; threonine synthase complement(1494569..1495957) Paracoccus denitrificans PD1222 4582865 YP_918076.1 CDS Pden_4316 NC_008687.1 1495967 1496638 R KEGG: rsp:RSP_1830 SURF1 protein; SURF1 protein complement(1495967..1496638) Paracoccus denitrificans PD1222 4582866 YP_918077.1 CDS Pden_4317 NC_008687.1 1496704 1497528 R PFAM: cytochrome c oxidase, subunit III; KEGG: rsp:RSP_1829 cytochrome c oxidase, aa3-type, subunit III; cytochrome c oxidase subunit III complement(1496704..1497528) Paracoccus denitrificans PD1222 4582867 YP_918078.1 CDS Pden_4318 NC_008687.1 1497563 1498150 R involved in the insertion of copper into subunit I of cytochrome C oxidase; cytochrome C oxidase assembly protein complement(1497563..1498150) Paracoccus denitrificans PD1222 4582868 YP_918079.1 CDS Pden_4319 NC_008687.1 1498147 1498422 R KEGG: jan:Jann_3153 hypothetical protein; hypothetical protein complement(1498147..1498422) Paracoccus denitrificans PD1222 4582869 YP_918080.1 CDS Pden_4320 NC_008687.1 1498416 1499333 R converts protoheme IX and farnesyl diphosphate to heme O; protoheme IX farnesyltransferase complement(1498416..1499333) Paracoccus denitrificans PD1222 4582870 YP_918081.1 CDS Pden_4321 NC_008687.1 1499343 1500239 R PFAM: cytochrome c oxidase, subunit II; cytochrome C oxidase subunit II, transmembrane region; KEGG: sil:SPO3076 cytochrome c oxidase, subunit II; cytochrome-c oxidase complement(1499343..1500239) Paracoccus denitrificans PD1222 4582871 YP_918082.1 CDS Pden_4322 NC_008687.1 1500382 1501821 D PFAM: peptidase U62, modulator of DNA gyrase; KEGG: rsp:RSP_1825 probable modulator of DNA gyrase; C69 family peptidase 1500382..1501821 Paracoccus denitrificans PD1222 4582872 YP_918083.1 CDS Pden_4323 NC_008687.1 1501919 1503175 D TIGRFAM: DNA protecting protein DprA; PFAM: SMF family protein; KEGG: jan:Jann_3158 DNA processing protein DprA; DNA protecting protein DprA 1501919..1503175 Paracoccus denitrificans PD1222 4582873 YP_918084.1 CDS Pden_4324 NC_008687.1 1503467 1505602 D PFAM: OmpA/MotB domain protein; KEGG: rsp:RSP_1933 outer membrane protein, OmpA/MotB family; OmpA/MotB domain-containing protein 1503467..1505602 Paracoccus denitrificans PD1222 4582874 YP_918085.1 CDS Pden_4325 NC_008687.1 1505694 1506383 R 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 complement(1505694..1506383) Paracoccus denitrificans PD1222 4582875 YP_918086.1 CDS Pden_4326 NC_008687.1 1506387 1507097 R TIGRFAM: phosphate transport system regulatory protein PhoU; PFAM: PhoU family protein; KEGG: rsp:RSP_2600 phosphate transport system regulatory protein; phosphate uptake regulator PhoU complement(1506387..1507097) Paracoccus denitrificans PD1222 4582876 YP_918087.1 CDS Pden_4327 NC_008687.1 1507115 1507912 R 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 complement(1507115..1507912) Paracoccus denitrificans PD1222 4582877 YP_918088.1 CDS Pden_4328 NC_008687.1 1507933 1509276 R 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 complement(1507933..1509276) Paracoccus denitrificans PD1222 4582878 YP_918089.1 CDS Pden_4329 NC_008687.1 1509273 1510463 R 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 complement(1509273..1510463) Paracoccus denitrificans PD1222 4582879 YP_918090.1 CDS Pden_4330 NC_008687.1 1510524 1511552 R KEGG: sit:TM1040_1262 phosphate ABC transporter, periplasmic phosphate-binding protein; phosphate ABC transporter, periplasmic phosphate-binding protein complement(1510524..1511552) Paracoccus denitrificans PD1222 4582880 YP_918091.1 CDS Pden_4331 NC_008687.1 1511549 1511791 R hypothetical protein complement(1511549..1511791) Paracoccus denitrificans PD1222 4582881 YP_918092.1 CDS Pden_4332 NC_008687.1 1511803 1512903 R catalyzes the formation of chorismate from 5-O-(1-carboxyvinyl)-3-phosphoshikimate in aromatic amino acid biosynthesis; chorismate synthase complement(1511803..1512903) Paracoccus denitrificans PD1222 4582882 YP_918093.1 CDS Pden_4333 NC_008687.1 1513319 1513648 R hypothetical protein complement(1513319..1513648) Paracoccus denitrificans PD1222 4582883 YP_918094.1 CDS Pden_4334 NC_008687.1 1513676 1515139 D PFAM: amino acid permease-associated region; KEGG: rha:RHA1_ro06596 cationic amino acid transporter, APC family; amino acid permease 1513676..1515139 Paracoccus denitrificans PD1222 4582884 YP_918095.1 CDS Pden_4335 NC_008687.1 1515167 1516498 R 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 complement(1515167..1516498) Paracoccus denitrificans PD1222 4582885 YP_918096.1 CDS Pden_4336 NC_008687.1 1516482 1518473 R 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 complement(1516482..1518473) Paracoccus denitrificans PD1222 4582886 YP_918097.1 CDS Pden_4337 NC_008687.1 1518470 1520503 R KEGG: mes:Meso_2598 hypothetical protein; hypothetical protein complement(1518470..1520503) Paracoccus denitrificans PD1222 4582887 YP_918098.1 CDS Pden_4338 NC_008687.1 1520613 1522424 R KEGG: mes:Meso_2597 PE-PGRS family protein; PE-PGRS family protein complement(1520613..1522424) Paracoccus denitrificans PD1222 4582888 YP_918099.1 CDS Pden_4339 NC_008687.1 1523038 1523739 D PFAM: regulatory protein, LuxR; KEGG: dra:DRB0081 DNA-binding response regulator; response regulator receiver protein 1523038..1523739 Paracoccus denitrificans PD1222 4582889 YP_918100.1 CDS Pden_4340 NC_008687.1 1523736 1524257 D KEGG: mes:Meso_2596 hypothetical protein; hypothetical protein 1523736..1524257 Paracoccus denitrificans PD1222 4582890 YP_918101.1 CDS Pden_4341 NC_008687.1 1524344 1525063 R 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 complement(1524344..1525063) Paracoccus denitrificans PD1222 4582891 YP_918102.1 CDS Pden_4342 NC_008687.1 1525080 1525973 R 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 complement(1525080..1525973) Paracoccus denitrificans PD1222 4582892 YP_918103.1 CDS Pden_4343 NC_008687.1 1525966 1526805 R 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 complement(1525966..1526805) Paracoccus denitrificans PD1222 4582893 YP_918104.1 CDS Pden_4344 NC_008687.1 1526809 1527795 R 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 complement(1526809..1527795) Paracoccus denitrificans PD1222 4582894 YP_918105.1 CDS Pden_4345 NC_008687.1 1528285 1529583 D PFAM: secretion protein HlyD family protein; KEGG: pae:PA4142 probable secretion protein; secretion protein HlyD family protein 1528285..1529583 Paracoccus denitrificans PD1222 4582895 YP_918106.1 CDS Pden_4346 NC_008687.1 1529573 1531753 D 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 1529573..1531753 Paracoccus denitrificans PD1222 4582896 YP_918107.1 CDS Pden_4347 NC_008687.1 1532148 1533389 D PFAM: Radical SAM domain protein; KEGG: sma:SAV5715 hypothetical protein; radical SAM domain-containing protein 1532148..1533389 Paracoccus denitrificans PD1222 4582897 YP_918108.1 CDS Pden_4348 NC_008687.1 1533474 1535159 D 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 1533474..1535159 Paracoccus denitrificans PD1222 4582898 YP_918109.1 CDS Pden_4349 NC_008687.1 1535156 1535776 R 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 complement(1535156..1535776) Paracoccus denitrificans PD1222 4582899 YP_918110.1 CDS mdoD NC_008687.1 1535955 1537556 R involved in the control of the structural glucose backbone of osmoregulated periplasmic glucans; glucan biosynthesis protein D complement(1535955..1537556) Paracoccus denitrificans PD1222 4582900 YP_918111.1 CDS Pden_4351 NC_008687.1 1537755 1539227 R PFAM: permease for cytosine/purines, uracil, thiamine, allantoin; KEGG: rsp:RSP_3174 nucleoside transporter, NCS1 family; cytosine/purines uracil thiamine allantoin permease complement(1537755..1539227) Paracoccus denitrificans PD1222 4582901 YP_918112.1 CDS Pden_4352 NC_008687.1 1539330 1541114 R PFAM: Hydantoinase B/oxoprolinase; KEGG: hwa:HQ2241A N-methylhydantoinase B (ATP-hydrolyzing); 5-oxoprolinase complement(1539330..1541114) Paracoccus denitrificans PD1222 4582902 YP_918113.1 CDS Pden_4353 NC_008687.1 1541127 1543205 R PFAM: Hydantoinase/oxoprolinase; Hydantoinaseoxoprolinase domain protein; KEGG: hwa:HQ2242A N-methylhydantoinase A (ATP-hydrolyzing); 5-oxoprolinase complement(1541127..1543205) Paracoccus denitrificans PD1222 4582903 YP_918114.1 CDS Pden_4354 NC_008687.1 1543296 1544039 R PFAM: isochorismatase hydrolase; KEGG: rha:RHA1_ro10206 phthalate ester hydrolase (isochorismatase hydrolase); N-carbamoylsarcosine amidase complement(1543296..1544039) Paracoccus denitrificans PD1222 4582904 YP_918115.1 CDS Pden_4355 NC_008687.1 1544204 1545109 D PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: jan:Jann_3249 transcriptional regulator, LysR family; LysR family transcriptional regulator 1544204..1545109 Paracoccus denitrificans PD1222 4582905 YP_918116.1 CDS Pden_4356 NC_008687.1 1545213 1545761 R PFAM: cytochrome B561; KEGG: jan:Jann_0302 cytochrome b561; cytochrome B561 complement(1545213..1545761) Paracoccus denitrificans PD1222 4582906 YP_918117.1 CDS Pden_4357 NC_008687.1 1545866 1546603 D KEGG: jan:Jann_0303 CDP-alcohol phosphatidyltransferase; CDP-alcohol phosphatidyltransferase 1545866..1546603 Paracoccus denitrificans PD1222 4582907 YP_918118.1 CDS Pden_4358 NC_008687.1 1546600 1548177 D PFAM: sulfatase; KEGG: jan:Jann_0304 hypothetical protein; sulfatase 1546600..1548177 Paracoccus denitrificans PD1222 4582908 YP_918119.1 CDS Pden_4359 NC_008687.1 1548197 1549192 D KEGG: jan:Jann_0306 twin-arginine translocation pathway signal; twin-arginine translocation pathway signal 1548197..1549192 Paracoccus denitrificans PD1222 4582909 YP_918120.1 CDS Pden_4360 NC_008687.1 1549185 1549958 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: jan:Jann_0307 ABC transporter related; ABC transporter 1549185..1549958 Paracoccus denitrificans PD1222 4582910 YP_918121.1 CDS Pden_4361 NC_008687.1 1549955 1551499 D 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 1549955..1551499 Paracoccus denitrificans PD1222 4582911 YP_918122.1 CDS Pden_4362 NC_008687.1 1551496 1552545 D PFAM: glycosyl transferase, group 1; KEGG: jan:Jann_0309 glycosyl transferase, group 1; group 1 glycosyl transferase 1551496..1552545 Paracoccus denitrificans PD1222 4582912 YP_918123.1 CDS Pden_4363 NC_008687.1 1552589 1553200 R PFAM: bifunctional deaminase-reductase domain protein; KEGG: sme:SMc04173 hypothetical protein; deaminase-reductase domain-containing protein complement(1552589..1553200) Paracoccus denitrificans PD1222 4582913 YP_918124.1 CDS Pden_4364 NC_008687.1 1553381 1554592 R PFAM: ThiJ/PfpI domain protein; KEGG: bbr:BB2338 probable transcriptional regulator; ThiJ/PfpI domain-containing protein complement(1553381..1554592) Paracoccus denitrificans PD1222 4582914 YP_918125.1 CDS Pden_4365 NC_008687.1 1554607 1555581 D 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 1554607..1555581 Paracoccus denitrificans PD1222 4582915 YP_918126.1 CDS Pden_4366 NC_008687.1 1555817 1557880 R 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 complement(1555817..1557880) Paracoccus denitrificans PD1222 4582916 YP_918127.1 CDS Pden_4367 NC_008687.1 1558036 1558938 R PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: sme:SMb20683 transcriptional regulator, LysR family protein; LysR family transcriptional regulator complement(1558036..1558938) Paracoccus denitrificans PD1222 4582917 YP_918128.1 CDS Pden_4368 NC_008687.1 1559113 1560438 D involved in the transport of C4-dicarboxylates across the membrane; C4-dicarboxylate transporter DctA 1559113..1560438 Paracoccus denitrificans PD1222 4582918 YP_918129.1 CDS Pden_4369 NC_008687.1 1560541 1561515 R PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: rpe:RPE_1784 transcriptional regulator, LysR family; LysR family transcriptional regulator complement(1560541..1561515) Paracoccus denitrificans PD1222 4582919 YP_918130.1 CDS Pden_4370 NC_008687.1 1561546 1562565 D PFAM: conserved hypothetical protein 698; KEGG: rpe:RPE_1785 conserved hypothetical protein 698; hypothetical protein 1561546..1562565 Paracoccus denitrificans PD1222 4582920 YP_918131.1 CDS Pden_4371 NC_008687.1 1562633 1563463 D KEGG: rsp:RSP_0408 hypothetical protein; hypothetical protein 1562633..1563463 Paracoccus denitrificans PD1222 4582921 YP_918132.1 CDS Pden_4372 NC_008687.1 1563453 1563677 R KEGG: mlo:mll4732 glycolate oxidase, (S)-2-hydroxy-acid oxidase, peroxisomal; hypothetical protein complement(1563453..1563677) Paracoccus denitrificans PD1222 4582922 YP_918133.1 CDS Pden_4373 NC_008687.1 1563763 1566018 R 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 complement(1563763..1566018) Paracoccus denitrificans PD1222 4582923 YP_918134.1 CDS Pden_4374 NC_008687.1 1566089 1566385 R hypothetical protein complement(1566089..1566385) Paracoccus denitrificans PD1222 4582924 YP_918135.1 CDS Pden_4375 NC_008687.1 1566679 1566900 D TIGRFAM: Glutaredoxin-like protein NrdH; PFAM: glutaredoxin; KEGG: sit:TM1040_0521 glutaredoxin-like protein NrdH; glutaredoxin-like protein NrdH 1566679..1566900 Paracoccus denitrificans PD1222 4582925 YP_918136.1 CDS nrdI NC_008687.1 1566910 1567326 D in Salmonella NrdI has a stimulatory effect on the ribonucleotide reductase activity of NrdH with NrdEF; ribonucleotide reductase stimulatory protein 1566910..1567326 Paracoccus denitrificans PD1222 4582926 YP_918137.1 CDS Pden_4377 NC_008687.1 1567308 1569434 D Catalyzes the rate-limiting step in dNTP synthesis; ribonucleotide-diphosphate reductase subunit alpha 1567308..1569434 Paracoccus denitrificans PD1222 4582927 YP_918138.1 CDS nrdF NC_008687.1 1569481 1570470 D 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 1569481..1570470 Paracoccus denitrificans PD1222 4582928 YP_918139.1 CDS Pden_4379 NC_008687.1 1570467 1571435 R PFAM: Bile acid:sodium symporter; KEGG: mes:Meso_2484 bile acid:sodium symporter; bile acid:sodium symporter complement(1570467..1571435) Paracoccus denitrificans PD1222 4582929 YP_918140.1 CDS Pden_4380 NC_008687.1 1571526 1572773 D PFAM: aminotransferase, class I and II; KEGG: xcv:XCV1904 aminotransferase; GntR family transcriptional regulator 1571526..1572773 Paracoccus denitrificans PD1222 4582930 YP_918141.1 CDS Pden_4381 NC_008687.1 1572796 1574571 R PFAM: Citrate transporter; TrkA-C domain protein; KEGG: sme:SMa1916 hypothetical protein; TrkA domain-containing protein complement(1572796..1574571) Paracoccus denitrificans PD1222 4582931 YP_918142.1 CDS Pden_4382 NC_008687.1 1575068 1576975 D PFAM: TonB-dependent receptor; TonB-dependent receptor, plug; KEGG: rru:Rru_A0488 TonB-dependent receptor; TonB-dependent receptor 1575068..1576975 Paracoccus denitrificans PD1222 4582932 YP_918143.1 CDS Pden_4383 NC_008687.1 1576969 1577805 D PFAM: periplasmic binding protein; KEGG: rsp:RSP_2403 ABC cobalamin/Fe3+-siderophore transporter, periplasmic substrate-binding subunit; periplasmic binding protein 1576969..1577805 Paracoccus denitrificans PD1222 4582933 YP_918144.1 CDS Pden_4384 NC_008687.1 1577802 1578797 D PFAM: transport system permease; KEGG: rsp:RSP_2404 ABC cobalamin/Fe3+-siderophore transporter, inner membrane subunit; transport system permease 1577802..1578797 Paracoccus denitrificans PD1222 4582934 YP_918145.1 CDS Pden_4385 NC_008687.1 1578800 1579555 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rsp:RSP_2405 ABC cobalamin/Fe3+-siderophore transporter, ATPase subunit; ABC transporter 1578800..1579555 Paracoccus denitrificans PD1222 4582935 YP_918146.1 CDS Pden_4386 NC_008687.1 1579716 1581206 R TIGRFAM: glycerol kinase; PFAM: carbohydrate kinase, FGGY; KEGG: rsp:RSP_2662 glycerol kinase; glycerol kinase complement(1579716..1581206) Paracoccus denitrificans PD1222 4582936 YP_918147.1 CDS Pden_4387 NC_008687.1 1581285 1583006 R KEGG: rsp:RSP_2663 ABC sugar (glycerol) transporter, periplasmic binding protein; ABC sugar (glycerol) transporter, periplasmic binding protein complement(1581285..1583006) Paracoccus denitrificans PD1222 4582937 YP_918148.1 CDS Pden_4388 NC_008687.1 1583090 1583371 R KEGG: rsp:RSP_2664 hypothetical protein; hypothetical protein complement(1583090..1583371) Paracoccus denitrificans PD1222 4582938 YP_918149.1 CDS Pden_4389 NC_008687.1 1583515 1584318 R 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 complement(1583515..1584318) Paracoccus denitrificans PD1222 4582939 YP_918150.1 CDS Pden_4390 NC_008687.1 1584318 1585205 R 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 complement(1584318..1585205) Paracoccus denitrificans PD1222 4582940 YP_918151.1 CDS Pden_4391 NC_008687.1 1585205 1586308 R PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rsp:RSP_2667 ABC sugar (glycerol) transporter, ATPase subunit; ABC transporter complement(1585205..1586308) Paracoccus denitrificans PD1222 4582941 YP_918152.1 CDS Pden_4392 NC_008687.1 1586292 1587371 R PFAM: ABC transporter related; Transport-associated OB domain protein; SMART: AAA ATPase; KEGG: rsp:RSP_2669 ABC sugar (glycerol) transporter, ATPase subunit; ABC transporter complement(1586292..1587371) Paracoccus denitrificans PD1222 4582942 YP_918153.1 CDS glpD NC_008687.1 1587386 1588969 R 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 complement(1587386..1588969) Paracoccus denitrificans PD1222 4582943 YP_918154.1 CDS Pden_4394 NC_008687.1 1589081 1589401 D hypothetical protein 1589081..1589401 Paracoccus denitrificans PD1222 4582944 YP_918155.1 CDS Pden_4395 NC_008687.1 1589413 1590348 D with CysN catalyzes the formation of adenylylsulfate from sulfate and ATP; sulfate adenylyltransferase subunit 2 1589413..1590348 Paracoccus denitrificans PD1222 4582945 YP_918156.1 CDS Pden_4396 NC_008687.1 1590350 1592272 D 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 1590350..1592272 Paracoccus denitrificans PD1222 4582946 YP_918157.1 CDS Pden_4397 NC_008687.1 1592380 1593675 R 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 complement(1592380..1593675) Paracoccus denitrificans PD1222 4582947 YP_918158.1 CDS Pden_4398 NC_008687.1 1593677 1594810 R PFAM: FAD linked oxidase domain protein; KEGG: sit:TM1040_2501 FAD linked oxidase-like; FAD linked oxidase domain-containing protein complement(1593677..1594810) Paracoccus denitrificans PD1222 4582948 YP_918159.1 CDS Pden_4399 NC_008687.1 1594807 1596261 R PFAM: FAD linked oxidase domain protein; KEGG: rsp:RSP_1020 glycolate oxidase subunit protein; FAD linked oxidase domain-containing protein complement(1594807..1596261) Paracoccus denitrificans PD1222 4582949 YP_918160.1 CDS Pden_4400 NC_008687.1 1596412 1597221 D 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 1596412..1597221 Paracoccus denitrificans PD1222 4582950 YP_918161.1 CDS Pden_4401 NC_008687.1 1597278 1598243 R PFAM: Uncharacterized protein UPF0065; KEGG: sme:SMa1927 hypothetical protein; hypothetical protein complement(1597278..1598243) Paracoccus denitrificans PD1222 4582951 YP_918162.1 CDS Pden_4402 NC_008687.1 1598266 1599774 R PFAM: protein of unknown function DUF112, transmembrane; KEGG: atc:AGR_C_184 hypothetical protein; hypothetical protein complement(1598266..1599774) Paracoccus denitrificans PD1222 4582952 YP_918163.1 CDS Pden_4403 NC_008687.1 1599787 1600251 R PFAM: protein of unknown function DUF1468; KEGG: sme:SMb20026 hypothetical protein; hypothetical protein complement(1599787..1600251) Paracoccus denitrificans PD1222 4582953 YP_918164.1 CDS Pden_4404 NC_008687.1 1600310 1601284 R PFAM: Uncharacterized protein UPF0065; KEGG: sme:SMb20025 hypothetical protein; hypothetical protein complement(1600310..1601284) Paracoccus denitrificans PD1222 4582954 YP_918165.1 CDS Pden_4405 NC_008687.1 1601479 1602825 R 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 complement(1601479..1602825) Paracoccus denitrificans PD1222 4582955 YP_918166.1 CDS Pden_4406 NC_008687.1 1602822 1604690 R 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 complement(1602822..1604690) Paracoccus denitrificans PD1222 4582956 YP_918167.1 CDS Pden_4407 NC_008687.1 1604791 1606113 R KEGG: bur:Bcep18194_A6285 permease for cytosine/purines, uracil, thiamine, allantoin tranporter; cytosine/purines, uracil, thiamine, allantoin permease complement(1604791..1606113) Paracoccus denitrificans PD1222 4582957 YP_918168.1 CDS Pden_4408 NC_008687.1 1606211 1608346 R PFAM: Hydantoinase/oxoprolinase; Hydantoinaseoxoprolinase domain protein; KEGG: ppu:PP_3515 hydantoin utilization protein A; 5-oxoprolinase complement(1606211..1608346) Paracoccus denitrificans PD1222 4582958 YP_918169.1 CDS Pden_4409 NC_008687.1 1608429 1610177 R PFAM: Hydantoinase B/oxoprolinase; KEGG: pfl:PFL_2733 hydantoin utilization protein B; 5-oxoprolinase complement(1608429..1610177) Paracoccus denitrificans PD1222 4582959 YP_918170.1 CDS Pden_4410 NC_008687.1 1610483 1611439 D PFAM: helix-turn-helix- domain containing protein, AraC type; KEGG: ppu:PP_3516 transcriptional regulator, AraC family; helix-turn-helix domain-containing protein 1610483..1611439 Paracoccus denitrificans PD1222 4582960 YP_918171.1 CDS Pden_4411 NC_008687.1 1611443 1612588 R PFAM: L-carnitine dehydratase/bile acid-inducible protein F; KEGG: sil:SPO0820 CaiB/BaiF family protein; L-carnitine dehydratase/bile acid-inducible protein F complement(1611443..1612588) Paracoccus denitrificans PD1222 4582961 YP_918172.1 CDS Pden_4412 NC_008687.1 1612588 1613799 R PFAM: acyl-CoA dehydrogenase domain protein; Acyl-CoA dehydrogenase, type 2, C-terminal domain; KEGG: mlo:mll2878 glutaryl Co-A dehydrogenase; acyl-CoA dehydrogenase complement(1612588..1613799) Paracoccus denitrificans PD1222 4582962 YP_918173.1 CDS Pden_4413 NC_008687.1 1613891 1614793 D PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: mes:Meso_2482 transcriptional regulator, LysR family; LysR family transcriptional regulator 1613891..1614793 Paracoccus denitrificans PD1222 4582963 YP_918174.1 CDS Pden_4414 NC_008687.1 1614817 1616097 R TIGRFAM: 4-aminobutyrate aminotransferase; PFAM: aminotransferase class-III; KEGG: jan:Jann_3070 4-aminobutyrate aminotransferase; 4-aminobutyrate aminotransferase complement(1614817..1616097) Paracoccus denitrificans PD1222 4582964 YP_918175.1 CDS Pden_4415 NC_008687.1 1616178 1616819 D PFAM: helix-turn-helix domain protein; Cupin 2, conserved barrel domain protein; KEGG: rde:RD1_0838 transcription regulator; XRE family transcriptional regulator 1616178..1616819 Paracoccus denitrificans PD1222 4582965 YP_918176.1 CDS Pden_4416 NC_008687.1 1616830 1618263 R PFAM: aldehyde dehydrogenase; KEGG: atc:AGR_L_2660 hypothetical protein; aldehyde dehydrogenase complement(1616830..1618263) Paracoccus denitrificans PD1222 4582966 YP_918177.1 CDS Pden_4417 NC_008687.1 1618631 1620475 R binds to the ribosome on the universally-conserved alpha-sarcin loop; GTP-binding protein LepA complement(1618631..1620475) Paracoccus denitrificans PD1222 4582967 YP_918178.1 CDS Pden_4418 NC_008687.1 1620472 1621392 R PFAM: protein of unknown function DUF6, transmembrane; KEGG: rde:RD1_3141 integral membrane protein; hypothetical protein complement(1620472..1621392) Paracoccus denitrificans PD1222 4582968 YP_918179.1 CDS Pden_4419 NC_008687.1 1621789 1622154 D KEGG: rsp:RSP_2018 hypothetical protein; hypothetical protein 1621789..1622154 Paracoccus denitrificans PD1222 4582969 YP_918180.1 CDS Pden_4420 NC_008687.1 1622162 1622842 D PFAM: Silent information regulator protein Sir2; KEGG: rde:RD1_1683 NAD-dependent deacetylase; silent information regulator protein Sir2 1622162..1622842 Paracoccus denitrificans PD1222 4582970 YP_918181.1 CDS Pden_4421 NC_008687.1 1623017 1624159 D TIGRFAM: phosphonate metabolism protein PhnM; PFAM: amidohydrolase; Amidohydrolase 3; KEGG: sil:SPO0476 alkylphosphonate utilization protein PhnM; phosphonate metabolism protein PhnM 1623017..1624159 Paracoccus denitrificans PD1222 4582971 YP_918182.1 CDS Pden_4422 NC_008687.1 1624263 1624601 D TIGRFAM: alkylhydroperoxidase like protein, AhpD family; PFAM: Carboxymuconolactone decarboxylase; KEGG: sil:SPO0640 4-carboxymuconolactone decarboxylase domain/alkylhydroperoxidase AhpD family core domain protein; alkylhydroperoxidase 1624263..1624601 Paracoccus denitrificans PD1222 4582972 YP_918183.1 CDS Pden_4423 NC_008687.1 1624638 1626269 R catalyzes the interconversion of alpha-D-glucose 1-phosphate to alpha-D-glucose 6-phosphate; phosphoglucomutase complement(1624638..1626269) Paracoccus denitrificans PD1222 4582973 YP_918184.1 CDS Pden_4424 NC_008687.1 1626280 1628115 R KEGG: rde:RD1_2871 4-alpha-glucanotransferase; TIGRFAM: 4-alpha-glucanotransferase; PFAM: glycoside hydrolase, family 77; 4-alpha-glucanotransferase complement(1626280..1628115) Paracoccus denitrificans PD1222 4582974 YP_918185.1 CDS Pden_4425 NC_008687.1 1628108 1630201 R 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 complement(1628108..1630201) Paracoccus denitrificans PD1222 4582975 YP_918186.1 CDS glgA NC_008687.1 1630201 1631604 R catalyzes the formation of alpha-1,4-glucan chains from ADP-glucose; glycogen synthase complement(1630201..1631604) Paracoccus denitrificans PD1222 4582976 YP_918187.1 CDS glgC NC_008687.1 1631601 1632863 R catalyzes the formation of ADP-glucose and diphosphate from ATP and alpha-D-glucose 1-phosphate; glucose-1-phosphate adenylyltransferase complement(1631601..1632863) Paracoccus denitrificans PD1222 4582977 YP_918188.1 CDS Pden_4428 NC_008687.1 1632907 1635102 R 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 complement(1632907..1635102) Paracoccus denitrificans PD1222 4582978 YP_918189.1 CDS Pden_4429 NC_008687.1 1635124 1637520 R KEGG: rsp:RSP_2887 glycogen phosphorylase; TIGRFAM: glycogen/starch/alpha-glucan phosphorylases; PFAM: glycosyl transferase, family 35; glycogen/starch/alpha-glucan phosphorylase complement(1635124..1637520) Paracoccus denitrificans PD1222 4582979 YP_918190.1 CDS Pden_4430 NC_008687.1 1637767 1638618 R KEGG: sil:SPO3245 nicotinate-nucleotide pyrophosphorylase; TIGRFAM: nicotinate-nucleotide pyrophosphorylase; PFAM: Quinolinate phosphoribosyl transferase; nicotinate-nucleotide pyrophosphorylase complement(1637767..1638618) Paracoccus denitrificans PD1222 4582980 YP_918191.1 CDS Pden_4431 NC_008687.1 1638615 1640180 R catalyzes the formation of oxaloacetate from L-aspartate; L-aspartate oxidase complement(1638615..1640180) Paracoccus denitrificans PD1222 4582981 YP_918192.1 CDS Pden_4432 NC_008687.1 1640184 1641236 R 3 different subfamilies; catalyzes the formation of quinolinate from iminoaspartate and dihydroxyacetone phosphate; quinolinate synthetase complement(1640184..1641236) Paracoccus denitrificans PD1222 4582982 YP_918193.1 CDS Pden_4433 NC_008687.1 1641493 1642257 D PFAM: regulatory proteins, IclR; KEGG: sil:SPO2355 transcriptional regulator, IclR family; regulatory proteins, IclR 1641493..1642257 Paracoccus denitrificans PD1222 4582983 YP_918194.1 CDS Pden_4434 NC_008687.1 1642263 1642841 R KEGG: rsp:RSP_0816 aminotransferase, class IV; hypothetical protein complement(1642263..1642841) Paracoccus denitrificans PD1222 4582984 YP_918195.1 CDS Pden_4435 NC_008687.1 1642850 1644016 R catalyzes the formation of 4-amino-4-deoxychorismate from chorismate and glutamine; aminodeoxychorismate synthase complement(1642850..1644016) Paracoccus denitrificans PD1222 4582985 YP_918196.1 CDS Pden_4436 NC_008687.1 1644105 1645277 R PFAM: oxidoreductase domain protein; Oxidoreductase, C-terminal domain; KEGG: rsp:RSP_1245 predicted oxidoreductase, Gfo/Idh/MocA family; oxidoreductase domain-containing protein complement(1644105..1645277) Paracoccus denitrificans PD1222 4582986 YP_918197.1 CDS Pden_4437 NC_008687.1 1645344 1646393 R PFAM: oxidoreductase domain protein; Oxidoreductase, C-terminal domain; KEGG: sme:SMb20330 probable trehalosemaltose utilization protein, function; oxidoreductase domain-containing protein complement(1645344..1646393) Paracoccus denitrificans PD1222 4582987 YP_918198.1 CDS Pden_4438 NC_008687.1 1646393 1647178 R PFAM: protein of unknown function DUF1037; KEGG: atc:AGR_L_2958 probable ThuA protein, function; hypothetical protein complement(1646393..1647178) Paracoccus denitrificans PD1222 4582988 YP_918199.1 CDS Pden_4439 NC_008687.1 1647221 1648222 R 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 complement(1647221..1648222) Paracoccus denitrificans PD1222 4582989 YP_918200.1 CDS Pden_4440 NC_008687.1 1648226 1649059 R PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: bms:BRA0306 sugar ABC transporter, permease; binding-protein-dependent transport systems inner membrane component complement(1648226..1649059) Paracoccus denitrificans PD1222 4582990 YP_918201.1 CDS Pden_4441 NC_008687.1 1649056 1650018 R PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: sme:SMb20326 probable trehalosemaltose transporter permease; binding-protein-dependent transport systems inner membrane component complement(1649056..1650018) Paracoccus denitrificans PD1222 4582991 YP_918202.1 CDS Pden_4442 NC_008687.1 1650089 1651366 R PFAM: extracellular solute-binding protein, family 1; KEGG: sme:SMb20325 probable trehalosemaltose-binding protein; extracellular solute-binding protein complement(1650089..1651366) Paracoccus denitrificans PD1222 4582992 YP_918203.1 CDS Pden_4443 NC_008687.1 1651797 1652429 R PFAM: electron transport protein SCO1/SenC; KEGG: mes:Meso_1992 electron transport protein SCO1/SenC; electron transport protein SCO1/SenC complement(1651797..1652429) Paracoccus denitrificans PD1222 4582993 YP_918204.1 CDS Pden_4444 NC_008687.1 1652416 1653402 R PFAM: protein of unknown function DUF461; nuclear export factor GLE1; KEGG: sme:SMc01242 signal peptide protein; hypothetical protein complement(1652416..1653402) Paracoccus denitrificans PD1222 4582994 YP_918205.1 CDS Pden_4445 NC_008687.1 1653460 1653879 R hypothetical protein complement(1653460..1653879) Paracoccus denitrificans PD1222 4582995 YP_918206.1 CDS Pden_4446 NC_008687.1 1653933 1655585 R PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: atc:AGR_C_717 hypothetical protein; binding-protein-dependent transport system inner membrane protein complement(1653933..1655585) Paracoccus denitrificans PD1222 4582996 YP_918207.1 CDS Pden_4447 NC_008687.1 1655608 1656621 R PFAM: extracellular solute-binding protein, family 1; KEGG: atc:AGR_C_715 iron binding protein; extracellular solute-binding protein complement(1655608..1656621) Paracoccus denitrificans PD1222 4582997 YP_918208.1 CDS Pden_4448 NC_008687.1 1656714 1657835 D PFAM: ABC transporter related; Transport-associated OB domain protein; SMART: AAA ATPase; KEGG: rsp:RSP_2539 ABC transporter, ATPase subunit; ABC transporter 1656714..1657835 Paracoccus denitrificans PD1222 4582998 YP_918209.1 CDS Pden_4449 NC_008687.1 1657849 1660461 R 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 complement(1657849..1660461) Paracoccus denitrificans PD1222 4582999 YP_918210.1 CDS Pden_4450 NC_008687.1 1660470 1661327 R PFAM: formate/nitrite transporter; KEGG: bcn:Bcen_5755 formate/nitrite transporter; formate/nitrite transporter complement(1660470..1661327) Paracoccus denitrificans PD1222 4583000 YP_918211.1 CDS Pden_4451 NC_008687.1 1661340 1661675 R 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 complement(1661340..1661675) Paracoccus denitrificans PD1222 4583001 YP_918212.1 CDS Pden_4452 NC_008687.1 1661672 1664104 R 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 complement(1661672..1664104) Paracoccus denitrificans PD1222 4583002 YP_918213.1 CDS Pden_4453 NC_008687.1 1664120 1665328 R PFAM: major facilitator superfamily MFS_1; KEGG: sme:SMb20436 nitrate transporter protein; major facilitator transporter complement(1664120..1665328) Paracoccus denitrificans PD1222 4583003 YP_918214.1 CDS Pden_4454 NC_008687.1 1665613 1666785 R KEGG: jan:Jann_3039 nitrate transport protein; nitrate transport protein complement(1665613..1666785) Paracoccus denitrificans PD1222 4583004 YP_918215.1 CDS Pden_4455 NC_008687.1 1666776 1667366 R PFAM: ANTAR domain protein; KEGG: jan:Jann_3038 response regulator receiver (CheY-like) and ANTAR domain protein; response regulator receiver/ANTAR domain-containing protein complement(1666776..1667366) Paracoccus denitrificans PD1222 4583005 YP_918216.1 CDS Pden_4456 NC_008687.1 1667596 1668348 D PFAM: 3-alpha; MOSC domain containing protein; KEGG: rsp:RSP_1921 MOSC domain protein; MOSC domain-containing protein 1667596..1668348 Paracoccus denitrificans PD1222 4583006 YP_918217.1 CDS Pden_4457 NC_008687.1 1668345 1669181 D TIGRFAM: pyridoxal kinase; PFAM: Phosphomethylpyrimidine kinase type-1; KEGG: rsp:RSP_1920 pyridoxal/pyridoxine/pyridoxamine kinase; pyridoxal kinase 1668345..1669181 Paracoccus denitrificans PD1222 4583007 YP_918218.1 CDS Pden_4458 NC_008687.1 1669248 1671560 R 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 complement(1669248..1671560) Paracoccus denitrificans PD1222 4583008 YP_918219.1 CDS Pden_4459 NC_008687.1 1671634 1672110 R hypothetical protein complement(1671634..1672110) Paracoccus denitrificans PD1222 4583009 YP_918220.1 CDS Pden_4460 NC_008687.1 1672770 1674299 R 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 complement(1672770..1674299) Paracoccus denitrificans PD1222 4583010 YP_918221.1 CDS Pden_4461 NC_008687.1 1674441 1674779 D PFAM: nitrogen regulatory protein P-II; KEGG: rsp:RSP_0146 nitrogen regulatory protein P-II; nitrogen regulatory protein P-II 1674441..1674779 Paracoccus denitrificans PD1222 4583011 YP_918222.1 CDS Pden_4462 NC_008687.1 1674857 1676263 D 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 1674857..1676263 Paracoccus denitrificans PD1222 4583012 YP_918223.1 CDS Pden_4463 NC_008687.1 1676470 1677786 D Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide; adenylosuccinate lyase 1676470..1677786 Paracoccus denitrificans PD1222 4583013 YP_918224.1 CDS Pden_4464 NC_008687.1 1677847 1678902 D PFAM: flagellar motor switch protein FliG; KEGG: rsp:RSP_2220 possible flagellar motor switch protein (FliG); flagellar motor switch protein FliG 1677847..1678902 Paracoccus denitrificans PD1222 4583014 YP_918225.1 CDS Pden_4465 NC_008687.1 1679499 1680500 D 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 1679499..1680500 Paracoccus denitrificans PD1222 4583015 YP_918226.1 CDS Pden_4466 NC_008687.1 1680590 1680904 R KEGG: rsp:RSP_0307 antifreeze protein, type I; antifreeze protein, type I complement(1680590..1680904) Paracoccus denitrificans PD1222 4583016 YP_918227.1 CDS Pden_4467 NC_008687.1 1681035 1682078 D catalyzes the formation of N-carbamoyl-L-aspartate from (S)-dihydroorotate in pyrimidine biosynthesis; dihydroorotase 1681035..1682078 Paracoccus denitrificans PD1222 4583017 YP_918228.1 CDS pyrE NC_008687.1 1682075 1682746 D 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 1682075..1682746 Paracoccus denitrificans PD1222 4583018 YP_918229.1 CDS Pden_4469 NC_008687.1 1682979 1684478 D unwinds double stranded DNA; replicative DNA helicase 1682979..1684478 Paracoccus denitrificans PD1222 4583019 YP_918230.1 CDS Pden_4470 NC_008687.1 1684475 1684837 D PFAM: protein of unknown function DUF486; KEGG: rsp:RSP_2188 hypothetical protein; hypothetical protein 1684475..1684837 Paracoccus denitrificans PD1222 4583020 YP_918231.1 CDS Pden_4471 NC_008687.1 1684901 1686109 D 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 1684901..1686109 Paracoccus denitrificans PD1222 4583021 YP_918232.1 CDS Pden_4472 NC_008687.1 1686171 1687565 D PFAM: helix-turn-helix domain protein; protein of unknown function DUF955; KEGG: rsp:RSP_2186 transcriptional regulator, MerR family; hypothetical protein 1686171..1687565 Paracoccus denitrificans PD1222 4583022 YP_918233.1 CDS Pden_4473 NC_008687.1 1687807 1689282 D PFAM: peptidase M23B; KEGG: rde:RD1_3002 peptidase, M23/M37 family; peptidase M23B 1687807..1689282 Paracoccus denitrificans PD1222 4583023 YP_918234.1 CDS Pden_4474 NC_008687.1 1689272 1689769 D PFAM: protein of unknown function DUF583; KEGG: rsp:RSP_2975 hypothetical protein; hypothetical protein 1689272..1689769 Paracoccus denitrificans PD1222 4583024 YP_918235.1 CDS Pden_4475 NC_008687.1 1689816 1690679 R KEGG: rsp:RSP_2976 hypothetical protein; hypothetical protein complement(1689816..1690679) Paracoccus denitrificans PD1222 4583025 YP_918236.1 CDS coaD NC_008687.1 1690734 1691228 R Catalyzes the conversion of ATP and pantetheine 4'-phosphate to diphosphate and 3'-dephospho-coA; phosphopantetheine adenylyltransferase complement(1690734..1691228) Paracoccus denitrificans PD1222 4583026 YP_918237.1 CDS Pden_4477 NC_008687.1 1691338 1691775 R PFAM: CBS domain containing protein; KEGG: rsp:RSP_2961 protein containing a CBS domain; signal-transduction protein complement(1691338..1691775) Paracoccus denitrificans PD1222 4583027 YP_918238.1 CDS Pden_4478 NC_008687.1 1691868 1692761 R PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: rsp:RSP_2965 transcriptional regulator, LysR family; LysR family transcriptional regulator complement(1691868..1692761) Paracoccus denitrificans PD1222 4583028 YP_918239.1 CDS Pden_4479 NC_008687.1 1692871 1694370 D TIGRFAM: methylmalonate-semialdehyde dehydrogenase; PFAM: aldehyde dehydrogenase; KEGG: sit:TM1040_1106 methylmalonate-semialdehyde dehydrogenase; methylmalonate-semialdehyde dehydrogenase 1692871..1694370 Paracoccus denitrificans PD1222 4583029 YP_918240.1 CDS Pden_4480 NC_008687.1 1694494 1695639 D PFAM: acyl-CoA dehydrogenase domain protein; Acyl-CoA dehydrogenase, type 2, C-terminal domain; KEGG: rsp:RSP_0156 acyl-CoA dehydrogenase; acyl-CoA dehydrogenase 1694494..1695639 Paracoccus denitrificans PD1222 4583030 YP_918241.1 CDS Pden_4481 NC_008687.1 1695640 1696647 D PFAM: Enoyl-CoA hydratase/isomerase; KEGG: sil:SPO2212 enoyl-CoA hydratase/isomerase family protein; enoyl-CoA hydratase/isomerase 1695640..1696647 Paracoccus denitrificans PD1222 4583031 YP_918242.1 CDS Pden_4482 NC_008687.1 1696644 1697519 D 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 1696644..1697519 Paracoccus denitrificans PD1222 4583032 YP_918243.1 CDS Pden_4483 NC_008687.1 1697600 1697908 D hypothetical protein 1697600..1697908 Paracoccus denitrificans PD1222 4583033 YP_918244.1 CDS Pden_4484 NC_008687.1 1697905 1699548 R TIGRFAM: DNA repair protein RecN; PFAM: SMC domain protein; KEGG: rsp:RSP_2118 DNA repair protein RecN; DNA repair protein RecN complement(1697905..1699548) Paracoccus denitrificans PD1222 4583034 YP_918245.1 CDS Pden_4485 NC_008687.1 1699556 1700398 R KEGG: rsp:RSP_2117 ComL lipoprotein; ComL lipoprotein complement(1699556..1700398) Paracoccus denitrificans PD1222 4583035 YP_918246.1 CDS lpxC NC_008687.1 1700528 1701466 R 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 complement(1700528..1701466) Paracoccus denitrificans PD1222 4583036 YP_918247.1 CDS Pden_4487 NC_008687.1 1701702 1703336 R 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 complement(1701702..1703336) Paracoccus denitrificans PD1222 4583037 YP_918248.1 CDS Pden_4488 NC_008687.1 1703557 1704891 R PFAM: cell division protein FtsA; KEGG: rsp:RSP_2113 cell division protein FtsA; cell division protein FtsA complement(1703557..1704891) Paracoccus denitrificans PD1222 4583038 YP_918249.1 CDS Pden_4489 NC_008687.1 1704913 1705935 R PFAM: cell division protein FtsQ; KEGG: rsp:RSP_2112 cell division septal protein FtsQ; cell division protein FtsQ complement(1704913..1705935) Paracoccus denitrificans PD1222 4583039 YP_918250.1 CDS ddl NC_008687.1 1705923 1706858 R 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 complement(1705923..1706858) Paracoccus denitrificans PD1222 4583040 YP_918251.1 CDS murB NC_008687.1 1706977 1707897 R catalyzes the reduction of UDP-N-acetylglucosamine enolpyruvate to form UDP-N-acetylmuramate in peptidoglycan biosynthesis; UDP-N-acetylenolpyruvoylglucosamine reductase complement(1706977..1707897) Paracoccus denitrificans PD1222 4583041 YP_918252.1 CDS Pden_4492 NC_008687.1 1708076 1708444 R hypothetical protein complement(1708076..1708444) Paracoccus denitrificans PD1222 4583042 YP_918253.1 CDS Pden_4493 NC_008687.1 1708449 1708712 R KEGG: jan:Jann_2756 hypothetical protein; hypothetical protein complement(1708449..1708712) Paracoccus denitrificans PD1222 4583043 YP_918254.1 CDS murC NC_008687.1 1708709 1710136 R 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 complement(1708709..1710136) Paracoccus denitrificans PD1222 4583044 YP_918255.1 CDS murG NC_008687.1 1710133 1711221 R 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 complement(1710133..1711221) Paracoccus denitrificans PD1222 4583045 YP_918256.1 CDS Pden_4496 NC_008687.1 1711218 1712387 R TIGRFAM: cell division protein FtsW; PFAM: cell cycle protein; KEGG: rsp:RSP_2106 cell division protein FtsW; cell division protein FtsW complement(1711218..1712387) Paracoccus denitrificans PD1222 4583046 YP_918257.1 CDS Pden_4497 NC_008687.1 1712522 1712911 R PFAM: DoxX family protein; KEGG: ret:RHE_CH00824 hypothetical conserved membrane protein; DoxX family protein complement(1712522..1712911) Paracoccus denitrificans PD1222 4583047 YP_918258.1 CDS Pden_4498 NC_008687.1 1713154 1714056 D KEGG: rsp:RSP_0009 hypothetical protein; hypothetical protein 1713154..1714056 Paracoccus denitrificans PD1222 4583048 YP_918259.1 CDS Pden_4499 NC_008687.1 1714056 1714982 D catalyzes the formation of O-succinyl-L-homoserine from succinyl-CoA and L-homoserine in methionine biosynthesis; homoserine O-succinyltransferase 1714056..1714982 Paracoccus denitrificans PD1222 4583049 YP_918260.1 CDS Pden_4500 NC_008687.1 1714985 1715908 D PFAM: protein of unknown function DUF344; KEGG: rsp:RSP_0013 hypothetical protein; hypothetical protein 1714985..1715908 Paracoccus denitrificans PD1222 4583050 YP_918261.1 CDS Pden_4501 NC_008687.1 1715930 1716865 D PFAM: protein of unknown function DUF477; KEGG: sil:SPO2950 hypothetical protein; hypothetical protein 1715930..1716865 Paracoccus denitrificans PD1222 4583051 YP_918262.1 CDS Pden_4502 NC_008687.1 1716908 1717990 D KEGG: rsp:RSP_2141 ABC polyamine transporter, periplasmic substrate-binding protein; ABC polyamine transporter, periplasmic substrate-binding protein 1716908..1717990 Paracoccus denitrificans PD1222 4583052 YP_918263.1 CDS proA NC_008687.1 1718596 1719867 D Catalyzes the phosphorylation of L-glutamate during the proline biosynthesis pathway; gamma-glutamyl phosphate reductase 1718596..1719867 Paracoccus denitrificans PD1222 4583053 YP_918264.1 CDS Pden_4504 NC_008687.1 1719911 1720567 R KEGG: rsp:RSP_3825 hypothetical protein; hypothetical protein complement(1719911..1720567) Paracoccus denitrificans PD1222 4583054 YP_918265.1 CDS Pden_4505 NC_008687.1 1720608 1720787 D KEGG: rsp:RSP_6239 hypothetical protein; hypothetical protein 1720608..1720787 Paracoccus denitrificans PD1222 4583055 YP_918266.1 CDS Pden_4506 NC_008687.1 1720925 1721704 D KEGG: rsp:RSP_3826 hypothetical protein; hypothetical protein 1720925..1721704 Paracoccus denitrificans PD1222 4583056 YP_918267.1 CDS Pden_4507 NC_008687.1 1721701 1722534 D PFAM: phospholipid/glycerol acyltransferase; KEGG: rde:RD1_2655 acyltransferase; phospholipid/glycerol acyltransferase 1721701..1722534 Paracoccus denitrificans PD1222 4583057 YP_918268.1 CDS Pden_4508 NC_008687.1 1722683 1724461 R 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 complement(1722683..1724461) Paracoccus denitrificans PD1222 4583058 YP_918269.1 CDS Pden_4509 NC_008687.1 1724563 1725381 R KEGG: rde:RD1_2012 hypothetical protein; hypothetical protein complement(1724563..1725381) Paracoccus denitrificans PD1222 4583059 YP_918270.1 CDS Pden_4510 NC_008687.1 1725447 1726982 R TIGRFAM: 2-polyprenylphenol 6-hydroxylase; PFAM: ABC-1 domain protein; KEGG: jan:Jann_4208 2-polyprenylphenol 6-hydroxylase; 2-polyprenylphenol 6-hydroxylase complement(1725447..1726982) Paracoccus denitrificans PD1222 4583060 YP_918271.1 CDS Pden_4511 NC_008687.1 1726984 1727736 R 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 complement(1726984..1727736) Paracoccus denitrificans PD1222 4583061 YP_918272.1 CDS Pden_4512 NC_008687.1 1727837 1728682 D KEGG: rsp:RSP_1339 formamidopyrimidine-DNA glycolase; TIGRFAM: formamidopyrimidine-DNA glycosylase; PFAM: Formamidopyrimidine-DNA glycolase; formamidopyrimidine-DNA glycosylase 1727837..1728682 Paracoccus denitrificans PD1222 4583062 YP_918273.1 CDS Pden_4513 NC_008687.1 1728790 1729566 D PFAM: Enoyl-CoA hydratase/isomerase; KEGG: rsp:RSP_1340 enoyl-CoA hydratase/isomerase; enoyl-CoA hydratase/isomerase 1728790..1729566 Paracoccus denitrificans PD1222 4583063 YP_918274.1 CDS rpsT NC_008687.1 1729720 1729989 D binds directly to the 16S rRNA and is involved in post-translational inhibition of arginine and ornithine decarboxylase; 30S ribosomal protein S20 1729720..1729989 Paracoccus denitrificans PD1222 4583064 YP_918275.1 CDS Pden_4515 NC_008688.1 65 511 R 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 complement(65..511) Paracoccus denitrificans PD1222 4583099 YP_918276.1 CDS Pden_4516 NC_008688.1 536 931 R PFAM: 3-demethylubiquinone-9 3-methyltransferase; KEGG: pau:PA14_46720 hypothetical protein; 3-demethylubiquinone-9 3-methyltransferase complement(536..931) Paracoccus denitrificans PD1222 4583100 YP_918277.1 CDS Pden_4517 NC_008688.1 988 1506 D PFAM: regulatory protein, MarR; KEGG: nha:Nham_3666 transcriptional regulator, MarR family; MarR family transcriptional regulator 988..1506 Paracoccus denitrificans PD1222 4583101 YP_918278.1 CDS Pden_4518 NC_008688.1 1528 1887 R PFAM: regulatory protein, ArsR; KEGG: sme:SMc02639 transcription regulator protein; regulatory protein, ArsR complement(1528..1887) Paracoccus denitrificans PD1222 4583102 YP_918279.1 CDS Pden_4519 NC_008688.1 1936 2382 D PFAM: Activator of Hsp90 ATPase 1 family protein; KEGG: sal:Sala_0458 hypothetical protein; activator of Hsp90 ATPase 1 family protein 1936..2382 Paracoccus denitrificans PD1222 4583103 YP_918280.1 CDS Pden_4520 NC_008688.1 2524 2937 D PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase; KEGG: mlo:mlr1197 hypothetical protein; glyoxalase/bleomycin resistance protein/dioxygenase 2524..2937 Paracoccus denitrificans PD1222 4583104 YP_918281.1 CDS Pden_4521 NC_008688.1 3076 4578 D KEGG: mlo:mll0865 hypothetical protein; hypothetical protein 3076..4578 Paracoccus denitrificans PD1222 4583105 YP_918282.1 CDS Pden_4522 NC_008688.1 4693 5118 R PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase; KEGG: bur:Bcep18194_A5393 glyoxalase/bleomycin resistance protein/dioxygenase; glyoxalase/bleomycin resistance protein/dioxygenase complement(4693..5118) Paracoccus denitrificans PD1222 4583080 YP_918283.1 CDS Pden_4523 NC_008688.1 5412 5861 R PFAM: regulatory protein, MerR; KEGG: mes:Meso_2848 transcriptional regulator, MerR family; MerR family transcriptional regulator complement(5412..5861) Paracoccus denitrificans PD1222 4583081 YP_918284.1 CDS Pden_4524 NC_008688.1 5936 6553 D hypothetical protein 5936..6553 Paracoccus denitrificans PD1222 4583082 YP_918285.1 CDS Pden_4525 NC_008688.1 6621 7568 D PFAM: GCN5-related N-acetyltransferase; regulatory protein, MarR; KEGG: pfo:Pfl_2408 transcriptional regulator, MarR family; MarR family transcriptional regulator 6621..7568 Paracoccus denitrificans PD1222 4583083 YP_918286.1 CDS Pden_4526 NC_008688.1 7718 8479 R PFAM: Methyltransferase type 11; Methyltransferase type 12; KEGG: pae:PA2679 hypothetical protein; methyltransferase type 11 complement(7718..8479) Paracoccus denitrificans PD1222 4583084 YP_918287.1 CDS Pden_4527 NC_008688.1 8469 8966 R PFAM: regulatory protein, MarR; KEGG: xcb:XC_0601 transcriptional regulator MarR family; MarR family transcriptional regulator complement(8469..8966) Paracoccus denitrificans PD1222 4583085 YP_918288.1 CDS Pden_4528 NC_008688.1 9105 10142 R PFAM: helix-turn-helix- domain containing protein, AraC type; KEGG: bam:Bamb_5783 transcriptional regulator, AraC family; helix-turn-helix domain-containing protein complement(9105..10142) Paracoccus denitrificans PD1222 4583086 YP_918289.1 CDS Pden_4529 NC_008688.1 10534 12111 D PFAM: Na+/solute symporter; KEGG: btk:BT9727_3311 sodium/pantothenate symporter; Na+/solute symporter 10534..12111 Paracoccus denitrificans PD1222 4583087 YP_918290.1 CDS Pden_4530 NC_008688.1 12108 13175 D 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 12108..13175 Paracoccus denitrificans PD1222 4583088 YP_918291.1 CDS Pden_4531 NC_008688.1 13168 14097 D PFAM: protein of unknown function DUF849; KEGG: rpc:RPC_0103 protein of unknown function DUF849; hypothetical protein 13168..14097 Paracoccus denitrificans PD1222 4583089 YP_918292.1 CDS Pden_4532 NC_008688.1 14111 14359 D hypothetical protein 14111..14359 Paracoccus denitrificans PD1222 4583090 YP_918293.1 CDS Pden_4533 NC_008688.1 14488 15000 D 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 14488..15000 Paracoccus denitrificans PD1222 4583091 YP_918294.1 CDS Pden_4534 NC_008688.1 15000 15950 D PFAM: FecR protein; KEGG: pae:PA3409 probable transmembrane sensor; FecR 15000..15950 Paracoccus denitrificans PD1222 4583092 YP_918295.1 CDS Pden_4535 NC_008688.1 16049 18385 D 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 16049..18385 Paracoccus denitrificans PD1222 4583093 YP_918296.1 CDS Pden_4537 NC_008688.1 18797 19075 D KEGG: bxe:Bxe_A3169 IS66 transposase, TnpC; hypothetical protein 18797..19075 Paracoccus denitrificans PD1222 4583094 YP_918297.1 CDS Pden_4538 NC_008688.1 19142 19492 R hypothetical protein complement(19142..19492) Paracoccus denitrificans PD1222 4583095 YP_918298.1 CDS Pden_4539 NC_008688.1 19602 20843 D 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) 19602..20843 Paracoccus denitrificans PD1222 4583096 YP_918299.1 CDS Pden_4540 NC_008688.1 20858 21871 D PFAM: transposase IS66; KEGG: mag:amb3320 transposase and inactivated derivative; transposase IS66 20858..21871 Paracoccus denitrificans PD1222 4583097 YP_918300.1 CDS Pden_4541 NC_008688.1 21921 22283 R hypothetical protein complement(21921..22283) Paracoccus denitrificans PD1222 4583098 YP_918301.1 CDS Pden_4542 NC_008688.1 22329 23213 R PFAM: helix-turn-helix protein RpiR; sugar isomerase (SIS); KEGG: rsp:RSP_2324 transcriptional regulator, RpiR family; RpiR family transcriptional regulator complement(22329..23213) Paracoccus denitrificans PD1222 4583281 YP_918302.1 CDS Pden_4543 NC_008688.1 23335 24075 D PFAM: N-formylglutamate amidohydrolase; KEGG: rsp:RSP_2323 hypothetical protein; N-formylglutamate amidohydrolase 23335..24075 Paracoccus denitrificans PD1222 4583282 YP_918303.1 CDS Pden_4544 NC_008688.1 24075 24611 D 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 24075..24611 Paracoccus denitrificans PD1222 4583283 YP_918304.1 CDS Pden_4545 NC_008688.1 24608 25933 D 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 24608..25933 Paracoccus denitrificans PD1222 4583284 YP_918305.1 CDS Pden_4546 NC_008688.1 25957 26997 D PFAM: TRAP dicarboxylate transporter- DctP subunit; KEGG: rsp:RSP_2320 TRAP-T family transporter, periplasmic binding protein; TRAP dicarboxylate transporter- DctP subunit 25957..26997 Paracoccus denitrificans PD1222 4583285 YP_918306.1 CDS Pden_4547 NC_008688.1 27051 28412 D PFAM: glutamine synthetase, catalytic region; KEGG: rsp:RSP_2319 glutamine synthetase class-I; glutamate--ammonia ligase 27051..28412 Paracoccus denitrificans PD1222 4583286 YP_918307.1 CDS Pden_4548 NC_008688.1 28450 29838 D PFAM: aldehyde dehydrogenase; KEGG: rsp:RSP_2318 aldehyde dehydrogenase; aldehyde dehydrogenase 28450..29838 Paracoccus denitrificans PD1222 4583287 YP_918308.1 CDS Pden_4549 NC_008688.1 29835 30980 D PFAM: iron-containing alcohol dehydrogenase; KEGG: rsp:RSP_2317 iron-containing alcohol dehydrogenase; iron-containing alcohol dehydrogenase 29835..30980 Paracoccus denitrificans PD1222 4583288 YP_918309.1 CDS Pden_4550 NC_008688.1 31432 33387 D TIGRFAM: acetate--CoA ligase; PFAM: AMP-dependent synthetase and ligase; KEGG: rsp:RSP_0579 acetyl-coenzyme A synthetase; acetate--CoA ligase 31432..33387 Paracoccus denitrificans PD1222 4583289 YP_918310.1 CDS Pden_4551 NC_008688.1 33496 33753 D KEGG: sit:TM1040_3665 conserved hypothetical protein; hypothetical protein 33496..33753 Paracoccus denitrificans PD1222 4583290 YP_918311.1 CDS Pden_4552 NC_008688.1 33764 35575 D PFAM: Na+/solute symporter; KEGG: rsp:RSP_0576 Na+/solute symporter; Na+/solute symporter 33764..35575 Paracoccus denitrificans PD1222 4583291 YP_918312.1 CDS Pden_4553 NC_008688.1 35633 37444 D 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 35633..37444 Paracoccus denitrificans PD1222 4583292 YP_918313.1 CDS Pden_4554 NC_008688.1 37452 37949 D KEGG: rsp:RSP_0574 hypothetical protein; hypothetical protein 37452..37949 Paracoccus denitrificans PD1222 4583293 YP_918314.1 CDS Pden_4555 NC_008688.1 37949 38320 D PFAM: response regulator receiver; KEGG: rsp:RSP_0573 response regulator receiver protein; response regulator receiver protein 37949..38320 Paracoccus denitrificans PD1222 4583294 YP_918315.1 CDS Pden_4556 NC_008688.1 38314 40293 D 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 38314..40293 Paracoccus denitrificans PD1222 4583295 YP_918316.1 CDS Pden_4557 NC_008688.1 40436 41701 R PFAM: peptidase S8 and S53, subtilisin, kexin, sedolisin; KEGG: sme:SMa0142 possible protease; peptidase S8/S53 subtilisin kexin sedolisin complement(40436..41701) Paracoccus denitrificans PD1222 4583296 YP_918317.1 CDS Pden_4558 NC_008688.1 41802 42293 D 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 41802..42293 Paracoccus denitrificans PD1222 4583297 YP_918318.1 CDS Pden_4559 NC_008688.1 42290 43018 D KEGG: sme:SMa0144 hypothetical protein; hypothetical protein 42290..43018 Paracoccus denitrificans PD1222 4583298 YP_918319.1 CDS Pden_4560 NC_008688.1 43068 44735 D PFAM: sodium/sulphate symporter; KEGG: sco:SCO2144 integral membrane transporter; sodium/sulphate symporter 43068..44735 Paracoccus denitrificans PD1222 4583299 YP_918320.1 CDS Pden_4561 NC_008688.1 44868 46031 D PFAM: glycerate kinase; KEGG: bat:BAS2054 glycerate kinase; glycerate kinase 44868..46031 Paracoccus denitrificans PD1222 4583300 YP_918321.1 CDS Pden_4562 NC_008688.1 46125 46862 D PFAM: Hemolysin-type calcium-binding region; KEGG: rpb:RPB_0805 glycerophosphoryl diester phosphodiesterase; hemolysin-type calcium-binding region 46125..46862 Paracoccus denitrificans PD1222 4583301 YP_918322.1 CDS Pden_4563 NC_008688.1 47053 47964 R PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: bbr:BB1277 LysR-family transcriptional regulator; LysR family transcriptional regulator complement(47053..47964) Paracoccus denitrificans PD1222 4583302 YP_918323.1 CDS Pden_4564 NC_008688.1 48060 48686 D stationary phase that binds TrpR repressor; TrpR binding protein WrbA 48060..48686 Paracoccus denitrificans PD1222 4583303 YP_918324.1 CDS Pden_4565 NC_008688.1 48686 49864 D PFAM: major facilitator superfamily MFS_1; KEGG: mag:amb2984 permease of the major facilitator superfamily; major facilitator transporter 48686..49864 Paracoccus denitrificans PD1222 4583304 YP_918325.1 CDS Pden_4566 NC_008688.1 49852 51039 R PFAM: protein of unknown function DUF6, transmembrane; KEGG: sme:SMc00381 hypothetical protein; hypothetical protein complement(49852..51039) Paracoccus denitrificans PD1222 4583305 YP_918326.1 CDS Pden_4567 NC_008688.1 51125 53917 R catalyzes the conversion of citrate to isocitrate and the conversion of 2-methylaconitate to 2-methylisocitrate; bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase complement(51125..53917) Paracoccus denitrificans PD1222 4583306 YP_918327.1 CDS Pden_4568 NC_008688.1 54000 54425 D hypothetical protein 54000..54425 Paracoccus denitrificans PD1222 4583307 YP_918328.1 CDS Pden_4569 NC_008688.1 54428 54691 D hypothetical protein 54428..54691 Paracoccus denitrificans PD1222 4583308 YP_918329.1 CDS Pden_4570 NC_008688.1 54785 55594 R KEGG: bur:Bcep18194_A6516 hypothetical protein; hypothetical protein complement(54785..55594) Paracoccus denitrificans PD1222 4583309 YP_918330.1 CDS Pden_4571 NC_008688.1 55723 56352 R PFAM: NAD-dependent epimerase/dehydratase; KEGG: mlo:mlr0241 hypothetical protein; NAD-dependent epimerase/dehydratase complement(55723..56352) Paracoccus denitrificans PD1222 4583310 YP_918331.1 CDS Pden_4572 NC_008688.1 56439 57800 R PFAM: major facilitator superfamily MFS_1; KEGG: neu:NE2492 general substrate transporters; major facilitator transporter complement(56439..57800) Paracoccus denitrificans PD1222 4583311 YP_918332.1 CDS Pden_4573 NC_008688.1 57816 58733 D PFAM: protein of unknown function DUF6, transmembrane; KEGG: sil:SPO0261 hypothetical protein; hypothetical protein 57816..58733 Paracoccus denitrificans PD1222 4583312 YP_918333.1 CDS Pden_4574 NC_008688.1 58879 59838 D PFAM: aldo/keto reductase; KEGG: jan:Jann_0800 aldo/keto reductase; aldo/keto reductase 58879..59838 Paracoccus denitrificans PD1222 4583313 YP_918334.1 CDS Pden_4575 NC_008688.1 59908 60876 R PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: sme:SMa1632 LysR-family transcriptional regulator; LysR family transcriptional regulator complement(59908..60876) Paracoccus denitrificans PD1222 4583314 YP_918335.1 CDS Pden_4576 NC_008688.1 60909 61229 D KEGG: rsp:RSP_2028 hypothetical protein; hypothetical protein 60909..61229 Paracoccus denitrificans PD1222 4583315 YP_918336.1 CDS Pden_4577 NC_008688.1 61229 62008 D PFAM: NAD-dependent epimerase/dehydratase; short-chain dehydrogenase/reductase SDR; KEGG: rsp:RSP_2029 short chain dehydrogenase; short chain dehydrogenase 61229..62008 Paracoccus denitrificans PD1222 4583316 YP_918337.1 CDS Pden_4578 NC_008688.1 62405 62806 R PFAM: Cupin 2, conserved barrel domain protein; KEGG: jan:Jann_0773 cupin 2 protein; cupin 2 domain-containing protein complement(62405..62806) Paracoccus denitrificans PD1222 4583317 YP_918338.1 CDS Pden_4579 NC_008688.1 62781 63167 R PFAM: helix-turn-helix, HxlR type; KEGG: ret:RHE_CH02586 transcriptional regulator protein; HxlR family transcriptional regulator complement(62781..63167) Paracoccus denitrificans PD1222 4583318 YP_918339.1 CDS Pden_4580 NC_008688.1 63261 64172 D PFAM: NADPH-dependent FMN reductase; Antibiotic biosynthesis monooxygenase; KEGG: mlo:mll2599 probable reductase; NADPH-dependent FMN reductase 63261..64172 Paracoccus denitrificans PD1222 4583319 YP_918340.1 CDS Pden_4581 NC_008688.1 64195 65091 R PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: rme:Rmet_5666 transcriptional regulator, LysR family; LysR family transcriptional regulator complement(64195..65091) Paracoccus denitrificans PD1222 4583320 YP_918341.1 CDS Pden_4582 NC_008688.1 65190 65714 D KEGG: cvi:CV1605 hypothetical protein; hypothetical protein 65190..65714 Paracoccus denitrificans PD1222 4583321 YP_918342.1 CDS Pden_4583 NC_008688.1 66007 66354 D PFAM: protein of unknown function DUF1330; KEGG: mlo:mll3541 hypothetical protein; hypothetical protein 66007..66354 Paracoccus denitrificans PD1222 4583322 YP_918343.1 CDS Pden_4584 NC_008688.1 66478 67236 D PFAM: short-chain dehydrogenase/reductase SDR; KR; KEGG: sil:SPO3609 short chain dehydrogenase; short chain dehydrogenase 66478..67236 Paracoccus denitrificans PD1222 4583323 YP_918344.1 CDS groEL NC_008688.1 67559 69196 R 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 complement(67559..69196) Paracoccus denitrificans PD1222 4583324 YP_918345.1 CDS groES NC_008688.1 69237 69524 R 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 complement(69237..69524) Paracoccus denitrificans PD1222 4583325 YP_918346.1 CDS Pden_4587 NC_008688.1 69832 70299 D hypothetical protein 69832..70299 Paracoccus denitrificans PD1222 4583326 YP_918347.1 CDS Pden_4588 NC_008688.1 70413 70760 D KEGG: ret:RHE_CH01244 probable molecular chaperone small heat shock protein, HSP20 family; Hsp20 family heat-shock protein 70413..70760 Paracoccus denitrificans PD1222 4583327 YP_918348.1 CDS Pden_4589 NC_008688.1 70744 70947 D KEGG: ret:RHE_CH01245 probable molecular chaperone small heat shock protein, HSP20 family; hypothetical protein 70744..70947 Paracoccus denitrificans PD1222 4583328 YP_918349.1 CDS Pden_4590 NC_008688.1 71280 72935 R activates fatty acids by binding to coenzyme A; acyl-CoA synthetase complement(71280..72935) Paracoccus denitrificans PD1222 4583329 YP_918350.1 CDS Pden_4591 NC_008688.1 72975 73367 R PFAM: Rhodanese domain protein; KEGG: mes:Meso_2537 rhodanese-like; rhodanese domain-containing protein complement(72975..73367) Paracoccus denitrificans PD1222 4583330 YP_918351.1 CDS Pden_4592 NC_008688.1 73370 73948 R TIGRFAM: alkylhydroperoxidase like protein, AhpD family; uncharacterized peroxidase-related enzyme; PFAM: Carboxymuconolactone decarboxylase; KEGG: rsp:RSP_3419 hypothetical protein; uncharacterized peroxidase-related enzyme complement(73370..73948) Paracoccus denitrificans PD1222 4583331 YP_918352.1 CDS Pden_4593 NC_008688.1 73945 76260 R 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 complement(73945..76260) Paracoccus denitrificans PD1222 4583332 YP_918353.1 CDS Pden_4594 NC_008688.1 76273 77817 R thiamine-pyrophosphate requiring enzyme; hypothetical protein complement(76273..77817) Paracoccus denitrificans PD1222 4583333 YP_918354.1 CDS Pden_4595 NC_008688.1 77814 79304 R PFAM: carbohydrate kinase, FGGY; KEGG: sme:SMc01623 erythritol kinase; carbohydrate kinase, FGGY complement(77814..79304) Paracoccus denitrificans PD1222 4583334 YP_918355.1 CDS Pden_4596 NC_008688.1 79304 79981 R PFAM: class II aldolase/adducin family protein; KEGG: bja:bll6170 L-fuculose phosphate aldolase; Fis family transcriptional regulator complement(79304..79981) Paracoccus denitrificans PD1222 4583335 YP_918356.1 CDS Pden_4597 NC_008688.1 79990 81036 R 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 complement(79990..81036) Paracoccus denitrificans PD1222 4583336 YP_918357.1 CDS Pden_4598 NC_008688.1 81033 82232 R PFAM: L-carnitine dehydratase/bile acid-inducible protein F; KEGG: pae:PA3592 hypothetical protein; L-carnitine dehydratase/bile acid-inducible protein F complement(81033..82232) Paracoccus denitrificans PD1222 4583337 YP_918358.1 CDS Pden_4599 NC_008688.1 82229 82996 R KEGG: rpa:RPA4652 possible CoA transferase, subunit B; CoA transferase, subunit B complement(82229..82996) Paracoccus denitrificans PD1222 4583338 YP_918359.1 CDS Pden_4600 NC_008688.1 82993 83802 R KEGG: rpa:RPA4651 possible glutaconate CoA-transferase, subunit A; glutaconate CoA-transferase, subunit A complement(82993..83802) Paracoccus denitrificans PD1222 4583339 YP_918360.1 CDS Pden_4601 NC_008688.1 84009 85157 D 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 84009..85157 Paracoccus denitrificans PD1222 4583106 YP_918361.1 CDS Pden_4602 NC_008688.1 85154 86929 D PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: rpa:RPA4649 probable ABC transporter permease; binding-protein-dependent transport systems inner membrane component 85154..86929 Paracoccus denitrificans PD1222 4583107 YP_918362.1 CDS Pden_4603 NC_008688.1 86961 88037 D KEGG: rpa:RPA4648 possible ABC transporter binding protein component; ABC transporter binding protein component 86961..88037 Paracoccus denitrificans PD1222 4583108 YP_918363.1 CDS Pden_4604 NC_008688.1 88135 88890 D PFAM: regulatory protein, ArsR; regulatory proteins, IclR; KEGG: rpa:RPA4647 probable transcriptional regulator KdgR, IclR family; regulatory proteins, IclR 88135..88890 Paracoccus denitrificans PD1222 4583109 YP_918364.1 CDS Pden_4605 NC_008688.1 89102 89422 D KEGG: atc:AGR_L_2660 hypothetical protein; hypothetical protein 89102..89422 Paracoccus denitrificans PD1222 4583110 YP_918365.1 CDS Pden_4606 NC_008688.1 89556 90788 D 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 89556..90788 Paracoccus denitrificans PD1222 4583111 YP_918366.1 CDS Pden_4607 NC_008688.1 90785 92224 D PFAM: Uracil-DNA glycosylase superfamily; KEGG: gbe:GbCGDNIH1_1530 uracil DNA glycosylase superfamily protein; uracil-DNA glycosylase 90785..92224 Paracoccus denitrificans PD1222 4583112 YP_918367.1 CDS Pden_4608 NC_008688.1 92297 92779 D KEGG: jan:Jann_0955 general stress protein 26; general stress protein 26 92297..92779 Paracoccus denitrificans PD1222 4583113 YP_918368.1 CDS Pden_4609 NC_008688.1 93059 94534 D PFAM: phospholipase D/Transphosphatidylase; KEGG: rsp:RSP_0113 phospholipase D/transphosphatidylase; phospholipase D/transphosphatidylase 93059..94534 Paracoccus denitrificans PD1222 4583114 YP_918369.1 CDS Pden_4610 NC_008688.1 94555 95784 R PFAM: FAD dependent oxidoreductase; KEGG: hne:HNE_2468 oxidoreductase; FAD dependent oxidoreductase complement(94555..95784) Paracoccus denitrificans PD1222 4583115 YP_918370.1 CDS Pden_4611 NC_008688.1 95816 97948 R PFAM: Catalase domain protein; KEGG: hne:HNE_2467 catalase HPII; catalase complement(95816..97948) Paracoccus denitrificans PD1222 4583116 YP_918371.1 CDS Pden_4612 NC_008688.1 98287 99021 D PFAM: Peptidoglycan-binding domain 1 protein; KEGG: jan:Jann_3999 peptidoglycan-binding domain 1; peptidoglycan binding domain-containing protein 98287..99021 Paracoccus denitrificans PD1222 4583117 YP_918372.1 CDS Pden_4613 NC_008688.1 99235 99792 D KEGG: bja:bll8025 hypothetical protein; hypothetical protein 99235..99792 Paracoccus denitrificans PD1222 4583118 YP_918373.1 CDS Pden_4614 NC_008688.1 99830 100234 D KEGG: rsp:RSP_0683 hypothetical protein; hypothetical protein 99830..100234 Paracoccus denitrificans PD1222 4583119 YP_918374.1 CDS Pden_4615 NC_008688.1 100218 101297 D TIGRFAM: esterase, PHB depolymerase family; PFAM: esterase; phospholipase/Carboxylesterase; KEGG: rru:Rru_A1969 esterase, PHB depolymerase; PHB depolymerase family esterase 100218..101297 Paracoccus denitrificans PD1222 4583120 YP_918375.1 CDS Pden_4616 NC_008688.1 101404 102804 R catalyzes the hydrolytic cleavage of hydantoin with aromatic side chains at the 5'position; phenylhydantoinase complement(101404..102804) Paracoccus denitrificans PD1222 4583121 YP_918376.1 CDS Pden_4617 NC_008688.1 102801 103520 R PFAM: regulatory protein GntR, HTH; GntR domain protein; KEGG: bja:blr6040 transcriptional regulatory protein; GntR family transcriptional regulator complement(102801..103520) Paracoccus denitrificans PD1222 4583122 YP_918377.1 CDS Pden_4618 NC_008688.1 103562 104329 R PFAM: Asp/Glu racemase; KEGG: pol:Bpro_0550 Asp/Glu racemase; Asp/Glu racemase complement(103562..104329) Paracoccus denitrificans PD1222 4583123 YP_918378.1 CDS Pden_4619 NC_008688.1 104611 105654 D PFAM: TRAP dicarboxylate transporter- DctP subunit; KEGG: pol:Bpro_0556 TRAP dicarboxylate transporter-DctP subunit; TRAP dicarboxylate transporter- DctP subunit 104611..105654 Paracoccus denitrificans PD1222 4583124 YP_918379.1 CDS Pden_4620 NC_008688.1 105705 106304 D KEGG: pol:Bpro_0557 hypothetical protein; hypothetical protein 105705..106304 Paracoccus denitrificans PD1222 4583125 YP_918380.1 CDS Pden_4621 NC_008688.1 106301 107602 D 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 106301..107602 Paracoccus denitrificans PD1222 4583126 YP_918381.1 CDS Pden_4622 NC_008688.1 107603 109075 D PFAM: amidohydrolase; KEGG: rde:RD1_2424 amidohydrolase family protein; amidohydrolase 107603..109075 Paracoccus denitrificans PD1222 4583127 YP_918382.1 CDS Pden_4623 NC_008688.1 109319 109621 D KEGG: hne:HNE_1970 dipeptidase family protein; dipeptidase family protein 109319..109621 Paracoccus denitrificans PD1222 4583128 YP_918383.1 CDS Pden_4624 NC_008688.1 109691 110152 R PFAM: regulatory protein, AsnC/Lrp family; KEGG: sit:TM1040_2780 transcriptional regulator, AsnC family; AsnC family transcriptional regulator complement(109691..110152) Paracoccus denitrificans PD1222 4583129 YP_918384.1 CDS Pden_4625 NC_008688.1 110273 111340 D 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 110273..111340 Paracoccus denitrificans PD1222 4583130 YP_918385.1 CDS Pden_4626 NC_008688.1 111423 112142 D PFAM: protein of unknown function DUF161; KEGG: sme:SMc02240 hypothetical protein; hypothetical protein 111423..112142 Paracoccus denitrificans PD1222 4583131 YP_918386.1 CDS Pden_4627 NC_008688.1 112278 112646 R hypothetical protein complement(112278..112646) Paracoccus denitrificans PD1222 4583132 YP_918387.1 CDS Pden_4628 NC_008688.1 112710 113948 R PFAM: FAD dependent oxidoreductase; KEGG: bja:bll4301 oxidoreductase; D-amino-acid dehydrogenase complement(112710..113948) Paracoccus denitrificans PD1222 4583133 YP_918388.1 CDS Pden_4629 NC_008688.1 113965 116208 R 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 complement(113965..116208) Paracoccus denitrificans PD1222 4583134 YP_918389.1 CDS Pden_4630 NC_008688.1 116301 116921 R PFAM: regulatory protein, TetR; KEGG: mpa:MAP1349c hypothetical protein; TetR family transcriptional regulator complement(116301..116921) Paracoccus denitrificans PD1222 4583135 YP_918390.1 CDS Pden_4631 NC_008688.1 117112 118494 D PFAM: major facilitator superfamily MFS_1; KEGG: bam:Bamb_5358 major facilitator superfamily MFS_1; major facilitator transporter 117112..118494 Paracoccus denitrificans PD1222 4583136 YP_918391.1 CDS Pden_4632 NC_008688.1 118543 119655 D PFAM: beta-lactamase; KEGG: bce:BC3013 D-alanyl-D-alanine carboxypeptidase; beta-lactamase 118543..119655 Paracoccus denitrificans PD1222 4583137 YP_918392.1 CDS Pden_4633 NC_008688.1 119665 121167 D PFAM: Uncharacterized conserved protein UCP012702; MlrC domain protein; KEGG: bur:Bcep18194_A4349 hypothetical protein; hypothetical protein 119665..121167 Paracoccus denitrificans PD1222 4583138 YP_918393.1 CDS Pden_4634 NC_008688.1 121265 122743 D PFAM: peptidase M17, leucyl aminopeptidase domain protein; KEGG: ret:RHE_CH01456 leucine aminopeptidase; leucyl aminopeptidase 121265..122743 Paracoccus denitrificans PD1222 4583139 YP_918394.1 CDS Pden_4635 NC_008688.1 122749 123795 D PFAM: peptidase M42 family protein; KEGG: ava:Ava_3182 peptidases M20 and M42; peptidase M42 family protein 122749..123795 Paracoccus denitrificans PD1222 4583140 YP_918395.1 CDS Pden_4636 NC_008688.1 124022 125368 D PFAM: Carbohydrate-selective porin OprB; KEGG: plu:plu0581 porin; carbohydrate-selective porin OprB 124022..125368 Paracoccus denitrificans PD1222 4583141 YP_918396.1 CDS Pden_4637 NC_008688.1 125503 126549 D catalyzes the formation of L-proline from L-ornithine; ornithine cyclodeaminase 125503..126549 Paracoccus denitrificans PD1222 4583142 YP_918397.1 CDS Pden_4638 NC_008688.1 126559 126942 D hypothetical protein 126559..126942 Paracoccus denitrificans PD1222 4583143 YP_918398.1 CDS Pden_4641 NC_008688.1 128042 129550 R KEGG: sdn:Sden_2083 hypothetical protein; hypothetical protein complement(128042..129550) Paracoccus denitrificans PD1222 4583144 YP_918399.1 CDS Pden_4642 NC_008688.1 129609 131342 R KEGG: mxa:MXAN_2365 hypothetical protein; hypothetical protein complement(129609..131342) Paracoccus denitrificans PD1222 4583145 YP_918400.1 CDS Pden_4643 NC_008688.1 131369 133168 R PFAM: tyrosinase; KEGG: hsa:7299 tyrosinase (oculocutaneous albinism IA); tyrosinase complement(131369..133168) Paracoccus denitrificans PD1222 4583146 YP_918401.1 CDS Pden_4644 NC_008688.1 133291 133749 D SMART: regulatory protein, AsnC/Lrp family; KEGG: eca:ECA1157 AsnC-family transcriptional regulator; AsnC family transcriptional regulator 133291..133749 Paracoccus denitrificans PD1222 4583147 YP_918402.1 CDS Pden_4645 NC_008688.1 133967 134641 R PFAM: regulatory protein, TetR; KEGG: reu:Reut_A1792 regulatory protein, TetR; TetR family transcriptional regulator complement(133967..134641) Paracoccus denitrificans PD1222 4583148 YP_918403.1 CDS Pden_4646 NC_008688.1 134870 135652 D PFAM: cyclase family protein; KEGG: jan:Jann_2038 cyclase; cyclase family protein 134870..135652 Paracoccus denitrificans PD1222 4583149 YP_918404.1 CDS Pden_4647 NC_008688.1 135709 136926 D PFAM: major facilitator superfamily MFS_1; KEGG: pol:Bpro_2062 major facilitator superfamily MFS_1; major facilitator transporter 135709..136926 Paracoccus denitrificans PD1222 4583150 YP_918405.1 CDS Pden_4648 NC_008688.1 136951 137886 D PFAM: protein of unknown function DUF849; KEGG: rpc:RPC_0103 protein of unknown function DUF849; hypothetical protein 136951..137886 Paracoccus denitrificans PD1222 4583151 YP_918406.1 CDS Pden_4649 NC_008688.1 138208 139215 D PFAM: extracellular solute-binding protein, family 1; KEGG: sth:STH3219 iron ABC transporter substrate-binding protein; extracellular solute-binding protein 138208..139215 Paracoccus denitrificans PD1222 4583152 YP_918407.1 CDS Pden_4650 NC_008688.1 139237 140928 D PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: sth:STH3218 ABC transporter permease; binding-protein-dependent transport systems inner membrane component 139237..140928 Paracoccus denitrificans PD1222 4583153 YP_918408.1 CDS Pden_4651 NC_008688.1 140935 142038 D PFAM: ABC transporter related; Transport-associated OB domain protein; SMART: AAA ATPase; KEGG: sth:STH3217 ABC transporter ATP-binding protein; ABC transporter related 140935..142038 Paracoccus denitrificans PD1222 4583154 YP_918409.1 CDS Pden_4652 NC_008688.1 142041 142892 D PFAM: inositol monophosphatase; KEGG: sme:SMb20159 inositol monophosphatase; inositol-phosphate phosphatase 142041..142892 Paracoccus denitrificans PD1222 4583155 YP_918410.1 CDS Pden_4653 NC_008688.1 142879 143721 D PFAM: helix-turn-helix protein RpiR; sugar isomerase (SIS); KEGG: cvi:CV0148 probable transcriptional regulator; RpiR family transcriptional regulator 142879..143721 Paracoccus denitrificans PD1222 4583156 YP_918411.1 CDS aphA NC_008688.1 143841 144527 D Class B; non-specific; catalyzes the dephosphorylation of organic phosphomonoesters; also has phosphotransferase activity; acid phosphatase/phosphotransferase 143841..144527 Paracoccus denitrificans PD1222 4583157 YP_918412.1 CDS Pden_4655 NC_008688.1 144688 145875 D KEGG: bbr:BB1453 regulatory lipoprotein; regulatory lipoprotein 144688..145875 Paracoccus denitrificans PD1222 4583158 YP_918413.1 CDS Pden_4656 NC_008688.1 145872 147824 D 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 145872..147824 Paracoccus denitrificans PD1222 4583159 YP_918414.1 CDS Pden_4657 NC_008688.1 147826 149097 D 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 147826..149097 Paracoccus denitrificans PD1222 4583160 YP_918415.1 CDS Pden_4658 NC_008688.1 149263 150585 D PFAM: extracellular solute-binding protein, family 1; KEGG: bpe:BP2271 regulatory lipoprotein; extracellular solute-binding protein 149263..150585 Paracoccus denitrificans PD1222 4583161 YP_918416.1 CDS Pden_4659 NC_008688.1 150662 152392 D 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 150662..152392 Paracoccus denitrificans PD1222 4583162 YP_918417.1 CDS Pden_4660 NC_008688.1 152405 153448 D 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 152405..153448 Paracoccus denitrificans PD1222 4583163 YP_918418.1 CDS Pden_4661 NC_008688.1 153452 154009 D PFAM: Phosphoglycerate mutase; KEGG: sus:Acid_7225 phosphoglycerate mutase; phosphoglycerate mutase 153452..154009 Paracoccus denitrificans PD1222 4583164 YP_918419.1 CDS Pden_4662 NC_008688.1 154010 154678 D PFAM: pyridoxamine 5'-phosphate oxidase-related, FMN-binding; KEGG: aor:AO090023000033 pyridoxamine-phosphate oxidase Pfam: Pyridox_oxidase; pyridoxamine-phosphate oxidase 154010..154678 Paracoccus denitrificans PD1222 4583165 YP_918420.1 CDS Pden_4663 NC_008688.1 154917 156053 R KEGG: ret:RHE_PB00156 hypothetical protein; hypothetical protein complement(154917..156053) Paracoccus denitrificans PD1222 4583166 YP_918421.1 CDS Pden_4664 NC_008688.1 156075 156881 R PFAM: Shikimate/quinate 5-dehydrogenase; Shikimate dehydrogenase substrate binding, N-terminal domain protein; KEGG: mes:Meso_3972 shikimate dehydrogenase substrate binding-like; shikimate dehydrogenase complement(156075..156881) Paracoccus denitrificans PD1222 4583167 YP_918422.1 CDS Pden_4665 NC_008688.1 156878 158452 R PFAM: aldehyde dehydrogenase; KEGG: ccr:CC2791 fatty aldehyde dehydrogenase; aldehyde dehydrogenase complement(156878..158452) Paracoccus denitrificans PD1222 4583168 YP_918423.1 CDS Pden_4666 NC_008688.1 158454 159386 R PFAM: dihydrodipicolinate synthetase; KEGG: mes:Meso_3971 dihydrodipicolinate synthetase; dihydrodipicolinate synthetase complement(158454..159386) Paracoccus denitrificans PD1222 4583169 YP_918424.1 CDS Pden_4667 NC_008688.1 159459 160268 R PFAM: extracellular solute-binding protein, family 3; KEGG: rfr:Rfer_1029 extracellular solute-binding protein, family 3; extracellular solute-binding protein complement(159459..160268) Paracoccus denitrificans PD1222 4583170 YP_918425.1 CDS Pden_4668 NC_008688.1 160296 161084 R PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: mes:Meso_3975 ABC transporter related; ABC transporter related complement(160296..161084) Paracoccus denitrificans PD1222 4583171 YP_918426.1 CDS Pden_4669 NC_008688.1 161088 161732 R 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 complement(161088..161732) Paracoccus denitrificans PD1222 4583172 YP_918427.1 CDS Pden_4670 NC_008688.1 161744 162424 R 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 complement(161744..162424) Paracoccus denitrificans PD1222 4583173 YP_918428.1 CDS Pden_4671 NC_008688.1 162586 164157 D PFAM: D-galactarate dehydratase/Altronate hydrolase domain protein; SAF domain; KEGG: bms:BRA0806 hydrolase, UxaA family; altronate dehydratase 162586..164157 Paracoccus denitrificans PD1222 4583174 YP_918429.1 CDS Pden_4672 NC_008688.1 164133 165164 D PFAM: regulatory protein GntR, HTH; GntR domain protein; KEGG: mes:Meso_3969 transcriptional regulator, GntR family; GntR family transcriptional regulator 164133..165164 Paracoccus denitrificans PD1222 4583175 YP_918430.1 CDS Pden_4673 NC_008688.1 165193 166875 R PFAM: band 7 protein; KEGG: sit:TM1040_2195 band 7 protein; band 7 protein complement(165193..166875) Paracoccus denitrificans PD1222 4583176 YP_918431.1 CDS Pden_4674 NC_008688.1 166911 167633 R PFAM: protein of unknown function DUF1449; KEGG: jan:Jann_1795 hypothetical protein; hypothetical protein complement(166911..167633) Paracoccus denitrificans PD1222 4583177 YP_918432.1 CDS Pden_4675 NC_008688.1 167769 168779 D PFAM: helix-turn-helix protein RpiR; sugar isomerase (SIS); KEGG: ecp:ECP_3116 hypothetical phosphosugar isomerases; RpiR family transcriptional regulator 167769..168779 Paracoccus denitrificans PD1222 4583178 YP_918433.1 CDS Pden_4676 NC_008688.1 168892 169983 R 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 complement(168892..169983) Paracoccus denitrificans PD1222 4583179 YP_918434.1 CDS Pden_4677 NC_008688.1 169987 170670 R PFAM: 2OG-Fe(II) oxygenase; SMART: Prolyl 4-hydroxylase, alpha subunit; KEGG: rme:Rmet_0838 2OG-Fe(II) oxygenase; hydroxylase complement(169987..170670) Paracoccus denitrificans PD1222 4583180 YP_918435.1 CDS Pden_4678 NC_008688.1 170821 171414 R KEGG: mfa:Mfla_2318 TonB-dependent siderophore receptor; hypothetical protein complement(170821..171414) Paracoccus denitrificans PD1222 4583181 YP_918436.1 CDS Pden_4679 NC_008688.1 171868 172305 D 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 171868..172305 Paracoccus denitrificans PD1222 4583182 YP_918437.1 CDS Pden_4680 NC_008688.1 172602 173063 D PFAM: MaoC domain protein dehydratase; KEGG: rru:Rru_A2194 MaoC-like dehydratase; dehydratase 172602..173063 Paracoccus denitrificans PD1222 4583183 YP_918438.1 CDS Pden_4681 NC_008688.1 173066 173680 D PFAM: regulatory protein, TetR; KEGG: reu:Reut_B4322 regulatory protein, TetR; TetR family transcriptional regulator 173066..173680 Paracoccus denitrificans PD1222 4583184 YP_918439.1 CDS Pden_4682 NC_008688.1 174512 175090 R 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 complement(174512..175090) Paracoccus denitrificans PD1222 4583185 YP_918440.1 CDS Pden_4683 NC_008688.1 175210 175947 D 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 175210..175947 Paracoccus denitrificans PD1222 4583186 YP_918441.1 CDS Pden_4684 NC_008688.1 175947 176591 D 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 175947..176591 Paracoccus denitrificans PD1222 4583187 YP_918442.1 CDS Pden_4685 NC_008688.1 177048 178337 D PFAM: secretion protein HlyD family protein; KEGG: rpc:RPC_4665 secretion protein HlyD; secretion protein HlyD family protein 177048..178337 Paracoccus denitrificans PD1222 4583188 YP_918443.1 CDS Pden_4686 NC_008688.1 178334 181072 D PFAM: ABC transporter related; ABC-2 type transporter; SMART: AAA ATPase; KEGG: rpb:RPB_0170 ABC-2 type transport system; ABC transporter related 178334..181072 Paracoccus denitrificans PD1222 4583189 YP_918444.1 CDS Pden_4687 NC_008688.1 181069 182181 D PFAM: ABC-2 type transporter; KEGG: bmb:BruAb1_1347 hypothetical ABC transporter, permease; ABC-2 type transporter 181069..182181 Paracoccus denitrificans PD1222 4583190 YP_918445.1 CDS Pden_4688 NC_008688.1 182270 182818 R PFAM: YbaK/prolyl-tRNA synthetase associated region; KEGG: sme:SMc00385 hypothetical protein; prolyl-tRNA synthetase complement(182270..182818) Paracoccus denitrificans PD1222 4583191 YP_918446.1 CDS Pden_4689 NC_008688.1 182815 183270 R KEGG: zmo:ZMO1010 hypothetical protein; hypothetical protein complement(182815..183270) Paracoccus denitrificans PD1222 4583192 YP_918447.1 CDS Pden_4690 NC_008688.1 183281 183901 R PFAM: UbiE/COQ5 methyltransferase; Methyltransferase type 11; Methyltransferase type 12; KEGG: sit:TM1040_3086 phosphatidylethanolamine N-methyltransferase; phosphatidylethanolamine N-methyltransferase complement(183281..183901) Paracoccus denitrificans PD1222 4583193 YP_918448.1 CDS Pden_4691 NC_008688.1 183911 184654 R KEGG: sit:TM1040_3085 CDP-diacylglycerol--serine O-phosphatidyltransferase; TIGRFAM: CDP-diacylglycerol--serine O-phosphatidyltransferase; PFAM: CDP-alcohol phosphatidyltransferase; CDP-diacylglycerol--serine O-phosphatidyltransferase complement(183911..184654) Paracoccus denitrificans PD1222 4583194 YP_918449.1 CDS Pden_4692 NC_008688.1 184654 185334 R catalyzes the decarboxylaton of phospatidyl-L-sering to phosphatidylethanolamine; phosphatidylserine decarboxylase complement(184654..185334) Paracoccus denitrificans PD1222 4583195 YP_918450.1 CDS Pden_4693 NC_008688.1 185444 186895 R TIGRFAM: uracil-xanthine permease; PFAM: Xanthine/uracil/vitamin C permease; KEGG: bme:BMEII0825 uracil permease; uracil-xanthine permease complement(185444..186895) Paracoccus denitrificans PD1222 4583196 YP_918451.1 CDS Pden_4694 NC_008688.1 187089 188438 D PFAM: FAD-dependent pyridine nucleotide-disulphide oxidoreductase; KEGG: rpe:RPE_3985 FAD-dependent pyridine nucleotide-disulphide oxidoreductase; FAD-dependent pyridine nucleotide-disulphide oxidoreductase 187089..188438 Paracoccus denitrificans PD1222 4583197 YP_918452.1 CDS Pden_4695 NC_008688.1 188452 188814 D KEGG: rpb:RPB_0927 hypothetical protein; hypothetical protein 188452..188814 Paracoccus denitrificans PD1222 4583198 YP_918453.1 CDS Pden_4696 NC_008688.1 188951 192142 R PFAM: acriflavin resistance protein; KEGG: rsp:RSP_0460 AcrB/AcrD/AcrF family cation/multidrug efflux pump; acriflavin resistance protein complement(188951..192142) Paracoccus denitrificans PD1222 4583199 YP_918454.1 CDS Pden_4697 NC_008688.1 192139 193098 R 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 complement(192139..193098) Paracoccus denitrificans PD1222 4583200 YP_918455.1 CDS Pden_4698 NC_008688.1 193110 193310 R KEGG: rsp:RSP_0589 hypothetical protein; hypothetical protein complement(193110..193310) Paracoccus denitrificans PD1222 4583201 YP_918456.1 CDS Pden_4699 NC_008688.1 193418 194020 R PFAM: cytochrome B561; KEGG: rsp:RSP_0475 cytochrome b; cytochrome B561 complement(193418..194020) Paracoccus denitrificans PD1222 4583202 YP_918457.1 CDS Pden_4700 NC_008688.1 194022 194477 R PFAM: cytochrome c, class II; KEGG: rsp:RSP_0474 cytochrome c'; cytochrome c, class II complement(194022..194477) Paracoccus denitrificans PD1222 4583203 YP_918458.1 CDS Pden_4701 NC_008688.1 194673 194993 D PFAM: regulatory protein, ArsR; KEGG: bja:bll5773 transcriptional regulatory protein; regulatory protein, ArsR 194673..194993 Paracoccus denitrificans PD1222 4583204 YP_918459.1 CDS Pden_4702 NC_008688.1 195037 195411 R PFAM: protein of unknown function DUF442; KEGG: bms:BRA0697 hypothetical protein; hypothetical protein complement(195037..195411) Paracoccus denitrificans PD1222 4583205 YP_918460.1 CDS Pden_4703 NC_008688.1 195412 195867 R PFAM: protein of unknown function DUF395, YeeE/YedE; KEGG: sit:TM1040_3646 protein of unknown function DUF395, YeeE/YedE; hypothetical protein complement(195412..195867) Paracoccus denitrificans PD1222 4583206 YP_918461.1 CDS Pden_4704 NC_008688.1 195869 196294 R PFAM: protein of unknown function DUF395, YeeE/YedE; KEGG: bur:Bcep18194_B1883 YeeE/YedE family membrane protein; hypothetical protein complement(195869..196294) Paracoccus denitrificans PD1222 4583207 YP_918462.1 CDS Pden_4705 NC_008688.1 196291 196494 R KEGG: rso:RSc1506 probable transmembrane protein; transmembrane protein complement(196291..196494) Paracoccus denitrificans PD1222 4583208 YP_918463.1 CDS Pden_4706 NC_008688.1 196513 197445 R PFAM: beta-lactamase domain protein; KEGG: mlo:mll3743 hypothetical protein; beta-lactamase domain-containing protein complement(196513..197445) Paracoccus denitrificans PD1222 4583209 YP_918464.1 CDS Pden_4707 NC_008688.1 197669 197983 D KEGG: rde:RD1_2193 hypothetical protein; hypothetical protein 197669..197983 Paracoccus denitrificans PD1222 4583210 YP_918465.1 CDS Pden_4708 NC_008688.1 198083 198478 D PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase; KEGG: rsp:RSP_3237 lactoylglutathione lyase; glyoxalase/bleomycin resistance protein/dioxygenase 198083..198478 Paracoccus denitrificans PD1222 4583211 YP_918466.1 CDS Pden_4709 NC_008688.1 198528 199070 D KEGG: rde:RD1_2191 hypothetical protein; hypothetical protein 198528..199070 Paracoccus denitrificans PD1222 4583212 YP_918467.1 CDS Pden_4710 NC_008688.1 199082 200662 D PFAM: glucose-methanol-choline oxidoreductase; KEGG: rde:RD1_2190 oxidoreductase; glucose-methanol-choline oxidoreductase 199082..200662 Paracoccus denitrificans PD1222 4583213 YP_918468.1 CDS Pden_4711 NC_008688.1 200737 201006 R 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 complement(200737..201006) Paracoccus denitrificans PD1222 4583214 YP_918469.1 CDS Pden_4712 NC_008688.1 201008 201745 R TIGRFAM: septum site-determining protein MinD; KEGG: pfl:PFL_4380 septum site-determining protein MinD; septum site-determining protein MinD complement(201008..201745) Paracoccus denitrificans PD1222 4583215 YP_918470.1 CDS Pden_4713 NC_008688.1 201853 202599 R 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 complement(201853..202599) Paracoccus denitrificans PD1222 4583216 YP_918471.1 CDS Pden_4714 NC_008688.1 202820 203488 D PFAM: phosphoribosyltransferase; KEGG: mes:Meso_3530 phosphoribosyltransferase; phosphoribosyltransferase 202820..203488 Paracoccus denitrificans PD1222 4583217 YP_918472.1 CDS Pden_4715 NC_008688.1 203601 204569 D 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 203601..204569 Paracoccus denitrificans PD1222 4583218 YP_918473.1 CDS Pden_4716 NC_008688.1 204576 205070 D 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 204576..205070 Paracoccus denitrificans PD1222 4583219 YP_918474.1 CDS Pden_4717 NC_008688.1 205063 206352 D 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 205063..206352 Paracoccus denitrificans PD1222 4583220 YP_918475.1 CDS Pden_4718 NC_008688.1 206504 206752 D hypothetical protein 206504..206752 Paracoccus denitrificans PD1222 4583221 YP_918476.1 CDS Pden_4719 NC_008688.1 206786 206965 D PFAM: periplasmic nitrate reductase NapE; KEGG: sme:SMa1241 NapE component of periplasmic nitrate reductase; periplasmic nitrate reductase NapE 206786..206965 Paracoccus denitrificans PD1222 4583222 YP_918477.1 CDS Pden_4720 NC_008688.1 206975 207313 D PFAM: NapD family protein; KEGG: sme:SMa1239 NapD component of periplasmic nitrate reductase; NapD family protein 206975..207313 Paracoccus denitrificans PD1222 4583223 YP_918478.1 CDS Pden_4721 NC_008688.1 207310 209805 D periplasmic; catalytic subunit; with NapBC catalyzes the reduction of nitrate to nitrite; NapAB receives electrons from NapC; nitrate reductase catalytic subunit 207310..209805 Paracoccus denitrificans PD1222 4583224 YP_918479.1 CDS Pden_4722 NC_008688.1 209778 210263 D PFAM: Nitrate reductase cytochrome c-type subunit (NapB); KEGG: sme:SMa1233 NapB periplasmic nitrate reductase; nitrate reductase cytochrome c-type subunit (NapB) 209778..210263 Paracoccus denitrificans PD1222 4583225 YP_918480.1 CDS Pden_4723 NC_008688.1 210265 210978 D 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 210265..210978 Paracoccus denitrificans PD1222 4583226 YP_918481.1 CDS Pden_4724 NC_008688.1 211265 211678 D Regulates the synthesis of nucleoside triphosphates for nucleic acid synthesis, CTP for lipid synthesis, and GTP for protein elongation; nucleoside diphosphate kinase regulator 211265..211678 Paracoccus denitrificans PD1222 4583227 YP_918482.1 CDS Pden_4725 NC_008688.1 211902 212627 D KEGG: rpd:RPD_2427 hypothetical protein; hypothetical protein 211902..212627 Paracoccus denitrificans PD1222 4583228 YP_918483.1 CDS Pden_4726 NC_008688.1 212549 213526 R PFAM: MscS Mechanosensitive ion channel; KEGG: eba:ebA6709 mechanosensitive channel protein; MscS mechanosensitive ion channel complement(212549..213526) Paracoccus denitrificans PD1222 4583229 YP_918484.1 CDS Pden_4727 NC_008688.1 213959 215170 R PFAM: glucose sorbosone dehydrogenase; KEGG: neu:NE1997 glucose dehydrogenase B; glucose sorbosone dehydrogenase complement(213959..215170) Paracoccus denitrificans PD1222 4583230 YP_918485.1 CDS Pden_4728 NC_008688.1 215703 216554 R PFAM: regulatory protein, LysR; helix-turn-helix, Fis-type; LysR, substrate-binding; KEGG: bja:bll5630 transcriptional regulatory protein; LysR family transcriptional regulator complement(215703..216554) Paracoccus denitrificans PD1222 4583231 YP_918486.1 CDS Pden_4729 NC_008688.1 216737 217570 D KEGG: mfa:Mfla_0547 hypothetical protein; hypothetical protein 216737..217570 Paracoccus denitrificans PD1222 4583232 YP_918487.1 CDS Pden_4730 NC_008688.1 217650 218903 D KEGG: mfa:Mfla_0548 amine dehydrogenase; TIGRFAM: methylamine dehydrogenase heavy chain; PFAM: methylamine dehydrogenase heavy subunit; methylamine dehydrogenase heavy chain 217650..218903 Paracoccus denitrificans PD1222 4583233 YP_918488.1 CDS Pden_4731 NC_008688.1 218908 219468 D PFAM: methylamine utilisation MauE; KEGG: mfa:Mfla_0549 methylamine utilisation MauE; methylamine utilisation MauE 218908..219468 Paracoccus denitrificans PD1222 4583234 YP_918489.1 CDS Pden_4732 NC_008688.1 219470 220072 D TIGRFAM: methylamine dehydrogenase accessory protein MauD; PFAM: Redoxin domain protein; KEGG: mfa:Mfla_0550 hypothetical protein; methylamine dehydrogenase accessory protein MauD 219470..220072 Paracoccus denitrificans PD1222 4583235 YP_918490.1 CDS Pden_4733 NC_008688.1 220115 220681 D KEGG: mfa:Mfla_0551 amine dehydrogenase; TIGRFAM: methylamine dehydrogenase light chain; PFAM: Methylamine dehydrogenase light chain, C terminal domain protein; methylamine dehydrogenase light chain 220115..220681 Paracoccus denitrificans PD1222 4583236 YP_918491.1 CDS Pden_4734 NC_008688.1 220736 221131 D TIGRFAM: amicyanin; PFAM: blue (type 1) copper domain protein; KEGG: mpa:MAP4219 hypothetical protein; amicyanin 220736..221131 Paracoccus denitrificans PD1222 4583237 YP_918492.1 CDS Pden_4735 NC_008688.1 221149 222012 D hypothetical protein 221149..222012 Paracoccus denitrificans PD1222 4583238 YP_918493.1 CDS Pden_4736 NC_008688.1 222012 223175 D PFAM: Di-haem cytochrome c peroxidase; KEGG: atc:AGR_C_5068 hypothetical protein; di-haem cytochrome c peroxidase 222012..223175 Paracoccus denitrificans PD1222 4583239 YP_918494.1 CDS Pden_4737 NC_008688.1 223205 223879 D 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 223205..223879 Paracoccus denitrificans PD1222 4583240 YP_918495.1 CDS Pden_4738 NC_008688.1 223876 224727 D 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 223876..224727 Paracoccus denitrificans PD1222 4583241 YP_918496.1 CDS Pden_4739 NC_008688.1 224785 225129 R TIGRFAM: alkylphosphonate utilization operon protein PhnA; PFAM: PhnA protein-like; KEGG: rsp:RSP_3090 alkylphosphonate uptake protein, PhnA; alkylphosphonate utilization protein PhnA complement(224785..225129) Paracoccus denitrificans PD1222 4583242 YP_918497.1 CDS Pden_4740 NC_008688.1 225218 225700 R PFAM: regulatory protein, LuxR; KEGG: rme:Rmet_5323 two component transcriptional regulator, LuxR family; two component LuxR family transcriptional regulator complement(225218..225700) Paracoccus denitrificans PD1222 4583243 YP_918498.1 CDS Pden_4741 NC_008688.1 225816 227240 R 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 complement(225816..227240) Paracoccus denitrificans PD1222 4583244 YP_918499.1 CDS Pden_4742 NC_008688.1 227240 227755 R KEGG: cvi:CV2214 hypothetical protein; hypothetical protein complement(227240..227755) Paracoccus denitrificans PD1222 4583245 YP_918500.1 CDS Pden_4743 NC_008688.1 228171 229892 D PFAM: Peptidoglycan-binding domain 1 protein; KEGG: jan:Jann_3999 peptidoglycan-binding domain 1; peptidoglycan binding domain-containing protein 228171..229892 Paracoccus denitrificans PD1222 4583246 YP_918501.1 CDS Pden_4744 NC_008688.1 229896 231137 R KEGG: mlo:mlr2623 hypothetical protein; hypothetical protein complement(229896..231137) Paracoccus denitrificans PD1222 4583247 YP_918502.1 CDS Pden_4745 NC_008688.1 231134 232693 R PFAM: Sel1 domain protein repeat-containing protein; Sel1 domain-containing protein complement(231134..232693) Paracoccus denitrificans PD1222 4583248 YP_918503.1 CDS Pden_4746 NC_008688.1 232852 233691 R 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 complement(232852..233691) Paracoccus denitrificans PD1222 4583249 YP_918504.1 CDS Pden_4747 NC_008688.1 233688 234515 R 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 complement(233688..234515) Paracoccus denitrificans PD1222 4583250 YP_918505.1 CDS Pden_4748 NC_008688.1 234525 235589 R 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 complement(234525..235589) Paracoccus denitrificans PD1222 4583251 YP_918506.1 CDS Pden_4749 NC_008688.1 235660 236511 R 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 complement(235660..236511) Paracoccus denitrificans PD1222 4583252 YP_918507.1 CDS Pden_4750 NC_008688.1 236793 237773 R PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: bur:Bcep18194_C7696 transcriptional regulator, LysR family; LysR family transcriptional regulator complement(236793..237773) Paracoccus denitrificans PD1222 4583253 YP_918508.1 CDS Pden_4751 NC_008688.1 237770 239113 R PFAM: FAD dependent oxidoreductase; KEGG: rsp:RSP_4005 oxidoreductase, NAD-binding site; FAD dependent oxidoreductase complement(237770..239113) Paracoccus denitrificans PD1222 4583254 YP_918509.1 CDS Pden_4752 NC_008688.1 239115 240620 R PFAM: aldehyde dehydrogenase; KEGG: rsp:RSP_4003 aldehyde dehydrogenase; aldehyde dehydrogenase complement(239115..240620) Paracoccus denitrificans PD1222 4583255 YP_918510.1 CDS Pden_4753 NC_008688.1 240622 241539 R PFAM: dihydrodipicolinate synthetase; KEGG: rsp:RSP_4002 dihydrodipicolinate synthetase; dihydrodipicolinate synthetase complement(240622..241539) Paracoccus denitrificans PD1222 4583256 YP_918511.1 CDS Pden_4754 NC_008688.1 241670 243025 R KEGG: reu:Reut_B3732 hypothetical protein; hypothetical protein complement(241670..243025) Paracoccus denitrificans PD1222 4583257 YP_918512.1 CDS Pden_4755 NC_008688.1 243208 251547 D PFAM: carbohydrate binding; glycosyltransferase 36; glycosyltransferase 36 associated; KEGG: sme:SMc04382 beta-(1,2)-glucan production associated transmembrane protein; carbohydrate binding 243208..251547 Paracoccus denitrificans PD1222 4583258 YP_918513.1 CDS Pden_4756 NC_008688.1 251599 252096 R PFAM: regulatory protein, AsnC/Lrp family; KEGG: atu:Atu4818 transcriptional regulator, AsnC family; AsnC family transcriptional regulator complement(251599..252096) Paracoccus denitrificans PD1222 4583259 YP_918514.1 CDS Pden_4757 NC_008688.1 252278 253531 D PFAM: dehydrogenase, E1 component; KEGG: bme:BMEII0748 2-oxoisovalerate dehydrogenase alpha subunit; 3-methyl-2-oxobutanoate dehydrogenase 252278..253531 Paracoccus denitrificans PD1222 4583260 YP_918515.1 CDS Pden_4758 NC_008688.1 253533 254549 D PFAM: Transketolase, central region; Transketolase domain protein; KEGG: mlo:mll4472 2-oxoisovalerate dehydrogenase (beta subunit); transketolase, central region 253533..254549 Paracoccus denitrificans PD1222 4583261 YP_918516.1 CDS Pden_4759 NC_008688.1 254551 255840 D 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 254551..255840 Paracoccus denitrificans PD1222 4583262 YP_918517.1 CDS Pden_4760 NC_008688.1 255845 257233 D TIGRFAM: dihydrolipoamide dehydrogenase; PFAM: FAD-dependent pyridine nucleotide-disulphide oxidoreductase; pyridine nucleotide-disulphide oxidoreductase dimerisation region; KEGG: mlo:mll4470 dihydrolipoamide dehydrogenase; dihydrolipoamide dehydrogenase 255845..257233 Paracoccus denitrificans PD1222 4583263 YP_918518.1 CDS Pden_4761 NC_008688.1 257267 257992 D PFAM: protein of unknown function DUF105; KEGG: rsp:RSP_2406 hypothetical protein; hypothetical protein 257267..257992 Paracoccus denitrificans PD1222 4583264 YP_918519.1 CDS Pden_4762 NC_008688.1 258120 259136 D KEGG: sit:TM1040_3771 conserved hypothetical protein; hypothetical protein 258120..259136 Paracoccus denitrificans PD1222 4583265 YP_918520.1 CDS Pden_4763 NC_008688.1 259133 260473 R 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 complement(259133..260473) Paracoccus denitrificans PD1222 4583266 YP_918521.1 CDS Pden_4764 NC_008688.1 260470 262152 R 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 complement(260470..262152) Paracoccus denitrificans PD1222 4583267 YP_918522.1 CDS Pden_4765 NC_008688.1 262357 263724 D PFAM: sodium:dicarboxylate symporter; KEGG: atc:AGR_L_3041 C4-dicarboxylate transport protein; sodium:dicarboxylate symporter 262357..263724 Paracoccus denitrificans PD1222 4583268 YP_918523.1 CDS Pden_4766 NC_008688.1 263791 264801 R PFAM: regulatory protein, LacI; periplasmic binding protein/LacI transcriptional regulator; KEGG: rsp:RSP_1243 transcriptional regulator, LacI family; periplasmic binding protein/LacI transcriptional regulator complement(263791..264801) Paracoccus denitrificans PD1222 4583269 YP_918524.1 CDS Pden_4767 NC_008688.1 264898 265950 D PFAM: AP endonuclease 2 domain protein; Xylose isomerase domain protein TIM barrel; KEGG: bms:BR0545 hypothetical protein; xylose isomerase domain-containing protein 264898..265950 Paracoccus denitrificans PD1222 4583270 YP_918525.1 CDS Pden_4768 NC_008688.1 265947 267041 D PFAM: oxidoreductase domain protein; Oxidoreductase, C-terminal domain; KEGG: atc:AGR_L_984 hypothetical protein; oxidoreductase domain-containing protein 265947..267041 Paracoccus denitrificans PD1222 4583271 YP_918526.1 CDS Pden_4769 NC_008688.1 267038 268522 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rsp:RSP_1247 ABC sugar transporter, ATPase subunit; ABC transporter related 267038..268522 Paracoccus denitrificans PD1222 4583272 YP_918527.1 CDS Pden_4770 NC_008688.1 268519 269487 D PFAM: inner-membrane translocator; KEGG: rsp:RSP_6150 ABC sugar (ribose) transporter, inner membrane subunit; inner-membrane translocator 268519..269487 Paracoccus denitrificans PD1222 4583273 YP_918528.1 CDS Pden_4771 NC_008688.1 269506 270465 D KEGG: rsp:RSP_1249 ABC ribose transporter, periplasmic solute-binding protein; ABC ribose transporter, periplasmic solute-binding protein 269506..270465 Paracoccus denitrificans PD1222 4583274 YP_918529.1 CDS Pden_4772 NC_008688.1 270444 271328 R 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 complement(270444..271328) Paracoccus denitrificans PD1222 4583275 YP_918530.1 CDS Pden_4773 NC_008688.1 271318 271791 R TIGRFAM: alkylhydroperoxidase like protein, AhpD family; PFAM: Carboxymuconolactone decarboxylase; KEGG: rsp:RSP_0606 redox protein; alkylhydroperoxidase complement(271318..271791) Paracoccus denitrificans PD1222 4583276 YP_918531.1 CDS Pden_4774 NC_008688.1 271895 273037 R TIGRFAM: phosphonate metabolism protein PhnM; PFAM: Amidohydrolase 3; KEGG: sil:SPO0476 alkylphosphonate utilization protein PhnM; phosphonate metabolism protein PhnM complement(271895..273037) Paracoccus denitrificans PD1222 4583277 YP_918532.1 CDS Pden_4775 NC_008688.1 273133 273813 D PFAM: protein of unknown function DUF1045; KEGG: rsp:RSP_2937 hypothetical protein; hypothetical protein 273133..273813 Paracoccus denitrificans PD1222 4583278 YP_918533.1 CDS Pden_4776 NC_008688.1 273795 274328 R 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 complement(273795..274328) Paracoccus denitrificans PD1222 4583279 YP_918534.1 CDS Pden_4777 NC_008688.1 274325 275008 R 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 complement(274325..275008) Paracoccus denitrificans PD1222 4583280 YP_918535.1 CDS phnK NC_008688.1 275013 275795 R 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 complement(275013..275795) Paracoccus denitrificans PD1222 4583340 YP_918536.1 CDS Pden_4779 NC_008688.1 275792 276664 R PFAM: phosphonate metabolism PhnJ; KEGG: rde:RD1_2391 phosphonate metabolism protein PhnJ; phosphonate metabolism PhnJ complement(275792..276664) Paracoccus denitrificans PD1222 4583341 YP_918537.1 CDS Pden_4780 NC_008688.1 276661 277743 R PFAM: phosphonate metabolism; KEGG: rde:RD1_2392 phosphonate metabolism protein; phosphonate metabolism complement(276661..277743) Paracoccus denitrificans PD1222 4583342 YP_918538.1 CDS phnH NC_008688.1 277743 278309 R PFAM: phosphonate metabolism; KEGG: rde:RD1_2393 phosphonate metabolism protein; carbon-phosphorus lyase complex subunit complement(277743..278309) Paracoccus denitrificans PD1222 4583343 YP_918539.1 CDS Pden_4782 NC_008688.1 278306 278758 R PFAM: phosphonate metabolism PhnG; KEGG: sit:TM1040_3703 phosphonate metabolism PhnG; phosphonate metabolism PhnG complement(278306..278758) Paracoccus denitrificans PD1222 4583344 YP_918540.1 CDS Pden_4783 NC_008688.1 278877 279608 D 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 278877..279608 Paracoccus denitrificans PD1222 4583345 YP_918541.1 CDS Pden_4784 NC_008688.1 279605 280930 R 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 complement(279605..280930) Paracoccus denitrificans PD1222 4583346 YP_918542.1 CDS Pden_4785 NC_008688.1 280934 281776 R 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 complement(280934..281776) Paracoccus denitrificans PD1222 4583347 YP_918543.1 CDS Pden_4786 NC_008688.1 281840 282751 R TIGRFAM: phosphonate ABC transporter, periplasmic phosphonate-binding protein; KEGG: sit:TM1040_3708 phosphonate-binding periplasmic protein; phosphonate ABC transporter, periplasmic phosphonate-binding protein complement(281840..282751) Paracoccus denitrificans PD1222 4583348 YP_918544.1 CDS Pden_4787 NC_008688.1 282787 283605 R 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 complement(282787..283605) Paracoccus denitrificans PD1222 4583349 YP_918545.1 CDS Pden_4788 NC_008688.1 283918 284115 D hypothetical protein 283918..284115 Paracoccus denitrificans PD1222 4583350 YP_918546.1 CDS Pden_4789 NC_008688.1 284182 284724 R PFAM: NADPH-dependent FMN reductase; KEGG: rsp:RSP_3069 NADPH-dependent FMN reductase; NADPH-dependent FMN reductase complement(284182..284724) Paracoccus denitrificans PD1222 4583351 YP_918547.1 CDS Pden_4790 NC_008688.1 284832 285551 R PFAM: 5-formyltetrahydrofolate cyclo-ligase; KEGG: mlo:mll0364 hypothetical protein; 5-formyltetrahydrofolate cyclo-ligase complement(284832..285551) Paracoccus denitrificans PD1222 4583352 YP_918548.1 CDS Pden_4791 NC_008688.1 285774 286877 D 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 285774..286877 Paracoccus denitrificans PD1222 4583353 YP_918549.1 CDS Pden_4792 NC_008688.1 286921 288861 R 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 complement(286921..288861) Paracoccus denitrificans PD1222 4583354 YP_918550.1 CDS Pden_4793 NC_008688.1 288866 289567 R PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: bbr:BB3153 high-affinity branched-chain amino acid transport, ATP-binding protein; ABC transporter related complement(288866..289567) Paracoccus denitrificans PD1222 4583355 YP_918551.1 CDS Pden_4794 NC_008688.1 289554 290333 R PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: bpe:BP1649 high-affinity branched-chain amino acid transport, ATP-binding protein; ABC transporter related complement(289554..290333) Paracoccus denitrificans PD1222 4583356 YP_918552.1 CDS Pden_4795 NC_008688.1 290330 291289 R PFAM: inner-membrane translocator; KEGG: bbr:BB3151 ABC-transporter permease component; inner-membrane translocator complement(290330..291289) Paracoccus denitrificans PD1222 4583357 YP_918553.1 CDS Pden_4796 NC_008688.1 291289 292161 R PFAM: inner-membrane translocator; KEGG: bbr:BB3150 ABC-transporter permease component; inner-membrane translocator complement(291289..292161) Paracoccus denitrificans PD1222 4583358 YP_918554.1 CDS Pden_4797 NC_008688.1 292229 293374 R PFAM: Extracellular ligand-binding receptor; KEGG: bpa:BPP2828 ABC-transporter substrate-binding protein; extracellular ligand-binding receptor complement(292229..293374) Paracoccus denitrificans PD1222 4583359 YP_918555.1 CDS Pden_4798 NC_008688.1 293415 295094 R TIGRFAM: phenylacetic acid degradation protein paaN; PFAM: aldehyde dehydrogenase; KEGG: bbr:BB3430 oxidoreductase; phenylacetic acid degradation protein paaN complement(293415..295094) Paracoccus denitrificans PD1222 4583360 YP_918556.1 CDS Pden_4799 NC_008688.1 295167 295955 D Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA; enoyl-CoA hydratase 295167..295955 Paracoccus denitrificans PD1222 4583361 YP_918557.1 CDS Pden_4800 NC_008688.1 295952 296416 D 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 295952..296416 Paracoccus denitrificans PD1222 4583362 YP_918558.1 CDS Pden_4801 NC_008688.1 296445 297755 D TIGRFAM: phenylacetate-CoA ligase; KEGG: jan:Jann_0656 phenylacetate-CoA ligase; phenylacetate-CoA ligase 296445..297755 Paracoccus denitrificans PD1222 4583363 YP_918559.1 CDS Pden_4802 NC_008688.1 297880 298479 D PFAM: regulatory protein, TetR; KEGG: nha:Nham_0935 transcriptional regulator, TetR family; TetR family transcriptional regulator 297880..298479 Paracoccus denitrificans PD1222 4583364 YP_918560.1 CDS Pden_4803 NC_008688.1 298650 299360 D KEGG: sme:SMa2315 aminoglycoside adenylyltransferase; adenylyltransferase 298650..299360 Paracoccus denitrificans PD1222 4583365 YP_918561.1 CDS Pden_4804 NC_008688.1 299460 301520 R catalyzes the ring cleavage reaction in phenylacetate degradation and the formation of 3-hydroxyacyl-CoA from crotonyl-CoA; bifunctional aldehyde dehydrogenase/enoyl-CoA hydratase complement(299460..301520) Paracoccus denitrificans PD1222 4583366 YP_918562.1 CDS Pden_4805 NC_008688.1 301596 302348 R PFAM: phenylacetic acid catabolic family protein; KEGG: nha:Nham_0933 phenylacetic acid catabolic; phenylacetic acid catabolic family protein complement(301596..302348) Paracoccus denitrificans PD1222 4583367 YP_918563.1 CDS Pden_4806 NC_008688.1 302371 303447 R 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 complement(302371..303447) Paracoccus denitrificans PD1222 4583368 YP_918564.1 CDS Pden_4807 NC_008688.1 303479 304000 R 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 complement(303479..304000) Paracoccus denitrificans PD1222 4583369 YP_918565.1 CDS Pden_4808 NC_008688.1 304007 304819 R 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 complement(304007..304819) Paracoccus denitrificans PD1222 4583370 YP_918566.1 CDS paaB NC_008688.1 304819 305103 R with PaaBCDE catalyzes the hydroxylation of phenylacetyl-CoA; involved in phenylacetate degradation; phenylacetate-CoA oxygenase subunit PaaB complement(304819..305103) Paracoccus denitrificans PD1222 4583371 YP_918567.1 CDS paaA NC_008688.1 305175 306164 R with PaaBCDE catalyzes the hydroxylation of phenylacetyl-CoA; phenylacetate-CoA oxygenase subunit PaaA complement(305175..306164) Paracoccus denitrificans PD1222 4583372 YP_918568.1 CDS Pden_4811 NC_008688.1 306183 307388 R KEGG: dar:Daro_0375 thiolase; TIGRFAM: acetyl-CoA acetyltransferases; beta-ketoadipyl CoA thiolase; PFAM: Thiolase; beta-ketoadipyl CoA thiolase complement(306183..307388) Paracoccus denitrificans PD1222 4583373 YP_918569.1 CDS Pden_4812 NC_008688.1 307534 308388 R 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 complement(307534..308388) Paracoccus denitrificans PD1222 4583374 YP_918570.1 CDS Pden_4813 NC_008688.1 308495 310867 R PFAM: peptidase S45, penicillin amidase; KEGG: sbo:SBO_4393 penicillin G acylase; penicillin amidase complement(308495..310867) Paracoccus denitrificans PD1222 4583375 YP_918571.1 CDS Pden_4814 NC_008688.1 311088 311471 D KEGG: hne:HNE_3363 hypothetical protein; hypothetical protein 311088..311471 Paracoccus denitrificans PD1222 4583376 YP_918572.1 CDS Pden_4815 NC_008688.1 311475 311948 D KEGG: hne:HNE_3362 hypothetical protein; hypothetical protein 311475..311948 Paracoccus denitrificans PD1222 4583377 YP_918573.1 CDS Pden_4816 NC_008688.1 312233 314110 D 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 312233..314110 Paracoccus denitrificans PD1222 4583378 YP_918574.1 CDS Pden_4817 NC_008688.1 314140 315156 D 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 314140..315156 Paracoccus denitrificans PD1222 4583379 YP_918575.1 CDS Pden_4818 NC_008688.1 315156 315995 D PFAM: regulatory proteins, IclR; KEGG: sme:SMc00263 transcription regulator protein; regulatory proteins, IclR 315156..315995 Paracoccus denitrificans PD1222 4583380 YP_918576.1 CDS Pden_4819 NC_008688.1 315992 317161 D 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 315992..317161 Paracoccus denitrificans PD1222 4583381 YP_918577.1 CDS Pden_4820 NC_008688.1 317158 318759 D activates fatty acids by binding to coenzyme A; acyl-CoA synthetase 317158..318759 Paracoccus denitrificans PD1222 4583382 YP_918578.1 CDS Pden_4821 NC_008688.1 318756 319583 D KEGG: atc:AGR_L_127 hypothetical protein; hypothetical protein 318756..319583 Paracoccus denitrificans PD1222 4583383 YP_918579.1 CDS Pden_4822 NC_008688.1 319580 320341 D 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 319580..320341 Paracoccus denitrificans PD1222 4583384 YP_918580.1 CDS Pden_4823 NC_008688.1 320376 321647 R KEGG: nha:Nham_1901 membrane protein; membrane protein complement(320376..321647) Paracoccus denitrificans PD1222 4583385 YP_918581.1 CDS Pden_4824 NC_008688.1 321817 323316 D 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 321817..323316 Paracoccus denitrificans PD1222 4583386 YP_918582.1 CDS Pden_4825 NC_008688.1 323332 325164 R 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 complement(323332..325164) Paracoccus denitrificans PD1222 4583387 YP_918583.1 CDS Pden_4826 NC_008688.1 325307 325822 R KEGG: sit:TM1040_2140 hypothetical protein; hypothetical protein complement(325307..325822) Paracoccus denitrificans PD1222 4583388 YP_918584.1 CDS Pden_4827 NC_008688.1 326381 328453 D 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 326381..328453 Paracoccus denitrificans PD1222 4583389 YP_918585.1 CDS Pden_4828 NC_008688.1 328455 329231 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sco:SCO0998 Fe uptake system permease; ABC transporter related 328455..329231 Paracoccus denitrificans PD1222 4583390 YP_918586.1 CDS Pden_4829 NC_008688.1 329242 330195 D PFAM: periplasmic binding protein; KEGG: rde:RD1_3480 iron ABC transporter, periplasmic binding protein; periplasmic binding protein 329242..330195 Paracoccus denitrificans PD1222 4583391 YP_918587.1 CDS Pden_4830 NC_008688.1 330205 331230 D PFAM: transport system permease; KEGG: rde:RD1_3479 hemin ABC transport protein, permease component; transport system permease 330205..331230 Paracoccus denitrificans PD1222 4583392 YP_918588.1 CDS Pden_4832 NC_008688.1 331703 332341 R PFAM: Negative transcriptional regulator; KEGG: rme:Rmet_4524 negative transcriptional regulator; FMN-binding negative transcriptional regulator complement(331703..332341) Paracoccus denitrificans PD1222 4583393 YP_918589.1 CDS Pden_4833 NC_008688.1 332445 333902 D PFAM: regulatory protein GntR, HTH; aminotransferase, class I and II; KEGG: mlo:mlr6174 transcriptional regulator; GntR family transcriptional regulator 332445..333902 Paracoccus denitrificans PD1222 4583394 YP_918590.1 CDS Pden_4834 NC_008688.1 333973 334761 R 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 complement(333973..334761) Paracoccus denitrificans PD1222 4583395 YP_918591.1 CDS Pden_4835 NC_008688.1 334892 336103 D PFAM: major facilitator superfamily MFS_1; KEGG: sus:Acid_6582 major facilitator superfamily MFS_1; major facilitator transporter 334892..336103 Paracoccus denitrificans PD1222 4583396 YP_918592.1 CDS Pden_4836 NC_008688.1 336108 337487 R 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 complement(336108..337487) Paracoccus denitrificans PD1222 4583397 YP_918593.1 CDS Pden_4837 NC_008688.1 337651 338505 D PFAM: protein of unknown function DUF6, transmembrane; KEGG: bja:bll0403 hypothetical protein; hypothetical protein 337651..338505 Paracoccus denitrificans PD1222 4583398 YP_918594.1 CDS Pden_4838 NC_008688.1 338602 338784 D KEGG: xfa:XF1750 hypothetical protein; hypothetical protein 338602..338784 Paracoccus denitrificans PD1222 4583399 YP_918595.1 CDS Pden_4839 NC_008688.1 338830 339504 R 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 complement(338830..339504) Paracoccus denitrificans PD1222 4583400 YP_918596.1 CDS Pden_4840 NC_008688.1 339581 340573 R PFAM: Alcohol dehydrogenase, zinc-binding domain protein; Alcohol dehydrogenase GroES domain protein; KEGG: atc:AGR_L_3295 hypothetical protein; alcohol dehydrogenase complement(339581..340573) Paracoccus denitrificans PD1222 4583401 YP_918597.1 CDS Pden_4841 NC_008688.1 340631 341401 R Converts D-sorbitol to L-sorbose; sorbitol dehydrogenase complement(340631..341401) Paracoccus denitrificans PD1222 4583402 YP_918598.1 CDS Pden_4842 NC_008688.1 341398 342396 R 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 complement(341398..342396) Paracoccus denitrificans PD1222 4583403 YP_918599.1 CDS Pden_4843 NC_008688.1 342404 343234 R 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 complement(342404..343234) Paracoccus denitrificans PD1222 4583404 YP_918600.1 CDS Pden_4844 NC_008688.1 343242 344114 R 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 complement(343242..344114) Paracoccus denitrificans PD1222 4583405 YP_918601.1 CDS Pden_4845 NC_008688.1 344219 345523 R PFAM: extracellular solute-binding protein, family 1; KEGG: atc:AGR_L_3289 periplasmic sorbitol-binding protein; extracellular solute-binding protein complement(344219..345523) Paracoccus denitrificans PD1222 4583406 YP_918602.1 CDS Pden_4846 NC_008688.1 345633 346655 R 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 complement(345633..346655) Paracoccus denitrificans PD1222 4583407 YP_918603.1 CDS Pden_4847 NC_008688.1 346837 348114 R PFAM: D-tagatose-bisphosphate aldolase class II accessory protein AgaZ; KEGG: sme:SMb21373 sugar kinase; tagatose-6-phosphate kinase complement(346837..348114) Paracoccus denitrificans PD1222 4583408 YP_918604.1 CDS Pden_4848 NC_008688.1 348120 349061 R PFAM: PfkB domain protein; KEGG: sme:SMb21374 sugar kinase, PfkB family protein; ribokinase-like domain-containing protein complement(348120..349061) Paracoccus denitrificans PD1222 4583409 YP_918605.1 CDS Pden_4849 NC_008688.1 349066 350043 R PFAM: inner-membrane translocator; KEGG: sme:SMb21375 sugar uptake ABC transporter permease; inner-membrane translocator complement(349066..350043) Paracoccus denitrificans PD1222 4583410 YP_918606.1 CDS Pden_4850 NC_008688.1 350040 351551 R PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sme:SMb21376 sugar uptake ABC transporter ATP-binding protein; ABC transporter related complement(350040..351551) Paracoccus denitrificans PD1222 4583411 YP_918607.1 CDS Pden_4851 NC_008688.1 351612 352499 R 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 complement(351612..352499) Paracoccus denitrificans PD1222 4583412 YP_918608.1 CDS Pden_4852 NC_008688.1 352963 355263 R 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 complement(352963..355263) Paracoccus denitrificans PD1222 4583413 YP_918609.1 CDS Pden_4853 NC_008688.1 355266 355892 R KEGG: rno:678915 hypothetical protein LOC678915; hypothetical protein complement(355266..355892) Paracoccus denitrificans PD1222 4583414 YP_918610.1 CDS Pden_4854 NC_008688.1 355962 357653 R PFAM: protein of unknown function DUF126; protein of unknown function DUF521; KEGG: sme:SMb20269 hypothetical protein; hypothetical protein complement(355962..357653) Paracoccus denitrificans PD1222 4583415 YP_918611.1 CDS Pden_4855 NC_008688.1 357807 358877 R PFAM: Malate/L-lactate dehydrogenase; KEGG: pau:PA14_48020 L-malate dehydrogenase; malate/L-lactate dehydrogenase complement(357807..358877) Paracoccus denitrificans PD1222 4583416 YP_918612.1 CDS Pden_4856 NC_008688.1 358921 359907 R PFAM: TRAP dicarboxylate transporter- DctP subunit; KEGG: bja:bll4424 hypothetical protein; TRAP dicarboxylate transporter- DctP subunit complement(358921..359907) Paracoccus denitrificans PD1222 4583417 YP_918613.1 CDS Pden_4857 NC_008688.1 359934 361199 R 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 complement(359934..361199) Paracoccus denitrificans PD1222 4583418 YP_918614.1 CDS Pden_4858 NC_008688.1 361199 361816 R PFAM: Tripartite ATP-independent periplasmic transporter, DctQ component; KEGG: bja:bll4426 hypothetical protein; tripartite ATP-independent periplasmic transporter DctQ complement(361199..361816) Paracoccus denitrificans PD1222 4583419 YP_918615.1 CDS Pden_4859 NC_008688.1 361992 362996 R PFAM: proline racemase; KEGG: sme:SMb20268 proline racemase; hydroxyproline-2-epimerase complement(361992..362996) Paracoccus denitrificans PD1222 4583420 YP_918616.1 CDS Pden_4860 NC_008688.1 363004 364224 R PFAM: FAD dependent oxidoreductase; KEGG: sme:SMb20267 D-amino acid dehydrogenase; D-amino-acid dehydrogenase complement(363004..364224) Paracoccus denitrificans PD1222 4583421 YP_918617.1 CDS Pden_4861 NC_008688.1 364221 364946 R PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: atc:AGR_L_402 probable ATP-binding component of ABC transporter; ABC transporter related complement(364221..364946) Paracoccus denitrificans PD1222 4583422 YP_918618.1 CDS Pden_4862 NC_008688.1 364939 365592 R 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 complement(364939..365592) Paracoccus denitrificans PD1222 4583423 YP_918619.1 CDS Pden_4863 NC_008688.1 365603 366295 R 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 complement(365603..366295) Paracoccus denitrificans PD1222 4583424 YP_918620.1 CDS Pden_4864 NC_008688.1 366331 367137 R PFAM: extracellular solute-binding protein, family 3; KEGG: sme:SMb20263 ABC transporter periplasmic amino acid-binding protein; extracellular solute-binding protein complement(366331..367137) Paracoccus denitrificans PD1222 4583425 YP_918621.1 CDS Pden_4865 NC_008688.1 367288 368802 R PFAM: aldehyde dehydrogenase; KEGG: sme:SMb20262 semialdehyde dehydrogenase; aldehyde dehydrogenase complement(367288..368802) Paracoccus denitrificans PD1222 4583426 YP_918622.1 CDS Pden_4866 NC_008688.1 368936 369967 D PFAM: Malate/L-lactate dehydrogenase; KEGG: sme:SMb20261 malate dehydrogenase; malate/L-lactate dehydrogenase 368936..369967 Paracoccus denitrificans PD1222 4583427 YP_918623.1 CDS Pden_4867 NC_008688.1 370019 370981 R PFAM: dihydrodipicolinate synthetase; KEGG: sme:SMb20259 dihydrodipicolinate synthase; dihydrodipicolinate synthase complement(370019..370981) Paracoccus denitrificans PD1222 4583428 YP_918624.1 CDS Pden_4868 NC_008688.1 371084 371782 R PFAM: regulatory protein GntR, HTH; GntR domain protein; KEGG: sme:SMb20258 transcriptional regulator protein; GntR family transcriptional regulator complement(371084..371782) Paracoccus denitrificans PD1222 4583429 YP_918625.1 CDS Pden_4869 NC_008688.1 372107 372817 D KEGG: mlo:mll7204 ABC transporter, substrate binding protein; ABC-type branched-chain amino acid transport systems periplasmic component-like 372107..372817 Paracoccus denitrificans PD1222 4583430 YP_918626.1 CDS Pden_4870 NC_008688.1 372730 373365 R PFAM: helix-turn-helix domain protein; Cupin 2, conserved barrel domain protein; KEGG: ppr:PBPRB1321 transcriptional regulator, HTH_3family; XRE family transcriptional regulator complement(372730..373365) Paracoccus denitrificans PD1222 4583431 YP_918627.1 CDS Pden_4871 NC_008688.1 373525 374331 R KEGG: rsp:RSP_3364 pyrroline-5-carboxylate reductase; TIGRFAM: pyrroline-5-carboxylate reductase; PFAM: NADP oxidoreductase, coenzyme F420-dependent; pyrroline-5-carboxylate reductase complement(373525..374331) Paracoccus denitrificans PD1222 4583432 YP_918628.1 CDS Pden_4872 NC_008688.1 374536 375981 D PFAM: FAD linked oxidase domain protein; KEGG: eba:ebA4737 FAD dependent oxidoreductase; FAD linked oxidase domain-containing protein 374536..375981 Paracoccus denitrificans PD1222 4583433 YP_918629.1 CDS Pden_4873 NC_008688.1 376018 377100 D KEGG: pae:PA4985 spermidine/putrescine transport system substrate-binding protein; spermidine/putrescine transport system substrate-binding protein 376018..377100 Paracoccus denitrificans PD1222 4583434 YP_918630.1 CDS Pden_4874 NC_008688.1 377124 378206 D 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 377124..378206 Paracoccus denitrificans PD1222 4583435 YP_918631.1 CDS Pden_4875 NC_008688.1 378206 379969 D 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 378206..379969 Paracoccus denitrificans PD1222 4583436 YP_918632.1 CDS Pden_4876 NC_008688.1 379987 380877 D PFAM: dihydrodipicolinate synthetase; KEGG: bbr:BB1108 dihydrodipicolinate synthase; dihydrodipicolinate synthetase 379987..380877 Paracoccus denitrificans PD1222 4583437 YP_918633.1 CDS Pden_4877 NC_008688.1 380890 382029 D PFAM: FMN-dependent alpha-hydroxy acid dehydrogenase; KEGG: bpe:BP1669 lactate dehydrogenase; L-lactate dehydrogenase (cytochrome) 380890..382029 Paracoccus denitrificans PD1222 4583438 YP_918634.1 CDS Pden_4878 NC_008688.1 382304 383257 R PFAM: pyruvate carboxyltransferase; KEGG: jan:Jann_3783 pyruvate carboxyltransferase; pyruvate carboxyltransferase complement(382304..383257) Paracoccus denitrificans PD1222 4583439 YP_918635.1 CDS Pden_4879 NC_008688.1 383259 384446 R PFAM: L-carnitine dehydratase/bile acid-inducible protein F; KEGG: bja:blr0697 hypothetical protein; L-carnitine dehydratase/bile acid-inducible protein F complement(383259..384446) Paracoccus denitrificans PD1222 4583440 YP_918636.1 CDS Pden_4880 NC_008688.1 384553 385485 D PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: bja:bll0696 transcriptional regulatory protein; LysR family transcriptional regulator 384553..385485 Paracoccus denitrificans PD1222 4583441 YP_918637.1 CDS Pden_4881 NC_008688.1 385533 386534 R 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 complement(385533..386534) Paracoccus denitrificans PD1222 4583442 YP_918638.1 CDS Pden_4882 NC_008688.1 386548 387327 R PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: bja:bll6487 ABC transporter permease; binding-protein-dependent transport systems inner membrane component complement(386548..387327) Paracoccus denitrificans PD1222 4583443 YP_918639.1 CDS Pden_4883 NC_008688.1 387324 388133 R PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: bmb:BruAb2_0894 ABC transporter, ATP binding protein; ABC transporter related complement(387324..388133) Paracoccus denitrificans PD1222 4583444 YP_918640.1 CDS Pden_4884 NC_008688.1 388334 388714 R hypothetical protein complement(388334..388714) Paracoccus denitrificans PD1222 4583445 YP_918641.1 CDS Pden_4885 NC_008688.1 388791 389441 D 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 388791..389441 Paracoccus denitrificans PD1222 4583446 YP_918642.1 CDS Pden_4886 NC_008688.1 389467 390615 D 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 389467..390615 Paracoccus denitrificans PD1222 4583447 YP_918643.1 CDS Pden_4887 NC_008688.1 390612 391334 D 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 390612..391334 Paracoccus denitrificans PD1222 4583448 YP_918644.1 CDS Pden_4888 NC_008688.1 391373 392257 D 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 391373..392257 Paracoccus denitrificans PD1222 4583449 YP_918645.1 CDS Pden_4889 NC_008688.1 392278 393198 D 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 392278..393198 Paracoccus denitrificans PD1222 4583450 YP_918646.1 CDS Pden_4890 NC_008688.1 393211 394401 D PFAM: acyl-CoA dehydrogenase domain protein; Acyl-CoA dehydrogenase, type 2, C-terminal domain; KEGG: bxe:Bxe_B1084 butyryl-CoA dehydrogenase; acyl-CoA dehydrogenase 393211..394401 Paracoccus denitrificans PD1222 4583451 YP_918647.1 CDS Pden_4891 NC_008688.1 394418 395980 D PFAM: AMP-dependent synthetase and ligase; KEGG: bce:BC0890 acyl-CoA synthase; AMP-dependent synthetase/ligase 394418..395980 Paracoccus denitrificans PD1222 4583452 YP_918648.1 CDS Pden_4892 NC_008688.1 395991 397316 D PFAM: MmgE/PrpD family protein; KEGG: csa:Csal_2358 MmgE/PrpD; MmgE/PrpD family protein 395991..397316 Paracoccus denitrificans PD1222 4583453 YP_918649.1 CDS Pden_4893 NC_008688.1 397338 398360 R PFAM: helix-turn-helix- domain containing protein, AraC type; ThiJ/PfpI domain protein; KEGG: mlo:mlr6509 transcriptional regulator; AraC family transcriptional regulator complement(397338..398360) Paracoccus denitrificans PD1222 4583454 YP_918650.1 CDS Pden_4894 NC_008688.1 398413 399606 R PFAM: FAD dependent oxidoreductase; KEGG: bxe:Bxe_B0746 oxidoreductase; FAD dependent oxidoreductase complement(398413..399606) Paracoccus denitrificans PD1222 4583455 YP_918651.1 CDS Pden_4895 NC_008688.1 399593 401176 R 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 complement(399593..401176) Paracoccus denitrificans PD1222 4583456 YP_918652.1 CDS Pden_4896 NC_008688.1 401288 402316 R 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 complement(401288..402316) Paracoccus denitrificans PD1222 4583457 YP_918653.1 CDS Pden_4897 NC_008688.1 402322 403554 R PFAM: Rieske [2Fe-2S] domain protein; KEGG: ppu:PP_0315 rieske 2Fe-2S family protein; Rieske (2Fe-2S) domain-containing protein complement(402322..403554) Paracoccus denitrificans PD1222 4583458 YP_918654.1 CDS Pden_4898 NC_008688.1 403708 403959 D hypothetical protein 403708..403959 Paracoccus denitrificans PD1222 4583459 YP_918655.1 CDS Pden_4899 NC_008688.1 403962 404570 R TIGRFAM: alkylhydroperoxidase like protein, AhpD family; uncharacterized peroxidase-related enzyme; PFAM: Carboxymuconolactone decarboxylase; KEGG: bja:bll6900 hypothetical protein; uncharacterized peroxidase-related enzyme complement(403962..404570) Paracoccus denitrificans PD1222 4583460 YP_918656.1 CDS Pden_4900 NC_008688.1 404580 405149 R KEGG: bja:bll6901 hypothetical protein; hypothetical protein complement(404580..405149) Paracoccus denitrificans PD1222 4583461 YP_918657.1 CDS Pden_4901 NC_008688.1 405160 406185 R PFAM: luciferase family protein; KEGG: bja:bll6902 hypothetical protein; luciferase family protein complement(405160..406185) Paracoccus denitrificans PD1222 4583462 YP_918658.1 CDS Pden_4902 NC_008688.1 406182 406913 R PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: eca:ECA0072 ABC transporter ATP-binding protein; ABC transporter related complement(406182..406913) Paracoccus denitrificans PD1222 4583463 YP_918659.1 CDS Pden_4903 NC_008688.1 406910 407698 R PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: eca:ECA0073 ABC transporter permease; binding-protein-dependent transport systems inner membrane component complement(406910..407698) Paracoccus denitrificans PD1222 4583464 YP_918660.1 CDS Pden_4904 NC_008688.1 407735 408619 R 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 complement(407735..408619) Paracoccus denitrificans PD1222 4583465 YP_918661.1 CDS Pden_4905 NC_008688.1 408691 409599 R 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 complement(408691..409599) Paracoccus denitrificans PD1222 4583466 YP_918662.1 CDS Pden_4906 NC_008688.1 409602 410168 R PFAM: Sarcosine oxidase, gamma subunit; KEGG: rde:RD1_0009 sarcosine oxidase, gamma subunit; sarcosine oxidase, gamma subunit complement(409602..410168) Paracoccus denitrificans PD1222 4583467 YP_918663.1 CDS Pden_4907 NC_008688.1 410161 413091 R 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 complement(410161..413091) Paracoccus denitrificans PD1222 4583468 YP_918664.1 CDS Pden_4908 NC_008688.1 413088 413402 R PFAM: Sarcosine oxidase, delta subunit, heterotetrameric; KEGG: rde:RD1_0011 sarcosine oxidase, delta subunit; sarcosine oxidase, delta subunit, heterotetrameric complement(413088..413402) Paracoccus denitrificans PD1222 4583469 YP_918665.1 CDS Pden_4909 NC_008688.1 413380 414630 R 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 complement(413380..414630) Paracoccus denitrificans PD1222 4583470 YP_918666.1 CDS Pden_4910 NC_008688.1 414756 415922 D PFAM: helix-turn-helix- domain containing protein, AraC type; ThiJ/PfpI domain protein; KEGG: mlo:mlr6241 transcription regulator; AraC family transcriptional regulator 414756..415922 Paracoccus denitrificans PD1222 4583471 YP_918667.1 CDS Pden_4911 NC_008688.1 416120 417121 R KEGG: bbr:BB1042 extracellular solute-binding protein; extracellular solute-binding protein complement(416120..417121) Paracoccus denitrificans PD1222 4583472 YP_918668.1 CDS Pden_4912 NC_008688.1 417208 418851 R 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 complement(417208..418851) Paracoccus denitrificans PD1222 4583473 YP_918669.1 CDS Pden_4913 NC_008688.1 418848 419909 R PFAM: ABC transporter related; Transport-associated OB domain protein; SMART: AAA ATPase; KEGG: bbr:BB1043 ATP-binding component of ABC transporter; ABC transporter related complement(418848..419909) Paracoccus denitrificans PD1222 4583474 YP_918670.1 CDS Pden_4914 NC_008688.1 419938 420747 R PFAM: inositol monophosphatase; KEGG: sme:SMa0483 inositol monophosphatase; inositol monophosphatase complement(419938..420747) Paracoccus denitrificans PD1222 4583475 YP_918671.1 CDS Pden_4915 NC_008688.1 421058 421840 D PFAM: regulatory protein, DeoR; Helix-turn-helix, type 11 domain protein; KEGG: bxe:Bxe_A4204 transcriptional regulator, DeoR family; DeoR family transcriptional regulator 421058..421840 Paracoccus denitrificans PD1222 4583476 YP_918672.1 CDS Pden_4916 NC_008688.1 421864 424311 R 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 complement(421864..424311) Paracoccus denitrificans PD1222 4583477 YP_918673.1 CDS Pden_4917 NC_008688.1 424551 425105 D PFAM: helix-turn-helix domain protein; Cupin 2, conserved barrel domain protein; KEGG: sil:SPO3403 DNA-binding protein; XRE family transcriptional regulator 424551..425105 Paracoccus denitrificans PD1222 4583478 YP_918674.1 CDS Pden_4918 NC_008688.1 425252 425728 R KEGG: rru:Rru_B0014 transposase, mutator type; hypothetical protein complement(425252..425728) Paracoccus denitrificans PD1222 4583479 YP_918675.1 CDS Pden_4919 NC_008688.1 425785 426534 D 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 425785..426534 Paracoccus denitrificans PD1222 4583480 YP_918676.1 CDS Pden_4920 NC_008688.1 426820 427398 D KEGG: vvy:VV0790 hypothetical protein; hypothetical protein 426820..427398 Paracoccus denitrificans PD1222 4583481 YP_918677.1 CDS Pden_4921 NC_008688.1 427353 428321 R PFAM: alpha/beta hydrolase fold; KEGG: lbl:LBL_2370 hydrolase; alpha/beta hydrolase complement(427353..428321) Paracoccus denitrificans PD1222 4583482 YP_918678.1 CDS Pden_4922 NC_008688.1 428408 429511 R KEGG: gox:GOX0022 hypothetical protein; hypothetical protein complement(428408..429511) Paracoccus denitrificans PD1222 4583483 YP_918679.1 CDS Pden_4923 NC_008688.1 429786 430586 R PFAM: regulatory proteins, IclR; KEGG: bam:Bamb_0518 transcriptional regulator, IclR family; regulatory proteins, IclR complement(429786..430586) Paracoccus denitrificans PD1222 4583484 YP_918680.1 CDS Pden_4924 NC_008688.1 430779 431534 D 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 430779..431534 Paracoccus denitrificans PD1222 4583485 YP_918681.1 CDS Pden_4925 NC_008688.1 431545 432189 D 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 431545..432189 Paracoccus denitrificans PD1222 4583486 YP_918682.1 CDS Pden_4926 NC_008688.1 432173 432907 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: mes:Meso_3975 ABC transporter related; ABC transporter related 432173..432907 Paracoccus denitrificans PD1222 4583487 YP_918683.1 CDS Pden_4927 NC_008688.1 432970 433770 D PFAM: extracellular solute-binding protein, family 3; KEGG: rfr:Rfer_1029 extracellular solute-binding protein, family 3; extracellular solute-binding protein 432970..433770 Paracoccus denitrificans PD1222 4583488 YP_918684.1 CDS Pden_4928 NC_008688.1 433821 435347 D PFAM: D-galactarate dehydratase/Altronate hydrolase domain protein; SAF domain; KEGG: rfr:Rfer_1027 galactarate dehydratase; galactarate dehydratase 433821..435347 Paracoccus denitrificans PD1222 4583489 YP_918685.1 CDS Pden_4929 NC_008688.1 435375 436289 D PFAM: 2-keto-3-deoxy-galactonokinase; KEGG: ret:RHE_CH00854 2-dehydro-3-deoxygalactonokinase; 2-keto-3-deoxy-galactonokinase 435375..436289 Paracoccus denitrificans PD1222 4583490 YP_918686.1 CDS Pden_4930 NC_008688.1 436286 436948 D 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 436286..436948 Paracoccus denitrificans PD1222 4583491 YP_918687.1 CDS Pden_4931 NC_008688.1 437007 438020 D PFAM: Alcohol dehydrogenase, zinc-binding domain protein; Alcohol dehydrogenase GroES domain protein; KEGG: bth:BT3617 sorbitol dehydrogenase; alcohol dehydrogenase 437007..438020 Paracoccus denitrificans PD1222 4583492 YP_918688.1 CDS Pden_4932 NC_008688.1 438017 438784 D PFAM: short-chain dehydrogenase/reductase SDR; KR; KEGG: mmr:Mmar10_0232 2-deoxy-D-gluconate 3-dehydrogenase; short-chain dehydrogenase/reductase SDR 438017..438784 Paracoccus denitrificans PD1222 4583493 YP_918689.1 CDS Pden_4933 NC_008688.1 438858 439418 R KEGG: sme:SMa2229 hypothetical protein; hypothetical protein complement(438858..439418) Paracoccus denitrificans PD1222 4583494 YP_918690.1 CDS Pden_4934 NC_008688.1 439421 440803 R 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 complement(439421..440803) Paracoccus denitrificans PD1222 4583495 YP_918691.1 CDS Pden_4935 NC_008688.1 440800 441114 R KEGG: bxe:Bxe_B2707 hypothetical protein; hypothetical protein complement(440800..441114) Paracoccus denitrificans PD1222 4583496 YP_918692.1 CDS Pden_4936 NC_008688.1 441095 442210 R PFAM: FAD dependent oxidoreductase; KEGG: sme:SMa2223 opine oxidase subunit; FAD dependent oxidoreductase complement(441095..442210) Paracoccus denitrificans PD1222 4583497 YP_918693.1 CDS Pden_4937 NC_008688.1 442207 442920 R KEGG: sme:SMa2221 hypothetical protein; hypothetical protein complement(442207..442920) Paracoccus denitrificans PD1222 4583498 YP_918694.1 CDS Pden_4938 NC_008688.1 442917 443510 R TIGRFAM: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; PFAM: flavoprotein; KEGG: sme:SMa2219 probable decarboxylase; 3-octaprenyl-4-hydroxybenzoate carboxy-lyase complement(442917..443510) Paracoccus denitrificans PD1222 4583499 YP_918695.1 CDS Pden_4939 NC_008688.1 443512 444843 R TIGRFAM: UbiD family decarboxylases; PFAM: Carboxylyase-related protein; KEGG: sme:SMa2217 decarboxylase; UbiD family decarboxylase complement(443512..444843) Paracoccus denitrificans PD1222 4583500 YP_918696.1 CDS Pden_4940 NC_008688.1 444877 445641 R 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 complement(444877..445641) Paracoccus denitrificans PD1222 4583501 YP_918697.1 CDS Pden_4941 NC_008688.1 445920 447416 D PFAM: aldehyde dehydrogenase; KEGG: sme:SMA2213 aldehyde; betaine-aldehyde dehydrogenase 445920..447416 Paracoccus denitrificans PD1222 4583502 YP_918698.1 CDS Pden_4942 NC_008688.1 447413 449116 D catalyzes the formation of 2-acetolactate from pyruvate, leucine sensitive; also known as acetolactate synthase large subunit; thiamine pyrophosphate protein 447413..449116 Paracoccus denitrificans PD1222 4583503 YP_918699.1 CDS Pden_4943 NC_008688.1 449214 450236 D PFAM: extracellular solute-binding protein, family 1; KEGG: sme:SMa2209 ABC transporter, periplasmic solute-binding protein; extracellular solute-binding protein 449214..450236 Paracoccus denitrificans PD1222 4583504 YP_918700.1 CDS Pden_4944 NC_008688.1 450315 451409 D 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 450315..451409 Paracoccus denitrificans PD1222 4583505 YP_918701.1 CDS Pden_4945 NC_008688.1 451413 452273 D PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: sme:SMa2205 ABC transporter, permease; binding-protein-dependent transport systems inner membrane component 451413..452273 Paracoccus denitrificans PD1222 4583506 YP_918702.1 CDS Pden_4946 NC_008688.1 452270 453064 D PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: sme:SMa2203 ABC transporter, permease; binding-protein-dependent transport systems inner membrane component 452270..453064 Paracoccus denitrificans PD1222 4583507 YP_918703.1 CDS Pden_4947 NC_008688.1 453396 453593 D PFAM: protein of unknown function DUF1127; KEGG: rde:RD1_2086 hypothetical protein; hypothetical protein 453396..453593 Paracoccus denitrificans PD1222 4583508 YP_918704.1 CDS Pden_4948 NC_008688.1 453745 454716 R hypothetical protein complement(453745..454716) Paracoccus denitrificans PD1222 4583509 YP_918705.1 CDS Pden_4949 NC_008688.1 454856 455650 R PFAM: protein of unknown function DUF72; KEGG: rsp:RSP_0939 hypothetical protein; hypothetical protein complement(454856..455650) Paracoccus denitrificans PD1222 4583510 YP_918706.1 CDS Pden_4950 NC_008688.1 455680 455967 D hypothetical protein 455680..455967 Paracoccus denitrificans PD1222 4583511 YP_918707.1 CDS Pden_4951 NC_008688.1 455943 457997 R 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 complement(455943..457997) Paracoccus denitrificans PD1222 4583512 YP_918708.1 CDS Pden_4952 NC_008688.1 458149 459108 R PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: bja:blr6829 transcriptional regulatory protein; LysR family transcriptional regulator complement(458149..459108) Paracoccus denitrificans PD1222 4583513 YP_918709.1 CDS Pden_4953 NC_008688.1 459163 460233 R PFAM: ammonia monooxygenase; KEGG: rsp:RSP_7367 AbrB protein (AidB regulator); ammonia monooxygenase complement(459163..460233) Paracoccus denitrificans PD1222 4583514 YP_918710.1 CDS Pden_4954 NC_008688.1 460383 461261 D KEGG: ret:RHE_PF00334 acetyltransferase; acetyltransferase 460383..461261 Paracoccus denitrificans PD1222 4583515 YP_918711.1 CDS Pden_4955 NC_008688.1 461312 462640 R PFAM: FAD dependent oxidoreductase; FAD-dependent pyridine nucleotide-disulphide oxidoreductase; KEGG: atc:AGR_L_1801 deaminase; FAD dependent oxidoreductase complement(461312..462640) Paracoccus denitrificans PD1222 4583516 YP_918712.1 CDS Pden_4956 NC_008688.1 462656 463975 R PFAM: FAD dependent oxidoreductase; KEGG: ret:RHE_PF00361 probable deaminase; FAD dependent oxidoreductase complement(462656..463975) Paracoccus denitrificans PD1222 4583517 YP_918713.1 CDS Pden_4957 NC_008688.1 464212 464688 D PFAM: regulatory protein, AsnC/Lrp family; KEGG: ret:RHE_PF00360 probable transcriptional regulator protein (leucine-responsive), AsnC family; AsnC family transcriptional regulator 464212..464688 Paracoccus denitrificans PD1222 4583518 YP_918714.1 CDS Pden_4958 NC_008688.1 464707 466368 R PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sme:SMa1864 ABC transporter, ATP-binding protein; ABC transporter related complement(464707..466368) Paracoccus denitrificans PD1222 4583519 YP_918715.1 CDS Pden_4959 NC_008688.1 466368 467210 R 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 complement(466368..467210) Paracoccus denitrificans PD1222 4583520 YP_918716.1 CDS Pden_4960 NC_008688.1 467210 468163 R PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: sme:SMa1862 ABC transporter, permease; binding-protein-dependent transport systems inner membrane component complement(467210..468163) Paracoccus denitrificans PD1222 4583521 YP_918717.1 CDS Pden_4961 NC_008688.1 468219 469832 R PFAM: extracellular solute-binding protein, family 5; KEGG: ret:RHE_PF00351 probable oligopeptide ABC transporter, substrate-binding protein; extracellular solute-binding protein complement(468219..469832) Paracoccus denitrificans PD1222 4583522 YP_918718.1 CDS Pden_4962 NC_008688.1 469890 470690 R 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 complement(469890..470690) Paracoccus denitrificans PD1222 4583523 YP_918719.1 CDS Pden_4963 NC_008688.1 470825 471739 R PFAM: D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding; KEGG: mlo:mll7048 probable dehydrogenase; D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding complement(470825..471739) Paracoccus denitrificans PD1222 4583524 YP_918720.1 CDS Pden_4964 NC_008688.1 471739 473115 R PFAM: aminotransferase class-III; KEGG: sme:SMa1855 hypothetical protein; hypothetical protein complement(471739..473115) Paracoccus denitrificans PD1222 4583525 YP_918721.1 CDS Pden_4965 NC_008688.1 473133 473966 R PFAM: GCN5-related N-acetyltransferase; KEGG: atc:AGR_L_2832 hypothetical protein; GCN5-related N-acetyltransferase complement(473133..473966) Paracoccus denitrificans PD1222 4583526 YP_918722.1 CDS Pden_4966 NC_008688.1 474080 474433 R PFAM: protein of unknown function DUF861, cupin_3; KEGG: mlo:mll7047 hypothetical protein; hypothetical protein complement(474080..474433) Paracoccus denitrificans PD1222 4583527 YP_918723.1 CDS Pden_4967 NC_008688.1 474442 475719 R PFAM: FAD dependent oxidoreductase; KEGG: mlo:mlr7042 probable oxidoreductase; FAD dependent oxidoreductase complement(474442..475719) Paracoccus denitrificans PD1222 4583528 YP_918724.1 CDS Pden_4968 NC_008688.1 475722 476426 R 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 complement(475722..476426) Paracoccus denitrificans PD1222 4583529 YP_918725.1 CDS Pden_4969 NC_008688.1 476532 477980 R KEGG: sme:SMa1848 GabD5 succinate semialdehyde dehdyrogenase; TIGRFAM: succinic semialdehyde dehydrogenase; PFAM: aldehyde dehydrogenase; succinic semialdehyde dehydrogenase complement(476532..477980) Paracoccus denitrificans PD1222 4583530 YP_918726.1 CDS Pden_4970 NC_008688.1 477977 479017 R catalyzes the oxidation of 3-isopropylmalate to 3-carboxy-4-methyl-2-oxopentanoate in leucine biosynthesis; 3-isopropylmalate dehydrogenase complement(477977..479017) Paracoccus denitrificans PD1222 4583531 YP_918727.1 CDS Pden_4971 NC_008688.1 479029 480492 R PFAM: aldehyde dehydrogenase; KEGG: ret:RHE_PF00338 probable aldehyde dehydrogenase; aldehyde dehydrogenase complement(479029..480492) Paracoccus denitrificans PD1222 4583532 YP_918728.1 CDS Pden_4972 NC_008688.1 480618 481538 R PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: mlo:mlr7023 transcriptional regulator; LysR family transcriptional regulator complement(480618..481538) Paracoccus denitrificans PD1222 4583533 YP_918729.1 CDS Pden_4973 NC_008688.1 481546 483504 R PFAM: Hydantoinase B/oxoprolinase; KEGG: bpe:BP0821 hydantoin utilization protein B; 5-oxoprolinase complement(481546..483504) Paracoccus denitrificans PD1222 4583534 YP_918730.1 CDS Pden_4974 NC_008688.1 483508 485547 R PFAM: Hydantoinase/oxoprolinase; Hydantoinaseoxoprolinase domain protein; KEGG: bbr:BB3858 hydantoin utilization protein A; 5-oxoprolinase complement(483508..485547) Paracoccus denitrificans PD1222 4583535 YP_918731.1 CDS Pden_4975 NC_008688.1 485636 486100 R PFAM: GCN5-related N-acetyltransferase; KEGG: vpa:VP2001 hypothetical protein; GCN5-related N-acetyltransferase complement(485636..486100) Paracoccus denitrificans PD1222 4583536 YP_918732.1 CDS Pden_4976 NC_008688.1 486259 487389 D catalyzes the formation of L-ornithine from N(2)-acetyl-L-ornithine; acetylornithine deacetylase 486259..487389 Paracoccus denitrificans PD1222 4583537 YP_918733.1 CDS Pden_4977 NC_008688.1 487592 487843 D hypothetical protein 487592..487843 Paracoccus denitrificans PD1222 4583538 YP_918734.1 CDS Pden_4978 NC_008688.1 487868 489118 D KEGG: pfa:PF10_0374 gene 11-1 protein precursor; hypothetical protein 487868..489118 Paracoccus denitrificans PD1222 4583539 YP_918735.1 CDS Pden_4979 NC_008688.1 489237 491096 R 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 complement(489237..491096) Paracoccus denitrificans PD1222 4583540 YP_918736.1 CDS Pden_4980 NC_008688.1 491175 492248 R PFAM: Alcohol dehydrogenase, zinc-binding domain protein; Alcohol dehydrogenase GroES domain protein; KEGG: atc:AGR_L_281 hypothetical protein; alcohol dehydrogenase complement(491175..492248) Paracoccus denitrificans PD1222 4583541 YP_918737.1 CDS Pden_4981 NC_008688.1 492258 492587 R TIGRFAM: alkylhydroperoxidase like protein, AhpD family; PFAM: Carboxymuconolactone decarboxylase; KEGG: sil:SPO3789 4-carboxymuconolactone decarboxylase domain/alkylhydroperoxidase AhpD family core domain protein; alkylhydroperoxidase complement(492258..492587) Paracoccus denitrificans PD1222 4583542 YP_918738.1 CDS Pden_4982 NC_008688.1 492584 493372 R PFAM: NAD-dependent epimerase/dehydratase; short-chain dehydrogenase/reductase SDR; KR; KEGG: rha:RHA1_ro05279 acetoin dehydrogenase; short-chain dehydrogenase/reductase SDR complement(492584..493372) Paracoccus denitrificans PD1222 4583543 YP_918739.1 CDS Pden_4983 NC_008688.1 493422 494525 R 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 complement(493422..494525) Paracoccus denitrificans PD1222 4583544 YP_918740.1 CDS Pden_4984 NC_008688.1 494527 495534 R PFAM: Transketolase, central region; Transketolase domain protein; KEGG: sil:SPO3791 acetoin dehydrogenase complex, E1 component, beta subunit; transketolase, central region complement(494527..495534) Paracoccus denitrificans PD1222 4583545 YP_918741.1 CDS Pden_4985 NC_008688.1 495557 496534 R PFAM: dehydrogenase, E1 component; KEGG: sil:SPO3792 acetoin dehydrogenase complex, E1 component, alpha subunit; pyruvate dehydrogenase (acetyl-transferring) complement(495557..496534) Paracoccus denitrificans PD1222 4583546 YP_918742.1 CDS Pden_4986 NC_008688.1 496555 497568 R PFAM: ATP-NAD/AcoX kinase; KEGG: sil:SPO3793 acetoin catabolism protein X; ATP-NAD/AcoX kinase complement(496555..497568) Paracoccus denitrificans PD1222 4583547 YP_918743.1 CDS Pden_4987 NC_008688.1 497659 498849 D 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 497659..498849 Paracoccus denitrificans PD1222 4583548 YP_918744.1 CDS Pden_4988 NC_008688.1 498993 500036 R PFAM: protein of unknown function UPF0118; KEGG: bms:BRA0460 hypothetical protein; hypothetical protein complement(498993..500036) Paracoccus denitrificans PD1222 4583549 YP_918745.1 CDS Pden_4989 NC_008688.1 500225 500854 R PFAM: DSBA oxidoreductase; KEGG: sil:SPOA0362 27kDa outer membrane protein; Fis family transcriptional regulator complement(500225..500854) Paracoccus denitrificans PD1222 4583550 YP_918746.1 CDS Pden_4990 NC_008688.1 500906 501400 R PFAM: ErfK/YbiS/YcfS/YnhG family protein; KEGG: rsp:RSP_3073 ErfK/YbiS/YcfS/YnhG family protein; ErfK/YbiS/YcfS/YnhG family protein complement(500906..501400) Paracoccus denitrificans PD1222 4583551 YP_918747.1 CDS Pden_4991 NC_008688.1 502213 503199 R PFAM: Alcohol dehydrogenase, zinc-binding domain protein; Alcohol dehydrogenase GroES domain protein; KEGG: rfr:Rfer_1643 alcohol dehydrogenase, zinc-binding; alcohol dehydrogenase complement(502213..503199) Paracoccus denitrificans PD1222 4583552 YP_918748.1 CDS Pden_4992 NC_008688.1 503222 504040 R PFAM: Enoyl-CoA hydratase/isomerase; KEGG: mes:Meso_1938 enoyl-CoA hydratase/isomerase; enoyl-CoA hydratase/isomerase complement(503222..504040) Paracoccus denitrificans PD1222 4583553 YP_918749.1 CDS Pden_4993 NC_008688.1 504070 505269 R PFAM: major facilitator superfamily MFS_1; KEGG: mmr:Mmar10_2043 major facilitator superfamily MFS_1; major facilitator transporter complement(504070..505269) Paracoccus denitrificans PD1222 4583554 YP_918750.1 CDS Pden_4994 NC_008688.1 505308 506510 R PFAM: Extracellular ligand-binding receptor; KEGG: sit:TM1040_2237 extracellular ligand-binding receptor; extracellular ligand-binding receptor complement(505308..506510) Paracoccus denitrificans PD1222 4583555 YP_918751.1 CDS Pden_4995 NC_008688.1 506611 507375 R PFAM: regulatory protein GntR, HTH; GntR domain protein; KEGG: sil:SPO2543 transcriptional regulator, GntR family; GntR family transcriptional regulator complement(506611..507375) Paracoccus denitrificans PD1222 4583556 YP_918752.1 CDS Pden_4996 NC_008688.1 507372 509489 R PFAM: CoA-binding domain protein; ATP-grasp domain protein; KEGG: sma:SAV1821 acyl-CoA synthetase (NDP forming type); CoA-binding domain-containing protein complement(507372..509489) Paracoccus denitrificans PD1222 4583557 YP_918753.1 CDS Pden_4997 NC_008688.1 509578 510285 R PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rfr:Rfer_2387 ABC transporter related; ABC transporter related complement(509578..510285) Paracoccus denitrificans PD1222 4583558 YP_918754.1 CDS Pden_4998 NC_008688.1 510282 511034 R PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: tth:TTC0969 branched-chain amino acid transport ATP-binding protein livG; ABC transporter related complement(510282..511034) Paracoccus denitrificans PD1222 4583559 YP_918755.1 CDS Pden_4999 NC_008688.1 511031 512032 R PFAM: inner-membrane translocator; KEGG: reu:Reut_C6328 inner-membrane translocator; inner-membrane translocator complement(511031..512032) Paracoccus denitrificans PD1222 4583560 YP_918756.1 CDS Pden_5000 NC_008688.1 512029 512994 R PFAM: inner-membrane translocator; KEGG: bja:bll6235 ABC transporter permease; inner-membrane translocator complement(512029..512994) Paracoccus denitrificans PD1222 4583561 YP_918757.1 CDS Pden_5001 NC_008688.1 513391 513969 R PFAM: HupE/UreJ protein; KEGG: pfo:Pfl_0560 HupE/UreJ protein; HupE/UreJ protein complement(513391..513969) Paracoccus denitrificans PD1222 4583562 YP_918758.1 CDS Pden_5002 NC_008688.1 514015 514329 R SMART: Rhodanese domain protein; rhodanese domain-containing protein complement(514015..514329) Paracoccus denitrificans PD1222 4583563 YP_918759.1 CDS Pden_5003 NC_008688.1 514340 514846 R PFAM: Cupin domain protein; Cupin 2, conserved barrel domain protein; KEGG: bja:blr2407 hypothetical protein; cupin 2 domain-containing protein complement(514340..514846) Paracoccus denitrificans PD1222 4583564 YP_918760.1 CDS Pden_5004 NC_008688.1 514961 515698 R PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sma:SAV1559 ABC transporter ATP-binding protein; ABC transporter related complement(514961..515698) Paracoccus denitrificans PD1222 4583565 YP_918761.1 CDS Pden_5005 NC_008688.1 515671 516540 R 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 complement(515671..516540) Paracoccus denitrificans PD1222 4583566 YP_918762.1 CDS Pden_5006 NC_008688.1 516542 517513 R 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 complement(516542..517513) Paracoccus denitrificans PD1222 4583567 YP_918763.1 CDS Pden_5007 NC_008688.1 517529 518857 R KEGG: pst:PSPTO_2425 monooxygenase, NtaA/SnaA/SoxA family; NtaA/SnaA/SoxA family monooxygenase complement(517529..518857) Paracoccus denitrificans PD1222 4583568 YP_918764.1 CDS Pden_5008 NC_008688.1 519031 520572 R PFAM: copper resistance protein CopC; copper resistance D domain protein; KEGG: rpa:RPA2929 copper resistance protein; copper resistance protein CopC complement(519031..520572) Paracoccus denitrificans PD1222 4583569 YP_918765.1 CDS Pden_5009 NC_008688.1 520569 521009 R KEGG: rpc:RPC_2425 nuclear export factor GLE1; nuclear export factor GLE1 complement(520569..521009) Paracoccus denitrificans PD1222 4583570 YP_918766.1 CDS Pden_5010 NC_008688.1 521021 521812 R PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: bam:Bamb_3676 ABC transporter related; ABC transporter related complement(521021..521812) Paracoccus denitrificans PD1222 4583571 YP_918767.1 CDS Pden_5011 NC_008688.1 521806 522801 R 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 complement(521806..522801) Paracoccus denitrificans PD1222 4583572 YP_918768.1 CDS Pden_5012 NC_008688.1 522811 523842 R KEGG: bja:bll6455 ABC transporter substrate-binding protein; ABC transporter substrate-binding protein complement(522811..523842) Paracoccus denitrificans PD1222 4583573 YP_918769.1 CDS Pden_5013 NC_008688.1 523853 524959 R PFAM: luciferase family protein; KEGG: psb:Psyr_3599 alkanesulfonate monooxygenase; alkanesulfonate monooxygenase complement(523853..524959) Paracoccus denitrificans PD1222 4583574 YP_918770.1 CDS Pden_5014 NC_008688.1 524976 526130 R PFAM: acyl-CoA dehydrogenase domain protein; Acyl-CoA dehydrogenase, type 2, C-terminal domain; KEGG: bja:bll6452 acyl-CoA dehydrogenase; acyl-CoA dehydrogenase complement(524976..526130) Paracoccus denitrificans PD1222 4583575 YP_918771.1 CDS Pden_5015 NC_008688.1 526530 527465 R hypothetical protein complement(526530..527465) Paracoccus denitrificans PD1222 4583576 YP_918772.1 CDS Pden_5016 NC_008688.1 527529 528437 D KEGG: rpc:RPC_3638 serine O-acetyltransferase; Serine O-acetyltransferase 527529..528437 Paracoccus denitrificans PD1222 4583577 YP_918773.1 CDS Pden_5017 NC_008688.1 528519 529106 D KEGG: bmb:BruAb2_0725 hypothetical protein; hypothetical protein 528519..529106 Paracoccus denitrificans PD1222 4583578 YP_918774.1 CDS Pden_5018 NC_008688.1 529599 530375 D PFAM: Xylose isomerase domain protein TIM barrel; KEGG: rde:RD1_3783 hypothetical protein; hydroxypyruvate isomerase 529599..530375 Paracoccus denitrificans PD1222 4583579 YP_918775.1 CDS Pden_5019 NC_008688.1 530421 531179 R 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 complement(530421..531179) Paracoccus denitrificans PD1222 4583580 YP_918776.1 CDS Pden_5020 NC_008688.1 531289 532038 D 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 531289..532038 Paracoccus denitrificans PD1222 4583581 YP_918777.1 CDS Pden_5021 NC_008688.1 532035 532706 D 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 532035..532706 Paracoccus denitrificans PD1222 4583582 YP_918778.1 CDS Pden_5022 NC_008688.1 532708 533907 D catalyzes the thiolytic cleavage of beta-ketoadipyl-CoA to succinate and acetyl-CoA; beta-ketoadipyl CoA thiolase 532708..533907 Paracoccus denitrificans PD1222 4583583 YP_918779.1 CDS Pden_5023 NC_008688.1 534012 534962 R 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 complement(534012..534962) Paracoccus denitrificans PD1222 4583584 YP_918780.1 CDS Pden_5024 NC_008688.1 535096 535398 D hypothetical protein 535096..535398 Paracoccus denitrificans PD1222 4583585 YP_918781.1 CDS Pden_5025 NC_008688.1 535604 536038 D TIGRFAM: cytidyltransferase-related domain; glycerol-3-phosphate cytidylyltransferase; PFAM: cytidylyltransferase; KEGG: blo:BL0210 probable glycerol-3-phosphate cytidylyltransferase; glycerol-3-phosphate cytidylyltransferase 535604..536038 Paracoccus denitrificans PD1222 4583586 YP_918782.1 CDS Pden_5026 NC_008688.1 536137 536541 R hypothetical protein complement(536137..536541) Paracoccus denitrificans PD1222 4583587 YP_918783.1 CDS Pden_5027 NC_008688.1 536632 539202 D PFAM: glycosyl transferase, group 1; CDP-glycerol:poly(glycerophosphate) glycerophosphotransferase; KEGG: lxx:Lxx17460 teichoic acid synthase; glycosyl transferase, group 1 536632..539202 Paracoccus denitrificans PD1222 4583588 YP_918784.1 CDS Pden_5028 NC_008688.1 539210 540220 R KEGG: sit:TM1040_1773 conserved hypothetical protein; hypothetical protein complement(539210..540220) Paracoccus denitrificans PD1222 4583589 YP_918785.1 CDS Pden_5029 NC_008688.1 540232 541374 R KEGG: ecc:c3693 hypothetical protein; hypothetical protein complement(540232..541374) Paracoccus denitrificans PD1222 4583590 YP_918786.1 CDS Pden_5030 NC_008688.1 541478 542752 R KEGG: ecc:c3695 hypothetical protein; hypothetical protein complement(541478..542752) Paracoccus denitrificans PD1222 4583591 YP_918787.1 CDS Pden_5031 NC_008688.1 543056 543865 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rsp:RSP_2175 ABC transporter, ATPase subunit; ABC transporter related 543056..543865 Paracoccus denitrificans PD1222 4583592 YP_918788.1 CDS Pden_5032 NC_008688.1 543840 544457 D PFAM: cobalt transport protein; KEGG: rsp:RSP_2174 ABC transporter, inner membrane subunit; cobalt transport protein 543840..544457 Paracoccus denitrificans PD1222 4583593 YP_918789.1 CDS Pden_5033 NC_008688.1 544464 545039 D PFAM: BioY protein; KEGG: rsp:RSP_2173 biotin biosynthesis protein BioY; BioY protein 544464..545039 Paracoccus denitrificans PD1222 4583594 YP_918790.1 CDS Pden_5034 NC_008688.1 545354 546376 R PFAM: initiator RepB protein; KEGG: cbu:CBUA0039 RepA protein; initiator RepB protein complement(545354..546376) Paracoccus denitrificans PD1222 4583595 YP_918791.1 CDS Pden_5035 NC_008688.1 546983 548182 D PFAM: Cobyrinic acid a,c-diamide synthase; KEGG: sme:SMb20046 probable replication protein A; cobyrinic acid a,c-diamide synthase 546983..548182 Paracoccus denitrificans PD1222 4583596 YP_918792.1 CDS Pden_5036 NC_008688.1 548179 549144 D TIGRFAM: parB-like partition proteins; PFAM: ParB domain protein nuclease; KEGG: cbu:CBUA0038 RepB protein; parB-like partition proteins 548179..549144 Paracoccus denitrificans PD1222 4583597 YP_918793.1 CDS Pden_5037 NC_008688.1 549321 549998 R PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sme:SMb20832 cell surface polysaccharide export ABC-2 transporter ATP-binding protein; ABC transporter related complement(549321..549998) Paracoccus denitrificans PD1222 4583598 YP_918794.1 CDS Pden_5038 NC_008688.1 550003 551244 R KEGG: mes:Meso_2756 capsule polysaccharide export protein-like; capsule polysaccharide export protein-like complement(550003..551244) Paracoccus denitrificans PD1222 4583599 YP_918795.1 CDS Pden_5039 NC_008688.1 552149 552901 D PFAM: ABC-2 type transporter; KEGG: sme:SMb20833 cell surface polysaccharide export ABC-2 transporter permease, close relative of Y20822wzm2; ABC-2 type transporter 552149..552901 Paracoccus denitrificans PD1222 4583600 YP_918796.1 CDS Pden_5040 NC_008688.1 552932 554020 R PFAM: glycosyl transferase, group 1; KEGG: dvu:DVU0328 glycosyl transferase, group 1 family protein; glycosyl transferase, group 1 complement(552932..554020) Paracoccus denitrificans PD1222 4583601 YP_918797.1 CDS Pden_5041 NC_008688.1 554121 555020 D KEGG: msu:MS0656 hypothetical protein; hypothetical protein 554121..555020 Paracoccus denitrificans PD1222 4583602 YP_918798.1 CDS Pden_5042 NC_008688.1 554998 555288 R hypothetical protein complement(554998..555288) Paracoccus denitrificans PD1222 4583603 YP_918799.1 CDS Pden_5043 NC_008688.1 555356 556501 D PFAM: UDP-galactopyranose mutase; KEGG: atc:AGR_L_1762 probable UDP-galactopyranose mutase; UDP-galactopyranose mutase 555356..556501 Paracoccus denitrificans PD1222 4583604 YP_918800.1 CDS Pden_5044 NC_008688.1 556550 557500 R PFAM: aldo/keto reductase; KEGG: mlo:mll3531 hypothetical protein; aldo/keto reductase complement(556550..557500) Paracoccus denitrificans PD1222 4583605 YP_918801.1 CDS Pden_5045 NC_008688.1 557500 558684 R PFAM: FMN-dependent alpha-hydroxy acid dehydrogenase; KEGG: mes:Meso_3045 FMN-dependent alpha-hydroxy acid dehydrogenase; (S)-2-hydroxy-acid oxidase complement(557500..558684) Paracoccus denitrificans PD1222 4583606 YP_918802.1 CDS Pden_5046 NC_008688.1 558688 559206 R PFAM: regulatory protein, MarR; KEGG: mlo:mlr3448 regulatory protein (MarR-family); MarR family transcriptional regulator complement(558688..559206) Paracoccus denitrificans PD1222 4583607 YP_918803.1 CDS Pden_5047 NC_008688.1 559396 560412 D PFAM: extracellular solute-binding protein, family 1; KEGG: bja:bll3286 ABC transporter substrate-binding protein; extracellular solute-binding protein 559396..560412 Paracoccus denitrificans PD1222 4583608 YP_918804.1 CDS Pden_5048 NC_008688.1 560494 561555 D 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 560494..561555 Paracoccus denitrificans PD1222 4583609 YP_918805.1 CDS Pden_5049 NC_008688.1 561552 562403 D 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 561552..562403 Paracoccus denitrificans PD1222 4583610 YP_918806.1 CDS Pden_5050 NC_008688.1 562400 563188 D 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 562400..563188 Paracoccus denitrificans PD1222 4583611 YP_918807.1 CDS Pden_5051 NC_008688.1 563200 564021 D PFAM: polysaccharide deacetylase; KEGG: bja:bll7202 hypothetical protein; polysaccharide deacetylase 563200..564021 Paracoccus denitrificans PD1222 4583612 YP_918808.1 CDS Pden_5052 NC_008688.1 564018 564758 D PFAM: NAD-dependent epimerase/dehydratase; short-chain dehydrogenase/reductase SDR; KR; KEGG: rsp:RSP_7370 short-chain alcohol dehydrogenase; short-chain dehydrogenase/reductase SDR 564018..564758 Paracoccus denitrificans PD1222 4583613 YP_918809.1 CDS Pden_5053 NC_008688.1 564766 565512 D PFAM: NAD-dependent epimerase/dehydratase; short-chain dehydrogenase/reductase SDR; KEGG: rsp:RSP_3963 short-chain dehydrogenase/reductase SDR; short-chain dehydrogenase/reductase SDR 564766..565512 Paracoccus denitrificans PD1222 4583614 YP_918810.1 CDS Pden_5054 NC_008688.1 565525 566901 D PFAM: Amidase; KEGG: bja:blr3229 glutamyl-tRNA(Gln) amidotransferase subunit; amidase 565525..566901 Paracoccus denitrificans PD1222 4583615 YP_918811.1 CDS Pden_5055 NC_008688.1 566911 568026 R PFAM: ABC-2 type transporter; KEGG: mlo:mlr4596 ABC transporter, ATP-binding protein; ABC-2 type transporter complement(566911..568026) Paracoccus denitrificans PD1222 4583616 YP_918812.1 CDS Pden_5056 NC_008688.1 568023 568931 R PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: mlo:mlr4595 ATP-binding component of a transport system; ABC transporter related complement(568023..568931) Paracoccus denitrificans PD1222 4583617 YP_918813.1 CDS Pden_5057 NC_008688.1 568928 569869 R PFAM: secretion protein HlyD family protein; KEGG: bmb:BruAb2_0759 HlyD family secretion protein; secretion protein HlyD family protein complement(568928..569869) Paracoccus denitrificans PD1222 4583618 YP_918814.1 CDS Pden_5058 NC_008688.1 569862 570503 R PFAM: regulatory protein, TetR; KEGG: mes:Meso_4073 transcriptional regulator, TetR family; TetR family transcriptional regulator complement(569862..570503) Paracoccus denitrificans PD1222 4583619 YP_918815.1 CDS Pden_5059 NC_008688.1 570617 571534 R PFAM: PfkB domain protein; KEGG: sil:SPO2420 2-dehydro-3-deoxygluconokinase; ribokinase-like domain-containing protein complement(570617..571534) Paracoccus denitrificans PD1222 4583620 YP_918816.1 CDS Pden_5060 NC_008688.1 571531 572982 R PFAM: Mannitol dehydrogenase, C-terminal domain; Mannitol dehydrogenase rossman, N-terminal domain; KEGG: sil:SPO1724 D-mannonate oxidoreductase; mannitol dehydrogenase complement(571531..572982) Paracoccus denitrificans PD1222 4583621 YP_918817.1 CDS Pden_5061 NC_008688.1 572979 574187 R catalyzes the formation of 2-dehydro-3-deoxy-D-gluconate from mannonate; mannonate dehydratase complement(572979..574187) Paracoccus denitrificans PD1222 4583622 YP_918818.1 CDS Pden_5062 NC_008688.1 574206 575363 R PFAM: FMN-dependent alpha-hydroxy acid dehydrogenase; KEGG: pau:PA14_33860 L-lactate dehydrogenase; L-lactate dehydrogenase (cytochrome) complement(574206..575363) Paracoccus denitrificans PD1222 4583623 YP_918819.1 CDS Pden_5063 NC_008688.1 575368 576411 R PFAM: Alcohol dehydrogenase, zinc-binding domain protein; Alcohol dehydrogenase GroES domain protein; KEGG: sil:SPO2424 L-idonate 5-dehydrogenase; alcohol dehydrogenase complement(575368..576411) Paracoccus denitrificans PD1222 4583624 YP_918820.1 CDS Pden_5064 NC_008688.1 576413 577693 R 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 complement(576413..577693) Paracoccus denitrificans PD1222 4583625 YP_918821.1 CDS Pden_5065 NC_008688.1 577698 578204 R PFAM: Tripartite ATP-independent periplasmic transporter, DctQ component; KEGG: sil:SPO1720 TRAP dicarboxylate transporter, DctQ subunit; tripartite ATP-independent periplasmic transporter DctQ complement(577698..578204) Paracoccus denitrificans PD1222 4583626 YP_918822.1 CDS Pden_5066 NC_008688.1 578272 579252 R 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 complement(578272..579252) Paracoccus denitrificans PD1222 4583627 YP_918823.1 CDS Pden_5067 NC_008688.1 579277 579957 R PFAM: regulatory protein GntR, HTH; GntR domain protein; KEGG: sme:SMa0065 GntR-family transcriptional regulator; GntR family transcriptional regulator complement(579277..579957) Paracoccus denitrificans PD1222 4583628 YP_918824.1 CDS Pden_5068 NC_008688.1 580126 581079 R PFAM: regulatory protein, LysR; LysR, substrate-binding; KEGG: sme:SMc02596 transcription regulator protein; LysR family transcriptional regulator complement(580126..581079) Paracoccus denitrificans PD1222 4583629 YP_918825.1 CDS Pden_5069 NC_008688.1 581257 582414 D 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 581257..582414 Paracoccus denitrificans PD1222 4583630 YP_918826.1 CDS Pden_5070 NC_008688.1 582418 583371 R PFAM: helix-turn-helix- domain containing protein, AraC type; ThiJ/PfpI domain protein; KEGG: atc:AGR_pAT_bx241 hypothetical protein; AraC family transcriptional regulator complement(582418..583371) Paracoccus denitrificans PD1222 4583631 YP_918827.1 CDS Pden_5071 NC_008688.1 583458 584345 D PFAM: protein of unknown function DUF849; KEGG: atc:AGR_pAT_488 hypothetical protein; hypothetical protein 583458..584345 Paracoccus denitrificans PD1222 4583632 YP_918828.1 CDS Pden_5072 NC_008688.1 584405 585964 D PFAM: extracellular solute-binding protein, family 5; KEGG: atc:AGR_pAT_490 OphA, peptide transport system substrate-binding protein; extracellular solute-binding protein 584405..585964 Paracoccus denitrificans PD1222 4583633 YP_918829.1 CDS Pden_5073 NC_008688.1 585961 587415 D Converts (S)-3-hydroxyacyl-CoA to 3-oxyacyl-CoA; may also act as a thioesterase; bifunctional 3-hydroxyacyl-CoA dehydrogenase/thioesterase 585961..587415 Paracoccus denitrificans PD1222 4583634 YP_918830.1 CDS Pden_5074 NC_008688.1 587412 588389 D 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 587412..588389 Paracoccus denitrificans PD1222 4583635 YP_918831.1 CDS Pden_5075 NC_008688.1 588394 589212 D 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 588394..589212 Paracoccus denitrificans PD1222 4583636 YP_918832.1 CDS Pden_5076 NC_008688.1 589216 590832 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: atc:AGR_pAT_497 ABC transporter ATP-binding protein; ABC transporter related 589216..590832 Paracoccus denitrificans PD1222 4583637 YP_918833.1 CDS Pden_5077 NC_008688.1 590829 591707 D PFAM: Alpha/beta hydrolase fold-3 domain protein; KEGG: atc:AGR_pAT_499 hypothetical protein; alpha/beta hydrolase 590829..591707 Paracoccus denitrificans PD1222 4583638 YP_918834.1 CDS Pden_5078 NC_008688.1 591783 592796 D PFAM: regulatory protein, LacI; periplasmic binding protein/LacI transcriptional regulator; KEGG: sme:SMa0078 LacI-family transcriptional regulator; periplasmic binding protein/LacI transcriptional regulator 591783..592796 Paracoccus denitrificans PD1222 4583639 YP_918835.1 CDS Pden_5079 NC_008688.1 592864 593532 D 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 592864..593532 Paracoccus denitrificans PD1222 4583640 YP_918836.1 CDS Pden_5080 NC_008688.1 593534 594190 D 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 593534..594190 Paracoccus denitrificans PD1222 4583641 YP_918837.1 CDS Pden_5081 NC_008688.1 594227 595024 D PFAM: extracellular solute-binding protein, family 3; KEGG: sme:SMa0082 ABC transporter, periplasmic solute-binding protein; extracellular solute-binding protein 594227..595024 Paracoccus denitrificans PD1222 4583642 YP_918838.1 CDS Pden_5082 NC_008688.1 595077 595811 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sme:SMa0083 ABC transporter ATP-binding protein; ABC transporter related 595077..595811 Paracoccus denitrificans PD1222 4583643 YP_918839.1 CDS Pden_5083 NC_008688.1 595808 596752 D 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 595808..596752 Paracoccus denitrificans PD1222 4583644 YP_918840.1 CDS Pden_5084 NC_008688.1 596730 597665 D PFAM: PfkB domain protein; KEGG: psb:Psyr_2510 carbohydrate kinase, PfkB; ribokinase-like domain-containing protein 596730..597665 Paracoccus denitrificans PD1222 4583645 YP_918841.1 CDS Pden_5085 NC_008688.1 597662 598402 D KEGG: bte:BTH_II1322 hydratase/decarboxylase family protein; hydratase/decarboxylase family protein 597662..598402 Paracoccus denitrificans PD1222 4583646 YP_918842.1 CDS Pden_5086 NC_008688.1 598404 599519 R 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 complement(598404..599519) Paracoccus denitrificans PD1222 4583647 YP_918843.1 CDS Pden_5087 NC_008688.1 599659 601944 D catalyzes the conversion of salicylyl-CoA to gentisyl-CoA; salicylyl-CoA 5-hydroxylase 599659..601944 Paracoccus denitrificans PD1222 4583648 YP_918844.1 CDS Pden_5088 NC_008688.1 601941 602678 D PFAM: short-chain dehydrogenase/reductase SDR; KR; KEGG: mlo:mll5433 similar to granaticin polyketide ketoreductase; short-chain dehydrogenase/reductase SDR 601941..602678 Paracoccus denitrificans PD1222 4583649 YP_918845.1 CDS Pden_5089 NC_008688.1 602675 603112 D PFAM: regulatory protein, MarR; KEGG: mlo:mll5432 transcriptional regulator; MarR family transcriptional regulator 602675..603112 Paracoccus denitrificans PD1222 4583650 YP_918846.1 CDS Pden_5090 NC_008688.1 603109 603921 D Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA; enoyl-CoA hydratase 603109..603921 Paracoccus denitrificans PD1222 4583651 YP_918847.1 CDS Pden_5091 NC_008688.1 603925 605061 D PFAM: acyl-CoA dehydrogenase domain protein; Acyl-CoA dehydrogenase, type 2, C-terminal domain; KEGG: mlo:mll5430 acyl-CoA dehydrogenase; acyl-CoA dehydrogenase 603925..605061 Paracoccus denitrificans PD1222 4583652 YP_918848.1 CDS Pden_5092 NC_008688.1 605058 605477 D PFAM: thioesterase superfamily protein; KEGG: sil:SPO0786 thioesterase family protein; thioesterase superfamily protein 605058..605477 Paracoccus denitrificans PD1222 4583653 YP_918849.1 CDS Pden_5093 NC_008688.1 605467 605865 D PFAM: Endoribonuclease L-PSP; KEGG: mlo:mll5429 hypothetical protein; endoribonuclease L-PSP 605467..605865 Paracoccus denitrificans PD1222 4583654 YP_918850.1 CDS Pden_5094 NC_008688.1 605932 607572 D PFAM: AMP-dependent synthetase and ligase; KEGG: sil:SPOA0401 benzoate-coenzyme A ligase; AMP-dependent synthetase/ligase 605932..607572 Paracoccus denitrificans PD1222 4583655 YP_918851.1 CDS Pden_5095 NC_008688.1 607669 608814 D KEGG: rde:RD1_0540 ABC transporter substrate binding protei; ABC transporter substrate binding protei 607669..608814 Paracoccus denitrificans PD1222 4583656 YP_918852.1 CDS Pden_5096 NC_008688.1 608878 609789 D PFAM: inner-membrane translocator; KEGG: sit:TM1040_2236 inner-membrane translocator; inner-membrane translocator 608878..609789 Paracoccus denitrificans PD1222 4583657 YP_918853.1 CDS Pden_5097 NC_008688.1 609793 610785 D PFAM: inner-membrane translocator; KEGG: rde:RD1_0542 branched-chain amino acid ABC transporter, permease; inner-membrane translocator 609793..610785 Paracoccus denitrificans PD1222 4583658 YP_918854.1 CDS Pden_5098 NC_008688.1 610778 611542 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sit:TM1040_2234 ABC transporter related; ABC transporter related 610778..611542 Paracoccus denitrificans PD1222 4583659 YP_918855.1 CDS Pden_5099 NC_008688.1 611539 612228 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sit:TM1040_2233 ABC transporter related; ABC transporter related 611539..612228 Paracoccus denitrificans PD1222 4583660 YP_918856.1 CDS Pden_5100 NC_008688.1 612229 613047 D KEGG: bcn:Bcen_1215 esterase/lipase-like protein; esterase/lipase-like protein 612229..613047 Paracoccus denitrificans PD1222 4583661 YP_918857.1 CDS Pden_5101 NC_008688.1 613069 613356 R KEGG: sil:SPO0085 hypothetical protein; hypothetical protein complement(613069..613356) Paracoccus denitrificans PD1222 4583662 YP_918858.1 CDS Pden_5102 NC_008688.1 613437 616136 R 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 complement(613437..616136) Paracoccus denitrificans PD1222 4583663 YP_918859.1 CDS Pden_5103 NC_008688.1 616216 618018 R 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 complement(616216..618018) Paracoccus denitrificans PD1222 4583664 YP_918860.1 CDS Pden_5104 NC_008688.1 618213 618905 R PFAM: Surfeit locus 1 family protein; KEGG: sal:Sala_1504 surfeit locus 1; Surfeit locus 1 family protein complement(618213..618905) Paracoccus denitrificans PD1222 4583665 YP_918861.1 CDS Pden_5105 NC_008688.1 618902 619285 R PFAM: cytochrome C oxidase subunit IV; KEGG: ret:RHE_PE00027 cytochrome o ubiquinol oxidase, subunit IV protein; cytochrome C oxidase subunit IV complement(618902..619285) Paracoccus denitrificans PD1222 4583666 YP_918862.1 CDS Pden_5106 NC_008688.1 619285 619902 R PFAM: cytochrome c oxidase, subunit III; KEGG: rpb:RPB_0240 cytochrome c oxidase, subunit III; cytochrome c oxidase, subunit III complement(619285..619902) Paracoccus denitrificans PD1222 4583667 YP_918863.1 CDS Pden_5107 NC_008688.1 619906 621912 R PFAM: cytochrome c oxidase, subunit I; KEGG: sal:Sala_1507 cytochrome-c oxidase; cytochrome-c oxidase complement(619906..621912) Paracoccus denitrificans PD1222 4583668 YP_918864.1 CDS Pden_5108 NC_008688.1 621925 623127 R 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 complement(621925..623127) Paracoccus denitrificans PD1222 4583669 YP_918865.1 CDS Pden_5109 NC_008688.1 623349 624674 D PFAM: General substrate transporter; major facilitator superfamily MFS_1; KEGG: bja:bll0148 MFS permease; major facilitator transporter 623349..624674 Paracoccus denitrificans PD1222 4583670 YP_918866.1 CDS Pden_5110 NC_008688.1 624911 626368 D 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 624911..626368 Paracoccus denitrificans PD1222 4583671 YP_918867.1 CDS Pden_5111 NC_008688.1 626365 626610 D KEGG: rfr:Rfer_3780 hypothetical protein; hypothetical protein 626365..626610 Paracoccus denitrificans PD1222 4583672 YP_918868.1 CDS Pden_5112 NC_008688.1 626607 629312 D 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 626607..629312 Paracoccus denitrificans PD1222 4583673 YP_918869.1 CDS Pden_5113 NC_008688.1 629302 629667 D PFAM: response regulator receiver; KEGG: eba:ebA168 protein containing response regulator domain, but no DNA binding domain; response regulator receiver protein 629302..629667 Paracoccus denitrificans PD1222 4583674 YP_918870.1 CDS Pden_5114 NC_008688.1 629664 631784 D 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 629664..631784 Paracoccus denitrificans PD1222 4583675 YP_918871.1 CDS Pden_5115 NC_008688.1 631818 633980 R KEGG: rsp:RSP_1753 hypothetical protein; hypothetical protein complement(631818..633980) Paracoccus denitrificans PD1222 4583676 YP_918872.1 CDS Pden_5116 NC_008688.1 634258 635226 R TIGRFAM: agmatinase; PFAM: Arginase/agmatinase/formiminoglutamase; KEGG: pfl:PFL_0325 agmatinase; agmatinase complement(634258..635226) Paracoccus denitrificans PD1222 4583677 YP_918873.1 CDS Pden_5117 NC_008688.1 635564 636178 D PFAM: protein of unknown function DUF1234; KEGG: rsp:RSP_3119 conserved hypothetical protein / esterase; hypothetical protein 635564..636178 Paracoccus denitrificans PD1222 4583678 YP_918874.1 CDS Pden_5118 NC_008688.1 636385 637719 D KEGG: rsp:RSP_3118 hypothetical protein; hypothetical protein 636385..637719 Paracoccus denitrificans PD1222 4583679 YP_918875.1 CDS Pden_5119 NC_008688.1 637973 638530 D PFAM: NAD(P)H dehydrogenase (quinone); NADPH-dependent FMN reductase; KEGG: mlo:mlr5227 NADH-dependent FMN reductase MsuE; NADPH-dependent FMN reductase 637973..638530 Paracoccus denitrificans PD1222 4583680 YP_918876.1 CDS Pden_5120 NC_008688.1 638626 638979 R hypothetical protein complement(638626..638979) Paracoccus denitrificans PD1222 4583681 YP_918877.1 CDS Pden_5121 NC_008688.1 638963 639214 R hypothetical protein complement(638963..639214) Paracoccus denitrificans PD1222 4583682 YP_918878.1 CDS Pden_5122 NC_008688.1 639347 639820 D PFAM: regulatory protein, AsnC/Lrp family; KEGG: bja:blr8125 transcriptional regulatory protein; AsnC family transcriptional regulator 639347..639820 Paracoccus denitrificans PD1222 4583683 YP_918879.1 CDS Pden_5123 NC_008688.1 639969 640247 R hypothetical protein complement(639969..640247) Paracoccus denitrificans PD1222 4583684 YP_918880.1 CDS Pden_5124 NC_008688.1 640248 640676 D hypothetical protein 640248..640676 Paracoccus denitrificans PD1222 4583685 YP_918881.1 CDS Pden_5125 NC_008688.1 640801 642153 D KEGG: ret:RHE_PC00169 probable monooxygenase; monooxygenase 640801..642153 Paracoccus denitrificans PD1222 4583686 YP_918882.1 CDS Pden_5126 NC_008688.1 642158 643000 D 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 642158..643000 Paracoccus denitrificans PD1222 4583687 YP_918883.1 CDS Pden_5127 NC_008688.1 643025 644002 D KEGG: ret:RHE_PC00167 probable aliphatic sulphonate ABC transporter, substrate-binding protein; Fis family transcriptional regulator 643025..644002 Paracoccus denitrificans PD1222 4583688 YP_918884.1 CDS Pden_5128 NC_008688.1 644002 644772 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sme:SMb20569 ABC transporter ATP-binding protein; ABC transporter related 644002..644772 Paracoccus denitrificans PD1222 4583689 YP_918885.1 CDS Pden_5129 NC_008688.1 645014 645514 D 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 645014..645514 Paracoccus denitrificans PD1222 4583690 YP_918886.1 CDS Pden_5130 NC_008688.1 645516 646472 D PFAM: FecR protein; KEGG: neu:NE1070 transmembrane sensor; FecR 645516..646472 Paracoccus denitrificans PD1222 4583691 YP_918887.1 CDS Pden_5131 NC_008688.1 646603 649128 D 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 646603..649128 Paracoccus denitrificans PD1222 4583692 YP_918888.1 CDS Pden_5132 NC_008688.1 649292 650629 D TIGRFAM: efflux transporter, RND family, MFP subunit; KEGG: nwi:Nwi_2042 secretion protein HlyD; RND family efflux transporter MFP subunit 649292..650629 Paracoccus denitrificans PD1222 4583693 YP_918889.1 CDS Pden_5133 NC_008688.1 650650 652572 D PFAM: ABC transporter related; protein of unknown function DUF214; SMART: AAA ATPase; KEGG: nwi:Nwi_2041 ABC transporter, ATPase subunit; ABC transporter 650650..652572 Paracoccus denitrificans PD1222 4583694 YP_918890.1 CDS Pden_5134 NC_008688.1 652635 653789 D KEGG: ssn:SSO_1681 receptor; hypothetical protein 652635..653789 Paracoccus denitrificans PD1222 4583695 Pden_R0001 tRNA Pden_R0001 NC_008686.1 48588 48662 R tRNA-Val complement(48588..48662) Paracoccus denitrificans PD1222 4581164 Pden_R0003 tRNA Pden_R0003 NC_008686.1 60071 60147 D tRNA-Ile 60071..60147 Paracoccus denitrificans PD1222 4581166 Pden_R0004 tRNA Pden_R0004 NC_008686.1 60210 60285 D tRNA-Ala 60210..60285 Paracoccus denitrificans PD1222 4581167 Pden_R0007 tRNA Pden_R0007 NC_008686.1 63740 63816 D tRNA-Met 63740..63816 Paracoccus denitrificans PD1222 4581170 Pden_R0008 tRNA Pden_R0008 NC_008686.1 361057 361146 D tRNA-Ser 361057..361146 Paracoccus denitrificans PD1222 4581172 Pden_R0009 tRNA Pden_R0009 NC_008686.1 364942 365017 R tRNA-Lys complement(364942..365017) Paracoccus denitrificans PD1222 4581173 Pden_R0010 tRNA Pden_R0010 NC_008686.1 411262 411338 D tRNA-Pro 411262..411338 Paracoccus denitrificans PD1222 4581174 Pden_R0011 tRNA Pden_R0011 NC_008686.1 466890 466974 D tRNA-Leu 466890..466974 Paracoccus denitrificans PD1222 4581177 Pden_R0012 tRNA Pden_R0012 NC_008686.1 506103 506176 R tRNA-Gly complement(506103..506176) Paracoccus denitrificans PD1222 4581178 Pden_R0013 tRNA Pden_R0013 NC_008686.1 722941 723016 D tRNA-Trp 722941..723016 Paracoccus denitrificans PD1222 4581179 Pden_R0014 tRNA Pden_R0014 NC_008686.1 848876 848952 D tRNA-Pro 848876..848952 Paracoccus denitrificans PD1222 4581180 Pden_R0015 tRNA Pden_R0015 NC_008686.1 857717 857793 R tRNA-Arg complement(857717..857793) Paracoccus denitrificans PD1222 4581181 Pden_R0016 tRNA Pden_R0016 NC_008686.1 894322 894398 D tRNA-Met 894322..894398 Paracoccus denitrificans PD1222 4581182 Pden_R0017 tRNA Pden_R0017 NC_008686.1 948593 948682 D tRNA-Ser 948593..948682 Paracoccus denitrificans PD1222 4581183 Pden_R0018 tRNA Pden_R0018 NC_008686.1 1178499 1178575 D tRNA-Asp 1178499..1178575 Paracoccus denitrificans PD1222 4581186 Pden_R0019 tRNA Pden_R0019 NC_008686.1 1195017 1195091 R tRNA-Gln complement(1195017..1195091) Paracoccus denitrificans PD1222 4581187 Pden_R0020 tRNA Pden_R0020 NC_008686.1 1274404 1274493 R tRNA-Ser complement(1274404..1274493) Paracoccus denitrificans PD1222 4580651 Pden_R0021 tRNA Pden_R0021 NC_008686.1 1343520 1343603 R tRNA-Leu complement(1343520..1343603) Paracoccus denitrificans PD1222 4580654 Pden_R0022 tRNA Pden_R0022 NC_008686.1 1523471 1523547 R tRNA-His complement(1523471..1523547) Paracoccus denitrificans PD1222 4580656 Pden_R0023 tRNA Pden_R0023 NC_008686.1 1565680 1565769 D tRNA-Ser 1565680..1565769 Paracoccus denitrificans PD1222 4580657 Pden_R0024 tRNA Pden_R0024 NC_008686.1 1725856 1725931 D tRNA-Ala 1725856..1725931 Paracoccus denitrificans PD1222 4580661 Pden_R0026 tRNA Pden_R0026 NC_008686.1 1761801 1761875 D tRNA-Asn 1761801..1761875 Paracoccus denitrificans PD1222 4580663 Pden_R0027 tRNA Pden_R0027 NC_008686.1 1769711 1769785 R tRNA-Glu complement(1769711..1769785) Paracoccus denitrificans PD1222 4580664 Pden_R0028 tRNA Pden_R0028 NC_008686.1 1771692 1771765 R tRNA-Gly complement(1771692..1771765) Paracoccus denitrificans PD1222 4580665 Pden_R0029 tRNA Pden_R0029 NC_008686.1 1786959 1787034 D tRNA-Phe 1786959..1787034 Paracoccus denitrificans PD1222 4580666 Pden_R0030 tRNA Pden_R0030 NC_008686.1 1788974 1789050 R tRNA-Arg complement(1788974..1789050) Paracoccus denitrificans PD1222 4580667 Pden_R0032 tRNA Pden_R0032 NC_008686.1 1863668 1863745 D tRNA-Pro 1863668..1863745 Paracoccus denitrificans PD1222 4580669 Pden_R0033 tRNA Pden_R0033 NC_008686.1 1879838 1879912 D tRNA-Glu 1879838..1879912 Paracoccus denitrificans PD1222 4580672 Pden_R0034 tRNA Pden_R0034 NC_008686.1 1907794 1907870 R tRNA-Asp complement(1907794..1907870) Paracoccus denitrificans PD1222 4580673 Pden_R0035 tRNA Pden_R0035 NC_008686.1 1907899 1907975 R tRNA-Asp complement(1907899..1907975) Paracoccus denitrificans PD1222 4580674 Pden_R0036 tRNA Pden_R0036 NC_008686.1 1931540 1931626 R tRNA-Leu complement(1931540..1931626) Paracoccus denitrificans PD1222 4580676 Pden_R0037 tRNA Pden_R0037 NC_008686.1 1965201 1965275 D tRNA-Thr 1965201..1965275 Paracoccus denitrificans PD1222 4580678 Pden_R0038 tRNA Pden_R0038 NC_008686.1 1974456 1974532 R tRNA-Met complement(1974456..1974532) Paracoccus denitrificans PD1222 4580679 Pden_R0041 tRNA Pden_R0041 NC_008686.1 1977987 1978062 R tRNA-Ala complement(1977987..1978062) Paracoccus denitrificans PD1222 4580682 Pden_R0042 tRNA Pden_R0042 NC_008686.1 1978125 1978201 R tRNA-Ile complement(1978125..1978201) Paracoccus denitrificans PD1222 4579131 Pden_R0044 tRNA Pden_R0044 NC_008686.1 1982093 1982169 R tRNA-Arg complement(1982093..1982169) Paracoccus denitrificans PD1222 4579133 Pden_R0045 tRNA Pden_R0045 NC_008686.1 2000687 2000762 R tRNA-Thr complement(2000687..2000762) Paracoccus denitrificans PD1222 4579134 Pden_R0046 tRNA Pden_R0046 NC_008686.1 2057161 2057246 D tRNA-Leu 2057161..2057246 Paracoccus denitrificans PD1222 4579135 Pden_R0047 tRNA Pden_R0047 NC_008686.1 2281331 2281406 R tRNA-Met complement(2281331..2281406) Paracoccus denitrificans PD1222 4579136 Pden_R0048 tRNA Pden_R0048 NC_008686.1 2341732 2341807 R tRNA-Ala complement(2341732..2341807) Paracoccus denitrificans PD1222 4579137 Pden_R0049 tRNA Pden_R0049 NC_008686.1 2387713 2387787 D tRNA-Gly 2387713..2387787 Paracoccus denitrificans PD1222 4579139 Pden_R0050 tRNA Pden_R0050 NC_008686.1 2423242 2423315 D tRNA-Cys 2423242..2423315 Paracoccus denitrificans PD1222 4579140 Pden_R0051 tRNA Pden_R0051 NC_008686.1 2841537 2841628 R tRNA-Sec complement(2841537..2841628) Paracoccus denitrificans PD1222 4579145 Pden_R0002 rRNA Pden_R0002 NC_008686.1 58447 59902 D 16S ribosomal RNA 58447..59902 Paracoccus denitrificans PD1222 4581165 Pden_R0005 rRNA Pden_R0005 NC_008686.1 60609 63451 D 23S ribosomal RNA 60609..63451 Paracoccus denitrificans PD1222 4581168 Pden_R0006 rRNA Pden_R0006 NC_008686.1 63561 63682 D 5S ribosomal RNA 63561..63682 Paracoccus denitrificans PD1222 4581169 Pden_R0039 rRNA Pden_R0039 NC_008686.1 1974590 1974711 R 5S ribosomal RNA complement(1974590..1974711) Paracoccus denitrificans PD1222 4580680 Pden_R0040 rRNA Pden_R0040 NC_008686.1 1974821 1977663 R 23S ribosomal RNA complement(1974821..1977663) Paracoccus denitrificans PD1222 4580681 Pden_R0043 rRNA Pden_R0043 NC_008686.1 1978370 1979825 R 16S ribosomal RNA complement(1978370..1979825) Paracoccus denitrificans PD1222 4579132 Pden_r1 rRNA Pden_r1 NC_008687.1 141979 143453 D 16S ribosomal RNA 141979..143453 Paracoccus denitrificans PD1222 4794292 Pden_r2 rRNA Pden_r2 NC_008687.1 144166 146983 D 23S ribosomal RNA 144166..146983 Paracoccus denitrificans PD1222 4794290 Pden_r3 rRNA Pden_r3 NC_008687.1 147102 147223 D 5S ribosomal RNA 147102..147223 Paracoccus denitrificans PD1222 4794291