-- dump date 20140619_065654 -- 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 398580000001 SEQ_END SEQ_END NC_009952.1 3789584 3789584 DR NC_009952.1; contig end 3789584..3789584 Dinoroseobacter shibae DFL 12 = DSM 16493 398580000002 SEQ_END SEQ_END NC_009955.1 190506 190506 DR NC_009955.1; contig end 190506..190506 Dinoroseobacter shibae DFL 12 = DSM 16493 398580000003 SEQ_END SEQ_END NC_009956.1 152970 152970 DR NC_009956.1; contig end 152970..152970 Dinoroseobacter shibae DFL 12 = DSM 16493 398580000004 SEQ_END SEQ_END NC_009957.1 126304 126304 DR NC_009957.1; contig end 126304..126304 Dinoroseobacter shibae DFL 12 = DSM 16493 398580000005 SEQ_END SEQ_END NC_009958.1 86208 86208 DR NC_009958.1; contig end 86208..86208 Dinoroseobacter shibae DFL 12 = DSM 16493 398580000006 SEQ_END SEQ_END NC_009959.1 72296 72296 DR NC_009959.1; contig end 72296..72296 Dinoroseobacter shibae DFL 12 = DSM 16493 YP_001531351.1 CDS gltD NC_009952.1 128 1567 D function undetermined; similar to glutamate synthase beta subunit and related oxidoreductases which transfer electrons from NADPH to an acceptor protein or protein domain; putative oxidoreductase 128..1567 Dinoroseobacter shibae DFL 12 = DSM 16493 5713708 YP_001531352.1 CDS gltB NC_009952.1 1782 6320 D PFAM: glutamine amidotransferase class-II; glutamate synthase alpha subunit domain protein; ferredoxin-dependent glutamate synthase; glutamate synthase KEGG: sit:TM1040_2823 glutamate synthase (ferredoxin), involved in nitrogen metabolism PATH: rn00910; glutamate synthase 1782..6320 Dinoroseobacter shibae DFL 12 = DSM 16493 5711754 YP_001531354.1 CDS Dshi_0004 NC_009952.1 7257 8114 R PFAM: conserved hypothetical protein KEGG: sil:SPO3342 decarboxylase family protein, Homologous Superfamily (CATH Code: 3.40.50.80), Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module; hypothetical protein complement(7257..8114) Dinoroseobacter shibae DFL 12 = DSM 16493 5711756 YP_001531355.1 CDS Dshi_0005 NC_009952.1 8220 8924 D interPro: short signalpeptide N-terminal, bad swissprot hit to Sterol 3-beta-glucosyltransferase from Candida albicans and bad Ref NP hit to 4-alpha-glucanotransferase from Fusobacterium nucleatum subsp. nucleatum ATCC 25586; hypothetical protein 8220..8924 Dinoroseobacter shibae DFL 12 = DSM 16493 5711757 YP_001531356.1 CDS dapD NC_009952.1 9028 9855 D 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 9028..9855 Dinoroseobacter shibae DFL 12 = DSM 16493 5711758 YP_001531358.1 CDS Dshi_0008 NC_009952.1 10683 11255 D bad swissprot to LPS-assembly protein precursor (Organic solvent tolerance protein) from Pseudomonas aeruginosa UCBPP-PA14 and bad ref ZP hit to putative chemotaxis protein from Erythrobacter sp. NAP1, short signalpeptide and transmembranedomain, conserved domain: Guanylate kinase/L-type calcium channel region (Active enzymes catalyze ATP-dependent phosphorylation of GMP to GDP); hypothetical protein 10683..11255 Dinoroseobacter shibae DFL 12 = DSM 16493 5711760 YP_001531359.1 CDS csp2 NC_009952.1 11747 11953 R PFAM: Cold-shock protein DNA-binding SMART: Cold shock protein KEGG: rde:RD1_1402 cold shock protein CspA-related protein, putative; cold-shock DNA-binding domain-containing protein complement(11747..11953) Dinoroseobacter shibae DFL 12 = DSM 16493 5711761 YP_001531360.1 CDS Dshi_0010 NC_009952.1 12121 12642 R PFAM: protein of unknown function DUF305 KEGG: psa:PST_3374 hypothetical protein, conserved in bacteria; hypothetical protein complement(12121..12642) Dinoroseobacter shibae DFL 12 = DSM 16493 5711588 YP_001531361.1 CDS Dshi_0011 NC_009952.1 12777 13124 D KEGG: rsq:Rsph17025_0047 hypothetical protein, bad swissprot hit to Multiple PDZ domain protein from rattus norvegicus involved in cell junction/cell projection; Immunoglobulin V-Type, subgroup domain (Eukaryota) from T cell surface glycoproteins, junction adhesion molecules , cell surface presentation?; hypothetical protein 12777..13124 Dinoroseobacter shibae DFL 12 = DSM 16493 5711589 YP_001531362.1 CDS dapE1 NC_009952.1 13129 14268 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 13129..14268 Dinoroseobacter shibae DFL 12 = DSM 16493 5711590 YP_001531363.1 CDS elaA NC_009952.1 14265 14693 D PFAM: GCN5-related N-acetyltransferase KEGG: rsh:Rsph17029_2788 GCN5-related N-acetyltransferase; N-acetyltransferase GCN5 14265..14693 Dinoroseobacter shibae DFL 12 = DSM 16493 5711591 YP_001531364.1 CDS Dshi_0014 NC_009952.1 14693 15271 D KEGG: sil:SPO3331 hypothetical protein, Uncharacterized protein conserved in bacteria COG3222, bad swissprot hit to Carboxylesterase bioH (Biotin synthesis protein bioH) from Escherichia coli, Also displays a weak thioesterase activity. Can form a complex with CoA, and may be involved in the condensation of CoA and pimelic acid into pimeloyl-CoA; hypothetical protein 14693..15271 Dinoroseobacter shibae DFL 12 = DSM 16493 5711592 YP_001531365.1 CDS rnr NC_009952.1 15472 17727 D KEGG: sit:TM1040_2994 ribonuclease R TIGRFAM: VacB and RNase II family 3-5 exoribonuclease; ribonuclease R PFAM: ribonuclease II; RNA binding S1 domain protein, high sw hit to Ribonuclease R (RNase R) (VacB protein homolog) from Haemophilus influenzae; ribonuclease R 15472..17727 Dinoroseobacter shibae DFL 12 = DSM 16493 5711593 YP_001531366.1 CDS mltB2 NC_009952.1 18179 19426 D TIGRFAM: lytic murein transglycosylase PFAM: Peptidoglycan-binding domain 1 protein KEGG: rde:RD1_0181 transglycosylase, putative, good sw hit to Membrane-bound lytic murein transglycosylase B precursor from E. coli; lytic murein transglycosylase 18179..19426 Dinoroseobacter shibae DFL 12 = DSM 16493 5711594 YP_001531367.1 CDS Dshi_0017 NC_009952.1 19516 20166 R KEGG: jan:Jann_0593 hypothetical protein, one single bad swissprot hit to ATP synthase protein 8 (ATPase subunit 8) from mitochondrion Artemia franciscana, short signalpeptide and transmembrane domains, uDENN Domain: found in a variety of signalling proteins, is a good candidate for a GTP/GDP exchange activity; hypothetical protein complement(19516..20166) Dinoroseobacter shibae DFL 12 = DSM 16493 5711595 YP_001531368.1 CDS Dshi_0018 NC_009952.1 20326 22629 R PFAM: multicopper oxidase type 2 KEGG: hch:HCH_03584 putative multicopper oxidases, diverse cupredoxin and multicopper oxidase 1-3 domains, bad swissprot hit to Blue copper oxidase cueO precursor (Copper efflux oxidase) from Escherichia coli O157:H7, Copper resistance protein A (copA) from a plasmid in Pseudomonas syringae. This protein seems to be involved in the resistance of the microbial host to copper; multicopper oxidase complement(20326..22629) Dinoroseobacter shibae DFL 12 = DSM 16493 5711596 YP_001531369.1 CDS Dshi_0019 NC_009952.1 22866 24683 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: rde:RD1_2707 GTP-binding protein TypA, putative, high swissprot hit to GTP-binding protein TypA/BipA homolog from Helicobacter pylori, diverse translation and elongation factor domains; GTP-binding protein TypA 22866..24683 Dinoroseobacter shibae DFL 12 = DSM 16493 5711597 YP_001531370.1 CDS Dshi_0020 NC_009952.1 25297 26019 R KEGG: sil:SPO3454 hypothetical protein, no significant swissprot hit, next good Ref YP hit to putative transcriptional regulator, CadC from Silicibacter sp. TM1040, three domains to trans_reg_C, Effector domain of response regulator, CadC, DNA-binding winged-HTH domains and OmpR, Response regulators consisting of a CheY-like receiver domain; CadC; putative transcriptional regulator complement(25297..26019) Dinoroseobacter shibae DFL 12 = DSM 16493 5711598 YP_001531371.1 CDS Dshi_0021 NC_009952.1 25973 26377 R KEGG: rsp:RSP_6002 hypothetical protein, one single transmembrane domain; hypothetical protein complement(25973..26377) Dinoroseobacter shibae DFL 12 = DSM 16493 5711643 YP_001531372.1 CDS Dshi_0022 NC_009952.1 26400 26954 D no swissprot hit, next ref ZP hit to hypothetical protein RB2150_13021 from Rhodobacterales bacterium HTCC2150, short signalpeptide and two transmembrane regions, NO hit to Sodium/hydrogen exchanger family Pfam00999; hypothetical protein 26400..26954 Dinoroseobacter shibae DFL 12 = DSM 16493 5711644 YP_001531373.1 CDS rnhB NC_009952.1 26998 27618 D RNH2; RNase HII; binds manganese; endonuclease which specifically degrades the RNA of RNA-DNA hybrids; ribonuclease HII 26998..27618 Dinoroseobacter shibae DFL 12 = DSM 16493 5711645 YP_001531374.1 CDS dam NC_009952.1 27713 28819 D PFAM: DNA methylase N-4/N-6 domain protein KEGG: rsq:Rsph17025_0066 DNA methylase N-4/N-6 domain protein, high swissprot hit to Modification methylase CcrMI (Adenine-specific methyltransferase CcrMI from Caulobacter vibrioides (Caulobacter crescentus); adenine-specific methyltransferase 27713..28819 Dinoroseobacter shibae DFL 12 = DSM 16493 5711646 YP_001531375.1 CDS chrR2 NC_009952.1 29143 29814 D KEGG: abo:ABO_0664 hypothetical protein, Cupin, RmlC-type domain, best swissprot hit to Transcriptional activator chrR from Rhodobacter sphaeroides 2.4.1 and high similarity to Predicted transcription negative regulator (refZP hit) from Roseovarius sp. 217; transcriptional activator anti-ECFsigma factor 29143..29814 Dinoroseobacter shibae DFL 12 = DSM 16493 5711647 YP_001531376.1 CDS Dshi_0026 NC_009952.1 29888 30529 D KEGG: jan:Jann_0393 NAD-dependent epimerase/dehydratase, best swissprot hit to Flavin reductase (FR) (NADPH-dependent diaphorase) from Mus musculus; NAD-dependent epimerase/dehydratase 29888..30529 Dinoroseobacter shibae DFL 12 = DSM 16493 5711648 YP_001531377.1 CDS alkB1 NC_009952.1 30653 31807 R PFAM: fatty acid desaturase KEGG: sit:TM1040_2646 alkane-1 monooxygenase, good swissprot hit to Alkane 1-monooxygenase (Alkane omega-hydroxylase) from Pseudomonas oleovorans, also fatty acid desaturase typ 1 domain Pfam00487; alkane 1-monooxygenase complement(30653..31807) Dinoroseobacter shibae DFL 12 = DSM 16493 5711649 YP_001531378.1 CDS mutY NC_009952.1 31815 32909 R TIGRFAM: A/G-specific adenine glycosylase PFAM: helix-hairpin-helix motif; HhH-GPD family protein KEGG: sit:TM1040_2645 A/G-specific adenine glycosylase, swissprot to A/G-specific adenine glycosylase from Escherichia coli; A/G-specific adenine glycosylase complement(31815..32909) Dinoroseobacter shibae DFL 12 = DSM 16493 5711650 YP_001531379.1 CDS Dshi_0029 NC_009952.1 32995 33507 D PFAM: protein of unknown function DUF1159 KEGG: sit:TM1040_2644 protein of unknown function DUF1159; hypothetical protein 32995..33507 Dinoroseobacter shibae DFL 12 = DSM 16493 5711651 YP_001531380.1 CDS dsbA1 NC_009952.1 33519 34190 D KEGG: rde:RD1_0295 thiol-disulfide oxidoreductase D, putative, swissprot hit to Putative protein-disulfide oxidoreductase RBE_1288 precursor from Rickettsia bellii RML369-C, conserved domains: dsbA: a monomeric thiol disulfide oxidoreductase protein and dsbG: Protein-disulfide isomerase; putative thiol-disulfide oxidoreductase D 33519..34190 Dinoroseobacter shibae DFL 12 = DSM 16493 5711652 YP_001531381.1 CDS lpxK NC_009952.1 34226 35239 R 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 complement(34226..35239) Dinoroseobacter shibae DFL 12 = DSM 16493 5711653 YP_001531382.1 CDS kdtA NC_009952.1 35239 36555 R PFAM: Three-deoxy-D-manno-octulosonic-acid transferase domain protein KEGG: jan:Jann_0400 three-deoxy-D-manno-octulosonic-acid transferase-like; three-deoxy-D-manno-octulosonic-acid transferase domain-containing protein complement(35239..36555) Dinoroseobacter shibae DFL 12 = DSM 16493 5711654 YP_001531383.1 CDS Dshi_0033 NC_009952.1 36716 36907 R PFAM: protein of unknown function DUF343 KEGG: sit:TM1040_0056 protein of unknown function DUF343, DUF343 domain: Trm112p-like protein, The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length. The C terminus contains the strongest conservation. Trm112p is required for tRNA methylation n S. cerevisiae and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W.; hypothetical protein complement(36716..36907) Dinoroseobacter shibae DFL 12 = DSM 16493 5711655 YP_001531384.1 CDS Dshi_0034 NC_009952.1 36904 37551 R PFAM: peptidase S16 lon domain protein KEGG: rsq:Rsph17025_2895 peptidase S16, lon domain protein, swissprot hit to ATP-dependent protease La 2 from Myxococcus xanthus, COG2802: Uncharacterized protein, similar to the N-terminal domain of Lon protease and LON-domains; ATP-dependent protease La complement(36904..37551) Dinoroseobacter shibae DFL 12 = DSM 16493 5711656 YP_001531385.1 CDS trxA2 NC_009952.1 37578 38489 R PFAM: Thioredoxin domain KEGG: rsp:RSP_1489 protein containing thioredoxin domain, swissprot hit to Thioredoxin (TRX) from Pasteurella multocida; thioredoxin domain-containing protein complement(37578..38489) Dinoroseobacter shibae DFL 12 = DSM 16493 5711657 YP_001531386.1 CDS xthA NC_009952.1 38563 39351 R TIGRFAM: exodeoxyribonuclease III Xth PFAM: Endonuclease/exonuclease/phosphatase KEGG: sit:TM1040_0053 exodeoxyribonuclease III, best swissprot hit to Exodeoxyribonuclease III (Exonuclease III) from Escherichia coli; exodeoxyribonuclease III complement(38563..39351) Dinoroseobacter shibae DFL 12 = DSM 16493 5711658 YP_001531387.1 CDS Dshi_0037 NC_009952.1 39692 40216 D unsure, bad GC frame plot, no significant Ref hits; some kind of LPxTG anchor domains detected by TIGRfam, but unconvincing; some leucine repeats at C-terminal; hypothetical protein 39692..40216 Dinoroseobacter shibae DFL 12 = DSM 16493 5711659 YP_001531388.1 CDS Dshi_0038 NC_009952.1 40432 41118 R PFAM: response regulator receiver; transcriptional regulator domain protein KEGG: jan:Jann_0417 two component transcriptional regulator, winged helix family, Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain, best swissprot hit to Transcriptional regulatory protein yycF from Bacillus subtilis; winged helix family; two component transcriptional regulator complement(40432..41118) Dinoroseobacter shibae DFL 12 = DSM 16493 5711660 YP_001531389.1 CDS ribA NC_009952.1 41277 42347 D PFAM: GTP cyclohydrolase II KEGG: sil:SPO3427 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II; GTP cyclohydrolase II 41277..42347 Dinoroseobacter shibae DFL 12 = DSM 16493 5711661 YP_001531390.1 CDS Dshi_0040 NC_009952.1 42375 42662 D PFAM: protein of unknown function DUF1330 KEGG: sit:TM1040_1707 protein of unknown function DUF1330, no significant swissprot hit, best ref ZP hit to hypothetical protein OM2255_07195 from alpha proteobacterium HTCC2255; hypothetical protein 42375..42662 Dinoroseobacter shibae DFL 12 = DSM 16493 5711662 YP_001531391.1 CDS Dshi_0041 NC_009952.1 42669 43163 D KEGG: rde:RD1_0044 hypothetical protein, no significant swissprot hit, conserved domain found in several roseobacter function unknown; hypothetical protein 42669..43163 Dinoroseobacter shibae DFL 12 = DSM 16493 5711663 YP_001531392.1 CDS Dshi_0042 NC_009952.1 43160 43816 R PFAM: alanine racemase domain protein KEGG: jan:Jann_0414 protein of unknown function UPF0001, swissprot hit to UPF0001 protein yggS from E. coli O6 related to PLP dependent enzymes class III; alanine racemase domain-containing protein complement(43160..43816) Dinoroseobacter shibae DFL 12 = DSM 16493 5711664 YP_001531393.1 CDS Dshi_0043 NC_009952.1 43903 44862 R swissprot hit to porin from Rhodobacter capsulatus and high ref ZP hit to putative porin from D. shibae DshiDRAFT_2133 which doesnt exist in the finished sequence and to outer membrane porin, putative from Roseobacter sp. CCS2, also conserved domain to porin, Gram-negative type (interPro); Gram-negative type; porin complement(43903..44862) Dinoroseobacter shibae DFL 12 = DSM 16493 5711665 YP_001531394.1 CDS Dshi_0044 NC_009952.1 45163 45633 D KEGG: rsq:Rsph17025_3134 hypothetical protein; hypothetical protein 45163..45633 Dinoroseobacter shibae DFL 12 = DSM 16493 5711666 YP_001531395.1 CDS Dshi_0045 NC_009952.1 45640 46014 R bad BLAST hits to hypothetical proteins, no significant swissprot hit, no domains detected by TIGRfam (no UspA domain); hypothetical protein complement(45640..46014) Dinoroseobacter shibae DFL 12 = DSM 16493 5711667 YP_001531396.1 CDS Dshi_0046 NC_009952.1 46315 46704 D no Interpro hits reported, unsure, bad GC frame plot, bad ref ZP hits to hypothetical protein ROS217_08770 from Roseovarius sp. 217; hypothetical protein 46315..46704 Dinoroseobacter shibae DFL 12 = DSM 16493 5711668 YP_001531397.1 CDS Dshi_0047 NC_009952.1 46984 47406 R no Interpro hits reported, unsure, bad GC frame plot, bad ref XP hits to hypothetical protein MGG_12456 from Magnaporthe grisea 70-15 (Fungi); hypothetical protein complement(46984..47406) Dinoroseobacter shibae DFL 12 = DSM 16493 5711669 YP_001531398.1 CDS Dshi_0048 NC_009952.1 47483 48445 R KEGG: rpc:RPC_0725 putative transposase, good ref ZP hit to possible transposase from Roseovarius sp. 217, InterPro:several Zinc finger domains (DNA binding?); putative transposase complement(47483..48445) Dinoroseobacter shibae DFL 12 = DSM 16493 5711670 YP_001531399.1 CDS Dshi_0049 NC_009952.1 48547 48753 D KEGG: har:HEAR2212 hypothetical protein, no InterPro hit, no good swissprot hit, Ref ZP hit to hypothetical protein ROS217_08790 fromRoseovarius sp. 217, next Ref ZP hit to GMP synthase, PP-ATPase domain/subunit from Magnetospirillum magnetotacticum MS-1; hypothetical protein 48547..48753 Dinoroseobacter shibae DFL 12 = DSM 16493 5711671 YP_001531400.1 CDS Dshi_0050 NC_009952.1 48750 49232 R PFAM: protein of unknown function DUF955 KEGG: mag:amb3753 predicted Zn peptidase, no significant swissprot hit, good ref Yp hit to Predicted Zn peptidase from Magnetospirillum magneticum AMB-1, DUF955 domain shows similarity to Peptidase_M48; hypothetical protein complement(48750..49232) Dinoroseobacter shibae DFL 12 = DSM 16493 5711672 YP_001531401.1 CDS Dshi_0051 NC_009952.1 49229 49645 R no significant BLAST hits, short signal peptide and two transmembrane regions, bad GC frame plot; hypothetical protein complement(49229..49645) Dinoroseobacter shibae DFL 12 = DSM 16493 5711673 YP_001531402.1 CDS Dshi_0052 NC_009952.1 49656 49868 R no hits reported for InterPro Scan, BLAST hits similar to several hypothetical proteins in Roseobacter strains, bad GC frame plot; hypothetical protein complement(49656..49868) Dinoroseobacter shibae DFL 12 = DSM 16493 5711674 YP_001531403.1 CDS Dshi_0053 NC_009952.1 49943 51163 D PFAM: HI0933 family protein; FAD-dependent pyridine nucleotide-disulphide oxidoreductase KEGG: sil:SPO3436 hypothetical protein, best ref ZP hit to hypothetical protein ISM_02290 from Roseovarius nubinhibens ISM: related to COG2081 Predicted flavoproteins, HI0933 like domain: This is a family of conserved hypothetical proteins that may include proteins with a dinucleotide-binding motif (Rossman fold), including oxidoreductases and dehydrogenases; hypothetical protein 49943..51163 Dinoroseobacter shibae DFL 12 = DSM 16493 5711675 YP_001531404.1 CDS gst2 NC_009952.1 51142 51732 R PFAM: Glutathione S-transferase domain KEGG: pde:Pden_2769 glutathione S-transferase, N-terminal domain and C-terminal domain; Thioredoxin fold; glutathione S-transferase-like protein complement(51142..51732) Dinoroseobacter shibae DFL 12 = DSM 16493 5711676 YP_001531405.1 CDS holA NC_009952.1 51747 52772 R KEGG: sit:TM1040_0043 DNA polymerase III, delta subunit; DNA polymerase III subunit delta complement(51747..52772) Dinoroseobacter shibae DFL 12 = DSM 16493 5711677 YP_001531406.1 CDS Dshi_0056 NC_009952.1 52769 53263 R KEGG: rsq:Rsph17025_3136 hypothetical protein, best ref ZP hit to lipoprotein, putative from Sulfitobacter sp. NAS-14.1, no significant InterPro Scan hits; hypothetical protein complement(52769..53263) Dinoroseobacter shibae DFL 12 = DSM 16493 5711678 YP_001531407.1 CDS leuS NC_009952.1 53250 55859 R 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 complement(53250..55859) Dinoroseobacter shibae DFL 12 = DSM 16493 5711679 YP_001531408.1 CDS lolA NC_009952.1 55941 56645 R PFAM: outer membrane lipoprotein carrier protein LolA KEGG: rsq:Rsph17025_2901 outer membrane lipoprotein carrier protein LolA; outer membrane lipoprotein carrier protein complement(55941..56645) Dinoroseobacter shibae DFL 12 = DSM 16493 5711680 YP_001531409.1 CDS ftsK NC_009952.1 56686 59673 R PFAM: cell divisionFtsK/SpoIIIE KEGG: rde:RD1_0033 cell division protein FtsK; very good swissprot hit to DNA translocase ftsK from Agrobacterium tumefaciens str. C58; DNA translocase complement(56686..59673) Dinoroseobacter shibae DFL 12 = DSM 16493 5711681 YP_001531410.1 CDS Dshi_0060 NC_009952.1 59687 60868 R PFAM: aminotransferase class I and II KEGG: sil:SPO3417 aminotransferase, classes I and II; swissprot hit to Putative aminotransferase aatC from Sinorhizobium meliloti; class I/II aminotransferase complement(59687..60868) Dinoroseobacter shibae DFL 12 = DSM 16493 5711682 YP_001531411.1 CDS Dshi_0061 NC_009952.1 60992 62323 R PFAM: Amidase KEGG: rsq:Rsph17025_2898 amidase; COG0154 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases; best swissprot hit to Glutamyl-tRNA(Gln) amidotransferase subunit A from Dehalococcoides ethenogenes 195 : function: Furnishes a means for formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln) (By similarity).; amidase complement(60992..62323) Dinoroseobacter shibae DFL 12 = DSM 16493 5711683 YP_001531412.1 CDS ubiH NC_009952.1 62385 63650 D TIGRFAM: Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family PFAM: monooxygenase FAD-binding KEGG: sil:SPO3419 ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases COG0654; best swissprot hit to 2-octaprenyl-6-methoxyphenol hydroxylase from Escherichia coli K12; 2-octaprenyl-6-methoxyphenol hydroxylase 62385..63650 Dinoroseobacter shibae DFL 12 = DSM 16493 5711684 YP_001531413.1 CDS suhB2 NC_009952.1 63773 64567 R PFAM: inositol monophosphatase KEGG: sil:SPO3443 inositol monophosphatase family protein; COG0483 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family; best BLAST hits to inositol monophosphatase family protein from Oceanicola batsensis HTCC2597 (refZP) and Inositol-1-monophosphatase (IMPase) from Sinorhizobium meliloti (Rhizobium meliloti) (swissprot); inositol-phosphate phosphatase complement(63773..64567) Dinoroseobacter shibae DFL 12 = DSM 16493 5711685 YP_001531414.1 CDS pmbA NC_009952.1 64554 65900 R PFAM: peptidase U62 modulator of DNA gyrase KEGG: sit:TM1040_2639 peptidase U62, modulator of DNA gyrase; COG0312 Predicted Zn-dependent proteases and their inactivated homologs; good swissprot hit to Protein pmbA (Protein tldE) from Escherichia coli K12; peptidase U62 modulator of DNA gyrase complement(64554..65900) Dinoroseobacter shibae DFL 12 = DSM 16493 5711686 YP_001531415.1 CDS Dshi_0065 NC_009952.1 65978 67468 R KEGG: sil:SPO3441 hypothetical protein, no swissprot hit, ref hits to several hypothetical proteins in roseobacter strains; hypothetical protein complement(65978..67468) Dinoroseobacter shibae DFL 12 = DSM 16493 5711687 YP_001531416.1 CDS Dshi_0066 NC_009952.1 67584 68342 D PFAM: short-chain dehydrogenase/reductase SDR; KR domain protein KEGG: sil:SPO3440 20-beta-hydroxysteroid dehydrogenase, putative, BLAST hits to several dehydrogenase proteins: swissprot hit to Uncharacterized oxidoreductase SSP1627 from Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305 (Belongs to the short-chain dehydrogenases/reductases (SDR) family and ref hits to 20-beta-hydroxysteroid dehydrogenase, putative from Silicibacter pomeroyi DSS-3; dehydrogenase/reductase 67584..68342 Dinoroseobacter shibae DFL 12 = DSM 16493 5711688 YP_001531417.1 CDS caiD NC_009952.1 68339 69085 D PFAM: Enoyl-CoA hydratase/isomerase KEGG: rsh:Rsph17029_2572 enoyl-CoA hydratase/isomerase; COG1024 Enoyl-CoA hydratase/carnithine racemase; enoyl-CoA hydratase/isomerase 68339..69085 Dinoroseobacter shibae DFL 12 = DSM 16493 5711689 YP_001531418.1 CDS Dshi_0068 NC_009952.1 69090 69674 R KEGG: sil:SPO3414 lipoprotein, putative; Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. LTs catalyze the cleavage of the beta-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetyl-D-glucosamine (GlcNAc), as do goose-type lysozymes. However, in addition to this, they also make a new glycosidic bond with the C6 hydroxyl group of the same muramic acid residue.; lipoprotein complement(69090..69674) Dinoroseobacter shibae DFL 12 = DSM 16493 5711690 YP_001531419.1 CDS Dshi_0069 NC_009952.1 69751 70632 R PFAM: Auxin Efflux Carrier; COG0679 Predicted permeases, good Ref ZP hit to auxin efflux carrier family protein fromSulfitobacter sp. EE-36, swissprot hit to Uncharacterized transporter MTH_1382 from Methanothermobacter thermautotrophicus str. Delta H; auxin efflux carrier complement(69751..70632) Dinoroseobacter shibae DFL 12 = DSM 16493 5711691 YP_001531420.1 CDS yccV NC_009952.1 70719 71045 D TIGRFAM: hemimethylated DNA binding protein PFAM: Hemimethylated DNA-binding region KEGG: sil:SPO3412 hypothetical protein, no swissprot; hemimethylated DNA-binding protein 70719..71045 Dinoroseobacter shibae DFL 12 = DSM 16493 5711692 YP_001531421.1 CDS ggt1 NC_009952.1 71093 72676 R PFAM: gamma-glutamyltranspeptidase KEGG: sit:TM1040_0064 gamma-glutamyltransferase, good swissprot hit to Gamma-glutamyltranspeptidase precursor from Bacillus subtilis; gamma-glutamyltransferase complement(71093..72676) Dinoroseobacter shibae DFL 12 = DSM 16493 5711693 YP_001531422.1 CDS rsbW NC_009952.1 72738 73247 R KEGG: rde:RD1_0027 serine-protein kinase, putative; COG2172 Anti-sigma regulatory factor (Ser/Thr protein kinase); ATP-binding region is related to ATPase domains of histidine kinase; Anti-sigma-B factor; serine-protein kinase complement(72738..73247) Dinoroseobacter shibae DFL 12 = DSM 16493 5711694 YP_001531423.1 CDS Dshi_0073 NC_009952.1 73262 73594 R TIGRFAM: anti-anti-sigma factor PFAM: Sulfate transporter/antisigma-factor antagonist STAS KEGG: rsq:Rsph17025_2906 anti-sigma-factor antagonist, SpoIIAA domain: The establishment of differential gene expression in sporulating Bacillus subtilis involves four protein components one of which is SpoIIAA (). The four components regulate the sporulation sigma factor F. Early in sporulation, SpoIIAA is in the phosphorylated state (SpoIIAA-P), as a result; anti-sigma-factor antagonist complement(73262..73594) Dinoroseobacter shibae DFL 12 = DSM 16493 5711695 YP_001531424.1 CDS thlA NC_009952.1 73694 74872 D KEGG: jan:Jann_4050 acetyl-CoA C-acetyltransferase TIGRFAM: acetyl-CoA acetyltransferase PFAM: Thiolase; good swissprot hit to Acetyl-CoA acetyltransferase (Acetoacetyl-CoA thiolase) from Clostridium acetobutylicum; found domain accords to thiolase II; acetyl-CoA acetyltransferase 73694..74872 Dinoroseobacter shibae DFL 12 = DSM 16493 5711696 YP_001531425.1 CDS Dshi_0075 NC_009952.1 75136 75378 R KEGG: rde:RD1_0777 hypothetical protein; bad BLAST hits, no swissprot: Calcium-binding EF-hand domain; hypothetical protein complement(75136..75378) Dinoroseobacter shibae DFL 12 = DSM 16493 5711697 YP_001531426.1 CDS Dshi_0076 NC_009952.1 75771 76007 D KEGG: rsq:Rsph17025_3561 IstB domain protein ATP-binding protein; no IPR domain, best Blast hit to Integrase, catalytic region from Rhodobacter sphaeroides ATCC 17025; bad GC frame plot; hypothetical protein 75771..76007 Dinoroseobacter shibae DFL 12 = DSM 16493 5711698 YP_001531427.1 CDS Dshi_0077 NC_009952.1 76020 76910 D no significant BLAST hits, unsure GC frame plot, IPR found small domain of intermediate filament from eukaryotes, integrated by Dshi_0076 possible integrase?; hypothetical protein 76020..76910 Dinoroseobacter shibae DFL 12 = DSM 16493 5711699 YP_001531428.1 CDS Dshi_0078 NC_009952.1 76953 77537 D no significant BLAST hits, unsure GC frame plot, no InterPro Scan hits detected, but good RBS binding site AGGAT; hypothetical protein 76953..77537 Dinoroseobacter shibae DFL 12 = DSM 16493 5711700 YP_001531429.1 CDS Dshi_0079 NC_009952.1 78091 78972 D PFAM: lipid A biosynthesis acyltransferase KEGG: sil:SPO1058 acyltransferase, HtrB family; lipid A biosynthesis acyltransferase 78091..78972 Dinoroseobacter shibae DFL 12 = DSM 16493 5711702 YP_001531430.1 CDS Dshi_0080 NC_009952.1 78969 79955 R PFAM: protein of unknown function DUF6 transmembrane KEGG: jan:Jann_0131 protein of unknown function DUF6, transmembrane; good hits to putative transporter, RhaT family, DMT superfamily from Loktanella vestfoldensis SKA53; also middle-rate swissprot hit to S-adenosylmethionine uptake transporter from Rickettsia typhi; hypothetical protein complement(78969..79955) Dinoroseobacter shibae DFL 12 = DSM 16493 5711703 YP_001531431.1 CDS imdh NC_009952.1 80080 81186 R catalyzes the oxidation of 3-isopropylmalate to 3-carboxy-4-methyl-2-oxopentanoate in leucine biosynthesis; 3-isopropylmalate dehydrogenase complement(80080..81186) Dinoroseobacter shibae DFL 12 = DSM 16493 5711704 YP_001531432.1 CDS Dshi_0082 NC_009952.1 81262 82386 R KEGG: rde:RD1_0227 hypothetical protein, small signalpeptide; hypothetical protein complement(81262..82386) Dinoroseobacter shibae DFL 12 = DSM 16493 5711705 YP_001531433.1 CDS leuD NC_009952.1 82492 83097 R catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate in leucine biosynthesis; forms a heterodimer of LeuC/D; isopropylmalate isomerase small subunit complement(82492..83097) Dinoroseobacter shibae DFL 12 = DSM 16493 5711706 YP_001531434.1 CDS Dshi_0084 NC_009952.1 83135 83662 R KEGG: bja:blr2987 hypothetical protein, uncharacterized conserved protein function unknown, transmembrane regions, signalpeptide; hypothetical protein complement(83135..83662) Dinoroseobacter shibae DFL 12 = DSM 16493 5711707 YP_001531435.1 CDS ipmi1 NC_009952.1 83697 85100 R dehydratase component, catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; isopropylmalate isomerase large subunit complement(83697..85100) Dinoroseobacter shibae DFL 12 = DSM 16493 5711708 YP_001531436.1 CDS Dshi_0086 NC_009952.1 85412 86014 D PFAM: SOUL heme-binding protein KEGG: bra:BRADO5496 putative heme-binding protein, SOUL family, swissprot hit to Heme-binding-like protein At3g10130 chloroplast precursor from Arabidopsis thaliana; SOUL heme-binding protein 85412..86014 Dinoroseobacter shibae DFL 12 = DSM 16493 5711709 YP_001531437.1 CDS Dshi_0087 NC_009952.1 86213 86545 D TIGRFAM: iojap-like protein PFAM: Iojap-related protein KEGG: sit:TM1040_2506 iojap-related protein; good ref ZP hit to iojap-related protein from Rhodobacterales bacterium HTCC2654; iojap family protein 86213..86545 Dinoroseobacter shibae DFL 12 = DSM 16493 5711710 YP_001531438.1 CDS Dshi_0088 NC_009952.1 86564 87034 D 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 86564..87034 Dinoroseobacter shibae DFL 12 = DSM 16493 5711711 YP_001531439.1 CDS ipgm NC_009952.1 87158 88675 D catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate; phosphoglyceromutase 87158..88675 Dinoroseobacter shibae DFL 12 = DSM 16493 5711712 YP_001531440.1 CDS Dshi_0090 NC_009952.1 88672 89775 D PFAM: peptidase M23B KEGG: rsh:Rsph17029_2592 peptidase M23B; peptidase M23B 88672..89775 Dinoroseobacter shibae DFL 12 = DSM 16493 5711713 YP_001531441.1 CDS prc NC_009952.1 89783 91120 D KEGG: rde:RD1_0333 carboxyl-terminal protease family protein, putative TIGRFAM: carboxyl-terminal protease PFAM: PDZ/DHR/GLGF domain protein; peptidase S41, high swissprot hit to Carboxy-terminal-processing protease precursor from Bartonella bacilliformis KC583; RBS site AGGAT; carboxyl-terminal protease 89783..91120 Dinoroseobacter shibae DFL 12 = DSM 16493 5711714 YP_001531442.1 CDS Dshi_0092 NC_009952.1 91122 91604 D PFAM: NUDIX hydrolase KEGG: rde:RD1_0960 hydrolase, NUDIX family domain; good swissprot hit to Probable (di)nucleoside polyphosphate hydrolase from Silicibacter pomeroyi and Ap4A domain; NUDIX hydrolase 91122..91604 Dinoroseobacter shibae DFL 12 = DSM 16493 5711715 YP_001531443.1 CDS Dshi_0093 NC_009952.1 91896 92264 R no significant BLAST hit, small signalpeptide, bad GC frame plot, Dshi_0100 putative transposase; hypothetical protein complement(91896..92264) Dinoroseobacter shibae DFL 12 = DSM 16493 5711716 YP_001531444.1 CDS Dshi_0094 NC_009952.1 92411 93343 R KEGG: rde:RD1_0345 hypothetical protein, domain of protease I prophage; no swissprot; hypothetical protein complement(92411..93343) Dinoroseobacter shibae DFL 12 = DSM 16493 5711717 YP_001531445.1 CDS Dshi_0095 NC_009952.1 93348 94247 R KEGG: rde:RD1_0344 hypothetical protein, no swissprot, no IPR Scan result, COG4397 Mu-like prophage major head subunit gpT; hypothetical protein complement(93348..94247) Dinoroseobacter shibae DFL 12 = DSM 16493 5711718 YP_001531446.1 CDS Dshi_0096 NC_009952.1 94244 94774 R unsure GC frame plot, no significant BLAST hits, no IPR Scan results; hypothetical protein complement(94244..94774) Dinoroseobacter shibae DFL 12 = DSM 16493 5711719 YP_001531447.1 CDS Dshi_0097 NC_009952.1 95154 95567 R KEGG: rde:RD1_0343 hypothetical protein, no swissprot, no IPR results, DUF1018 domain: This family consists of several bacterial and phage proteins of unknown function.; hypothetical protein complement(95154..95567) Dinoroseobacter shibae DFL 12 = DSM 16493 5711720 YP_001531448.1 CDS Dshi_0098 NC_009952.1 95564 96019 R no significant BLAST hit, unsure GC frame plot, no IPR scan result; hypothetical protein complement(95564..96019) Dinoroseobacter shibae DFL 12 = DSM 16493 5711721 YP_001531449.1 CDS Dshi_0099 NC_009952.1 96161 96931 R KEGG: ecs:ECs4946 putative DNA transposition protein, bad BLAST hits, AAA ATPase domain (COG2842 Uncharacterized ATPase, putative transposase ); hypothetical protein complement(96161..96931) Dinoroseobacter shibae DFL 12 = DSM 16493 5711722 YP_001531450.1 CDS Dshi_0100 NC_009952.1 96999 98882 R KEGG: rde:RD1_0339 transposase, putative; swissprot hit to Transposase from Enterobacteria phage Mu; pfam02914 Mu_transposase; putative transposase complement(96999..98882) Dinoroseobacter shibae DFL 12 = DSM 16493 5711723 YP_001531451.1 CDS Dshi_0101 NC_009952.1 99281 99538 D unsure GC frame plot, no significant BLAST hits, no IPR Scan result; hypothetical protein 99281..99538 Dinoroseobacter shibae DFL 12 = DSM 16493 5711724 YP_001531452.1 CDS dnaE1 NC_009952.1 99840 102824 D KEGG: rde:RD1_0336 DNA polymerase III, alpha subunit TIGRFAM: DNA polymerase III, alpha subunit PFAM: DNA polymerase III alpha subunit SMART: phosphoesterase PHP domain protein; DNA polymerase III subunit alpha 99840..102824 Dinoroseobacter shibae DFL 12 = DSM 16493 5711725 YP_001531453.1 CDS adhI NC_009952.1 102930 104042 D TIGRFAM: Alcohol dehydrogenase class III/S-(hydroxymethyl)glutathione dehydrogenase PFAM: Alcohol dehydrogenase zinc-binding domain protein; Alcohol dehydrogenase GroES domain protein KEGG: sil:SPOA0272 glutathione-dependent formaldehyde dehydrogenase; alcohol dehydrogenase class III/S-(hydroxymethyl)glutathione dehydrogenase 102930..104042 Dinoroseobacter shibae DFL 12 = DSM 16493 5711726 YP_001531454.1 CDS Dshi_0104 NC_009952.1 104039 104527 D PFAM: GCN5-related N-acetyltransferase KEGG: rle:pRL110290 putative acetyltransferase, no significant swissprot, but middle Ref YP hit to putative acetyltransferase from Rhizobium leguminosarum bv. viciae 3841; N-acetyltransferase GCN5 104039..104527 Dinoroseobacter shibae DFL 12 = DSM 16493 5711727 YP_001531455.1 CDS Dshi_0105 NC_009952.1 104539 105249 D PFAM: protein of unknown function DUF88 KEGG: jan:Jann_0048 protein of unknown function DUF88; no swissprot; hypothetical protein 104539..105249 Dinoroseobacter shibae DFL 12 = DSM 16493 5711728 YP_001531456.1 CDS Dshi_0106 NC_009952.1 105246 105869 R PFAM: regulatory protein TetR KEGG: rsh:Rsph17029_2507 transcriptional regulator, TetR family; TetR family; transcriptional regulator complement(105246..105869) Dinoroseobacter shibae DFL 12 = DSM 16493 5711729 YP_001531457.1 CDS Dshi_0107 NC_009952.1 105989 106960 D PFAM: Rubrerythrin; protein of unknown function DUF125 transmembrane KEGG: sil:SPO3842 hypothetical protein, may be Rubrerythrin, but Rub has a C-terminal domain homologous to rubredoxin PUBMED:1657933, which is not detected in this case, just the CCC1 like domain at C-terminal, which could be involved in iron and manganese transport; ferritin-like protein 105989..106960 Dinoroseobacter shibae DFL 12 = DSM 16493 5711730 YP_001531458.1 CDS Dshi_0108 NC_009952.1 106968 107909 R KEGG: syw:SYNW1655 hypothetical protein, best ref ZP hit to Methyltransferase type 11 from Methylobacterium sp. 4-46, no IPR scan results; hypothetical protein complement(106968..107909) Dinoroseobacter shibae DFL 12 = DSM 16493 5711731 YP_001531459.1 CDS Dshi_0109 NC_009952.1 108100 109035 D PFAM: Auxin Efflux Carrier KEGG: jan:Jann_0051 auxin efflux carrier, best swissprot hit to Putative malonate transporter from Sinorhizobium meliloti (Rhizobium meliloti) and best ref YP hit to Auxin Efflux Carrier from Jannaschia sp. CCS1; COG0679 Predicted permeases; auxin efflux carrier 108100..109035 Dinoroseobacter shibae DFL 12 = DSM 16493 5711732 YP_001531460.1 CDS Dshi_0110 NC_009952.1 109035 109487 D PFAM: protein of unknown function DUF188 KEGG: rde:RD1_0321 YaiI/YqxD family protein, putative; hypothetical protein 109035..109487 Dinoroseobacter shibae DFL 12 = DSM 16493 5711733 YP_001531461.1 CDS Dshi_0111 NC_009952.1 109578 110813 R PFAM: major facilitator superfamily MFS_1 KEGG: rde:RD1_0325 transmembrane transporter, major facilitator family, putative, COG2814 Arabinose efflux permease; major facilitator superfamily (MFS); transmembrane transporter complement(109578..110813) Dinoroseobacter shibae DFL 12 = DSM 16493 5711734 YP_001531462.1 CDS Dshi_0112 NC_009952.1 110834 112003 D PFAM: AFG1-family ATPase KEGG: rde:RD1_0326 ATPase, AFG1 family protein; AFG1 family ATPase 110834..112003 Dinoroseobacter shibae DFL 12 = DSM 16493 5711735 YP_001531463.1 CDS ahpC NC_009952.1 112059 112541 R PFAM: alkyl hydroperoxide reductase/ Thiol specific antioxidant/ Mal allergen; Redoxin domain protein KEGG: rsh:Rsph17029_2558 redoxin domain protein; good swissprot hit to Peroxiredoxin-2E-2, chloroplast precursor from Oryza sativa and Ref ZP hit toantioxidant, AhpC/Tsa family, putative from Roseobacter sp. AzwK-3b; redoxin complement(112059..112541) Dinoroseobacter shibae DFL 12 = DSM 16493 5711736 YP_001531464.1 CDS Dshi_0114 NC_009952.1 112628 113833 D PFAM: FAD-dependent pyridine nucleotide-disulphide oxidoreductase KEGG: sil:SPO3737 pyridine nucleotide-disulphide oxidoreductase family protein; also good swissprot hits to Rhodocoxin reductase from Rhodococcus erythropolis; pyridine nucleotide-disulfide oxidoreductase family protein 112628..113833 Dinoroseobacter shibae DFL 12 = DSM 16493 5711737 YP_001531465.1 CDS Dshi_0115 NC_009952.1 113830 114387 D TIGRFAM: putative methyltransferase PFAM: conserved hypothetical protein KEGG: sil:SPO3738 methyltransferase, putative; putative methyltransferase 113830..114387 Dinoroseobacter shibae DFL 12 = DSM 16493 5711738 YP_001531466.1 CDS Dshi_0116 NC_009952.1 114678 115730 R PFAM: TRAP dicarboxylate transporter- DctP subunit KEGG: pol:Bpro_2121 TRAP dicarboxylate transporter-DctP subunit; TRAP dicarboxylate transporter subunit DctP complement(114678..115730) Dinoroseobacter shibae DFL 12 = DSM 16493 5711739 YP_001531467.1 CDS map NC_009952.1 116582 117397 R KEGG: sit:TM1040_2469 methionine aminopeptidase, type I TIGRFAM: methionine aminopeptidase, type I PFAM: peptidase M24; also high swissprot to Methionine aminopeptidase (MAP) (Peptidase M) from Rickettsia prowazekii; methionine aminopeptidase complement(116582..117397) Dinoroseobacter shibae DFL 12 = DSM 16493 5711740 YP_001531468.1 CDS sfsA NC_009952.1 117444 118178 R Regulatory factor involved in maltose metabolism; sugar fermentation stimulation protein A complement(117444..118178) Dinoroseobacter shibae DFL 12 = DSM 16493 5711741 YP_001531469.1 CDS mogA NC_009952.1 118227 118955 D PFAM: molybdopterin binding domain KEGG: rsh:Rsph17029_2583 molybdopterin binding domain COG1058 - Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA; molybdenum cofactor biosynthesis protein MogA 118227..118955 Dinoroseobacter shibae DFL 12 = DSM 16493 5711742 YP_001531470.1 CDS Dshi_0120 NC_009952.1 118952 119677 D PFAM: GCN5-related N-acetyltransferase KEGG: rsq:Rsph17025_2991 GCN5-related N-acetyltransferase; N-acetyltransferase GCN5 118952..119677 Dinoroseobacter shibae DFL 12 = DSM 16493 5711743 YP_001531471.1 CDS Dshi_0121 NC_009952.1 119674 120249 D TIGRFAM: alkylhydroperoxidase like protein, AhpD family; uncharacterized peroxidase-related enzyme PFAM: Carboxymuconolactone decarboxylase KEGG: sit:TM1040_2465 uncharacterised peroxidase-related, no swissprot, but high Ref hits; peroxidase-like protein 119674..120249 Dinoroseobacter shibae DFL 12 = DSM 16493 5711744 YP_001531472.1 CDS Dshi_0122 NC_009952.1 120246 121178 D PFAM: OmpA/MotB domain protein KEGG: rsh:Rsph17029_2585 OmpA/MotB domain protein; COG2885 Outer membrane protein and related peptidoglycan-associated (lipo)proteins; OmpA/MotB domain-containing protein 120246..121178 Dinoroseobacter shibae DFL 12 = DSM 16493 5711745 YP_001531473.1 CDS Dshi_0123 NC_009952.1 121186 122094 R PFAM: regulatory protein LysR; LysR substrate-binding KEGG: sit:TM1040_2460 transcriptional regulator, LysR family, good RBS site AGGAT; LysR family; transcriptional regulator complement(121186..122094) Dinoroseobacter shibae DFL 12 = DSM 16493 5711746 YP_001531474.1 CDS Dshi_0124 NC_009952.1 122240 122824 R TIGRFAM: intracellular protease, PfpI family PFAM: ThiJ/PfpI domain protein KEGG: jan:Jann_1867 peptidase C56, PfpI; PfpI family; intracellular protease complement(122240..122824) Dinoroseobacter shibae DFL 12 = DSM 16493 5711747 YP_001531475.1 CDS fadH NC_009952.1 122863 124881 R PFAM: NADH:flavin oxidoreductase/NADH oxidase; FAD-dependent pyridine nucleotide-disulphide oxidoreductase KEGG: sit:TM1040_2458 NADH:flavin oxidoreductase/NADH oxidase, high swissprot to 2,4-dienoyl-CoA reductase [NADPH] from Escherichia coli K12; NADPH:2,4-dienoyl-CoA reductase complement(122863..124881) Dinoroseobacter shibae DFL 12 = DSM 16493 5711748 YP_001531476.1 CDS Dshi_0126 NC_009952.1 124985 125401 R KEGG: sit:TM1040_2681 hypothetical protein, bad BLAST hits, no IPR Scan results; hypothetical protein complement(124985..125401) Dinoroseobacter shibae DFL 12 = DSM 16493 5711749 YP_001531477.1 CDS Dshi_0127 NC_009952.1 125398 126168 R KEGG: sit:TM1040_2680 hypothetical protein; no swissprot, no IPR Scan results; hypothetical protein complement(125398..126168) Dinoroseobacter shibae DFL 12 = DSM 16493 5711750 YP_001531478.1 CDS Dshi_0128 NC_009952.1 126287 126946 R KEGG: jan:Jann_0063 hypothetical protein, no significant swissprot, middle Ref hit; hypothetical protein complement(126287..126946) Dinoroseobacter shibae DFL 12 = DSM 16493 5711751 YP_001531479.1 CDS ilvD1 NC_009952.1 126918 128651 R catalyzes the dehydration of 2,3-dihydroxy-3-methylbutanoate to 3-methyl-2-oxobutanoate in valine and isoleucine biosynthesis; dihydroxy-acid dehydratase complement(126918..128651) Dinoroseobacter shibae DFL 12 = DSM 16493 5711752 YP_001531480.1 CDS abi NC_009952.1 128795 129697 D PFAM: Abortive infection protein KEGG: jan:Jann_0061 abortive infection protein, no significant swissprot; abortive infection protein 128795..129697 Dinoroseobacter shibae DFL 12 = DSM 16493 5711753 YP_001531481.1 CDS accD NC_009952.1 129763 130725 D TIGRFAM: acetyl-CoA carboxylase, carboxyl transferase, beta subunit KEGG: pde:Pden_1987 acetyl-CoA carboxylase, carboxyl transferase, beta subunit, high swissprot; carboxyl transferase, beta subunit; acetyl-CoA carboxylase 129763..130725 Dinoroseobacter shibae DFL 12 = DSM 16493 5711599 YP_001531482.1 CDS folC NC_009952.1 130730 131998 D TIGRFAM: FolC bifunctional protein PFAM: cytoplasmic peptidoglycan synthetase domain protein; Mur ligase middle domain protein KEGG: sil:SPO3818 FolC bifunctional protein; folylpolyglutamate synthase 130730..131998 Dinoroseobacter shibae DFL 12 = DSM 16493 5711600 YP_001531483.1 CDS Dshi_0133 NC_009952.1 132102 133061 D KEGG: sil:SPO2586 type I secretion target repeat protein, middle Ref ZP hit, no swissprot, hedgehog domain: in eukaryotes involved in cell growth and differentiation; putative type I secretion target repeat protein 132102..133061 Dinoroseobacter shibae DFL 12 = DSM 16493 5711601 YP_001531484.1 CDS pcd NC_009952.1 133058 133351 R PFAM: transcriptional coactivator/pterin dehydratase KEGG: rde:RD1_0944 pterin-4-alpha-carbinolamine dehydratase; pterin-4-alpha-carbinolamine dehydratase complement(133058..133351) Dinoroseobacter shibae DFL 12 = DSM 16493 5711602 YP_001531485.1 CDS Dshi_0135 NC_009952.1 133351 134571 R PFAM: protein of unknown function DUF482 KEGG: sil:SPO3732 hypothetical protein, no swissprot; hypothetical protein complement(133351..134571) Dinoroseobacter shibae DFL 12 = DSM 16493 5711603 YP_001531486.1 CDS ugpQ NC_009952.1 134622 135395 R PFAM: glycerophosphoryl diester phosphodiesterase KEGG: jan:Jann_0436 glycerophosphoryl diester phosphodiesterase PRK: ugpQ; cytosolic glycerophosphoryl diester phosphodiesterase complement(134622..135395) Dinoroseobacter shibae DFL 12 = DSM 16493 5711604 YP_001531487.1 CDS Dshi_0137 NC_009952.1 135392 135859 R PFAM: Endoribonuclease L-PSP COG0251-Putative translation initiation inhibitor, yjgF family; endoribonuclease L-PSP complement(135392..135859) Dinoroseobacter shibae DFL 12 = DSM 16493 5711605 YP_001531488.1 CDS hlyD NC_009952.1 135882 137189 R TIGRFAM: type I secretion membrane fusion protein, HlyD family PFAM: secretion protein HlyD family protein KEGG: sil:SPO3729 type I secretion membrane fusion protein, HlyD family; also middle swissprot hit to Proteases secretion protein prtE from Erwinia chrysanthemi; HlyD family; type I secretion membrane fusion protein complement(135882..137189) Dinoroseobacter shibae DFL 12 = DSM 16493 5711606 YP_001531489.1 CDS Dshi_0139 NC_009952.1 137186 138925 R TIGRFAM: type I secretion system ATPase PFAM: ABC transporter related contains:pfam00005 pfam00664; type I secretion system ATPase complement(137186..138925) Dinoroseobacter shibae DFL 12 = DSM 16493 5711607 YP_001531490.1 CDS Dshi_0140 NC_009952.1 139098 139919 D PFAM: VacJ family lipoprotein KEGG: rsp:RSP_0891 putative lipoprotein, middle swissprot to Lipoprotein vacJ precursor from Shigella flexneri; VacJ family lipoprotein 139098..139919 Dinoroseobacter shibae DFL 12 = DSM 16493 5711608 YP_001531491.1 CDS ttg2D NC_009952.1 139909 140529 D PFAM: toluene tolerance family protein KEGG: rde:RD1_0939 toluene tolerance family protein, putative; swissprot hit to Protein yrbC precursor from Escherichia coli K12 (ABC transporter related); toluene tolerance family protein 139909..140529 Dinoroseobacter shibae DFL 12 = DSM 16493 5711609 YP_001531492.1 CDS mrcB NC_009952.1 140693 142882 R KEGG: rde:RD1_0938 penicillin-binding protein, 1A family TIGRFAM: penicillin-binding protein, 1A family PFAM: glycosyl transferase family 51; penicillin-binding protein transpeptidase; 1A family; penicillin-binding protein complement(140693..142882) Dinoroseobacter shibae DFL 12 = DSM 16493 5711610 YP_001531493.1 CDS glnK NC_009952.1 143197 143535 D PFAM: nitrogen regulatory protein P-II KEGG: jan:Jann_4056 nitrogen regulatory protein P-II (GlnB, GlnK), glnK-amtB-Operon (amtB: Dshi_1838); highly conserved gene cluster (e.g. E. coli, R. capsulatus); nitrogen regulatory protein P-II 143197..143535 Dinoroseobacter shibae DFL 12 = DSM 16493 5711611 YP_001531494.1 CDS amtB NC_009952.1 143570 144883 D TIGRFAM: ammonium transporter PFAM: Rh family protein/ammonium transporter KEGG: sit:TM1040_2630 ammonium transporter, high swissprot to Putative ammonium transporter sll0108 from Synechocystis sp. PCC 6803; sequence homolgies; gene arrangement (-> glnK, Dshi_0143); ammonium transporter 143570..144883 Dinoroseobacter shibae DFL 12 = DSM 16493 5711612 YP_001531495.1 CDS Dshi_0145 NC_009952.1 145044 146222 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(145044..146222) Dinoroseobacter shibae DFL 12 = DSM 16493 5711613 YP_001531496.1 CDS sseA NC_009952.1 146231 147106 R PFAM: Rhodanese domain protein KEGG: rsh:Rsph17029_2544 3-mercaptopyruvate sulfurtransferase; both, high swissprot and Ref YP hits to 3-mercaptopyruvate sulfurtransferase (sseA); 3-mercaptopyruvate sulfurtransferase complement(146231..147106) Dinoroseobacter shibae DFL 12 = DSM 16493 5711614 YP_001531497.1 CDS smpB NC_009952.1 147392 147874 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(147392..147874) Dinoroseobacter shibae DFL 12 = DSM 16493 5711615 YP_001531498.1 CDS Dshi_0148 NC_009952.1 147905 148354 R PFAM: GCN5-related N-acetyltransferase KEGG: bur:Bcep18194_B2857 GCN5-related N-acetyltransferase, bad BLAST hits; N-acetyltransferase GCN5 complement(147905..148354) Dinoroseobacter shibae DFL 12 = DSM 16493 5711616 YP_001531499.1 CDS dapA NC_009952.1 148351 149226 R catalyzes the formation of dihydrodipicolinate from L-aspartate 4-semialdehyde and pyruvate in lysine and diaminopimelate biosynthesis; dihydrodipicolinate synthase complement(148351..149226) Dinoroseobacter shibae DFL 12 = DSM 16493 5711617 YP_001531500.1 CDS Dshi_0150 NC_009952.1 149400 151349 D PFAM: Lytic transglycosylase catalytic KEGG: rsh:Rsph17029_2541 lytic transglycosylase, catalytic; swissprot to Putative soluble lytic murein transglycosylase precursor from Haemophilus influenzae; IPR Scan: domain to bacterial muramidases superfamily; putative lytic transglycosylase catalytic subunit 149400..151349 Dinoroseobacter shibae DFL 12 = DSM 16493 5711618 YP_001531501.1 CDS Dshi_0151 NC_009952.1 151387 152265 R PFAM: protein of unknown function DUF6 transmembrane KEGG: jan:Jann_0141 protein of unknown function DUF6, transmembrane, swissprot hit to S-adenosylmethionine uptake transporter from Rickettsia typhi (DMT related); hypothetical protein complement(151387..152265) Dinoroseobacter shibae DFL 12 = DSM 16493 5711619 YP_001531502.1 CDS Dshi_0152 NC_009952.1 152262 152954 R PFAM: protein of unknown function DUF752 KEGG: sil:SPO3553 hypothetical protein; hypothetical protein complement(152262..152954) Dinoroseobacter shibae DFL 12 = DSM 16493 5711620 YP_001531503.1 CDS dao NC_009952.1 153035 154093 D PFAM: FAD dependent oxidoreductase KEGG: sil:SPO3552 oxidoreductase, FAD-binding; FAD dependent oxidoreductase 153035..154093 Dinoroseobacter shibae DFL 12 = DSM 16493 5711621 YP_001531504.1 CDS Dshi_0154 NC_009952.1 154275 154820 R PFAM: NAD(P)H dehydrogenase (quinone); NADPH-dependent FMN reductase KEGG: sit:TM1040_2447 NADPH-dependent FMN reductase; predicted flavoprotein COG0431; NADPH-dependent FMN reductase complement(154275..154820) Dinoroseobacter shibae DFL 12 = DSM 16493 5711622 YP_001531505.1 CDS lrgA NC_009952.1 155531 155887 D PFAM: LrgA family protein; bad Ref ZP hit to hypothetical protein RAZWK3B_06232 from Roseobacter sp. AzwK-3b no significant swissprot hit; putative LrgA family protein 155531..155887 Dinoroseobacter shibae DFL 12 = DSM 16493 5711623 YP_001531506.1 CDS lrgB NC_009952.1 155880 156596 D PFAM: LrgB family protein KEGG: pde:Pden_2740 LrgB family protein; gene arrangement wtih Dshi_0155 putative LrgA protein; LrgB family protein 155880..156596 Dinoroseobacter shibae DFL 12 = DSM 16493 5711624 YP_001531507.1 CDS cobA2 NC_009952.1 156608 157222 D KEGG: ret:RHE_CH02488 cob(I)alamin adenosyltransferase protein TIGRFAM: cob(I)alamin adenosyltransferase PFAM: ATP:corrinoid adenosyltransferase BtuR/CobO/CobP, good swissprot hits, good RBS site AGGAT, the following genes are also involved in the vit. B12 biosynthese; alternative gene name: cobO/btuR; cob(I)alamin adenosyltransferase 156608..157222 Dinoroseobacter shibae DFL 12 = DSM 16493 5711625 YP_001531508.1 CDS cobN NC_009952.1 157466 161173 R KEGG: bov:BOV_1269 cobaltochelatase, CobN subunit TIGRFAM: cobaltochelatase, CobN subunit PFAM: CobN/magnesium chelatase; swissprot: high similarity to aerobic cobaltochelatase subunit cobN from Pseudomonas denitrificans; gene arangement from Dshi_0157 to Dshi_0166 Vit B12 synthesis; cobaltochelatase complement(157466..161173) Dinoroseobacter shibae DFL 12 = DSM 16493 5711626 YP_001531509.1 CDS Dshi_0159 NC_009952.1 161242 161751 R no significant BLAST hits, no IPR Scan result; unsure GC frame plot; hypothetical protein complement(161242..161751) Dinoroseobacter shibae DFL 12 = DSM 16493 5711627 YP_001531510.1 CDS cobW NC_009952.1 162047 163126 R TIGRFAM: cobalamin biosynthesis protein CobW PFAM: cobalamin synthesis protein P47K; cobalamin synthesis CobW domain protein KEGG: bov:BOV_1270 cobalamin biosynthesis protein CobW, high swissprot hit to Protein cobW from Pseudomonas denitrificans; cobalamin biosynthesis protein CobW complement(162047..163126) Dinoroseobacter shibae DFL 12 = DSM 16493 5711628 YP_001531511.1 CDS cbtA NC_009952.1 163128 163817 R TIGRFAM: cobalt transporter, subunit CbtA PFAM: Cobalt transporter subunit CbtA putative KEGG: sit:TM1040_2222 cobalt transporter subunit CbtA, putative, no swissprot, middle Ref hits; putative cobalt transporter subunit CbtA complement(163128..163817) Dinoroseobacter shibae DFL 12 = DSM 16493 5711629 YP_001531512.1 CDS cbtB NC_009952.1 163833 164030 R KEGG: pde:Pden_2524 hypothetical protein, no swissprot, bad EDO hit to cobalt transporter, subunit CbtB from Methylobacterium populi BJ001, a single transmembrane domain and four times His at C-terminal; hypothetical protein complement(163833..164030) Dinoroseobacter shibae DFL 12 = DSM 16493 5711630 YP_001531513.1 CDS smc NC_009952.1 164463 167915 D TIGRFAM: chromosome segregation protein SMC PFAM: SMC domain protein; SMCs flexible hinge domain protein KEGG: rde:RD1_1327 chromosome segregation protein, putative; chromosome segregation protein SMC 164463..167915 Dinoroseobacter shibae DFL 12 = DSM 16493 5711631 YP_001531514.1 CDS mltB1 NC_009952.1 168135 169304 R TIGRFAM: lytic murein transglycosylase PFAM: Peptidoglycan-binding domain 1 protein KEGG: sil:SPO3226 hypothetical protein; lytic murein transglycosylase complement(168135..169304) Dinoroseobacter shibae DFL 12 = DSM 16493 5711632 YP_001531515.1 CDS cobD NC_009952.1 169365 170276 R CobD; CbiD in Salmonella; converts cobyric acid to cobinamide by the addition of aminopropanol on the F carboxylic group; cobalamin biosynthesis protein complement(169365..170276) Dinoroseobacter shibae DFL 12 = DSM 16493 5711633 YP_001531516.1 CDS cobC NC_009952.1 170273 171229 R PFAM: aminotransferase class I and II KEGG: sil:SPO3224 cobalamin biosynthetic protein CobC; gene arrangement with several genes upstream (Dshi_0157) to downstream (Dshi_0175); L-threonine-O-3-phosphate decarboxylase; threonine-phosphate decarboxylase complement(170273..171229) Dinoroseobacter shibae DFL 12 = DSM 16493 5711634 YP_001531517.1 CDS Dshi_0167 NC_009952.1 171226 171609 R PFAM: protein of unknown function DUF1636 KEGG: hne:HNE_2170 hypothetical protein; conserved domain COG5469: predicted metal-binding protein; middle Ref ZP hit to hypothetical protein ROS217_22062 from Roseovarius sp. 217 (same COG domain); bad Swissprot hit to Magnesium-chelatase subunit H (Mg-protoporphyrin IX chelatase subunit H) from Rhodobacter sphaeroides 2.4.1: This family contains a domain common to the cobN protein and to magn; hypothetical protein complement(171226..171609) Dinoroseobacter shibae DFL 12 = DSM 16493 5711635 YP_001531518.1 CDS Dshi_0168 NC_009952.1 171888 172247 D KEGG: rde:RD1_1333 response regulator, putative; COG2204 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains; response regulator receiver protein 171888..172247 Dinoroseobacter shibae DFL 12 = DSM 16493 5711636 YP_001531519.1 CDS Dshi_0169 NC_009952.1 172349 173338 R KEGG: jan:Jann_0368 putative glutathione S-transferase; putative glutathione S-transferase complement(172349..173338) Dinoroseobacter shibae DFL 12 = DSM 16493 5711637 YP_001531520.1 CDS Dshi_0170 NC_009952.1 173674 173919 D no significant BLAST hits, bad GC frame plot, no conserved domains detected; hypothetical protein 173674..173919 Dinoroseobacter shibae DFL 12 = DSM 16493 5711638 YP_001531521.1 CDS cbiX2 NC_009952.1 173916 175166 D PFAM: cobalamin (vitamin B12) biosynthesis CbiX protein KEGG: sye:Syncc9902_0843 hypothetical protein; swissprot to Sirohydrochlorin cobaltochelatase (CbiXL) from Bacillus megaterium; sirohydrochlorin cobaltochelatase 173916..175166 Dinoroseobacter shibae DFL 12 = DSM 16493 5711639 YP_001531522.1 CDS cobH NC_009952.1 175166 176704 D PFAM: Precorrin-8X methylmutase CbiC/CobH KEGG: bvi:Bcep1808_1609 precorrin-8X methylmutase; alternative gene name: cbiC; precorrin-8X methylmutase 175166..176704 Dinoroseobacter shibae DFL 12 = DSM 16493 5711640 YP_001531523.1 CDS cobL NC_009952.1 176787 177989 D KEGG: ava:Ava_3558 uroporphyrin-III C/tetrapyrrole (corrin/porphyrin) 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; decarboxylating precorrin-6Y C(5,15)-methyltransferase 176787..177989 Dinoroseobacter shibae DFL 12 = DSM 16493 5711641 YP_001531524.1 CDS cobI NC_009952.1 177986 178687 D TIGRFAM: precorrin-2 C20-methyltransferase PFAM: Uroporphyrin-III C/tetrapyrrole (Corrin/Porphyrin) methyltransferase KEGG: mag:amb0297 precorrin-2 methylase; alternative gene name: cbiL; precorrin-2 C(20)-methyltransferase 177986..178687 Dinoroseobacter shibae DFL 12 = DSM 16493 5711642 YP_001531525.1 CDS cbiG NC_009952.1 178678 180483 D TIGRFAM: precorrin-3B C17-methyltransferase PFAM: Uroporphyrin-III C/tetrapyrrole (Corrin/Porphyrin) methyltransferase; cobalamin (vitamin B12) biosynthesis CbiG protein KEGG: mag:amb0298 precorrin-3B methylase; precorrin-3B C(17)-methyltransferase 178678..180483 Dinoroseobacter shibae DFL 12 = DSM 16493 5712100 YP_001531526.1 CDS cobM NC_009952.1 180607 181383 D TIGRFAM: precorrin-4 C11-methyltransferase PFAM: Uroporphyrin-III C/tetrapyrrole (Corrin/Porphyrin) methyltransferase KEGG: mag:amb0514 precorrin-4 methylase, anaerobic equivalent cbiF; precorrin-4 C(11)-methyltransferase 180607..181383 Dinoroseobacter shibae DFL 12 = DSM 16493 5712101 YP_001531527.1 CDS Dshi_0177 NC_009952.1 181444 181797 D KEGG: jan:Jann_0367 hypothetical protein, no significant swissprot, no IPR Scan results; hypothetical protein 181444..181797 Dinoroseobacter shibae DFL 12 = DSM 16493 5712102 YP_001531528.1 CDS Dshi_0178 NC_009952.1 181801 182973 R PFAM: aminotransferase class I and II KEGG: sit:TM1040_2581 aminotransferase, class I and II; middle swissprot to Putative aminotransferase B from Bacillus subtilis (patB); class I/II aminotransferase complement(181801..182973) Dinoroseobacter shibae DFL 12 = DSM 16493 5712103 YP_001531529.1 CDS def1 NC_009952.1 183047 183610 D KEGG: rsh:Rsph17029_2532 peptide deformylase TIGRFAM: peptide deformylase PFAM: formylmethionine deformylase; peptide deformylase 183047..183610 Dinoroseobacter shibae DFL 12 = DSM 16493 5712104 YP_001531530.1 CDS def2 NC_009952.1 183683 184189 D TIGRFAM: peptide deformylase PFAM: formylmethionine deformylase KEGG: sit:TM1040_2578 formylmethionine deformylase, worse BLAST hits than Dshi_0179, but same product result; peptide deformylase 183683..184189 Dinoroseobacter shibae DFL 12 = DSM 16493 5712105 YP_001531531.1 CDS fmt NC_009952.1 184186 185085 D TIGRFAM: methionyl-tRNA formyltransferase PFAM: formyl transferase domain protein KEGG: sil:SPO3216 methionyl-tRNA formyltransferase; high swissprot; methionyl-tRNA formyltransferase 184186..185085 Dinoroseobacter shibae DFL 12 = DSM 16493 5712106 YP_001531532.1 CDS rnhA NC_009952.1 185190 185663 R An endonuclease that specifically degrades the RNA strand of RNA-DNA hybrids; ribonuclease H complement(185190..185663) Dinoroseobacter shibae DFL 12 = DSM 16493 5712107 YP_001531533.1 CDS Dshi_0183 NC_009952.1 185656 186255 R PFAM: Methyltransferase type 11; Methyltransferase type 12 KEGG: sil:SPO3211 hypothetical protein; type 11 methyltransferase complement(185656..186255) Dinoroseobacter shibae DFL 12 = DSM 16493 5712108 YP_001531534.1 CDS Dshi_0184 NC_009952.1 186252 186704 R KEGG: rde:RD1_1353 hypothetical protein; hypothetical protein complement(186252..186704) Dinoroseobacter shibae DFL 12 = DSM 16493 5712109 YP_001531535.1 CDS cdsA2 NC_009952.1 186744 187694 R PFAM: phosphatidate cytidylyltransferase KEGG: reu:Reut_B4016 phosphatidate cytidylyltransferase; phosphatidate cytidylyltransferase complement(186744..187694) Dinoroseobacter shibae DFL 12 = DSM 16493 5712110 YP_001531536.1 CDS plsC NC_009952.1 187691 188344 R PFAM: phospholipid/glycerol acyltransferase KEGG: reh:H16_A2089 1-acyl-sn-glycerol-3-phosphate acyltransferase; phospholipid/glycerol acyltransferase complement(187691..188344) Dinoroseobacter shibae DFL 12 = DSM 16493 5712111 YP_001531537.1 CDS Dshi_0187 NC_009952.1 188367 188981 R PFAM: Lysine exporter protein (LYSE/YGGA) KEGG: jan:Jann_0505 lysine exporter protein (LysE/YggA); COG1280 putative threonine efflux protein; Ref hit to Lysine exporter protein (LYSE/YGGA) from Jannaschia sp. CCS1, also swissprot to Homoserine/homoserine lactone efflux protein from Escherichia coli K12; amino-acid exporter protein complement(188367..188981) Dinoroseobacter shibae DFL 12 = DSM 16493 5712112 YP_001531538.1 CDS ispH NC_009952.1 189644 190600 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(189644..190600) Dinoroseobacter shibae DFL 12 = DSM 16493 5712113 YP_001531539.1 CDS Dshi_0189 NC_009952.1 190754 191188 D PFAM: cytochrome c class I KEGG: rsh:Rsph17029_3996 cytochrome c, class I; COG2863 Cytochrome c553; just middle Ref hits to probable c-type cytochrome from Roseovarius sp. HTCC2601; good RBS site AGGAGGAT; putative cytochrome c class I 190754..191188 Dinoroseobacter shibae DFL 12 = DSM 16493 5712114 YP_001531540.1 CDS Dshi_0190 NC_009952.1 191192 191707 R KEGG: pmy:Pmen_0684 membrane protein-like protein, middle Ref hits; hypothetical protein complement(191192..191707) Dinoroseobacter shibae DFL 12 = DSM 16493 5712115 YP_001531541.1 CDS Dshi_0191 NC_009952.1 191718 192290 R PFAM: protein of unknown function DUF88 KEGG: rsq:Rsph17025_2579 protein of unknown function DUF88; hypothetical protein complement(191718..192290) Dinoroseobacter shibae DFL 12 = DSM 16493 5712116 YP_001531542.1 CDS hppk NC_009952.1 192409 192978 D TIGRFAM: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase PFAM: 78-dihydro-6-hydroxymethylpterin-pyrophosphokinase HPPK KEGG: sil:SPO3205 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase; 2-amino-4-hydroxy-6- hydroxymethyldihydropteridine pyrophosphokinase 192409..192978 Dinoroseobacter shibae DFL 12 = DSM 16493 5712117 YP_001531543.1 CDS rpoZ NC_009952.1 193056 193412 D 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 193056..193412 Dinoroseobacter shibae DFL 12 = DSM 16493 5712118 YP_001531544.1 CDS relA NC_009952.1 193417 195561 D KEGG: rsq:Rsph17025_2576 (p)ppGpp synthetase I, SpoT/RelA TIGRFAM: RelA/SpoT family protein PFAM: TGS domain protein; metal-dependent phosphohydrolase HD sub domain; RelA/SpoT domain protein SMART: metal-dependent phosphohydrolase HD region; ppGpp synthetase I; ATP:GTP 3-pyrophosphotransferase; GTP pyrophosphokinase 193417..195561 Dinoroseobacter shibae DFL 12 = DSM 16493 5712119 YP_001531545.1 CDS Dshi_0195 NC_009952.1 195599 196255 D KEGG: sil:SPO3202 hypothetical protein; hypothetical protein 195599..196255 Dinoroseobacter shibae DFL 12 = DSM 16493 5712120 YP_001531546.1 CDS pdxJ NC_009952.1 196281 197045 D involved in the de novo synthesis of pyridoxine (Vitamin B6); pyridoxine 5'-phosphate synthase 196281..197045 Dinoroseobacter shibae DFL 12 = DSM 16493 5712121 YP_001531547.1 CDS Dshi_0197 NC_009952.1 197042 197704 D KEGG: sit:TM1040_1321 hypothetical protein, no swissprot, no conserved domains; hypothetical protein 197042..197704 Dinoroseobacter shibae DFL 12 = DSM 16493 5712122 YP_001531548.1 CDS acpS NC_009952.1 197844 198263 D 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 197844..198263 Dinoroseobacter shibae DFL 12 = DSM 16493 5712123 YP_001531549.1 CDS lepB NC_009952.1 198319 199104 D KEGG: rsq:Rsph17025_2572 signal peptidase I TIGRFAM: signal peptidase I PFAM: peptidase S24 and S26 domain protein; signal peptidase I 198319..199104 Dinoroseobacter shibae DFL 12 = DSM 16493 5712124 YP_001531550.1 CDS rnc NC_009952.1 199101 199790 D PFAM: ribonuclease III; double-stranded RNA binding domain protein KEGG: rde:RD1_1366 ribonuclease III; ribonuclease III 199101..199790 Dinoroseobacter shibae DFL 12 = DSM 16493 5712125 YP_001531551.1 CDS era NC_009952.1 199783 200709 D 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 199783..200709 Dinoroseobacter shibae DFL 12 = DSM 16493 5712126 YP_001531552.1 CDS Dshi_0202 NC_009952.1 200713 201045 D PFAM: protein of unknown function DUF1491 KEGG: sil:SPO0690 hypothetical protein; hypothetical protein 200713..201045 Dinoroseobacter shibae DFL 12 = DSM 16493 5712127 YP_001531553.1 CDS recO NC_009952.1 201114 201839 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 201114..201839 Dinoroseobacter shibae DFL 12 = DSM 16493 5712128 YP_001531554.1 CDS mmgC NC_009952.1 201901 203595 R PFAM: acyl-CoA dehydrogenase domain protein; Acyl-CoA dehydrogenase type 2 domain KEGG: rde:RD1_1372 isobutyryl-CoA dehydrogenase; acyl-CoA dehydrogenase complement(201901..203595) Dinoroseobacter shibae DFL 12 = DSM 16493 5712129 YP_001531555.1 CDS Dshi_0205 NC_009952.1 203871 204635 D PFAM: protein of unknown function DUF81 KEGG: sit:TM1040_2445 protein of unknown function DUF81; no significant swissprot; hypothetical protein 203871..204635 Dinoroseobacter shibae DFL 12 = DSM 16493 5712130 YP_001531556.1 CDS Dshi_0206 NC_009952.1 204628 205515 R KEGG: rde:RD1_1384 hypothetical protein, no significant swissprot, but conserved domains and good RBS site AGGAT; hypothetical protein complement(204628..205515) Dinoroseobacter shibae DFL 12 = DSM 16493 5712131 YP_001531557.1 CDS ptsH NC_009952.1 205596 205865 R TIGRFAM: phosphocarrier, HPr family PFAM: phosphocarrier HPr protein KEGG: sit:TM1040_2436 phosphotransferase system, HPr; phosphocarrier protein HPr; phosphotransferase system complement(205596..205865) Dinoroseobacter shibae DFL 12 = DSM 16493 5712132 YP_001531558.1 CDS ptsL NC_009952.1 205876 206265 R PFAM: PTS system fructose subfamily IIA component KEGG: sil:SPO0714 PTS system IIA component, Man family; Man family protein; PTS system transporter subunit IIA complement(205876..206265) Dinoroseobacter shibae DFL 12 = DSM 16493 5712133 YP_001531559.1 CDS Dshi_0209 NC_009952.1 206303 207205 R PFAM: conserved hypothetical protein KEGG: rsh:Rsph17029_0317 uncharacterised P-loop ATPase protein UPF0042; high swissprot, part of the PTS system in gene neighborhood?; hypothetical protein complement(206303..207205) Dinoroseobacter shibae DFL 12 = DSM 16493 5712134 YP_001531560.1 CDS hprK NC_009952.1 207218 207655 R KEGG: sil:SPO0712 HPr serine kinase/phosphatase domain protein; HPr kinase/phosphorylase complement(207218..207655) Dinoroseobacter shibae DFL 12 = DSM 16493 5712135 YP_001531561.1 CDS Dshi_0211 NC_009952.1 207658 209376 R PFAM: ATP-binding region ATPase domain protein; histidine kinase HAMP region domain protein; histidine kinase A domain protein KEGG: rsh:Rsph17029_0315 histidine kinase; integral membrane sensor signal transduction histidine kinase complement(207658..209376) Dinoroseobacter shibae DFL 12 = DSM 16493 5712136 YP_001531562.1 CDS Dshi_0212 NC_009952.1 209373 210074 R PFAM: response regulator receiver; transcriptional regulator domain protein KEGG: sit:TM1040_2441 two component transcriptional regulator, winged helix family; winged helix family; two component transcriptional regulator complement(209373..210074) Dinoroseobacter shibae DFL 12 = DSM 16493 5712137 YP_001531563.1 CDS pckA NC_009952.1 210410 212008 D PEP carboxykinase; PEP carboxylase; PEPCK; catalyzes the phosphorylation and decarboxylation of oxaloacetate to form phosphoenolpyruvate using ATP; phosphoenolpyruvate carboxykinase 210410..212008 Dinoroseobacter shibae DFL 12 = DSM 16493 5712138 YP_001531564.1 CDS hbdA NC_009952.1 212131 213006 R converts (S)-3-hydroxybutanoyl-CoA to 3-acetoacetyl-CoA; 3-hydroxybutyryl-CoA dehydrogenase complement(212131..213006) Dinoroseobacter shibae DFL 12 = DSM 16493 5712139 YP_001531565.1 CDS Dshi_0215 NC_009952.1 213167 214024 D KEGG: rde:RD1_1386 hypothetical protein; no significant swissprot; no IPR Scan results; hypothetical protein 213167..214024 Dinoroseobacter shibae DFL 12 = DSM 16493 5712140 YP_001531566.1 CDS eftA NC_009952.1 214091 215017 R PFAM: Electron transfer flavoprotein alpha/beta-subunit ; Electron transfer flavoprotein alpha subunit KEGG: rde:RD1_1387 electron transfer flavoprotein, alpha subunit, high swissprot; electron transfer flavoprotein subunit alpha complement(214091..215017) Dinoroseobacter shibae DFL 12 = DSM 16493 5712141 YP_001531567.1 CDS eftB NC_009952.1 215017 215775 R PFAM: Electron transfer flavoprotein alpha/beta-subunit KEGG: sil:SPO0720 electron transfer flavoprotein, beta subunit; high swissprot to Electron transfer flavoprotein subunit beta from Paracoccus denitrificans; electron transfer flavoprotein subunit beta complement(215017..215775) Dinoroseobacter shibae DFL 12 = DSM 16493 5712142 YP_001531568.1 CDS Dshi_0218 NC_009952.1 216003 216575 R TIGRFAM: ATP--cobalamin adenosyltransferase PFAM: cobalamin adenosyltransferase KEGG: rde:RD1_1389 cob(I)alamin adenosyltransferase, putative; putative ATP--cobalamin adenosyltransferase complement(216003..216575) Dinoroseobacter shibae DFL 12 = DSM 16493 5712143 YP_001531569.1 CDS Dshi_0219 NC_009952.1 216579 216794 R KEGG: rsq:Rsph17025_2554 hypothetical protein; no significant swissprot; no conserved domains; hypothetical protein complement(216579..216794) Dinoroseobacter shibae DFL 12 = DSM 16493 5712144 YP_001531570.1 CDS Dshi_0220 NC_009952.1 216879 217712 R PFAM: short-chain dehydrogenase/reductase SDR KEGG: rde:RD1_1391 oxidoreductase, putative; putative oxidoreductase NAD-/NADP-dependent complement(216879..217712) Dinoroseobacter shibae DFL 12 = DSM 16493 5712145 YP_001531571.1 CDS parC NC_009952.1 217806 220139 D decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling; DNA topoisomerase IV subunit A 217806..220139 Dinoroseobacter shibae DFL 12 = DSM 16493 5712146 YP_001531572.1 CDS Dshi_0222 NC_009952.1 220158 220832 D KEGG: rsh:Rsph17029_0330 hypothetical protein, no significant swissprot; hypothetical protein 220158..220832 Dinoroseobacter shibae DFL 12 = DSM 16493 5712147 YP_001531573.1 CDS tufA2 NC_009952.1 220923 222098 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 220923..222098 Dinoroseobacter shibae DFL 12 = DSM 16493 5712148 YP_001531574.1 CDS Dshi_0224 NC_009952.1 222170 223045 R bad Ref ZP hit to methyltransferase FkbM from Lyngbya sp. PCC 8106, no significant swissprot hit, conserved domain related to S-adenosyl-L-methionine-dependent methyltransferases; hypothetical protein complement(222170..223045) Dinoroseobacter shibae DFL 12 = DSM 16493 5712149 YP_001531575.1 CDS Dshi_0225 NC_009952.1 223884 224186 D KEGG: pde:Pden_3026 hypothetical protein, no swissprot, bad Ref hits, no conserved domains detected; hypothetical protein 223884..224186 Dinoroseobacter shibae DFL 12 = DSM 16493 5712151 YP_001531576.1 CDS Dshi_0226 NC_009952.1 224310 224642 R PFAM: protein of unknown function DUF1244 KEGG: sil:SPO3602 hypothetical protein; no significant swissprot hit; hypothetical protein complement(224310..224642) Dinoroseobacter shibae DFL 12 = DSM 16493 5712152 YP_001531577.1 CDS Dshi_0227 NC_009952.1 224639 225388 R PFAM: N-formylglutamate amidohydrolase KEGG: jan:Jann_0446 N-formylglutamate amidohydrolase; high Ref hit, but no significant swissprot hit; N-formylglutamate amidohydrolase complement(224639..225388) Dinoroseobacter shibae DFL 12 = DSM 16493 5712153 YP_001531578.1 CDS pykA NC_009952.1 225543 226991 D KEGG: rsp:RSP_1766 pyruvate kinase TIGRFAM: pyruvate kinase PFAM: Pyruvate kinase barrel; Pyruvate kinase alpha/beta; high swissprot; pyruvate kinase 225543..226991 Dinoroseobacter shibae DFL 12 = DSM 16493 5712154 YP_001531579.1 CDS Dshi_0229 NC_009952.1 226996 227220 D bad BLAST hits, best swissprot to Prolyl-tRNA synthetase from Haemophilus ducreyi, but very unsure; no conserved domains detected; hypothetical protein 226996..227220 Dinoroseobacter shibae DFL 12 = DSM 16493 5712155 YP_001531580.1 CDS rpmI NC_009952.1 227567 227767 D PFAM: ribosomal protein L35 KEGG: sil:SPO3599 ribosomal protein L35; high swissprot; 50S ribosomal protein L35 227567..227767 Dinoroseobacter shibae DFL 12 = DSM 16493 5712156 YP_001531581.1 CDS rplT NC_009952.1 227780 228145 D binds directly to 23S ribosomal RNA prior to in vitro assembly of the 50S ribosomal subunit; 50S ribosomal protein L20 227780..228145 Dinoroseobacter shibae DFL 12 = DSM 16493 5712157 YP_001531582.1 CDS Dshi_0232 NC_009952.1 228403 229473 D KEGG: sil:SPO2161 hypothetical protein; no significant swissprot, best Ref ZP hit to type I secretion target repeat protein from Roseovarius sp. 217; Hedgehog hintN domain detected; hypothetical protein 228403..229473 Dinoroseobacter shibae DFL 12 = DSM 16493 5712158 YP_001531583.1 CDS Dshi_0233 NC_009952.1 229629 231512 D PFAM: Citrate transporter KEGG: mgm:Mmc1_1728 citrate transporter; best Ref ZP hit to sulfur deprivation response regulator from Rhodobacterales bacterium HTCC2150, best swissprot toUncharacterized transporter sll0640 from Synechocystis sp. PCC 6803; CitMHS domain detected (citrate transporter); putative citrate transporter 229629..231512 Dinoroseobacter shibae DFL 12 = DSM 16493 5712159 YP_001531584.1 CDS Dshi_0234 NC_009952.1 231585 232649 D KEGG: sil:SPO2161 hypothetical protein; no significant swissprot hit, Hedgehog/intein (Hint) domain, Ref ZP hit to type I secretion target repeat protein fromRoseovarius sp. 217; same like Dshi_232; hypothetical protein 231585..232649 Dinoroseobacter shibae DFL 12 = DSM 16493 5712160 YP_001531585.1 CDS pheS NC_009952.1 232709 233782 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 heterotetramer of alpha(2)beta(2); binds two magnesium ions per tetramer; type 1 subfamily; phenylalanyl-tRNA synthetase subunit alpha 232709..233782 Dinoroseobacter shibae DFL 12 = DSM 16493 5712161 YP_001531586.1 CDS Dshi_0236 NC_009952.1 233956 234210 D no swissprot, bad Ref ZP hit to phenylalanyl-tRNA synthetase beta subunit from Loktanella vestfoldensis SKA53, no conserved domains, just short signalpeptide and two transmembrane regions, bad GC frame plot, maybe Dshi_0236 is part of Dshi_0237?; hypothetical protein 233956..234210 Dinoroseobacter shibae DFL 12 = DSM 16493 5712162 YP_001531587.1 CDS pheT NC_009952.1 234571 236967 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 234571..236967 Dinoroseobacter shibae DFL 12 = DSM 16493 5712163 YP_001531588.1 CDS Dshi_0238 NC_009952.1 237254 237724 D KEGG: sil:SPO3492 hypothetical protein; no swissprot; best Ref hit to succinate dehydrogenase iron-sulfur subunit from Roseobacter sp. AzwK-3b; no conserved domains; hypothetical protein 237254..237724 Dinoroseobacter shibae DFL 12 = DSM 16493 5712164 YP_001531589.1 CDS nadX NC_009952.1 237729 238490 R PFAM: aspartate dehydrogenase; homoserine dehydrogenase NAD-binding KEGG: mes:Meso_0824 aspartate dehydrogenase; aspartate dehydrogenase complement(237729..238490) Dinoroseobacter shibae DFL 12 = DSM 16493 5712165 YP_001531590.1 CDS gst3 NC_009952.1 238487 239185 R PFAM: Glutathione S-transferase domain KEGG: sil:SPO3494 glutathione S-transferase family protein; glutathione S-transferase domain-containing protein complement(238487..239185) Dinoroseobacter shibae DFL 12 = DSM 16493 5712166 YP_001531591.1 CDS mscL NC_009952.1 239334 239729 D TIGRFAM: large conductance mechanosensitive channel protein PFAM: large-conductance mechanosensitive channel KEGG: jan:Jann_0457 large conductance mechanosensitive channel protein; large conductance mechanosensitive channel protein 239334..239729 Dinoroseobacter shibae DFL 12 = DSM 16493 5712167 YP_001531592.1 CDS Dshi_0242 NC_009952.1 239815 240792 D PFAM: fatty acid hydroxylase KEGG: hne:HNE_0606 hypothetical protein; no significant swissprot hit, middle Ref YP hit to hypothetical protein HNE_0606 from Hyphomonas neptunium ATCC 15444, Erg3 domain: sterol desaturase and fatty acid hydroxylase superfamily domain; hypothetical protein 239815..240792 Dinoroseobacter shibae DFL 12 = DSM 16493 5712168 YP_001531593.1 CDS Dshi_0243 NC_009952.1 240789 241940 D PFAM: acyltransferase 3 KEGG: hne:HNE_0605 acyltransferase family protein; bad swissprot to transferases, middle Ref YP hit to acyltransferase family protein from Hyphomonas neptunium ATCC 15444; acyltransferase family protein 240789..241940 Dinoroseobacter shibae DFL 12 = DSM 16493 5712169 YP_001531594.1 CDS adh NC_009952.1 241950 243065 R TIGRFAM: alanine dehydrogenase PFAM: D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding; alanine dehydrogenase/PNT domain protein KEGG: sit:TM1040_3628 alanine dehydrogenase; high swissprot; alanine dehydrogenase complement(241950..243065) Dinoroseobacter shibae DFL 12 = DSM 16493 5712170 YP_001531595.1 CDS asnC NC_009952.1 243155 243664 D PFAM: regulatory protein AsnC/Lrp family KEGG: jan:Jann_0459 transcriptional regulator, AsnC family; AsnC family; transcriptional regulator 243155..243664 Dinoroseobacter shibae DFL 12 = DSM 16493 5712171 YP_001531596.1 CDS rpsU NC_009952.1 243756 243962 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(243756..243962) Dinoroseobacter shibae DFL 12 = DSM 16493 5712172 YP_001531597.1 CDS Dshi_0247 NC_009952.1 244084 244782 D TIGRFAM: rpsU-divergently transcribed protein PFAM: COQ9 domain protein KEGG: rde:RD1_1038 hypothetical protein, best Ref hits to hypothetical proteins, middel swissprot hit to Ubiquinone biosynthesis protein COQ9 from Drosophila melanogaster (fruit fly), gene arrangement with following gene (Dshi_0248 quinone oxidoreductase)?; hypothetical protein 244084..244782 Dinoroseobacter shibae DFL 12 = DSM 16493 5712173 YP_001531598.1 CDS Dshi_0248 NC_009952.1 244793 245779 D TIGRFAM: Quinone oxidoreductase putative PIG3 PFAM: Alcohol dehydrogenase zinc-binding domain protein; Alcohol dehydrogenase GroES domain protein KEGG: rsq:Rsph17025_2435 alcohol dehydrogenase, zinc-binding domain protein; quinone oxidoreductase putative PIG3 244793..245779 Dinoroseobacter shibae DFL 12 = DSM 16493 5712174 YP_001531599.1 CDS Dshi_0249 NC_009952.1 246115 246699 R located downstream of an ORF representing the N-terminal part of RND subunit, putative sequencing error colocated with MFP subunit; pfam00873,; RND family, C-terminal part of RND subunit; efflux transporter complement(246115..246699) Dinoroseobacter shibae DFL 12 = DSM 16493 5712175 YP_001531600.1 CDS Dshi_0250 NC_009952.1 246745 249237 R located upstream of an ORF representing the C-terminal part of RND subunit, putative sequencing error colocated with MFP subunit; pfam00873,; RND family, N-terminal part of RND subunit; efflux transporter complement(246745..249237) Dinoroseobacter shibae DFL 12 = DSM 16493 5712176 YP_001531601.1 CDS Dshi_0251 NC_009952.1 249241 250392 R colocated with RND subunit; TIGRFAM: efflux transporter, RND family, MFP subunit PFAM: secretion protein HlyD family protein KEGG: jan:Jann_1310 secretion protein HlyD; RND family, MFP subunit; efflux transporter complement(249241..250392) Dinoroseobacter shibae DFL 12 = DSM 16493 5712177 YP_001531602.1 CDS Dshi_0252 NC_009952.1 250470 251144 D PFAM: regulatory protein TetR KEGG: jan:Jann_1309 transcriptional regulator, TetR family; TetR family; transcriptional regulator 250470..251144 Dinoroseobacter shibae DFL 12 = DSM 16493 5712178 YP_001531603.1 CDS Dshi_0253 NC_009952.1 251200 252759 D PFAM: AMP-dependent synthetase and ligase KEGG: sil:SPO0801 4-coumarate:CoA ligase; high swissprot to 4-coumarate--CoA ligase 1 from Nicotiana tabacum; acyl-CoA synthetase/AMP-acid ligase II 251200..252759 Dinoroseobacter shibae DFL 12 = DSM 16493 5712179 YP_001531604.1 CDS Dshi_0254 NC_009952.1 252790 253431 R PFAM: ribonuclease T2 KEGG: jan:Jann_3879 ribonuclease T2, unsure GC frame plot; ribonuclease T2 complement(252790..253431) Dinoroseobacter shibae DFL 12 = DSM 16493 5712180 YP_001531605.1 CDS Dshi_0255 NC_009952.1 253588 254340 D PFAM: protein of unknown function DUF1013 KEGG: rde:RD1_1043 hypothetical protein; hypothetical protein 253588..254340 Dinoroseobacter shibae DFL 12 = DSM 16493 5712181 YP_001531606.1 CDS Dshi_0256 NC_009952.1 254419 254667 R no significant BLAST hits, no conserved domains; hypothetical protein complement(254419..254667) Dinoroseobacter shibae DFL 12 = DSM 16493 5712182 YP_001531607.1 CDS Dshi_0257 NC_009952.1 254727 256076 R PFAM: peptidase S8 and S53 subtilisin kexin sedolisin KEGG: sma:SAV5709 protease; good swissprot to Subtilisin E precursor from Bacillus subtilis; peptidase S8/S53 subtilisin kexin sedolisin complement(254727..256076) Dinoroseobacter shibae DFL 12 = DSM 16493 5712183 YP_001531608.1 CDS secE NC_009952.1 256271 256471 D part of the sec system translocase; preprotein translocase subunit SecE 256271..256471 Dinoroseobacter shibae DFL 12 = DSM 16493 5712184 YP_001531609.1 CDS nusG NC_009952.1 256673 257206 D TIGRFAM: transcription termination/antitermination factor NusG PFAM: KOW domain protein; NGN domain protein KEGG: rsq:Rsph17025_2547 NusG antitermination factor; NusG antitermination factor 256673..257206 Dinoroseobacter shibae DFL 12 = DSM 16493 5712185 YP_001531610.1 CDS rplK NC_009952.1 257310 257735 D binds directly to 23S ribosomal RNA; 50S ribosomal protein L11 257310..257735 Dinoroseobacter shibae DFL 12 = DSM 16493 5712186 YP_001531611.1 CDS rplA NC_009952.1 257737 258435 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 257737..258435 Dinoroseobacter shibae DFL 12 = DSM 16493 5712187 YP_001531612.1 CDS Dshi_0262 NC_009952.1 258788 259516 D KEGG: jan:Jann_2686 hypothetical protein; PEP-CTERM putative exosortase interaction domain; no significant swissprot, bad Ref hits; hypothetical protein 258788..259516 Dinoroseobacter shibae DFL 12 = DSM 16493 5712188 YP_001531613.1 CDS fkbM NC_009952.1 259644 260429 D TIGRFAM: methyltransferase FkbM family KEGG: jan:Jann_0310 methyltransferase FkbM; no significant swissprot; FkbM family methyltransferase 259644..260429 Dinoroseobacter shibae DFL 12 = DSM 16493 5712189 YP_001531614.1 CDS Dshi_0264 NC_009952.1 260484 261542 D KEGG: jan:Jann_2490 hemolysin-type calcium-binding protein, middle Ref hits to hypothetical proteins, no swissprot, C-terminal beginning of unsure GC frame plot; hypothetical protein 260484..261542 Dinoroseobacter shibae DFL 12 = DSM 16493 5712190 YP_001531615.1 CDS rplJ NC_009952.1 261837 262355 D binds the two ribosomal protein L7/L12 dimers and anchors them to the large ribosomal subunit; 50S ribosomal protein L10 261837..262355 Dinoroseobacter shibae DFL 12 = DSM 16493 5712191 YP_001531616.1 CDS rplL NC_009952.1 262428 262808 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 262428..262808 Dinoroseobacter shibae DFL 12 = DSM 16493 5712192 YP_001531617.1 CDS Dshi_0267 NC_009952.1 262945 264294 D KEGG: pde:Pden_2598 PpiC-type peptidyl-prolyl cis-trans isomerase; bad BLAST hits, unsure GC frame plot, RBS site AGGAT; hypothetical protein 262945..264294 Dinoroseobacter shibae DFL 12 = DSM 16493 5712193 YP_001531618.1 CDS rpoB NC_009952.1 264787 268923 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 264787..268923 Dinoroseobacter shibae DFL 12 = DSM 16493 5712194 YP_001531619.1 CDS rpoC NC_009952.1 269021 273268 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' 269021..273268 Dinoroseobacter shibae DFL 12 = DSM 16493 5711519 YP_001531620.1 CDS Dshi_0270 NC_009952.1 273419 274324 D PFAM: protein of unknown function DUF6 transmembrane KEGG: sil:SPO3504 hypothetical protein; best Ref ZP hit to membrane protein, putative and bad swissprot to S-adenosylmethionine uptake transporter from Rickettsia typhi; hypothetical protein 273419..274324 Dinoroseobacter shibae DFL 12 = DSM 16493 5711520 YP_001531621.1 CDS rpsL NC_009952.1 274606 274977 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 274606..274977 Dinoroseobacter shibae DFL 12 = DSM 16493 5711521 YP_001531622.1 CDS rpsG NC_009952.1 274990 275460 D binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit; 30S ribosomal protein S7 274990..275460 Dinoroseobacter shibae DFL 12 = DSM 16493 5711522 YP_001531623.1 CDS fusA NC_009952.1 275486 277603 D EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene; elongation factor G 275486..277603 Dinoroseobacter shibae DFL 12 = DSM 16493 5711523 YP_001531624.1 CDS tufA1 NC_009952.1 277686 278861 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 277686..278861 Dinoroseobacter shibae DFL 12 = DSM 16493 5711524 YP_001531625.1 CDS rpsJ NC_009952.1 278960 279280 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 278960..279280 Dinoroseobacter shibae DFL 12 = DSM 16493 5711525 YP_001531626.1 CDS rplC NC_009952.1 279295 280134 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 279295..280134 Dinoroseobacter shibae DFL 12 = DSM 16493 5711526 YP_001531627.1 CDS rplD NC_009952.1 280131 280748 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 280131..280748 Dinoroseobacter shibae DFL 12 = DSM 16493 5711527 YP_001531628.1 CDS rplW NC_009952.1 280745 281041 D binds third domain of 23S rRNA and protein L29; part of exit tunnel; 50S ribosomal protein L23 280745..281041 Dinoroseobacter shibae DFL 12 = DSM 16493 5711528 YP_001531629.1 CDS Dshi_0279 NC_009952.1 281137 281487 R no significant BLAST hits, no conserved domains, unsure GC frame plot; hypothetical protein complement(281137..281487) Dinoroseobacter shibae DFL 12 = DSM 16493 5711529 YP_001531630.1 CDS Dshi_0280 NC_009952.1 281779 282159 R KEGG: rde:RD1_1404 hypothetical protein, no significant swissprot hit, unsure GC frame plot; hypothetical protein complement(281779..282159) Dinoroseobacter shibae DFL 12 = DSM 16493 5711530 YP_001531631.1 CDS Dshi_0281 NC_009952.1 282323 282814 R KEGG: rde:RD1_3741 YHS domain protein, no swissprot; is located in the midst of a unsure GC frame plot region; YHS domain-containing protein complement(282323..282814) Dinoroseobacter shibae DFL 12 = DSM 16493 5711531 YP_001531632.1 CDS Dshi_0282 NC_009952.1 283471 283737 D no swissprot, bad Ref hits, no conserved domains, unsure GC frame plot; hypothetical protein 283471..283737 Dinoroseobacter shibae DFL 12 = DSM 16493 5711532 YP_001531633.1 CDS Dshi_0283 NC_009952.1 283818 284120 D no swissprot, bad Ref hits, no conserved domains, unsure GC frame plot; hypothetical protein 283818..284120 Dinoroseobacter shibae DFL 12 = DSM 16493 5711533 YP_001531634.1 CDS Dshi_0284 NC_009952.1 284463 285113 D KEGG: rsq:Rsph17025_2139 hypothetical protein; bad swissprot to 31 kDa outer-membrane immunogenic protein precursor from Brucella melitensis; middle Ref ZP hit to possible outer membrane protein from Roseovarius sp. 217; Autotransporter beta-domain; putative outer membrane protein 284463..285113 Dinoroseobacter shibae DFL 12 = DSM 16493 5711534 YP_001531635.1 CDS rplB NC_009952.1 285409 286251 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 285409..286251 Dinoroseobacter shibae DFL 12 = DSM 16493 5711535 YP_001531636.1 CDS rpsS NC_009952.1 286255 286533 D protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA; 30S ribosomal protein S19 286255..286533 Dinoroseobacter shibae DFL 12 = DSM 16493 5711536 YP_001531637.1 CDS rplV NC_009952.1 286537 286917 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 286537..286917 Dinoroseobacter shibae DFL 12 = DSM 16493 5711537 YP_001531638.1 CDS rpsC NC_009952.1 286917 287639 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 286917..287639 Dinoroseobacter shibae DFL 12 = DSM 16493 5711538 YP_001531639.1 CDS rplP NC_009952.1 287653 288066 D located in the peptidyl transferase center and may be involved in peptidyl transferase activity; similar to archaeal L10e; 50S ribosomal protein L16 287653..288066 Dinoroseobacter shibae DFL 12 = DSM 16493 5711539 YP_001531640.1 CDS Dshi_0290 NC_009952.1 288217 288447 D KEGG: sit:TM1040_3827 hypothetical protein; short signalpeptide and three transmembrane region; no swissprot, bad Ref hits to hypothetical proteins; hypothetical protein 288217..288447 Dinoroseobacter shibae DFL 12 = DSM 16493 5711540 YP_001531641.1 CDS Dshi_0291 NC_009952.1 289020 289409 R KEGG: rde:RD1_0735 hypothetical protein; bad Ref hits to hypothetical proteins; short signalpeptide and four transmembrane regions; no significant swissprot; hypothetical protein complement(289020..289409) Dinoroseobacter shibae DFL 12 = DSM 16493 5711541 YP_001531642.1 CDS Dshi_0292 NC_009952.1 289461 290186 R KEGG: sil:SPO0491 hypothetical protein; no swissprot; TIGR02466 conserved hypothetical protein; hypothetical protein complement(289461..290186) Dinoroseobacter shibae DFL 12 = DSM 16493 5711542 YP_001531643.1 CDS rpmC NC_009952.1 290274 290480 D one of the stabilizing components for the large ribosomal subunit; 50S ribosomal protein L29 290274..290480 Dinoroseobacter shibae DFL 12 = DSM 16493 5711543 YP_001531644.1 CDS rpsQ NC_009952.1 290493 290723 D PFAM: ribosomal protein S17 KEGG: sit:TM1040_0263 ribosomal protein S17; 30S ribosomal protein S17 290493..290723 Dinoroseobacter shibae DFL 12 = DSM 16493 5711544 YP_001531645.1 CDS rplN NC_009952.1 290797 291165 D binds to the 23S rRNA between the centers for peptidyl transferase and GTPase; 50S ribosomal protein L14 290797..291165 Dinoroseobacter shibae DFL 12 = DSM 16493 5711545 YP_001531646.1 CDS rplX NC_009952.1 291165 291470 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 291165..291470 Dinoroseobacter shibae DFL 12 = DSM 16493 5711546 YP_001531647.1 CDS rplE NC_009952.1 291470 292033 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 291470..292033 Dinoroseobacter shibae DFL 12 = DSM 16493 5711547 YP_001531648.1 CDS rpsN NC_009952.1 292052 292357 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 292052..292357 Dinoroseobacter shibae DFL 12 = DSM 16493 5711548 YP_001531649.1 CDS rpsH NC_009952.1 292371 292763 D binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit; 30S ribosomal protein S8 292371..292763 Dinoroseobacter shibae DFL 12 = DSM 16493 5711549 YP_001531650.1 CDS rplF NC_009952.1 292776 293309 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 292776..293309 Dinoroseobacter shibae DFL 12 = DSM 16493 5711550 YP_001531651.1 CDS rplR NC_009952.1 293321 293680 D binds 5S rRNA along with protein L5 and L25; 50S ribosomal protein L18 293321..293680 Dinoroseobacter shibae DFL 12 = DSM 16493 5711551 YP_001531652.1 CDS rpsE NC_009952.1 293839 294414 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 293839..294414 Dinoroseobacter shibae DFL 12 = DSM 16493 5711552 YP_001531653.1 CDS rpmD NC_009952.1 294427 294615 D L30 binds domain II of the 23S rRNA and the 5S rRNA; similar to eukaryotic protein L7; 50S ribosomal protein L30 294427..294615 Dinoroseobacter shibae DFL 12 = DSM 16493 5711553 YP_001531654.1 CDS rplO NC_009952.1 294758 295231 D late assembly protein; 50S ribosomal protein L15 294758..295231 Dinoroseobacter shibae DFL 12 = DSM 16493 5711554 YP_001531655.1 CDS secY NC_009952.1 295343 296704 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 295343..296704 Dinoroseobacter shibae DFL 12 = DSM 16493 5711555 YP_001531656.1 CDS adk NC_009952.1 296701 297342 D essential enzyme that recycles AMP in active cells; converts ATP and AMP to two molecules of ADP; adenylate kinase 296701..297342 Dinoroseobacter shibae DFL 12 = DSM 16493 5711556 YP_001531657.1 CDS rpsM NC_009952.1 297504 297947 D PFAM: ribosomal protein S13 KEGG: sil:SPO0509 ribosomal protein S13; 30S ribosomal protein S13 297504..297947 Dinoroseobacter shibae DFL 12 = DSM 16493 5711557 YP_001531658.1 CDS rpsK NC_009952.1 297963 298352 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 297963..298352 Dinoroseobacter shibae DFL 12 = DSM 16493 5711558 YP_001531659.1 CDS rpoA NC_009952.1 298455 299486 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 298455..299486 Dinoroseobacter shibae DFL 12 = DSM 16493 5711559 YP_001531660.1 CDS rplQ NC_009952.1 299605 300021 D is a component of the macrolide binding site in the peptidyl transferase center; 50S ribosomal protein L17 299605..300021 Dinoroseobacter shibae DFL 12 = DSM 16493 5711560 YP_001531661.1 CDS luxR1 NC_009952.1 300364 300975 D PFAM: regulatory protein LuxR; Autoinducer-binding domain protein KEGG: pde:Pden_0786 response regulator receiver protein, Autoinducer binding domain pfam03472, HTH-LuxR domain pfam00196; LuxR family; transcriptional regulator 300364..300975 Dinoroseobacter shibae DFL 12 = DSM 16493 5711561 YP_001531662.1 CDS luxI NC_009952.1 301032 301619 D KEGG: pde:Pden_0787 N-acyl-L-homoserine lactone synthetase-like; N-acyl-L-homoserine lactone synthetase-like protein 301032..301619 Dinoroseobacter shibae DFL 12 = DSM 16493 5711562 YP_001531663.1 CDS Dshi_0313 NC_009952.1 301799 303109 D PFAM: magnesium chelatase ChlI subunit; AAA ATPase central domain protein; ATPase associated with various cellular activities AAA_5 SMART: AAA ATPase KEGG: sil:SPO0515 ATPase, AAA family; recombination factor protein RarA 301799..303109 Dinoroseobacter shibae DFL 12 = DSM 16493 5711563 YP_001531664.1 CDS Dshi_0314 NC_009952.1 303192 303521 D PFAM: Camphor resistance CrcB protein KEGG: rde:RD1_1440 CrcB-like protein; COG0239 Integral membrane protein possibly involved in chromosome condensation; integral membrane protein 303192..303521 Dinoroseobacter shibae DFL 12 = DSM 16493 5711564 YP_001531665.1 CDS rluC NC_009952.1 303518 304564 D high Ref YP hit to Pseudouridine synthase, RluD from Jannaschia sp. CCS1 and middle swissprot hit to Ribosomal large subunit pseudouridine synthase C from Pasteurella multocida; RNA binding and rluC domain (PF00849); ribosomal large subunit pseudouridine synthase C 303518..304564 Dinoroseobacter shibae DFL 12 = DSM 16493 5711565 YP_001531666.1 CDS gph NC_009952.1 304561 305241 D TIGRFAM: HAD-superfamily hydrolase, subfamily IA, variant 3; HAD-superfamily hydrolase, subfamily IA, variant 1 PFAM: Haloacid dehalogenase domain protein hydrolase KEGG: rde:RD1_1442 hydrolase, putative; PGPase; phosphoglycolate phosphatase 304561..305241 Dinoroseobacter shibae DFL 12 = DSM 16493 5711566 YP_001531667.1 CDS Dshi_0317 NC_009952.1 305238 305942 D PFAM: ATP12 ATPase KEGG: rsp:RSP_1746 hypothetical protein; good Ref hits to ATP12 proteins, also middle swissprot hit toATP synthase mitochondrial F1 complex assembly factor 2, mitochondrial precursor (ATP12 homolog) from Homo sapiens; ATP12 chaperone protein 305238..305942 Dinoroseobacter shibae DFL 12 = DSM 16493 5711567 YP_001531668.1 CDS bztA NC_009952.1 306292 307308 D TIGRFAM: cationic amino acid ABC transporter, periplasmic binding protein SMART: extracellular solute-binding protein family 3 KEGG: sil:SPO0519 glutamate/glutamine/aspartate/asparagine ABC transporter, periplasmic substrate-binding protein; high swissprot hit to Glutamate/glutamine/aspartate/asparagine-binding protein bztA from Rhodobacter capsulatus; RBS site AGGAT; glutamate/glutamine/aspartate/asparagine ABC transporter 306292..307308 Dinoroseobacter shibae DFL 12 = DSM 16493 5711568 YP_001531669.1 CDS bztB NC_009952.1 307429 308664 D TIGRFAM: polar amino acid ABC transporter, inner membrane subunit PFAM: binding-protein-dependent transport systems inner membrane component KEGG: rde:RD1_1445 glutamate/glutamine/aspartate/asparagine transport system permease protein, high swissprot; glutamate/glutamine/aspartate/asparagine ABC transport system permease 307429..308664 Dinoroseobacter shibae DFL 12 = DSM 16493 5711569 YP_001531670.1 CDS bztC NC_009952.1 308666 309964 D TIGRFAM: polar amino acid ABC transporter, inner membrane subunit PFAM: binding-protein-dependent transport systems inner membrane component KEGG: rde:RD1_1446 amino acid ABC transporter, permease protein, high swissprot to Glutamate/glutamine/aspartate/asparagine transport system permease from Rhodobacter capsulatus; glutamate/glutamine/aspartate/asparagine ABC transport system permease 308666..309964 Dinoroseobacter shibae DFL 12 = DSM 16493 5711570 YP_001531671.1 CDS bztD NC_009952.1 309980 310756 D PFAM: ABC transporter related SMART: AAA ATPase KEGG: jan:Jann_0630 ABC transporter related, high swissprot hit to Glutamate/glutamine/aspartate/asparagine transport ATP-binding from Rhodobacter capsulatus; glutamate/glutamine/aspartate/asparagine ABC transport ATP-binding 309980..310756 Dinoroseobacter shibae DFL 12 = DSM 16493 5711571 YP_001531672.1 CDS Dshi_0322 NC_009952.1 310800 311300 R PFAM: Phosphoglycerate mutase KEGG: sil:SPO0523 phosphoglycerate mutase family protein; COG2062 Phosphohistidine phosphatase SixA; best Ref hits to hypothetical proteins; putative phosphatase complement(310800..311300) Dinoroseobacter shibae DFL 12 = DSM 16493 5711572 YP_001531673.1 CDS Dshi_0323 NC_009952.1 311297 311920 R KEGG: rde:RD1_1449 hypothetical protein, no significant swissprot; no conserved domains detected; hypothetical protein complement(311297..311920) Dinoroseobacter shibae DFL 12 = DSM 16493 5711573 YP_001531674.1 CDS argB NC_009952.1 311973 312836 R catalyzes the phosphorylation of N-acetyl-L-glutamate to form N-acetyl-L-glutamate 5-phosphate; acetylglutamate kinase complement(311973..312836) Dinoroseobacter shibae DFL 12 = DSM 16493 5711574 YP_001531675.1 CDS fabG3 NC_009952.1 312924 313655 D PFAM: short-chain dehydrogenase/reductase SDR , good swissprot hit to Protein fixR from Bradyrhizobium japonicum, fabG NCBI domain, good Ref ZP hit toShort-chain alcohol dehydrogenase from Rhodobacterales bacterium HTCC2150; 3-ketoacyl-ACP reductase 312924..313655 Dinoroseobacter shibae DFL 12 = DSM 16493 5711575 YP_001531676.1 CDS engB NC_009952.1 313718 314371 R 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 complement(313718..314371) Dinoroseobacter shibae DFL 12 = DSM 16493 5711576 YP_001531677.1 CDS mosc NC_009952.1 314368 315117 R PFAM: MOSC domain containing protein; MOSC domain protein beta barrel domain protein KEGG: sil:SPO0531 MOSC domain protein, swissprot hit to Molybdenum cofactor sulfurase from Mus musculus; MOSC domain-containing protein complement(314368..315117) Dinoroseobacter shibae DFL 12 = DSM 16493 5711577 YP_001531678.1 CDS yidC NC_009952.1 315114 316934 R 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; putative inner membrane protein translocase component YidC complement(315114..316934) Dinoroseobacter shibae DFL 12 = DSM 16493 5711578 YP_001531679.1 CDS ydaM NC_009952.1 317056 318645 R TIGRFAM: diguanylate cyclase PFAM: GGDEF domain containing protein; EAL domain protein KEGG: sil:SPO0533 diguanylate cyclase, putative; diguanylate cyclase/phosphodiesterase complement(317056..318645) Dinoroseobacter shibae DFL 12 = DSM 16493 5711579 YP_001531680.1 CDS ydaO NC_009952.1 318693 319556 R TtcA; YdaO; catalyzes the thiolation of cytosine 32 in specific tRNAs; C32 tRNA thiolase complement(318693..319556) Dinoroseobacter shibae DFL 12 = DSM 16493 5711580 YP_001531681.1 CDS Dshi_0331 NC_009952.1 319810 320031 R PFAM: protein of unknown function DUF37; middle swissprot hit to UPF0161 protein RD1_1458 from Roseobacter denitrificans OCh 114 and middle Ref ZP hit to hypothetical protein SKA53_00415 from Loktanella vestfoldensis SKA53; hypothetical protein complement(319810..320031) Dinoroseobacter shibae DFL 12 = DSM 16493 5711582 YP_001531682.1 CDS rnpA NC_009952.1 320028 320417 R TIGRFAM: ribonuclease P protein component PFAM: ribonuclease P protein , middle swissprot hit to Ribonuclease P protein component from Silicibacter pomeroyi and middle Ref ZP hit toribonuclease P protein component from Roseobacter sp. CCS2; ribonuclease P protein component complement(320028..320417) Dinoroseobacter shibae DFL 12 = DSM 16493 5711583 YP_001531683.1 CDS rpmH NC_009952.1 320480 320614 R in Escherichia coli transcription of this gene is enhanced by polyamines; 50S ribosomal protein L34 complement(320480..320614) Dinoroseobacter shibae DFL 12 = DSM 16493 5711584 YP_001531684.1 CDS Dshi_0334 NC_009952.1 320898 322301 R PFAM: ATP-binding region ATPase domain protein; histidine kinase HAMP region domain protein; histidine kinase A domain protein; low swissprot hit to Sensor protein zraS (a membrane-associated protein kinase that phosphorylates zraR in response to high concentrations of zinc or lead in the medium) from Salmonella typhimurium and high Ref ZP hit to periplasmic sensor signal transduction histidine kinase from R; integral membrane sensor signal transduction histidine kinase complement(320898..322301) Dinoroseobacter shibae DFL 12 = DSM 16493 5711586 YP_001531685.1 CDS merA NC_009952.1 322338 323750 R PFAM: FAD-dependent pyridine nucleotide-disulphide oxidoreductase; pyridine nucleotide-disulphide oxidoreductase dimerisation region; high swissprot to Mercuric reductase from Bacillus cereus and high Ref ZP hit to mercuric reductase, putative from Roseovarius sp. TM1035; putative mercuric reductase MerA complement(322338..323750) Dinoroseobacter shibae DFL 12 = DSM 16493 5711587 YP_001531686.1 CDS Dshi_0336 NC_009952.1 323755 324486 R PFAM: SNARE associated Golgi protein KEGG: rde:RD1_1463 mercuric reductase; the mercuric reductase MerA also comprises a SNARE associated Golgi protein motif, low swissprot hit to UPF0043 membrane protein ydjX from Escherichia coli K12 and good Ref ZP hit to hypothetical protein RCCS2_07124 from Roseobacter sp. CCS2; also good Ref YP hit to mercuric reductase from Roseobacter denitrificans OCh 114; possible Gene arrangement with Dshi_0335; hypothetical protein complement(323755..324486) Dinoroseobacter shibae DFL 12 = DSM 16493 5711245 YP_001531687.1 CDS parA2 NC_009952.1 325428 326237 R PFAM: ATPase MipZ KEGG: jan:Jann_0738 ATPases involved in chromosome partitioning-like;alternative gene name: mipZ; chromosome partitioning ATPase complement(325428..326237) Dinoroseobacter shibae DFL 12 = DSM 16493 5711246 YP_001531688.1 CDS Dshi_0338 NC_009952.1 326619 327452 D PFAM: beta-lactamase domain protein KEGG: sil:SPO2170 metallo-beta-lactamase family protein; NCBI conserved domains:GloB, Zn-dependent hydrolases, including glyoxylases; no significant swissprot; metallo-beta-lactamase family protein 326619..327452 Dinoroseobacter shibae DFL 12 = DSM 16493 5711247 YP_001531689.1 CDS Dshi_0339 NC_009952.1 327660 328538 R PFAM: protein of unknown function DUF849 KEGG: bur:Bcep18194_B0612 protein of unknown function DUF849, no significant swissprot; hypothetical protein complement(327660..328538) Dinoroseobacter shibae DFL 12 = DSM 16493 5711248 YP_001531690.1 CDS rpmE NC_009952.1 328656 328877 R RpmE; there appears to be two types of ribosomal proteins L31 in bacterial genomes; some contain a CxxC motif while others do not; Bacillus subtilis has both types; the proteins in this cluster do not have the CXXC motif; RpmE is found in exponentially growing Bacilli while YtiA was found after exponential growth; expression of ytiA is controlled by a zinc-specific transcriptional repressor; RpmE contains one zinc ion and a CxxC motif is responsible for this binding; forms an RNP particle along with proteins L5, L18, and L25 and 5S rRNA; found crosslinked to L2 and L25 and EF-G; may be near the peptidyltransferase site of the 50S ribosome; 50S ribosomal protein L31 complement(328656..328877) Dinoroseobacter shibae DFL 12 = DSM 16493 5711249 YP_001531691.1 CDS rplS NC_009952.1 328889 329263 R 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 complement(328889..329263) Dinoroseobacter shibae DFL 12 = DSM 16493 5711250 YP_001531692.1 CDS trmD NC_009952.1 329524 330321 R KEGG: rsq:Rsph17025_0184 tRNA (guanine-N1)-methyltransferase TIGRFAM: tRNA (guanine-N1)-methyltransferase PFAM: tRNA (guanine-N1-)-methyltransferase; tRNA (guanine-N1)-methyltransferase complement(329524..330321) Dinoroseobacter shibae DFL 12 = DSM 16493 5711251 YP_001531693.1 CDS aph NC_009952.1 330412 331401 D PFAM: aminoglycoside phosphotransferase KEGG: sit:TM1040_2610 hypothetical protein; no significant swissprot hit; aminoglycoside phosphotransferase 330412..331401 Dinoroseobacter shibae DFL 12 = DSM 16493 5711252 YP_001531694.1 CDS rimM NC_009952.1 331421 331921 R Essential for efficient processing of 16S rRNA; 16S rRNA-processing protein RimM complement(331421..331921) Dinoroseobacter shibae DFL 12 = DSM 16493 5711253 YP_001531695.1 CDS Dshi_0345 NC_009952.1 331918 332064 R no significant BLAST hits, unsure prosite hit to ribosomal protein S2; hypothetical protein complement(331918..332064) Dinoroseobacter shibae DFL 12 = DSM 16493 5711254 YP_001531696.1 CDS Dshi_0346 NC_009952.1 332071 332535 R PFAM: protein of unknown function DUF55 KEGG: mjl:Mjls_0045 protein of unknown function DUF55, bad swissprot hit to UPF0310 protein in gntR 5region fromBacillus licheniformis; bad Ref ZP hit to UPF0310 protein in gntR 5region fromBacillus licheniformis; hypothetical protein complement(332071..332535) Dinoroseobacter shibae DFL 12 = DSM 16493 5711255 YP_001531697.1 CDS bluB NC_009952.1 332537 333166 R KEGG: sil:SPO3254 cobalamin biosynthesis protein BluB TIGRFAM: cob(II)yrinic acid a,c-diamide reductase PFAM: nitroreductase; good swissprot hit toPutative cob(II)yrinic acid a,c-diamide reductase from Rhodobacter capsulatus; cob(II)yrinic acid a,c-diamide reductase complement(332537..333166) Dinoroseobacter shibae DFL 12 = DSM 16493 5711256 YP_001531698.1 CDS rpsP NC_009952.1 333195 333587 R 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 complement(333195..333587) Dinoroseobacter shibae DFL 12 = DSM 16493 5711257 YP_001531699.1 CDS pheA1 NC_009952.1 333629 333925 R catalyzes the interconversion of chorismate to prephenate; chorismate mutase complement(333629..333925) Dinoroseobacter shibae DFL 12 = DSM 16493 5711258 YP_001531700.1 CDS Dshi_0350 NC_009952.1 334046 334651 R KEGG: sit:TM1040_2605 hypothetical protein, no significant swissprot, good Ref YP hit to acetyltransferase, GNAT family from Roseobacter denitrificans OCh 114, NCBI conserved domains: rimL; hypothetical protein complement(334046..334651) Dinoroseobacter shibae DFL 12 = DSM 16493 5711259 YP_001531701.1 CDS Dshi_0351 NC_009952.1 334651 335166 R PFAM: GCN5-related N-acetyltransferase KEGG: jan:Jann_0752 GCN5-related N-acetyltransferase; middle Ref YP hit to GCN5-related N-acetyltransferase from Jannaschia sp. CCS1; NCBI conserved domains: rimL; N-acetyltransferase GCN5 complement(334651..335166) Dinoroseobacter shibae DFL 12 = DSM 16493 5711260 YP_001531702.1 CDS Dshi_0352 NC_009952.1 335163 335696 R middle Ref ZP hit to acetyltransferase, GNAT family protein from Roseobacter sp. CCS2, no significant swissprot, NCBI domains: rimL; prosite51186 GCN5-related N-acetyltransferase ; GNAT family; acetyltransferase complement(335163..335696) Dinoroseobacter shibae DFL 12 = DSM 16493 5711261 YP_001531703.1 CDS ffh NC_009952.1 335696 337210 R KEGG: rde:RD1_1315 signal recognition particle protein, putative 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; high swissprot to Signal recognition particle protein from Rickettsia typhi; signal recognition particle protein complement(335696..337210) Dinoroseobacter shibae DFL 12 = DSM 16493 5711262 YP_001531704.1 CDS azoR1 NC_009952.1 337582 338226 R Pfam02525 Flavodoxin-like fold, NCBI conserved domains PRK00170 azoreductase, middle Ref ZP hit to (Acyl-carrier protein) phosphodiesterase from Roseobacter sp. SK209-2-6, middle swissprot hit toFMN-dependent NADH-azoreductase 1 from Jannaschia sp. CCS1; at N-terminal unsure GC frame plot; FMN-dependent NADH-azoreductase 1 complement(337582..338226) Dinoroseobacter shibae DFL 12 = DSM 16493 5711263 YP_001531705.1 CDS lysR NC_009952.1 338282 339163 D PFAM: regulatory protein LysR; LysR substrate-binding KEGG: sit:TM1040_2599 transcriptional regulator, LysR family; high Ref Yp hit to transcriptional regulator, LysR family from Silicibacter sp. TM1040; LysR family; transcriptional regulator 338282..339163 Dinoroseobacter shibae DFL 12 = DSM 16493 5711264 YP_001531706.1 CDS Dshi_0356 NC_009952.1 339214 340104 D PFAM: protein of unknown function DUF6 transmembrane KEGG: rde:RD1_1318 integral membrane protein, putative; no significant swissprot; high Ref Yp hit to integral membrane protein, putative from Roseobacter denitrificans OCh 114, no conserved domains by NCBI; ten transmembrane regions; hypothetical protein 339214..340104 Dinoroseobacter shibae DFL 12 = DSM 16493 5711265 YP_001531707.1 CDS arsR NC_009952.1 340107 340445 R PFAM: regulatory protein ArsR KEGG: sit:TM1040_2597 transcriptional regulator, ArsR family; middle Ref ZP hit to transcriptional regulator, ArsR family protein from Roseovarius sp. TM1035; bad swissprot hit to cadC: Cadmium efflux system accessory protein from Listeria monocytogenes; ArsR family; transcriptional regulator complement(340107..340445) Dinoroseobacter shibae DFL 12 = DSM 16493 5711266 YP_001531708.1 CDS purH NC_009952.1 340610 342199 D involved in de novo purine biosynthesis; bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase 340610..342199 Dinoroseobacter shibae DFL 12 = DSM 16493 5711267 YP_001531709.1 CDS lspA NC_009952.1 342204 342680 D lipoprotein signal peptidase; integral membrane protein that removes signal peptides from prolipoproteins during lipoprotein biosynthesis; lipoprotein signal peptidase 342204..342680 Dinoroseobacter shibae DFL 12 = DSM 16493 5711268 YP_001531710.1 CDS Dshi_0360 NC_009952.1 342734 343279 D KEGG: rsq:Rsph17025_2930 hypothetical protein; no significant swissprot, no conserved domains; hypothetical protein 342734..343279 Dinoroseobacter shibae DFL 12 = DSM 16493 5711269 YP_001531711.1 CDS pqqL2 NC_009952.1 343363 344724 D PFAM: peptidase M16 domain protein; high swissprot to Uncharacterized zinc protease y4wA fromRhizobium sp. NGR234 and high Ref ZP hit to putative zinc protease from Rhodobacterales bacterium HTCC2150; NCBI conserved domains: pqqL; peptidase M16 protein 343363..344724 Dinoroseobacter shibae DFL 12 = DSM 16493 5711270 YP_001531712.1 CDS pqqL1 NC_009952.1 344721 346034 D PFAM: peptidase M16 domain protein; good swissprot to Uncharacterized zinc protease-like protein y4wB from Rhizobium sp. NGR234 and Ref YP hit to peptidase M16 domain protein from Rhodobacter sphaeroides ATCC 17025, NCBI conserved domains: pqqL; peptidase M16 protein 344721..346034 Dinoroseobacter shibae DFL 12 = DSM 16493 5711271 YP_001531713.1 CDS mutL NC_009952.1 346074 347939 D 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 346074..347939 Dinoroseobacter shibae DFL 12 = DSM 16493 5711272 YP_001531714.1 CDS rmuC NC_009952.1 347936 349168 D PFAM: protein of unknown function DUF195 ; NCBI conserved domains: rmuC; swissprot to DNA recombination protein rmuC homolog from Xylella fastidiosa Temecula1 and high Ref ZP hit to RmuC domain protein from Oceanicola batsensis HTCC2597; hypothetical protein 347936..349168 Dinoroseobacter shibae DFL 12 = DSM 16493 5711273 YP_001531715.1 CDS chrR1 NC_009952.1 349194 349865 R TIGRFAM: anti-sigma factor, putative, ChrR family PFAM: Cupin 2 conserved barrel domain protein; good swissprot to Transcriptional activator chrR from Rhodobacter sphaeroides 2.4.1 and good Ref ZP hit to Anti-sigma factor ChrR from Roseovarius sp. TM1035; NCBI conserved domains: chrR; ChrR; anti-ECFsigma factor complement(349194..349865) Dinoroseobacter shibae DFL 12 = DSM 16493 5711274 YP_001531716.1 CDS rpoE2 NC_009952.1 349872 350441 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; this sigma factor is involved in heat shock and oxidative stress response; RNA polymerase sigma factor RpoE complement(349872..350441) Dinoroseobacter shibae DFL 12 = DSM 16493 5711275 YP_001531717.1 CDS Dshi_0367 NC_009952.1 350649 351953 D PFAM: amine oxidase; FAD dependent oxidoreductase, no significant swissprot, high ref ZP hit to Putative cyclopropane/cyclopropene fatty acid synthesis protein, flavin amine oxidase from Sulfitobacter sp. NAS-14.1; amine oxidase 350649..351953 Dinoroseobacter shibae DFL 12 = DSM 16493 5711276 YP_001531718.1 CDS Dshi_0368 NC_009952.1 351950 352708 D PFAM: protein of unknown function DUF1365; no significant swissprot, high Ref YP hit to protein of unknown function DUF1365 from Jannaschia sp. CCS1; hypothetical protein 351950..352708 Dinoroseobacter shibae DFL 12 = DSM 16493 5711277 YP_001531719.1 CDS Dshi_0369 NC_009952.1 352726 353964 D bad swissprot hit to Uncharacterized symporter ynaJ from Bacillus subtilis and high Ref ZP hit to sodium:galactoside symporter family protein, putative from Roseobacter sp. CCS2; PF07690 MFS_1: transporter, major facilitator family; putative sodium:galactoside symporter family protein 352726..353964 Dinoroseobacter shibae DFL 12 = DSM 16493 5711278 YP_001531720.1 CDS Dshi_0370 NC_009952.1 353964 354554 D no significant swissprot, good Ref ZP hit to hypothetical protein RCCS2_10850 from Roseobacter sp. CCS2; no NCBI conserved domains; hypothetical protein 353964..354554 Dinoroseobacter shibae DFL 12 = DSM 16493 5711279 YP_001531721.1 CDS Dshi_0371 NC_009952.1 354573 355304 D PFAM: short-chain dehydrogenase/reductase SDR; KR domain protein; middle swissprot hit to Uncharacterized oxidoreductase MXAN_5909 from Myxococcus xanthus DK 1622, good Ref ZP hit to Short-chain dehydrogenase/reductase family member from Loktanella vestfoldensis SKA53; NCBI conserved domains: COG4221, Short-chain alcohol dehydrogenase of unknown specificity; short-chain dehydrogenase/reductase SDR 354573..355304 Dinoroseobacter shibae DFL 12 = DSM 16493 5711280 YP_001531722.1 CDS Dshi_0372 NC_009952.1 355405 355728 D no conserved domains detected, no significant swissprot, middle Ref ZP hit to hypothetical protein SKA53_12618 from Loktanella vestfoldensis SKA53; hypothetical protein 355405..355728 Dinoroseobacter shibae DFL 12 = DSM 16493 5711281 YP_001531723.1 CDS fadD3 NC_009952.1 355873 357843 D PFAM: AMP-dependent synthetase and ligase, good swissprot hit to Putative long-chain-fatty-acid--CoA ligase from Haemophilus influenzae and high Ref ZP hit to AMP-binding enzyme from Rhodobacterales bacterium HTCC2654; NCBI conserved domains: COG0318, CaiC, Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II; acyl-CoA synthetase 355873..357843 Dinoroseobacter shibae DFL 12 = DSM 16493 5711282 YP_001531724.1 CDS Dshi_0374 NC_009952.1 357902 358156 D no significant BLAST hits, no conserved domains detected; normal GC frame plot; hypothetical protein 357902..358156 Dinoroseobacter shibae DFL 12 = DSM 16493 5711283 YP_001531725.1 CDS livG NC_009952.1 358153 358974 D PFAM: ABC transporter related SMART: AAA ATPase, good swissprot to High-affinity branched-chain amino acid transport ATP-binding protein from Pseudomonas aeruginosa and high Ref ZP hit tobranched-chain amino acid ABC transporter, ATP-binding protein from Rhodobacterales bacterium HTCC2654; NCBI conserved domains: livG; gene arrangement (ABC transporter) with following genes to Dshi_0381; high-affinity branched-chain amino acid transport ATP-binding protein livG 358153..358974 Dinoroseobacter shibae DFL 12 = DSM 16493 5711284 YP_001531726.1 CDS livH NC_009952.1 359118 360107 D PFAM: inner-membrane translocator KEGG: rde:RD1_0704 branched-chain amino acid ABC transporter, permease protein, putative, low swissprot hit to High-affinity branched-chain amino acid transport system permease protein livH from Escherichia coli K12 and high Ref ZP hit to ABC branched amino acid transporter family, inner membrane subunit from Rhodobacterales bacterium HTCC2654, NCBI conserved doma; high-affinity branched-chain amino acid transport system permease livH 359118..360107 Dinoroseobacter shibae DFL 12 = DSM 16493 5711285 YP_001531727.1 CDS Dshi_0377 NC_009952.1 360124 360432 R no significant BLAST hits, unsure GC frame plot, no conserved domains detected, lies in the middle of ABC transporter; hypothetical protein complement(360124..360432) Dinoroseobacter shibae DFL 12 = DSM 16493 5711286 YP_001531728.1 CDS Dshi_0378 NC_009952.1 360675 360929 D no significant BLAST hits, unsure GC frame plot, no conserved domains detected, lies in the middle of ABC transporter; hypothetical protein 360675..360929 Dinoroseobacter shibae DFL 12 = DSM 16493 5711287 YP_001531729.1 CDS livM NC_009952.1 361062 362138 D PFAM: inner-membrane translocator KEGG: sil:SPO3292 branched-chain amino acid ABC transporter, permease protein; middle swissprot hit to High-affinity branched-chain amino acid transport system permease protein livM from Salmonella typhimurium and high Ref YP hit to inner-membrane translocator from Jannaschia sp. CCS1; NCBI conserved domains:livM; gene arrangement with Dshi_0375 to Dshi_0381; high-affinity branched-chain amino acid transport system permease livM 361062..362138 Dinoroseobacter shibae DFL 12 = DSM 16493 5711288 YP_001531730.1 CDS livK NC_009952.1 362188 363468 D pfam01094 Receptor family ligand binding region; bad swissprot hit to Leu/Ile/Val-binding protein homolog 3 precursor from Brucella suis and high Ref ZP hit to branched-chain amino acid ABC transporter, periplasmic from Roseobacter sp. MED193; gene arrangement with Dshi_0375 to Dshi_0381; high-affinity branched-chain amino acid transport system periplasmic-binding protein livK 362188..363468 Dinoroseobacter shibae DFL 12 = DSM 16493 5711289 YP_001531731.1 CDS livF1 NC_009952.1 363531 364355 D PFAM: ABC transporter related SMART: AAA ATPase KEGG: jan:Jann_4003 ABC transporter related, good swissprot hit to High-affinity branched-chain amino acid transport ATP-binding protein livF from Salmonella typhimurium and high Ref ZP hit to ABC transporter related protein from Roseobacter sp. CCS2, NCBI conserved domains: livF; gene cluster from Dshi_0375 to Dshi_0381; high-affinity branched-chain amino acid transport ATP-binding protein livF 363531..364355 Dinoroseobacter shibae DFL 12 = DSM 16493 5711290 YP_001531732.1 CDS paaK NC_009952.1 364512 365732 D SSF56801 Acetyl-CoA sythase-like, low swissprot hit to Phenylacetate-coenzyme A ligase from Escherichia coli K12 and high Ref Yp hit to phenylacetate-CoA ligase, putative from Silicibacter sp. TM1040; NCBI conserved domains:paaK; phenylacetate-CoA ligase 364512..365732 Dinoroseobacter shibae DFL 12 = DSM 16493 5711291 YP_001531733.1 CDS Dshi_0383 NC_009952.1 365857 366321 D no significant BLAST hits, unsure GC frame plot, no conserved domains; hypothetical protein 365857..366321 Dinoroseobacter shibae DFL 12 = DSM 16493 5711292 YP_001531734.1 CDS Dshi_0384 NC_009952.1 366443 366901 R KEGG: bur:Bcep18194_B1502 NUDIX hydrolase; no significant swissprot, bad Ref YP hit to NUDIX hydrolase from Burkholderia sp. 383; no conserved domains by Interpro Scan, NCBI conserved domains:NUDIX hydrolase 23; hypothetical protein complement(366443..366901) Dinoroseobacter shibae DFL 12 = DSM 16493 5711293 YP_001531735.1 CDS dinB NC_009952.1 366959 368212 D involved in translesion DNA polymerization with beta clamp of polymerase III; belongs to Y family of polymerases; does not contain proofreading function; DNA polymerase IV 366959..368212 Dinoroseobacter shibae DFL 12 = DSM 16493 5711294 YP_001531736.1 CDS hutG NC_009952.1 368291 369154 R PFAM: N-formylglutamate amidohydrolase KEGG: rde:RD1_0718 N-formylglutamate amidohydrolase, putative; no signifcant swissprot; good Ref ZP hit to N-formylglutamate amidohydrolase family protein from Loktanella vestfoldensis SKA53; NCBI conserved domains: hutG; N-formylglutamate amidohydrolase complement(368291..369154) Dinoroseobacter shibae DFL 12 = DSM 16493 5711295 YP_001531737.1 CDS rpmJ NC_009952.1 369431 369556 D smallest protein in the large subunit; similar to what is found with protein L31 and L33 several bacterial genomes contain paralogs which may be regulated by zinc; the protein from Thermus thermophilus has a zinc-binding motif and contains a bound zinc ion; the proteins in this group do not have the motif; 50S ribosomal protein L36 369431..369556 Dinoroseobacter shibae DFL 12 = DSM 16493 5711297 YP_001531738.1 CDS rbsA5 NC_009952.1 369763 370548 R PFAM: ABC transporter related SMART: AAA ATPase KEGG: sit:TM1040_0370 ABC transporter related; good swissprot hit to Ribose import ATP-binding protein rbsA from Anabaena variabilis and high Ref ZP hit to sugar ABC transporter, ATP-binding protein, putative from Roseobacter sp. CCS2; ribose import ATP-binding protein rbsA complement(369763..370548) Dinoroseobacter shibae DFL 12 = DSM 16493 5711298 YP_001531739.1 CDS rbsC2 NC_009952.1 370545 371618 R PFAM: inner-membrane translocator KEGG: sit:TM1040_0369 inner-membrane translocator; middle swissprot hit to Ribose transport system permease protein rbsC from Bacillus subtilis and high Ref YP hit to inner-membrane translocator from Silicibacter sp. TM1040; ribose transport system permease rbsC complement(370545..371618) Dinoroseobacter shibae DFL 12 = DSM 16493 5711299 YP_001531740.1 CDS rbsB3 NC_009952.1 371715 372728 R PFAM: periplasmic binding protein/LacI transcriptional regulator KEGG: sit:TM1040_0368 periplasmic binding protein/LacI transcriptional regulator; low swissprot hit to D-ribose-binding periplasmic protein precursor from Salmonella typhimurium and high Ref YP hit to periplasmic binding protein/LacI transcriptional regulator from Silicibacter sp. TM1040; NCBI conserved domains:rbsB; D-ribose-binding periplasmic protein complement(371715..372728) Dinoroseobacter shibae DFL 12 = DSM 16493 5711300 YP_001531741.1 CDS Dshi_0391 NC_009952.1 379683 382190 D no significant swissprot, high Ref ZP hit to hypothetical protein MELB17_00320 from Marinobacter sp. ELB17; pfam02810 SEC-C motif; hypothetical protein 379683..382190 Dinoroseobacter shibae DFL 12 = DSM 16493 5711307 YP_001531742.1 CDS Dshi_0392 NC_009952.1 382289 383437 R no significant swissprot, high Ref hit to hypothetical protein TM1040_3581 from Silicibacter sp. TM1040; no conserved domains, unsure GC frame plot; hypothetical protein complement(382289..383437) Dinoroseobacter shibae DFL 12 = DSM 16493 5711308 YP_001531743.1 CDS Dshi_0393 NC_009952.1 383697 383918 R no significant swissprot, no conserved domains, bad Ref Yp hit to hypothetical protein TM1040_3583 from Silicibacter sp. TM1040, bad GC frame plot, CRISPR region; hypothetical protein complement(383697..383918) Dinoroseobacter shibae DFL 12 = DSM 16493 5711309 YP_001531744.1 CDS Dshi_0394 NC_009952.1 383978 384751 R no significant swissprot, no conserved domains, bad GC frame plot; bad Ref Yp hit to hypothetical protein TM1040_3584 from Silicibacter sp. TM1040; CRISPR region; hypothetical protein complement(383978..384751) Dinoroseobacter shibae DFL 12 = DSM 16493 5711310 YP_001531745.1 CDS Dshi_0395 NC_009952.1 384765 385958 R PFAM: integrase family protein KEGG: sit:TM1040_3585 phage integrase; COG4974 - Site-specific recombinase XerD; high Ref YP hit to phage integrase from Silicibacter sp. TM1040 and bad swissprot hit to Putative prophage CPZ-55 integrase from Escherichia coli K12; bad GC frame plot, CRISPR region; phage integrase family protein complement(384765..385958) Dinoroseobacter shibae DFL 12 = DSM 16493 5711311 YP_001531746.1 CDS Dshi_0396 NC_009952.1 386137 387813 R PFAM: Resolvase domain; Recombinase KEGG: pde:Pden_3123 recombinase; COG1961 - Site-specific recombinases, DNA invertase Pin homologs; bad swissprot hit toPutative DNA recombinase from Bacillus subtilis and high Ref ZP hit toResolvase, N-terminal:Recombinase from Paracoccus denitrificans PD1222; bad GC frame plot, CRISPR region; recombinase complement(386137..387813) Dinoroseobacter shibae DFL 12 = DSM 16493 5711312 YP_001531747.1 CDS xerDC2 NC_009952.1 387910 388986 R PFAM: integrase family protein ; low swissprot hit to Tyrosine recombinase xerD from Bacillus subtilis and middle Ref EDP hit to phage integrase from alpha proteobacterium BAL199; NCBI conserved domains: xerDC; CRISPR region; integrase family protein complement(387910..388986) Dinoroseobacter shibae DFL 12 = DSM 16493 5711313 YP_001531748.1 CDS xerDC1 NC_009952.1 388979 390658 R PFAM: integrase family protein; COG4974 - Site-specific recombinase XerD; bad swissprot hit to Tyrosine recombinase xerC from Pseudomonas aeruginosa and good Ref ZP hit to phage integrase from Roseovarius sp. HTCC2601; CRISPR region; integrase family protein complement(388979..390658) Dinoroseobacter shibae DFL 12 = DSM 16493 5711314 YP_001531749.1 CDS Dshi_0399 NC_009952.1 390817 391029 R TIGRFAM: DNA binding domain, excisionase family PFAM: regulatory protein MerR; NCBI conserved domains: HTH_MerR-trunc; bad Ref YP hit to DNA binding domain, excisionase family from Alkaliphilus oremlandii OhILAs and bad swissprot hit to Gene 36 protein from Mycobacterium phage D29; bad GC frame plot; Dshi_0400 to Dshi_0402 CRISPRs; excisionase family; DNA-binding domain-containing protein complement(390817..391029) Dinoroseobacter shibae DFL 12 = DSM 16493 5711315 YP_001531750.1 CDS Dshi_0400 NC_009952.1 391798 395037 D TIGRFAM: CRISPR-associated protein, Csn1 family ; no significant swissprot, high Ref YP hit to CRISPR-associated protein, Csn1 family from Verminephrobacter eiseniae EF01-2; Csn1 family; CRISPR-associated protein 391798..395037 Dinoroseobacter shibae DFL 12 = DSM 16493 5711316 YP_001531751.1 CDS Dshi_0401 NC_009952.1 395098 396009 D TIGRFAM: CRISPR-associated protein Cas1 KEGG: vei:Veis_1231 CRISPR-associated protein Cas1, no significant swissprot, good Ref YP hit to CRISPR-associated protein Cas1 from Verminephrobacter eiseniae EF01-2; CRISPR-associated protein Cas1 395098..396009 Dinoroseobacter shibae DFL 12 = DSM 16493 5711317 YP_001531752.1 CDS Dshi_0402 NC_009952.1 396006 396350 D TIGRFAM: CRISPR-associated protein Cas2 KEGG: vei:Veis_1232 CRISPR-associated protein Cas2; no significant swissprot; low Ref YP hit to CRISPR-associated protein Cas2 from Verminephrobacter eiseniae EF01-2; CRISPR-associated protein Cas2 396006..396350 Dinoroseobacter shibae DFL 12 = DSM 16493 5711318 YP_001531753.1 CDS Dshi_0403 NC_009952.1 397989 398255 D PFAM: transposase IS3/IS911 family protein; NCBI conserved domains: transposase_8; middle Ref ZP hit to Insertion element ISR1 hypothetical 10 kDa protein A3 from Sagittula stellata E-37; middle swissprot to Insertion element ISR1 uncharacterized 10 kDa protein A3 from Rhizobium sp.; insertion element ISR1 10 kDa protein A3 397989..398255 Dinoroseobacter shibae DFL 12 = DSM 16493 5711319 YP_001531754.1 CDS Dshi_0404 NC_009952.1 398279 399088 D PFAM: Integrase catalytic region KEGG: bbt:BBta_7691 integrase, catalytic domain; good swissprot hit toInsertion element IS476 uncharacterized 39.2 kDa protein from Xanthomonas euvesicatoria; high Ref Yp hit to Integrase catalytic region from Xanthobacter autotrophicus Py2; downstream of CRISPR region; integrase catalytic subunit 398279..399088 Dinoroseobacter shibae DFL 12 = DSM 16493 5711320 YP_001531755.1 CDS Dshi_0405 NC_009952.1 399227 400612 R no significant BLAST hits, no conserved domains, unsure GC frame plot, downstream of CRISPR region; hypothetical protein complement(399227..400612) Dinoroseobacter shibae DFL 12 = DSM 16493 5711321 YP_001531756.1 CDS Dshi_0406 NC_009952.1 400543 401841 R no significant BLAST hits, no conserved domains, unsure GC frame plot; hypothetical protein complement(400543..401841) Dinoroseobacter shibae DFL 12 = DSM 16493 5711322 YP_001531757.1 CDS Dshi_0407 NC_009952.1 402104 402430 D PFAM: helix-turn-helix domain protein KEGG: nmu:Nmul_D2824 transcriptional regulator, XRE family; no significant swissprot, middle Ref YP hit to transcriptional regulator, XRE family from Nitrosospira multiformis ATCC 25196; XRE family; transcriptional regulator 402104..402430 Dinoroseobacter shibae DFL 12 = DSM 16493 5711323 YP_001531758.1 CDS Dshi_0408 NC_009952.1 402441 403163 D PFAM: protein of unknown function DUF955 KEGG: nmu:Nmul_D2822 hypothetical protein; no significant swissprot; middle Ref YP hit to hypothetical protein Nmul_D2822 from Nitrosospira multiformis ATCC 25196; hypothetical protein 402441..403163 Dinoroseobacter shibae DFL 12 = DSM 16493 5711324 YP_001531759.1 CDS Dshi_0409 NC_009952.1 403268 403912 D KEGG: nwi:Nwi_1958 hypothetical protein; no significant swissprot, middle Ref YP hit to hypothetical protein Nwi_1958 from Nitrobacter winogradskyi Nb-255, no conserved domains detected; hypothetical protein 403268..403912 Dinoroseobacter shibae DFL 12 = DSM 16493 5711325 YP_001531760.1 CDS Dshi_0410 NC_009952.1 404246 405190 R good Ref Yp hit to hypothetical protein RD1_0494 from Roseobacter denitrificans OCh 114; no significant swissprot; short signalpeptide and two transmembrane regions; unsure GC frame plot; hypothetical protein complement(404246..405190) Dinoroseobacter shibae DFL 12 = DSM 16493 5711326 YP_001531761.1 CDS Dshi_0411 NC_009952.1 405174 406022 R good Ref YP hit to hypothetical protein RD1_0495 from Roseobacter denitrificans OCh 114; no significant swissprot; no NCBI conserved domains; PS00092 N-6 Adenine-specific DNA methylase; hypothetical protein complement(405174..406022) Dinoroseobacter shibae DFL 12 = DSM 16493 5711327 YP_001531762.1 CDS fas NC_009952.1 406254 407786 D PFAM: beta-Ig-H3/fasciclin; Hemolysin-type calcium-binding region KEGG: pde:Pden_0560 hemolysin-type calcium-binding region; NCBI conserved domains: Fasciclin; middle Ref YP hit to Beta-Ig-H3/fasciclin from Ralstonia eutropha JMP134; no significant swissprot; beta-Ig-H3/fasciclin 406254..407786 Dinoroseobacter shibae DFL 12 = DSM 16493 5711328 YP_001531763.1 CDS Dshi_0413 NC_009952.1 407836 408195 D no significant swissprot, unsure GC frame Plot, no conserved domains detected by InterPro Scan; NCBI conserved domains: COG1373 - Predicted ATPase (AAA+ superfamily); middle Ref ZP hit tohypothetical protein RTM1035_00450 from Roseovarius sp. TM1035; hypothetical protein 407836..408195 Dinoroseobacter shibae DFL 12 = DSM 16493 5711329 YP_001531764.1 CDS Dshi_0414 NC_009952.1 408427 408873 R KEGG: pde:Pden_4724 GreA/GreB family elongation factor; bad swissprot hit to Transcription elongation factor greA from Brucella suis; middle Ref ZP hit to putative nucleoside diphosphate kinase regulator from Oceanicola batsensis HTCC2597; NCBI conserved domains: PRK05753, nucleoside diphosphate kinase regulator and GreA/B; GreA/GreB family elongation factor complement(408427..408873) Dinoroseobacter shibae DFL 12 = DSM 16493 5711330 YP_001531765.1 CDS Dshi_0415 NC_009952.1 409020 409262 D no significant BLAST hits, no conserved domains; unsure GC frame plot; hypothetical protein 409020..409262 Dinoroseobacter shibae DFL 12 = DSM 16493 5711331 YP_001531766.1 CDS Dshi_0416 NC_009952.1 409608 409919 D PFAM: protein of unknown function DUF1127; bad Ref ZP hit to hypothetical protein OB2597_05265 from Oceanicola batsensis HTCC2597; no significant swissprot, unsure GC frame plot; hypothetical protein 409608..409919 Dinoroseobacter shibae DFL 12 = DSM 16493 5711332 YP_001531767.1 CDS Dshi_0417 NC_009952.1 410003 410209 D no significant BLAST hits, no conserved domains, unsure GC frame plot; hypothetical protein 410003..410209 Dinoroseobacter shibae DFL 12 = DSM 16493 5711333 YP_001531768.1 CDS uspA2 NC_009952.1 410284 411177 D PFAM: UspA domain protein KEGG: hha:Hhal_1414 UspA domain protein; COG0589 - Universal stress protein UspA and related nucleotide-binding proteins, bad swissprot hit to Stress response protein nhaX from Bacillus subtilis; low Ref YP hit to UspA domain protein from Halorhodospira halophila SL1, NCBI conserved domains:Usp/UspA like; universal stress protein uspA 410284..411177 Dinoroseobacter shibae DFL 12 = DSM 16493 5711334 YP_001531769.1 CDS Dshi_0419 NC_009952.1 411331 412584 D PFAM: major facilitator superfamily MFS_1 KEGG: sal:Sala_2954 major facilitator superfamily MFS_1; middle swissprot hit to Uncharacterized MFS-type transporter ycaD from Salmonella typhi and good Ref ZP hit to major facilitator family transporter from Sphingomonas sp. SKA58; major facilitator superfamily protein 411331..412584 Dinoroseobacter shibae DFL 12 = DSM 16493 5711335 YP_001531770.1 CDS Dshi_0420 NC_009952.1 412724 413434 D PFAM: Endonuclease/exonuclease/phosphatase KEGG: sil:SPO2482 endonuclease/exonuclease/phosphatase family protein; no significant swissprot; good Ref EDP hit to metal-dependent hydrolase from Oceanibulbus indolifex HEL-45, NCBI conserved domains: elsH, Metal-dependent hydrolase; endonuclease/exonuclease/phosphatase 412724..413434 Dinoroseobacter shibae DFL 12 = DSM 16493 5711336 YP_001531771.1 CDS Dshi_0421 NC_009952.1 413435 414979 D PFAM: phospholipase D/Transphosphatidylase KEGG: pmy:Pmen_2055 phospholipase D/transphosphatidylase; high swissprot hit to Uncharacterized protein ymdC from Escherichia coli K12 and high Ref EDP hit to phospholipase D/Transphosphatidylase from Oceanibulbus indolifex HEL-45; NCBI conserved domains: PLDc; phospholipase D/transphosphatidylase 413435..414979 Dinoroseobacter shibae DFL 12 = DSM 16493 5711337 YP_001531772.1 CDS Dshi_0422 NC_009952.1 415164 415685 D PFAM: Propeptide PepSY amd peptidase M4 KEGG: swi:Swit_4515 hypothetical protein; no significant swissprot; bad gb hit to Propeptide, PepSY amd peptidase M4 from Oceanibulbus indolifex HEL-45; propeptide PepSY amd peptidase M4 415164..415685 Dinoroseobacter shibae DFL 12 = DSM 16493 5711338 YP_001531773.1 CDS pap NC_009952.1 415763 416488 R PFAM: phosphoesterase PA-phosphatase related KEGG: rsh:Rsph17029_1755 phosphoesterase, PA-phosphatase related, no significant swissprot; good Ref YP hit to PA-phosphatase related phosphoesterase from Rhodobacter sphaeroides 2.4.1; NCBI conserved domains: Pap2-like; PA-phosphatase-like phosphoesterase complement(415763..416488) Dinoroseobacter shibae DFL 12 = DSM 16493 5711339 YP_001531774.1 CDS Dshi_0424 NC_009952.1 417105 417566 D peptidase M41 417105..417566 Dinoroseobacter shibae DFL 12 = DSM 16493 5711340 YP_001531775.1 CDS Dshi_0426 NC_009952.1 418488 418850 D no significant swissprot; PD068243 REGULATORY BACTERIAL FAMILY MERR CYTOPLASMIC; middle Ref ZP hit to hypothetical protein ROS217_15345 from Roseovarius sp. 217; hypothetical protein 418488..418850 Dinoroseobacter shibae DFL 12 = DSM 16493 5711342 YP_001531776.1 CDS Dshi_0427 NC_009952.1 418998 419249 D no significant swissprot, no conserved domains (except for one signalpeptide/ two transmembr. region), bad Ref YP hit to hypothetical protein AZC_2085 from Azorhizobium caulinodans ORS 571; hypothetical protein 418998..419249 Dinoroseobacter shibae DFL 12 = DSM 16493 5711343 YP_001531777.1 CDS phaC NC_009952.1 419269 421152 D PFAM: alpha/beta hydrolase fold; Poly-beta-hydroxybutyrate polymerase domain protein KEGG: sil:SPO0112 poly(3-hydroxyalkanoate) polymerase family protein; high Ref YP hit to poly(3-hydroxyalkanoate) polymerase family protein from Silicibacter pomeroyi DSS-3 and high swissprot hit to Poly(3-hydroxyalkanoate) polymerase (PHA polymerase) from Methylobacterium extorquens; NCBI conserved domains: phaC; poly(3-hydroxyalkanoate) polymerase 419269..421152 Dinoroseobacter shibae DFL 12 = DSM 16493 5711344 YP_001531778.1 CDS Dshi_0429 NC_009952.1 421265 421552 R no significant swissprot, no conserved domains, low Ref Yp hit to uncharacterized conserved coiled coil protein from Marinomonas sp. MWYL1; hypothetical protein complement(421265..421552) Dinoroseobacter shibae DFL 12 = DSM 16493 5711345 YP_001531779.1 CDS Dshi_0430 NC_009952.1 421575 422009 R no significant swissprot, no conserved domains, low Ref YP hit to hypothetical protein SPO0412 from Silicibacter pomeroyi DSS-3; hypothetical protein complement(421575..422009) Dinoroseobacter shibae DFL 12 = DSM 16493 5711346 YP_001531780.1 CDS dcuC NC_009952.1 422213 423661 D PFAM: C4-dicarboxylate anaerobic carrier KEGG: mes:Meso_2242 C4-dicarboxylate anaerobic carrier; good swissprot hit to Uncharacterized protein HI0594 from Haemophilus influenzae; high Ref Yp hit to C4-dicarboxylate anaerobic carrier from Mesorhizobium sp. BNC1; NCBI conserved domains: dcuC; C4-dicarboxylate anaerobic carrier 422213..423661 Dinoroseobacter shibae DFL 12 = DSM 16493 5711347 YP_001531781.1 CDS arcA NC_009952.1 423677 424906 D catalyzes the degradation of arginine to citruline and ammonia; arginine deiminase 423677..424906 Dinoroseobacter shibae DFL 12 = DSM 16493 5711348 YP_001531782.1 CDS arcB NC_009952.1 424920 425921 D TIGRFAM: ornithine carbamoyltransferase PFAM: aspartate/ornithine carbamoyltransferase Asp/Orn-binding region; aspartate/ornithine carbamoyltransferase carbamoyl-P binding domain KEGG: mes:Meso_2240 ornithine carbamoyltransferase; high swissprot hit to Ornithine carbamoyltransferase, catabolic from Haemophilus influenzae; ornithine carbamoyltransferase 424920..425921 Dinoroseobacter shibae DFL 12 = DSM 16493 5711349 YP_001531783.1 CDS arcC NC_009952.1 425925 426863 D reversible synthesis of carbamate and ATP from carbamoyl phosphate and ADP; carbamate kinase 425925..426863 Dinoroseobacter shibae DFL 12 = DSM 16493 5711350 YP_001531784.1 CDS atpD1 NC_009952.1 427117 428505 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 427117..428505 Dinoroseobacter shibae DFL 12 = DSM 16493 5711351 YP_001531785.1 CDS atpC2 NC_009952.1 428502 428912 D TIGRFAM: ATP synthase F1, epsilon subunit PFAM: H+transporting two-sector ATPase delta/epsilon subunit KEGG: net:Neut_2014 H+-transporting two-sector ATPase, delta/epsilon subunit, low swissprot hit to ATP synthase epsilon chain 2 from Burkholderia xenovorans LB400; ATP synthase F1 subunit epsilon 428502..428912 Dinoroseobacter shibae DFL 12 = DSM 16493 5711352 YP_001531786.1 CDS Dshi_0437 NC_009952.1 428909 429196 D TIGRFAM: F0F1-ATPase subunit, putative PFAM: F0F1-ATPase subunit putative KEGG: net:Neut_2015 F0F1-ATPase subunit, putative; no significant swissprot; low Ref ZP hit to H(+)-transporting ATP synthase, gene 1 from Marinobacter sp. ELB17; ATP synthase F0F1 subunit 428909..429196 Dinoroseobacter shibae DFL 12 = DSM 16493 5711353 YP_001531787.1 CDS Dshi_0438 NC_009952.1 429193 429498 D no significant swissprot and no conserved domains (except from signalpep. and three transmembr. regions); low, but best Ref ZP hit to F0F1 ATP synthase subunit A from Marinobacter sp. ELB17, lies in the middle of F0F1 ATPase cluster; ATP synthase F0F1 subunit 429193..429498 Dinoroseobacter shibae DFL 12 = DSM 16493 5711354 YP_001531788.1 CDS atpB2 NC_009952.1 429489 430178 D 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 429489..430178 Dinoroseobacter shibae DFL 12 = DSM 16493 5711355 YP_001531789.1 CDS atpE1 NC_009952.1 430175 430465 D 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 430175..430465 Dinoroseobacter shibae DFL 12 = DSM 16493 5711356 YP_001531790.1 CDS atpF1 NC_009952.1 430470 431237 D PFAM: H+transporting two-sector ATPase B/B subunit KEGG: net:Neut_2019 H+-transporting two-sector ATPase, B/B subunit; low swissprot hit to ATP synthase B chain from Vibrio vulnificus and good Ref ZP hit to H(+)-transporting ATP synthase, subunit B from Marinobacter sp. ELB17; ATP synthase F0 subunit B 430470..431237 Dinoroseobacter shibae DFL 12 = DSM 16493 5711357 YP_001531791.1 CDS atpA2 NC_009952.1 431227 432756 D KEGG: net:Neut_2020 ATP synthase F1, alpha subunit TIGRFAM: ATP synthase F1, alpha subunit PFAM: H+transporting two-sector ATPase alpha/beta subunit central region; H+transporting two-sector ATPase alpha/beta subunit domain protein; high swissprot hit to ATP synthase subunit alpha 2 from Syntrophus aciditrophicus SB; ATP synthase F1 subunit alpha 431227..432756 Dinoroseobacter shibae DFL 12 = DSM 16493 5711358 YP_001531792.1 CDS atpG1 NC_009952.1 432740 433687 D PFAM: H+transporting two-sector ATPase gamma subunit KEGG: net:Neut_2021 H+-transporting two-sector ATPase, gamma subunit; low swissprot hit to ATP synthase gamma chain from Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough and good Ref ZP hit to H(+)-transporting ATP synthase, subunit gamma fromMarinobacter sp. ELB17; NCBI conserved domains: atpG; ATP synthase F1 subunit gamma 432740..433687 Dinoroseobacter shibae DFL 12 = DSM 16493 5711359 YP_001531793.1 CDS Dshi_0444 NC_009952.1 433725 434012 D no significant swissprot, no conserved domains, low Ref YP hit to hypothetical protein Nham_4077 from Nitrobacter hamburgensis X14; hypothetical protein 433725..434012 Dinoroseobacter shibae DFL 12 = DSM 16493 5711360 YP_001531794.1 CDS Dshi_0445 NC_009952.1 434046 434438 D no significant swissprot, no conserved domains, low Ref ZP hit to hypothetical protein NB311A_09431 from Nitrobacter sp. Nb-311A; hypothetical protein 434046..434438 Dinoroseobacter shibae DFL 12 = DSM 16493 5711361 YP_001531795.1 CDS Dshi_0446 NC_009952.1 434569 434979 D PFAM: CBS domain containing protein; middle Ref YP hit to CBS domain containing protein from Mesorhizobium sp. BNC1 and bad swissprot to Uncharacterized protein yhcV from Bacillus subtilis; NCBI conserved domains: cbs_pair_9; putative signal transduction protein 434569..434979 Dinoroseobacter shibae DFL 12 = DSM 16493 5711362 YP_001531796.1 CDS Dshi_0447 NC_009952.1 434981 435769 R PFAM: cyclic nucleotide-binding SMART: regulatory protein Crp; low swissprot hit to Transcriptional activatory protein aadR from Rhodopseudomonas palustris and middle Ref ZP hit to transcriptional regulator, Crp/Fnr family protein from Roseobacter sp. AzwK-3b; Crp/Fnr family; transcriptional regulator complement(434981..435769) Dinoroseobacter shibae DFL 12 = DSM 16493 5711363 YP_001531797.1 CDS Dshi_0448 NC_009952.1 436086 437696 D PFAM: ATP-binding region ATPase domain protein; histidine kinase HAMP region domain protein; histidine kinase A domain protein; middle swissprot hit to Uncharacterized sensor-like histidine kinase yclK from Bacillus subtilis and high Ref YP hit to Sensor protein resE, putative from Roseobacter denitrificans OCh 114; integral membrane sensor signal transduction histidine kinase 436086..437696 Dinoroseobacter shibae DFL 12 = DSM 16493 5711364 YP_001531798.1 CDS Dshi_0449 NC_009952.1 437751 438434 D PFAM: response regulator receiver; transcriptional regulator domain protein; middle swissprot hit to Transcriptional regulatory protein dltR from Streptococcus agalactiae serogroup III (Phosphorylated by dltS kinase); good Ref YP hit to transcriptional regulatory protein PrrA, putative from Roseobacter denitrificans OCh 114; winged helix family; two component transcriptional regulator 437751..438434 Dinoroseobacter shibae DFL 12 = DSM 16493 5711365 YP_001531799.1 CDS pqqA NC_009952.1 438538 438636 D Required for coenzyme pyrroloquinoline quinone (PQQ) biosynthesis; probably provides the glutamate and tyrosine residues that are cross-linked and modified to form the coenzyme; coenzyme PQQ synthesis protein PqqA 438538..438636 Dinoroseobacter shibae DFL 12 = DSM 16493 5711366 YP_001531800.1 CDS pqqB NC_009952.1 438663 439556 D possibly involved in transport of pyrroloquinoline quinone transport; pyrroloquinoline quinone biosynthesis protein PqqB 438663..439556 Dinoroseobacter shibae DFL 12 = DSM 16493 5711367 YP_001531801.1 CDS pqqC NC_009952.1 439556 440308 D Required in the synthesis of PPQ, but its exact function is unknown; pyrroloquinoline quinone biosynthesis protein PqqC 439556..440308 Dinoroseobacter shibae DFL 12 = DSM 16493 5711368 YP_001531802.1 CDS pqqD NC_009952.1 440305 440583 D PFAM: coenzyme PQQ synthesis D; low swissprot hit to Coenzyme PQQ synthesis protein D from Silicibacter pomeroyi; middle Ref ZP hit to coenzyme PQQ synthesis protein D from Roseovarius sp. HTCC2601; NCBI conserved domains: pqqD; coenzyme PQQ biosynthesis protein PqqD 440305..440583 Dinoroseobacter shibae DFL 12 = DSM 16493 5711369 YP_001531803.1 CDS pqqE NC_009952.1 440580 441686 D TIGRFAM: coenzyme PQQ biosynthesis protein E PFAM: Radical SAM domain protein KEGG: rde:RD1_1150 coenzyme PQQ biosynthesis protein E; high swissprot hit to Coenzyme PQQ synthesis protein E from Silicibacter pomeroyi; pyrroloquinoline quinone biosynthesis protein PqqE 440580..441686 Dinoroseobacter shibae DFL 12 = DSM 16493 5711370 YP_001531804.1 CDS Dshi_0455 NC_009952.1 442029 442946 D no significant swissprot; no conserved domains except for short signalpeptide; high Ref YP hit to hypothetical protein RD1_0870 from Roseobacter denitrificans OCh 114; hypothetical protein 442029..442946 Dinoroseobacter shibae DFL 12 = DSM 16493 5711371 YP_001531805.1 CDS moxR NC_009952.1 443039 443995 D PFAM: ATPase associated with various cellular activities AAA_3; ATPase associated with various cellular activities AAA_5 SMART: AAA ATPase KEGG: rde:RD1_0871 MoxR-like ATPase, middle swissprot hit to Protein moxR from Methylobacterium extorquens and high Ref YP hit to MoxR-like ATPase from Roseobacter denitrificans OCh 114; MoxR-like ATPase 443039..443995 Dinoroseobacter shibae DFL 12 = DSM 16493 5711372 YP_001531806.1 CDS Dshi_0457 NC_009952.1 443992 444900 D PFAM: protein of unknown function DUF58; no significant swissprot; high Ref YP hit to hypothetical protein RD1_0873 from Roseobacter denitrificans OCh 114; hypothetical protein 443992..444900 Dinoroseobacter shibae DFL 12 = DSM 16493 5711373 YP_001531807.1 CDS Dshi_0458 NC_009952.1 444897 445268 D no significant swissprot, no conserved domains; middle Ref YP hit to hypothetical protein RD1_0874 from Roseobacter denitrificans OCh 114; hypothetical protein 444897..445268 Dinoroseobacter shibae DFL 12 = DSM 16493 5711374 YP_001531808.1 CDS Dshi_0459 NC_009952.1 445261 446223 D PFAM: von Willebrand factor type A KEGG: rde:RD1_0875 hypothetical protein; bad swissprot hit to Uncharacterized protein BB_0173 from Borrelia burgdorferi, unsure GC frame plot; von Willebrand factor type A 445261..446223 Dinoroseobacter shibae DFL 12 = DSM 16493 5711375 YP_001531809.1 CDS Dshi_0460 NC_009952.1 446220 447119 D no significant swissprot, unsure GC frame plot; NCBI conserved domains: VWA domain (von Willebrand factor); high Ref YP hit to hypothetical protein RD1_0876 from Roseobacter denitrificans OCh 114; hypothetical protein 446220..447119 Dinoroseobacter shibae DFL 12 = DSM 16493 5711376 YP_001531810.1 CDS Dshi_0461 NC_009952.1 447116 447790 D unsure GC frame plot, no conserved domains (except for one signalpep. and one transmembr. region); good Ref YP hit to hypothetical protein RD1_0877 from Roseobacter denitrificans OCh 114; bad swissprot hit to Transposon Ty2-GR1 Gag-Pol polyprotein from Saccharomyces cerevisiae; Dshi_0463 transposase family protein; hypothetical protein 447116..447790 Dinoroseobacter shibae DFL 12 = DSM 16493 5711377 YP_001531811.1 CDS Dshi_0462 NC_009952.1 447787 448983 D no significant swissprot, unsure GC frame plot; high Ref YP hit to hypothetical protein RD1_0878 from Roseobacter denitrificans OCh 114; hypothetical protein 447787..448983 Dinoroseobacter shibae DFL 12 = DSM 16493 5711378 YP_001531812.1 CDS Dshi_0463 NC_009952.1 449156 449422 D PFAM: transposase IS3/IS911 family protein KEGG: rde:RD1_3450 inverted repeat region; middle swissprot hit to Insertion element ISR1 uncharacterized 10 kDa protein A3 from Rhizobium sp.; transposase IS3/IS911 family protein 449156..449422 Dinoroseobacter shibae DFL 12 = DSM 16493 5711379 YP_001531813.1 CDS Dshi_0464 NC_009952.1 449446 450267 D PFAM: Integrase catalytic region KEGG: rde:RD1_3449 integrase, catalytic domain, putative; good swissprot hit to Insertion element IS476 uncharacterized 39.2 kDa protein from Xanthomonas euvesicatoria and high Ref YP hit to integrase, catalytic domain, putative from Roseobacter denitrificans OCh 114; NCBI conserved domains: rve; integrase catalytic subunit 449446..450267 Dinoroseobacter shibae DFL 12 = DSM 16493 5711380 YP_001531814.1 CDS luxR2 NC_009952.1 450313 451032 D blast hits, no swissprot, Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain, PFAM: regulatory protein LuxR; response regulator receiver; LuxR family; two component transcriptional regulator 450313..451032 Dinoroseobacter shibae DFL 12 = DSM 16493 5711381 YP_001531815.1 CDS Dshi_0466 NC_009952.1 451045 452202 D PFAM: domain of unknown function DUF1745, no significant swissprot, unsure GC frame plot; high Ref YP hit to hypothetical protein RD1_0880 from Roseobacter denitrificans OCh 114; hypothetical protein 451045..452202 Dinoroseobacter shibae DFL 12 = DSM 16493 5711382 YP_001531816.1 CDS Dshi_0467 NC_009952.1 452199 454475 D PFAM: response regulator receiver; ATP-binding region ATPase domain protein; histidine kinase A domain protein; middle swissprot to Sensor protein rcsC from Salmonella typhimurium; high RefZP hit to putative sensor histidine kinase protein from Sagittula stellata E-37; unsure GC frame plot; sensor histidine kinase 452199..454475 Dinoroseobacter shibae DFL 12 = DSM 16493 5711383 YP_001531817.1 CDS Dshi_0468 NC_009952.1 454509 455171 D no significant swissprot; high Ref YP hit to hypothetical protein RD1_0882 from Roseobacter denitrificans OCh 114; hypothetical protein 454509..455171 Dinoroseobacter shibae DFL 12 = DSM 16493 5711384 YP_001531818.1 CDS Dshi_0469 NC_009952.1 455168 455518 D no significant swissprot, good ref YP hit to hypothetical protein RD1_0883 from Roseobacter denitrificans OCh 114; no conserved domains (except from signalpep.); hypothetical protein 455168..455518 Dinoroseobacter shibae DFL 12 = DSM 16493 5711385 YP_001531819.1 CDS soxZ NC_009952.1 455582 456454 R PFAM: Sulphur oxidation protein SoxZ ; no significant swissprot; good Ref YP hit to Sulphur oxidation protein SoxZ from Sinorhizobium medicae WSM419; NCBI conserved domains: SoxZ and PRK07474, sulfur oxidation protein SoxY; sulfur oxidation protein SoxZ complement(455582..456454) Dinoroseobacter shibae DFL 12 = DSM 16493 5711386 YP_001531820.1 CDS Dshi_0471 NC_009952.1 456517 457557 D PFAM: beta-lactamase domain protein; KEGG: rde:RD1_0885 hypothetical protein; no significant swissprot, unsure GC frame plot; high Ref YP hit to beta-lactamase domain protein from Sinorhizobium medicae WSM419; NCBI conserved domains: GloB, Zn-dependent hydrolases, including glyoxylases; beta-lactamase domain-containing protein 456517..457557 Dinoroseobacter shibae DFL 12 = DSM 16493 5711387 YP_001531821.1 CDS Dshi_0472 NC_009952.1 457583 458197 R no significant swissprot, no conserved domains, high REf YP hit to hypothetical protein RD1_0886 from Roseobacter denitrificans OCh 114; hypothetical protein complement(457583..458197) Dinoroseobacter shibae DFL 12 = DSM 16493 5711388 YP_001531822.1 CDS Dshi_0473 NC_009952.1 458365 459477 D TIGRFAM: Alcohol dehydrogenase class III/S-(hydroxymethyl)glutathione dehydrogenase PFAM: Alcohol dehydrogenase zinc-binding domain protein; Alcohol dehydrogenase GroES domain protein; high swissprot hit to Alcohol dehydrogenase class-3 from Rhodobacter sphaeroides 2.4.1; alcohol dehydrogenase class III/S-(hydroxymethyl)glutathione dehydrogenase 458365..459477 Dinoroseobacter shibae DFL 12 = DSM 16493 5711389 YP_001531823.1 CDS Dshi_0474 NC_009952.1 459481 460308 D KEGG: rde:RD1_0888 S-formylglutathione hydrolase, putative TIGRFAM: S-formylglutathione hydrolase PFAM: putative esterase; good swissprot hit to S-formylglutathione hydrolase from Mus musculus; high Ref YP hit to S-formylglutathione hydrolase, putative from Roseobacter denitrificans OCh 114; S-formylglutathione hydrolase 459481..460308 Dinoroseobacter shibae DFL 12 = DSM 16493 5711390 YP_001531824.1 CDS cytC NC_009952.1 460328 460729 D PFAM: cytochrome c class I; low swissprot hit to Cytochrome c-552 from Paracoccus denitrificans; high Ref YP hit to cytochrome c family protein from Roseobacter denitrificans OCh 114; cytochrome c class I 460328..460729 Dinoroseobacter shibae DFL 12 = DSM 16493 5711391 YP_001531825.1 CDS gcd NC_009952.1 460857 462659 D PFAM: Pyrrolo-quinoline quinone; high swissprot hit to Putative dehydrogenase xoxF precursor from Paracoccus denitrificans; high Ref YP hit to Pyrrolo-quinoline quinone from Rhodobacter sphaeroides ATCC 17025; NCBI conserved domains: pqqDH; quinoprotein glucose dehydrogenase 460857..462659 Dinoroseobacter shibae DFL 12 = DSM 16493 5711392 YP_001531826.1 CDS cccA NC_009952.1 462744 463289 D SSF46626 Cytochrome c, monohaem; NCBI conserved domains: CccA, Cytochrome c, mono- and diheme variants, good swissprot hit to Cytochrome c-553I precursor from Paracoccus denitrificans; good Ref ZP hit to putative cytochrome c protein from Sagittula stellata E-37; cytochrome c protein 462744..463289 Dinoroseobacter shibae DFL 12 = DSM 16493 5711393 YP_001531827.1 CDS Dshi_0478 NC_009952.1 463273 464121 D SMART: extracellular solute-binding protein family ; NCBI conserved domains: PbPb; low swissprot hit to Protein moxJ precursor from Methylobacterium extorquens (May be involved in the assemblage of active methanoldehydrogenase and/or its cofactor PQQ in the periplasm); high Ref YP hit to putative methanol oxidation protein from Roseobacter denitrificans OCh 114; family 3 extracellular solute-binding protein 463273..464121 Dinoroseobacter shibae DFL 12 = DSM 16493 5711394 YP_001531828.1 CDS Dshi_0479 NC_009952.1 464118 464666 D no significant swissprot, unsure GC frame plot, good gb hit to hypothetical protein RLO149_07849 from Roseobacter litoralis Och 149; NCBI conserved domains: RHOD, Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein; hypothetical protein 464118..464666 Dinoroseobacter shibae DFL 12 = DSM 16493 5711395 YP_001531829.1 CDS Dshi_0480 NC_009952.1 464801 465967 D no significant swissprot, unsure GC frame plot; middle gb hit to hypothetical protein RLO149_03449 from Roseobacter litoralis Och 149; no conserved domains detected (except for one signalpep. and transmemb. region); hypothetical protein 464801..465967 Dinoroseobacter shibae DFL 12 = DSM 16493 5711396 YP_001531830.1 CDS Dshi_0481 NC_009952.1 466019 466831 R no significant swissprot, high Ref YP hit to hypothetical protein RD1_0894 from Roseobacter denitrificans OCh 114; NCBI conserved domains: COG5501, Predicted secreted protein; hypothetical protein complement(466019..466831) Dinoroseobacter shibae DFL 12 = DSM 16493 5711397 YP_001531831.1 CDS Dshi_0482 NC_009952.1 467299 467784 R no significant swissprot, unsure GC frame plot; no conserved domains; good Ref YP hit to hypothetical protein RD1_0897 from Roseobacter denitrificans OCh 114; hypothetical protein complement(467299..467784) Dinoroseobacter shibae DFL 12 = DSM 16493 5711398 YP_001531832.1 CDS Dshi_0483 NC_009952.1 467943 469130 D no significant swissprot, unsure GC frame plot (N-terminal); SSF53822 Periplasmic binding protein-like I; high gb hit to hypothetical protein RLO149_07824 [Roseobacter litoralis Och 149]; hypothetical protein 467943..469130 Dinoroseobacter shibae DFL 12 = DSM 16493 5711399 YP_001531833.1 CDS Dshi_0484 NC_009952.1 469158 470129 D TIGRFAM: 40-residue YVTN family beta-propeller repeat protein; SSF50969 Quinoprotein amine dehydrogenase, beta chain-like, no significant swissprot, high Ref YP hit to 40-residue YVTN family beta-propeller repeat protein from Sinorhizobium medicae WSM419; 40-residue YVTN family beta-propeller repeat-containing protein 469158..470129 Dinoroseobacter shibae DFL 12 = DSM 16493 5711400 YP_001531834.1 CDS Dshi_0485 NC_009952.1 470179 470616 D no significant swissprot, no conserved domains, high Ref YP hit to hypothetical protein RD1_0900 [Roseobacter denitrificans OCh 114]; hypothetical protein 470179..470616 Dinoroseobacter shibae DFL 12 = DSM 16493 5711401 YP_001531835.1 CDS Dshi_0486 NC_009952.1 470635 470883 D no significant swissprot, no conserved domains, middle gb hit to hypothetical protein RLO149_07809 [Roseobacter litoralis Och 149].; hypothetical protein 470635..470883 Dinoroseobacter shibae DFL 12 = DSM 16493 5711402 YP_001531836.1 CDS Dshi_0487 NC_009952.1 471449 472675 R no significant swissprot; bad Ref XP hit to TPR repeat protein [Entamoeba histolytica HM-1:IMSS]; InterPro Scan: G3DSA:1.25.40.10 Tetratricopeptide-like helical; hypothetical protein complement(471449..472675) Dinoroseobacter shibae DFL 12 = DSM 16493 5711403 YP_001531837.1 CDS Dshi_0488 NC_009952.1 472665 473018 R no significant BLAST hits, no conserved domains (except for two transmembr. regions); good RBS site : AGGAT; hypothetical protein complement(472665..473018) Dinoroseobacter shibae DFL 12 = DSM 16493 5711404 YP_001531838.1 CDS Dshi_0489 NC_009952.1 473039 474289 R no significant BLAST hits, unsure GC frame plot; NCBI conserved domains: mncomplete BisC domain, Anaerobic dehydrogenases, typically selenocysteine-containing; hypothetical protein complement(473039..474289) Dinoroseobacter shibae DFL 12 = DSM 16493 5711405 YP_001531839.1 CDS Dshi_0490 NC_009952.1 475571 475996 D low swissprot hit to Inner membrane protein ybaN from Escherichia coli K12; low Ref YP hit toprotein of unknown function DUF454 from Rhodobacter sphaeroides ATCC 17029; PF04304 Protein of unknown function DUF454; NCBI conserved domains: DUF454, Protein of unknown function (DUF454). Predicted membrane protein; unsure GC frame plot; hypothetical protein 475571..475996 Dinoroseobacter shibae DFL 12 = DSM 16493 5711406 YP_001531840.1 CDS ssuA1 NC_009952.1 476139 477122 D low swissprot hit to Putative aliphatic sulfonates-binding protein precursor from Escherichia coli K12; good Ref YP hit toTwin-arginine translocation pathway signal [Paracoccus denitrificans PD1222]; COG0715 - ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components;TIGR01409 Twin-arginine translocation pathway signal; putative sulfonate/nitrate transport system substrate-binding protein 476139..477122 Dinoroseobacter shibae DFL 12 = DSM 16493 5711407 YP_001531841.1 CDS ssuC1 NC_009952.1 477181 478005 D PFAM: binding-protein-dependent transport systems inner membrane component; COG0600, TauC, ABC-type nitrate/sulfonate/bicarbonate transport system, permease component; low swissprot toNitrate transport permease protein nrtB from Phormidium laminosum; high Ref ZP hit toBinding-protein-dependent transport systems inner membrane component [Paracoccus denitrificans PD1222]; sulfonate/nitrate/taurine transport system permease 477181..478005 Dinoroseobacter shibae DFL 12 = DSM 16493 5711408 YP_001531842.1 CDS ssuB1 NC_009952.1 478002 478751 D PFAM: ABC transporter related SMART: AAA ATPase; COG1116 - ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component; NCBI conserved domains: ssuB; middle swissprot hit to Aliphatic sulfonates import ATP-binding protein ssuB 1 from Xanthomonas axonopodis pv. citri; good Ref ZP hit to ABC transporter [Paracoccus denitrificans PD1222]; sulfonate/nitrate/taurine transport system ATP-binding 478002..478751 Dinoroseobacter shibae DFL 12 = DSM 16493 5711409 YP_001531843.1 CDS nnrS NC_009952.1 478748 480028 D PFAM: NnrS family protein KEGG: pde:Pden_4166 NnrS family protein; no swissprot; good gb hit to NnrS [Rhodobacter capsulatus]; NCBI conserved domains: NnrS; NnrS family protein 478748..480028 Dinoroseobacter shibae DFL 12 = DSM 16493 5711410 YP_001531844.1 CDS Dshi_0495 NC_009952.1 480087 480497 D no significant swissprot; low Ref NP hit to ferrienterobactin-like protein [Agrobacterium tumefaciens str. C58]; Pfam07715 TonB-dependent Receptor Plug Domain; hypothetical protein 480087..480497 Dinoroseobacter shibae DFL 12 = DSM 16493 5711411 YP_001531845.1 CDS Dshi_0496 NC_009952.1 480704 482722 R PFAM: 4Fe-4S ferredoxin iron-sulfur binding domain protein; no significant swissprot, unsure GC frame plot; high Ref ZP hit to putative ferredoxin [Loktanella vestfoldensis SKA53]; 4Fe-4S ferredoxin complement(480704..482722) Dinoroseobacter shibae DFL 12 = DSM 16493 5711412 YP_001531846.1 CDS Dshi_0497 NC_009952.1 482822 483556 D no significant swissprot, unsure GC frame plot, no conserved domains; good Ref ZP hit to hypothetical protein SKA53_09144 [Loktanella vestfoldensis SKA53]; hypothetical protein 482822..483556 Dinoroseobacter shibae DFL 12 = DSM 16493 5711413 YP_001531847.1 CDS Dshi_0498 NC_009952.1 483553 484110 D no significant swissprot; unsure GC frame plot; no conserved domains; good Ref ZP hit to hypothetical protein SKA53_09139 [Loktanella vestfoldensis SKA53]; hypothetical protein 483553..484110 Dinoroseobacter shibae DFL 12 = DSM 16493 5711414 YP_001531848.1 CDS Dshi_0499 NC_009952.1 484107 485120 D no significant swissprot, unsure GC frame plot; no conserved domains; high Ref ZP hit to hypothetical protein SKA53_09134 [Loktanella vestfoldensis SKA53]; hypothetical protein 484107..485120 Dinoroseobacter shibae DFL 12 = DSM 16493 5711415 YP_001531849.1 CDS Dshi_0500 NC_009952.1 485120 485656 D no significant swissprot; no conserved domains; unsure GC frame plot; low Ref ZP hit to molybdopterin-guanine dinucleotide biosynthesis protein A from Methylobacterium extorquens PA1; hypothetical protein 485120..485656 Dinoroseobacter shibae DFL 12 = DSM 16493 5711416 YP_001531850.1 CDS Dshi_0501 NC_009952.1 485653 486264 D no significant swissprot, no conserved domains; low Ref ZP hit to hypothetical protein SKA53_09124 [Loktanella vestfoldensis SKA53].; hypothetical protein 485653..486264 Dinoroseobacter shibae DFL 12 = DSM 16493 5711417 YP_001531851.1 CDS torD NC_009952.1 486380 487042 D PFAM: cytoplasmic chaperone TorD family protein; low swissprot to Chaperone protein torD from Vibrio cholerae and high Ref ZP hit toputative chaperone [Loktanella vestfoldensis SKA53]; NCBI conserved domains: torD; cytoplasmic chaperone TorD family protein 486380..487042 Dinoroseobacter shibae DFL 12 = DSM 16493 5711418 YP_001531852.1 CDS Dshi_0503 NC_009952.1 487101 487310 D no significant swissprot; bad Ref ZP hit to hypothetical protein SKA53_09114 [Loktanella vestfoldensis SKA53]; no conserved domains (except for one transmem. region); hypothetical protein 487101..487310 Dinoroseobacter shibae DFL 12 = DSM 16493 5711419 YP_001531853.1 CDS fdnG NC_009952.1 487314 490274 D PFAM: molybdopterin oxidoreductase; molydopterin dinucleotide-binding region; molybdopterin oxidoreductase Fe4S4; high swissprot hit to Formate dehydrogenase alpha chain from Methanocaldococcus jannaschii; high Ref ZP hit to formate dehydrogenase, alpha subunit, putative [Loktanella vestfoldensis SKA53]; NCBI conserved domains: mopB; formate dehydrogenase subunit alpha 487314..490274 Dinoroseobacter shibae DFL 12 = DSM 16493 5711420 YP_001531854.1 CDS fdnH NC_009952.1 490289 490885 D PFAM: 4Fe-4S ferredoxin iron-sulfur binding domain protein; good swissprot hit to Formate dehydrogenase iron-sulfur subunit from Wolinella succinogenes; high Ref ZP hit to formate dehydrogenase iron-sulfur subunit [Loktanella vestfoldensis SKA53]; NCBI conserved domains: HybA, Fe-S-cluster-containing hydrogenase components 1; formate dehydrogenase iron-sulfur subunit 490289..490885 Dinoroseobacter shibae DFL 12 = DSM 16493 5711421 YP_001531855.1 CDS fdnI NC_009952.1 490899 491927 D TIGRFAM: formate dehydrogenase, gamma subunit; middle swissprot hit to Formate dehydrogenase, nitrate-inducible, cytochrome b556(fdn) subunit (Formate dehydrogenase-N subunit gamma) from Escherichia coli K12; high Ref ZP hit to putative formate dehydrogenase [Loktanella vestfoldensis SKA53]; NCBI conserved domains: fdnI; formate dehydrogenase subunit gamma 490899..491927 Dinoroseobacter shibae DFL 12 = DSM 16493 5711422 YP_001531856.1 CDS Dshi_0507 NC_009952.1 492087 493133 D high swissprot hit to Protein mrp homolog from Haemophilus influenzae; high Ref ZP hit to probable multidrug-resistance related protein [Loktanella Loktanella vestfoldensis SKA53]; InterPro Scan: PS01215 Mrp; NCBI conserved domains: mrp-like; ATP/GTP-binding protein; MRP-like protein 492087..493133 Dinoroseobacter shibae DFL 12 = DSM 16493 5711423 YP_001531857.1 CDS Dshi_0508 NC_009952.1 493317 494531 D PFAM: cytochrome c class I; SMART: WD-40 repeat protein, unsure GC frame plot; low swissprot hit to Cytochrome c from Cochliobolus lunatus; good Ref ZP hit to cytochrome c, class I [Methylobacterium extorquens PA1]; NCBI conserved domains: WD40; cytochrome c class I 493317..494531 Dinoroseobacter shibae DFL 12 = DSM 16493 5711424 YP_001531858.1 CDS Dshi_0509 NC_009952.1 494625 495407 R no significant swissprot, no conserved domains (except for one signalpep.); unsure GC frame plot; good Ref YP hit to hypothetical protein Spro_3113 [Serratia proteamaculans 568].; hypothetical protein complement(494625..495407) Dinoroseobacter shibae DFL 12 = DSM 16493 5711425 YP_003422323.1 CDS Dshi_0510 NC_009952.1 495589 496662 R good swissprot hit to Alkyl/aryl-sulfatase BDS1 (Bacterially-derived sulfatase 1) from Saccharomyces cerevisiae, high Ref ZP hit to beta-lactamase domain protein [Methylobacterium sp. 4-46];InterPRo Scan: Tetratricopeptide region TPR; NCBI conserved domains: COG2015, Alkyl sulfatase and related hydrolases; beta-lactamase complement(495589..496662) Dinoroseobacter shibae DFL 12 = DSM 16493 5711426 YP_003422324.1 CDS Dshi_0511 NC_009952.1 496690 496893 R may be part of Gene Dshi_0510; low swissprot hit to Alkyl/aryl-sulfatase BDS1 (Bacterially-derived sulfatase 1) from Saccharomyces cerevisiae; middle Ref YP hit to metallo-beta-lactamase superfamily protein [Azorhizobium caulinodans ORS 571]; NCBI conserved domains: COG2015, Alkyl sulfatase and related hydrolases; InterPro Scan: no hits reported; hypothetical protein complement(496690..496893) Dinoroseobacter shibae DFL 12 = DSM 16493 8130634 YP_001531859.1 CDS Dshi_0512 NC_009952.1 496905 497582 R pfam00753, Lactamase_B, Metallo-beta-lactamase superfamily; COG2333, ComEC, Predicted hydrolase; low swissprot hit to Alkyl/aryl-sulfatase BDS1 (Bacterially-derived sulfatase 1) from Saccharomyces cerevisiae; good Ref YP hit to beta-lactamase domain protein [Polynucleobacter sp. QLW-P1DMWA-1]; beta-lactamase domain-containing protein complement(496905..497582) Dinoroseobacter shibae DFL 12 = DSM 16493 5711427 YP_001531860.1 CDS Dshi_0513 NC_009952.1 498319 498786 R pfam00196, GerE, Bacterial regulatory proteins, luxR family; low swissprot hit to Transcriptional regulatory protein fixJ from Sinorhizobium meliloti; middle Ref ZP hit to putative two-component response regulator [Roseovarius sp. HTCC2601], unsure GC frame plot; LuxR family; transcriptional regulator complement(498319..498786) Dinoroseobacter shibae DFL 12 = DSM 16493 5711428 YP_001531861.1 CDS Dshi_0514 NC_009952.1 498765 498947 R bad swissprot to Transcriptional regulatory protein fixJ from Azorhizobium caulinodans; low Ref ZP hit to putative two-component response regulator [Roseovarius sp. HTCC2601]; PFAM00072 response regulator receiver; COG4566, TtrR, Response regulator; response regulator receiver protein complement(498765..498947) Dinoroseobacter shibae DFL 12 = DSM 16493 5711429 YP_001531862.1 CDS Dshi_0515 NC_009952.1 498944 499843 R unsure GC frame plot; - PFAM: ATP-binding region ATPase domain protein; histidine kinase A domain protein; NCBI conserved domains: HisKA; middle swissprot hit to Sensor protein fixL; good Ref ZP hit to probable sensor histidine kinase of two-component system from Roseovarius sp. HTCC2601; histidine kinase complement(498944..499843) Dinoroseobacter shibae DFL 12 = DSM 16493 5711430 YP_001531863.1 CDS Dshi_0516 NC_009952.1 499850 500836 R pfam04392, ABC_sub_bind, ABC transporter substrate binding protein; no significant swissprot; good Ref ZP hit to probable sensor histidine kinase of two-component system from Roseovarius sp. HTCC2601; unsure GC frame plot; putative two-component sensor kinase complement(499850..500836) Dinoroseobacter shibae DFL 12 = DSM 16493 5711431 YP_001531864.1 CDS araF2 NC_009952.1 501109 502149 R PFAM: periplasmic binding protein/LacI transcriptional regulator; COG4213, XylF, ABC-type xylose transport system, periplasmic component; low swissprot hit to D-ribose-binding protein precursor from Bacillus subtilis; High Ref YP Hit to sugar ABC transporter, substrate-binding protein, putative from Roseobacter denitrificans OCh 114; periplasmic component; ribose/xylose/arabinose/galactoside ABC-type transport system protein complement(501109..502149) Dinoroseobacter shibae DFL 12 = DSM 16493 5711432 YP_001531865.1 CDS araH1 NC_009952.1 502175 503185 R PFAM: inner-membrane translocator; NCBI conserved domains: COG1172, AraH, Ribose/xylose/arabinose/galactoside ABC-type transport systems, permease components; PRK09512, rbsC, ribose ABC transporter permease protein; middle swissprot hit to Ribose transport system permease protein rbsC from Bacillus subtilis; High gb hit to ribose ABC transporter, permease protein [Roseob; permease components; ribose/xylose/arabinose/galactoside ABC-type transport system protein complement(502175..503185) Dinoroseobacter shibae DFL 12 = DSM 16493 5711433 YP_001531866.1 CDS araG1 NC_009952.1 503182 504678 R PFAM: ABC transporter related SMART: AAA ATPase, high swissprot to Arabinose import ATP-binding protein araG from Pseudomonas syringae pv. tomato; high gb hit to sugar uptake ABC transporter ATP-binding protein from Roseobacter litoralis Och 149; ATP-binding; ribose/xylose/arabinose/galactoside ABC-type transport system protein complement(503182..504678) Dinoroseobacter shibae DFL 12 = DSM 16493 5711434 YP_001531867.1 CDS mtnK NC_009952.1 504830 506089 D phosphorylates methylthioribose to form methylthioribose-1-phosphate; involved in methionine salvage pathway; methylthioribose kinase 504830..506089 Dinoroseobacter shibae DFL 12 = DSM 16493 5711973 YP_001531868.1 CDS mtnA NC_009952.1 506086 507189 D isomerizes methylthioribose-1-phosphate into methylthioribulose-1-phosphate; involved in methionine salvage pathway; methylthioribose-1-phosphate isomerase 506086..507189 Dinoroseobacter shibae DFL 12 = DSM 16493 5711974 YP_001531869.1 CDS deoR3 NC_009952.1 507247 508206 D PFAM: putative sugar-binding domain protein; NCBI conserved domains: pfam04198, Sugar-bind, Putative sugar-binding domain; COG2390, DeoR, Transcriptional regulator, contains sigma factor-related N-terminal domain, good swissprot hit to Uncharacterized transcriptional regulator yjhU from Escherichia coli K12 (related to SorC); high Ref YP hit to transcriptional regulator, putative [Roseobacter denitrificans OCh 114]; DeoR family; transcriptional regulator 507247..508206 Dinoroseobacter shibae DFL 12 = DSM 16493 5711975 YP_001531870.1 CDS fucA NC_009952.1 508203 508898 D PFAM: class II aldolase/adducin family protein; COG0235, AraD, Ribulose-5-phosphate 4-epimerase and related epimerases and aldolases; good swissprot hit to L-fuculose phosphate aldolase from Escherichia coli K12; good Ref ZP hit to L-fuculose phosphate aldolase [Stappia aggregata IAM 12614]; unsure GC frame plot; L-fuculose phosphate aldolase 508203..508898 Dinoroseobacter shibae DFL 12 = DSM 16493 5711976 YP_001531871.1 CDS Dshi_0524 NC_009952.1 508895 509974 D pfam00248: aldo/keto reductase; COG0667, Tas, Predicted oxidoreductases; good swissprot hit to Uncharacterized oxidoreductase yajO from Escherichia coli K12; high Ref NP hit to oxido-reductase, and dehydratase mocA from Mesorhizobium loti MAFF303099; aldo/keto reductase 508895..509974 Dinoroseobacter shibae DFL 12 = DSM 16493 5711977 YP_001531872.1 CDS Dshi_0525 NC_009952.1 510058 510609 D no significant swissprot, unsure GC frame plot; COG3911, Predicted ATPase; cd00009, AAA, AAA-superfamily of ATPases; good Ref ZP hit to ATPase-like protein [Sagittula stellata E-37].; ATPase-like protein 510058..510609 Dinoroseobacter shibae DFL 12 = DSM 16493 5711978 YP_001531873.1 CDS dahL NC_009952.1 510637 511236 R PFAM:PF02734 Dak phosphatase; NCBI conserved domains: PRK10005, dihydroxyacetone kinase, C-terminal domain; low swissprot hit to PTS-dependent dihydroxyacetone kinase, ADP-binding subunit dhaL from Escherichia coli K12; middle Ref ZP hit to Dihydroxyacetone kinase [Psychroflexus torquis ATCC 700755]; unsure GC frame plot; ADP-binding subunit dhaL; PTS-dependent dihydroxyacetone kinase complement(510637..511236) Dinoroseobacter shibae DFL 12 = DSM 16493 5711979 YP_001531874.1 CDS dahK NC_009952.1 511233 512234 R PFAM: Dak kinase; NCBI conserved domains: PRK11468, dihydroxyacetone kinase subunit DhaK; good swissprot hit to PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit dhaK from Escherichia coli K12; high Ref ZP hit to putative dihydroxyacetone kinase [Aurantimonas sp. SI85-9A1]; dihydroxyacetone-binding subunit dhaK; PTS-dependent dihydroxyacetone kinase complement(511233..512234) Dinoroseobacter shibae DFL 12 = DSM 16493 5711980 YP_001531875.1 CDS araH2 NC_009952.1 512265 513269 R PFAM: inner-membrane translocator; NCBI conserved domains: COG1172, AraH; middle swissprot hit to Ribose transport system permease protein rbsC from Bacillus subtilis; good Ref NP hit to ABC transporter, membrane spanning protein (sugar) [Agrobacterium tumefaciens str. C58]; permease components; ribose/xylose/arabinose/galactoside ABC-type transport system protein complement(512265..513269) Dinoroseobacter shibae DFL 12 = DSM 16493 5711981 YP_001531876.1 CDS araH3 NC_009952.1 513283 514284 R PFAM: inner-membrane translocator; NCBI conserved domains: COG1172, AraH; middle swissprot hit to Ribose transport system permease protein rbsC from Bacillus subtilis; good Ref ZP hit to putative permease protein, ABC-type sugar transporter [Aurantimonas sp. SI85-9A1]; permease components; ribose/xylose/arabinose/galactoside ABC-type transport system protein complement(513283..514284) Dinoroseobacter shibae DFL 12 = DSM 16493 5711982 YP_001531877.1 CDS araG2 NC_009952.1 514281 515777 R PFAM: ABC transporter related SMART: AAA ATPase; high swissprot hit to Ribose import ATP-binding protein rbsA 3 from Rubrobacter xylanophilus DSM 9941; high Ref YP hit to ABC transporter related [Nocardioides sp. JS614]; ATP-binding; ribose/xylose/arabinose/galactoside ABC-type transport system protein complement(514281..515777) Dinoroseobacter shibae DFL 12 = DSM 16493 5711983 YP_001531878.1 CDS araF1 NC_009952.1 515852 516841 R NCBI conserved domains: COG4213, XylF, ABC-type xylose transport system, periplasmic component; low swissprot hit to Uncharacterized protein yneA precursor from Escherichia coli K12; high Ref ZP hit to putative periplasmic substrate-binding protein, ABC-type sugar transporter [Aurantimonas sp. SI85-9A1]; periplasmic component; ribose/xylose/arabinose/galactoside ABC-type transport system protein complement(515852..516841) Dinoroseobacter shibae DFL 12 = DSM 16493 5711984 YP_001531879.1 CDS deoR2 NC_009952.1 517065 518039 D PFAM: putative sugar-binding domain protein; NCBI conserved domains: pfam04198, Sugar-bind and COG2390, DeoR; middle swissprot hit to Deoxyribonucleoside regulator from Bacillus subtilis; good Ref YP hit to transcriptional regulator, DeoR family [Sinorhizobium medicae WSM419]; DeoR family; transcriptional regulator 517065..518039 Dinoroseobacter shibae DFL 12 = DSM 16493 5711985 YP_001531880.1 CDS Dshi_0533 NC_009952.1 518039 518887 D PFAM: Xylose isomerase domain protein TIM barrel; NCBI conserved domains: cd00019, AP2Ec, AP endonuclease family 2; middle swissprot hit to Uncharacterized protein sll1304 from Synechocystis sp. PCC 6803; high Ref YP hit to Xylose isomerase domain protein TIM barrel [Sinorhizobium medicae WSM419]; xylose isomerase domain-containing protein 518039..518887 Dinoroseobacter shibae DFL 12 = DSM 16493 5711986 YP_001531881.1 CDS pdhA2 NC_009952.1 518910 519929 D PFAM: dehydrogenase E1 component; good swissprot hit to Pyruvate dehydrogenase E1 component subunit alpha from Zymomonas mobilis; high Ref YP hit to dehydrogenase E1 component [Sinorhizobium medicae WSM419]; pyruvate dehydrogenase E1 component subunit alpha 518910..519929 Dinoroseobacter shibae DFL 12 = DSM 16493 5711987 YP_001531882.1 CDS pdhB1 NC_009952.1 519929 520912 D PFAM: Transketolase central region; Transketolase domain protein; high swissprot hit to Pyruvate dehydrogenase E1 component subunit beta from Rickettsia bellii RML369-C; high Ref YP hit to Transketolase central region [Sinorhizobium medicae WSM419]; Transketolase central region; pyruvate dehydrogenase E1 component subunit beta 519929..520912 Dinoroseobacter shibae DFL 12 = DSM 16493 5711988 YP_001531883.1 CDS pdhC2 NC_009952.1 520939 522135 D PFAM: alpha/beta hydrolase fold; biotin/lipoyl attachment domain-containing protein; E3 binding domain protein; middle swissprot hit to Acetoin dehydrogenase E2 component from Pseudomonas putida; high Ref YP hit to branched-chain alpha-keto acid dehydrogenase subunit E2 from Sinorhizobium medicae WSM419; unsure GC frame plot; pyruvate dehydrogenase E2 component; branched-chain alpha-keto acid dehydrogenase subunit E2 520939..522135 Dinoroseobacter shibae DFL 12 = DSM 16493 5711989 YP_001531884.1 CDS Dshi_0537 NC_009952.1 522165 523658 D PFAM: carbohydrate kinase FGGY; NCBI conserved domains: AraB, XylB; good swissprot hit to Ribulokinase from Bacillus clausii KSM-K16; high Ref YP hit to carbohydrate kinase FGGY [Sinorhizobium medicae WSM419]; carbohydrate kinase FGGY 522165..523658 Dinoroseobacter shibae DFL 12 = DSM 16493 5711990 YP_001531885.1 CDS Dshi_0538 NC_009952.1 523844 524515 D unsure GC frame plot; no significant swissprot; PFAM: protein of unknown function DUF1045; high Ref ZP hit to hypothetical protein SSE37_12456 [Sagittula stellata E-37]; hypothetical protein 523844..524515 Dinoroseobacter shibae DFL 12 = DSM 16493 5711991 YP_001531886.1 CDS Dshi_0539 NC_009952.1 524529 525467 R PFAM: aldo/keto reductase; COG0667, Tas, Predicted oxidoreductases; high Ref ZP hit to oxidoreductase, aldo/keto reductase family protein [Sagittula stellata E-37]; good swissprot hit to Uncharacterized oxidoreductase yajO from Escherichia coli K12; aldo/keto reductase family protein; oxidoreductase complement(524529..525467) Dinoroseobacter shibae DFL 12 = DSM 16493 5711992 YP_001531887.1 CDS Dshi_0540 NC_009952.1 525545 526321 D unsure GC frame plot; no significant swissprot; PFAM: NnrUfamily protein; NCBI conserved domains: pfam07298, NnrU, NnrU protein; good Ref ZP hit to NnrU family protein [Roseovarius sp. TM1035]; NnrU family protein 525545..526321 Dinoroseobacter shibae DFL 12 = DSM 16493 5711993 YP_001531888.1 CDS hemN1 NC_009952.1 526456 527820 D catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III; coproporphyrinogen III oxidase 526456..527820 Dinoroseobacter shibae DFL 12 = DSM 16493 5711994 YP_001531889.1 CDS Dshi_0542 NC_009952.1 528241 529869 R NCBI conserved domains: pfam01384, PHO4, Phosphate transporter family; COG0306, PitA, Phosphate/sulphate permeases; high swissprot hit to Putative phosphate permease jhp_1384 from Helicobacter pylori J99; high Ref YP hit to phosphate permease [Azoarcus sp. EbN1].; phosphate transporter complement(528241..529869) Dinoroseobacter shibae DFL 12 = DSM 16493 5711995 YP_001531890.1 CDS Dshi_0543 NC_009952.1 529946 531796 D NCBI conserved domains: pfam02690, Na_Pi_cotrans, Na+/Pi-cotransporter; COG1283, NptA, Na+/phosphate symporter, bad swissprot hit to Na(+)/Pi cotransporter 2B from Bos taurus; high Ref ZP hit to Na+/Pi-cotransporter [Oceanospirillum sp. MED92]; Na+/Pi-cotransporter 529946..531796 Dinoroseobacter shibae DFL 12 = DSM 16493 5711996 YP_001531891.1 CDS Dshi_0544 NC_009952.1 531843 532091 D no significant BLAST hits, no conserved domains detected; hypothetical protein 531843..532091 Dinoroseobacter shibae DFL 12 = DSM 16493 5711997 YP_001531892.1 CDS Dshi_0545 NC_009952.1 532144 532884 R TIGRFAM: HAD-superfamily hydrolase, subfamily IA, variant 3; HAD-superfamily hydrolase, subfamily IA, variant 1 PFAM: Haloacid dehalogenase domain protein hydrolase, NCBI conserved domains: COG0637, Predicted phosphatase/phosphohexomutase; low swissprot hit to Phosphatase yieH from Escherichia coli K12; good gb hit to HAD-superfamily hydrolase subfamily IA, variant 3 [Hoeflea phototrophica DFL-43]; subfamily IA, variant 3; HAD-superfamily hydrolase complement(532144..532884) Dinoroseobacter shibae DFL 12 = DSM 16493 5711998 YP_001531893.1 CDS ugpC2 NC_009952.1 532894 533910 R PFAM: ABC transporter related; TOBE domain protein; Transport-associated OB domain protein SMART: AAA ATPase; high swissprot hit to sn-glycerol-3-phosphate import ATP-binding protein ugpC from Silicibacter pomeroyi; high gb hit to sorbitol/mannitol ABC transporter, ATP-binding protein [Hoeflea phototrophica DFL-43]; following three ABC transporter genes (Dshi_0547 to Dshi_0549) com; sugar/sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC complement(532894..533910) Dinoroseobacter shibae DFL 12 = DSM 16493 5711999 YP_001531894.1 CDS ugpB4 NC_009952.1 534071 535414 D PFAM: extracellular solute-binding protein family, NCBI conserved domains: COG1653, UgpB, ABC-type sugar transport system, periplasmic component; low swissprot hit to Putative binding protein BruAb2_0484 precursor from Brucella abortus; high gb hit to sugar ABC transporter, periplasmic binding protein, putative from Hoeflea phototrophica DFL-43; periplasmic component ugpB; sugar/sn-glycerol 3-phosphate ABC transporter protein 534071..535414 Dinoroseobacter shibae DFL 12 = DSM 16493 5712000 YP_001531895.1 CDS ugpA1 NC_009952.1 535489 536355 D PFAM: binding-protein-dependent transport systems inner membrane component, NCBI conserved domains: COG1175, UgpA, ABC-type sugar transport systems, permease components; middle swissprot hit to Probable ABC transporter permease protein y4oQ from Rhizobium sp. NGR234; high gb hit to putative sugar ABC transporter, permease protein [Hoeflea phototrophica DFL-43]; sugar/sn-glycerol-3-phosphate ABC transporter permease UgpA 535489..536355 Dinoroseobacter shibae DFL 12 = DSM 16493 5712001 YP_001531896.1 CDS ugpE4 NC_009952.1 536359 537177 D PFAM: binding-protein-dependent transport systems inner membrane component; NCBI conserved domains: COG0395, UgpE, ABC-type sugar transport system, permease component and COG3833, MalG, ABC-type maltose transport systems, permease component; middle swissprot hit to Probable ABC transporter permease protein y4oR from Rhizobium sp. NGR234; high gb hit to sugar ABC transporter permease protein [Hoef; sugar/sn-glycerol-3-phosphate ABC transporter permease UgpE 536359..537177 Dinoroseobacter shibae DFL 12 = DSM 16493 5712002 YP_001531897.1 CDS deoR1 NC_009952.1 537246 538217 D PFAM: putative sugar-binding domain protein; low swissprot hit to Deoxyribonucleoside regulator DeoR from Bacillus subtilis; high gb hit to putative transcriptional regulator protein, DeoR family [Hoefleaphototrophica DFL-43]; DeoR family; transcriptional regulator 537246..538217 Dinoroseobacter shibae DFL 12 = DSM 16493 5712003 YP_001531898.1 CDS xylD NC_009952.1 538237 539280 D PFAM: Alcohol dehydrogenase zinc-binding domain protein; Alcohol dehydrogenase GroES domain protein; high swissprot hit to Putative D-xylulose reductase from Sinorhizobium meliloti; high gb hit to D-xylulose reductase, putative [Hoeflea phototrophica DFL-43]; Xylitol dehydrogenase; D-xylulose reductase 538237..539280 Dinoroseobacter shibae DFL 12 = DSM 16493 5712004 YP_001531899.1 CDS Dshi_0552 NC_009952.1 539277 539843 D PFAM: sugar isomerase (SIS); middle swissprot to 3-hexulose-6-phosphate isomerase from Bacillus subtilis; good gb hit to 6-phospho-3-hexuloisomerase [Hoeflea phototrophica DFL-43].; sugar isomerase 539277..539843 Dinoroseobacter shibae DFL 12 = DSM 16493 5712005 YP_001531900.1 CDS Dshi_0553 NC_009952.1 539847 540614 D PFAM: short-chain dehydrogenase/reductase SDR; KR domain protein; NCBI conserved domains: PRK12825, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase; middle swissprot hit to3-oxoacyl-[acyl-carrier-protein] reductase from Bacillus subtilis; good ref ZP hit to Short-chain dehydrogenase/reductase SDR [Synechococcus sp. WH 5701]; short-chain dehydrogenase/reductase SDR 539847..540614 Dinoroseobacter shibae DFL 12 = DSM 16493 5712006 YP_001531901.1 CDS rbtD NC_009952.1 541133 541858 D PFAM: short-chain dehydrogenase/reductase SDR; KR domain protein; high swissprot hit to Ribitol 2-dehydrogenase (RDH) from Klebsiella aerogenes; high Ref YP hit to probable ribitol 2-dehydrogenase protein [Rhizobium etli CFN 42].; ribitol 2-dehydrogenase 541133..541858 Dinoroseobacter shibae DFL 12 = DSM 16493 5712007 YP_001531902.1 CDS araB NC_009952.1 541855 543489 D TIGRFAM: FGGY-family pentulose kinase PFAM: carbohydrate kinase FGGY; good swissprot hit to Uncharacterized sugar kinase YDR109C from Saccharomyces cerevisiae; high gb hit to ribitol kinase [Escherichia coli]; unsure Gc frame plot; ribulokinase 541855..543489 Dinoroseobacter shibae DFL 12 = DSM 16493 5712008 YP_001531903.1 CDS Dshi_0556 NC_009952.1 544002 544445 D unsure GC frame plot, no significant swissprot, bad gb hit to nucleoside diphosphate kinase regulator from Oceanibulbus indolifex HEL-45; NCBI conserved domains: PRK05753, nucleoside diphosphate kinase regulator; hypothetical protein 544002..544445 Dinoroseobacter shibae DFL 12 = DSM 16493 5712009 YP_001531904.1 CDS greA2 NC_009952.1 544496 544927 D PFAM: transcription elongation factor GreA/GreB domain protein, NCBI conserved domains: COG0782, GreA, Transcription elongation factor, bad swissprot hit to Transcription elongation factor greA from Sinorhizobium meliloti; middle gb hit to GreA/GreB family elongation factor [Oceanibulbus indolifex HEL-45].; GreA/GreB family elongation factor 544496..544927 Dinoroseobacter shibae DFL 12 = DSM 16493 5712010 YP_001531905.1 CDS dadA NC_009952.1 545054 546313 D PFAM: FAD dependent oxidoreductase; NCBI conserved domains: PRK00711, D-amino acid dehydrogenase small subunit; high swissprot hit to D-amino acid dehydrogenase small subunit from Bradyrhizobium japonicum; high gb hit to D-amino-acid dehydrogenase, small subunit protein [Oceanibulbus indolifex HEL-45].; D-amino-acid dehydrogenase 545054..546313 Dinoroseobacter shibae DFL 12 = DSM 16493 5712011 YP_001531906.1 CDS Dshi_0559 NC_009952.1 546760 547167 D unsure GC frame plot, no significant swissprot, PFAM: protein of unknown function DUF1636; NCBI conserved domains: COG5469, Predicted metal-binding protein; middle Ref ZP hit to hypothetical protein RCCS2_05834 [Roseobacter sp. CCS2].; hypothetical protein 546760..547167 Dinoroseobacter shibae DFL 12 = DSM 16493 5712012 YP_001531907.1 CDS fhuC NC_009952.1 547164 547937 D PFAM: ABC transporter related SMART: AAA ATPase; good swissprot hit to Ferrichrome transport ATP-binding protein fhuC from Escherichia coli K12; high Ref ZP hit to iron ABC transporter, ATP-binding protein, putative [Roseobactersp. CCS2], unsure GC frame plot; ATPase components; alternative gene name: fecE/fepC/btuD; cobalamin/Fe3+-siderophores ABC transporter protein 547164..547937 Dinoroseobacter shibae DFL 12 = DSM 16493 5712013 YP_001531908.1 CDS fhuD NC_009952.1 547953 548888 D PFAM: periplasmic binding protein; low swissprot hit to Vitamin B12-binding protein precursor from Escherichia coli O6; high Ref YP hit to putative iron ABC transporter, periplasmic binding protein from Roseobacter denitrificans OCh 114; NCBI conserved domains: fhuD, btuF; periplasmic binding protein; alternative gene name: fecB/fepB/btuF; cobalamin/Fe3+-siderophores ABC transporter protein 547953..548888 Dinoroseobacter shibae DFL 12 = DSM 16493 5712014 YP_001531909.1 CDS fhuB NC_009952.1 548885 549931 D PFAM: transport system permease protein; NCBI conserved domains: fecCD, fepDG, btuC; good swissprot hit to Ferrichrome transport system permease protein fhuB from Bacillus subtilis; high gb hit to putative hemin ABC transport protein, permease component from Roseobacter litoralis Och 149; permease protein; alternative gene name: fecCD/fepDG/btuC; cobalamin/Fe3+-siderophores ABC transporter protein 548885..549931 Dinoroseobacter shibae DFL 12 = DSM 16493 5712015 YP_001531910.1 CDS irpA NC_009952.1 550566 551828 D unsure GC frame plot; NCBI conserved domains: COG3487, IrpA, Uncharacterized iron-regulated protein; low swissprot hit to Iron-regulated protein A precursor from Synechococcus elongatus PCC 7942; high Ref ZP hit to lipoprotein, putative [Rhodobacterales bacterium HTCC2150]; iron-regulated protein 550566..551828 Dinoroseobacter shibae DFL 12 = DSM 16493 5712016 YP_001531911.1 CDS Dshi_0564 NC_009952.1 551932 553464 D PFAM: protein of unknown function DUF1111; NCBI conserved domains: COG3488, Predicted thiol oxidoreductase; no significant swissprot; high Ref ZP hit to probable thiol oxidoreductase with 2 cytochrome c heme-binding sites [Sulfitobacter sp. EE-36]; hypothetical protein 551932..553464 Dinoroseobacter shibae DFL 12 = DSM 16493 5712017 YP_001531912.1 CDS Dshi_0565 NC_009952.1 553461 554477 D low swissprot hit to Iron-regulated protein A precursor from Synechococcus elongatus PCC 7942; high Ref ZP hit to hypothetical protein RB2150_00045 [Rhodobacterales bacterium HTCC2150]; NCBI conserved domains: COG3489, Predicted periplasmic lipoprotein; hypothetical protein 553461..554477 Dinoroseobacter shibae DFL 12 = DSM 16493 5712018 YP_001531913.1 CDS Dshi_0566 NC_009952.1 554479 555561 D NCBI conserved domains: pfam07433, DUF1513, COG3490, Uncharacterized protein conserved in bacteria, no significant swissprot; high Ref ZP hit to hypothetical protein RB2150_00040 [Rhodobacterales bacterium HTCC2150]; unsure GC frame plot; hypothetical protein 554479..555561 Dinoroseobacter shibae DFL 12 = DSM 16493 5712019 YP_001531914.1 CDS Dshi_0567 NC_009952.1 555614 556162 R unsure GC frame plot; TIGRFAM: TonB family protein; low swissprot hit to Protein tonB from Pseudomonas putida; low Ref ZP hit toPutative TonB protein [Roseobacter sp. SK209-2-6]; TonB family protein complement(555614..556162) Dinoroseobacter shibae DFL 12 = DSM 16493 5712020 YP_001531915.1 CDS exbD NC_009952.1 556657 557049 R PFAM: Biopolymer transport protein ExbD/TolR; low swissprot hit to Biopolymer transport protein exbD1 from Vibrio cholerae; low gb hit to Biopolymer transport protein ExbD/TolR [alpha proteobacterium BAL199]; biopolymer transport protein ExbD/TolR complement(556657..557049) Dinoroseobacter shibae DFL 12 = DSM 16493 5712021 YP_001531916.1 CDS exbB NC_009952.1 557437 558129 R PFAM: MotA/TolQ/ExbB proton channel; low swissprot hit to Putative biopolymer transport protein exbB homolog from Methanothermobacter thermautotrophicus str. Delta H; good Ref ZP hit to MotA/TolQ/ExbB proton channel [Roseobacter sp. SK209-2-6]; NCBI conserved domains: MotA/ ExbB; MotA/TolQ/ExbB proton channel complement(557437..558129) Dinoroseobacter shibae DFL 12 = DSM 16493 5712022 YP_001531917.1 CDS fhuA NC_009952.1 558999 561026 D PFAM: TonB-dependent receptor; TonB-dependent receptor plug; low swissprot hit to Vitamin B12 transporter btuB precursor from Photobacterium profundum; high Ref NP hit to putative outer membrane receptor for iron compound or colicin [Escherichia coli O157:H7 EDL933]; TonB-dependent outermembrane recepter protein; alternative gene name: fecA/fepA/btuB; cobalamin/Fe3+-siderophores ABC transporter protein 558999..561026 Dinoroseobacter shibae DFL 12 = DSM 16493 5712023 YP_001531918.1 CDS hmuV NC_009952.1 561072 561854 R with HmuTU is involved in the transport of hemin; hemin importer ATP-binding subunit complement(561072..561854) Dinoroseobacter shibae DFL 12 = DSM 16493 5712024 YP_001531919.1 CDS hmuU NC_009952.1 561851 562933 R PFAM: transport system permease protein; good swissprot hit to Hemin transport system permease protein hmuU from Yersinia pestis; high embl hit to HmuU protein [Rhizobium leguminosarum].; hemin transport system permease hmuU complement(561851..562933) Dinoroseobacter shibae DFL 12 = DSM 16493 5712025 YP_001531920.1 CDS hmuT NC_009952.1 562923 563759 R PFAM: periplasmic binding protein; good swissprot hit to Hemin-binding periplasmic protein hmuT precursor from Yersinia pestis; high Ref YP hit to hemin ABC transporter, periplasmic hemin-binding protein [Roseobacter denitrificans OCh 114]; hemin-binding periplasmic protein HmuT complement(562923..563759) Dinoroseobacter shibae DFL 12 = DSM 16493 5712026 YP_001531921.1 CDS hmuS NC_009952.1 563756 564787 R PFAM: Haemin-degrading family protein; NCBI conserved domains: hemS; good swissprot hit to Hemin transport protein hmuS fromYersinia pestis; high Ref ZP hit to Haemin-degrading [Roseovarius sp. TM1035]; hemin-degrading; hemin transport protein hmuS complement(563756..564787) Dinoroseobacter shibae DFL 12 = DSM 16493 5712027 YP_001531922.1 CDS Dshi_0575 NC_009952.1 564854 565354 R no significant swissprot, no conserved domains; low Ref ZP hit to hypothetical protein SSE37_21645 [Sagittula stellata E-37].; hypothetical protein complement(564854..565354) Dinoroseobacter shibae DFL 12 = DSM 16493 5712028 YP_001531923.1 CDS Dshi_0576 NC_009952.1 565766 566635 R PFAM: regulatory protein LysR; LysR substrate-binding; low swissprot hit to Uncharacterized HTH-type transcriptional regulator ydcI from Escherichia coli K12; middle Ref ZP hit to transcriptional regulator, LysR family protein [Roseobacter sp. AzwK-3b]; LysR family; transcriptional regulator complement(565766..566635) Dinoroseobacter shibae DFL 12 = DSM 16493 5712029 YP_001531924.1 CDS aldH2 NC_009952.1 566726 568177 D PFAM: aldehyde dehydrogenase, NCBI conserved domains: pfam00171, Aldedh, Aldehyde dehydrogenase family; high swissprot hit to Aldehyde dehydrogenase, thermostable from Geobacillus stearothermophilus; high Ref ZP hit to aldehyde dehydrogenase family protein [Roseovarius sp. 217].; aldehyde dehydrogenase 566726..568177 Dinoroseobacter shibae DFL 12 = DSM 16493 5712030 YP_001531925.1 CDS rDP NC_009952.1 568174 569184 D PFAM: peptidase M19 renal dipeptidase; NCBI conserved domains: rDP-like; low swissprot hit to Dipeptidase 1 precursor from Oryctolagus cuniculus; high Ref ZP hit to peptidase M19, renal dipeptidase [Roseovarius sp. TM1035]; peptidase M19 568174..569184 Dinoroseobacter shibae DFL 12 = DSM 16493 5712031 YP_001531926.1 CDS betT NC_009952.1 569219 570778 D PFAM: BCCT transporter; NCBI conserved domains: COG1292, BetT, Choline-glycine betaine transporter and pfam02028, BCCT; good swissprot hit to Glycine betaine transporter opuD from Bacillus subtilis; high gb hit to putative glycine betaine transporter [Phaeobacter gallaeciensis 2.10]; choline-glycine betaine transporter 569219..570778 Dinoroseobacter shibae DFL 12 = DSM 16493 5712032 YP_001531927.1 CDS Dshi_0580 NC_009952.1 570846 572522 D unsure GC frame plot, no significant swissprot, no conserved domains; high Ref ZP hit to hypothetical protein ROS217_07275 [Roseovarius sp. 217]; hypothetical protein 570846..572522 Dinoroseobacter shibae DFL 12 = DSM 16493 5712033 YP_001531928.1 CDS Dshi_0581 NC_009952.1 572519 573250 D unsure GC frame plot, no significant swissprot, no conserved domains; middle Ref YP hit to hypothetical protein PFL_0797 [Pseudomonas fluorescens Pf-5].; hypothetical protein 572519..573250 Dinoroseobacter shibae DFL 12 = DSM 16493 5712034 YP_001531929.1 CDS Dshi_0582 NC_009952.1 573264 573629 D unsure GC frame plot, PFAM: Endoribonuclease L-PSP; NCBI conserved domains: cd02198, YjgH; low swissprot hit to UPF0076 protein HI1627 from Haemophilus influenzae; low Ref YP hit to yjgF family protein [Azorhizobium caulinodans ORS 571].; putative Endoribonuclease L-PSP 573264..573629 Dinoroseobacter shibae DFL 12 = DSM 16493 5712035 YP_001531930.1 CDS kdsA NC_009952.1 574071 574904 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(574071..574904) Dinoroseobacter shibae DFL 12 = DSM 16493 5712037 YP_001531931.1 CDS kpsE NC_009952.1 574921 576630 R PFAM: lipopolysaccharide biosynthesis protein; NCBI conserved domains: COG3524, KpsE, Capsule polysaccharide export protein; middle swissprot hit to Capsule polysaccharide export inner-membrane protein ctrB from Neisseria meningitidis serogroup A; high Ref ZP hit to Capsule polysaccharide export protein-like [Rhodobacterales bacterium HTCC2150]; permease protein; alternative gene name: ctrB; capsule polysaccharide export complement(574921..576630) Dinoroseobacter shibae DFL 12 = DSM 16493 5712038 YP_001531932.1 CDS kpsT NC_009952.1 576608 577267 R PFAM: ABC transporter related; NCBI conserved domains: kpsT; good swissprot hit to Capsule polysaccharide export ATP-binding protein ctrD from Neisseria meningitidis serogroup B; high Ref ZP hit to capsular polysaccharide export ATP-binding protein [Oceanicola granulosus HTCC2516]; ATP-binding protein; alternative gene name: ctrD; capsule polysaccharide export complement(576608..577267) Dinoroseobacter shibae DFL 12 = DSM 16493 5712039 YP_001531933.1 CDS kpsM NC_009952.1 577452 578498 R PFAM: permease; NCBI conserved domains: COG0701, Predicted permeases; no significant swissprot; high Ref ZP hit to permease, putative [Roseovarius nubinhibens ISM]; ambiguous hits, but in connection with the gene context (Dshi_0584 kpsE, Dshi_0858 kpsT) the permease should be kpsM; permease protein; alternative gene name: ctrC; capsule polysaccharide transport complement(577452..578498) Dinoroseobacter shibae DFL 12 = DSM 16493 5712040 YP_001531934.1 CDS Dshi_0587 NC_009952.1 578470 578814 R SMART: regulatory protein ArsR; unsure GC frame plot; no significant swissprot; NCBI conserved domains: ArsR; middle Ref ZP hit to transcriptional regulator, ArsR family protein [Roseovarius sp. HTCC2601].; ArsR family; putative transcriptional regulator complement(578470..578814) Dinoroseobacter shibae DFL 12 = DSM 16493 5712041 YP_001531935.1 CDS Dshi_0588 NC_009952.1 578892 579500 D unsure GC frame plot; InterPro Scan results: SSF52141 UDNA_glycsylseSF; NCBI conserved domains: COG1573, Uracil-DNA glycosylase and pfam03167, UDG, Uracil DNA glycosylase superfamily; middle swissprot hit to Uncharacterized protein HI0220.2. from Haemophilus influenzae; high Ref YP hit to Uracil-DNA glycosylase superfamily [Jannaschia sp. CCS1].; uracil-DNA glycosylase superfamily 578892..579500 Dinoroseobacter shibae DFL 12 = DSM 16493 5712042 YP_001531936.1 CDS Dshi_0589 NC_009952.1 579497 580282 D unsure GC frame plot, no significant swissprot; no conserved domains detected; high Ref ZP hit to hypothetical protein R2601_11544 [Roseovarius sp. HTCC2601]; hypothetical protein 579497..580282 Dinoroseobacter shibae DFL 12 = DSM 16493 5712043 YP_001531937.1 CDS Dshi_0590 NC_009952.1 580316 581251 R PFAM: D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding; middle swissprot hit to Putative 2-hydroxyacid dehydrogenase ycdW from Escherichia coli K12; high Ref ZP hit to D-isomer specific 2-hydroxyacid dehydrogenase family protein from Roseovarius sp. 217; D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding subunit complement(580316..581251) Dinoroseobacter shibae DFL 12 = DSM 16493 5712044 YP_001531938.1 CDS mreD1 NC_009952.1 581261 582400 R TIGRFAM: rod shape-determining protein RodA PFAM: cell cycle protein; NCBI conserved domains: COG0772, FtsW, Bacterial cell division membrane protein; good swissprot hit to Rod shape-determining protein rodA from Haemophilus influenzae; high Ref ZP hit to rod shape-determining protein MreD [Roseobacter sp. AzwK-3b].; rod shape-determining protein MreD complement(581261..582400) Dinoroseobacter shibae DFL 12 = DSM 16493 5712045 YP_001531939.1 CDS ftsI1 NC_009952.1 582397 584340 R PFAM: penicillin-binding protein transpeptidase; Penicillin-binding protein dimerisation domain, NCBI conserved domains: COG0768, FtsI, Cell division protein FtsI/penicillin-binding protein 2; high swissprot hit to Penicillin-binding protein 2 from Haemophilus influenzae; high Ref ZP hit to penicillin-binding protein 2 [Roseobacter sp. CCS2].; penicillin-binding protein (pbp-2); division-specific transpeptidase complement(582397..584340) Dinoroseobacter shibae DFL 12 = DSM 16493 5712046 YP_001531940.1 CDS mreD2 NC_009952.1 584337 584876 R no significant swissprot; no conserved domains, except from one signalpep. and four transmembr. regions; low Ref ZP hit to putative rod shape-determining protein MreD [Roseobacter sp. CCS2].; putative rod shape-determining protein MreD complement(584337..584876) Dinoroseobacter shibae DFL 12 = DSM 16493 5712047 YP_001531941.1 CDS mreC NC_009952.1 584869 585768 R 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 complement(584869..585768) Dinoroseobacter shibae DFL 12 = DSM 16493 5712048 YP_001531942.1 CDS mreB NC_009952.1 585804 586841 R functions in MreBCD complex in some organisms; rod shape-determining protein MreB complement(585804..586841) Dinoroseobacter shibae DFL 12 = DSM 16493 5712049 YP_001531943.1 CDS leuA NC_009952.1 587090 588667 R catalyzes the formation of 2-isopropylmalate from acetyl-CoA and 2-oxoisovalerate in leucine biosynthesis; 2-isopropylmalate synthase complement(587090..588667) Dinoroseobacter shibae DFL 12 = DSM 16493 5712050 YP_001531944.1 CDS Dshi_0597 NC_009952.1 588851 589648 R InterPro Scan: G3DSA:2.120.10.30 Six-bladed beta-propeller, TolB-like; NCBI conserved domains: COG3391, Uncharacterized conserved protein; no significant swissprot hit; middle Ref YP hit to hypothetical protein RD1_3731 [Roseobacter denitrificans OCh 114].; hypothetical protein complement(588851..589648) Dinoroseobacter shibae DFL 12 = DSM 16493 5712051 YP_001531945.1 CDS Dshi_0598 NC_009952.1 589775 590440 D PFAM: short-chain dehydrogenase/reductase SDR; NCBI conserved domains: PRK09009, C factor cell-cell signaling protein and PRK06953, short chain dehydrogenase; low swissprot hit to C-factor (C signal) from Myxococcus xanthus; high Ref YP hit to C factor, cell signaling protein, putative [Roseobacter denitrificans OCh 114].; short-chain dehydrogenase/reductase SDR 589775..590440 Dinoroseobacter shibae DFL 12 = DSM 16493 5712052 YP_001531946.1 CDS Dshi_0599 NC_009952.1 590437 591963 D PFAM: deoxyribodipyrimidine photolyase-related protein; NCBI conserved domains: pfam04244, DPRP, Deoxyribodipyrimidine photolyase-related protein and COG0415, PhrB, Deoxyribodipyrimidine photolyase; no significant swissprot; high Ref YP hit to deoxyribodipyrimidine photolyase-related protein [Jannaschia sp. CCS1]; deoxyribodipyrimidine photolyase-like protein 590437..591963 Dinoroseobacter shibae DFL 12 = DSM 16493 5712053 YP_001531947.1 CDS Dshi_0600 NC_009952.1 592010 593416 R PFAM: MORN repeat-containing protein, NCBI conserved domains: several repeats of COG4642, Uncharacterized protein conserved in bacteria; low swissprot hit to Radial spoke head 10 homolog B from Rattus norvegicus; high Ref YP hit to MORN repeat-containing protein [Rhodobacter sphaeroides ATCC Q66HB5]; MORN repeat-containing protein complement(592010..593416) Dinoroseobacter shibae DFL 12 = DSM 16493 5712054 YP_001531948.1 CDS nadE NC_009952.1 593670 595343 D 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 593670..595343 Dinoroseobacter shibae DFL 12 = DSM 16493 5712055 YP_001531949.1 CDS Dshi_0602 NC_009952.1 595527 595928 R PFAM: protein of unknown function DUF1025; NCBI conserved domains: COG3824, Uncharacterized protein conserved in bacteria; bad swissprot hit to Putative metalloprotease XOO2769 from Xanthomonas oryzae pv. oryzae; middle Ref ZP hit to Neutral zinc metallopeptidase [Rhodobacterales bacterium HTCC2654].; hypothetical protein complement(595527..595928) Dinoroseobacter shibae DFL 12 = DSM 16493 5712056 YP_001531950.1 CDS Dshi_0603 NC_009952.1 596472 596903 R PFAM: thioesterase superfamily protein, NCBI conserved domains: cd03442, BFIT_BACH, Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH) and cd03440, hot_dog; middle swissprot hit to Uncharacterized acyl-CoA thioester hydrolase HI0827 from Haemophilus influenzae; middle emb cad hit to acyl-CoA thioester-like hydrolase [Defluvibacter lusatiensis]; unsure GC frame plot; thioesterase superfamily protein complement(596472..596903) Dinoroseobacter shibae DFL 12 = DSM 16493 5712057 YP_001531951.1 CDS Dshi_0604 NC_009952.1 596939 597799 R PFAM: amidohydrolase 2; CNBI conserved domains: cd01311, PDC_hydrolase, COG2159, Predicted metal-dependent hydrolase, no significant swissprot; unsure GC frame plot; high Ref YP hit to amidohydrolase 2 [Burkholderia multivorans ATCC 17616].; amidohydrolase family protein complement(596939..597799) Dinoroseobacter shibae DFL 12 = DSM 16493 5712058 YP_001531952.1 CDS dctM5 NC_009952.1 597820 599106 R TIGRFAM: TRAP dicarboxylate transporter, DctM subunit PFAM: TRAP C4-dicarboxylate transport system permease DctM subunit; middle swissprot hit to Sialic acid TRAP transporter permease protein siaT from Haemophilus influenzae 86-028NP; high Ref ZP hit to TRAP dicarboxylate transporter, DctM subunit [Shewanella woodyi ATCC 51908]; DctM subunit; TRAP dicarboxylate transporter complement(597820..599106) Dinoroseobacter shibae DFL 12 = DSM 16493 5712059 YP_001531953.1 CDS Dshi_0606 NC_009952.1 599132 599698 R unsure GC frame plot, no significant swissprot, no conserved domains; low Ref ZP hit to TRAP transporter, transmembrane protein, putative [Roseovarius sp. HTCC2601]; hypothetical protein complement(599132..599698) Dinoroseobacter shibae DFL 12 = DSM 16493 5712060 YP_001531954.1 CDS dctP5 NC_009952.1 599763 600845 R PFAM: TRAP dicarboxylate transporter- DctP subunit; NCBI conserved domains: COG1638, DctP, TRAP-type C4-dicarboxylate transport system, periplasmic component; no significant swissprot; good Ref ZP hit to TRAP dicarboxylate transporter- DctP subunit [Shewanella woodyi ATCC 51908]; TRAP dicarboxylate transporter subunit DctP complement(599763..600845) Dinoroseobacter shibae DFL 12 = DSM 16493 5712061 YP_001531955.1 CDS Dshi_0608 NC_009952.1 600943 601713 R unsure GC frame plot; no significant swissprot; no conserved domains; low Ref YP hit to hypothetical protein TM1040_3278 [Silicibacter sp. TM1040].; hypothetical protein complement(600943..601713) Dinoroseobacter shibae DFL 12 = DSM 16493 5712062 YP_001531956.1 CDS Dshi_0609 NC_009952.1 601843 603387 D unsure GC frame plot; PFAM: regulatory protein GntR HTH; aminotransferase class I and II; SSF53383 Pyridoxal phosphate-dependent transferase, major region; good swissprot hit to HTH-type pyridoxine biosynthesis transcriptional regulator pdxR from Corynebacterium glutamicum (position Ser-301 of subject correlates to position Ser-300 of Query in alignment) ; high Ref YP hit to transcriptional regulator, GntR family [Rubrobacter xylanophilus DSM 9941]; GntR family transcriptional regulator 601843..603387 Dinoroseobacter shibae DFL 12 = DSM 16493 5712063 YP_001531957.1 CDS Dshi_0610 NC_009952.1 603311 604093 R unsure GC frame plot, good swissprot hit to UPF0317 protein BP1875 from Bordetella pertussis; high gb hit to hypothetical protein HPDFL43_09917 [Hoeflea phototrophica DFL-43]; hypothetical protein complement(603311..604093) Dinoroseobacter shibae DFL 12 = DSM 16493 5712064 YP_001531958.1 CDS Dshi_0611 NC_009952.1 604086 604418 R unsure GC frame plot; PFAM: NIPSNAP family containing protein; NCBI conserved domains: NIPSNAP; bad swissprot hit to Protein NipSnap3A from Homo sapiens; low Ref YP hit to NIPSNAP family containing protein [Delftia acidovorans SPH-1].; NIPSNAP family containing protein complement(604086..604418) Dinoroseobacter shibae DFL 12 = DSM 16493 5712065 YP_001531959.1 CDS Dshi_0612 NC_009952.1 605184 606101 R PFAM: beta-lactamase domain protein; NCBI conserved domains: COG0491, GloB, Zn-dependent hydrolases, including glyoxylases; no significant swissprot; high Ref ZP hit to metallo-beta-lactamase family protein, putative [Roseobacter sp. CCS2]; beta-lactamase domain-containing protein complement(605184..606101) Dinoroseobacter shibae DFL 12 = DSM 16493 5712066 YP_001531960.1 CDS Dshi_0613 NC_009952.1 606284 607171 D PFAM: band 7 protein; NCBI conserved domains: band_7 and COG0330, HflC, Membrane protease subunits, stomatin/prohibitin homologs; good swissprot hit to Uncharacterized protein ybbK from Escherichia coli K12; high Ref ZP hit to SPFH domain/band 7 family protein [Sagittula stellata E-37].; hypothetical protein 606284..607171 Dinoroseobacter shibae DFL 12 = DSM 16493 5712067 YP_001531961.1 CDS Dshi_0614 NC_009952.1 607171 607452 D PFAM01957 Nodulation efficiency, NfeD; no significant swissprot; low Ref YP hit to hypothetical protein Rsph17025_2810 [Rhodobacter sphaeroides ATCC 17025].; hypothetical protein 607171..607452 Dinoroseobacter shibae DFL 12 = DSM 16493 5712068 YP_001531962.1 CDS pyrF NC_009952.1 607474 608172 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(607474..608172) Dinoroseobacter shibae DFL 12 = DSM 16493 5712069 YP_001531963.1 CDS Dshi_0616 NC_009952.1 608284 608697 D unsure GC frame plot, no significant BLAST hits; no conserved domains; hypothetical protein 608284..608697 Dinoroseobacter shibae DFL 12 = DSM 16493 5712070 YP_001531964.1 CDS clpB NC_009952.1 609070 611685 D PFAM: AAA ATPase central domain protein; Clp domain protein; ATPase associated with various cellular activities AAA_5; ATPase AAA-2 domain protein SMART: AAA ATPase; high swissprot hit to Chaperone protein clpB from Brucella suis; high Ref ZP hit to ATP-dependent Clp protease, ATP-binding subunit ClpB [Roseobacter sp. CCS2].; chaperone protein clpB 609070..611685 Dinoroseobacter shibae DFL 12 = DSM 16493 5712071 YP_001531965.1 CDS Dshi_0618 NC_009952.1 611730 612320 D unsure GC frame plot, no significant swissprot, no conserved domains (except from one signalpep. and two transmem. regions); middle gb hit to hypothetical protein RLO149_06672 [Roseobacter litoralis Och 149].; hypothetical protein 611730..612320 Dinoroseobacter shibae DFL 12 = DSM 16493 5712072 YP_001531966.1 CDS Dshi_0619 NC_009952.1 612549 612863 D no significant swissprot, no conserved domains detected; bad Ref ZP hit to SNase-like nuclease [Roseobacter sp. AzwK-3b].; hypothetical protein 612549..612863 Dinoroseobacter shibae DFL 12 = DSM 16493 5712073 YP_001531967.1 CDS fabG2 NC_009952.1 612860 613612 R PFAM: short-chain dehydrogenase/reductase SDR; KR domain protein; NCBI conserved domains: fabG; middle swissprot hit to 3-oxoacyl-[acyl-carrier-protein] reductase from Chlamydia trachomatis; high Ref ZP hit to oxidoreductase [Rhodobacterales bacterium HTCC2150].; 3-oxoacyl-ACP reductase complement(612860..613612) Dinoroseobacter shibae DFL 12 = DSM 16493 5712074 YP_001531968.1 CDS Dshi_0621 NC_009952.1 613772 614260 R PFAM02469 Fasciclin domain; NCBI conserved domains: COG2335, Secreted and surface protein containing fasciclin-like repeats; middle swissprot hit to Uncharacterized protein sll1483 precursor from Synechocystis sp. PCC 6803; middle Ref ZP hit to beta-Ig-H3/fasciclin [Roseovarius sp. TM1035]; fasciclin domain-containing protein complement(613772..614260) Dinoroseobacter shibae DFL 12 = DSM 16493 5712075 YP_001531969.1 CDS Dshi_0622 NC_009952.1 614334 614825 R PFAM02469 Fasciclin domain; NCBI conserved domains: COG2335, Secreted and surface protein containing fasciclin-like repeats; middle swissprot hit to Uncharacterized protein sll1483 precursor from Synechocystis sp. PCC 6803; good Ref ZP hit to beta-Ig-H3/fasciclin [Roseovarius sp. TM1035]; fasciclin domain-containing protein complement(614334..614825) Dinoroseobacter shibae DFL 12 = DSM 16493 5712076 YP_001531970.1 CDS yedY NC_009952.1 615171 616088 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; putative sulfite oxidase subunit YedY 615171..616088 Dinoroseobacter shibae DFL 12 = DSM 16493 5712077 YP_001531971.1 CDS yedZ NC_009952.1 616088 616696 D PFAM: Ferric reductase domain protein transmembrane component domain; NCBI conserved domains: PRK05419, putative sulfite oxidase subunit YedZ, middle swissprot hit to UPF0191 membrane protein yedZ from Escherichia coli O157:H7; good Ref YP hit to putative sulfite oxidase subunit YedZ [Roseobacter denitrificans OCh 114]; putative sulfite oxidase subunit YedZ 616088..616696 Dinoroseobacter shibae DFL 12 = DSM 16493 5712078 YP_001531972.1 CDS Dshi_0625 NC_009952.1 623104 623826 D unsure GC frame plot, no significant BLAST hits; hypothetical protein 623104..623826 Dinoroseobacter shibae DFL 12 = DSM 16493 5712084 YP_001531973.1 CDS Dshi_0626 NC_009952.1 624057 624743 D PFAM: binding-protein-dependent transport systems inner membrane component; NCBI conserved domains: COG4662, TupA, ABC-type tungstate transport system, periplasmic component; low swissprot hit to Sulfate transport system permease protein cysW from Escherichia coli K12; high Ref ZP hit to sulfate/tungstate uptake family ABC transporter, permease protein from Roseovarius sp. 217; permease protein; basic organic compound ABC-transporter 624057..624743 Dinoroseobacter shibae DFL 12 = DSM 16493 5712085 YP_001531974.1 CDS Dshi_0627 NC_009952.1 624736 625491 D PFAM: ABC transporter related SMART: AAA ATPase; NCBI conserved domains: cd03260, ABC_PstB_phosphate_transporter; middle swissprot hit to Phosphate import ATP-binding protein pstB from Thermus thermophilus HB27; high Ref ZP hit to sulfate/tungstate uptake family ABC transporter, ATP-binding from Roseovarius sp. 217; ATP-binding protein; basic organic compound ABC-transporter 624736..625491 Dinoroseobacter shibae DFL 12 = DSM 16493 5712086 YP_001531975.1 CDS Dshi_0628 NC_009952.1 625528 626358 D PFAM: extracellular solute-binding protein family 1, NCBI conserved domains: tupB; no significant swissprot; high Ref ZP hit to sulfate/tungstate uptake family ABC transporter, periplasmic substrate-binding protein from Stappia aggregata IAM 12614; periplasmic substrate-binding protein; basic organic compound ABC-transporter 625528..626358 Dinoroseobacter shibae DFL 12 = DSM 16493 5712087 YP_001531976.1 CDS Dshi_0629 NC_009952.1 626365 627237 R TIGRFAM: DNA binding domain, excisionase family, NCBI conserved domains: COG1910, Periplasmic molybdate-binding protein/domain; bad swissprot hit to Putative molybdopterin biosynthesis protein MJ0886 from Methanocaldococcus jannaschii; high Ref ZP hit to Periplasmic molybdate-binding protein/domain [Stappia aggregata IAM 12614].; periplasmic substrate-binding protein complement(626365..627237) Dinoroseobacter shibae DFL 12 = DSM 16493 5712088 YP_001531977.1 CDS glpD NC_009952.1 627302 628897 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(627302..628897) Dinoroseobacter shibae DFL 12 = DSM 16493 5712089 YP_001531978.1 CDS glpR NC_009952.1 629081 629854 D PFAM: regulatory protein DeoR; Helix-turn-helix type 11 domain protein, NCBI conserved domains: COG1349, GlpR, Transcriptional regulators of sugar metabolism; high swissprot hit to Glycerol-3-phosphate regulon repressor from Escherichia coli K12; high Ref ZP hit to probable glycerol-3-phosphate regulon repressor [Roseovarius sp. HTCC2601].; glycerol-3-phosphate regulon repressor 629081..629854 Dinoroseobacter shibae DFL 12 = DSM 16493 5712090 YP_001531979.1 CDS ackA NC_009952.1 629832 630980 R TIGRFAM: acetate kinase PFAM: acetate and butyrate kinase KEGG: rde:RD1_3831 acetate kinase; Acetokinase; acetate kinase complement(629832..630980) Dinoroseobacter shibae DFL 12 = DSM 16493 5712091 YP_001531980.1 CDS pta2 NC_009952.1 630977 632392 R Swissprot: Phosphate acetyltransferase (Phosphotransacetylase) PFAM: phosphate acetyl/butaryl transferase; MaoC domain protein dehydratase KEGG: rpe:RPE_3163 phosphate butyryltransferase; bifunctional enoyl-CoA hydratase/phosphate acetyltransferase complement(630977..632392) Dinoroseobacter shibae DFL 12 = DSM 16493 5712092 YP_001531981.1 CDS Dshi_0634 NC_009952.1 632597 633406 D no significant swissprot, no conserved domains; high gb hit to glycosyltransferase, putative [Roseobacter litoralis Och 149].; hypothetical protein 632597..633406 Dinoroseobacter shibae DFL 12 = DSM 16493 5712093 YP_001531982.1 CDS Dshi_0635 NC_009952.1 633409 635610 R PFAM: cyclic nucleotide-binding; Sulfate transporter/antisigma-factor antagonist STAS; Xanthine/uracil/vitamin C permease; sulphate transporter; low swissprot hit to Uncharacterized vacuolar membrane protein YGR125W from Saccharomyces cerevisiae; high Ref YP hit to Sulfate permease and related transporters [Magnetospirillum magneticum AMB-1].; putative sulfate permease with cyclic nucleotide-binding domain complement(633409..635610) Dinoroseobacter shibae DFL 12 = DSM 16493 5712094 YP_001531983.1 CDS Dshi_0636 NC_009952.1 635809 636474 R PFAM: phospholipase/Carboxylesterase; NCBI conserved domains: COG0400, Predicted esterase; low swissprot hit to Acyl-protein thioesterase 1 from Yarrowia lipolytica; good gb hit to phospholipase/Carboxylesterase [Roseobacter litoralis Och 149].; phospholipase/carboxylesterase complement(635809..636474) Dinoroseobacter shibae DFL 12 = DSM 16493 5712095 YP_001531984.1 CDS Dshi_0637 NC_009952.1 636471 637394 R PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase; NCBI conserved domains: see PFAM result before; middle swissprot hit to Chlorohydroquinone/hydroquinone 1,2-dioxygenase from Sphingomonas paucimobilis; high Ref YP hit to glyoxylase family protein [Roseobacter denitrificans OCh 114]; glyoxalase/bleomycin resistance protein/dioxygenase complement(636471..637394) Dinoroseobacter shibae DFL 12 = DSM 16493 5712096 YP_001531985.1 CDS Dshi_0638 NC_009952.1 637586 638542 D PFAM: ABC transporter related SMART: AAA ATPase; NCBI conserved domains: cd03265, ABC_DrrA; good swissprot hit to Uncharacterized ABC transporter ATP-binding protein yadG from Escherichia coli K12; high gb hit to ABC transporter, ATP-binding protein, putative [Oceanibulbus indolifex HEL-45].; ATP-binding protein; ABC-A-subfamily transporter 637586..638542 Dinoroseobacter shibae DFL 12 = DSM 16493 5712097 YP_001531986.1 CDS Dshi_0639 NC_009952.1 638539 639300 D PFAM: ABC-2 type transporter, NCBI conserved domains: COG1682, TagG, ABC-type polysaccharide/polyol phosphate export systems, permease component; good swissprot hit to Inner membrane transport permease yadH from Escherichia coli K12; high Ref ZP hit to ABC transporter, permease protein [Roseobacter sp. SK209-2-6].; permease protein; ABC transporter 638539..639300 Dinoroseobacter shibae DFL 12 = DSM 16493 5712098 YP_001531987.1 CDS Dshi_0640 NC_009952.1 639402 640199 D PFAM: peptidase S49; NCBI conserved domains: COG0616, SppA; middle swissprot hit to Putative signal peptide peptidase sppA from Bacillus halodurans; high Ref ZP hit to peptidase S49 [Rhodobacterales bacterium HTCC2150].; peptidase S49 639402..640199 Dinoroseobacter shibae DFL 12 = DSM 16493 5712099 YP_001531988.1 CDS Dshi_0641 NC_009952.1 640204 640374 D no swissprot, no conserved domains, bad Ref ZP hit to hypothetical protein ISM_10031 [Roseovarius nubinhibens ISM].; hypothetical protein 640204..640374 Dinoroseobacter shibae DFL 12 = DSM 16493 5711476 YP_001531989.1 CDS Dshi_0642 NC_009952.1 640377 641315 D TIGRFAM: Na+/Ca+ antiporter, CaCA family PFAM: sodium/calcium exchanger membrane region, NCBI conserved domains: COG0530, ECM27, Ca2+/Na+ antiporter; bad swissprot hit to Sodium/potassium/calcium exchanger 1 from Homo sapiens; high Ref ZP hit to K+-dependent Na+/Ca+ exchanger related-protein [Roseobacter sp. AzwK-3b]; CaCA family; Na+/Ca+ antiporter 640377..641315 Dinoroseobacter shibae DFL 12 = DSM 16493 5711477 YP_001531990.1 CDS Dshi_0643 NC_009952.1 641326 642117 D PFAM: short-chain dehydrogenase/reductase SDR; KR domain protein; NCBI conserved domains: PRK09134, short chain dehydrogenase; middle swissprot hit to 3-oxoacyl-[acyl-carrier-protein] reductase from Staphylococcus epidermidis ATCC 12228; high Ref ZP hit to short chain dehydrogenase [Roseobacter sp. AzwK-3b].; short chain dehydrogenase 641326..642117 Dinoroseobacter shibae DFL 12 = DSM 16493 5711478 YP_001531991.1 CDS uvrC NC_009952.1 642411 644306 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 642411..644306 Dinoroseobacter shibae DFL 12 = DSM 16493 5711479 YP_001531992.1 CDS Dshi_0645 NC_009952.1 644406 645413 D TIGRFAM: TRAP transporter solute receptor, TAXI family; NCBI conserved domains: COG2358, Imp, TRAP-type uncharacterized transport system, periplasmic component; no significant swissprot; high Ref YP hit to TRAP-type uncharacterized transport system, periplasmic component from Hahella chejuensis KCTC 2396; periplasmic component; TRAP-type transport system 644406..645413 Dinoroseobacter shibae DFL 12 = DSM 16493 5711480 YP_001531993.1 CDS Dshi_0646 NC_009952.1 645472 647574 D TIGRFAM: TRAP transporter, 4TM/12TM fusion protein PFAM: TRAP C4-dicarboxylate transport system permease DctM subunit; NCBI conserved domains: COG4666, TRAP-type uncharacterized transport system, fused permease componen; bad swissprot hit to Sialic acid TRAP transporter permease protein siaT from Haemophilus influenzae; high Ref ZP hit to TRAP-type uncharacterized transport system, fused permease components [Roseobacter sp. CCS2].; TRAP-type transport system permease 645472..647574 Dinoroseobacter shibae DFL 12 = DSM 16493 5711481 YP_001531994.1 CDS Dshi_0647 NC_009952.1 647766 650513 D InterPro Scan: Integrin alpha N-terminal domain superfamily; no significant swissprot; low Ref ZP hit to hypothetical protein RED65_02278 [Oceanobacter sp. RED65]; hypothetical protein 647766..650513 Dinoroseobacter shibae DFL 12 = DSM 16493 5711482 YP_001531995.1 CDS recR NC_009952.1 650663 651262 R involved in a recombinational process of DNA repair, independent of the recBC complex; recombination protein RecR complement(650663..651262) Dinoroseobacter shibae DFL 12 = DSM 16493 5711483 YP_001531996.1 CDS Dshi_0649 NC_009952.1 651279 651623 R PFAM: conserved hypothetical protein; NCBI conserved domains: pfam02575, DUF149, Uncharacterised BCR, YbaB family COG0718; low swissprot hit to UPF0133 protein HD_0326 from Haemophilus ducreyi; middle Ref YP hit to conserved hypothetical protein 103 [Jannaschia sp. CCS1].; hypothetical protein complement(651279..651623) Dinoroseobacter shibae DFL 12 = DSM 16493 5711484 YP_001531997.1 CDS dnaX NC_009952.1 651643 653406 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(651643..653406) Dinoroseobacter shibae DFL 12 = DSM 16493 5711485 YP_001531998.1 CDS Dshi_0651 NC_009952.1 653737 654693 D PFAM: NUDIX hydrolase; NADH pyrophosphatase-like ; Zinc ribbon NADH pyrophosphatase; NCBI conserved domains: cd03429, NADH_pyrophosphatase; middle swissprot hit to NADH pyrophosphatase from Escherichia coli O6; high Ref ZP hit to hydrolase, NUDIX family [Loktanella vestfoldensis SKA53].; NUDIX hydrolase 653737..654693 Dinoroseobacter shibae DFL 12 = DSM 16493 5711487 YP_001531999.1 CDS Dshi_0652 NC_009952.1 654714 655202 D no significant swissprot; no conserved domains; low Ref ZP hit to hypothetical protein NAS141_10191 [Sulfitobacter sp. NAS-14.1].; hypothetical protein 654714..655202 Dinoroseobacter shibae DFL 12 = DSM 16493 5711488 YP_001532000.1 CDS pheA2 NC_009952.1 655248 656090 R catalyzes the formation of phenylpyruvate from prephenate in phenylalanine biosynthesis; prephenate dehydratase complement(655248..656090) Dinoroseobacter shibae DFL 12 = DSM 16493 5711489 YP_001532001.1 CDS cycM NC_009952.1 656214 656738 D PFAM: cytochrome c class I; NCBI conserved domains: pfam00034, Cytochrom_C; middle swissprot hit to Cytochrome c-552 from Paracoccus denitrificans; middle Ref ZP hit to cytochrome c552 [Roseobacter sp. AzwK-3b].; cytochrome c552 656214..656738 Dinoroseobacter shibae DFL 12 = DSM 16493 5711490 YP_001532002.1 CDS oppA NC_009952.1 656989 658890 D PFAM: extracellular solute-binding protein family 5; NCBI conserved domains: COG4166, OppA, ABC-type oligopeptide transport system; high swissprot hit to Uncharacterized protein yejA precursor from Escherichia coli K12; high Ref hit to ABC peptide transporter, substrate binding protein [Rhodobacter sphaeroides 2.4.1].; substrate binding protein; alternative gene name: dppA; ABC peptide transporter 656989..658890 Dinoroseobacter shibae DFL 12 = DSM 16493 5711491 YP_001532003.1 CDS oppBC1 NC_009952.1 658895 659992 D PFAM: binding-protein-dependent transport systems inner membrane component; NCBI conserved domains: COG0601, DppB, ABC-type dipeptide/oligopeptide/nickel transport systems, permease components; high swissprot hit to Inner membrane ABC transporter permease protein yejB from Escherichia coli K12; high Ref ZP hit to ABC peptide transporter, inner membrane subunit [Sulfitobacter sp. NAS-14.1]; permease protein; alternative gene name: dppBC; ABC peptide transporter 658895..659992 Dinoroseobacter shibae DFL 12 = DSM 16493 5711492 YP_001532004.1 CDS oppBC2 NC_009952.1 659994 661172 D PFAM: binding-protein-dependent transport systems inner membrane component; NCBI conserved domains: COG1173, DppC, ABC-type dipeptide/oligopeptide/nickel transport systems, permease components; high swissprot hit to Inner membrane ABC transporter permease protein yejE from Escherichia coli K12; high Ref YP hit to ABC peptide transporter, inner membrane subunit [Rhodobacter Rhodobacter sphaeroides 2.4.1]; permease protein; alternative gene name: dppBC; ABC peptide transporter 659994..661172 Dinoroseobacter shibae DFL 12 = DSM 16493 5711493 YP_001532005.1 CDS oppDF NC_009952.1 661169 662770 D PFAM: ABC transporter related; Oligopeptide/dipeptide ABC transporter domain protein; NCBI conserved domains: cd03257, ABC_NikE_OppD_transporters; high swissprot hit to Uncharacterized ABC transporter ATP-binding protein yejF from Escherichia coli K12; high Ref ZP hit to peptide ABC transporter, ATP-binding protein, putative [Roseobacter sp. CCS2]; ATP-binding protein; alternative gene name: dppDF; ABC peptide transporter 661169..662770 Dinoroseobacter shibae DFL 12 = DSM 16493 5711494 YP_001532006.1 CDS hemN2 NC_009952.1 662948 664309 R catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III; coproporphyrinogen III oxidase complement(662948..664309) Dinoroseobacter shibae DFL 12 = DSM 16493 5711495 YP_001532007.1 CDS fixK NC_009952.1 664362 665111 D PFAM: cyclic nucleotide-binding; regulatory protein Crp, NCBI conserved domains: PRK09391, fixK, transcriptional regulator FixK; high swissprot hit to Transcriptional activator protein fnrL from Rhodobacter sphaeroides 2.4.1; high Ref ZP hit to transcriptional activator protein FnrL [Roseovarius sp. 217].; Crp/Fnr family; alternative gene name: fnrL; transcriptional regulator 664362..665111 Dinoroseobacter shibae DFL 12 = DSM 16493 5711496 YP_001532008.1 CDS fixN NC_009952.1 665449 667050 D CcoN; FixN; cbb3-type cytochrome c oxidase subunit I 665449..667050 Dinoroseobacter shibae DFL 12 = DSM 16493 5711497 YP_001532009.1 CDS fixO NC_009952.1 667065 667790 D CcoO; FixO; cbb3-type cytochrome c oxidase subunit II 667065..667790 Dinoroseobacter shibae DFL 12 = DSM 16493 5711498 YP_001532010.1 CDS fixQ NC_009952.1 667803 668036 D PFAM: Cbb3-type cytochrome oxidase component; NCBI conserved domains: fixQ; no significant swissprot hit; low Ref ZP hit to cytochrome c oxidase, cbb3-type, subunit IV [Loktanella vestfoldensis SKA53].; cbb3-type, subunit IV; cytochrome c oxidase 667803..668036 Dinoroseobacter shibae DFL 12 = DSM 16493 5711499 YP_001532011.1 CDS fixP NC_009952.1 668033 668896 D TIGRFAM: cytochrome c oxidase, cbb3-type, subunit III PFAM: cytochrome c class I; NCBI conserved domains: COG2010, CccA, Cytochrome c, mono- and diheme variants; high Ref ZP hit to cytochrome c oxidase, cbb3-type, subunit III [Jannaschia sp. CCS1].; cbb3-type, subunit III; cytochrome c oxidase 668033..668896 Dinoroseobacter shibae DFL 12 = DSM 16493 5711500 YP_001532012.1 CDS fixG NC_009952.1 669212 670654 D TIGRFAM: Cytochrome c oxidase cbb3 type accessory protein FixG; PFAM00037 4Fe-4S binding domain; high swissprot hit to Nitrogen fixation protein fixG from Sinorhizobium meliloti; high Ref ZP hit to iron-sulfur-binding protein, RdxA/RdxB/FixG family [Roseobacter sp. AzwK-3b].; nitrogen fixation protein fixG 669212..670654 Dinoroseobacter shibae DFL 12 = DSM 16493 5711501 YP_001532013.1 CDS fixH NC_009952.1 670651 671118 D PFAM: FixH family protein; NCBI conserved domains: fixH; low swissprot hit to Nitrogen fixation protein fixH from Sinorhizobium meliloti, middle Ref ZP hit to FixH [Silicibacter sp. TM1040].; nitrogen fixation protein fixH 670651..671118 Dinoroseobacter shibae DFL 12 = DSM 16493 5711502 YP_001532014.1 CDS fixI NC_009952.1 671120 673309 D 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; high swissprot hit to Nitrogen fixation protein fixI from Sinorhizobium meliloti; high Ref ZP hit to copper-t; E1-E2 type cation ATPase fixI; nitrogen fixation protein fixI 671120..673309 Dinoroseobacter shibae DFL 12 = DSM 16493 5711503 YP_001532015.1 CDS fixS NC_009952.1 673314 673472 D TIGRFAM: cytochrome oxidase maturation protein, cbb3-type PFAM: cytochrome oxidase maturation protein cbb3-type; NCBI conserved domains: fixS, ccoS; low swissprot hit to Nitrogen fixation protein fixS from Sinorhizobium meliloti; low Ref YP hit to cytochrome oxidase maturation protein, cbb3-type [Rhodobacter sphaeroides ATCC 17025].; nitrogen fixation protein fixS 673314..673472 Dinoroseobacter shibae DFL 12 = DSM 16493 5711504 YP_001532016.1 CDS dacC2 NC_009952.1 673560 675041 R PFAM: beta-lactamase; peptidase S11 D-alanyl-D-alanine carboxypeptidase 1; NCBI conserved domains: dacC; middle swissprot hit to D-alanyl-D-alanine carboxypeptidase dacC precursor from Escherichia coli K12; high Ref YP hit to D-alanyl-D-alanine carboxypeptidase family protein [Roseobacter denitrificans OCh 114].; D-alanyl-D-alanine carboxypeptidase complement(673560..675041) Dinoroseobacter shibae DFL 12 = DSM 16493 5711505 YP_001532017.1 CDS Dshi_0670 NC_009952.1 675215 675919 R ibu; PFAM: Haloacid dehalogenase domain protein hydrolase; NCBI conserved domains: COG1011, Predicted hydrolase (HAD superfamily); bad swissprot hit to Uncharacterized HAD-hydrolase MTH_209 from Methanothermobacter thermautotrophicus str. Delta H; high Ref YP hit to Haloacid dehalogenase domain protein hydrolase [Rhodobacter sphaeroides ATCC 17025].; haloacid dehalogenase domain-containing protein hydrolase complement(675215..675919) Dinoroseobacter shibae DFL 12 = DSM 16493 5711506 YP_001532018.1 CDS rsmC NC_009952.1 676410 677411 D PFAM: methyltransferase small; Methyltransferase type 11; Methyltransferase type 12; NCBI conserved domains: rsmC; low swissprot hit to Ribosomal RNA small subunit methyltransferase C from Escherichia coli K12; high Ref ZP hit to Possible ribosomal RNA small subunit methyltransferase C RsmC from Roseobacter sp. CCS2; ribosomal RNA small subunit methyltransferase C 676410..677411 Dinoroseobacter shibae DFL 12 = DSM 16493 5711507 YP_001532019.1 CDS Dshi_0672 NC_009952.1 677442 678248 D PFAM: short-chain dehydrogenase/reductase SDR; KR domain protein; low swissprot hit to 7-alpha-hydroxysteroid dehydrogenase from Escherichia coli K12; high Ref ZP hit to 7-alpha-hydroxysteroid dehydrogenase, putative [Roseovarius nubinhibens ISM].; short-chain dehydrogenase/reductase SDR 677442..678248 Dinoroseobacter shibae DFL 12 = DSM 16493 5711508 YP_001532020.1 CDS Dshi_0673 NC_009952.1 678229 678606 R no significant swissprot, no conserved domains; bad Ref ZP hit to hypothetical protein RTM1035_19081 [Roseovarius sp. TM1035].; hypothetical protein complement(678229..678606) Dinoroseobacter shibae DFL 12 = DSM 16493 5711509 YP_001532021.1 CDS hemF NC_009952.1 678666 679559 D catalyzes the conversion of the propionic acid groups of rings I and III to vinyl groups during heme synthesis; coproporphyrinogen III oxidase 678666..679559 Dinoroseobacter shibae DFL 12 = DSM 16493 5711510 YP_001532022.1 CDS ggt2 NC_009952.1 679714 681504 D TIGRFAM: gamma-glutamyltransferase PFAM: gamma-glutamyltranspeptidase; NCBI conserved domains: ggT; high swissprot hit to Gamma-glutamyltranspeptidase precursor from Escherichia coli K12; high Ref YP hit to Gamma-glutamyltransferase [Jannaschia sp. CCS1].; gamma-glutamyltransferase 679714..681504 Dinoroseobacter shibae DFL 12 = DSM 16493 5711511 YP_001532023.1 CDS Dshi_0676 NC_009952.1 681643 683742 D PFAM: beta-lactamase; NCBI conserved domains: COG1680, AmpC, Beta-lactamase class C and other penicillin binding proteins; bad swissprot hit to Penicillin-binding protein 4* (PBP 4*) from Bacillus subtilis; bad Ref YP hit to beta-lactamase [Chloroflexus aurantiacus J-10-fl]; beta-lactamase 681643..683742 Dinoroseobacter shibae DFL 12 = DSM 16493 5711512 YP_001532024.1 CDS Dshi_0677 NC_009952.1 683755 684570 R Pfam03567 Sulfotransferase; NCBI conserved domains: pfam03567; bad swissprot hit to Carbohydrate sulfotransferase 9 from Mus musculus; high Ref ZP hit to hypothetical protein R2601_13619 [Roseovarius sp. HTCC2601].; hypothetical protein complement(683755..684570) Dinoroseobacter shibae DFL 12 = DSM 16493 5711513 YP_001532025.1 CDS Dshi_0678 NC_009952.1 684684 686261 D PFAM: glycosyl transferase family 14; NCBI conserved domains: pfam02485, Branch, Core-2/I-Branching enzyme, pfam03267, DUF266, Domain of unknown function, bad swissprot hit to Xylosyltransferase from Ciona intestinalis; high Ref YP hit to epsK domain protein [Silicibacter pomeroyi DSS-3].; glycosyl transferase family protein 684684..686261 Dinoroseobacter shibae DFL 12 = DSM 16493 5711514 YP_001532026.1 CDS Dshi_0679 NC_009952.1 686270 686641 D PFAM: histidine triad (HIT) protein; NCBI conserved domains: cd01276, PKCI_related, Protein Kinase C Interacting protein related (PKCI), COG0537, Hit, Diadenosine tetraphosphate (Ap4A) hydrolase and other HIT family hydrolases; middle swissprot hit to Uncharacterized 13.2 kDa HIT-like protein in hisE 3region from Azospirillum brasilense; good Ref ZP hit to HIT-like protein, putative [Roseobacter sp. AzwK-3b].; histidine triad (HIT) protein 686270..686641 Dinoroseobacter shibae DFL 12 = DSM 16493 5711515 YP_001532027.1 CDS purK NC_009952.1 686761 687834 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(686761..687834) Dinoroseobacter shibae DFL 12 = DSM 16493 5711516 YP_001532028.1 CDS purE NC_009952.1 687827 688312 R TIGRFAM: phosphoribosylaminoimidazole carboxylase, catalytic subunit PFAM: 1-(5-phosphoribosyl)-5-amino-4-imidazole-carboxylate (AIR) carboxylase; NCBI conserved domains: purE; middle swissprot hit to Phosphoribosylaminoimidazole carboxylase catalytic subunit from Bacillus subtilis; high Ref YP hit to Phosphoribosylaminoimidazole carboxylase, catalytic subunit from Rhodobacter sphaeroides 2.4.1; catalytic subunit; phosphoribosylaminoimidazole carboxylase complement(687827..688312) Dinoroseobacter shibae DFL 12 = DSM 16493 5711517 YP_001532029.1 CDS Dshi_0682 NC_009952.1 688389 688613 R PFAM: protein of unknown function DUF465; no significant swissprot; low Ref ZP hit to Protein of unknown function DUF465 [Paracoccus denitrificans PD1222].; hypothetical protein complement(688389..688613) Dinoroseobacter shibae DFL 12 = DSM 16493 5711518 YP_001532030.1 CDS ibpAB NC_009952.1 688790 689233 D PFAM: heat shock protein Hsp20; NCBI conserved domains: ibpA; low swissprot hit to Small heat shock protein ibpA from Salmonella choleraesuis; good Ref YP hit to heat shock protein Hsp20 [Jannaschia sp. CCS1].; heat shock protein 688790..689233 Dinoroseobacter shibae DFL 12 = DSM 16493 5711118 YP_001532031.1 CDS Dshi_0684 NC_009952.1 689230 689457 D NCBI conserved domains: pfam06620 DUF1150, Protein of unknown function, COG5568, Uncharacterized small protein; no significant swissprot; low Ref ZP hit to hypothetical protein OB2597_07215 [Oceanicola batsensis HTCC2597].; hypothetical protein 689230..689457 Dinoroseobacter shibae DFL 12 = DSM 16493 5711119 YP_001532032.1 CDS apbE2 NC_009952.1 689465 690361 R PFAM: ApbE family lipoprotein KEGG: pde:Pden_2485 ApbE family lipoprotein; ApbE family lipoprotein complement(689465..690361) Dinoroseobacter shibae DFL 12 = DSM 16493 5711120 YP_001532033.1 CDS nosR1 NC_009952.1 690358 692448 R InterPro Scan: PIRSF036354 nitrous oxide reductase expression regulator NosR; NCBI conserved domains: nosR; high swissprot hit to Regulatory protein nosR from Pseudomonas stutzeri; high Ref ZP hit to regulatory protein, putative [Sagittula stellata E-37].; regulator of nitric oxide reductase transcription complement(690358..692448) Dinoroseobacter shibae DFL 12 = DSM 16493 5711121 YP_001532034.1 CDS Dshi_0687 NC_009952.1 692556 693332 D PFAM: binding-protein-dependent transport systems inner membrane component; NCBI conserved domains: COG0600, TauC, ABC-type nitrate/sulfonate/bicarbonate transport system, permease component; low swissprot hit to Putative aliphatic sulfonates transport permease protein ssuC from Bacillus subtilis; high Ref ZP hit to putative ABC transporter protein [Sagittula stellata E-37]; other two ABC-transporter components (ATP-binding, substrate-binding) are missing; two-component system, permease 692556..693332 Dinoroseobacter shibae DFL 12 = DSM 16493 5711122 YP_001532035.1 CDS Dshi_0688 NC_009952.1 693474 694838 R PFAM: fumarate reductase/succinate dehydrogenase flavoprotein domain protein; FAD dependent oxidoreductase; FAD-dependent pyridine nucleotide-disulphide oxidoreductase; NCBI conserved domains: PRK06481, fumarate reductase flavoprotein subunit, COG1053, SdhA, Succinate dehydrogenase/fumarate reductase, flavoprotein subunit; middle swissprot hit to Fumarate reductase flavoprotein subunit precursor from Shewanella oneidensis; high Ref YP hit to fumarate reductase/succinate dehydrogenase flavoprotein-like from Jannaschia sp. CCS1; fumarate reductase/succinate dehydrogenase flavoprotein domain-containing protein complement(693474..694838) Dinoroseobacter shibae DFL 12 = DSM 16493 5711123 YP_001532036.1 CDS prpB NC_009952.1 694835 695713 R NCBI conserved domains: COG2513, PrpB, PEP phosphonomutase and related enzymes; PRK11320, prpB, 2-methylisocitrate lyase; middle swissprot hit to Methylisocitrate lyase from Vibrio cholerae; high Ref YP hit to isocitrate lyase family protein [Jannaschia sp. CCS1].; methylisocitrate lyase complement(694835..695713) Dinoroseobacter shibae DFL 12 = DSM 16493 5711124 YP_001532037.1 CDS entB NC_009952.1 695710 696312 R PFAM: isochorismatase hydrolase; NCBI conserved domains: COG1535, EntB, Isochorismate hydrolase; low swissprot hit to Isochorismatase (Isochorismate lyase) from Escherichia coli K12; high Ref ZP hit to isochorismatase family protein [Sulfitobacter sp. EE-36].; isochorismatase complement(695710..696312) Dinoroseobacter shibae DFL 12 = DSM 16493 5711125 YP_001532038.1 CDS hyuA NC_009952.1 696309 698378 R PFAM: Hydantoinase/oxoprolinase; Hydantoinaseoxoprolinase domain protein; NCBI conserved domains: COG0145, HyuA, N-methylhydantoinase A/acetone carboxylase, beta subunit; high swissprot hit to Hydantoin utilization protein A from Pseudomonas sp. NS671; high Ref ZP hit to hydantoin utilization protein A [Roseovarius sp. HTCC2601].; hydantoin utilization protein A complement(696309..698378) Dinoroseobacter shibae DFL 12 = DSM 16493 5711126 YP_001532039.1 CDS hyuB NC_009952.1 698375 700072 R PFAM: Hydantoinase B/oxoprolinase, NCBI conserved domains: COG0146, HyuB, N-methylhydantoinase B/acetone carboxylase, alpha subunit; good swissprot hit to Hydantoin utilization protein B from Pseudomonas sp. NS671; high Ref ZP hit to hydantoin utilization protein B, putative [Roseovarius sp. HTCC2601].; hydantoin utilization protein B complement(698375..700072) Dinoroseobacter shibae DFL 12 = DSM 16493 5711127 YP_001532040.1 CDS pptA NC_009952.1 700069 700644 R PFAM: 4-oxalocrotonate tautomerase; NCBI conserved domains: pfam01361, Tautomerase; no significant swissprot, good Ref ZP hit to tautomerase, putative [Loktanella vestfoldensis SKA53].; 4-oxalocrotonate tautomerase complement(700069..700644) Dinoroseobacter shibae DFL 12 = DSM 16493 5711128 YP_001532041.1 CDS Dshi_0694 NC_009952.1 700802 701602 D PFAM: regulatory protein GntR HTH; UbiC transcription regulator-associated domain protein; NCBI conserved domains: pfam07702, UTRA; low swissprot hit to Uncharacterized HTH-type transcriptional regulator yidP from Escherichia coli K12; high Ref YP hit to transcriptional regulator, GntR family [Jannaschia sp. CCS1].; GntR family; transcriptional regulator 700802..701602 Dinoroseobacter shibae DFL 12 = DSM 16493 5711129 YP_001532042.1 CDS leuC NC_009952.1 701599 702993 D dehydratase component, catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; isopropylmalate isomerase large subunit 701599..702993 Dinoroseobacter shibae DFL 12 = DSM 16493 5711130 YP_001532043.1 CDS leuD NC_009952.1 702990 703649 D TIGRFAM: 3-isopropylmalate dehydratase, small subunit PFAM: aconitate hydratase domain protein; NCBI conserved domains: PRK01641, leuD, isopropylmalate isomerase small subunit; good swissprot hit to 3-isopropylmalate dehydratase small subunit from Symbiobacterium thermophilum; good Ref ZP hit to 3-isopropylmalate dehydratase, small subunit [Sulfitobacter sp. NAS-14.1].; 3-isopropylmalate dehydratase small subunit 702990..703649 Dinoroseobacter shibae DFL 12 = DSM 16493 5711131 YP_001532044.1 CDS dctP1 NC_009952.1 703665 704675 D PFAM: TRAP dicarboxylate transporter- DctP subunit, NCBI conserved domains: COG1638, DctP; bad swissprot hit to C4-dicarboxylate-binding periplasmic protein precursor from Rhodobacter capsulatus; high Ref ZP hit to TRAP dicarboxylate transporter- DctP subunit [Hoeflea phototrophica DFL-43].; TRAP dicarboxylate transporter subunit DctP 703665..704675 Dinoroseobacter shibae DFL 12 = DSM 16493 5711132 YP_001532045.1 CDS dctQ3 NC_009952.1 704719 705225 D PFAM: Tripartite ATP-independent periplasmic transporter DctQ component, NCBI conserved domains: dctQ and dctM small permease component; no significant swissprot; good Ref ZP hit to TRAP dicarboxylate transporter, DctQ subunit, putative from Sulfitobacter sp. EE-36; TRAP dicarboxylate transporter subunit DctQ 704719..705225 Dinoroseobacter shibae DFL 12 = DSM 16493 5711133 YP_001532046.1 CDS dctM1 NC_009952.1 705226 706539 D PFAM: TRAP C4-dicarboxylate transport system permease DctM subunit; NCBI conserved domains: COG4664, FcbT3, TRAP-type mannitol/chloroaromatic compound transport system, large permease component and dctMQ; middle swissprot hit to Putative TRAP transporter large permease protein HI0050 from Haemophilus influenzae; high Ref ZP hit to TRAP dicarboxylate transporter, DctM subunit [Loktanella vestfoldensis SKA53].; TRAP dicarboxylate transporter subunit DctM 705226..706539 Dinoroseobacter shibae DFL 12 = DSM 16493 5711134 YP_001532047.1 CDS Dshi_0700 NC_009952.1 706599 708116 D PFAM: AMP-dependent synthetase and ligase; NCBI conserved domains: COG0318, CaiC, Acyl-CoA synthetases (AMP-forming); middle swissprot hit to 2-succinylbenzoate--CoA ligase (OSB-CoA synthetase) from Bacillus anthracis; high Ref ZP hit to AMP-binding enzyme [Rhodobacterales bacterium HTCC2654].; AMP-dependent synthetase and ligase 706599..708116 Dinoroseobacter shibae DFL 12 = DSM 16493 5711135 YP_001532048.1 CDS Dshi_0701 NC_009952.1 708169 708822 R PFAM: Methyltransferase type 11; Methyltransferase type 12; NCBI conserved domains: COG2226, UbiE; no significant swissprot; middle Ref YP hit to Methyltransferase type 12 [Flavobacterium johnsoniae UW101]; methyltransferase domain-containing protein complement(708169..708822) Dinoroseobacter shibae DFL 12 = DSM 16493 5711136 YP_001532049.1 CDS Dshi_0702 NC_009952.1 708819 709466 R InterPro Scan and NCBI conserved domains: pfam08889, WbqC; no significant swissprot; low gb hit to WbnG [Shigella dysenteriae].; WbqC-like family protein complement(708819..709466) Dinoroseobacter shibae DFL 12 = DSM 16493 5711137 YP_001532050.1 CDS Dshi_0703 NC_009952.1 709466 710386 R NCBI conserved domains: pfam00535, Glycos_transf_2, Glycosyl transferase family 2; no significant swissprot; low Ref YP hit to hypothetical protein Rsph17025_3846 [Rhodobacter sphaeroides ATCC 17025].; hypothetical protein complement(709466..710386) Dinoroseobacter shibae DFL 12 = DSM 16493 5711138 YP_001532051.1 CDS Dshi_0704 NC_009952.1 710642 711829 D PFAM: DegT/DnrJ/EryC1/StrS aminotransferase; aminotransferase class-III; NCBI conserved domains: pfam01041, DegT_DnrJ_EryC1, DegT/DnrJ/EryC1/StrS aminotransferase family; COG0399, WecE, Predicted pyridoxal phosphate-dependent enzyme; low swissprot hit to UDP-Ara4O aminotransferase from Salmonella typhi; middle Ref YP hit to DegT/DnrJ/EryC1/StrS aminotransferase [Methylobacillus flagellatus KT]; pyridoxal-phosphate-dependent aminotransferase 710642..711829 Dinoroseobacter shibae DFL 12 = DSM 16493 5711139 YP_001532052.1 CDS Dshi_0705 NC_009952.1 711826 713256 D NCBI conserved domains: COG4421, Capsular polysaccharide biosynthesis protein; no significant swissprot; low Ref ZP hit to Capsular polysaccharide biosynthesis protein-like protein from Roseobacter sp. AzwK-3b; hypothetical protein 711826..713256 Dinoroseobacter shibae DFL 12 = DSM 16493 5711140 YP_001532053.1 CDS Dshi_0707 NC_009952.1 714601 715269 D NCBI conserved domains: cd00208, LbetaH, Left-Handed Parallel beta-Helix and COG1044, LpxD, UDP-3-O-[3-hydroxymyristoyl]; low swissprot hit to UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase from Nitrosococcus oceani ATCC 19707; middle Ref ZP hit to transferase hexapeptide repeat [Pseudomonas putida W619]; hypothetical protein 714601..715269 Dinoroseobacter shibae DFL 12 = DSM 16493 5711142 YP_001532054.1 CDS Dshi_0708 NC_009952.1 715275 716246 D unsure GC frame Plot, no conserved domains; no significant swissprot; middle Ref YP hit to hypothetical protein BTH_I3215 [Burkholderia thailandensis E264].; hypothetical protein 715275..716246 Dinoroseobacter shibae DFL 12 = DSM 16493 5711143 YP_001532055.1 CDS atoDA NC_009952.1 716718 718664 D PFAM: coenzyme A transferase; NCBI conserved domains: atoDA; low swissprot hit to SCOT-S from Sus scrofa; high Ref ZP hit to Coenzyme A transferase [Roseobacter litoralis Och 149].; acyl CoA:acetate/3-ketoacid CoA transferase, alpha and subunit beta 716718..718664 Dinoroseobacter shibae DFL 12 = DSM 16493 5711144 YP_001532056.1 CDS Dshi_0710 NC_009952.1 718730 719377 D no significant swissprot; no conserved domains detected (except from one signalpep. and six transmembr. regions); middle Ref ZP hit to hypothetical protein RLO149_12985 [Roseobacter litoralis Och 149].; hypothetical protein 718730..719377 Dinoroseobacter shibae DFL 12 = DSM 16493 5711145 YP_001532057.1 CDS Dshi_0711 NC_009952.1 719323 720249 R 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 complement(719323..720249) Dinoroseobacter shibae DFL 12 = DSM 16493 5711146 YP_001532058.1 CDS lysE NC_009952.1 720340 720966 D NCBI conserved domains: COG1279, Lysine efflux permease; pfam01810, LysE; middle swissprot hit to Putative amino-acid transporter yggA from Aeromonas salmonicida; good Ref ZP hit to L-lysine exporter, putative [Oceanibulbus indolifex HEL-45].; LYSE/YGGA; lysine exporter protein 720340..720966 Dinoroseobacter shibae DFL 12 = DSM 16493 5711147 YP_001532059.1 CDS Dshi_0713 NC_009952.1 721072 721935 D NCBI conserved domains: COG3509, LpqC; no significant swissprot; low REf YP hit to polyhydroxybutyrate depolymerase [Frankia sp. EAN1pec].; poly(3-hydroxybutyrate) depolymerase-like protein 721072..721935 Dinoroseobacter shibae DFL 12 = DSM 16493 5711148 YP_001532060.1 CDS Dshi_0714 NC_009952.1 721916 722884 D NCBI conserved domains: pfam00892, DUF6, Integral membrane protein DUF6; COG0697, RhaT, Permeases of the drug/metabolite transporter (DMT) superfamily; low swissprot hit to S-adenosylmethionine uptake transporter from Rickettsia typhi; high Ref ZP hit to membrane protein, putative [Roseobacter sp. MED193].; hypothetical protein 721916..722884 Dinoroseobacter shibae DFL 12 = DSM 16493 5711149 YP_001532061.1 CDS Dshi_0715 NC_009952.1 722969 723211 D PFAM04325 Protein of unknown function (DUF465); NCBI conserved domains: COG2841, Uncharacterized protein conserved in bacteria; no swissprot hit; low Ref YP hit to protein of unknown function DUF465 [Silicibacter sp. TM1040].; hypothetical protein 722969..723211 Dinoroseobacter shibae DFL 12 = DSM 16493 5711150 YP_001532062.1 CDS Dshi_0716 NC_009952.1 723225 724619 R PFAM: helix-turn-helix domain protein; protein of unknown function DUF955; NCBI conserved domains: COG3800, Predicted transcriptional regulator; no significant swissprot; high Ref YP hit to transcriptional regulator, XRE family [Silicibacter sp. TM1040].; XRE (HTH-3) family; transcriptional regulator complement(723225..724619) Dinoroseobacter shibae DFL 12 = DSM 16493 5711151 YP_001532063.1 CDS Dshi_0717 NC_009952.1 724680 725906 R TIGRFAM: drug resistance transporter, Bcr/CflA subfamily PFAM: major facilitator superfamily MFS_1, NCBI conserved domains: PRK11652, emrD, multidrug resistance protein D; low swissprot hit to Bicyclomycin resistance protein (bcr) from Escherichia coli K12; high Ref ZP hit to MFS protein, putative [Roseobacter sp. AzwK-3b].; multidrug resistance protein complement(724680..725906) Dinoroseobacter shibae DFL 12 = DSM 16493 5711152 YP_001532064.1 CDS pccB NC_009952.1 726256 727788 D Probably a dodecamer composed of six biotin-containing alpha subunits and six beta subunits.; carboxyl transferase 726256..727788 Dinoroseobacter shibae DFL 12 = DSM 16493 5711153 YP_001532065.1 CDS Dshi_0719 NC_009952.1 727888 728286 D hypothetical protein 727888..728286 Dinoroseobacter shibae DFL 12 = DSM 16493 5711154 YP_001532066.1 CDS Dshi_0720 NC_009952.1 728279 728668 D Active on single-stranded mRNA. Inhibits protein synthesis by cleavage of mRNA.; endoribonuclease L-PSP 728279..728668 Dinoroseobacter shibae DFL 12 = DSM 16493 5711155 YP_001532067.1 CDS Dshi_0721 NC_009952.1 728665 729036 D weak similarity to genes in Rhodobacteraceae; hypothetical protein 728665..729036 Dinoroseobacter shibae DFL 12 = DSM 16493 5711156 YP_001532068.1 CDS Dshi_0722 NC_009952.1 729051 729410 D conserved in Rhodobacteraceae and Bradyrhizobiaceae; hypothetical protein 729051..729410 Dinoroseobacter shibae DFL 12 = DSM 16493 5711157 YP_001532069.1 CDS pccA NC_009952.1 729769 731814 D biotin-dependent enzyme, Probably a dodecamer composed of six biotin-containing alpha subunits and six beta subunits.; carbamoyl-phosphate synthase L chain ATP-binding 729769..731814 Dinoroseobacter shibae DFL 12 = DSM 16493 5711158 YP_001532070.1 CDS Dshi_0724 NC_009952.1 731879 732328 R hypothetical protein complement(731879..732328) Dinoroseobacter shibae DFL 12 = DSM 16493 5711159 YP_001532071.1 CDS Dshi_0725 NC_009952.1 732437 733432 D hypothetical protein 732437..733432 Dinoroseobacter shibae DFL 12 = DSM 16493 5711160 YP_001532072.1 CDS bhbA NC_009952.1 733404 735542 D MDM; functions in conversion of succinate to propionate; methylmalonyl-CoA mutase 733404..735542 Dinoroseobacter shibae DFL 12 = DSM 16493 5711161 YP_001532073.1 CDS Dshi_0727 NC_009952.1 735721 736650 R HTH and substrate binding domain; LysR family; transcriptional regulator complement(735721..736650) Dinoroseobacter shibae DFL 12 = DSM 16493 5711162 YP_001532074.1 CDS mnhA NC_009952.1 737004 739244 D quinone dependent NADH dehydrogenase 737004..739244 Dinoroseobacter shibae DFL 12 = DSM 16493 5711163 YP_001532075.1 CDS mnhB NC_009952.1 739241 739693 D Na+/H+ antiporter MnhB subunit-like protein 739241..739693 Dinoroseobacter shibae DFL 12 = DSM 16493 5711164 YP_001532076.1 CDS mnhC NC_009952.1 739693 740112 D subunit C of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; putative monovalent cation/H+ antiporter subunit C 739693..740112 Dinoroseobacter shibae DFL 12 = DSM 16493 5711165 YP_001532077.1 CDS mnhD NC_009952.1 740109 741644 D quinone dependent NADH dehydrogenase 740109..741644 Dinoroseobacter shibae DFL 12 = DSM 16493 5711166 YP_001532078.1 CDS mnhE NC_009952.1 741641 741994 D Members of the PhaE/MrpE family are predicted to be integral membrane proteins with three transmembrane regions, involved in regulation of pH. PhaE is part of a potassium efflux system involved in pH regulation; cation antiporter 741641..741994 Dinoroseobacter shibae DFL 12 = DSM 16493 5711167 YP_001532079.1 CDS mnhF NC_009952.1 741987 742343 D Members of the PhaF/MrpF family are predicted to be integral membrane proteins with three transmembrane regions, involved in regulation of pH. PhaF is part of a potassium efflux system involved in pH regulation; multiple resistance and pH regulation protein F 741987..742343 Dinoroseobacter shibae DFL 12 = DSM 16493 5711168 YP_001532080.1 CDS mnhG NC_009952.1 742340 742687 D family of small, transmembrane proteins believed to be components of Na+/H+ and K+/H+ antiporters. Members, including proteins designated MnhG from Staphylococcus aureus and PhaG from Rhizobium meliloti, show some similarity to chain L of the NADH dehydrogenase I, which also translocates protons.; MnhG/PhaG subunit; monovalent cation/proton antiporter 742340..742687 Dinoroseobacter shibae DFL 12 = DSM 16493 5711169 YP_001532081.1 CDS Dshi_0735 NC_009952.1 742674 743288 D hypothetical protein 742674..743288 Dinoroseobacter shibae DFL 12 = DSM 16493 5711170 YP_001532082.1 CDS Dshi_0736 NC_009952.1 743285 743770 D protein N-Acetyl-transferase; N-acetyltransferase GCN5 743285..743770 Dinoroseobacter shibae DFL 12 = DSM 16493 5711171 YP_001532083.1 CDS Dshi_0737 NC_009952.1 743834 744517 D heat shock protein DnaJ domain-containing protein 743834..744517 Dinoroseobacter shibae DFL 12 = DSM 16493 5711172 YP_001532084.1 CDS Dshi_0738 NC_009952.1 744578 744895 D hypothetical protein 744578..744895 Dinoroseobacter shibae DFL 12 = DSM 16493 5711173 YP_001532085.1 CDS ppx NC_009952.1 744912 746432 R This family consists of the N-terminal region of exopolyphosphatase (Ppx) and guanosine pentaphosphate phospho-hydrolase (GppA).; Ppx/GppA phosphatase complement(744912..746432) Dinoroseobacter shibae DFL 12 = DSM 16493 5711174 YP_001532086.1 CDS ppk1 NC_009952.1 746526 748700 R catalyzes the reversible transfer of the terminal phosphate of ATP to form a long chain polyphosphate; polyphosphate kinase complement(746526..748700) Dinoroseobacter shibae DFL 12 = DSM 16493 5711175 YP_001532087.1 CDS Dshi_0741 NC_009952.1 748740 749429 R weak evidence for predicted function; DnaA; chromosomal replication initiator complement(748740..749429) Dinoroseobacter shibae DFL 12 = DSM 16493 5711176 YP_001532088.1 CDS Dshi_0742 NC_009952.1 749426 750511 R predicted transmembrane protein (10TMH); hypothetical protein complement(749426..750511) Dinoroseobacter shibae DFL 12 = DSM 16493 5711177 YP_001532089.1 CDS mcsS NC_009952.1 750674 752056 D Mechanosensitive (MS) channels provide protection against hypo-osmotic shock, responding both to stretching of the cell membrane and to membrane depolarisation.; mechanosensitive ion channel protein MscS 750674..752056 Dinoroseobacter shibae DFL 12 = DSM 16493 5711178 YP_001532090.1 CDS proS NC_009952.1 752138 753475 D catalyzes the formation of prolyl-tRNA(Pro) from proline and tRNA(Pro); prolyl-tRNA synthetase 752138..753475 Dinoroseobacter shibae DFL 12 = DSM 16493 5711179 YP_001532091.1 CDS Dshi_0745 NC_009952.1 753664 754239 D This family of redoxins includes peroxiredoxin, thioredoxin and glutaredoxin proteins.; redoxin domain-containing protein 753664..754239 Dinoroseobacter shibae DFL 12 = DSM 16493 5711180 YP_001532092.1 CDS aqpZ NC_009952.1 754337 755023 D Transport of water across the membrane.; MIP family channel protein 754337..755023 Dinoroseobacter shibae DFL 12 = DSM 16493 5711181 YP_001532093.1 CDS lolC NC_009952.1 755116 756402 D Part of an ATP-dependent transport system responsible for the release of lipoproteins targeted to the outer membrane from the inner membrane.; transmembrane protein, LolC/E family; lipoprotein releasing system 755116..756402 Dinoroseobacter shibae DFL 12 = DSM 16493 5711182 YP_001532094.1 CDS lolD NC_009952.1 756395 757078 D Part of the ABC transporter complex lolCDE involved in the translocation of mature outer membrane-directed lipoproteins, from the inner membrane to the periplasmic chaperone, lolA. Responsible for the formation of the lolA-lipoprotein complex in an ATP-dependent manner; ABC transporter-like protein 756395..757078 Dinoroseobacter shibae DFL 12 = DSM 16493 5711183 YP_001532095.1 CDS Dshi_0749 NC_009952.1 758372 760336 R decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling; DNA topoisomerase IV subunit B complement(758372..760336) Dinoroseobacter shibae DFL 12 = DSM 16493 5711184 YP_001532096.1 CDS Dshi_0750 NC_009952.1 760995 761789 D hypothetical protein 760995..761789 Dinoroseobacter shibae DFL 12 = DSM 16493 5711185 YP_001532097.1 CDS ppk2 NC_009952.1 761970 762914 D Protein with ppk2 Domain, cytoplasmatic; hypothetical protein 761970..762914 Dinoroseobacter shibae DFL 12 = DSM 16493 5711186 YP_001532098.1 CDS Dshi_0752 NC_009952.1 762957 763637 D contains DUF1007 domain; hypothetical protein 762957..763637 Dinoroseobacter shibae DFL 12 = DSM 16493 5711187 YP_001532099.1 CDS nicO NC_009952.1 763625 764581 D incorporation of nickel into H2-uptake hydrogenase and urease, signal peptide cleveage after AA 22, inner membrane; high-affinity nickel-transporter 763625..764581 Dinoroseobacter shibae DFL 12 = DSM 16493 5711188 YP_001532100.1 CDS Dshi_0754 NC_009952.1 764591 765187 D SAM-dependent methyltransferase, Substrate not known KEGG: rsp:RSP_0765 SAM-dependent methyltransferase; type 11 methyltransferase 764591..765187 Dinoroseobacter shibae DFL 12 = DSM 16493 5711189 YP_001532101.1 CDS Dshi_0755 NC_009952.1 765229 766599 D MATE efflux family protein 765229..766599 Dinoroseobacter shibae DFL 12 = DSM 16493 5711190 YP_001532102.1 CDS Dshi_0756 NC_009952.1 766585 767244 R hypothetical protein complement(766585..767244) Dinoroseobacter shibae DFL 12 = DSM 16493 5711191 YP_001532103.1 CDS Dshi_0757 NC_009952.1 767248 768648 R selenium-binding protein complement(767248..768648) Dinoroseobacter shibae DFL 12 = DSM 16493 5711192 YP_001532104.1 CDS Dshi_0758 NC_009952.1 768813 769301 R MarR family; transcriptional regulator complement(768813..769301) Dinoroseobacter shibae DFL 12 = DSM 16493 5711193 YP_001532105.1 CDS Dshi_0759 NC_009952.1 769384 769752 D hypothetical protein 769384..769752 Dinoroseobacter shibae DFL 12 = DSM 16493 5711194 YP_001532106.1 CDS Dshi_0760 NC_009952.1 770254 770736 R hypothetical protein complement(770254..770736) Dinoroseobacter shibae DFL 12 = DSM 16493 5711195 YP_001532107.1 CDS Dshi_0761 NC_009952.1 770763 771179 R conserved in Rhodobacteraceae; hypothetical protein complement(770763..771179) Dinoroseobacter shibae DFL 12 = DSM 16493 5711196 YP_001532108.1 CDS aspC NC_009952.1 771187 772389 R catalyzes the formation of oxalozcetate and L-glutamate from L-aspartate and 2-oxoglutarate; aspartate aminotransferase complement(771187..772389) Dinoroseobacter shibae DFL 12 = DSM 16493 5711197 YP_001532109.1 CDS Dshi_0763 NC_009952.1 772480 772872 D Helix-Turn-Helix motif; XRE family; transcriptional regulator 772480..772872 Dinoroseobacter shibae DFL 12 = DSM 16493 5711198 YP_001532110.1 CDS Dshi_0764 NC_009952.1 772869 773168 D hypothetical protein 772869..773168 Dinoroseobacter shibae DFL 12 = DSM 16493 5711199 YP_001532111.1 CDS Dshi_0765 NC_009952.1 773281 773778 D HTH domain; MarR family; transcriptional regulator 773281..773778 Dinoroseobacter shibae DFL 12 = DSM 16493 5711200 YP_001532112.1 CDS Dshi_0766 NC_009952.1 773856 774593 R putative lipoprotein; hypothetical protein complement(773856..774593) Dinoroseobacter shibae DFL 12 = DSM 16493 5711201 YP_001532113.1 CDS Dshi_0767 NC_009952.1 774595 775023 R Lactoylglutathione lyase; glyoxalase/bleomycin resistance protein/dioxygenase complement(774595..775023) Dinoroseobacter shibae DFL 12 = DSM 16493 5711202 YP_001532114.1 CDS thyX NC_009952.1 775200 776117 D 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 775200..776117 Dinoroseobacter shibae DFL 12 = DSM 16493 5711203 YP_001532115.1 CDS csp1 NC_009952.1 776205 776414 R CSD(cold shock DNA-binding) domain containing Protein, binds single stranded DNA, 4 homologs in E. coli cspABCD; cold-shock DNA-binding domain-containing protein complement(776205..776414) Dinoroseobacter shibae DFL 12 = DSM 16493 5711204 YP_001532116.1 CDS Dshi_0770 NC_009952.1 776635 776946 D conserved arsC domain; arsenate reductase-like protein 776635..776946 Dinoroseobacter shibae DFL 12 = DSM 16493 5711205 YP_001532117.1 CDS Dshi_0771 NC_009952.1 776904 777470 R DoxX family protein complement(776904..777470) Dinoroseobacter shibae DFL 12 = DSM 16493 5711206 YP_001532118.1 CDS Dshi_0772 NC_009952.1 777464 778210 R hypothetical protein complement(777464..778210) Dinoroseobacter shibae DFL 12 = DSM 16493 5711207 YP_001532119.1 CDS Dshi_0773 NC_009952.1 778207 779157 R hypothetical protein complement(778207..779157) Dinoroseobacter shibae DFL 12 = DSM 16493 5711208 YP_001532120.1 CDS Dshi_0774 NC_009952.1 779200 779487 R predicted inner membrane protein, conserved in Rhodobacteraceae; hypothetical protein complement(779200..779487) Dinoroseobacter shibae DFL 12 = DSM 16493 5711209 YP_001532121.1 CDS ttuC NC_009952.1 780036 781115 D multiple catalytic activities: EC:1.1.1.93: Tartrate + NAD(+) <=> oxaloglycolate + NADH; EC:4.1.1.73: (R,R)-tartrate <=> D-glycerate + CO2; EC:1.1.1.83: (R)-malate + NAD(+) <=> pyruvate + CO(2) + NADH; cytoplasmatic; Belongs to the isocitrate and isopropylmalate dehydrogenases family; tartrate dehydrogenase 780036..781115 Dinoroseobacter shibae DFL 12 = DSM 16493 5711210 YP_001532122.1 CDS Dshi_0776 NC_009952.1 781394 782179 D similar to ppaA in the photosynthetic gene cluster, cytosolic; cobalamin B12-binding domain-containing protein 781394..782179 Dinoroseobacter shibae DFL 12 = DSM 16493 5711211 YP_001532123.1 CDS thrS NC_009952.1 782164 784128 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(782164..784128) Dinoroseobacter shibae DFL 12 = DSM 16493 5711212 YP_001532124.1 CDS Dshi_0778 NC_009952.1 784257 784445 R hypothetical protein complement(784257..784445) Dinoroseobacter shibae DFL 12 = DSM 16493 5711213 YP_001532125.1 CDS Dshi_0779 NC_009952.1 784566 785522 D protein with 2 functional domains: MarR and acetyltransferase (GNAT); MarR family with acetyltransferase activity; transcriptional regulator 784566..785522 Dinoroseobacter shibae DFL 12 = DSM 16493 5711214 YP_001532126.1 CDS Dshi_0780 NC_009952.1 785693 786637 R Hydrolase, alpha/beta fold motiv with catalytic triade; alpha/beta hydrolase fold protein complement(785693..786637) Dinoroseobacter shibae DFL 12 = DSM 16493 5711216 YP_001532127.1 CDS Dshi_0781 NC_009952.1 786642 786929 R contains SCP-2 sterol transfer family domain; sterol-binding domain-containing protein complement(786642..786929) Dinoroseobacter shibae DFL 12 = DSM 16493 5711217 YP_001532128.1 CDS Dshi_0782 NC_009952.1 787003 787569 D putative Tetratricopeptide TPR_2 repeat protein; hypothetical protein 787003..787569 Dinoroseobacter shibae DFL 12 = DSM 16493 5711218 YP_001532129.1 CDS Dshi_0783 NC_009952.1 787616 790579 D contains Helicase domain; helicase domain-containing protein 787616..790579 Dinoroseobacter shibae DFL 12 = DSM 16493 5711219 YP_001532130.1 CDS Dshi_0784 NC_009952.1 790711 790959 D RNA-binding protein S4 790711..790959 Dinoroseobacter shibae DFL 12 = DSM 16493 5711220 YP_001532131.1 CDS fdxA NC_009952.1 791008 791346 D contains [3Fe-4S] and [4Fe-4S] Cys cluster; 4Fe-4S ferredoxin 791008..791346 Dinoroseobacter shibae DFL 12 = DSM 16493 5711221 YP_001532132.1 CDS Dshi_0786 NC_009952.1 791654 792166 D similar to N-terminus of M. xanthus carD protein; CarD family; transcriptional regulator 791654..792166 Dinoroseobacter shibae DFL 12 = DSM 16493 5711222 YP_001532133.1 CDS cobS1 NC_009952.1 792216 792992 R Cobalamin biosynthesis, Reaction: Cobamide coenzyme + GMP <=> Adenosine-GDP-cobinamide + alpha-Ribazole; cobalamin-5-phosphate synthase CobS complement(792216..792992) Dinoroseobacter shibae DFL 12 = DSM 16493 5711223 YP_001532134.1 CDS cobT NC_009952.1 793089 794126 D catalyzes the synthesis of alpha-ribazole-5'-phosphate from nicotinate mononucleotide and 5,6-dimethylbenzimidazole; nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase 793089..794126 Dinoroseobacter shibae DFL 12 = DSM 16493 5711224 YP_001532135.1 CDS kefC NC_009952.1 794130 796142 R glutathione regulated, K+/H+ antiporter, NAD-binding domain; potassium efflux system protein complement(794130..796142) Dinoroseobacter shibae DFL 12 = DSM 16493 5711225 YP_001532136.1 CDS Dshi_0790 NC_009952.1 796285 798666 R conserved in Rhodobacteraceae; hypothetical protein complement(796285..798666) Dinoroseobacter shibae DFL 12 = DSM 16493 5711226 YP_001532137.1 CDS Dshi_0791 NC_009952.1 798789 799526 D protein of unknown function DUF541, bacterial membrane or periplasm protein; hypothetical protein 798789..799526 Dinoroseobacter shibae DFL 12 = DSM 16493 5711227 YP_001532138.1 CDS Dshi_0792 NC_009952.1 799585 799959 R hypothetical protein complement(799585..799959) Dinoroseobacter shibae DFL 12 = DSM 16493 5711228 YP_001532139.1 CDS metB2 NC_009952.1 800127 801422 R PLP-dependent, Reaction: O-Acetyl-L-homoserine + Methanethiol <=> L-Methionine + Acetate, Also reacts with other thiols and H2S, producing homocysteine or thioethers; O-acetylhomoserine/O-acetylserine sulfhydrylase complement(800127..801422) Dinoroseobacter shibae DFL 12 = DSM 16493 5711229 YP_001532140.1 CDS hisB NC_009952.1 801568 802155 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 801568..802155 Dinoroseobacter shibae DFL 12 = DSM 16493 5711230 YP_001532141.1 CDS hisH NC_009952.1 802157 802795 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 802157..802795 Dinoroseobacter shibae DFL 12 = DSM 16493 5711231 YP_001532142.1 CDS argF NC_009952.1 802986 803912 R catalyzes the formation of L-citrulline from carbamoyl phosphate and L-ornithine in arginine biosynthesis and degradation; ornithine carbamoyltransferase complement(802986..803912) Dinoroseobacter shibae DFL 12 = DSM 16493 5711232 YP_001532143.1 CDS Dshi_0797 NC_009952.1 803909 804442 R weakly conserved GCN5-related N-acetyltransferase, possibly EC:3.5.1.16; N-acetyltransferase GCN5 complement(803909..804442) Dinoroseobacter shibae DFL 12 = DSM 16493 5711233 YP_001532144.1 CDS argD NC_009952.1 804432 805613 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(804432..805613) Dinoroseobacter shibae DFL 12 = DSM 16493 5711234 YP_001532145.1 CDS Dshi_0799 NC_009952.1 805880 806218 R putative DNA-binding protein complement(805880..806218) Dinoroseobacter shibae DFL 12 = DSM 16493 5711235 YP_001532146.1 CDS Dshi_0800 NC_009952.1 806381 807163 R Helix-Turn-Helix motiv, iclR subfamily; IclR family; transcriptional regulator complement(806381..807163) Dinoroseobacter shibae DFL 12 = DSM 16493 5711236 YP_001532147.1 CDS Dshi_0801 NC_009952.1 807171 808529 R TRAP gene cluster - dctPQM; TRAP dicarboxylate transporter subunit DctM complement(807171..808529) Dinoroseobacter shibae DFL 12 = DSM 16493 5711237 YP_001532148.1 CDS Dshi_0802 NC_009952.1 808526 809254 R TRAP gene cluster - dctPQM; tripartite ATP-independent periplasmic transporter subunit DctQ complement(808526..809254) Dinoroseobacter shibae DFL 12 = DSM 16493 5711238 YP_001532149.1 CDS Dshi_0803 NC_009952.1 809305 810537 R TRAP gene cluster - dctPQM; TRAP dicarboxylate transporter subunit DctP complement(809305..810537) Dinoroseobacter shibae DFL 12 = DSM 16493 5711239 YP_001532150.1 CDS Dshi_0804 NC_009952.1 810647 812269 D contains N- and C-terminal GMC-oxidoreductase domain, FAD-binding; glucose-methanol-choline oxidoreductase 810647..812269 Dinoroseobacter shibae DFL 12 = DSM 16493 5711240 YP_001532151.1 CDS Dshi_0805 NC_009952.1 812303 814081 D catalyzes the formation of acetyl phosphate and sulfite from 2-sulfoacetaldehyde; is active when grown on taurine as a sole carbon source; sulfoacetaldehyde acetyltransferase 812303..814081 Dinoroseobacter shibae DFL 12 = DSM 16493 5711241 YP_001532152.1 CDS tauZ NC_009952.1 814089 815120 D 9 potential transmembrane domains; hypothetical protein 814089..815120 Dinoroseobacter shibae DFL 12 = DSM 16493 5711242 YP_001532153.1 CDS Dshi_0807 NC_009952.1 815127 816155 R hypothetical protein complement(815127..816155) Dinoroseobacter shibae DFL 12 = DSM 16493 5711243 YP_001532154.1 CDS mipA NC_009952.1 816307 817050 R integrates membrane bound lytic transglycosylase and penicillin-binding protein into a complex; MltA-interacting MipA family protein complement(816307..817050) Dinoroseobacter shibae DFL 12 = DSM 16493 5711244 YP_001532155.1 CDS lepA NC_009952.1 817541 819340 D binds to the ribosome on the universally-conserved alpha-sarcin loop; GTP-binding protein LepA 817541..819340 Dinoroseobacter shibae DFL 12 = DSM 16493 5711435 YP_001532156.1 CDS Dshi_0810 NC_009952.1 820707 820949 D hypothetical protein 820707..820949 Dinoroseobacter shibae DFL 12 = DSM 16493 5711436 YP_001532157.1 CDS Dshi_0811 NC_009952.1 820930 821163 D hypothetical protein 820930..821163 Dinoroseobacter shibae DFL 12 = DSM 16493 5711437 YP_001532158.1 CDS Dshi_0812 NC_009952.1 821347 821664 D TraR/DksA family; transcriptional regulator 821347..821664 Dinoroseobacter shibae DFL 12 = DSM 16493 5711438 YP_001532159.1 CDS Dshi_0813 NC_009952.1 821719 821967 D 2 predicted transmembrane domains; hypothetical protein 821719..821967 Dinoroseobacter shibae DFL 12 = DSM 16493 5711439 YP_001532160.1 CDS Dshi_0814 NC_009952.1 822057 822242 D conserved in Rhodobacteraceae and Bradyrhizobiaceae; hypothetical protein 822057..822242 Dinoroseobacter shibae DFL 12 = DSM 16493 5711440 YP_001532161.1 CDS Dshi_0815 NC_009952.1 822447 822863 R catalyzes the first step of the glyoxal pathway; glyoxalase/bleomycin resistance protein/dioxygenase complement(822447..822863) Dinoroseobacter shibae DFL 12 = DSM 16493 5711441 YP_001532162.1 CDS Dshi_0816 NC_009952.1 822910 823185 R hypothetical protein complement(822910..823185) Dinoroseobacter shibae DFL 12 = DSM 16493 5711442 YP_001532163.1 CDS Dshi_0817 NC_009952.1 823262 823522 D hypothetical protein 823262..823522 Dinoroseobacter shibae DFL 12 = DSM 16493 5711443 YP_001532164.1 CDS Dshi_0818 NC_009952.1 823519 823725 D hypothetical protein 823519..823725 Dinoroseobacter shibae DFL 12 = DSM 16493 5711444 YP_001532165.1 CDS Dshi_0819 NC_009952.1 823750 824046 D hypothetical protein 823750..824046 Dinoroseobacter shibae DFL 12 = DSM 16493 5711445 YP_001532166.1 CDS Dshi_0820 NC_009952.1 824267 825034 R hydrolase, alpha/beta fold motif with catalytic triade; alpha/beta hydrolase fold protein complement(824267..825034) Dinoroseobacter shibae DFL 12 = DSM 16493 5711446 YP_003422325.1 CDS Dshi_5001 NC_009952.1 825116 825505 D hypothetical protein 825116..825505 Dinoroseobacter shibae DFL 12 = DSM 16493 8130631 YP_001532167.1 CDS glyA NC_009952.1 825519 826814 R catalyzes the reaction of glycine with 5,10-methylenetetrahydrofolate to form L-serine and tetrahydrofolate; serine hydroxymethyltransferase complement(825519..826814) Dinoroseobacter shibae DFL 12 = DSM 16493 5711447 YP_001532168.1 CDS ppnK NC_009952.1 827012 827779 D catalyzes the phosphorylation of NAD to NADP; inorganic polyphosphate/ATP-NAD kinase 827012..827779 Dinoroseobacter shibae DFL 12 = DSM 16493 5711448 YP_001532169.1 CDS Dshi_0823 NC_009952.1 827784 829175 R Transcriptional regulater, ATP dependent Sigma54 interaction, part of two component system; Fis family; two component, sigma-54 specific, transcriptional regulator complement(827784..829175) Dinoroseobacter shibae DFL 12 = DSM 16493 5711449 YP_001532170.1 CDS Dshi_0824 NC_009952.1 829172 830701 R C-Terminal domain of arcB (aerobic respiration control), no PAS domain (sensor); histidine kinase complement(829172..830701) Dinoroseobacter shibae DFL 12 = DSM 16493 5711450 YP_001532171.1 CDS Dshi_0825 NC_009952.1 830837 832729 R AMP-binding domain, ligase similar to propionate-CoA and Acetyl-CoA ligase; AMP-dependent synthetase and ligase complement(830837..832729) Dinoroseobacter shibae DFL 12 = DSM 16493 5711451 YP_001532172.1 CDS Dshi_0826 NC_009952.1 832910 835189 R NAD-dependent; catalyzes the oxidative decarboxylation of malate to form pyruvate; does not decarboxylate oxaloacetate; malic enzyme complement(832910..835189) Dinoroseobacter shibae DFL 12 = DSM 16493 5711452 YP_001532173.1 CDS cdd NC_009952.1 835363 835755 D Reaction: Cytidine + H2O <=> Uridine + NH3; cytidine deaminase 835363..835755 Dinoroseobacter shibae DFL 12 = DSM 16493 5711453 YP_001532174.1 CDS deoA NC_009952.1 835752 837059 D Catalyzes the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate; thymidine phosphorylase 835752..837059 Dinoroseobacter shibae DFL 12 = DSM 16493 5711454 YP_001532175.1 CDS deoB NC_009952.1 837056 838255 D catalyzes the transfer of phosphate between the C1 and C5 carbons of pentose; phosphopentomutase 837056..838255 Dinoroseobacter shibae DFL 12 = DSM 16493 5711455 YP_001532176.1 CDS add NC_009952.1 838252 839247 D catalyzes the formation of inosine from adenosine; adenosine deaminase 838252..839247 Dinoroseobacter shibae DFL 12 = DSM 16493 5711456 YP_001532177.1 CDS upp NC_009952.1 839244 839876 D Catalyzes the formation of uracil and 5-phospho-alpha-D-ribosy 1-diphosphate from UMP and diphosphate; uracil phosphoribosyltransferase 839244..839876 Dinoroseobacter shibae DFL 12 = DSM 16493 5711457 YP_001532178.1 CDS Dshi_0832 NC_009952.1 839877 840893 R conserved in Rhodobacteraceae; hypothetical protein complement(839877..840893) Dinoroseobacter shibae DFL 12 = DSM 16493 5711458 YP_001532179.1 CDS Dshi_0833 NC_009952.1 841358 842983 R putative Acyl-CoA-Ligase (inferred from Swiss-Prot); AMP-dependent synthetase and ligase complement(841358..842983) Dinoroseobacter shibae DFL 12 = DSM 16493 5711459 YP_001532180.1 CDS Dshi_0834 NC_009952.1 843077 843994 D contains 1 N-terminal DUF6-domain; hypothetical protein 843077..843994 Dinoroseobacter shibae DFL 12 = DSM 16493 5711460 YP_001532181.1 CDS fadJ NC_009952.1 844051 846264 R multifunctional enzyme: Enoyl-CoA hydratase/3-hydroxybutyryl-CoA epimerase, Reaction: (3S)-3-Hydroxyacyl-CoA <=> trans-2,3-Dehydroacyl-CoA + H2O, Reaction: (S)-3-hydroxybutanoyl-CoA = (R)-3-hydroxybutanoyl-CoA; 3-hydroxyacyl-CoA dehydrogenase, Reaction(EC:1.1.1.35):(3S)-3-Hydroxyacyl-CoA + NAD+ <=> 3-Oxoacyl-CoA + NADH + H+; 3-hydroxyacyl-CoA dehydrogenase complement(844051..846264) Dinoroseobacter shibae DFL 12 = DSM 16493 5711461 YP_001532182.1 CDS fadA NC_009952.1 846270 847481 R 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 complement(846270..847481) Dinoroseobacter shibae DFL 12 = DSM 16493 5711462 YP_001532183.1 CDS Dshi_0837 NC_009952.1 847493 848128 R not all GST-like proteins show catalytic activity; glutathione S-transferase domain-containing protein complement(847493..848128) Dinoroseobacter shibae DFL 12 = DSM 16493 5711463 YP_001532184.1 CDS Dshi_0838 NC_009952.1 848409 849557 R contains all Acyl-CoA dehydrogenase domains; Reaction: Acyl-CoA + Acceptor <=> 2,3-Dehydroacyl-CoA + Reduced acceptor; acyl-CoA dehydrogenase domain-containing protein complement(848409..849557) Dinoroseobacter shibae DFL 12 = DSM 16493 5711464 YP_001532185.1 CDS Dshi_0839 NC_009952.1 849631 851409 R Oxidoreductase acting on the CH-CH group of donors with other acceptors; acyl-CoA dehydrogenase domain-containing protein complement(849631..851409) Dinoroseobacter shibae DFL 12 = DSM 16493 5711465 YP_001532186.1 CDS Dshi_0840 NC_009952.1 851439 851840 R contains winged helix DNA-binding motif; MerR family; transcriptional regulator complement(851439..851840) Dinoroseobacter shibae DFL 12 = DSM 16493 5711466 YP_001532187.1 CDS Dshi_0841 NC_009952.1 852286 853314 D hypothetical protein 852286..853314 Dinoroseobacter shibae DFL 12 = DSM 16493 5711467 YP_001532188.1 CDS Dshi_0842 NC_009952.1 853357 853728 R contains winged helix DNA-binding motif; MerR family; transcriptional regulator complement(853357..853728) Dinoroseobacter shibae DFL 12 = DSM 16493 5711468 YP_001532189.1 CDS Dshi_0843 NC_009952.1 853842 854276 D thioesterase superfamily protein 853842..854276 Dinoroseobacter shibae DFL 12 = DSM 16493 5711469 YP_001532190.1 CDS Dshi_0844 NC_009952.1 854276 854797 D thioesterase superfamily protein 854276..854797 Dinoroseobacter shibae DFL 12 = DSM 16493 5711470 YP_001532191.1 CDS Dshi_0845 NC_009952.1 854790 856109 D contains two multi antimicrobial extrusion (MATE) domains, drug/sodium antiporter; MATE efflux family protein 854790..856109 Dinoroseobacter shibae DFL 12 = DSM 16493 5711471 YP_001532192.1 CDS arsC NC_009952.1 856144 856491 R related to glutaredoxins, Reaction: Arsenate ion + Glutaredoxin <=> Arsenite + Glutaredoxin disulfide; arsenate reductase complement(856144..856491) Dinoroseobacter shibae DFL 12 = DSM 16493 5711472 YP_001532193.1 CDS pyrD2 NC_009952.1 856488 857546 R 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 complement(856488..857546) Dinoroseobacter shibae DFL 12 = DSM 16493 5711473 YP_001532194.1 CDS Dshi_0848 NC_009952.1 857543 857878 R hypothetical bacterial and plant proteins of unknown function; hypothetical protein complement(857543..857878) Dinoroseobacter shibae DFL 12 = DSM 16493 5711474 YP_001532195.1 CDS Dshi_0849 NC_009952.1 858004 859593 D membrane bound, hydrolyzes extracellular nucleotides into membrane permeable nucleosides, Reaction: 5-Ribonucleotide + H2O <=> Ribonucleoside + Orthophosphate; 5'-nucleotidase 858004..859593 Dinoroseobacter shibae DFL 12 = DSM 16493 5711475 YP_001532196.1 CDS deaD NC_009952.1 859653 861845 R he DEAD box helicases are involved in various aspects of RNA metabolism; DEAD/DEAH box helicase complement(859653..861845) Dinoroseobacter shibae DFL 12 = DSM 16493 5710539 YP_001532197.1 CDS Dshi_0851 NC_009952.1 862042 862707 D contains DUF159 domain; hypothetical protein 862042..862707 Dinoroseobacter shibae DFL 12 = DSM 16493 5710540 YP_001532198.1 CDS msbA NC_009952.1 863045 864853 D ABC transporter with fused ATPase and inner membrane subunits, Involved in lipid A export and inner membrane biogenesis; fused ATPase and inner membrane subunits; lipid A ABC exporter family 863045..864853 Dinoroseobacter shibae DFL 12 = DSM 16493 5710542 YP_001532199.1 CDS fadD2 NC_009952.1 865066 866964 D esterification and transport of exogeneous long chain fatty acids, Reaction: ATP + a long-chain carboxylic acid + CoA <=> AMP + diphosphate + an acyl-CoA; AMP-binding domain-containing protein 865066..866964 Dinoroseobacter shibae DFL 12 = DSM 16493 5710543 YP_001532200.1 CDS Dshi_0854 NC_009952.1 867049 867252 D hypothetical protein 867049..867252 Dinoroseobacter shibae DFL 12 = DSM 16493 5710544 YP_001532201.1 CDS Dshi_0855 NC_009952.1 867282 868169 R belongs to class of conserved hypothetical proteins with N-terminal transglutaminse domain, catalytic activity not proofed; transglutaminase domain-containing protein complement(867282..868169) Dinoroseobacter shibae DFL 12 = DSM 16493 5710545 YP_001532202.1 CDS Dshi_0856 NC_009952.1 868179 870593 R contains DUF404, 407, 403 domains; hypothetical protein complement(868179..870593) Dinoroseobacter shibae DFL 12 = DSM 16493 5710546 YP_001532203.1 CDS Dshi_0857 NC_009952.1 870602 873940 R belongs to clas of conserved hypothetical proteins with N-terminal transglutaminse domain, catalytic activity not proofed; transglutaminase domain-containing protein complement(870602..873940) Dinoroseobacter shibae DFL 12 = DSM 16493 5710547 YP_001532204.1 CDS Dshi_0858 NC_009952.1 874196 874888 R ABC transporter (importer) gene cluster: 2nd ATP binding cassette (ABC) domain; part of a heterotetramer; ABC transporter-like protein complement(874196..874888) Dinoroseobacter shibae DFL 12 = DSM 16493 5710548 YP_001532205.1 CDS Dshi_0859 NC_009952.1 874885 875637 R ABC transporter (importer) gene cluster: 1st ATP binding cassette (ABC) domain; part of a heterotetramer; ABC transporter-like protein complement(874885..875637) Dinoroseobacter shibae DFL 12 = DSM 16493 5710549 YP_001532206.1 CDS Dshi_0860 NC_009952.1 875634 876608 R ABC transporter (importer) gene cluster: 2nd membrane spanning domain (MSD); part of a heterotetramer; inner-membrane translocator complement(875634..876608) Dinoroseobacter shibae DFL 12 = DSM 16493 5710550 YP_001532207.1 CDS Dshi_0861 NC_009952.1 876610 877527 R ABC transporter (importer) gene cluster: 1st membrane spanning domain (MSD); part of a heterotetramer; inner-membrane translocator complement(876610..877527) Dinoroseobacter shibae DFL 12 = DSM 16493 5710551 YP_001532208.1 CDS Dshi_0862 NC_009952.1 877656 878795 R ABC transporter (importer) gene cluster: receptor; extracellular ligand-binding receptor complement(877656..878795) Dinoroseobacter shibae DFL 12 = DSM 16493 5710552 YP_001532209.1 CDS Dshi_0863 NC_009952.1 878828 879064 R helix-turn-helix DNA-binding motif; AsnC family; transcriptional regulator complement(878828..879064) Dinoroseobacter shibae DFL 12 = DSM 16493 5710553 YP_001532210.1 CDS Dshi_0864 NC_009952.1 879279 879737 D putative oxidoreductase; (2Fe-2S)-binding domain-containing protein 879279..879737 Dinoroseobacter shibae DFL 12 = DSM 16493 5710554 YP_001532211.1 CDS Dshi_0865 NC_009952.1 879739 881922 D function not clear, similar to several Swiss-Prot curated proteins; aldehyde oxidase and xanthine dehydrogenase molybdopterin-binding 879739..881922 Dinoroseobacter shibae DFL 12 = DSM 16493 5710555 YP_001532212.1 CDS Dshi_0866 NC_009952.1 882060 882755 D Hydrolase, alpha/beta fold motiv with catalytic triade, weak evidence; alpha/beta hydrolase fold protein 882060..882755 Dinoroseobacter shibae DFL 12 = DSM 16493 5710556 YP_001532213.1 CDS Dshi_0867 NC_009952.1 882752 883624 D contains amidohydrolase 2 domain; amidohydrolase 2 882752..883624 Dinoroseobacter shibae DFL 12 = DSM 16493 5710557 YP_001532214.1 CDS Dshi_0868 NC_009952.1 883631 885007 R peptidase related (trEMBL); putative peptidase complement(883631..885007) Dinoroseobacter shibae DFL 12 = DSM 16493 5710558 YP_001532215.1 CDS Dshi_0869 NC_009952.1 885019 885909 R phosphoesterase related (trEMBL); hypothetical protein complement(885019..885909) Dinoroseobacter shibae DFL 12 = DSM 16493 5710559 YP_001532216.1 CDS Dshi_0870 NC_009952.1 885921 887960 R weak similarity to transcriptional regulator, SARP family, TPR repeats; SARP family; transcriptional regulator complement(885921..887960) Dinoroseobacter shibae DFL 12 = DSM 16493 5710560 YP_001532217.1 CDS Dshi_0871 NC_009952.1 888034 888300 R hypothetical protein complement(888034..888300) Dinoroseobacter shibae DFL 12 = DSM 16493 5710561 YP_001532218.1 CDS Dshi_0872 NC_009952.1 888387 889970 D ABC transporter (importer) gene cluster: receptor (cluster disrupted); family 5 extracellular solute-binding protein 888387..889970 Dinoroseobacter shibae DFL 12 = DSM 16493 5710562 YP_001532219.1 CDS Dshi_0873 NC_009952.1 890141 890812 D hypothetical protein 890141..890812 Dinoroseobacter shibae DFL 12 = DSM 16493 5710563 YP_001532220.1 CDS Dshi_0874 NC_009952.1 890913 891137 D part of extracellular ligand-binding receptor; family 5; extracellular solute-binding protein 890913..891137 Dinoroseobacter shibae DFL 12 = DSM 16493 5710564 YP_001532221.1 CDS Dshi_0875 NC_009952.1 891165 891431 D transposase IS3/IS911 family protein 891165..891431 Dinoroseobacter shibae DFL 12 = DSM 16493 5710565 YP_001532222.1 CDS Dshi_0876 NC_009952.1 891455 892276 D integrase catalytic subunit 891455..892276 Dinoroseobacter shibae DFL 12 = DSM 16493 5710566 YP_001532223.1 CDS Dshi_0877 NC_009952.1 892303 893685 D ABC transporter (importer) gene cluster: receptor, N-terminal truncated; 4-phytase 892303..893685 Dinoroseobacter shibae DFL 12 = DSM 16493 5710567 YP_001532224.1 CDS Dshi_0878 NC_009952.1 894073 894540 R hypothetical protein complement(894073..894540) Dinoroseobacter shibae DFL 12 = DSM 16493 5710568 YP_001532225.1 CDS Dshi_0879 NC_009952.1 895189 895593 R membrane protein complement(895189..895593) Dinoroseobacter shibae DFL 12 = DSM 16493 5710569 YP_001532226.1 CDS Dshi_0880 NC_009952.1 895664 896512 R involved in the bacterial meta-cleavage pathways for degradation of aromatic compounds; hydratase/decarboxylase complement(895664..896512) Dinoroseobacter shibae DFL 12 = DSM 16493 5710570 YP_001532227.1 CDS Dshi_0881 NC_009952.1 896659 897645 D ABC transporter (importer) gene cluster: 1st membrane spanning domain (MSD); part of a heterotetramer; binding-protein-dependent transport system inner membrane protein 896659..897645 Dinoroseobacter shibae DFL 12 = DSM 16493 5710571 YP_001532228.1 CDS Dshi_0882 NC_009952.1 897647 898615 D ABC transporter (importer) gene cluster: 2nd membrane spanning domain (MSD); part of a heterotetramer; binding-protein-dependent transport system inner membrane protein 897647..898615 Dinoroseobacter shibae DFL 12 = DSM 16493 5710572 YP_001532229.1 CDS Dshi_0883 NC_009952.1 898620 898811 R hypothetical protein complement(898620..898811) Dinoroseobacter shibae DFL 12 = DSM 16493 5710573 YP_001532230.1 CDS Dshi_0884 NC_009952.1 899031 900113 D ABC transporter (importer) gene cluster: 1st ATP binding cassette (ABC) domain; part of a heterotetramer; ATPase subunit; oligopeptide/dipeptide ABC transporter 899031..900113 Dinoroseobacter shibae DFL 12 = DSM 16493 5710574 YP_001532231.1 CDS Dshi_0885 NC_009952.1 900110 901078 D ABC transporter (importer) gene cluster: 2nd ATP binding cassette (ABC) domain; part of a heterotetramer; ATPase subunit; oligopeptide/dipeptide ABC transporter 900110..901078 Dinoroseobacter shibae DFL 12 = DSM 16493 5710575 YP_001532232.1 CDS Dshi_0886 NC_009952.1 901082 901924 R Helix-Turn-Helix motif, iclR subfamily; IclR family; transcriptional regulator complement(901082..901924) Dinoroseobacter shibae DFL 12 = DSM 16493 5710576 YP_001532233.1 CDS sgaA2 NC_009952.1 902124 903314 D PLP-dependent enzyme, Reaction: L-serine + glyoxylate <=> 3-hydroxypyruvate + glycine; serine--glyoxylate transaminase 902124..903314 Dinoroseobacter shibae DFL 12 = DSM 16493 5710577 YP_001532234.1 CDS Dshi_0888 NC_009952.1 903322 904296 D PLP dependnet enzyme, catalytic activity not clear, Swiss-Prot hits to serine racemase, threonine dehydratase; pyridoxal-5'-phosphate-dependent protein subunit beta 903322..904296 Dinoroseobacter shibae DFL 12 = DSM 16493 5710578 YP_001532235.1 CDS Dshi_0889 NC_009952.1 904311 905474 D contains N-terminal domain of alanine racemase, C-terminal domain missing; alanine racemase domain-containing protein 904311..905474 Dinoroseobacter shibae DFL 12 = DSM 16493 5710579 YP_001532236.1 CDS Dshi_0890 NC_009952.1 905581 906573 D catalyses the deamination of ornithine to proline, Reaction: L-Ornithine <=> L-Proline + NH3; ornithine cyclodeaminase 905581..906573 Dinoroseobacter shibae DFL 12 = DSM 16493 5710580 YP_001532237.1 CDS cysK NC_009952.1 906667 907749 R PLP-dependent Enzyme, Reaction: O-Acetyl-L-serine + Hydrogen sulfide <=> L-Cysteine + Acetate; cysteine synthase A complement(906667..907749) Dinoroseobacter shibae DFL 12 = DSM 16493 5710581 YP_001532238.1 CDS Dshi_0892 NC_009952.1 908084 909016 D transposase IS4 family protein 908084..909016 Dinoroseobacter shibae DFL 12 = DSM 16493 5710582 YP_001532239.1 CDS Dshi_0893 NC_009952.1 909083 910375 D inner membrane protein; peptidoglycan-binding domain 1 protein 909083..910375 Dinoroseobacter shibae DFL 12 = DSM 16493 5710583 YP_001532240.1 CDS Dshi_0894 NC_009952.1 910592 911965 D inner membrane protein; peptidoglycan-binding domain 1 protein 910592..911965 Dinoroseobacter shibae DFL 12 = DSM 16493 5710584 YP_001532241.1 CDS Dshi_0895 NC_009952.1 912355 914220 D peptidase S1 and S6 chymotrypsin/Hap 912355..914220 Dinoroseobacter shibae DFL 12 = DSM 16493 5710585 YP_001532242.1 CDS Dshi_0896 NC_009952.1 914230 915495 D hypothetical protein 914230..915495 Dinoroseobacter shibae DFL 12 = DSM 16493 5710586 YP_001532243.1 CDS Dshi_0897 NC_009952.1 915495 918620 D Salmonella: activated by the global signal transduction/regulatory system SsrA/B, when in eukaryotic cells; virulence protein SrfB 915495..918620 Dinoroseobacter shibae DFL 12 = DSM 16493 5710587 YP_001532244.1 CDS Dshi_0898 NC_009952.1 918640 921318 D hypothetical protein 918640..921318 Dinoroseobacter shibae DFL 12 = DSM 16493 5710588 YP_001532245.1 CDS Dshi_0899 NC_009952.1 921315 922355 D hypothetical protein 921315..922355 Dinoroseobacter shibae DFL 12 = DSM 16493 5710589 YP_001532246.1 CDS Dshi_0900 NC_009952.1 922370 924292 D hypothetical protein 922370..924292 Dinoroseobacter shibae DFL 12 = DSM 16493 5710590 YP_001532247.1 CDS Dshi_0901 NC_009952.1 924297 925022 D ABC transporter (importer) gene cluster (disrupted): ATP binding cassette (ABC) domain; part of a heterotetramer; ABC transporter-like protein 924297..925022 Dinoroseobacter shibae DFL 12 = DSM 16493 5710591 YP_001532248.1 CDS Dshi_0902 NC_009952.1 925019 926218 D ABC transporter (importer) gene cluster (disrupted): membrane spanning domain (MSD); part of a heterotetramer; hypothetical protein 925019..926218 Dinoroseobacter shibae DFL 12 = DSM 16493 5710592 YP_001532249.1 CDS Dshi_0903 NC_009952.1 926215 927828 D hypothetical protein 926215..927828 Dinoroseobacter shibae DFL 12 = DSM 16493 5710593 YP_001532250.1 CDS Dshi_0904 NC_009952.1 927835 928704 R conserved only in R. denitrificans; hypothetical protein complement(927835..928704) Dinoroseobacter shibae DFL 12 = DSM 16493 5710594 YP_003422326.1 CDS Dshi_5007 NC_009952.1 928897 929556 D hypothetical protein 928897..929556 Dinoroseobacter shibae DFL 12 = DSM 16493 8130632 YP_001532251.1 CDS Dshi_0905 NC_009952.1 929570 930199 D membrane protein, contains a pair of UPF0126 domains; hypothetical protein 929570..930199 Dinoroseobacter shibae DFL 12 = DSM 16493 5710595 YP_001532252.1 CDS Dshi_0906 NC_009952.1 930196 930930 R ABC transporter (importer) gene cluster: membrane spanning domain (MSD); part of a heterotetramer; binding-protein-dependent transport system inner membrane protein complement(930196..930930) Dinoroseobacter shibae DFL 12 = DSM 16493 5710596 YP_001532253.1 CDS Dshi_0907 NC_009952.1 930927 931655 R ABC transporter (importer) gene cluster: 1st ATP binding cassette (ABC) domain; part of a heterotetramer; ABC transporter-like protein complement(930927..931655) Dinoroseobacter shibae DFL 12 = DSM 16493 5710597 YP_001532254.1 CDS Dshi_0908 NC_009952.1 931652 932350 R involved in thiamine biosynthesis; TenA family; transcriptional activator complement(931652..932350) Dinoroseobacter shibae DFL 12 = DSM 16493 5710598 YP_001532255.1 CDS Dshi_0909 NC_009952.1 932347 933282 R ABC transporter (importer) gene cluster: receptor, NMT1/THI5 like domain, involved in Thiamine biosynthesis; NMT1/THI5 like domain-containing protein complement(932347..933282) Dinoroseobacter shibae DFL 12 = DSM 16493 5710599 YP_001532256.1 CDS thiF NC_009952.1 933279 934244 R contains thiF and MoeZ/B-domain; UBA/THIF-type NAD/FAD-binding protein complement(933279..934244) Dinoroseobacter shibae DFL 12 = DSM 16493 5710600 YP_001532257.1 CDS thiE NC_009952.1 934241 934840 R Magnesium dependent, Reaction: 2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphate + 4-Methyl-5-(2-phosphoethyl)-thiazole <=> Pyrophosphate + Thiaminmonophosphate; thiamine-phosphate diphosphorylase complement(934241..934840) Dinoroseobacter shibae DFL 12 = DSM 16493 5710601 YP_001532258.1 CDS thiG NC_009952.1 934837 935631 R Required for the synthesis of the thiazole moiety of thiamine; thiazole biosynthesis family protein complement(934837..935631) Dinoroseobacter shibae DFL 12 = DSM 16493 5710602 YP_001532259.1 CDS Dshi_0913 NC_009952.1 935635 935829 R involved in sulphur transfer; thiamine biosynthesis protein ThiS complement(935635..935829) Dinoroseobacter shibae DFL 12 = DSM 16493 5710603 YP_001532260.1 CDS thiO NC_009952.1 935813 936790 R FAD dependent oxidoreductase, active with glycine, sarcosine, N-ethylglycine, D-alanine, D-alpha-aminobutyrate, D-proline, D-pipecolate and N-methyl-D-alanine; glycine oxidase ThiO complement(935813..936790) Dinoroseobacter shibae DFL 12 = DSM 16493 5710604 YP_001532261.1 CDS thiD NC_009952.1 936787 937584 R cofactor biosynthesis, Reaction: ATP + 4-amino-2-methyl-5-phosphomethylpyrimidine <=> ADP + 4-amino-2-methyl-5-diphosphomethylpyrimidine; phosphomethylpyrimidine kinase complement(936787..937584) Dinoroseobacter shibae DFL 12 = DSM 16493 5710605 YP_001532262.1 CDS Dshi_0916 NC_009952.1 937856 939046 D RND transporters are involved in multidrug resistance and heavy metal resistance. The resistance is performed by H+ driven export of the toxic compounds.; RND family, MFP subunit; efflux transporter 937856..939046 Dinoroseobacter shibae DFL 12 = DSM 16493 5710606 YP_001532263.1 CDS Dshi_0917 NC_009952.1 939057 942221 D RND transporters are involved in multidrug resistance, heavy metal resistance. The resistance is performed by H+ driven export of the toxic compounds.; acriflavin resistance protein 939057..942221 Dinoroseobacter shibae DFL 12 = DSM 16493 5710607 YP_001532264.1 CDS Dshi_0918 NC_009952.1 942472 943404 R belongs to a mostly uncharacterised family of membrane transport proteins found in eukaryotes, bacteria and archaea; auxin efflux carrier complement(942472..943404) Dinoroseobacter shibae DFL 12 = DSM 16493 5710608 YP_001532265.1 CDS Dshi_0919 NC_009952.1 943401 944207 R Metallo-beta-lactamase superfamily, apart from the beta-lactamases a number of other proteins contain this domain; beta-lactamase domain-containing protein complement(943401..944207) Dinoroseobacter shibae DFL 12 = DSM 16493 5710609 YP_001532266.1 CDS Dshi_0920 NC_009952.1 944204 945013 R related to a large superfamily of metalloenzymes, TatD, a member of this family has been shown experimentally to be a DNase enzyme; TatD family; hydrolase complement(944204..945013) Dinoroseobacter shibae DFL 12 = DSM 16493 5710610 YP_001532267.1 CDS Dshi_0921 NC_009952.1 945036 946181 R 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' complement(945036..946181) Dinoroseobacter shibae DFL 12 = DSM 16493 5710611 YP_001532268.1 CDS tmk NC_009952.1 946178 946801 R Phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis, Reaction: ATP + dTMP <=> ADP + dTDP; dTMP kinase complement(946178..946801) Dinoroseobacter shibae DFL 12 = DSM 16493 5710612 YP_001532269.1 CDS dacC1 NC_009952.1 946801 947982 R Removes C-terminal D-alanyl residues from sugar-peptide cell wall precursors, Preferential cleavage: (Ac)2-L-Lys-D-Ala-D-Ala; serine-type D-Ala-D-Ala carboxypeptidase complement(946801..947982) Dinoroseobacter shibae DFL 12 = DSM 16493 5710613 YP_001532270.1 CDS Dshi_0924 NC_009952.1 947994 948800 R contains SPOR domain, involved in binding peptidoglycan; sporulation domain-containing protein complement(947994..948800) Dinoroseobacter shibae DFL 12 = DSM 16493 5710614 YP_001532271.1 CDS Dshi_0925 NC_009952.1 949418 949618 D weak conservation; hypothetical protein 949418..949618 Dinoroseobacter shibae DFL 12 = DSM 16493 5710616 YP_001532272.1 CDS Dshi_0926 NC_009952.1 949670 950479 R integrase catalytic subunit complement(949670..950479) Dinoroseobacter shibae DFL 12 = DSM 16493 5710617 YP_001532273.1 CDS Dshi_0927 NC_009952.1 950503 950730 R transposase IS3/IS911 family protein complement(950503..950730) Dinoroseobacter shibae DFL 12 = DSM 16493 5710618 YP_001532274.1 CDS Dshi_0928 NC_009952.1 950829 951632 R inner membrane protein; hypothetical protein complement(950829..951632) Dinoroseobacter shibae DFL 12 = DSM 16493 5710619 YP_001532275.1 CDS Dshi_0929 NC_009952.1 952573 953553 R contains 2 UspA domains, expression is enhanced when the cell is exposed to stress agents, enhances the rate of cell survival during prolonged exposure to such conditions; UspA domain-containing protein complement(952573..953553) Dinoroseobacter shibae DFL 12 = DSM 16493 5710620 YP_001532276.1 CDS Dshi_0930 NC_009952.1 953550 955277 R Na/H antiporters are key transporters in maintaining the pH of actively metabolising cells; sodium/hydrogen exchanger complement(953550..955277) Dinoroseobacter shibae DFL 12 = DSM 16493 5710621 YP_001532277.1 CDS adhA NC_009952.1 955308 956327 R zinc-containing alcohol dehydrogenase family, Reaction: An alcohol + NAD+ <=> an aldehyde or ketone + NADH; alcohol dehydrogenase GroES domain-containing protein complement(955308..956327) Dinoroseobacter shibae DFL 12 = DSM 16493 5710622 YP_001532278.1 CDS Dshi_0932 NC_009952.1 956341 959109 R members of this ATPase-family are involved in Na+/K+, H+/K+, Ca++ and Mg++ transport; P-type (transporting), HAD superfamily, subfamily IC; ATPase complement(956341..959109) Dinoroseobacter shibae DFL 12 = DSM 16493 5710623 YP_001532279.1 CDS Dshi_0933 NC_009952.1 959106 959327 R weak evidence for function as DNA binding domain, excisionase family; excisionase family; DNA-binding domain-containing protein complement(959106..959327) Dinoroseobacter shibae DFL 12 = DSM 16493 5710624 YP_001532280.1 CDS Dshi_0934 NC_009952.1 959824 960150 D transposase IS3/IS911 family protein 959824..960150 Dinoroseobacter shibae DFL 12 = DSM 16493 5710625 YP_001532281.1 CDS Dshi_0935 NC_009952.1 960258 960719 R hypothetical protein complement(960258..960719) Dinoroseobacter shibae DFL 12 = DSM 16493 5710626 YP_001532282.1 CDS Dshi_0936 NC_009952.1 960784 963285 R exported or inner-membrane bound, catalyzes hydrolization of sulfate from organic compounds; sulfatase complement(960784..963285) Dinoroseobacter shibae DFL 12 = DSM 16493 5710627 YP_001532283.1 CDS Dshi_0937 NC_009952.1 963377 964288 R hypothetical protein complement(963377..964288) Dinoroseobacter shibae DFL 12 = DSM 16493 5710628 YP_001532284.1 CDS Dshi_0938 NC_009952.1 964490 965500 D helix-turn-helix DNA-binding motif; AraC family; transcriptional regulator 964490..965500 Dinoroseobacter shibae DFL 12 = DSM 16493 5710629 YP_001532285.1 CDS Dshi_0939 NC_009952.1 965791 965877 R 28aa of a transposase orfA IS5 family element (normally about 100-120aa); transposase orfA IS5 family element complement(965791..965877) Dinoroseobacter shibae DFL 12 = DSM 16493 5710630 YP_001532286.1 CDS Dshi_0940 NC_009952.1 965987 966301 D hypothetical protein 965987..966301 Dinoroseobacter shibae DFL 12 = DSM 16493 5710631 YP_001532287.1 CDS Dshi_0941 NC_009952.1 966631 967482 D hypothetical protein 966631..967482 Dinoroseobacter shibae DFL 12 = DSM 16493 5710632 YP_001532288.1 CDS Dshi_0942 NC_009952.1 967479 968444 D Members of the M23 peptidase family are zinc-metallopeptidases, most are endopeptidases, inner membrane location: possible function as cell wall peptidase; peptidase M23B 967479..968444 Dinoroseobacter shibae DFL 12 = DSM 16493 5710633 YP_001532289.1 CDS Dshi_0943 NC_009952.1 968525 969388 R contains CAAX amino terminal protease domain; abortive infection protein complement(968525..969388) Dinoroseobacter shibae DFL 12 = DSM 16493 5710634 YP_001532290.1 CDS Dshi_0944 NC_009952.1 969742 970260 R putative transmembrane protein (PSORT); hypothetical protein complement(969742..970260) Dinoroseobacter shibae DFL 12 = DSM 16493 5710635 YP_001532291.1 CDS Dshi_0945 NC_009952.1 970257 971039 R contains C-terminal putative peptidoglycan-binding domain, found in metalloproteases, N-terminus not characterized; peptidoglycan-binding domain 1 protein complement(970257..971039) Dinoroseobacter shibae DFL 12 = DSM 16493 5710636 YP_001532292.1 CDS Dshi_0946 NC_009952.1 971323 971721 R conserved in bacteria; hypothetical protein complement(971323..971721) Dinoroseobacter shibae DFL 12 = DSM 16493 5710637 YP_001532293.1 CDS pthA NC_009952.1 971779 972486 R Enables the recycling of peptidyl-tRNAs produced at termination of translation; peptidyl-tRNA hydrolase complement(971779..972486) Dinoroseobacter shibae DFL 12 = DSM 16493 5710638 YP_001532294.1 CDS lldD2 NC_009952.1 972616 973788 D FMN-dependent dehydrogenase, Reaction: (S)-lactate + 2 ferricytochrome c <=> pyruvate + 2 ferrocytochrome c + 2 H+; cytochrome; L-lactate dehydrogenase 972616..973788 Dinoroseobacter shibae DFL 12 = DSM 16493 5710639 YP_001532295.1 CDS Dshi_0949 NC_009952.1 973840 974457 D hypothetical protein 973840..974457 Dinoroseobacter shibae DFL 12 = DSM 16493 5710640 YP_001532296.1 CDS rplY NC_009952.1 974567 975202 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/general stress protein Ctc 974567..975202 Dinoroseobacter shibae DFL 12 = DSM 16493 5710641 YP_001532297.1 CDS Dshi_0951 NC_009952.1 975412 975882 R hypothetical protein complement(975412..975882) Dinoroseobacter shibae DFL 12 = DSM 16493 5710642 YP_001532298.1 CDS trpA NC_009952.1 976376 977194 R catalyzes the formation of indole and glyceraldehyde 3-phosphate from indoleglycerol phosphate in tryptophan biosynthesis; tryptophan synthase subunit alpha complement(976376..977194) Dinoroseobacter shibae DFL 12 = DSM 16493 5710643 YP_001532299.1 CDS Dshi_0953 NC_009952.1 977230 978582 R contains two multi antimicrobial extrusion (MATE) domains, drug/sodium antiporter; MATE efflux family protein complement(977230..978582) Dinoroseobacter shibae DFL 12 = DSM 16493 5710644 YP_001532300.1 CDS engD NC_009952.1 978833 979930 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 978833..979930 Dinoroseobacter shibae DFL 12 = DSM 16493 5710645 YP_001532301.1 CDS Dshi_0955 NC_009952.1 979967 980662 R similar to predicted racemases; hydantoin racemase complement(979967..980662) Dinoroseobacter shibae DFL 12 = DSM 16493 5710646 YP_001532302.1 CDS Dshi_0956 NC_009952.1 980662 981948 R TRAP gene cluster - dctPQM; DctM subunit; TRAP dicarboxylate transporter complement(980662..981948) Dinoroseobacter shibae DFL 12 = DSM 16493 5710647 YP_001532303.1 CDS Dshi_0957 NC_009952.1 981948 982469 R TRAP gene cluster - dctPQM; tripartite ATP-independent periplasmic transporter subunit DctQ complement(981948..982469) Dinoroseobacter shibae DFL 12 = DSM 16493 5710648 YP_001532304.1 CDS Dshi_0958 NC_009952.1 982492 983472 R TRAP gene cluster - dctPQM; DctP subunit; TRAP dicarboxylate transporter complement(982492..983472) Dinoroseobacter shibae DFL 12 = DSM 16493 5710649 YP_001532305.1 CDS Dshi_0959 NC_009952.1 983690 984535 R helix-turn-helix DNA-binding motif, SIS domain, found in proteins that regulate the expression of genes involved in synthesis of phosphosugars; RpiR family; transcriptional regulator complement(983690..984535) Dinoroseobacter shibae DFL 12 = DSM 16493 5710650 YP_001532306.1 CDS Dshi_0960 NC_009952.1 984738 985418 D N-terminal HTH region, C-terminal FCD effector binding domain; GntR family; transcriptional regulator 984738..985418 Dinoroseobacter shibae DFL 12 = DSM 16493 5710651 YP_001532307.1 CDS Dshi_0961 NC_009952.1 985534 986037 R C-terminal domain is missing, probable pseudogene; catechol dioxygenase domain-containing protein complement(985534..986037) Dinoroseobacter shibae DFL 12 = DSM 16493 5710652 YP_001532308.1 CDS Dshi_0964 NC_009952.1 987364 987915 R hypothetical protein complement(987364..987915) Dinoroseobacter shibae DFL 12 = DSM 16493 5710655 YP_001532309.1 CDS Dshi_0965 NC_009952.1 988027 988380 R hypothetical protein complement(988027..988380) Dinoroseobacter shibae DFL 12 = DSM 16493 5710656 YP_001532310.1 CDS Dshi_0967 NC_009952.1 989049 989933 R FAA is the last enzyme in the tyrosine catabolic pathway; fumarylacetoacetate (FAA) hydrolase complement(989049..989933) Dinoroseobacter shibae DFL 12 = DSM 16493 5710658 YP_001532311.1 CDS Dshi_0968 NC_009952.1 990030 990485 D The majority of proteins in this family consist of a single copy of this domain, though it is also found as a repeat; hypothetical protein 990030..990485 Dinoroseobacter shibae DFL 12 = DSM 16493 5710481 YP_001532312.1 CDS mtlK NC_009952.1 990448 991947 R Reaction: D-mannitol + NAD+ <=> D-fructose + NADH; mannitol dehydrogenase domain-containing protein complement(990448..991947) Dinoroseobacter shibae DFL 12 = DSM 16493 5710482 YP_001532313.1 CDS Dshi_0970 NC_009952.1 991935 992426 R N-terminal truncated; short-chain dehydrogenase/reductase SDR complement(991935..992426) Dinoroseobacter shibae DFL 12 = DSM 16493 5710483 YP_001532314.1 CDS Dshi_0971 NC_009952.1 992438 993442 R ABC transporter (importer) gene cluster: 1st ATP binding cassette (ABC) domain; part of a heterotetramer, no second ABC domain protein, single TOBE domain; ABC transporter-like protein complement(992438..993442) Dinoroseobacter shibae DFL 12 = DSM 16493 5710484 YP_001532315.1 CDS Dshi_0972 NC_009952.1 993455 994285 R ABC transporter (importer) gene cluster: 2nd membrane spanning domain (MSD); part of a heterotetramer; binding-protein-dependent transport system inner membrane protein complement(993455..994285) Dinoroseobacter shibae DFL 12 = DSM 16493 5710485 YP_001532316.1 CDS Dshi_0973 NC_009952.1 994296 995162 R ABC transporter (importer) gene cluster: 1st membrane spanning domain (MSD); part of a heterotetramer; binding-protein-dependent transport system inner membrane protein complement(994296..995162) Dinoroseobacter shibae DFL 12 = DSM 16493 5710486 YP_001532317.1 CDS Dshi_0974 NC_009952.1 995276 996583 R ABC transporter (importer) gene cluster: receptor; family 1 extracellular solute-binding protein complement(995276..996583) Dinoroseobacter shibae DFL 12 = DSM 16493 5710487 YP_001532318.1 CDS Dshi_0975 NC_009952.1 996698 997732 R LacI family; transcriptional regulator complement(996698..997732) Dinoroseobacter shibae DFL 12 = DSM 16493 5710488 YP_001532319.1 CDS Dshi_0976 NC_009952.1 997950 998168 D resolvase-like protein 997950..998168 Dinoroseobacter shibae DFL 12 = DSM 16493 5710489 YP_001532320.1 CDS murA NC_009952.1 998735 1000003 D 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 998735..1000003 Dinoroseobacter shibae DFL 12 = DSM 16493 5710491 YP_001532321.1 CDS Dshi_0978 NC_009952.1 1000000 1000476 D conserved in alphaproteobacteria; hypothetical protein 1000000..1000476 Dinoroseobacter shibae DFL 12 = DSM 16493 5710492 YP_001532322.1 CDS hisD NC_009952.1 1000537 1001853 D catalyzes the oxidation of L-histidinol to L-histidinaldehyde and then to L-histidine in histidine biosynthesis; functions as a dimer; histidinol dehydrogenase 1000537..1001853 Dinoroseobacter shibae DFL 12 = DSM 16493 5710493 YP_001532323.1 CDS Dshi_0980 NC_009952.1 1001850 1002329 D conserved uncharacterized protein; hypothetical protein 1001850..1002329 Dinoroseobacter shibae DFL 12 = DSM 16493 5710494 YP_001532324.1 CDS Dshi_0981 NC_009952.1 1002333 1002788 D function not clear, homology to protein tyrosine phosphatase and arsenate reductase; protein tyrosine phosphatase 1002333..1002788 Dinoroseobacter shibae DFL 12 = DSM 16493 5710495 YP_001532325.1 CDS infA NC_009952.1 1002938 1003156 D stimulates the activities of the other two initiation factors, IF-2 and IF-3; translation initiation factor IF-1 1002938..1003156 Dinoroseobacter shibae DFL 12 = DSM 16493 5710496 YP_001532326.1 CDS Dshi_0983 NC_009952.1 1003159 1003743 D putative inhibitor of septum formation; maf protein 1003159..1003743 Dinoroseobacter shibae DFL 12 = DSM 16493 5710497 YP_001532327.1 CDS Dshi_0984 NC_009952.1 1003740 1004783 D Ribonuclease G and E-like family; ribonuclease 1003740..1004783 Dinoroseobacter shibae DFL 12 = DSM 16493 5710498 YP_001532328.1 CDS Dshi_0985 NC_009952.1 1005574 1005831 R hypothetical protein complement(1005574..1005831) Dinoroseobacter shibae DFL 12 = DSM 16493 5710500 YP_001532329.1 CDS Dshi_0986 NC_009952.1 1006009 1006383 R DNA-binding, putative transcriptional regulator; helix-turn-helix domain-containing protein complement(1006009..1006383) Dinoroseobacter shibae DFL 12 = DSM 16493 5710501 YP_001532330.1 CDS Dshi_0987 NC_009952.1 1006380 1006733 R conserved in bacteria; hypothetical protein complement(1006380..1006733) Dinoroseobacter shibae DFL 12 = DSM 16493 5710502 YP_001532331.1 CDS Dshi_0988 NC_009952.1 1007057 1008169 R Phage integrase proteins cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment; integrase family protein complement(1007057..1008169) Dinoroseobacter shibae DFL 12 = DSM 16493 5710503 YP_001532332.1 CDS Dshi_0989 NC_009952.1 1008195 1008434 R hypothetical protein complement(1008195..1008434) Dinoroseobacter shibae DFL 12 = DSM 16493 5710504 YP_001532333.1 CDS Dshi_0990 NC_009952.1 1009203 1013882 R putative DNA helicase-like protein complement(1009203..1013882) Dinoroseobacter shibae DFL 12 = DSM 16493 5710505 YP_001532334.1 CDS Dshi_0991 NC_009952.1 1014095 1017562 R hypothetical protein complement(1014095..1017562) Dinoroseobacter shibae DFL 12 = DSM 16493 5710506 YP_001532335.1 CDS Dshi_0992 NC_009952.1 1017620 1020436 R protects the organism against invading foreign DNA, part of a heteromeric enzyme complex, mod (modification methyltransferase)subunit is missing; type III restriction protein res subunit complement(1017620..1020436) Dinoroseobacter shibae DFL 12 = DSM 16493 5710507 YP_001532336.1 CDS Dshi_0993 NC_009952.1 1022112 1023083 D TRAP gene cluster - dctPQM; TAXI family; TRAP transporter solute receptor 1022112..1023083 Dinoroseobacter shibae DFL 12 = DSM 16493 5710509 YP_001532337.1 CDS Dshi_0994 NC_009952.1 1023150 1025069 D TRAP gene cluster - dctPQM; 4TM/12TM fusion protein; TRAP transporter 1023150..1025069 Dinoroseobacter shibae DFL 12 = DSM 16493 5710510 YP_001532338.1 CDS Dshi_0995 NC_009952.1 1025066 1025971 R contains substrate binding domain, putative homotetramer; LysR family; transcriptional regulator complement(1025066..1025971) Dinoroseobacter shibae DFL 12 = DSM 16493 5710511 YP_001532339.1 CDS Dshi_0996 NC_009952.1 1026072 1027577 D subunit of NADH dehydrogenase, electron transport chain(ETC) complex I; NADH/Ubiquinone/plastoquinone 1026072..1027577 Dinoroseobacter shibae DFL 12 = DSM 16493 5710512 YP_001532340.1 CDS Dshi_0997 NC_009952.1 1027607 1029982 D putative inner membrane protein; hypothetical protein 1027607..1029982 Dinoroseobacter shibae DFL 12 = DSM 16493 5710513 YP_001532341.1 CDS ade NC_009952.1 1030013 1031707 R Adenine deaminases reaction is important for adenine utilisation as a purine and also as a nitrogen source, Reaction: Adenine + H2O <=> hypoxanthine + NH3, Manganese dependent; adenine deaminase complement(1030013..1031707) Dinoroseobacter shibae DFL 12 = DSM 16493 5710514 YP_001532342.1 CDS Dshi_0999 NC_009952.1 1031760 1032641 R found both in prokaryotes and eukaryotes; related to the human bile acid:sodium symporters; transmembrane proteins; bile acid:sodium symporter complement(1031760..1032641) Dinoroseobacter shibae DFL 12 = DSM 16493 5710515 YP_001532343.1 CDS fadD4 NC_009952.1 1032645 1034366 R esterification and transport of exogeneous long chain fatty acids, Reaction: ATP + a long-chain carboxylic acid + CoA <=> AMP + diphosphate + an acyl-CoA; AMP-dependent synthetase and ligase complement(1032645..1034366) Dinoroseobacter shibae DFL 12 = DSM 16493 5710516 YP_001532344.1 CDS serA2 NC_009952.1 1034458 1035408 R NAD-binding, Reaction: 2-hydroxyglutarate + NAD+ <=> 2-oxoglutarate + NADH; D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding subunit complement(1034458..1035408) Dinoroseobacter shibae DFL 12 = DSM 16493 5710517 YP_001532345.1 CDS metB1 NC_009952.1 1035541 1036683 R PLP-dependent enzyme, Methionine metabolism, Reaction: O4-succinyl-L-homoserine + L-cysteine <=> L-cystathionine + succinate; cystathionine gamma-synthase complement(1035541..1036683) Dinoroseobacter shibae DFL 12 = DSM 16493 5710518 YP_001532346.1 CDS Dshi_1003 NC_009952.1 1036698 1037711 R This family consists of bacterial antibiotic resistance proteins, which confer resistance to various aminoglycosides; aminoglycoside phosphotransferase complement(1036698..1037711) Dinoroseobacter shibae DFL 12 = DSM 16493 5710519 YP_001532347.1 CDS Dshi_1004 NC_009952.1 1037708 1038925 R contains middle and C-terminal domain, N-terminal domain not conserved; acyl-CoA dehydrogenase domain-containing protein complement(1037708..1038925) Dinoroseobacter shibae DFL 12 = DSM 16493 5710520 YP_001532348.1 CDS Dshi_1005 NC_009952.1 1039022 1039978 D This family contains integral membrane proteins with 5 to 6 predicted transmembrane spans. The family include ribonuclease BN that is involved in tRNA maturation. This family of proteins does not seem to contain any completely conserved polar residues that would be expected in a nuclease enzyme, suggesting that many members of this family may not have this catalytic activity; putative ribonuclease BN 1039022..1039978 Dinoroseobacter shibae DFL 12 = DSM 16493 5710521 YP_001532349.1 CDS Dshi_1006 NC_009952.1 1039975 1041198 R The MFS transporters are single-polypeptide secondary carriers capable only of transporting small solutes in response to chemiosmotic ion gradients, similar to tetracycline resistence protein; major facilitator superfamily protein complement(1039975..1041198) Dinoroseobacter shibae DFL 12 = DSM 16493 5710522 YP_001532350.1 CDS catD NC_009952.1 1041475 1042281 R Reaction: 3-oxoadipate enol-lactone + H2O = 3-oxoadipate; 3-oxoadipate enol-lactonase complement(1041475..1042281) Dinoroseobacter shibae DFL 12 = DSM 16493 5710523 YP_001532351.1 CDS fabI1 NC_009952.1 1042293 1043081 R Substrate: acyl-carrier-protein (ACP), Reaction: Acyl-ACP + NAD+ = trans-2,3-dehydroacyl-ACP + NADH; enoyl-(acyl-carrier-protein) reductase complement(1042293..1043081) Dinoroseobacter shibae DFL 12 = DSM 16493 5710524 YP_001532352.1 CDS fabB NC_009952.1 1043106 1044335 R Catalyzes the condensation reaction of fatty acid synthesis by the addition to an acyl acceptor of two carbons from malonyl-ACP. Specific for elongation from C-10 to unsaturated C-16 and C-18 fatty acids, Substrate: acyl-carrier-protein (ACP), Reaction: Acyl-ACP + malonyl-ACP <=> 3-oxoacyl-ACP + CO2 + ACP; beta-ketoacyl synthase complement(1043106..1044335) Dinoroseobacter shibae DFL 12 = DSM 16493 5710525 YP_001532353.1 CDS fabA NC_009952.1 1044358 1044867 R catalyzes the dehydration of (3R)-3-hydroxydecanoyl-ACP to 2,3-decenoyl-ACP or 3,4-decenoyl-ACP; 3-hydroxydecanoyl-ACP dehydratase complement(1044358..1044867) Dinoroseobacter shibae DFL 12 = DSM 16493 5710526 YP_001532354.1 CDS Dshi_1011 NC_009952.1 1045050 1045466 D Fur family includes metal ion uptake regulator proteins, that bind to the operator DNA and controls transcription of metal ion-responsive genes; Fur family; ferric uptake regulator 1045050..1045466 Dinoroseobacter shibae DFL 12 = DSM 16493 5710527 YP_001532355.1 CDS metK NC_009952.1 1045725 1046909 R catalyzes the formation of S-adenosylmethionine from methionine and ATP; methionine adenosyltransferase; S-adenosylmethionine synthetase complement(1045725..1046909) Dinoroseobacter shibae DFL 12 = DSM 16493 5710528 YP_001532356.1 CDS Dshi_1013 NC_009952.1 1046997 1048490 R Transfers the fatty acyl group on membrane lipoproteins; apolipoprotein N-acyltransferase complement(1046997..1048490) Dinoroseobacter shibae DFL 12 = DSM 16493 5710529 YP_001532357.1 CDS Dshi_1014 NC_009952.1 1048493 1049401 R CBS domains have been shown to bind ligands with an adenosyl group such as AMP, ATP and S-AdoMet; hypothetical protein complement(1048493..1049401) Dinoroseobacter shibae DFL 12 = DSM 16493 5710530 YP_001532358.1 CDS Dshi_1015 NC_009952.1 1049443 1049988 R hypothetical protein complement(1049443..1049988) Dinoroseobacter shibae DFL 12 = DSM 16493 5710531 YP_001532359.1 CDS Dshi_1016 NC_009952.1 1049966 1050979 R PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation.; PhoH family protein complement(1049966..1050979) Dinoroseobacter shibae DFL 12 = DSM 16493 5710532 YP_001532360.1 CDS hemB2 NC_009952.1 1051254 1053368 D Fur family includes metal ion uptake regulator proteins, that bind to the operator DNA and controls transcription of metal ion-responsive genes; TonB-dependent heme/hemoglobin receptor family protein 1051254..1053368 Dinoroseobacter shibae DFL 12 = DSM 16493 5710533 YP_001532361.1 CDS Dshi_1018 NC_009952.1 1053428 1053700 D putative inner membrane protein; hypothetical protein 1053428..1053700 Dinoroseobacter shibae DFL 12 = DSM 16493 5710534 YP_001532362.1 CDS Dshi_1019 NC_009952.1 1053712 1055025 R 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 complement(1053712..1055025) Dinoroseobacter shibae DFL 12 = DSM 16493 5710535 YP_001532363.1 CDS Dshi_1020 NC_009952.1 1055162 1056058 D hypothetical protein 1055162..1056058 Dinoroseobacter shibae DFL 12 = DSM 16493 5710536 YP_001532364.1 CDS trmB NC_009952.1 1056510 1057241 D 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 1056510..1057241 Dinoroseobacter shibae DFL 12 = DSM 16493 5710537 YP_001532365.1 CDS aroA NC_009952.1 1057354 1058706 D catalyzes the formation of 5-O-(1-carboxyvinyl)-3-phosphoshikimate from phosphoenolpyruvate and 3-phosphoshikimate in tryptophan biosynthesis; 3-phosphoshikimate 1-carboxyvinyltransferase 1057354..1058706 Dinoroseobacter shibae DFL 12 = DSM 16493 5710538 YP_001532366.1 CDS cmk NC_009952.1 1058724 1059362 D Catalyzes the formation of (d)CDP from ATP and (d)CMP; cytidylate kinase 1058724..1059362 Dinoroseobacter shibae DFL 12 = DSM 16493 5710991 YP_001532367.1 CDS Dshi_1024 NC_009952.1 1059484 1059801 D involved in formation of nucleoid structure and affects gene expression, similar to Rba. capsulatus Puf and Puh operon regulator hvrA; histone family protein nucleoid-structuring protein H-NS 1059484..1059801 Dinoroseobacter shibae DFL 12 = DSM 16493 5710992 YP_001532368.1 CDS rpsA NC_009952.1 1060024 1061700 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 1060024..1061700 Dinoroseobacter shibae DFL 12 = DSM 16493 5710993 YP_001532369.1 CDS Dshi_1026 NC_009952.1 1061749 1062312 R involved in septum formation; intracellular septation protein A complement(1061749..1062312) Dinoroseobacter shibae DFL 12 = DSM 16493 5710994 YP_001532370.1 CDS ihfB NC_009952.1 1062676 1062963 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 1062676..1062963 Dinoroseobacter shibae DFL 12 = DSM 16493 5710995 YP_001532371.1 CDS Dshi_1028 NC_009952.1 1062968 1063333 D conserved in Rhodobacteraceae; hypothetical protein 1062968..1063333 Dinoroseobacter shibae DFL 12 = DSM 16493 5710996 YP_001532372.1 CDS trpF NC_009952.1 1063346 1064032 D tryptophan biosynthesis, Reaction: N-(5-phospho-beta-D-ribosyl)anthranilate <=> 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate; phosphoribosylanthranilate isomerase 1063346..1064032 Dinoroseobacter shibae DFL 12 = DSM 16493 5710997 YP_001532373.1 CDS Dshi_1030 NC_009952.1 1064067 1064297 D hypothetical protein 1064067..1064297 Dinoroseobacter shibae DFL 12 = DSM 16493 5710998 YP_001532374.1 CDS trpB NC_009952.1 1064459 1065691 D catalyzes the formation of L-tryptophan from L-serine and 1-(indol-3-yl)glycerol 3-phosphate; tryptophan synthase subunit beta 1064459..1065691 Dinoroseobacter shibae DFL 12 = DSM 16493 5710999 YP_001532375.1 CDS Dshi_1032 NC_009952.1 1065916 1066362 D structure: signal peptide, Poly-DDR-repeat domain; hypothetical protein 1065916..1066362 Dinoroseobacter shibae DFL 12 = DSM 16493 5711000 YP_001532376.1 CDS Dshi_1033 NC_009952.1 1066444 1066914 D structure: signal peptide, Poly-DDR-repeat domain; hypothetical protein 1066444..1066914 Dinoroseobacter shibae DFL 12 = DSM 16493 5711001 YP_001532377.1 CDS Dshi_1034 NC_009952.1 1066907 1067449 D C-terminal LuxR Helix-Turn-helix motif; LuxR family; transcriptional regulator 1066907..1067449 Dinoroseobacter shibae DFL 12 = DSM 16493 5711002 YP_001532378.1 CDS Dshi_1035 NC_009952.1 1067835 1068809 D TRAP gene cluster - dctPQM; TRAP dicarboxylate transporter subunit DctP 1067835..1068809 Dinoroseobacter shibae DFL 12 = DSM 16493 5711003 YP_001532379.1 CDS Dshi_1036 NC_009952.1 1068862 1069407 D TRAP gene cluster - dctPQM; tripartite ATP-independent periplasmic transporter subunit DctQ 1068862..1069407 Dinoroseobacter shibae DFL 12 = DSM 16493 5711004 YP_001532380.1 CDS Dshi_1037 NC_009952.1 1069438 1070742 D TRAP gene cluster - dctPQM; DctM subunit; TRAP dicarboxylate transporter 1069438..1070742 Dinoroseobacter shibae DFL 12 = DSM 16493 5711005 YP_001532381.1 CDS Dshi_1038 NC_009952.1 1070739 1071509 R Glutamate racemase, which interconverts L-glutamate into D-glutamate, is required for the biosynthesis of peptidoglycan; Asp/Glu racemase complement(1070739..1071509) Dinoroseobacter shibae DFL 12 = DSM 16493 5711006 YP_001532382.1 CDS Dshi_1039 NC_009952.1 1071506 1072714 R Monooxygenases incorporate one hydroxyl group into substrates and are found in many metabolic pathways. In this reaction, two atoms of dioxygen are reduced to one hydroxyl group and one H2O molecule by the concomitant oxidation of NAD(P)H.; monooxygenase FAD-binding complement(1071506..1072714) Dinoroseobacter shibae DFL 12 = DSM 16493 5711007 YP_001532383.1 CDS Dshi_1040 NC_009952.1 1072711 1075002 R high similarity to predicted Carbon-monoxide dehydrogenase proteins; aldehyde oxidase and xanthine dehydrogenase molybdopterin-binding complement(1072711..1075002) Dinoroseobacter shibae DFL 12 = DSM 16493 5711008 YP_001532384.1 CDS Dshi_1041 NC_009952.1 1075005 1076324 R TRAP gene cluster - dctPQM; DctM subunit; TRAP dicarboxylate transporter complement(1075005..1076324) Dinoroseobacter shibae DFL 12 = DSM 16493 5711009 YP_001532385.1 CDS Dshi_1042 NC_009952.1 1076328 1076834 R TRAP gene cluster - dctPQM; tripartite ATP-independent periplasmic transporter subunit DctQ complement(1076328..1076834) Dinoroseobacter shibae DFL 12 = DSM 16493 5711010 YP_001532386.1 CDS Dshi_1043 NC_009952.1 1076851 1077846 R TRAP gene cluster - dctPQM; TRAP dicarboxylate transporter subunit DctP complement(1076851..1077846) Dinoroseobacter shibae DFL 12 = DSM 16493 5711011 YP_001532387.1 CDS Dshi_1044 NC_009952.1 1078350 1079054 D N-terminal HTH region, C-terminal FCD effector binding domain; GntR family; transcriptional regulator 1078350..1079054 Dinoroseobacter shibae DFL 12 = DSM 16493 5711012 YP_001532388.1 CDS Dshi_1045 NC_009952.1 1079051 1079896 D HpcH/HpaI aldolase 1079051..1079896 Dinoroseobacter shibae DFL 12 = DSM 16493 5711013 YP_001532389.1 CDS Dshi_1046 NC_009952.1 1079893 1081023 D contains Amidase signature (AS) motif, AS enzymes catalyse the hydrolysis of amide bonds (CO-NH2); amidase 1079893..1081023 Dinoroseobacter shibae DFL 12 = DSM 16493 5711014 YP_001532390.1 CDS Dshi_1047 NC_009952.1 1081020 1081880 R hypothetical protein complement(1081020..1081880) Dinoroseobacter shibae DFL 12 = DSM 16493 5711015 YP_001532391.1 CDS Dshi_1048 NC_009952.1 1081882 1082679 R Enoyl-CoA hydratase and 3-2trans-enoyl-CoA isomerase are two enzymes involved in fatty acid metabolism; enoyl-CoA hydratase/isomerase complement(1081882..1082679) Dinoroseobacter shibae DFL 12 = DSM 16493 5711016 YP_001532392.1 CDS Dshi_1049 NC_009952.1 1082676 1083461 R large family of oxidoreductases; short chain dehydrogenase complement(1082676..1083461) Dinoroseobacter shibae DFL 12 = DSM 16493 5711017 YP_001532393.1 CDS Dshi_1050 NC_009952.1 1083469 1083843 R hypothetical protein complement(1083469..1083843) Dinoroseobacter shibae DFL 12 = DSM 16493 5711018 YP_001532394.1 CDS Dshi_1051 NC_009952.1 1083833 1085182 R This family includes 2-methylcitrate dehydratase (PrpD) that is required for propionate catabolism. It catalyses the third step of the 2-methylcitric acid cycle.; MmgE/PrpD family protein complement(1083833..1085182) Dinoroseobacter shibae DFL 12 = DSM 16493 5711019 YP_001532395.1 CDS Dshi_1052 NC_009952.1 1085608 1086777 D ABC transporter (importer) gene cluster: receptor; spermidine/putrescine-binding periplasmic protein-like protein 1085608..1086777 Dinoroseobacter shibae DFL 12 = DSM 16493 5711020 YP_001532396.1 CDS Dshi_1053 NC_009952.1 1086781 1087698 D ABC transporter (importer) gene cluster: 1st membrane spanning domain (MSD); part of a heterotetramer; binding-protein-dependent transport system inner membrane protein 1086781..1087698 Dinoroseobacter shibae DFL 12 = DSM 16493 5711021 YP_001532397.1 CDS Dshi_1054 NC_009952.1 1087709 1088599 D ABC transporter (importer) gene cluster: 2nd membrane spanning domain (MSD); part of a heterotetramer; binding-protein-dependent transport system inner membrane protein 1087709..1088599 Dinoroseobacter shibae DFL 12 = DSM 16493 5711022 YP_001532398.1 CDS Dshi_1055 NC_009952.1 1088608 1089708 D ABC transporter (importer) gene cluster (disrupted): ATP binding cassette (ABC) domain; part of a heterotetramer; ABC transporter-like protein 1088608..1089708 Dinoroseobacter shibae DFL 12 = DSM 16493 5711023 YP_001532399.1 CDS Dshi_1056 NC_009952.1 1089720 1090628 D polysaccharide deacetylase 1089720..1090628 Dinoroseobacter shibae DFL 12 = DSM 16493 5711024 YP_001532400.1 CDS Dshi_1057 NC_009952.1 1090625 1091812 D Family III CoA-transferases occur in prokaryotes and eukaryotes, and catalyse CoA-transfer reactions in a highly substrate- and stereo-specific manner; L-carnitine dehydratase/bile acid-inducible protein F 1090625..1091812 Dinoroseobacter shibae DFL 12 = DSM 16493 5711025 YP_001532401.1 CDS Dshi_1058 NC_009952.1 1091824 1093014 D N-terminal, middle and C-terminal domain, Oxidoreductase acting on the CH-CH group of donors with other acceptors; acyl-CoA dehydrogenase domain-containing protein 1091824..1093014 Dinoroseobacter shibae DFL 12 = DSM 16493 5711026 YP_001532402.1 CDS Dshi_1059 NC_009952.1 1093034 1094338 R hypothetical protein complement(1093034..1094338) Dinoroseobacter shibae DFL 12 = DSM 16493 5711027 YP_001532403.1 CDS Dshi_1060 NC_009952.1 1094355 1095233 R hypothetical protein complement(1094355..1095233) Dinoroseobacter shibae DFL 12 = DSM 16493 5711028 YP_001532404.1 CDS Dshi_1061 NC_009952.1 1095405 1096250 R hypothetical protein complement(1095405..1096250) Dinoroseobacter shibae DFL 12 = DSM 16493 5711029 YP_001532405.1 CDS Dshi_1062 NC_009952.1 1096310 1096927 R high similarity to cobalt-zinc-cadmium resistance protein czcN, but no other czc genes in genome, inner membrane protein; isoprenylcysteine carboxyl methyltransferase complement(1096310..1096927) Dinoroseobacter shibae DFL 12 = DSM 16493 5711030 YP_001532406.1 CDS Dshi_1063 NC_009952.1 1097007 1097243 R hypothetical protein complement(1097007..1097243) Dinoroseobacter shibae DFL 12 = DSM 16493 5711031 YP_001532407.1 CDS rufX NC_009952.1 1097236 1097727 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(1097236..1097727) Dinoroseobacter shibae DFL 12 = DSM 16493 5711032 YP_001532408.1 CDS Dshi_1065 NC_009952.1 1098107 1098376 D hypothetical protein 1098107..1098376 Dinoroseobacter shibae DFL 12 = DSM 16493 5711033 YP_001532409.1 CDS Dshi_1066 NC_009952.1 1098458 1098886 D hypothetical protein 1098458..1098886 Dinoroseobacter shibae DFL 12 = DSM 16493 5711034 YP_001532410.1 CDS sod NC_009952.1 1099165 1099764 D Destroys radicals which are normally produced within the cells and which are toxic to biological systems, Reaction: 2 superoxide + 2 H+ = O2 + H2O2; superoxide dismutase 1099165..1099764 Dinoroseobacter shibae DFL 12 = DSM 16493 5711035 YP_001532411.1 CDS Dshi_1068 NC_009952.1 1099844 1100293 R conserved in Rhodobacteraceae; hypothetical protein complement(1099844..1100293) Dinoroseobacter shibae DFL 12 = DSM 16493 5711036 YP_001532412.1 CDS Dshi_1069 NC_009952.1 1100355 1100849 D This family consists of the SufE-related proteins. These have been implicated in Fe-S metabolism and export; Fe-S metabolism associated SufE 1100355..1100849 Dinoroseobacter shibae DFL 12 = DSM 16493 5711037 YP_001532413.1 CDS Dshi_1070 NC_009952.1 1101037 1101669 R hypothetical protein complement(1101037..1101669) Dinoroseobacter shibae DFL 12 = DSM 16493 5711038 YP_001532414.1 CDS Dshi_1071 NC_009952.1 1101666 1102001 R hypothetical protein complement(1101666..1102001) Dinoroseobacter shibae DFL 12 = DSM 16493 5711039 YP_001532415.1 CDS Dshi_1072 NC_009952.1 1101982 1102200 R hypothetical protein complement(1101982..1102200) Dinoroseobacter shibae DFL 12 = DSM 16493 5711040 YP_001532416.1 CDS Dshi_1073 NC_009952.1 1102259 1103038 R contains B12-binding domain, enzymatic domain not present; methionine synthase complement(1102259..1103038) Dinoroseobacter shibae DFL 12 = DSM 16493 5711041 YP_001532417.1 CDS Dshi_1074 NC_009952.1 1103070 1104095 R catalyzes the formation of methionine from L-homocysteine and S-adenosyl-L-methionine; methionine synthase I complement(1103070..1104095) Dinoroseobacter shibae DFL 12 = DSM 16493 5711042 YP_001532418.1 CDS Dshi_1075 NC_009952.1 1104398 1104712 R hypothetical protein complement(1104398..1104712) Dinoroseobacter shibae DFL 12 = DSM 16493 5711043 YP_001532419.1 CDS purC NC_009952.1 1104888 1105649 D 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; phosphoribosylaminoimidazolesuccinocarboxamide synthase 1104888..1105649 Dinoroseobacter shibae DFL 12 = DSM 16493 5711044 YP_001532420.1 CDS purS NC_009952.1 1105786 1106016 D part of heterotrimer with purL(2500131741) and purQ(2500131101), required for enzymatic activity of the complex; phosphoribosylformylglycinamidine synthase 1105786..1106016 Dinoroseobacter shibae DFL 12 = DSM 16493 5711045 YP_001532421.1 CDS Dshi_1078 NC_009952.1 1106016 1107053 D Reaction: An alcohol + NAD+ = an aldehyde or ketone + NADH; alcohol dehydrogenase zinc-binding domain-containing protein 1106016..1107053 Dinoroseobacter shibae DFL 12 = DSM 16493 5711046 YP_001532422.1 CDS purQ NC_009952.1 1107066 1107737 D Part of a heterotrimer with purL(2500131741) and purS(2500131099), Reaction: ATP + N2-formyl-N1-(5-phospho-D-ribosyl)glycinamide + L-glutamine + H2O = ADP + phosphate + 2-(formamido)-N1-(5-phospho-D-ribosyl)acetamidine + L-glutamate; phosphoribosylformylglycinamidine synthase I 1107066..1107737 Dinoroseobacter shibae DFL 12 = DSM 16493 5711047 YP_001532423.1 CDS Dshi_1080 NC_009952.1 1107811 1109568 D integral membrane bound sensor histidine kinase, similar to C4-dicarboxylate transport sensor protein dctB; integral membrane sensor signal transduction histidine kinase 1107811..1109568 Dinoroseobacter shibae DFL 12 = DSM 16493 5711048 YP_001532424.1 CDS Dshi_1081 NC_009952.1 1109596 1110921 D sigma54 specific, similar to C4-dicarboxylate transport transcriptional regulatory protein dctD; sigma54 specific, transcriptional regulator, Fis family; two component 1109596..1110921 Dinoroseobacter shibae DFL 12 = DSM 16493 5711049 YP_001532425.1 CDS ate NC_009952.1 1111025 1111882 R Conjugates Arg from its aminoacyl-tRNA to the N-termini of proteins containing an N-terminal aspartate or glutamate; arginyl-tRNA-protein transferase complement(1111025..1111882) Dinoroseobacter shibae DFL 12 = DSM 16493 5711050 YP_001532426.1 CDS Dshi_1083 NC_009952.1 1111953 1112393 R two transmembrane domains, RDD domain; RDD domain-containing protein complement(1111953..1112393) Dinoroseobacter shibae DFL 12 = DSM 16493 5711051 YP_001532427.1 CDS Dshi_1084 NC_009952.1 1112500 1112910 R hypothetical protein complement(1112500..1112910) Dinoroseobacter shibae DFL 12 = DSM 16493 5711052 YP_001532428.1 CDS Dshi_1085 NC_009952.1 1113043 1113513 R YbaK/prolyl-tRNA synthetase associated domain of unknown funktion; YbaK/prolyl-tRNA synthetase associated domain-containing protein complement(1113043..1113513) Dinoroseobacter shibae DFL 12 = DSM 16493 5711053 YP_001532429.1 CDS Dshi_1086 NC_009952.1 1113620 1114048 D hypothetical protein 1113620..1114048 Dinoroseobacter shibae DFL 12 = DSM 16493 5711054 YP_001532430.1 CDS Dshi_1087 NC_009952.1 1114171 1115130 D TRAP gene cluster - dctPQM; TAXI family; TRAP transporter solute receptor 1114171..1115130 Dinoroseobacter shibae DFL 12 = DSM 16493 5711055 YP_001532431.1 CDS Dshi_1088 NC_009952.1 1115143 1116930 D TRAP gene cluster - dctPQM; 4TM/12TM fusion protein; TRAP transporter 1115143..1116930 Dinoroseobacter shibae DFL 12 = DSM 16493 5711056 YP_001532432.1 CDS Dshi_1089 NC_009952.1 1117014 1118006 D TRAP gene cluster - dctPQM; TRAP dicarboxylate transporter subunit DctP 1117014..1118006 Dinoroseobacter shibae DFL 12 = DSM 16493 5711057 YP_001532433.1 CDS Dshi_1090 NC_009952.1 1118068 1118565 D TRAP gene cluster - dctPQM; tripartite ATP-independent periplasmic transporter subunit DctQ 1118068..1118565 Dinoroseobacter shibae DFL 12 = DSM 16493 5711058 YP_001532434.1 CDS Dshi_1091 NC_009952.1 1118562 1119836 D TRAP gene cluster - dctPQM; DctM subunit; TRAP dicarboxylate transporter 1118562..1119836 Dinoroseobacter shibae DFL 12 = DSM 16493 5711059 YP_001532435.1 CDS Dshi_1092 NC_009952.1 1119841 1120722 D Reaction: 1-Carboxyvinyl carboxyphosphonate <=> 3-(Hydrohydroxyphosphoryl)pyruvate + CO2; carboxyvinyl-carboxyphosphonatephosphorylmutase 1119841..1120722 Dinoroseobacter shibae DFL 12 = DSM 16493 5711060 YP_001532436.1 CDS Dshi_1093 NC_009952.1 1120783 1121310 D hypothetical protein 1120783..1121310 Dinoroseobacter shibae DFL 12 = DSM 16493 5711061 YP_001532437.1 CDS Dshi_1094 NC_009952.1 1121391 1122380 D Domains: GAF (present in phytochromes and cGMP-specific phosphodiesterases), FIS; Fis family; transcriptional regulator 1121391..1122380 Dinoroseobacter shibae DFL 12 = DSM 16493 5711062 YP_001532438.1 CDS Dshi_1095 NC_009952.1 1122494 1124014 D Reaction: An aldehyde + NAD+ + H2O = an acid + NADH; aldehyde dehydrogenase 1122494..1124014 Dinoroseobacter shibae DFL 12 = DSM 16493 5711063 YP_001532439.1 CDS Dshi_1096 NC_009952.1 1124071 1124751 R putative GDSL-like lipase; G-D-S-L; lipolytic protein complement(1124071..1124751) Dinoroseobacter shibae DFL 12 = DSM 16493 5711064 YP_001532440.1 CDS Dshi_1097 NC_009952.1 1124897 1125964 R two YeeE/YedE-domains; hypothetical protein complement(1124897..1125964) Dinoroseobacter shibae DFL 12 = DSM 16493 5711065 YP_001532441.1 CDS Dshi_1098 NC_009952.1 1126077 1127306 D inner membrane single-polypeptide secondary carrier; major facilitator superfamily protein 1126077..1127306 Dinoroseobacter shibae DFL 12 = DSM 16493 5711066 YP_001532442.1 CDS msrA2 NC_009952.1 1127361 1128023 D repairs damaged proteins. Methionine sulfoxide in proteins is reduced to methionine.; peptide methionine sulfoxide reductase 1127361..1128023 Dinoroseobacter shibae DFL 12 = DSM 16493 5711067 YP_001532443.1 CDS prmA NC_009952.1 1128118 1128987 D Methylates ribosomal protein L11; ribosomal L11 methyltransferase 1128118..1128987 Dinoroseobacter shibae DFL 12 = DSM 16493 5711068 YP_001532444.1 CDS Dshi_1101 NC_009952.1 1129052 1129375 D hypothetical protein 1129052..1129375 Dinoroseobacter shibae DFL 12 = DSM 16493 5711069 YP_001532445.1 CDS Dshi_1102 NC_009952.1 1129452 1129649 R hypothetical protein complement(1129452..1129649) Dinoroseobacter shibae DFL 12 = DSM 16493 5711070 YP_001532446.1 CDS ruvC NC_009952.1 1129962 1130492 D endonuclease; resolves Holliday structures; forms a complex of RuvABC; the junction binding protein RuvA forms a hexameric ring along with the RuvB helicase and catalyzes branch migration; RuvC then interacts with RuvAB to resolve the Holliday junction by nicking DNA strands of like polarity; Holliday junction resolvase 1129962..1130492 Dinoroseobacter shibae DFL 12 = DSM 16493 5711071 YP_001532447.1 CDS ruvA NC_009952.1 1130489 1131163 D plays an essential role in ATP-dependent branch migration of the Holliday junction; Holliday junction DNA helicase RuvA 1130489..1131163 Dinoroseobacter shibae DFL 12 = DSM 16493 5711072 YP_001532448.1 CDS ruvB NC_009952.1 1131167 1132240 D 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 1131167..1132240 Dinoroseobacter shibae DFL 12 = DSM 16493 5711073 YP_001532449.1 CDS Dshi_1106 NC_009952.1 1132304 1132930 D conserved in Rhodobacteraceae; hypothetical protein 1132304..1132930 Dinoroseobacter shibae DFL 12 = DSM 16493 5711074 YP_001532450.1 CDS Dshi_1107 NC_009952.1 1132927 1133337 D The significance of this thioesterase to the tol-pal system is unclear; Pol-Pal system-associated acyl-CoA thioesterase 1132927..1133337 Dinoroseobacter shibae DFL 12 = DSM 16493 5711075 YP_001532451.1 CDS tolQ NC_009952.1 1133433 1134107 D outer membrane integrity and transport system Tol-Pal: TolQRAB-Pal; Tol-Pal system protein TolQ 1133433..1134107 Dinoroseobacter shibae DFL 12 = DSM 16493 5711076 YP_001532452.1 CDS tolR NC_009952.1 1134195 1134599 D outer membrane integrity and transport system Tol-Pal: TolQRAB-Pal; biopolymer transport TolR 1134195..1134599 Dinoroseobacter shibae DFL 12 = DSM 16493 5711077 YP_001532453.1 CDS tolA NC_009952.1 1134607 1135662 D outer membrane integrity and transport system Tol-Pal: TolQRAB-Pal; hypothetical protein 1134607..1135662 Dinoroseobacter shibae DFL 12 = DSM 16493 5711078 YP_001532454.1 CDS tolB NC_009952.1 1135659 1136999 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 1135659..1136999 Dinoroseobacter shibae DFL 12 = DSM 16493 5711079 YP_001532455.1 CDS pal NC_009952.1 1137066 1137593 D outer membrane integrity and transport system Tol-Pal: TolQRAB-Pal; peptidoglycan-associated lipoprotein 1137066..1137593 Dinoroseobacter shibae DFL 12 = DSM 16493 5711080 YP_001532456.1 CDS Dshi_1113 NC_009952.1 1137614 1138432 D contains 1 Tetratricopeptide repeat; Tol-Pal system protein YbgF 1137614..1138432 Dinoroseobacter shibae DFL 12 = DSM 16493 5711081 YP_001532457.1 CDS tilS NC_009952.1 1138429 1139682 D Ligates Lysine to a tRNA cytidine, thus changing the amino acid specificity of the tRNA from methionine to isoleucine; tRNA(Ile)-lysidine synthetase 1138429..1139682 Dinoroseobacter shibae DFL 12 = DSM 16493 5711082 YP_001532458.1 CDS ftsH NC_009952.1 1139764 1141680 D membrane-bound ATP-dependent protease universally conserved in prokaryotes; ATP-dependent metalloprotease FtsH 1139764..1141680 Dinoroseobacter shibae DFL 12 = DSM 16493 5711083 YP_001532459.1 CDS Dshi_1116 NC_009952.1 1141820 1142431 D hypothetical protein 1141820..1142431 Dinoroseobacter shibae DFL 12 = DSM 16493 5711084 YP_001532460.1 CDS Dshi_1117 NC_009952.1 1142513 1142929 R thioesterase superfamily protein complement(1142513..1142929) Dinoroseobacter shibae DFL 12 = DSM 16493 5711085 YP_001532461.1 CDS Dshi_1118 NC_009952.1 1142926 1143639 R hypothetical protein complement(1142926..1143639) Dinoroseobacter shibae DFL 12 = DSM 16493 5711086 YP_001532462.1 CDS Dshi_1119 NC_009952.1 1143663 1146086 R contains DEAD/H associated domain; DEAD/DEAH box helicase complement(1143663..1146086) Dinoroseobacter shibae DFL 12 = DSM 16493 5711087 YP_001532463.1 CDS Dshi_1120 NC_009952.1 1146135 1147442 R hypothetical protein complement(1146135..1147442) Dinoroseobacter shibae DFL 12 = DSM 16493 5711088 YP_001532464.1 CDS Dshi_1121 NC_009952.1 1147479 1147988 R peptidase A24A prepilin type IV complement(1147479..1147988) Dinoroseobacter shibae DFL 12 = DSM 16493 5711089 YP_001532465.1 CDS Dshi_1122 NC_009952.1 1147996 1148847 R hypothetical protein complement(1147996..1148847) Dinoroseobacter shibae DFL 12 = DSM 16493 5711090 YP_001532466.1 CDS Dshi_1123 NC_009952.1 1148895 1149425 R contains 2 TPR domains, involved in protein-protein interaction; hypothetical protein complement(1148895..1149425) Dinoroseobacter shibae DFL 12 = DSM 16493 5711091 YP_001532467.1 CDS Dshi_1124 NC_009952.1 1149478 1150473 R type II secretion system protein complement(1149478..1150473) Dinoroseobacter shibae DFL 12 = DSM 16493 5711092 YP_001532468.1 CDS Dshi_1125 NC_009952.1 1150478 1151446 R type II secretion system protein complement(1150478..1151446) Dinoroseobacter shibae DFL 12 = DSM 16493 5711093 YP_001532469.1 CDS Dshi_1126 NC_009952.1 1151449 1152903 R type II secretion system protein E complement(1151449..1152903) Dinoroseobacter shibae DFL 12 = DSM 16493 5711094 YP_001532470.1 CDS Dshi_1127 NC_009952.1 1152923 1154230 R response regulator receiver protein complement(1152923..1154230) Dinoroseobacter shibae DFL 12 = DSM 16493 5711095 YP_001532471.1 CDS Dshi_1128 NC_009952.1 1154427 1155065 R It can function as an adhesin and invasin, participate in biofilm formation, act as both an immune target and evasin, and serves as a receptor for several bacteriophages.; OmpA/MotB domain-containing protein complement(1154427..1155065) Dinoroseobacter shibae DFL 12 = DSM 16493 5711096 YP_001532472.1 CDS Dshi_1129 NC_009952.1 1155070 1156494 R Bacterial type II and III secretion system protein; type II and III secretion system protein complement(1155070..1156494) Dinoroseobacter shibae DFL 12 = DSM 16493 5711097 YP_001532473.1 CDS Dshi_1130 NC_009952.1 1156688 1157530 R Domains: SAF; SAF domain-containing protein complement(1156688..1157530) Dinoroseobacter shibae DFL 12 = DSM 16493 5711098 YP_001532474.1 CDS Dshi_1131 NC_009952.1 1157706 1157918 R conserved in Rhodobacteraceae; hypothetical protein complement(1157706..1157918) Dinoroseobacter shibae DFL 12 = DSM 16493 5711099 YP_001532475.1 CDS Dshi_1132 NC_009952.1 1158153 1158365 R conserved in Rhodobacteraceae; hypothetical protein complement(1158153..1158365) Dinoroseobacter shibae DFL 12 = DSM 16493 5711100 YP_001532476.1 CDS Dshi_1133 NC_009952.1 1158693 1159541 D found in phages, type II, type III and type IV secretion systems; lytic transglycosylase catalytic subunit 1158693..1159541 Dinoroseobacter shibae DFL 12 = DSM 16493 5711101 YP_001532477.1 CDS Dshi_1134 NC_009952.1 1159632 1160258 R Reaction: Succinyl-CoA + a 3-oxo acid <=> succinate + a 3-oxoacyl-CoA; 3-oxoacid CoA-transferase subunit B complement(1159632..1160258) Dinoroseobacter shibae DFL 12 = DSM 16493 5711102 YP_001532478.1 CDS Dshi_1135 NC_009952.1 1160285 1161301 R contains putative PAS photoreceptor domain; putative signal transduction histidine kinase complement(1160285..1161301) Dinoroseobacter shibae DFL 12 = DSM 16493 5711103 YP_001532479.1 CDS Dshi_1136 NC_009952.1 1161319 1162014 R Reaction: Succinyl-CoA + a 3-oxo acid <=> succinate + a 3-oxoacyl-CoA; 3-oxoacid CoA-transferase subunit A complement(1161319..1162014) Dinoroseobacter shibae DFL 12 = DSM 16493 5711104 YP_001532480.1 CDS topA NC_009952.1 1162114 1164816 R catalyzes the ATP-dependent breakage of single-stranded DNA followed by passage and rejoining, maintains net negative superhelicity; DNA topoisomerase I complement(1162114..1164816) Dinoroseobacter shibae DFL 12 = DSM 16493 5711105 YP_001532481.1 CDS Dshi_1138 NC_009952.1 1165063 1166202 R required to protect incoming ssDNA from immediate degradation; DNA protecting protein DprA complement(1165063..1166202) Dinoroseobacter shibae DFL 12 = DSM 16493 5711106 YP_001532482.1 CDS tldD NC_009952.1 1166474 1167895 R Suppresses the inhibitory activity of the carbon storage regulator; peptidase U62 modulator of DNA gyrase complement(1166474..1167895) Dinoroseobacter shibae DFL 12 = DSM 16493 5711107 YP_001532483.1 CDS ctaC NC_009952.1 1168156 1168968 D part of oligomeric enzyme complex in the electron transport chain, transfers electrons from cytochrome c to the catalytic subunit I via hemA and copper; cytochrome c oxidase subunit II 1168156..1168968 Dinoroseobacter shibae DFL 12 = DSM 16493 5711108 YP_001532484.1 CDS ctaB NC_009952.1 1168989 1169975 D converts protoheme IX and farnesyl diphosphate to heme O; protoheme IX farnesyltransferase 1168989..1169975 Dinoroseobacter shibae DFL 12 = DSM 16493 5711109 YP_001532485.1 CDS Dshi_1142 NC_009952.1 1169979 1170164 D hypothetical protein 1169979..1170164 Dinoroseobacter shibae DFL 12 = DSM 16493 5711110 YP_001532486.1 CDS ctaG NC_009952.1 1170161 1170772 D involved in the insertion of copper into subunit I of cytochrome C oxidase; cytochrome C oxidase assembly protein 1170161..1170772 Dinoroseobacter shibae DFL 12 = DSM 16493 5711111 YP_001532487.1 CDS ctaE NC_009952.1 1170794 1171600 D part of oligomeric enzyme complex in the electron transport chain, subunit I and III form the catalytic active compound; cytochrome c oxidase subunit III 1170794..1171600 Dinoroseobacter shibae DFL 12 = DSM 16493 5711112 YP_001532488.1 CDS Dshi_1145 NC_009952.1 1171698 1172399 D similar to SURF1 protein, involved in cox complex assembly; hypothetical protein 1171698..1172399 Dinoroseobacter shibae DFL 12 = DSM 16493 5711113 YP_001532489.1 CDS thrC NC_009952.1 1172413 1173804 D catalyzes the formation of L-threonine from O-phospho-L-homoserine; threonine synthase 1172413..1173804 Dinoroseobacter shibae DFL 12 = DSM 16493 5711114 YP_001532490.1 CDS Dshi_1147 NC_009952.1 1173801 1175081 D uncharacterized zinc protease M16 family; processing peptidase 1173801..1175081 Dinoroseobacter shibae DFL 12 = DSM 16493 5711115 YP_001532491.1 CDS Dshi_1148 NC_009952.1 1175081 1175665 D protein N-Acetyl-transferase; N-acetyltransferase GCN5 1175081..1175665 Dinoroseobacter shibae DFL 12 = DSM 16493 5711116 YP_001532492.1 CDS infC NC_009952.1 1175811 1176419 R IF-3 has several functions that are required and promote translation initiation including; preventing association of 70S by binding to 30S; monitoring codon-anticodon interactions by promoting disassociation of fMet-tRNA(fMet) from initiation complexes formed on leaderless mRNAs or incorrectly bound noninitiatior tRNAs and complexes with noncanonical start sites; stimulates codon-anticodon interactions at P-site; involved in moving mRNA to the P-site; and in recycling subunits; translation initiation factor IF-3 complement(1175811..1176419) Dinoroseobacter shibae DFL 12 = DSM 16493 5711117 YP_001532493.1 CDS Dshi_1150 NC_009952.1 1176572 1177432 R Reaction: 2 reduced ferredoxin + NADP+ <=> 2 oxidized ferredoxin + NADPH; ferredoxin--NADP(+) reductase complement(1176572..1177432) Dinoroseobacter shibae DFL 12 = DSM 16493 5711918 YP_001532494.1 CDS Dshi_1151 NC_009952.1 1177500 1177916 R conserved in bacteria; hypothetical protein complement(1177500..1177916) Dinoroseobacter shibae DFL 12 = DSM 16493 5711919 YP_001532495.1 CDS cysH NC_009952.1 1177913 1178668 R catalyzes the reduction of 3'-phosphoadenylyl sulfate into sulfite; phosphoadenosine phosphosulfate reductase complement(1177913..1178668) Dinoroseobacter shibae DFL 12 = DSM 16493 5711920 YP_001532496.1 CDS cysI NC_009952.1 1178658 1180325 R catalyseses the six-electron reduction of sulphite to sulphide; nitrite/sulfite reductase hemoprotein beta-component ferrodoxin domain-containing protein complement(1178658..1180325) Dinoroseobacter shibae DFL 12 = DSM 16493 5711921 YP_001532497.1 CDS Dshi_1154 NC_009952.1 1180350 1180655 R conserved in Alphaproteobacteria; hypothetical protein complement(1180350..1180655) Dinoroseobacter shibae DFL 12 = DSM 16493 5711922 YP_001532498.1 CDS Dshi_1155 NC_009952.1 1180655 1182040 R For siroheme; for sulfite reductase.; uroporphyrin-III C-methyltransferase complement(1180655..1182040) Dinoroseobacter shibae DFL 12 = DSM 16493 5711923 YP_001532499.1 CDS Dshi_1156 NC_009952.1 1182178 1182645 D Helix-Turn-Helix motif, AsnC/Lrp subfamily; AsnC family; transcriptional regulator 1182178..1182645 Dinoroseobacter shibae DFL 12 = DSM 16493 5711924 YP_001532500.1 CDS Dshi_1157 NC_009952.1 1182730 1184175 R hypothetical protein complement(1182730..1184175) Dinoroseobacter shibae DFL 12 = DSM 16493 5711925 YP_001532501.1 CDS rih NC_009952.1 1184225 1185181 R preference for inosine/uridine; inosine/uridine-preferring nucleoside hydrolase complement(1184225..1185181) Dinoroseobacter shibae DFL 12 = DSM 16493 5711926 YP_001532502.1 CDS Dshi_1159 NC_009952.1 1185626 1186144 D hypothetical protein 1185626..1186144 Dinoroseobacter shibae DFL 12 = DSM 16493 5711927 YP_001532503.1 CDS Dshi_1160 NC_009952.1 1186149 1186988 R contains 2 MazG domains; MazG family protein complement(1186149..1186988) Dinoroseobacter shibae DFL 12 = DSM 16493 5711928 YP_001532504.1 CDS Dshi_1161 NC_009952.1 1187053 1188213 D Degradation of proteins, peptides, and glycopeptides; amidohydrolase 1187053..1188213 Dinoroseobacter shibae DFL 12 = DSM 16493 5711929 YP_001532505.1 CDS Dshi_1162 NC_009952.1 1188220 1191789 R RND transporters are involved in multidrug resistance, heavy metal resistance. The resistance is performed by H+ driven export of the toxic compounds.; acriflavin resistance protein complement(1188220..1191789) Dinoroseobacter shibae DFL 12 = DSM 16493 5711930 YP_001532506.1 CDS Dshi_1163 NC_009952.1 1191786 1192937 R RND transporters are involved in multidrug resistance and heavy metal resistance. The resistance is performed by H+ driven export of the toxic compounds.; RND family, MFP subunit; efflux transporter complement(1191786..1192937) Dinoroseobacter shibae DFL 12 = DSM 16493 5711931 YP_001532507.1 CDS Dshi_1164 NC_009952.1 1193168 1193821 D conserved in Rhodobacteraceae and Rhizobiales; hypothetical protein 1193168..1193821 Dinoroseobacter shibae DFL 12 = DSM 16493 5711932 YP_001532508.1 CDS Dshi_1165 NC_009952.1 1193808 1195160 D contains PQQ repeat domain involved in PQQ binding; pyrrolo-quinoline quinone 1193808..1195160 Dinoroseobacter shibae DFL 12 = DSM 16493 5711933 YP_001532509.1 CDS engA NC_009952.1 1195258 1196730 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 1195258..1196730 Dinoroseobacter shibae DFL 12 = DSM 16493 5711934 YP_001532510.1 CDS Dshi_1167 NC_009952.1 1196727 1198073 R Ste24p and the proteins related to it define a subfamily of proteins that are likely to function as intracellular, membrane-associated zinc metalloproteases; peptidase M48 Ste24p complement(1196727..1198073) Dinoroseobacter shibae DFL 12 = DSM 16493 5711935 YP_001532511.1 CDS Dshi_1168 NC_009952.1 1198126 1199301 D PLP-dependent enzyme; class I/II aminotransferase 1198126..1199301 Dinoroseobacter shibae DFL 12 = DSM 16493 5711936 YP_001532512.1 CDS amiC NC_009952.1 1199349 1200617 D cleaves the amide bond between N-acetylmuramoyl and L-amino acids in bacterial cell walls, probably involved in cell-wall hydrolysis, septation or recycling; N-acetylmuramoyl-L-alanine amidase 1199349..1200617 Dinoroseobacter shibae DFL 12 = DSM 16493 5711937 YP_001532513.1 CDS Dshi_1170 NC_009952.1 1200611 1201234 R SAM dependent enzyme; type 11 methyltransferase complement(1200611..1201234) Dinoroseobacter shibae DFL 12 = DSM 16493 5711938 YP_001532514.1 CDS Dshi_1171 NC_009952.1 1201406 1203928 D penicillin-binding proteins are bifunctional proteins consisting of transglycosylase and transpeptidase in the N- and C-terminus respectively; 1A family; penicillin-binding protein 1201406..1203928 Dinoroseobacter shibae DFL 12 = DSM 16493 5711939 YP_001532515.1 CDS prfB NC_009952.1 1204202 1205329 D 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 1204202..1205329 Dinoroseobacter shibae DFL 12 = DSM 16493 5711940 YP_001532516.1 CDS Dshi_1173 NC_009952.1 1205414 1206421 D proposed to be required for the biosynthesis of the pyrimidine moiety of thiamine; NMT1/THI5 like domain-containing protein 1205414..1206421 Dinoroseobacter shibae DFL 12 = DSM 16493 5711941 YP_001532517.1 CDS Dshi_1174 NC_009952.1 1206505 1207314 D putative inner membrane protein; hypothetical protein 1206505..1207314 Dinoroseobacter shibae DFL 12 = DSM 16493 5711942 YP_001532518.1 CDS Dshi_1175 NC_009952.1 1207399 1207956 R hypothetical protein complement(1207399..1207956) Dinoroseobacter shibae DFL 12 = DSM 16493 5711943 YP_001532519.1 CDS Dshi_1176 NC_009952.1 1207946 1209274 R catalytic activity has not been demonstrated; peptidase M23B complement(1207946..1209274) Dinoroseobacter shibae DFL 12 = DSM 16493 5711944 YP_001532520.1 CDS Dshi_1177 NC_009952.1 1209449 1210306 R hypothetical protein complement(1209449..1210306) Dinoroseobacter shibae DFL 12 = DSM 16493 5711945 YP_001532521.1 CDS Dshi_1178 NC_009952.1 1210336 1210797 R related to alkyl hydroperoxide reductase/ Thiol specific antioxidant; alkyl hydroperoxide reductase complement(1210336..1210797) Dinoroseobacter shibae DFL 12 = DSM 16493 5711946 YP_001532522.1 CDS Dshi_1179 NC_009952.1 1210889 1214206 D putative outer membrane protein; hypothetical protein 1210889..1214206 Dinoroseobacter shibae DFL 12 = DSM 16493 5711947 YP_001532523.1 CDS queA NC_009952.1 1214235 1215296 D Synthesizes oQ from preQ1 in a single S-adenosylmethionine-requiring step; S-adenosylmethionine--tRNA ribosyltransferase-isomerase 1214235..1215296 Dinoroseobacter shibae DFL 12 = DSM 16493 5711948 YP_001532524.1 CDS Dshi_1181 NC_009952.1 1215344 1216738 R Family M20 are Glutamate carboxypeptidases. Peptidase family M25 contains X-His dipeptidases; hypothetical protein complement(1215344..1216738) Dinoroseobacter shibae DFL 12 = DSM 16493 5711949 YP_001532525.1 CDS hemA2 NC_009952.1 1216936 1218159 D catalyzes the formation of 5-aminolevulinate from succinyl-CoA and glycine; 5-aminolevulinate synthase 1216936..1218159 Dinoroseobacter shibae DFL 12 = DSM 16493 5711950 YP_001532526.1 CDS Dshi_1183 NC_009952.1 1218363 1219592 D conserved in Rhodobacteraceae; hypothetical protein 1218363..1219592 Dinoroseobacter shibae DFL 12 = DSM 16493 5711951 YP_001532527.1 CDS ispG NC_009952.1 1219665 1220816 D 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 1219665..1220816 Dinoroseobacter shibae DFL 12 = DSM 16493 5711952 YP_001532528.1 CDS ksgA NC_009952.1 1220983 1221825 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(1220983..1221825) Dinoroseobacter shibae DFL 12 = DSM 16493 5711953 YP_001532529.1 CDS pdxA NC_009952.1 1221827 1222810 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(1221827..1222810) Dinoroseobacter shibae DFL 12 = DSM 16493 5711954 YP_001532530.1 CDS Dshi_1187 NC_009952.1 1222807 1224003 R contains SurA domain and Peptidyl-prolyl cis-trans isomerase domain, periplasmatic; SurA domain-containing protein complement(1222807..1224003) Dinoroseobacter shibae DFL 12 = DSM 16493 5711955 YP_001532531.1 CDS ostA NC_009952.1 1224020 1226170 R involved in outer membrane permeability; organic solvent tolerance protein complement(1224020..1226170) Dinoroseobacter shibae DFL 12 = DSM 16493 5711956 YP_001532532.1 CDS Dshi_1189 NC_009952.1 1226167 1227264 R permease YjgP/YjgQ family of unknown function; YjgP/YjgQ family permease complement(1226167..1227264) Dinoroseobacter shibae DFL 12 = DSM 16493 5711957 YP_001532533.1 CDS Dshi_1190 NC_009952.1 1227261 1228403 R permease YjgP/YjgQ family of unknown function; YjgP/YjgQ family permease complement(1227261..1228403) Dinoroseobacter shibae DFL 12 = DSM 16493 5711958 YP_001532534.1 CDS pepA1 NC_009952.1 1228563 1230029 D catalyzes the removal of N-terminal amino acids preferably leucine from various peptides; leucyl aminopeptidase 1228563..1230029 Dinoroseobacter shibae DFL 12 = DSM 16493 5711959 YP_001532535.1 CDS holC NC_009952.1 1230035 1230490 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 1230035..1230490 Dinoroseobacter shibae DFL 12 = DSM 16493 5711960 YP_001532536.1 CDS Dshi_1193 NC_009952.1 1230737 1231909 R Cytochrome P450 enzymes are a superfamily of haem-containing mono-oxygenase; cytochrome P450 complement(1230737..1231909) Dinoroseobacter shibae DFL 12 = DSM 16493 5711961 YP_001532537.1 CDS Dshi_1194 NC_009952.1 1231911 1234142 R TRAP gene cluster - dctPQM; 4TM/12TM fusion protein; TRAP transporter complement(1231911..1234142) Dinoroseobacter shibae DFL 12 = DSM 16493 5711962 YP_001532538.1 CDS Dshi_1195 NC_009952.1 1234239 1235231 R TRAP gene cluster - dctPQM; TAXI family; TRAP transporter solute receptor complement(1234239..1235231) Dinoroseobacter shibae DFL 12 = DSM 16493 5711963 YP_001532539.1 CDS dctD NC_009952.1 1235704 1237050 R Member of the two-component regulatory system dctB/dctD involved in the transport of C4-dicarboxylates. When activated by dctB acts in conjunction with sigma-54 to activate the transcription of dctA.; Fis family; two component, sigma-54 specific, transcriptional regulator complement(1235704..1237050) Dinoroseobacter shibae DFL 12 = DSM 16493 5711964 YP_001532540.1 CDS dctB NC_009952.1 1237047 1238915 R Member of the two-component regulatory system dctB/dctD involved in the transport of C4-dicarboxylates. DctB functions as a membrane-associated protein kinase that phosphorylates dctD in response to environmental signals.; integral membrane sensor signal transduction histidine kinase complement(1237047..1238915) Dinoroseobacter shibae DFL 12 = DSM 16493 5711965 YP_001532541.1 CDS Dshi_1198 NC_009952.1 1238964 1239965 R beta-lactamase complement(1238964..1239965) Dinoroseobacter shibae DFL 12 = DSM 16493 5711966 YP_001532542.1 CDS suhB1 NC_009952.1 1240118 1240912 D Mg-dependent, Reaction: Myo-inositol phosphate + H2O = myo-inositol + phosphate; inositol-phosphate phosphatase 1240118..1240912 Dinoroseobacter shibae DFL 12 = DSM 16493 5711967 YP_001532543.1 CDS Dshi_1200 NC_009952.1 1240915 1241691 R putative inner membrane serine protease; rhomboid family protein complement(1240915..1241691) Dinoroseobacter shibae DFL 12 = DSM 16493 5711968 YP_001532544.1 CDS Dshi_1201 NC_009952.1 1241780 1242331 D 2 TPR, TPR mediates protein-protein interactions and the assembly of multiprotein complexes; hypothetical protein 1241780..1242331 Dinoroseobacter shibae DFL 12 = DSM 16493 5711969 YP_001532545.1 CDS Dshi_1202 NC_009952.1 1242487 1243116 R contains DnaJ-Domain, wich mediats interaction with DnaK in heat shock proteins; heat shock protein DnaJ domain-containing protein complement(1242487..1243116) Dinoroseobacter shibae DFL 12 = DSM 16493 5711971 YP_001532546.1 CDS Dshi_1203 NC_009952.1 1243189 1243446 D In E. coli overexpression of this protein causes round morphology; BolA family protein 1243189..1243446 Dinoroseobacter shibae DFL 12 = DSM 16493 5711972 YP_001532547.1 CDS Dshi_1204 NC_009952.1 1243456 1243872 R conserved in Rhodobacteraceae; hypothetical protein complement(1243456..1243872) Dinoroseobacter shibae DFL 12 = DSM 16493 5711762 YP_001532548.1 CDS Dshi_1205 NC_009952.1 1244215 1244763 D hypothetical protein 1244215..1244763 Dinoroseobacter shibae DFL 12 = DSM 16493 5711763 YP_001532549.1 CDS Dshi_1206 NC_009952.1 1245054 1245302 R hypothetical protein complement(1245054..1245302) Dinoroseobacter shibae DFL 12 = DSM 16493 5711764 YP_001532550.1 CDS gatB NC_009952.1 1245310 1246827 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(1245310..1246827) Dinoroseobacter shibae DFL 12 = DSM 16493 5711765 YP_001532551.1 CDS Dshi_1208 NC_009952.1 1247009 1247605 D hypothetical protein 1247009..1247605 Dinoroseobacter shibae DFL 12 = DSM 16493 5711766 YP_001532552.1 CDS coxC NC_009952.1 1247697 1248803 D integral membrane sensor and DNA-binding protein; putative integral membrane sensor protein 1247697..1248803 Dinoroseobacter shibae DFL 12 = DSM 16493 5711767 YP_001532553.1 CDS coxM NC_009952.1 1249012 1249866 D Aerobic-type carbon monoxide dehydrogenase, middle subunit, part of heterotrimer coxLMS; molybdopterin dehydrogenase FAD-binding 1249012..1249866 Dinoroseobacter shibae DFL 12 = DSM 16493 5711768 YP_001532554.1 CDS coxS NC_009952.1 1249879 1250370 D Aerobic-type carbon monoxide dehydrogenase, small subunit, part of heterotrimer coxLMS, (2Fe-2S)-binding; (2Fe-2S)-binding domain-containing protein 1249879..1250370 Dinoroseobacter shibae DFL 12 = DSM 16493 5711769 YP_001532555.1 CDS coxL2 NC_009952.1 1250367 1252787 D Aerobic-type carbon monoxide dehydrogenase, large subunit, part of heterotrimer coxLMS; carbon-monoxide dehydrogenase large subunit 1250367..1252787 Dinoroseobacter shibae DFL 12 = DSM 16493 5711770 YP_001532556.1 CDS coxD NC_009952.1 1252829 1253737 D ATPase activity; ATPase 1252829..1253737 Dinoroseobacter shibae DFL 12 = DSM 16493 5711771 YP_001532557.1 CDS coxE NC_009952.1 1253734 1254912 D Protein containing von Willebrand factor type A (vWA) domain; VWA containing CoxE family protein 1253734..1254912 Dinoroseobacter shibae DFL 12 = DSM 16493 5711772 YP_001532558.1 CDS coxF NC_009952.1 1254912 1255724 D hypothetical protein 1254912..1255724 Dinoroseobacter shibae DFL 12 = DSM 16493 5711773 YP_001532559.1 CDS panE NC_009952.1 1255823 1256800 R ketopantoate reductase; catalyzes the NADPH reduction of ketopantoate to pantoate; functions in pantothenate (vitamin B5) biosynthesis; 2-dehydropantoate 2-reductase complement(1255823..1256800) Dinoroseobacter shibae DFL 12 = DSM 16493 5711774 YP_001532560.1 CDS Dshi_1217 NC_009952.1 1256903 1258444 R putative acyl-coA synthetase; AMP-dependent synthetase and ligase complement(1256903..1258444) Dinoroseobacter shibae DFL 12 = DSM 16493 5711775 YP_001532561.1 CDS Dshi_1218 NC_009952.1 1258541 1260055 R hypothetical protein complement(1258541..1260055) Dinoroseobacter shibae DFL 12 = DSM 16493 5711776 YP_001532562.1 CDS Dshi_1219 NC_009952.1 1260068 1260553 R conserved in Rhodobacteraceae; hypothetical protein complement(1260068..1260553) Dinoroseobacter shibae DFL 12 = DSM 16493 5711777 YP_001532563.1 CDS Dshi_1220 NC_009952.1 1260637 1261623 R hypothetical protein complement(1260637..1261623) Dinoroseobacter shibae DFL 12 = DSM 16493 5711778 YP_001532564.1 CDS Dshi_1221 NC_009952.1 1261791 1263197 D Helix-Turn-Helix motif, XRE family, Domain of unknown funktion DUF955; XRE family; transcriptional regulator 1261791..1263197 Dinoroseobacter shibae DFL 12 = DSM 16493 5711779 YP_001532565.1 CDS Dshi_1222 NC_009952.1 1263528 1264271 R most enzymes of this family are NAD/NADP-dependent oxidoreductases; short-chain dehydrogenase/reductase SDR complement(1263528..1264271) Dinoroseobacter shibae DFL 12 = DSM 16493 5711780 YP_001532566.1 CDS pepN NC_009952.1 1264297 1266852 R involved in the degradation of intracellular peptides generated by protein breakdown during normal growth or in response to nutrient starvation, Release of an N-terminal amino acid, Xaa-|-Yaa- from a peptide, amide or arylamide. Xaa is preferably Ala, but may be most amino acids including Pro (slow action).; aminopeptidase N complement(1264297..1266852) Dinoroseobacter shibae DFL 12 = DSM 16493 5711781 YP_001532567.1 CDS Dshi_1224 NC_009952.1 1267060 1267575 D hypothetical protein 1267060..1267575 Dinoroseobacter shibae DFL 12 = DSM 16493 5711782 YP_001532568.1 CDS Dshi_1225 NC_009952.1 1267586 1269130 D Photolyase/Cryptochrome family protein, catalytic activity not proved; deoxyribodipyrimidine photo-lyase 1267586..1269130 Dinoroseobacter shibae DFL 12 = DSM 16493 5711783 YP_001532569.1 CDS Dshi_1226 NC_009952.1 1269139 1269306 D hypothetical protein 1269139..1269306 Dinoroseobacter shibae DFL 12 = DSM 16493 5711784 YP_001532570.1 CDS glcB NC_009952.1 1269474 1271648 D catalyzes the formation of malate from glyoxylate and acetyl-CoA; malate synthase G 1269474..1271648 Dinoroseobacter shibae DFL 12 = DSM 16493 5711785 YP_001532571.1 CDS Dshi_1228 NC_009952.1 1271732 1272154 D hypothetical protein 1271732..1272154 Dinoroseobacter shibae DFL 12 = DSM 16493 5711786 YP_001532572.1 CDS Dshi_1229 NC_009952.1 1272260 1273039 D gamma-glutamyl hydrolase activity; peptidase C26 1272260..1273039 Dinoroseobacter shibae DFL 12 = DSM 16493 5711787 YP_001532573.1 CDS Dshi_1230 NC_009952.1 1273036 1274217 R Catalyzes the cleavage of L-kynurenine and L-3-hydroxykynurenine, PLP-dependent; kynureninase complement(1273036..1274217) Dinoroseobacter shibae DFL 12 = DSM 16493 5711788 YP_001532574.1 CDS Dshi_1231 NC_009952.1 1274344 1275300 D domain weakly conserved; beta-lactamase domain-containing protein 1274344..1275300 Dinoroseobacter shibae DFL 12 = DSM 16493 5711789 YP_001532575.1 CDS Dshi_1232 NC_009952.1 1275516 1275992 D predicted domain weakly conserved; isoprenylcysteine carboxyl methyltransferase family protein 1275516..1275992 Dinoroseobacter shibae DFL 12 = DSM 16493 5711790 YP_001532576.1 CDS pntA NC_009952.1 1276126 1277742 D 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 1276126..1277742 Dinoroseobacter shibae DFL 12 = DSM 16493 5711791 YP_001532577.1 CDS pntB NC_009952.1 1277755 1279251 D transhydrogenation between NADH and NADP is coupled to respiration and ATP hydrolysis and functions as a proton pump across the membrane, heterodimer pntA/B; AB-specific; NAD(P)(+) transhydrogenase 1277755..1279251 Dinoroseobacter shibae DFL 12 = DSM 16493 5711792 YP_001532578.1 CDS xylB1 NC_009952.1 1279366 1280808 D Reaction: ATP + D-xylulose = ADP + D-xylulose 5-phosphate; xylulokinase 1279366..1280808 Dinoroseobacter shibae DFL 12 = DSM 16493 5711793 YP_001532579.1 CDS dmsC NC_009952.1 1280772 1281659 R dimethyl sulphoxide reductase is a heterotrimeric enzyme, composed of a membrane extrinsic catalytic dimer (DmsAB) and a membrane intrinsic polytopic anchor subunit (DmsC); DMSO reductase anchor subunit complement(1280772..1281659) Dinoroseobacter shibae DFL 12 = DSM 16493 5711794 YP_001532580.1 CDS dmsB NC_009952.1 1281663 1282409 R dimethyl sulphoxide reductase is a heterotrimeric enzyme, composed of a membrane extrinsic catalytic dimer (DmsAB) and a membrane intrinsic polytopic anchor subunit (DmsC), 4Fe-4S ferredoxin iron-sulfur binding domain protein; 4Fe-4S ferredoxin complement(1281663..1282409) Dinoroseobacter shibae DFL 12 = DSM 16493 5711795 YP_001532581.1 CDS dmsA2 NC_009952.1 1282492 1285278 R dimethyl sulphoxide reductase is a heterotrimeric enzyme, composed of a membrane extrinsic catalytic dimer (DmsAB) and a membrane intrinsic polytopic anchor subunit (DmsC), molybdopterin oxidoreductase Fe4S4 region; molybdopterin oxidoreductase Fe4S4 region complement(1282492..1285278) Dinoroseobacter shibae DFL 12 = DSM 16493 5711796 YP_001532582.1 CDS lacZ NC_009952.1 1285260 1287167 R Hydrolysis of terminal non-reducing beta-D-galactose residues in beta-D-galactosides, homotrimer; beta-galactosidase complement(1285260..1287167) Dinoroseobacter shibae DFL 12 = DSM 16493 5711797 YP_001532583.1 CDS Dshi_1240 NC_009952.1 1287164 1288024 R domain found in various proteins; SMP-30/gluconolaconase/LRE domain-containing protein complement(1287164..1288024) Dinoroseobacter shibae DFL 12 = DSM 16493 5711798 YP_001532584.1 CDS dgoA NC_009952.1 1288021 1288626 R Keto-hydroxyglutarate-aldolase/keto-deoxy- phosphogluconate aldolase; KDPG and KHG aldolase complement(1288021..1288626) Dinoroseobacter shibae DFL 12 = DSM 16493 5711799 YP_001532585.1 CDS dgoK NC_009952.1 1288623 1289519 R catalyses the second step in D-galactonate degradation; 2-dehydro-3-deoxygalactonokinase complement(1288623..1289519) Dinoroseobacter shibae DFL 12 = DSM 16493 5711800 YP_001532586.1 CDS Dshi_1243 NC_009952.1 1289516 1290292 R large family of oxidoreductases, NAD, NADP-dependent; short-chain dehydrogenase/reductase SDR complement(1289516..1290292) Dinoroseobacter shibae DFL 12 = DSM 16493 5711801 YP_001532587.1 CDS ilvD2 NC_009952.1 1290292 1292001 R catalyzes the formation of 3-methyl-2-oxobutanoate from 2,3,-dihydroxy-3-methylbutanoate; dihydroxy-acid dehydratase complement(1290292..1292001) Dinoroseobacter shibae DFL 12 = DSM 16493 5711802 YP_001532588.1 CDS melA NC_009952.1 1292045 1293385 R glycoside hydrolase family 4 protein, Hydrolysis of terminal, non-reducing alpha-D-galactose residues, NAD and Mn-dependent; glycoside hydrolase family protein complement(1292045..1293385) Dinoroseobacter shibae DFL 12 = DSM 16493 5711803 YP_001532589.1 CDS Dshi_1246 NC_009952.1 1293382 1294230 R ABC-type sugar transport system, permease component, no ATPase in cluster; binding-protein-dependent transport system inner membrane protein complement(1293382..1294230) Dinoroseobacter shibae DFL 12 = DSM 16493 5711804 YP_001532590.1 CDS Dshi_1247 NC_009952.1 1294232 1295158 R ABC-type sugar transport system, permease component, no ATPase in cluster; binding-protein-dependent transport system inner membrane protein complement(1294232..1295158) Dinoroseobacter shibae DFL 12 = DSM 16493 5711805 YP_001532591.1 CDS Dshi_1248 NC_009952.1 1295236 1296480 R ABC-type sugar transport system, ligand binding component, no ATPase in cluster; family 1 extracellular solute-binding protein complement(1295236..1296480) Dinoroseobacter shibae DFL 12 = DSM 16493 5711806 YP_001532592.1 CDS Dshi_1249 NC_009952.1 1296622 1297437 D Helix-Turn-Helix motif, iclR subfamily; IclR family; transcriptional regulator 1296622..1297437 Dinoroseobacter shibae DFL 12 = DSM 16493 5711807 YP_001532593.1 CDS Dshi_1250 NC_009952.1 1297453 1298508 D ABC transporter (importer) gene cluster (disrupted): ATP binding cassette (ABC) domain; part of a heterotetramer; ABC transporter-like protein 1297453..1298508 Dinoroseobacter shibae DFL 12 = DSM 16493 5711808 YP_001532594.1 CDS Dshi_1251 NC_009952.1 1298515 1298802 R hypothetical protein complement(1298515..1298802) Dinoroseobacter shibae DFL 12 = DSM 16493 5711809 YP_001532595.1 CDS Dshi_1252 NC_009952.1 1299255 1299977 R hypothetical protein complement(1299255..1299977) Dinoroseobacter shibae DFL 12 = DSM 16493 5711810 YP_001532596.1 CDS Dshi_1253 NC_009952.1 1300089 1300952 D putative protein-phosphotyrosine-phosphatase activity, ArsR family regulators are sensitive to metal ions; ArsR family; transcriptional regulator 1300089..1300952 Dinoroseobacter shibae DFL 12 = DSM 16493 5711811 YP_001532597.1 CDS Dshi_1254 NC_009952.1 1300949 1301971 D tetrameric NAD-binding enzyme involved in glycolysis and glyconeogenesis; type I; glyceraldehyde-3-phosphate dehydrogenase 1300949..1301971 Dinoroseobacter shibae DFL 12 = DSM 16493 5711812 YP_001532598.1 CDS Dshi_1255 NC_009952.1 1301968 1303236 D The MFS transporters are single-polypeptide secondary carriers capable only of transporting small solutes in response to chemiosmotic ion gradients; major facilitator superfamily protein 1301968..1303236 Dinoroseobacter shibae DFL 12 = DSM 16493 5711813 YP_001532599.1 CDS Dshi_1256 NC_009952.1 1303304 1303924 D the exo genes are involved in exopolysaccharide biosynthesis, exoD of Rhizobium meliloti encodes a function needed for alfalfa nodule invasion; exopolysaccharide synthesis ExoD 1303304..1303924 Dinoroseobacter shibae DFL 12 = DSM 16493 5711814 YP_001532600.1 CDS Dshi_1257 NC_009952.1 1303935 1304216 R hypothetical protein complement(1303935..1304216) Dinoroseobacter shibae DFL 12 = DSM 16493 5711815 YP_001532601.1 CDS Dshi_1258 NC_009952.1 1304262 1305005 D most enzymes of this family are NAD/NADP-dependent oxidoreductases; short-chain dehydrogenase/reductase SDR 1304262..1305005 Dinoroseobacter shibae DFL 12 = DSM 16493 5711816 YP_001532602.1 CDS Dshi_1259 NC_009952.1 1305092 1307596 D heavy metal translocating P-type ATPase 1305092..1307596 Dinoroseobacter shibae DFL 12 = DSM 16493 5711817 YP_001532603.1 CDS Dshi_1260 NC_009952.1 1307607 1308002 D contains winged helix DNA-binding motif; MerR family; transcriptional regulator 1307607..1308002 Dinoroseobacter shibae DFL 12 = DSM 16493 5711818 YP_001532604.1 CDS gltS NC_009952.1 1308092 1309300 D sodium-dependent uptake of extracellular glutamate; sodium/glutamate symporter 1308092..1309300 Dinoroseobacter shibae DFL 12 = DSM 16493 5711819 YP_001532605.1 CDS Dshi_1262 NC_009952.1 1309307 1312360 R RND transporters are involved in multidrug resistance, heavy metal resistance. The resistance is performed by H+ driven export of the toxic compounds.; acriflavin resistance protein complement(1309307..1312360) Dinoroseobacter shibae DFL 12 = DSM 16493 5711820 YP_001532606.1 CDS Dshi_1263 NC_009952.1 1312365 1313612 R RND transporters are involved in multidrug resistance and heavy metal resistance. The resistance is performed by H+ driven export of the toxic compounds.; RND family, MFP subunit; efflux transporter complement(1312365..1313612) Dinoroseobacter shibae DFL 12 = DSM 16493 5711821 YP_001532607.1 CDS Dshi_1264 NC_009952.1 1313689 1314135 D two membrane helix type ion channel; ion transport 2 domain-containing protein 1313689..1314135 Dinoroseobacter shibae DFL 12 = DSM 16493 5711822 YP_001532608.1 CDS idhA NC_009952.1 1314155 1315138 R carbohydrate degradation; inositol 2-dehydrogenase complement(1314155..1315138) Dinoroseobacter shibae DFL 12 = DSM 16493 5711823 YP_001532609.1 CDS fbaA NC_009952.1 1315135 1315977 R zinc-dependent, homodimeric enzyme; ketose-bisphosphate aldolase complement(1315135..1315977) Dinoroseobacter shibae DFL 12 = DSM 16493 5711824 YP_001532610.1 CDS iolB NC_009952.1 1315974 1316834 R hypothetical protein complement(1315974..1316834) Dinoroseobacter shibae DFL 12 = DSM 16493 5711825 YP_001532611.1 CDS iolC NC_009952.1 1316838 1317839 R putative enzyme involved in myo-inositol catabolism; PfkB domain-containing protein complement(1316838..1317839) Dinoroseobacter shibae DFL 12 = DSM 16493 5711826 YP_001532612.1 CDS iolD NC_009952.1 1317836 1319701 R putative enzyme involved in myo-inositol catabolism, Thiamine-dependent; thiamine pyrophosphate protein central region complement(1317836..1319701) Dinoroseobacter shibae DFL 12 = DSM 16493 5711827 YP_001532613.1 CDS Dshi_1270 NC_009952.1 1319800 1320918 D NAD-dependent oxidoreductase; oxidoreductase domain-containing protein 1319800..1320918 Dinoroseobacter shibae DFL 12 = DSM 16493 5711828 YP_001532614.1 CDS Dshi_1271 NC_009952.1 1320915 1321811 D putative enzyme involved in myo-inositol catabolism; xylose isomerase domain-containing protein 1320915..1321811 Dinoroseobacter shibae DFL 12 = DSM 16493 5711829 YP_001532615.1 CDS Dshi_1272 NC_009952.1 1321819 1322952 D NAD-dependent oxidoreductase; oxidoreductase domain-containing protein 1321819..1322952 Dinoroseobacter shibae DFL 12 = DSM 16493 5711830 YP_001532616.1 CDS Dshi_1273 NC_009952.1 1322983 1323981 R Helix-Turn-Helix motif, Sugar -binding domain; LacI family; transcriptional regulator complement(1322983..1323981) Dinoroseobacter shibae DFL 12 = DSM 16493 5711831 YP_001532617.1 CDS Dshi_1274 NC_009952.1 1324124 1325101 D ATPase gene cluster: periplasmatic binding component, permease component, ATPase component; periplasmic-binding protein/LacI transcriptional regulator 1324124..1325101 Dinoroseobacter shibae DFL 12 = DSM 16493 5711832 YP_001532618.1 CDS Dshi_1275 NC_009952.1 1325167 1326291 D ATPase gene cluster: periplasmatic binding component, permease component, ATPase component; monosaccharide-transporting ATPase 1325167..1326291 Dinoroseobacter shibae DFL 12 = DSM 16493 5711833 YP_001532619.1 CDS Dshi_1276 NC_009952.1 1326293 1327087 D ATPase gene cluster: periplasmatic binding component, permease component, ATPase component; ABC transporter-like protein 1326293..1327087 Dinoroseobacter shibae DFL 12 = DSM 16493 5711834 YP_001532620.1 CDS Dshi_1277 NC_009952.1 1327074 1327316 D hypothetical protein 1327074..1327316 Dinoroseobacter shibae DFL 12 = DSM 16493 5711835 YP_001532621.1 CDS Dshi_1278 NC_009952.1 1327313 1328482 D phytanoyl-CoA dioxygenase 1327313..1328482 Dinoroseobacter shibae DFL 12 = DSM 16493 5711836 YP_001532622.1 CDS iolB2 NC_009952.1 1328494 1329306 D myo-inositol catabolism IolB domain-containing protein 1328494..1329306 Dinoroseobacter shibae DFL 12 = DSM 16493 5711837 YP_001532623.1 CDS Dshi_1280 NC_009952.1 1329323 1330588 R domain is found in amino transferases, and other enzymes including cysteine desulphurase, PLP dependent enzyme; class V aminotransferase complement(1329323..1330588) Dinoroseobacter shibae DFL 12 = DSM 16493 5711838 YP_001532624.1 CDS fdhB NC_009952.1 1330881 1332578 D high similarity to Respiratory-chain NADH dehydrogenase domain 24 kDa and 51 kDa subunits(PMID:2187144); respiratory-chain NADH dehydrogenase domain 51 kDa subunit 1330881..1332578 Dinoroseobacter shibae DFL 12 = DSM 16493 5711839 YP_001532625.1 CDS fdhA NC_009952.1 1332581 1335382 D complex with fdhB, Molybdopterin oxidoreductase, contains Fe-S clusters; formate dehydrogenase subunit alpha 1332581..1335382 Dinoroseobacter shibae DFL 12 = DSM 16493 5711840 YP_001532626.1 CDS fhs NC_009952.1 1335512 1337179 D catalyzes the formation of 10-formyltetrahydrofolate from formate and tetrahydrofolate; formate--tetrahydrofolate ligase 1335512..1337179 Dinoroseobacter shibae DFL 12 = DSM 16493 5711841 YP_001532627.1 CDS Dshi_1284 NC_009952.1 1337238 1337558 D chorismate mutase related enzyme 1337238..1337558 Dinoroseobacter shibae DFL 12 = DSM 16493 5711842 YP_001532628.1 CDS folD NC_009952.1 1337555 1338454 D 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 1337555..1338454 Dinoroseobacter shibae DFL 12 = DSM 16493 5711843 YP_001532629.1 CDS Dshi_1286 NC_009952.1 1338659 1339942 D hypothetical protein 1338659..1339942 Dinoroseobacter shibae DFL 12 = DSM 16493 5711844 YP_001532630.1 CDS Dshi_1287 NC_009952.1 1339875 1340969 R hypothetical protein complement(1339875..1340969) Dinoroseobacter shibae DFL 12 = DSM 16493 5711845 YP_001532631.1 CDS Dshi_1288 NC_009952.1 1341315 1342481 D amidohydrolase 1341315..1342481 Dinoroseobacter shibae DFL 12 = DSM 16493 5711846 YP_001532632.1 CDS Dshi_1289 NC_009952.1 1342529 1343269 D Catalyzes the transfer of the ammonia group from glutamine to a new carbon-nitrogen group; glutamine amidotransferase 1342529..1343269 Dinoroseobacter shibae DFL 12 = DSM 16493 5711847 YP_001532633.1 CDS moaA NC_009952.1 1343361 1344371 R together with moaC, is involved in the conversion of a guanosine derivative (GXP) into molybdopterin precursor Z; molybdenum cofactor biosynthesis protein A complement(1343361..1344371) Dinoroseobacter shibae DFL 12 = DSM 16493 5711848 YP_001532634.1 CDS Dshi_1291 NC_009952.1 1344604 1345305 R DNA alkylation repair protein complement(1344604..1345305) Dinoroseobacter shibae DFL 12 = DSM 16493 5711849 YP_001532635.1 CDS Dshi_1292 NC_009952.1 1345302 1345850 R pyridoxamine 5'-phosphate oxidase-like FMN-binding protein complement(1345302..1345850) Dinoroseobacter shibae DFL 12 = DSM 16493 5711850 YP_001532636.1 CDS glmS NC_009952.1 1345854 1347674 R Catalyzes the first step in hexosamine metabolism, converting fructose-6P into glucosamine-6P using glutamine as a nitrogen source; glucosamine--fructose-6-phosphate aminotransferase complement(1345854..1347674) Dinoroseobacter shibae DFL 12 = DSM 16493 5711851 YP_001532637.1 CDS glmU NC_009952.1 1347674 1349026 R 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 complement(1347674..1349026) Dinoroseobacter shibae DFL 12 = DSM 16493 5711852 YP_001532638.1 CDS Dshi_1295 NC_009952.1 1349154 1349828 D Specifically catalyzes the dephosphorylation of 2-phosphoglycolate; subfamily IA, variant 3; HAD-superfamily hydrolase 1349154..1349828 Dinoroseobacter shibae DFL 12 = DSM 16493 5711853 YP_001532639.1 CDS Dshi_1296 NC_009952.1 1349879 1351090 D DegT/DnrJ/EryC1/StrS aminotransferase 1349879..1351090 Dinoroseobacter shibae DFL 12 = DSM 16493 5711854 YP_001532640.1 CDS ivd NC_009952.1 1351256 1352419 D FAD-dependent, Reaction: 3-methylbutanoyl-CoA + acceptor = 3-methylbut-2-enoyl-CoA + reduced acceptor; acyl-CoA dehydrogenase domain-containing protein 1351256..1352419 Dinoroseobacter shibae DFL 12 = DSM 16493 5711855 YP_001532641.1 CDS Dshi_1298 NC_009952.1 1352444 1352782 D hypothetical protein 1352444..1352782 Dinoroseobacter shibae DFL 12 = DSM 16493 5711856 YP_001532642.1 CDS Dshi_1299 NC_009952.1 1352857 1353465 R OmpW family protein complement(1352857..1353465) Dinoroseobacter shibae DFL 12 = DSM 16493 5711857 YP_001532643.1 CDS mccB NC_009952.1 1353609 1355213 D involved in leucine catabolism; propionyl-CoA carboxylase 1353609..1355213 Dinoroseobacter shibae DFL 12 = DSM 16493 5711858 YP_001532644.1 CDS mccA NC_009952.1 1355325 1357310 D involved in leucine catabolism; carbamoyl-phosphate synthase L chain ATP-binding 1355325..1357310 Dinoroseobacter shibae DFL 12 = DSM 16493 5711859 YP_001532645.1 CDS Dshi_1302 NC_009952.1 1357307 1357975 D glutathione S-transferase domain-containing protein 1357307..1357975 Dinoroseobacter shibae DFL 12 = DSM 16493 5711860 YP_001532646.1 CDS mvaB NC_009952.1 1357972 1358835 D catalyzes the formation of acetoacetate and acetyl-CoA from 3-hydroxy-3-methylglutaryl-CoA; hydroxymethylglutaryl-CoA lyase 1357972..1358835 Dinoroseobacter shibae DFL 12 = DSM 16493 5711861 YP_001532647.1 CDS mvaA NC_009952.1 1358832 1359620 D Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA; enoyl-CoA hydratase 1358832..1359620 Dinoroseobacter shibae DFL 12 = DSM 16493 5711862 YP_001532648.1 CDS Dshi_1305 NC_009952.1 1359760 1359978 D 17 kDa surface antigen 1359760..1359978 Dinoroseobacter shibae DFL 12 = DSM 16493 5711863 YP_001532649.1 CDS Dshi_1306 NC_009952.1 1359980 1360588 R hypothetical protein complement(1359980..1360588) Dinoroseobacter shibae DFL 12 = DSM 16493 5711864 YP_001532650.1 CDS nuoA NC_009952.1 1360930 1361295 D Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit A 1360930..1361295 Dinoroseobacter shibae DFL 12 = DSM 16493 5711865 YP_001532651.1 CDS nuoB NC_009952.1 1361286 1361819 D 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 1361286..1361819 Dinoroseobacter shibae DFL 12 = DSM 16493 5711866 YP_001532652.1 CDS nuoC NC_009952.1 1361883 1362530 D Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit C 1361883..1362530 Dinoroseobacter shibae DFL 12 = DSM 16493 5711867 YP_001532653.1 CDS Dshi_1310 NC_009952.1 1362535 1363413 D hypothetical protein 1362535..1363413 Dinoroseobacter shibae DFL 12 = DSM 16493 5711868 YP_001532654.1 CDS nuoD NC_009952.1 1363417 1364631 D Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit D 1363417..1364631 Dinoroseobacter shibae DFL 12 = DSM 16493 5711869 YP_001532655.1 CDS Dshi_1312 NC_009952.1 1364628 1364816 D hypothetical protein 1364628..1364816 Dinoroseobacter shibae DFL 12 = DSM 16493 5711870 YP_001532656.1 CDS nuoE NC_009952.1 1365222 1366430 D catalyzes the transfer of electrons from NADH to ubiquinone; NADH dehydrogenase subunit E 1365222..1366430 Dinoroseobacter shibae DFL 12 = DSM 16493 5711871 YP_001532657.1 CDS Dshi_1314 NC_009952.1 1366460 1367179 D hypothetical protein 1366460..1367179 Dinoroseobacter shibae DFL 12 = DSM 16493 5711872 YP_001532658.1 CDS Dshi_1315 NC_009952.1 1367176 1367412 D conserved in Rhodobacteraceae; hypothetical protein 1367176..1367412 Dinoroseobacter shibae DFL 12 = DSM 16493 5711873 YP_001532659.1 CDS nuoF NC_009952.1 1367416 1368717 D 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 subunit I F 1367416..1368717 Dinoroseobacter shibae DFL 12 = DSM 16493 5711874 YP_001532660.1 CDS Dshi_1317 NC_009952.1 1368714 1369106 D hypothetical protein 1368714..1369106 Dinoroseobacter shibae DFL 12 = DSM 16493 5711875 YP_001532661.1 CDS Dshi_1318 NC_009952.1 1369103 1369564 D hypothetical protein 1369103..1369564 Dinoroseobacter shibae DFL 12 = DSM 16493 5711876 YP_001532662.1 CDS Dshi_1319 NC_009952.1 1369561 1370079 D hypothetical protein 1369561..1370079 Dinoroseobacter shibae DFL 12 = DSM 16493 5711877 YP_001532663.1 CDS nuoG NC_009952.1 1370083 1372101 D Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit G 1370083..1372101 Dinoroseobacter shibae DFL 12 = DSM 16493 5711878 YP_001532664.1 CDS nuoH NC_009952.1 1372375 1373412 D Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit H 1372375..1373412 Dinoroseobacter shibae DFL 12 = DSM 16493 5711879 YP_001532665.1 CDS nuoI NC_009952.1 1373416 1373910 D Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit I 1373416..1373910 Dinoroseobacter shibae DFL 12 = DSM 16493 5711880 YP_001532666.1 CDS Dshi_1323 NC_009952.1 1373907 1374320 D carboxymuconolactone decarboxylase 1373907..1374320 Dinoroseobacter shibae DFL 12 = DSM 16493 5711881 YP_001532667.1 CDS nuoJ NC_009952.1 1374343 1374957 D Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit J 1374343..1374957 Dinoroseobacter shibae DFL 12 = DSM 16493 5711882 YP_001532668.1 CDS Dshi_1325 NC_009952.1 1375139 1375633 D hypothetical protein 1375139..1375633 Dinoroseobacter shibae DFL 12 = DSM 16493 5711883 YP_001532669.1 CDS nuoK NC_009952.1 1375716 1376021 D Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit K 1375716..1376021 Dinoroseobacter shibae DFL 12 = DSM 16493 5711884 YP_001532670.1 CDS nuoL NC_009952.1 1376026 1378083 D Catalyzes the transfer of electrons from NADH to ubiquinone; NADH dehydrogenase subunit L 1376026..1378083 Dinoroseobacter shibae DFL 12 = DSM 16493 5711885 YP_001532671.1 CDS nuoM NC_009952.1 1378083 1379630 D Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit M 1378083..1379630 Dinoroseobacter shibae DFL 12 = DSM 16493 5711886 YP_001532672.1 CDS nuoN NC_009952.1 1379641 1381080 D Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit N 1379641..1381080 Dinoroseobacter shibae DFL 12 = DSM 16493 5711887 YP_001532673.1 CDS Dshi_1330 NC_009952.1 1381070 1381825 D biotin--acetyl-CoA-carboxylase ligase 1381070..1381825 Dinoroseobacter shibae DFL 12 = DSM 16493 5711888 YP_001532674.1 CDS Dshi_1331 NC_009952.1 1381846 1382616 D 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 1381846..1382616 Dinoroseobacter shibae DFL 12 = DSM 16493 5711889 YP_001532675.1 CDS Dshi_1332 NC_009952.1 1382616 1384286 D beta-lactamase domain-containing protein 1382616..1384286 Dinoroseobacter shibae DFL 12 = DSM 16493 5711890 YP_001532676.1 CDS rhlE NC_009952.1 1384375 1385856 R DEAD/DEAH box helicase complement(1384375..1385856) Dinoroseobacter shibae DFL 12 = DSM 16493 5711891 YP_001532677.1 CDS Dshi_1334 NC_009952.1 1386187 1387725 R TPR containing proteins are involved in assambly of multiprotein complexes; hypothetical protein complement(1386187..1387725) Dinoroseobacter shibae DFL 12 = DSM 16493 5711892 YP_001532678.2 CDS Dshi_1335 NC_009952.1 1388539 1389207 D hypothetical protein 1388539..1389207 Dinoroseobacter shibae DFL 12 = DSM 16493 5711893 YP_001532679.1 CDS prfC NC_009952.1 1389301 1390908 R Increases the formation of ribosomal termination complexes and stimulates activities of prfA and prfB, GTP binding; peptide chain release factor 3 complement(1389301..1390908) Dinoroseobacter shibae DFL 12 = DSM 16493 5711894 YP_001532680.1 CDS Dshi_1337 NC_009952.1 1391022 1391393 D hypothetical protein 1391022..1391393 Dinoroseobacter shibae DFL 12 = DSM 16493 5711895 YP_001532681.1 CDS uspA1 NC_009952.1 1391461 1392303 R contains 2 UspA domains, expression is enhanced when the cell is exposed to stress agents, enhances the rate of cell survival during prolonged exposure to such conditions; UspA domain-containing protein complement(1391461..1392303) Dinoroseobacter shibae DFL 12 = DSM 16493 5711896 YP_001532682.1 CDS Dshi_1339 NC_009952.1 1392438 1393217 D most enzymes of this family are NAD/NADP-dependent oxidoreductases; short-chain dehydrogenase/reductase SDR 1392438..1393217 Dinoroseobacter shibae DFL 12 = DSM 16493 5711897 YP_001532683.1 CDS Dshi_1340 NC_009952.1 1393332 1394720 D the energy stored in an inwardly directed electrochemical sodium gradient (sodium motive force, SMF) is used to drive solute accumulation against a concentration gradient; Na+/solute symporter 1393332..1394720 Dinoroseobacter shibae DFL 12 = DSM 16493 5711898 YP_001532684.1 CDS Dshi_1341 NC_009952.1 1394766 1395854 D unknown specificity, high similarity to iron ABC transporters; ABC transporter-like protein 1394766..1395854 Dinoroseobacter shibae DFL 12 = DSM 16493 5711899 YP_001532685.1 CDS Dshi_1342 NC_009952.1 1395858 1396517 R Helix-turn-helix type 11 domain protein; helix-turn-helix domain-containing protein complement(1395858..1396517) Dinoroseobacter shibae DFL 12 = DSM 16493 5711900 YP_001532686.1 CDS Dshi_1343 NC_009952.1 1396711 1396935 D Sec-independent translocation protein mttA/Hcf106, Members of this protein family are involved in a sec independent translocation mechanism. This sec-independent pathway is termed TAT for twin-arginine translocation system. This system mainly transports proteins with bound cofactors that require folding prior to export.; Sec-independent translocation protein mttA/Hcf106 1396711..1396935 Dinoroseobacter shibae DFL 12 = DSM 16493 5711901 YP_001532687.1 CDS tatB NC_009952.1 1396954 1397421 D Sec-independent protein secretion pathway components; TatB subunit; twin-arginine translocation protein 1396954..1397421 Dinoroseobacter shibae DFL 12 = DSM 16493 5711902 YP_001532688.1 CDS tatC NC_009952.1 1397430 1398470 D Sec-independent protein secretion pathway components; TatC subunit; sec-independent protein translocase 1397430..1398470 Dinoroseobacter shibae DFL 12 = DSM 16493 5711911 YP_001532689.1 CDS Dshi_1346 NC_009952.1 1398467 1399318 D hypothetical protein 1398467..1399318 Dinoroseobacter shibae DFL 12 = DSM 16493 5711912 YP_001532690.1 CDS Dshi_1347 NC_009952.1 1399416 1400000 R hypothetical protein complement(1399416..1400000) Dinoroseobacter shibae DFL 12 = DSM 16493 5711913 YP_001532691.1 CDS Dshi_1348 NC_009952.1 1400045 1400671 R Integral membrane protein family that includes the antibiotic resistance protein MarC. These proteins may be transporters.; multiple antibiotic resistance (MarC)-like protein complement(1400045..1400671) Dinoroseobacter shibae DFL 12 = DSM 16493 5711914 YP_001532692.1 CDS Dshi_1349 NC_009952.1 1400718 1402574 R duplicated ATPase domain; ABC transporter-like protein complement(1400718..1402574) Dinoroseobacter shibae DFL 12 = DSM 16493 5711915 YP_001532693.1 CDS ndk NC_009952.1 1402713 1403135 D catalyzes the formation of nucleoside triphosphate from ATP and nucleoside diphosphate; nucleoside diphosphate kinase 1402713..1403135 Dinoroseobacter shibae DFL 12 = DSM 16493 5711916 YP_001532694.1 CDS Dshi_1351 NC_009952.1 1403285 1403677 D hypothetical protein 1403285..1403677 Dinoroseobacter shibae DFL 12 = DSM 16493 5711917 YP_001532695.1 CDS Dshi_1352 NC_009952.1 1403674 1404003 R no evidence for predicted domain; TfoX domain-containing protein complement(1403674..1404003) Dinoroseobacter shibae DFL 12 = DSM 16493 5711903 YP_001532696.1 CDS Dshi_1353 NC_009952.1 1404655 1405959 D ABC transporter (importer) gene cluster: receptor; family 1 extracellular solute-binding protein 1404655..1405959 Dinoroseobacter shibae DFL 12 = DSM 16493 5711904 YP_001532697.1 CDS Dshi_1354 NC_009952.1 1406021 1407271 D ABC transporter (importer) gene cluster: 1st membrane spanning domain (MSD); part of a heterotetramer; binding-protein-dependent transport system inner membrane protein 1406021..1407271 Dinoroseobacter shibae DFL 12 = DSM 16493 5711905 YP_001532698.1 CDS Dshi_1355 NC_009952.1 1407459 1408673 D ABC transporter (importer) gene cluster: 2nd membrane spanning domain (MSD); part of a heterotetramer; binding-protein-dependent transport system inner membrane protein 1407459..1408673 Dinoroseobacter shibae DFL 12 = DSM 16493 5711906 YP_001532699.1 CDS Dshi_1356 NC_009952.1 1408670 1409944 D hypothetical protein 1408670..1409944 Dinoroseobacter shibae DFL 12 = DSM 16493 5711907 YP_001532700.1 CDS Dshi_1357 NC_009952.1 1409932 1410981 D ABC transporter (importer) gene cluster: ATP binding cassette (ABC) domain; part of a heterotetramer; ABC transporter-like protein 1409932..1410981 Dinoroseobacter shibae DFL 12 = DSM 16493 5711908 YP_001532701.1 CDS Dshi_1358 NC_009952.1 1410984 1411760 D most enzymes of this family are NAD/NADP-dependent oxidoreductases; short-chain dehydrogenase/reductase SDR 1410984..1411760 Dinoroseobacter shibae DFL 12 = DSM 16493 5711909 YP_001532702.1 CDS Dshi_1359 NC_009952.1 1411909 1412286 D hypothetical protein 1411909..1412286 Dinoroseobacter shibae DFL 12 = DSM 16493 5711910 YP_001532703.1 CDS Dshi_1360 NC_009952.1 1412275 1413312 R SnoaL-like polyketide cyclase family protein; hypothetical protein complement(1412275..1413312) Dinoroseobacter shibae DFL 12 = DSM 16493 5712536 YP_001532704.1 CDS dld1 NC_009952.1 1413419 1414825 D Catalyzes the stereospecific oxidation of D-lactate to pyruvate; cytochrome; D-lactate dehydrogenase 1413419..1414825 Dinoroseobacter shibae DFL 12 = DSM 16493 5712537 YP_001532705.1 CDS Dshi_1362 NC_009952.1 1414985 1416322 D function undetermined; similar to glutamate synthase beta subunit and related oxidoreductases which transfer electrons from NADPH to an acceptor protein or protein domain; putative oxidoreductase 1414985..1416322 Dinoroseobacter shibae DFL 12 = DSM 16493 5712538 YP_001532706.1 CDS pyrD1 NC_009952.1 1416350 1417648 D catalyzes the first step in pyrimidine degradation: the NADPH-dependent reduction of uracil and thymine to the corresponding 5,6-dihydropyrimidines; dihydropyrimidine dehydrogenase 1416350..1417648 Dinoroseobacter shibae DFL 12 = DSM 16493 5712539 YP_001532707.1 CDS Dshi_1364 NC_009952.1 1417662 1418054 R hypothetical protein complement(1417662..1418054) Dinoroseobacter shibae DFL 12 = DSM 16493 5712540 YP_001532708.1 CDS Dshi_1365 NC_009952.1 1418132 1418767 R Helix-Turn-Helix motif; TetR family; transcriptional regulator complement(1418132..1418767) Dinoroseobacter shibae DFL 12 = DSM 16493 5712541 YP_001532709.1 CDS Dshi_1366 NC_009952.1 1418987 1420312 D catalyzes the formation of pyruvate and beta-alanine from L-alanine and 3-oxopropanoate; beta alanine--pyruvate transaminase 1418987..1420312 Dinoroseobacter shibae DFL 12 = DSM 16493 5712542 YP_001532710.1 CDS amaB NC_009952.1 1420347 1421621 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 1420347..1421621 Dinoroseobacter shibae DFL 12 = DSM 16493 5712543 YP_001532711.1 CDS Dshi_1368 NC_009952.1 1421652 1421951 D hypothetical protein 1421652..1421951 Dinoroseobacter shibae DFL 12 = DSM 16493 5712544 YP_001532712.1 CDS Dshi_1369 NC_009952.1 1421968 1422711 D This family includes class II aldolases and adducins which have not been ascribed any enzymatic function.; class II aldolase/adducin family protein 1421968..1422711 Dinoroseobacter shibae DFL 12 = DSM 16493 5712545 YP_001532713.1 CDS dht NC_009952.1 1422758 1424209 D catalyzes the hydrolytic cleavage of hydantoin with aromatic side chains at the 5'position; phenylhydantoinase 1422758..1424209 Dinoroseobacter shibae DFL 12 = DSM 16493 5712546 YP_001532714.1 CDS Dshi_1371 NC_009952.1 1424219 1425220 D ABC transporter (importer) gene cluster (disrupted): ATP binding cassette (ABC) domain; part of a heterotetramer; ABC transporter-like protein 1424219..1425220 Dinoroseobacter shibae DFL 12 = DSM 16493 5712547 YP_001532715.1 CDS Dshi_1372 NC_009952.1 1425233 1426150 D ABC transporter (importer) gene cluster: 1st membrane spanning domain (MSD); part of a heterotetramer; binding-protein-dependent transport system inner membrane protein 1425233..1426150 Dinoroseobacter shibae DFL 12 = DSM 16493 5712548 YP_001532716.1 CDS Dshi_1373 NC_009952.1 1426147 1427058 D ABC transporter (importer) gene cluster: 2nd membrane spanning domain (MSD); part of a heterotetramer; binding-protein-dependent transport system inner membrane protein 1426147..1427058 Dinoroseobacter shibae DFL 12 = DSM 16493 5712549 YP_001532717.1 CDS Dshi_1374 NC_009952.1 1427332 1428321 D ABC transporter (importer) gene cluster: receptor; NMT1/THI5 like domain-containing protein 1427332..1428321 Dinoroseobacter shibae DFL 12 = DSM 16493 5712550 YP_001532718.1 CDS Dshi_1375 NC_009952.1 1428663 1429859 D ornithine decarboxylase 1428663..1429859 Dinoroseobacter shibae DFL 12 = DSM 16493 5712551 YP_001532719.1 CDS Dshi_1376 NC_009952.1 1429916 1430713 R catalyses the hydrolysis of creatinine to creatine; creatininase complement(1429916..1430713) Dinoroseobacter shibae DFL 12 = DSM 16493 5712552 YP_001532720.1 CDS Dshi_1377 NC_009952.1 1430706 1431608 R This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily; 2OG-Fe(II) oxygenase complement(1430706..1431608) Dinoroseobacter shibae DFL 12 = DSM 16493 5712553 YP_001532721.1 CDS Dshi_1378 NC_009952.1 1431608 1432243 R catalyseses the NAD(P)H-dependent two-electron reductions of quinones and protect cells against damage by free radicals and reactive oxygen species; quinone dependent NAD(P)H dehydrogenase complement(1431608..1432243) Dinoroseobacter shibae DFL 12 = DSM 16493 5712554 YP_001532722.1 CDS Dshi_1379 NC_009952.1 1432243 1432830 R catalyseses the NAD(P)H-dependent two-electron reductions of quinones and protect cells against damage by free radicals and reactive oxygen species; quinone dependent NADH dehydrogenase complement(1432243..1432830) Dinoroseobacter shibae DFL 12 = DSM 16493 5712555 YP_001532723.1 CDS Dshi_1380 NC_009952.1 1432949 1434355 R This family consists of various enzymes that use FAD as a co-factor, most of the enzymes are similar to oxygen oxidoreductase.; FAD linked oxidase domain-containing protein complement(1432949..1434355) Dinoroseobacter shibae DFL 12 = DSM 16493 5712556 YP_001532724.1 CDS Dshi_1381 NC_009952.1 1434352 1435626 R Amidohydrolases are a diverse superfamily of enzymes which catalyse the hydrolysis of amide or amine bonds in a large number of different substrates including urea, cytosine, AMP, formylmethanofuran; cytosine deaminase complement(1434352..1435626) Dinoroseobacter shibae DFL 12 = DSM 16493 5712557 YP_001532725.1 CDS Dshi_1382 NC_009952.1 1435626 1436483 R ABC transporter (importer) gene cluster: 2nd membrane spanning domain (MSD); part of a heterotetramer; binding-protein-dependent transport system inner membrane protein complement(1435626..1436483) Dinoroseobacter shibae DFL 12 = DSM 16493 5712558 YP_001532726.1 CDS Dshi_1383 NC_009952.1 1436480 1437289 R ABC transporter (importer) gene cluster: ATP binding cassette (ABC) domain; part of a heterotetramer; ABC transporter-like protein complement(1436480..1437289) Dinoroseobacter shibae DFL 12 = DSM 16493 5712559 YP_001532727.1 CDS Dshi_1384 NC_009952.1 1437354 1438355 R ABC transporter (importer) gene cluster: 1st membrane spanning domain (MSD); part of a heterotetramer; ABC transporter permease complement(1437354..1438355) Dinoroseobacter shibae DFL 12 = DSM 16493 5712560 YP_001532728.1 CDS Dshi_1385 NC_009952.1 1438594 1438992 D Endoribonuclease active on single-stranded mRNA. Inhibits protein synthesis by cleavage of mRNA; endoribonuclease L-PSP 1438594..1438992 Dinoroseobacter shibae DFL 12 = DSM 16493 5712561 YP_001532729.1 CDS Dshi_1386 NC_009952.1 1438996 1440408 R hypothetical protein complement(1438996..1440408) Dinoroseobacter shibae DFL 12 = DSM 16493 5712562 YP_001532730.1 CDS clpX NC_009952.1 1440553 1441812 R binds and unfolds substrates as part of the ClpXP protease; ATP-dependent protease ATP-binding subunit ClpX complement(1440553..1441812) Dinoroseobacter shibae DFL 12 = DSM 16493 5712563 YP_001532731.1 CDS clpP NC_009952.1 1442020 1442646 R hydrolyzes proteins to small peptides; with the ATPase subunits ClpA or ClpX, ClpP degrades specific substrates; ATP-dependent Clp protease proteolytic subunit complement(1442020..1442646) Dinoroseobacter shibae DFL 12 = DSM 16493 5712564 YP_001532732.1 CDS Dshi_1389 NC_009952.1 1442883 1444100 D putative deoxyribodipyrimidine photo-lyase 1442883..1444100 Dinoroseobacter shibae DFL 12 = DSM 16493 5712565 YP_001532733.1 CDS Dshi_1390 NC_009952.1 1444131 1444565 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 1444131..1444565 Dinoroseobacter shibae DFL 12 = DSM 16493 5712566 YP_001532734.1 CDS Dshi_1391 NC_009952.1 1444613 1445059 D Mammalian cell entry related domain; hypothetical protein 1444613..1445059 Dinoroseobacter shibae DFL 12 = DSM 16493 5712567 YP_001532735.1 CDS Dshi_1392 NC_009952.1 1445056 1445598 D hypothetical protein 1445056..1445598 Dinoroseobacter shibae DFL 12 = DSM 16493 5712568 YP_001532736.1 CDS Dshi_1393 NC_009952.1 1445608 1446195 R hypothetical protein complement(1445608..1446195) Dinoroseobacter shibae DFL 12 = DSM 16493 5712569 YP_001532737.1 CDS aat NC_009952.1 1446363 1447034 R transfers a Leu or Phe to the amino end of certain proteins to enable degradation. The N-terminal residue controls the biological half-life of many proteins via the N-end rule pathway.; leucyltransferase complement(1446363..1447034) Dinoroseobacter shibae DFL 12 = DSM 16493 5712570 YP_001532738.1 CDS accC NC_009952.1 1447094 1448440 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(1447094..1448440) Dinoroseobacter shibae DFL 12 = DSM 16493 5712571 YP_001532739.1 CDS accB NC_009952.1 1448450 1448977 R This protein is a component of the acetyl coenzyme A carboxylase complex; first, biotin carboxylase catalyzes the carboxylation of the carrier protein and then the transcarboxylase transfers the carboxyl group to form malonyl-CoA.; biotin carboxyl carrier protein; acetyl-CoA carboxylase complement(1448450..1448977) Dinoroseobacter shibae DFL 12 = DSM 16493 5712572 YP_001532740.1 CDS Dshi_1397 NC_009952.1 1449132 1450748 D contains several Hemolysin-type calcium-binding repeats found in proteins that are secreted into the growth medium by a mechanism that does not require a cleaved N-terminal signal sequence; phospholipase/lecithinase/hemolysin-like protein 1449132..1450748 Dinoroseobacter shibae DFL 12 = DSM 16493 5712573 YP_001532741.1 CDS Dshi_1398 NC_009952.1 1450880 1451332 D domain structure is similar to that of dehydrogenases, amidohydrolases, and oxidoreductases, however sequence and structural analyses have shown that it does not belong to the dehydrogenase or the amidohydrolase superfamilies of proteins; hypothetical protein 1450880..1451332 Dinoroseobacter shibae DFL 12 = DSM 16493 5712574 YP_001532742.1 CDS acsA NC_009952.1 1451413 1453374 R Enables the cell to use acetate during aerobic growth to generate energy via the TCA cycle, and biosynthetic compounds via the glyoxylate shunt. Acetylates cheY, the response regulator involved in flagellar movement and chemotaxis.; acetate--CoA ligase complement(1451413..1453374) Dinoroseobacter shibae DFL 12 = DSM 16493 5712575 YP_001532743.1 CDS Dshi_1400 NC_009952.1 1453619 1454374 R ABC transporter (importer) gene cluster: 2nd ATP binding cassette (ABC) domain; part of a heterotetramer; ABC transporter-like protein complement(1453619..1454374) Dinoroseobacter shibae DFL 12 = DSM 16493 5712576 YP_001532744.1 CDS Dshi_1401 NC_009952.1 1454386 1455144 R ABC transporter (importer) gene cluster: 1st ATP binding cassette (ABC) domain; part of a heterotetramer; ABC transporter-like protein complement(1454386..1455144) Dinoroseobacter shibae DFL 12 = DSM 16493 5712577 YP_001532745.1 CDS Dshi_1402 NC_009952.1 1455157 1456365 R ABC transporter (importer) gene cluster: 2nd membrane spanning domain (MSD); part of a heterotetramer; inner-membrane translocator complement(1455157..1456365) Dinoroseobacter shibae DFL 12 = DSM 16493 5712578 YP_001532746.1 CDS Dshi_1403 NC_009952.1 1456370 1457401 R ABC transporter (importer) gene cluster: 1st membrane spanning domain (MSD); part of a heterotetramer; inner-membrane translocator complement(1456370..1457401) Dinoroseobacter shibae DFL 12 = DSM 16493 5712579 YP_001532747.1 CDS Dshi_1404 NC_009952.1 1457511 1458866 R ABC transporter (importer) gene cluster: receptor; periplasmic binding protein, putative; branched-chain amino acid ABC transporter complement(1457511..1458866) Dinoroseobacter shibae DFL 12 = DSM 16493 5712580 YP_001532748.1 CDS Dshi_1405 NC_009952.1 1459097 1460392 D Helix-Turn-Helix motif; XRE family; transcriptional regulator 1459097..1460392 Dinoroseobacter shibae DFL 12 = DSM 16493 5712581 YP_001532749.1 CDS Dshi_1406 NC_009952.1 1460497 1460862 D DNA-binding motif, normally found at the C-terminus, is missing; response regulator receiver protein 1460497..1460862 Dinoroseobacter shibae DFL 12 = DSM 16493 5712582 YP_001532750.1 CDS Dshi_1407 NC_009952.1 1460864 1461184 D hypothetical protein 1460864..1461184 Dinoroseobacter shibae DFL 12 = DSM 16493 5712583 YP_001532751.1 CDS Dshi_1408 NC_009952.1 1461184 1463877 D Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms; integral membrane sensor signal transduction histidine kinase 1461184..1463877 Dinoroseobacter shibae DFL 12 = DSM 16493 5712584 YP_001532752.1 CDS Dshi_1409 NC_009952.1 1463926 1464975 D hypothetical protein 1463926..1464975 Dinoroseobacter shibae DFL 12 = DSM 16493 5712585 YP_001532753.1 CDS Dshi_1410 NC_009952.1 1464988 1465500 R hypothetical protein complement(1464988..1465500) Dinoroseobacter shibae DFL 12 = DSM 16493 5712586 YP_001532754.1 CDS Dshi_1411 NC_009952.1 1465574 1465852 D TraR/DksA family; transcriptional regulator 1465574..1465852 Dinoroseobacter shibae DFL 12 = DSM 16493 5712587 YP_001532755.1 CDS Dshi_1412 NC_009952.1 1465891 1466133 D hypothetical protein 1465891..1466133 Dinoroseobacter shibae DFL 12 = DSM 16493 5712588 YP_001532756.1 CDS Dshi_1413 NC_009952.1 1466558 1467793 D ABC transporter (importer) gene cluster: receptor; family 1 extracellular solute-binding protein 1466558..1467793 Dinoroseobacter shibae DFL 12 = DSM 16493 5712589 YP_001532757.1 CDS Dshi_1414 NC_009952.1 1467854 1468885 D ABC transporter (importer) gene cluster: 1st membrane spanning domain (MSD); part of a heterotetramer; binding-protein-dependent transport system inner membrane protein 1467854..1468885 Dinoroseobacter shibae DFL 12 = DSM 16493 5712590 YP_001532758.1 CDS Dshi_1415 NC_009952.1 1468888 1469772 D ABC transporter (importer) gene cluster: 2nd membrane spanning domain (MSD); part of a heterotetramer; binding-protein-dependent transport system inner membrane protein 1468888..1469772 Dinoroseobacter shibae DFL 12 = DSM 16493 5712591 YP_001532759.1 CDS Dshi_1416 NC_009952.1 1469815 1470858 D ABC transporter (importer) gene cluster: ATP binding cassette (ABC) domain; part of a heterotetramer; ABC transporter-like protein 1469815..1470858 Dinoroseobacter shibae DFL 12 = DSM 16493 5712592 YP_001532760.1 CDS Dshi_1417 NC_009952.1 1470855 1471379 D hypothetical protein 1470855..1471379 Dinoroseobacter shibae DFL 12 = DSM 16493 5712593 YP_001532761.1 CDS Dshi_1418 NC_009952.1 1471376 1471591 R conserved in Rhodobacteraceae; hypothetical protein complement(1471376..1471591) Dinoroseobacter shibae DFL 12 = DSM 16493 5712594 YP_001532762.1 CDS Dshi_1419 NC_009952.1 1471738 1472016 D hypothetical protein 1471738..1472016 Dinoroseobacter shibae DFL 12 = DSM 16493 5712595 YP_001532763.1 CDS Dshi_1420 NC_009952.1 1472033 1472908 R conserved in Rhodobacteraceae; hypothetical protein complement(1472033..1472908) Dinoroseobacter shibae DFL 12 = DSM 16493 5712596 YP_001532764.1 CDS Dshi_1421 NC_009952.1 1473533 1474705 D ABC transporter (importer) gene cluster: receptor; substrate-binding protein; ribose ABC transporter 1473533..1474705 Dinoroseobacter shibae DFL 12 = DSM 16493 5712598 YP_001532765.1 CDS rbsA3 NC_009952.1 1474762 1476309 D ABC transporter (importer) gene cluster: fused ATP binding cassette (ABC) domains; part of a heterotrimer; ABC transporter-like protein 1474762..1476309 Dinoroseobacter shibae DFL 12 = DSM 16493 5712599 YP_001532766.1 CDS rbsB2 NC_009952.1 1476309 1477271 D ABC transporter (importer) gene cluster: 1st membrane spanning domain (MSD); part of a heterotrimer; inner-membrane translocator 1476309..1477271 Dinoroseobacter shibae DFL 12 = DSM 16493 5712600 YP_001532767.1 CDS rbsC1 NC_009952.1 1477271 1478302 D ABC transporter (importer) gene cluster: 2nd membrane spanning domain (MSD); part of a heterotrimer; inner-membrane translocator 1477271..1478302 Dinoroseobacter shibae DFL 12 = DSM 16493 5712601 YP_001532768.1 CDS Dshi_1425 NC_009952.1 1478321 1479775 D This family of dehydrogenases act on aldehyde substrates. Members use NADP as a cofactor (PFAM, INTERPRO; COG: NAD-dependent enzyme).; aldehyde dehydrogenase 1478321..1479775 Dinoroseobacter shibae DFL 12 = DSM 16493 5712602 YP_001532769.1 CDS Dshi_1426 NC_009952.1 1479836 1481350 D Fumarase, or fumarate hydratase, is a component of the citric acid cycle.; Fe-S type, tartrate/fumarate subfamily, alpha subunit; hydro-lyase 1479836..1481350 Dinoroseobacter shibae DFL 12 = DSM 16493 5712603 YP_001532770.1 CDS citF NC_009952.1 1481361 1482908 D represents a citrate:acetyl-ACP transferase, alpha subunit of the holoenzyme citrate lyase composed of alpha, beta, and acyl carrier protein subunits in a stoichiometric relationship of 6:6:6TCA-cycle; citrate CoA-transferase 1481361..1482908 Dinoroseobacter shibae DFL 12 = DSM 16493 5712604 YP_001532771.1 CDS Dshi_1428 NC_009952.1 1483002 1484636 R Can catalyze the oxidation of choline to betaine aldehyde and betaine aldehyde to glycine betaine; glucose-methanol-choline oxidoreductase complement(1483002..1484636) Dinoroseobacter shibae DFL 12 = DSM 16493 5712605 YP_001532772.1 CDS fabG NC_009952.1 1484787 1485557 R Catalyzes the first of the two reduction steps in the elongation cycle of fatty acid synthesis; 3-ketoacyl-ACP reductase complement(1484787..1485557) Dinoroseobacter shibae DFL 12 = DSM 16493 5712606 YP_001532773.1 CDS Dshi_1430 NC_009952.1 1485573 1487036 R This family of dehydrogenases act on aldehyde substrates. Members use NADP as a cofactor.; aldehyde dehydrogenase complement(1485573..1487036) Dinoroseobacter shibae DFL 12 = DSM 16493 5712607 YP_001532774.1 CDS Dshi_1431 NC_009952.1 1487135 1488091 R contains substrate binding domain, putative homotetramer; LysR family; transcriptional regulator complement(1487135..1488091) Dinoroseobacter shibae DFL 12 = DSM 16493 5712608 YP_001532775.1 CDS Dshi_1432 NC_009952.1 1488222 1489370 D These CoA-transferases occur in prokaryotes and eukaryotes, and catalyse CoA-transfer reactions in a highly substrate- and stereo-specific manner, Members: formyl-CoA:oxalate CoA-transferase, succinyl-CoA:(R)-benzylsuccinate CoA-transferase, (E)-cinnamoyl-CoA:(R)-phenyllactate CoA-transferase, butyrobetainyl-CoA:(R)-carnitine CoA-transferase; L-carnitine dehydratase/bile acid-inducible protein F 1488222..1489370 Dinoroseobacter shibae DFL 12 = DSM 16493 5712609 YP_001532776.1 CDS Dshi_1433 NC_009952.1 1489582 1490181 D hypothetical protein 1489582..1490181 Dinoroseobacter shibae DFL 12 = DSM 16493 5712610 YP_001532777.1 CDS Dshi_1434 NC_009952.1 1490184 1490399 D remnant of Xaa-Pro dipeptidase; Xaa-Pro dipeptidase 1490184..1490399 Dinoroseobacter shibae DFL 12 = DSM 16493 5712611 YP_001532778.1 CDS Dshi_1435 NC_009952.1 1490378 1491148 R domain is common to a number of hydrolytic enzymes of widely differing phylogenetic origin and catalytic function; alpha/beta hydrolase fold protein complement(1490378..1491148) Dinoroseobacter shibae DFL 12 = DSM 16493 5712612 YP_001532779.1 CDS Dshi_1436 NC_009952.1 1491145 1492686 R ABC transporter gene cluster, permease component; binding-protein-dependent transport system inner membrane protein complement(1491145..1492686) Dinoroseobacter shibae DFL 12 = DSM 16493 5712613 YP_001532780.1 CDS Dshi_1437 NC_009952.1 1492683 1493738 R ABC transporter gene cluster, ATPase component; ATPase subunit; glycine betaine/L-proline ABC transporter complement(1492683..1493738) Dinoroseobacter shibae DFL 12 = DSM 16493 5712614 YP_001532781.1 CDS Dshi_1438 NC_009952.1 1493812 1494777 R ABC transporter gene cluster, periplasmatic substrate binding component; glycine betaine ABC transporter substrate binding protein complement(1493812..1494777) Dinoroseobacter shibae DFL 12 = DSM 16493 5712615 YP_001532782.1 CDS Dshi_1439 NC_009952.1 1494829 1495872 R catalyzes the formation of pyruvate from D-cysteine; D-cysteine desulfhydrase complement(1494829..1495872) Dinoroseobacter shibae DFL 12 = DSM 16493 5712616 YP_001532783.1 CDS Dshi_1440 NC_009952.1 1495960 1496892 D contains substrate binding domain, putative homotetramer; LysR family; transcriptional regulator 1495960..1496892 Dinoroseobacter shibae DFL 12 = DSM 16493 5712617 YP_001532784.1 CDS Dshi_1441 NC_009952.1 1497052 1498287 D C-Terminus conserved; hypothetical protein 1497052..1498287 Dinoroseobacter shibae DFL 12 = DSM 16493 5712618 YP_001532785.1 CDS Dshi_1442 NC_009952.1 1498290 1499732 D peroxidase 1498290..1499732 Dinoroseobacter shibae DFL 12 = DSM 16493 5712619 YP_001532786.1 CDS Dshi_1443 NC_009952.1 1499876 1500844 D TRAP gene cluster - dctPQM; TAXI family; TRAP transporter solute receptor 1499876..1500844 Dinoroseobacter shibae DFL 12 = DSM 16493 5712620 YP_001532787.1 CDS Dshi_1444 NC_009952.1 1500927 1503581 D TRAP gene cluster - dctPQM; 4TM/12TM fusion protein; TRAP transporter 1500927..1503581 Dinoroseobacter shibae DFL 12 = DSM 16493 5712621 YP_001532788.1 CDS uspG NC_009952.1 1503594 1504028 D contains 1 UspA domain, expression is enhanced when the cell is exposed to stress agents, enhances the rate of cell survival during prolonged exposure to such conditions; UspA domain-containing protein 1503594..1504028 Dinoroseobacter shibae DFL 12 = DSM 16493 5712622 YP_001532789.1 CDS Dshi_1446 NC_009952.1 1504032 1505366 D PLP-dependent enzyme; hypothetical protein 1504032..1505366 Dinoroseobacter shibae DFL 12 = DSM 16493 5712623 YP_001532790.1 CDS Dshi_1447 NC_009952.1 1505621 1505779 R transposase complement(1505621..1505779) Dinoroseobacter shibae DFL 12 = DSM 16493 5712624 YP_001532791.1 CDS Dshi_1448 NC_009952.1 1506500 1506724 D HTH-type transcriptional regulator ZntR 1506500..1506724 Dinoroseobacter shibae DFL 12 = DSM 16493 5712625 YP_001532792.1 CDS Dshi_1449 NC_009952.1 1506778 1509000 R TonB protein interacts with outer membrane receptor proteins that carry out high-affinity binding and energy-dependent uptake of specific substrates into the periplasmic space; TonB-dependent receptor complement(1506778..1509000) Dinoroseobacter shibae DFL 12 = DSM 16493 5712626 YP_001532793.1 CDS Dshi_1450 NC_009952.1 1509057 1510334 R NnrS is a putative heme-Cu protein (NnrS) and a member of the short-chain dehydrogenase family.; NnrS family protein complement(1509057..1510334) Dinoroseobacter shibae DFL 12 = DSM 16493 5712627 YP_001532794.1 CDS ssuB2 NC_009952.1 1510331 1511080 R Part of the ABC transporter complex ssuABC involved in aliphatic sulfonates import. Responsible for energy coupling to the transport system; ABC transporter-like protein complement(1510331..1511080) Dinoroseobacter shibae DFL 12 = DSM 16493 5712628 YP_001532795.1 CDS ssuC2 NC_009952.1 1511077 1511940 R Part of the ABC transporter complex ssuABC involved in aliphatic sulfonates import.; binding-protein-dependent transport system inner membrane protein complement(1511077..1511940) Dinoroseobacter shibae DFL 12 = DSM 16493 5712629 YP_001532796.1 CDS ssuA2 NC_009952.1 1511962 1512945 R Part of the ABC transporter complex ssuABC involved in aliphatic sulfonates import.; putative sulfonate/nitrate transport system substrate-binding protein complement(1511962..1512945) Dinoroseobacter shibae DFL 12 = DSM 16493 5712630 YP_001532797.1 CDS Dshi_1454 NC_009952.1 1513040 1513537 R hypothetical protein complement(1513040..1513537) Dinoroseobacter shibae DFL 12 = DSM 16493 5712631 YP_001532798.1 CDS Dshi_1455 NC_009952.1 1513747 1513896 D transposase 1513747..1513896 Dinoroseobacter shibae DFL 12 = DSM 16493 5712632 YP_001532799.1 CDS Dshi_1456 NC_009952.1 1513896 1514609 D Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains.; integrase catalytic subunit 1513896..1514609 Dinoroseobacter shibae DFL 12 = DSM 16493 5712633 YP_001532800.1 CDS Dshi_1457 NC_009952.1 1514658 1516022 D protects the organism against invading foreign DNA, part of a heteromeric enzyme complex, mod (modification methyltransferase)subunit is missing; type III restriction protein res subunit 1514658..1516022 Dinoroseobacter shibae DFL 12 = DSM 16493 5712634 YP_001532801.1 CDS Dshi_1458 NC_009952.1 1515973 1516368 R phage integrase family; site-specific recombinase complement(1515973..1516368) Dinoroseobacter shibae DFL 12 = DSM 16493 5712635 YP_001532802.1 CDS Dshi_1459 NC_009952.1 1516680 1517501 D outer membrane protein; hypothetical protein 1516680..1517501 Dinoroseobacter shibae DFL 12 = DSM 16493 5712637 YP_001532803.1 CDS rplU NC_009952.1 1517692 1518357 D fusion of ribosomal protein L21 and COG3743; 50S ribosomal protein L21 1517692..1518357 Dinoroseobacter shibae DFL 12 = DSM 16493 5712638 YP_001532804.1 CDS rpmA NC_009952.1 1518373 1518642 D involved in the peptidyltransferase reaction during translation; 50S ribosomal protein L27 1518373..1518642 Dinoroseobacter shibae DFL 12 = DSM 16493 5712639 YP_001532805.1 CDS Dshi_1462 NC_009952.1 1518721 1519377 D LysE family transport protein 1518721..1519377 Dinoroseobacter shibae DFL 12 = DSM 16493 5712640 YP_001532806.1 CDS Dshi_1463 NC_009952.1 1519374 1519913 D N-acetyltransferase GCN5 1519374..1519913 Dinoroseobacter shibae DFL 12 = DSM 16493 5712641 YP_001532807.1 CDS Dshi_1464 NC_009952.1 1519918 1520427 D N-acetyltransferase GCN5 1519918..1520427 Dinoroseobacter shibae DFL 12 = DSM 16493 5712642 YP_001532808.1 CDS Dshi_1465 NC_009952.1 1520424 1520951 D N-acetyltransferase GCN5 1520424..1520951 Dinoroseobacter shibae DFL 12 = DSM 16493 5712643 YP_001532809.1 CDS obgE NC_009952.1 1520948 1521985 D essential GTPase; exhibits high exchange rate for GTP/GDP; associates with 50S ribosomal subunit; involved in regulation of chromosomal replication; GTPase ObgE 1520948..1521985 Dinoroseobacter shibae DFL 12 = DSM 16493 5712644 YP_001532810.1 CDS proB NC_009952.1 1521973 1523079 D catalyzes the formation of glutamate 5-phosphate from glutamate in proline biosynthesis; gamma-glutamyl kinase 1521973..1523079 Dinoroseobacter shibae DFL 12 = DSM 16493 5712645 YP_001532811.1 CDS Dshi_1468 NC_009952.1 1523177 1523812 D hypothetical protein 1523177..1523812 Dinoroseobacter shibae DFL 12 = DSM 16493 5712646 YP_001532812.1 CDS proA NC_009952.1 1523915 1525180 D Catalyzes the phosphorylation of L-glutamate during the proline biosynthesis pathway; gamma-glutamyl phosphate reductase 1523915..1525180 Dinoroseobacter shibae DFL 12 = DSM 16493 5712647 YP_001532813.1 CDS Dshi_1470 NC_009952.1 1525195 1525809 R hypothetical protein complement(1525195..1525809) Dinoroseobacter shibae DFL 12 = DSM 16493 5712648 YP_001532814.1 CDS Dshi_1471 NC_009952.1 1525839 1526024 D hypothetical protein 1525839..1526024 Dinoroseobacter shibae DFL 12 = DSM 16493 5712649 YP_001532815.1 CDS Dshi_1472 NC_009952.1 1526145 1526921 D similar to ornithine acyl[acyl carrier protein] N-acyltransferase in S. pomeroyi; phospholipid/glycerol acyltransferase 1526145..1526921 Dinoroseobacter shibae DFL 12 = DSM 16493 5712650 YP_001532816.1 CDS Dshi_1473 NC_009952.1 1526918 1527763 D Glycerophospholipid metabolism; phospholipid/glycerol acyltransferase 1526918..1527763 Dinoroseobacter shibae DFL 12 = DSM 16493 5712651 YP_001532817.1 CDS Dshi_1474 NC_009952.1 1527727 1528590 R similar to Glutamyl-Q tRNA(Asp) synthetase which catalyzes the tRNA-independent activation of glutamate in presence of ATP and the subsequent transfer of glutamate onto a tRNA(Asp).; glutamyl-tRNA synthetase complement(1527727..1528590) Dinoroseobacter shibae DFL 12 = DSM 16493 5712652 YP_001532818.1 CDS gid NC_009952.1 1528630 1529985 R 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 complement(1528630..1529985) Dinoroseobacter shibae DFL 12 = DSM 16493 5712653 YP_001532819.1 CDS gyrA NC_009952.1 1530153 1532894 R negatively supercoils closed circular double-stranded DNA; DNA gyrase subunit A complement(1530153..1532894) Dinoroseobacter shibae DFL 12 = DSM 16493 5712654 YP_001532820.1 CDS Dshi_1477 NC_009952.1 1533086 1533355 D not in the trp operon, Usg is normally found in trpF, trpB, and trpA context; Usg family protein 1533086..1533355 Dinoroseobacter shibae DFL 12 = DSM 16493 5712655 YP_001532821.1 CDS Dshi_1478 NC_009952.1 1533483 1533950 R The DsbB protein oxidises the periplasmic protein DsbA which in turn oxidises cysteines in other periplasmic proteins in order to make disulfide bonds; disulfide bond formation protein DsbB complement(1533483..1533950) Dinoroseobacter shibae DFL 12 = DSM 16493 5712656 YP_001532822.1 CDS Dshi_1479 NC_009952.1 1534029 1534640 R the exo genes are involved in exopolysaccharide biosynthesis, exoD of Rhizobium meliloti encodes a function needed for alfalfa nodule invasion; exopolysaccharide synthesis ExoD complement(1534029..1534640) Dinoroseobacter shibae DFL 12 = DSM 16493 5712657 YP_001532823.1 CDS Dshi_1480 NC_009952.1 1535034 1536077 D TRAP gene cluster - dctPQM; TRAP dicarboxylate transporter subunit DctP 1535034..1536077 Dinoroseobacter shibae DFL 12 = DSM 16493 5712658 YP_001532824.1 CDS Dshi_1481 NC_009952.1 1536263 1536844 D TRAP gene cluster - dctPQM; hypothetical protein 1536263..1536844 Dinoroseobacter shibae DFL 12 = DSM 16493 5712659 YP_001532825.1 CDS Dshi_1482 NC_009952.1 1536841 1538193 D TRAP gene cluster - dctPQM; DctM subunit; TRAP dicarboxylate transporter 1536841..1538193 Dinoroseobacter shibae DFL 12 = DSM 16493 5712660 YP_001532826.1 CDS Dshi_1483 NC_009952.1 1538375 1538743 R hypothetical protein complement(1538375..1538743) Dinoroseobacter shibae DFL 12 = DSM 16493 5712662 YP_001532827.1 CDS Dshi_1484 NC_009952.1 1538907 1539512 R hypothetical protein complement(1538907..1539512) Dinoroseobacter shibae DFL 12 = DSM 16493 5712663 YP_001532828.1 CDS Dshi_1485 NC_009952.1 1539700 1542114 R DOMAINS: FAD dependent oxidoreductase, Glycine cleavage T-protein, involved in amine and polyamine degradation; FAD dependent oxidoreductase complement(1539700..1542114) Dinoroseobacter shibae DFL 12 = DSM 16493 5712664 YP_001532829.1 CDS Dshi_1486 NC_009952.1 1542296 1544161 R Betaine / Carnitine / Choline Transporter, The BCCT proteins contain 12 transmembrane regions and are energized by proton symport; BCCT transporter complement(1542296..1544161) Dinoroseobacter shibae DFL 12 = DSM 16493 5712665 YP_001532830.1 CDS Dshi_1487 NC_009952.1 1544432 1546513 R ABC transporter (importer) gene cluster: 2 fused ATPase/ Oligopeptide/dipeptide transporter, C-terminal region domains; ATPase subunit; oligopeptide/dipeptide ABC transporter complement(1544432..1546513) Dinoroseobacter shibae DFL 12 = DSM 16493 5712666 YP_001532831.1 CDS Dshi_1488 NC_009952.1 1546583 1547743 R ABC transporter (importer) gene cluster: 2nd membrane spanning domain (MSD); part of a heterotetramer; binding-protein-dependent transport system inner membrane protein complement(1546583..1547743) Dinoroseobacter shibae DFL 12 = DSM 16493 5712667 YP_001532832.1 CDS Dshi_1489 NC_009952.1 1547754 1548845 R ABC transporter (importer) gene cluster: 1st membrane spanning domain (MSD); part of a heterotetramer; binding-protein-dependent transport system inner membrane protein complement(1547754..1548845) Dinoroseobacter shibae DFL 12 = DSM 16493 5712668 YP_001532833.1 CDS Dshi_1490 NC_009952.1 1548941 1550608 R ABC transporter (importer) gene cluster: receptor; family 5 extracellular solute-binding protein complement(1548941..1550608) Dinoroseobacter shibae DFL 12 = DSM 16493 5712669 YP_001532834.1 CDS Dshi_1491 NC_009952.1 1550866 1551678 R only 1 DNA-binding domain, no substrate binding domain; AraC family; transcriptional regulator complement(1550866..1551678) Dinoroseobacter shibae DFL 12 = DSM 16493 5712670 YP_001532835.1 CDS miaA NC_009952.1 1551737 1552627 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(1551737..1552627) Dinoroseobacter shibae DFL 12 = DSM 16493 5712671 YP_001532836.1 CDS pyrH NC_009952.1 1552737 1553468 D Catalyzes the phosphorylation of UMP to UDP; uridylate kinase 1552737..1553468 Dinoroseobacter shibae DFL 12 = DSM 16493 5712672 YP_001532837.1 CDS frr NC_009952.1 1553599 1554165 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 1553599..1554165 Dinoroseobacter shibae DFL 12 = DSM 16493 5712673 YP_001532838.1 CDS uppS NC_009952.1 1554231 1554962 D Generates undecaprenyl pyrophosphate (UPP) from isopentenyl pyrophosphate (IPP). UPP is the precursor of glycosyl carrier lipid in the biosynthesis of bacterial cell wall polysaccharide components such as peptidoglycan and lipopolysaccharide; undecaprenyl diphosphate synthase 1554231..1554962 Dinoroseobacter shibae DFL 12 = DSM 16493 5712674 YP_001532839.1 CDS cdsA1 NC_009952.1 1554983 1555774 D catalyzes the synthesis of CDP-diacylglycerol from CTP and phosphatidate (PA): CDP-diacylglycerol is an important branch point intermediate in both prokaryotic and eukaryotic organisms.; phosphatidate cytidylyltransferase 1554983..1555774 Dinoroseobacter shibae DFL 12 = DSM 16493 5712675 YP_001532840.1 CDS dxr NC_009952.1 1555798 1556979 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 1555798..1556979 Dinoroseobacter shibae DFL 12 = DSM 16493 5712676 YP_001532841.1 CDS ecfE NC_009952.1 1557041 1558378 D Zinc-Metalloprotease; Degrades both heat shock sigma factors rpoE and rpoH.; putative membrane-associated zinc metalloprotease 1557041..1558378 Dinoroseobacter shibae DFL 12 = DSM 16493 5712677 YP_001532842.1 CDS yaeT NC_009952.1 1558817 1561063 D involved in the assembly of proteins into the outer membrane of Gram-negative bacteria; hypothetical protein 1558817..1561063 Dinoroseobacter shibae DFL 12 = DSM 16493 5712678 YP_001532843.1 CDS Dshi_1500 NC_009952.1 1561065 1561640 D Skp (OmpH) has been characterised as a molecular chaperone that interacts with unfolded proteins as they emerge in the periplasm from the Sec translocation machinery; outer membrane chaperone Skp 1561065..1561640 Dinoroseobacter shibae DFL 12 = DSM 16493 5712679 YP_001532844.1 CDS fabZ NC_009952.1 1561725 1562216 D in Pseudomonas aeruginosa this enzyme is a trimer of dimers; essential for membrane formation; performs third step of type II fatty acid biosynthesis; catalyzes dehydration of (3R)-hydroxyacyl-ACP to trans-2-acyl-ACP; (3R)-hydroxymyristoyl-ACP dehydratase 1561725..1562216 Dinoroseobacter shibae DFL 12 = DSM 16493 5712680 YP_001532845.1 CDS lpxA NC_009952.1 1562213 1563013 D catalyzes the addition of (R)-3-hydroxytetradecanoyl to the glucosamine disaccharide in lipid A biosynthesis; UDP-N-acetylglucosamine acyltransferase 1562213..1563013 Dinoroseobacter shibae DFL 12 = DSM 16493 5712681 YP_001532846.1 CDS Dshi_1503 NC_009952.1 1563017 1563814 D COG: COG3494 - Uncharacterized protein conserved in bacteria, PFAM: pfam06230 Protein of unknown function (DUF1009); hypothetical protein 1563017..1563814 Dinoroseobacter shibae DFL 12 = DSM 16493 5712682 YP_001532847.1 CDS lpxB NC_009952.1 1563814 1564956 D TIGRFAM: TIGR00215 lipid-A-disaccharide synthase, COG: COG0763 - Lipid A disaccharide synthetase, PFAM: LpxB, pfam02684 Lipid-A-disaccharide synthetase, KEGG Pathway: Lipopolysaccharide biosynthesis; lipid-A-disaccharide synthase 1563814..1564956 Dinoroseobacter shibae DFL 12 = DSM 16493 5712683 YP_001532848.1 CDS Dshi_1505 NC_009952.1 1564953 1566149 R SUPERFAMILY: SSF51294; hypothetical protein complement(1564953..1566149) Dinoroseobacter shibae DFL 12 = DSM 16493 5712684 YP_001532849.1 CDS mnmA NC_009952.1 1566319 1567473 R catalyzes a sulfuration reaction to synthesize 2-thiouridine at the U34 position of tRNAs; tRNA-specific 2-thiouridylase MnmA complement(1566319..1567473) Dinoroseobacter shibae DFL 12 = DSM 16493 5712685 YP_001532850.1 CDS Dshi_1507 NC_009952.1 1567599 1567877 D PFAM: PF06627; related to DUF1153; hypothetical protein 1567599..1567877 Dinoroseobacter shibae DFL 12 = DSM 16493 5712686 YP_001532851.1 CDS ctrA NC_009952.1 1567977 1568690 D SWISSPROT Q45994: Cell cycle transcriptional regulator; PRODOM: PD000039, PD000329; PFAM: PF00486, PF00072; SMART: SM00448, PROFILE: PS50110; SUPERFAMILY: SSF52172, COG: COG0745 - Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain; Response regulator sokA; cell cycle transcriptional regulator ctrA 1567977..1568690 Dinoroseobacter shibae DFL 12 = DSM 16493 5712687 YP_001532852.1 CDS ligA NC_009952.1 1568730 1570955 D SWISSPROT P15042: DNA ligase; PFAM: pfam01653, pfam03120, pfam00533, pfam03119; COG: COG0272 - NAD-dependent DNA ligase (contains BRCT domain type II), TIGRFAM: TIGR00575 DNA ligase, NAD-dependent; NAD-dependent; DNA ligase 1568730..1570955 Dinoroseobacter shibae DFL 12 = DSM 16493 5712688 YP_001532853.1 CDS recG NC_009952.1 1570952 1573042 D catalyzes branch migration in Holliday junction intermediates; ATP-dependent DNA helicase RecG 1570952..1573042 Dinoroseobacter shibae DFL 12 = DSM 16493 5712689 YP_001532854.1 CDS Dshi_1511 NC_009952.1 1573442 1574914 R SWISSPROT P42663: Thermostable carboxypeptidase 1; PFAM: pfam02074; COG: COG2317 - Zn-dependent carboxypeptidase; carboxypeptidase Taq complement(1573442..1574914) Dinoroseobacter shibae DFL 12 = DSM 16493 5712690 YP_001532855.1 CDS Dshi_1512 NC_009952.1 1574911 1576062 R PFAM: pfam02628; COG: COG1612 - Uncharacterized protein required for cytochrome oxidase assembly; putative cytochrome oxidase assembly protein complement(1574911..1576062) Dinoroseobacter shibae DFL 12 = DSM 16493 5713169 YP_001532856.1 CDS Dshi_1513 NC_009952.1 1576115 1576882 R PFAM: pfam00588; COG: COG0565 - rRNA methylase; TIGRFAM: TIGR00050 rRNA methylase, putative, group 1; SpoU family; putative tRNA/rRNA methyltransferase complement(1576115..1576882) Dinoroseobacter shibae DFL 12 = DSM 16493 5713170 YP_001532857.1 CDS Dshi_1514 NC_009952.1 1576962 1577585 D PFAM: pfam02581; COG: COG0352 Thiamine monophosphate synthase; TIGRFAM: TIGR00693 thiamine-phosphate pyrophosphorylase; putative thiamine monophosphate synthase 1576962..1577585 Dinoroseobacter shibae DFL 12 = DSM 16493 5713171 YP_001532858.1 CDS hisI NC_009952.1 1577589 1577948 R SWISSPROT Q53158: Phosphoribosyl-AMP cyclohydrolase; PFAM: pfam01502, COG: COG0139 - Phosphoribosyl-AMP cyclohydrolase; phosphoribosyl-AMP cyclohydrolase complement(1577589..1577948) Dinoroseobacter shibae DFL 12 = DSM 16493 5713172 YP_001532859.1 CDS Dshi_1516 NC_009952.1 1578009 1578458 D PFAM: PF01592, COG: COG0822 - NifU homolog involved in Fe-S cluster formation.; related to NIFU; hypothetical protein 1578009..1578458 Dinoroseobacter shibae DFL 12 = DSM 16493 5713173 YP_001532860.1 CDS Dshi_1517 NC_009952.1 1578568 1579872 R PFAM: pfam02653, COG: COG4177- ABC-type branched-chain amino acid transport system / permease component; related to amino acid / sugar transport system; hypothetical protein complement(1578568..1579872) Dinoroseobacter shibae DFL 12 = DSM 16493 5713174 YP_001532861.1 CDS Dshi_1518 NC_009952.1 1579869 1580879 R PFAM: pfam02653, COG: COG0559- Branched-chain amino acid ABC-type transport system, permease components; similar to branched -chain amino acid transporter, permease subunit; hypothetical protein complement(1579869..1580879) Dinoroseobacter shibae DFL 12 = DSM 16493 5713175 YP_001532862.1 CDS Dshi_1519 NC_009952.1 1580879 1581238 R associated with ABC-transport system cluster; hypothetical protein complement(1580879..1581238) Dinoroseobacter shibae DFL 12 = DSM 16493 5713176 YP_001532863.1 CDS livF2 NC_009952.1 1581242 1582075 R SWISSPROT P22731: High-affinity branched-chain amino acid transport ATP-binding protein livF; PFAM: PF00005; PROSITE: PS50893; SMART: SM00382; COG: COG0410 -ABC-type branched-chain amino acid transport systems, ATPase component.; high-affinity branched-chain amino acid transport ATP-binding protein complement(1581242..1582075) Dinoroseobacter shibae DFL 12 = DSM 16493 5713177 YP_001532864.1 CDS Dshi_1521 NC_009952.1 1582072 1582854 R SWISSPROT P0A9S7: High-affinity branched-chain amino acid transport ATP-binding protein livG; PFAM: PF00005; PROSITE: PS00211, PS50893; SMART: SM00382; COG: COG0411 - ABC-type branched-chain amino acid transport systems, ATPase component; livG; putative high-affinity branched-chain amino acid transport ATP-binding protein complement(1582072..1582854) Dinoroseobacter shibae DFL 12 = DSM 16493 5713178 YP_001532865.1 CDS Dshi_1522 NC_009952.1 1582914 1584101 R PFAM: pfam01094, COG: COG0683 - ABC-type branched-chain amino acid transport systems, periplasmic component, SWISSPROT: P04816: Leucine-specific-binding protein livK [Precursor]; SUPERFAMILY: SSF53822; associated with ABC transport system; LivK; putative periplasmic ligand-binding protein complement(1582914..1584101) Dinoroseobacter shibae DFL 12 = DSM 16493 5713179 YP_001532866.1 CDS yliI NC_009952.1 1584337 1585446 D COG: COG2133, PFAM (GSDH): pfam07995, Gene3D: G3DSA:2.120.10.30, SUPERFAMILY: SSF50952, SWISSPROT P75804: Soluble aldose sugar dehydrogenase yliI [Precursor]; aldose sugar dehydrogenase 1584337..1585446 Dinoroseobacter shibae DFL 12 = DSM 16493 5713180 YP_001532867.1 CDS Dshi_1524 NC_009952.1 1585464 1586033 R hypothetical protein complement(1585464..1586033) Dinoroseobacter shibae DFL 12 = DSM 16493 5713181 YP_001532868.1 CDS Dshi_1525 NC_009952.1 1586124 1587143 R PFAM: PF01965, PF00165; COG: COG4977 - Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain; AraC family; HTH-type transcriptional regulator complement(1586124..1587143) Dinoroseobacter shibae DFL 12 = DSM 16493 5713182 YP_001532869.1 CDS aroH NC_009952.1 1587318 1588694 D SWISSPROT P80574: Phospho-2-dehydro-3-deoxyheptonate aldolase aroH; PFAM: PF01474-Class-II DAHP synthetase family, COG: COG3200 - 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase, TIGRFAM: TIGR01358 3-deoxy-7-phosphoheptulonate synthase, class II; phospho-2-dehydro-3-deoxyheptonate aldolase 1587318..1588694 Dinoroseobacter shibae DFL 12 = DSM 16493 5713183 YP_001532870.1 CDS Dshi_1527 NC_009952.1 1588773 1589510 R pfam07310, COG5388; hypothetical protein complement(1588773..1589510) Dinoroseobacter shibae DFL 12 = DSM 16493 5713184 YP_001532871.1 CDS Dshi_1528 NC_009952.1 1589674 1590558 D PFAM: pfam03755, pfam08340; COG: COG1561 Uncharacterized stress-induced protein; TIGRFAM: TIGR00255 conserved hypothetical protein; similar to YicC-like; hypothetical protein 1589674..1590558 Dinoroseobacter shibae DFL 12 = DSM 16493 5713185 YP_001532872.1 CDS gmk NC_009952.1 1590625 1591278 D Essential for recycling GMP and indirectly, cGMP; guanylate kinase 1590625..1591278 Dinoroseobacter shibae DFL 12 = DSM 16493 5713186 YP_001532873.1 CDS Dshi_1530 NC_009952.1 1591275 1591799 D PFAM: PF00132, COG: COG0663 COG: Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily; SUPERFAMILY: SSF51161, SWISSPROT: P0A9W9 Protein yrdA; LpxA-like; gamma-class carbonic anhydrase family protein 1591275..1591799 Dinoroseobacter shibae DFL 12 = DSM 16493 5713187 YP_001532874.1 CDS Dshi_1531 NC_009952.1 1591903 1592376 R hypothetical protein complement(1591903..1592376) Dinoroseobacter shibae DFL 12 = DSM 16493 5713188 YP_001532875.1 CDS phoR NC_009952.1 1592488 1593549 D SWISSPROT P08400: Phosphate regulon sensor protein phoR; PFAM: PF02518, PF00512; SMART: SM00387, SM00091; SM00388; COG: COG5002-Signal transduction histidine kinase; putative phosphate regulon sensor protein (phoR); histidine kinase 1592488..1593549 Dinoroseobacter shibae DFL 12 = DSM 16493 5713189 YP_001532876.1 CDS Dshi_1533 NC_009952.1 1593702 1594727 D SWISSPROT Q4L694: Phosphate-binding protein pstS [precursor]; COG: COG0226 - ABC-type phosphate transport system, periplasmic component; Gene3D: G3DSA:3.40.190.10; SUPERFAMILY: SSF53850; associated with ABC transport system involved in phosphate import; periplasmic-binding protein 1593702..1594727 Dinoroseobacter shibae DFL 12 = DSM 16493 5713190 YP_001532877.1 CDS pstC NC_009952.1 1594799 1596268 D SWISSPROT: P0AGH8 Phosphate transport system permease protein pstC, TIGRFAM: TIGR02138, PFAM: PF00528, COG: COG0573, PROSITE: PS50928; phosphate ABC transporter permease 1594799..1596268 Dinoroseobacter shibae DFL 12 = DSM 16493 5713191 YP_001532878.1 CDS pstA NC_009952.1 1596265 1597617 D SWISSPROT P07654: Phosphate transport system permease protein pstCTIGRFAM: TIGR00974 - phosphate ABC transporter, permease protein PstA, PFAM: pfam00528, COG: COG0573 - ABC-type phosphate transport system, permease component; PROSITE: PS50928; phosphate ABC transporter permease 1596265..1597617 Dinoroseobacter shibae DFL 12 = DSM 16493 5713192 YP_001532879.1 CDS pstB NC_009952.1 1597634 1598428 D 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 1597634..1598428 Dinoroseobacter shibae DFL 12 = DSM 16493 5713193 YP_001532880.1 CDS phoU NC_009952.1 1598428 1599141 D SWISSPROT: P0A9K7, TIGRFAM: TIGR02135, PFAM: pfam01895; phosphate transport system protein 1598428..1599141 Dinoroseobacter shibae DFL 12 = DSM 16493 5713194 YP_001532881.1 CDS phoB NC_009952.1 1599146 1599832 D SWISSPROT: P0AFJ5 Phosphate regulon transcriptional regulatory protein, TIGRFAM: TIGR02154 phosphate regulon transcriptional regulatory protein PhoB, PFAM: PF00072, PF00486, COG: COG0745 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain; SUPERFAMILY: SSF52172; CheY-like; phosphate regulon transcriptional regulatory protein 1599146..1599832 Dinoroseobacter shibae DFL 12 = DSM 16493 5713195 YP_001532882.1 CDS Dshi_1539 NC_009952.1 1599990 1600946 D SWISSPROT: P45394 Inner membrane protein yrbG, PFAM: PF01699, TIGRFAM: TIGR00367 K+-dependent Na+/Ca+ exchanger related-protein, COG: COG0530 - Ca2+/Na+ antiporter; PANTHER: PTHR10846; sodium/potassium/calcium exchanger family; inner membrane protein 1599990..1600946 Dinoroseobacter shibae DFL 12 = DSM 16493 5713196 YP_001532883.1 CDS Dshi_1540 NC_009952.1 1601019 1602053 D COG: COG0265, SUPERFAMILY: SSF50494, PFAM: PF00595, PF00089; peptidase S1B family; precursor; protease 1601019..1602053 Dinoroseobacter shibae DFL 12 = DSM 16493 5713197 YP_001532884.1 CDS Dshi_1541 NC_009952.1 1602173 1604119 D PFAM: PF07969, SUPERFAMILY: SSF51556; COG: COG1574 - Predicted metal-dependent hydrolase with the TIM-barrel fold; putative amidohydrolase 3 1602173..1604119 Dinoroseobacter shibae DFL 12 = DSM 16493 5713198 YP_001532885.1 CDS Dshi_1542 NC_009952.1 1604184 1604711 D hypothetical protein 1604184..1604711 Dinoroseobacter shibae DFL 12 = DSM 16493 5713199 YP_001532886.1 CDS Dshi_1543 NC_009952.1 1604724 1605764 R PFAM: PF01734, SUPERFAMILY: SSF52151; COG: COG1752 Predicted esterase of the alpha-beta hydrolase superfamily; similar to Patatin-like phospholipase; hypothetical protein complement(1604724..1605764) Dinoroseobacter shibae DFL 12 = DSM 16493 5713200 YP_001532887.1 CDS Dshi_1544 NC_009952.1 1605788 1606561 R SWISSPROT P99093: 3-oxoacyl-[acyl-carrier-protein] reductase fabG; TIGRFAM: TIGR01963 3-hydroxybutyrate dehydrogenase; PRINTS: PR00080, PR00081; PANTHER: PTHR19410, PFAM: PF00106 short chain dehydrogenase/reductase, SUPERFAMILY: SSF51735, Gene3D: G3DSA:3.40.50.720, COG: COG1028 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases); short-chain dehydrogenase/reductase family protein complement(1605788..1606561) Dinoroseobacter shibae DFL 12 = DSM 16493 5713201 YP_001532888.1 CDS Dshi_1545 NC_009952.1 1606867 1608687 D COG: COG4166 - ABC-type oligopeptide transport system, periplasmic component; PFAM: PF00496; putative extracellular solute-binding protein 1606867..1608687 Dinoroseobacter shibae DFL 12 = DSM 16493 5713202 YP_001532889.1 CDS Dshi_1546 NC_009952.1 1608891 1609703 R PFAM: PF04367; COG: COG2928 - Uncharacterized conserved protein; hypothetical protein complement(1608891..1609703) Dinoroseobacter shibae DFL 12 = DSM 16493 5713203 YP_001532890.1 CDS Dshi_1547 NC_009952.1 1609759 1610724 R SUPERFAMILY: SSF53613 Ribokinase-like; COG: COG0524, Sugar kinase, ribokinase family; PFAM: PF00294; ribokinase family; putative carbohydrate kinase complement(1609759..1610724) Dinoroseobacter shibae DFL 12 = DSM 16493 5712691 YP_001532891.1 CDS rpsB NC_009952.1 1611039 1611818 D 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 1611039..1611818 Dinoroseobacter shibae DFL 12 = DSM 16493 5712692 YP_001532892.1 CDS tsf NC_009952.1 1611914 1612789 D 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 1611914..1612789 Dinoroseobacter shibae DFL 12 = DSM 16493 5712693 YP_001532893.1 CDS Dshi_1550 NC_009952.1 1613091 1613873 R PFAM: PF00196, PF03472; PROSITE: PS50043; SUPERFAMILY: SSF75516, SSF46894; COG: COG2197; luxR family; putative regulatory protein complement(1613091..1613873) Dinoroseobacter shibae DFL 12 = DSM 16493 5712694 YP_001532894.1 CDS Dshi_1551 NC_009952.1 1613870 1614322 R catalyzes the formation of 3-dehydroshikimate from 3-dehydroquinate in chorismate biosynthesis; 3-dehydroquinate dehydratase complement(1613870..1614322) Dinoroseobacter shibae DFL 12 = DSM 16493 5712695 YP_001532895.1 CDS Dshi_1552 NC_009952.1 1614497 1615753 D SWISSPROT: P44093, PFAM: PF07005; similar to uncharacterized protein HI1011; hypothetical protein 1614497..1615753 Dinoroseobacter shibae DFL 12 = DSM 16493 5712696 YP_001532896.1 CDS Dshi_1553 NC_009952.1 1615750 1616400 D SUPERFAMILY: SSF53639; PFAM: PF00596; COG: COG0235, Ribulose-5-phosphate 4-epimerase and related epimerases and aldolases; putative aldolase 1615750..1616400 Dinoroseobacter shibae DFL 12 = DSM 16493 5712697 YP_001532897.1 CDS Dshi_1554 NC_009952.1 1616397 1617161 D PFAM: PF01261, Gene3D: G3DSA:3.20.20.150, SUPERFAMILY: SSF51658, SWISSPROT: Q6NUD4, P30147; COG: COG3622; putative isomerase 1616397..1617161 Dinoroseobacter shibae DFL 12 = DSM 16493 5712698 YP_001532898.1 CDS Dshi_1555 NC_009952.1 1617231 1617857 R PFAM: PF01381, PF07883; SUPERFAMILY: SSF51182; Gene3D: G3DSA:1.10.260.40; HTH type; putative transcriptional regulator complement(1617231..1617857) Dinoroseobacter shibae DFL 12 = DSM 16493 5712699 YP_001532899.1 CDS Dshi_1556 NC_009952.1 1617876 1619435 D COG: COG0318, Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II; PFAM: PF00501, PANTHER: PTHR11968, PROSITE: PS00455, Gene3D: G3DSA:3.40.50.980, G3DSA:3.30.300.30; putative ATP-dependent AMP-binding enzyme 1617876..1619435 Dinoroseobacter shibae DFL 12 = DSM 16493 5712700 YP_001532900.1 CDS Dshi_1557 NC_009952.1 1619422 1620090 D PFAM: PF01323, SUPERFAMILY: SSF52833, COG: COG2761, Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis; putative DSBA oxidoreductase 1619422..1620090 Dinoroseobacter shibae DFL 12 = DSM 16493 5712701 YP_001532901.1 CDS Dshi_1558 NC_009952.1 1620057 1620377 R hypothetical protein complement(1620057..1620377) Dinoroseobacter shibae DFL 12 = DSM 16493 5712702 YP_001532902.1 CDS Dshi_1559 NC_009952.1 1620493 1621701 D SWISSPROT: P28246, TIGRFAM: TIGR00710- Drug resistance transporter Bcr/CflA subfamily, PANTHER: PTHR10074 Major facilitator subfamily member, Bicyclomycin resistance protein; COG: COG2814- Arabinose efflux permease; PFAM: PF07690; SUPERFAMILY: SSF103473; PROSITE: PS50850; putative bicyclomycin resistance protein; major facilitator superfamily transporter 1620493..1621701 Dinoroseobacter shibae DFL 12 = DSM 16493 5712703 YP_001532903.1 CDS Dshi_1560 NC_009952.1 1621839 1622270 D hypothetical protein 1621839..1622270 Dinoroseobacter shibae DFL 12 = DSM 16493 5712704 YP_001532904.1 CDS mfd NC_009952.1 1622403 1625885 R SWISSPROT P30958: Transcription-repair-coupling factor, TIGRFAM: TIGR00580 -Transcription-repair coupling factor; PFAM: PF03461, PF02559, PF00270, PF00271; transcription repair coupling factor complement(1622403..1625885) Dinoroseobacter shibae DFL 12 = DSM 16493 5712705 YP_001532905.1 CDS Dshi_1562 NC_009952.1 1626290 1626820 R hypothetical protein complement(1626290..1626820) Dinoroseobacter shibae DFL 12 = DSM 16493 5712706 YP_001532906.1 CDS hemB1 NC_009952.1 1626965 1627966 D catalyzes the formation of porphobilinogen from 5-aminolevulinate; delta-aminolevulinic acid dehydratase 1626965..1627966 Dinoroseobacter shibae DFL 12 = DSM 16493 5712707 YP_001532907.1 CDS Dshi_1564 NC_009952.1 1628155 1628724 D PROSITE: PS51257, PFAM: pfam04366, COG: COG2930 - Uncharacterized conserved protein; hypothetical protein 1628155..1628724 Dinoroseobacter shibae DFL 12 = DSM 16493 5712708 YP_001532908.1 CDS Dshi_1565 NC_009952.1 1628799 1631282 D PFAM: PF01804, COG: COG2366 - Protein related to penicillin acylase; putative penicillin acylase; acylase 1628799..1631282 Dinoroseobacter shibae DFL 12 = DSM 16493 5712709 YP_001532909.1 CDS hflX NC_009952.1 1631386 1632633 R SWISSPROT: P25519 - GTP-binding protein hflX, PANTHER: PTHR10229, PFAM: PF01926, SUPERFAMILY: SSF52540, Gene3D: G3DSA:3.40.50.300; GTP-binding protein complement(1631386..1632633) Dinoroseobacter shibae DFL 12 = DSM 16493 5712710 YP_001532910.1 CDS hfq NC_009952.1 1632675 1632953 R Stimulates the elongation of poly(A) tails; RNA-binding protein Hfq complement(1632675..1632953) Dinoroseobacter shibae DFL 12 = DSM 16493 5712711 YP_001532911.1 CDS trkH NC_009952.1 1633034 1634542 R SWISSPROT: Q9L6L2, P23849 - Trk system potassium uptake protein trkH; COG: COG0168 - Trk-type K+ transport systems, membrane components; PFAM: PF02386; potassium uptake protein complement(1633034..1634542) Dinoroseobacter shibae DFL 12 = DSM 16493 5712712 YP_001532912.1 CDS trkA NC_009952.1 1634542 1635918 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(1634542..1635918) Dinoroseobacter shibae DFL 12 = DSM 16493 5712713 YP_001532913.1 CDS Dshi_1570 NC_009952.1 1636081 1636563 D hypothetical protein 1636081..1636563 Dinoroseobacter shibae DFL 12 = DSM 16493 5712714 YP_001532914.1 CDS Dshi_1571 NC_009952.1 1636586 1637023 D hypothetical protein 1636586..1637023 Dinoroseobacter shibae DFL 12 = DSM 16493 5712715 YP_001532915.1 CDS ntrX NC_009952.1 1637185 1638600 R SWISSPROT: P03029 - Nitrogen assimilation regulatory protein ntrX; PFAM: PF00072, PF00158, PF02954; SUPERFAMILY: SSF52172, SSF52540; COG: COG2204; sigma factor 54; nitrogen assimilation regulator receiver protein complement(1637185..1638600) Dinoroseobacter shibae DFL 12 = DSM 16493 5712716 YP_001532916.1 CDS ntrY NC_009952.1 1638597 1640900 R SWISSPROT Q04850: Nitrogen regulation protein ntrY; PANTHER: Two-component Histidine Kinase; COG: COG5000 & PIRSF - Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation; PFAM: PF00512, PF00672, PF02518; TIGRFAM: TIGR00229; SMART: SM00091; PROSITE: PS50112; nitrogen regulation protein; histidine kinase complement(1638597..1640900) Dinoroseobacter shibae DFL 12 = DSM 16493 5712717 YP_001532917.1 CDS ntrC NC_009952.1 1640962 1642326 R SWISSPROT P10577: Nitrogen assimilation regulatory protein; COG: COG2204 - Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains; PFAM: PF02954, PF00072, PF00158; SUPERFAMILY: SSF52172; sigma factor 54; nitrogen assimilation regulator receiver protein complement(1640962..1642326) Dinoroseobacter shibae DFL 12 = DSM 16493 5712718 YP_001532918.1 CDS ntrB NC_009952.1 1642326 1643399 R SWISSPROT P09431, P0AFB5: Nitrogen regulation protein ntrB; COG: COG3852 - Signal transduction histidine kinase, nitrogen specific; PFAM: PF00512, PF02518; SMART: SM00091; nitrogen regulation protein complement(1642326..1643399) Dinoroseobacter shibae DFL 12 = DSM 16493 5712719 YP_001532919.1 CDS dus NC_009952.1 1643396 1644397 R TIGRFAM: Dihydrouridine synthase TIM-barrel, NifR3; COG: COG0042 - tRNA-dihydrouridine synthase, PFAM: pfam01207; alternative gene name: nifR; tRNA-dihydrouidine synthase complement(1643396..1644397) Dinoroseobacter shibae DFL 12 = DSM 16493 5712720 YP_001532920.1 CDS ispDF NC_009952.1 1644540 1645742 D SWISSPROT Q5LRN5: Bifunctional enzyme ispD/ispF; TIGRFAM: TIGR00151, TIGR00453; PFAM: pfam01128, pfam02542; bifunctional 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase/2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase 1644540..1645742 Dinoroseobacter shibae DFL 12 = DSM 16493 5712721 YP_001532921.1 CDS Dshi_1578 NC_009952.1 1645739 1646227 D SWISSPROT: P18200; COG: COG1267 - Phosphatidylglycerophosphatase A and related proteins; PFAM: PF04608; putative phosphatidylglycerophosphatase A 1645739..1646227 Dinoroseobacter shibae DFL 12 = DSM 16493 5712722 YP_001532922.1 CDS Dshi_1579 NC_009952.1 1646224 1646706 D TIGRFAM: TIGR00199 competence/damage-inducible protein CinA C-terminal domain; COG: COG1546 - Uncharacterized protein (competence- and mitomycin-induced); PFAM: pfam02464; CinA-like protein 1646224..1646706 Dinoroseobacter shibae DFL 12 = DSM 16493 5712723 YP_001532923.1 CDS Dshi_1580 NC_009952.1 1646685 1647200 R COG: COG2867-Oligoketide cyclase/lipid transport protein; PFAM: PF03364; putative polyketide cyclase / dehydrase complement(1646685..1647200) Dinoroseobacter shibae DFL 12 = DSM 16493 5712724 YP_001532924.1 CDS hpt NC_009952.1 1647224 1647760 D SWISSPROT P0A9M2: Hypoxanthine phosphoribosyltransferase, also high similarity to hypoxanthine-guanine phosphoribosyltransferase (SWISSPROT P37171); COG: COG0634 Hypoxanthine-guanine phosphoribosyltransferase; PFAM: PF00156; hypoxanthine phosphoribosyltransferase 1647224..1647760 Dinoroseobacter shibae DFL 12 = DSM 16493 5712725 YP_001532925.1 CDS Dshi_1582 NC_009952.1 1647958 1648476 R similar to transmembrane transport protein; hypothetical protein complement(1647958..1648476) Dinoroseobacter shibae DFL 12 = DSM 16493 5712726 YP_001532926.1 CDS lipA NC_009952.1 1648653 1649603 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(1648653..1649603) Dinoroseobacter shibae DFL 12 = DSM 16493 5712727 YP_001532927.1 CDS Dshi_1584 NC_009952.1 1649803 1650927 R hypothetical protein complement(1649803..1650927) Dinoroseobacter shibae DFL 12 = DSM 16493 5712728 YP_001532928.1 CDS Dshi_1585 NC_009952.1 1651121 1651423 D hypothetical protein 1651121..1651423 Dinoroseobacter shibae DFL 12 = DSM 16493 5712729 YP_001532929.1 CDS mttb NC_009952.1 1651441 1652988 R SWISSPROT O93658: Trimethylamine methyltransferase mttB; COG: COG5598 - Trimethylamine:corrinoid methyltransferase; PFAM: pfam06253; trimethylamine methyltransferase complement(1651441..1652988) Dinoroseobacter shibae DFL 12 = DSM 16493 5712730 YP_001532930.1 CDS guaA NC_009952.1 1653185 1654747 D contains glutamine-hydrolyzing domain and glutamine amidotransferase; GMP-binding domain; functions to produce GMP from XMP in the IMP pathway; GMP synthase 1653185..1654747 Dinoroseobacter shibae DFL 12 = DSM 16493 5712731 YP_001532931.1 CDS Dshi_1588 NC_009952.1 1654738 1655379 D COG: COG1434-Uncharacterized conserved protein; PFAM: pfam02698- Uncharacterized ACR, COG1434; hypothetical protein 1654738..1655379 Dinoroseobacter shibae DFL 12 = DSM 16493 5712732 YP_001532932.1 CDS Dshi_1589 NC_009952.1 1655376 1656263 D SWISSPROT Q68XV0: S-adenosylmethionine uptake transporter; PFAM: pfam00892; similar to S-adenosylmethionine uptake transporter; hypothetical protein 1655376..1656263 Dinoroseobacter shibae DFL 12 = DSM 16493 5712733 YP_001532933.1 CDS Dshi_1590 NC_009952.1 1656339 1657472 D SUPERFAMILY; SST56935-Porins; PFAM: PF03349-Outer membrane protein transport protein (OMPP1/FadL/TodX); COG: COG2067-Long-chain fatty acid transport protein; porin 1656339..1657472 Dinoroseobacter shibae DFL 12 = DSM 16493 5712734 YP_001532934.1 CDS Dshi_1591 NC_009952.1 1657563 1658480 D PFAM: PF00892, SUPERFAMILY: SSF103481; similar to Multidrug resistance efflux transporter EmrE; hypothetical protein 1657563..1658480 Dinoroseobacter shibae DFL 12 = DSM 16493 5712735 YP_001532935.1 CDS Dshi_1592 NC_009952.1 1658518 1659390 D SUPERFAMILY: SSF52540; hypothetical protein 1658518..1659390 Dinoroseobacter shibae DFL 12 = DSM 16493 5712736 YP_001532936.1 CDS metA NC_009952.1 1659426 1660343 D catalyzes the formation of O-succinyl-L-homoserine from succinyl-CoA and L-homoserine in methionine biosynthesis; homoserine O-succinyltransferase 1659426..1660343 Dinoroseobacter shibae DFL 12 = DSM 16493 5712737 YP_001532937.1 CDS Dshi_1594 NC_009952.1 1660318 1661280 D COG: COG0596- Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily); PFAM: pfam00561; SPRINTS: PR00111; putative alpha/beta hydrolase 1660318..1661280 Dinoroseobacter shibae DFL 12 = DSM 16493 5712738 YP_001532938.1 CDS Dshi_1595 NC_009952.1 1661362 1662231 D PFAM: PF03976; putative polyphosphate kinase 2 1661362..1662231 Dinoroseobacter shibae DFL 12 = DSM 16493 5712739 YP_001532939.1 CDS Dshi_1596 NC_009952.1 1662224 1662841 D PFAM: PF00440; COG: COG1309-Transcriptional regulator; similar to HTH-type transcriptional regulator (tetR family); hypothetical protein 1662224..1662841 Dinoroseobacter shibae DFL 12 = DSM 16493 5712740 YP_001532940.1 CDS potA1 NC_009952.1 1662856 1663923 R SWISSPROT P69874: Spermidine/putrescine import ATP-binding protein potA; COG: COG3842-ABC-type spermidine/putrescine transport systems, ATPase components; TIGRFAM: TIGR01187- spermidine/putrescine ABC transporter ATP-binding subunit; PFAM: PF00005, PF08402; SMART: SM00382; PANTHER: PTHR19222; spermidine/putrescine import ATP-binding protein complement(1662856..1663923) Dinoroseobacter shibae DFL 12 = DSM 16493 5712741 YP_001532941.1 CDS Dshi_1598 NC_009952.1 1663920 1664726 R SWISSPROT P0AFR9: Inner membrane ABC transporter permease protein ydcV, P0AFK6: Spermidine/putrescine transport system permease protein potC; COG: COG1177-ABC-type spermidine/putrescine transport system, permease component II; PFAM: PF00528; PROSITE: PS50928; associated with spermidine/putrescine transport system; inner membrane ABC-transporter permease complement(1663920..1664726) Dinoroseobacter shibae DFL 12 = DSM 16493 5712742 YP_001532942.1 CDS potB NC_009952.1 1664723 1665604 R SWISSPROT P0AFK4: Spermidine/putrescine transport system permease protein potB; COG: COG1176-ABC-type spermidine/putrescine transport system, permease component I; PFAM: pfam00528; PROSITE: PS50928; spermidine/putrescine transport system permease complement(1664723..1665604) Dinoroseobacter shibae DFL 12 = DSM 16493 5712743 YP_001532943.1 CDS Dshi_1600 NC_009952.1 1665720 1666031 R COG: COG2329-Uncharacterized enzyme involved in biosynthesis of extracellular polysaccharides; PFAM: pfam03992; SUPERFAMILY: SSF54909; monooxygenase complement(1665720..1666031) Dinoroseobacter shibae DFL 12 = DSM 16493 5712744 YP_001532944.1 CDS rpsI NC_009952.1 1666178 1666672 R forms a direct contact with the tRNA during translation; 30S ribosomal protein S9 complement(1666178..1666672) Dinoroseobacter shibae DFL 12 = DSM 16493 5712745 YP_001532945.1 CDS rplM NC_009952.1 1666677 1667135 R in Escherichia coli this protein is one of the earliest assembly proteins in the large subunit; 50S ribosomal protein L13 complement(1666677..1667135) Dinoroseobacter shibae DFL 12 = DSM 16493 5712746 YP_001532946.1 CDS Dshi_1603 NC_009952.1 1667361 1667783 R TIGRFAM: TIGR00369-Phenylacetic acid degradation-related protein; COG: COG2050-Uncharacterized protein, possibly involved in aromatic compounds catabolism; PFAM: PF03061; SWISSPROT Q9I644: UPF0152 protein PA0474, P76084: Phenylacetic acid degradation protein paaI; similar to Phenylacetic acid degradation protein paaI; putative thioesterase superfamily protein complement(1667361..1667783) Dinoroseobacter shibae DFL 12 = DSM 16493 5712747 YP_001532947.1 CDS Dshi_1604 NC_009952.1 1667840 1668634 D Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA; enoyl-CoA hydratase 1667840..1668634 Dinoroseobacter shibae DFL 12 = DSM 16493 5712748 YP_001532948.1 CDS Dshi_1605 NC_009952.1 1668641 1669249 R COG: COG0741-Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains); PFAM: PF01464; lytic murein transglycosylase complement(1668641..1669249) Dinoroseobacter shibae DFL 12 = DSM 16493 5712749 YP_001532949.1 CDS ssb NC_009952.1 1669410 1669916 D TIGRFAM: TIGR00621; COG: COG0629; PFAM: pfam00436; PANTHER: PTHR10302; PROSITE: PS50935; SWISSPROT P0AGE0; single stranded DNA-binding protein 1669410..1669916 Dinoroseobacter shibae DFL 12 = DSM 16493 5712750 YP_001532950.1 CDS Dshi_1607 NC_009952.1 1669966 1671222 R hypothetical protein complement(1669966..1671222) Dinoroseobacter shibae DFL 12 = DSM 16493 5712751 YP_001532951.1 CDS aroB NC_009952.1 1671408 1672559 R catalyzes the formation of 3-dehydroquinate from 3-deoxy-arabino-heptulonate 7-phosphate; functions in aromatic amino acid biosynthesis; 3-dehydroquinate synthase complement(1671408..1672559) Dinoroseobacter shibae DFL 12 = DSM 16493 5712752 YP_001532952.1 CDS aroK NC_009952.1 1672630 1673187 R catalyzes the formation of shikimate 3-phosphate from shikimate in aromatic amino acid biosynthesis; shikimate kinase complement(1672630..1673187) Dinoroseobacter shibae DFL 12 = DSM 16493 5712753 YP_001532953.1 CDS Dshi_1610 NC_009952.1 1673376 1674959 D hypothetical protein 1673376..1674959 Dinoroseobacter shibae DFL 12 = DSM 16493 5712754 YP_001532954.1 CDS xerD NC_009952.1 1674956 1675882 D SWISSPROT: P0A8P8 Tyrosine recombinase xerD; COG: COG4974 - Site-specific recombinase XerD; PFAM: pfam00589, pfam02899; SUPERFAMILY: SSF47823, SSF56349; tyrosine recombinase 1674956..1675882 Dinoroseobacter shibae DFL 12 = DSM 16493 5712755 YP_001532955.1 CDS Dshi_1612 NC_009952.1 1675879 1676685 R COG: COG0622 - Predicted phosphoesterase; SUPERFAMILY: Metallo-dependent phosphatases; Gene3D: [PDB] Hydrolase; putative phosphatase complement(1675879..1676685) Dinoroseobacter shibae DFL 12 = DSM 16493 5712756 YP_001532956.1 CDS Dshi_1613 NC_009952.1 1676755 1678056 D SWISSPROT P37908: UPF0053 inner membrane protein yfjD; PFAM: pfam01595, pfam03471, pfam00571; PANTHER: PTHR22777; hypothetical protein 1676755..1678056 Dinoroseobacter shibae DFL 12 = DSM 16493 5712757 YP_001532957.1 CDS yjgR NC_009952.1 1678074 1679633 R SWISSPROT P39342: Uncharacterized protein yjgR; PFAM: pfam05872; SUPERFAMILY: SSF52540; Gene3D: G3DSA:3.40.50.300; similar to uncharacterized protein yjgR (E.coli); hypothetical protein complement(1678074..1679633) Dinoroseobacter shibae DFL 12 = DSM 16493 5712758 YP_001532958.1 CDS Dshi_1615 NC_009952.1 1680082 1680672 D COG: COG5342 - Invasion protein B, involved in pathogenesis, PFAM: pfam06776; similar to Invasion protein B; hypothetical protein 1680082..1680672 Dinoroseobacter shibae DFL 12 = DSM 16493 5712759 YP_001532959.1 CDS Dshi_1616 NC_009952.1 1680682 1681893 R PANTHER: Polyketide synthase-related; COG: COG0304 - 3-oxoacyl-(acyl-carrier-protein) synthase; SWISSPROT P04684: Nodulation protein E, P0AAI5: 3-oxoacyl-[acyl-carrier-protein] synthase 2; PFAM: pfam02801, pfam00109; PROSITE: PS00606; beta ketoacyl synthase complement(1680682..1681893) Dinoroseobacter shibae DFL 12 = DSM 16493 5712760 YP_001532960.1 CDS Dshi_1617 NC_009952.1 1681897 1682166 R SWISSPROT P0A6A8: Acyl carrier protein; TIGRFAM: TIGR00517; PFAM: PF00550; PROSITE: PS50075, PS00012; phosphopantetheine attachment site; acyl carrier protein complement(1681897..1682166) Dinoroseobacter shibae DFL 12 = DSM 16493 5712761 YP_001532961.1 CDS lpxD NC_009952.1 1682224 1683315 R COG: COG1044 - UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; TIGRFAM: TIGR01853; PFAM: pfam04613, PF00132; UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase complement(1682224..1683315) Dinoroseobacter shibae DFL 12 = DSM 16493 5712762 YP_001532962.1 CDS Dshi_1619 NC_009952.1 1683367 1684977 R COG: COG2989 - Uncharacterized protein conserved in bacteria; PFAM: pfam01471; SWISSPROT P22525:Uncharacterized protein ycbB; related to uncharacterized protein ycbB (E.coli); hypothetical protein complement(1683367..1684977) Dinoroseobacter shibae DFL 12 = DSM 16493 5712763 YP_001532963.1 CDS Dshi_1620 NC_009952.1 1685275 1685844 D COG: COG3108 - Uncharacterized protein conserved in bacteria; PFAM: pfam05951; SWISSPROT P0AB06: Uncharacterized protein ycbK; similar to uncharcaterized protein ycbK; hypothetical protein 1685275..1685844 Dinoroseobacter shibae DFL 12 = DSM 16493 5712764 YP_001532964.1 CDS Dshi_1621 NC_009952.1 1685849 1686799 R SWISSPROT: 6-phosphofructokinase isozyme 2 (Phosphofructokinase-2) [pfkB]; PROSITE: PS00583; PFAM: PF00294; SUPERFAMILY: SSF53613; putative 6-phosphofructokinase isozyme 2 complement(1685849..1686799) Dinoroseobacter shibae DFL 12 = DSM 16493 5712765 YP_001532965.1 CDS Dshi_1622 NC_009952.1 1686892 1688406 R SWISSPROT Q99289: Thermolabile hemolysin [Precursor]; PFAM: PF00353; PROSITE: PS00330; SPRINT: PR00313 ; SUPERFAMILY: SSF51120; Gene3D: G3DSA:2.150.10.10; COG: COG2931; Calcium binding; putative hemolysin complement(1686892..1688406) Dinoroseobacter shibae DFL 12 = DSM 16493 5712766 YP_001532966.1 CDS sufS NC_009952.1 1688923 1690143 R SWISSPROT P77444: Cysteine desulfurase. Synonym: Selenocysteine lyase; TIGRFAM: TIGR01979; COG: COG0520 - Selenocysteine lyase; PFAM: PF00266; PROSITE: PS00595; SUPERFAMILY: SSF53383; cysteine desulfurase complement(1688923..1690143) Dinoroseobacter shibae DFL 12 = DSM 16493 5712768 YP_001532967.1 CDS Dshi_1624 NC_009952.1 1690144 1690743 R associated with suf system; hypothetical protein complement(1690144..1690743) Dinoroseobacter shibae DFL 12 = DSM 16493 5712769 YP_001532968.1 CDS Dshi_1625 NC_009952.1 1690773 1691270 R associated with suf sytem; hypothetical protein complement(1690773..1691270) Dinoroseobacter shibae DFL 12 = DSM 16493 5712770 YP_001532969.1 CDS sufD NC_009952.1 1691270 1692553 R SWISSPROT P77689: Protein sufD; COG: COG0719 - ABC-type transport system involved in Fe-S cluster assembly, permease component; PFAM: pfam01458; SUPERFAMILY SSF101960: Stabilizer of iron transporter SufD; sufD complement(1691270..1692553) Dinoroseobacter shibae DFL 12 = DSM 16493 5712771 YP_001532970.1 CDS sufC NC_009952.1 1692553 1693308 R SWISSPROT P77499: Probable ATP-dependent transporter sufC; TIGRFAM: TIGR01978 FeS assembly ATPase SufC; PANTHER: PTHR19222:SF6-ABC TRANSPORTER; PFAM: PF00005; PROSITE: PS00211, PS50893; SMART: SM00382; ATP-dependent transporter complement(1692553..1693308) Dinoroseobacter shibae DFL 12 = DSM 16493 5712772 YP_001532971.1 CDS Dshi_1628 NC_009952.1 1693326 1693640 R PFAM: PF01906; COG: COG0393 - Uncharacterized conserved protein; hypothetical protein complement(1693326..1693640) Dinoroseobacter shibae DFL 12 = DSM 16493 5712773 YP_001532972.1 CDS Dshi_1629 NC_009952.1 1693637 1693837 R hypothetical protein complement(1693637..1693837) Dinoroseobacter shibae DFL 12 = DSM 16493 5712774 YP_001532973.1 CDS Dshi_1630 NC_009952.1 1694332 1694541 R hypothetical protein complement(1694332..1694541) Dinoroseobacter shibae DFL 12 = DSM 16493 5712775 YP_001532974.1 CDS sufB NC_009952.1 1694568 1696079 R with SufCD activates cysteine desulfurase SufS; cysteine desulfurase activator complex subunit SufB complement(1694568..1696079) Dinoroseobacter shibae DFL 12 = DSM 16493 5712776 YP_001532975.1 CDS nifS NC_009952.1 1696137 1697183 R SWISSPROT P05341: Cysteine desulfurase; COG: COG1104 - Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes; PANTHER: Cysteine desulforase; PFAM: PF00266; Gene3D: G3DSA:3.40.640.10; alternative gene name: iscS; cysteine desulfurase complement(1696137..1697183) Dinoroseobacter shibae DFL 12 = DSM 16493 5712777 YP_001532976.1 CDS iscR NC_009952.1 1697195 1697683 R SWISSPROT P0AGK8: HTH-type transcriptional regulator iscR; TIGRFAM: TIGR00738 rrf2 family protein (putative transcriptional regulator); COG: COG1959 - Predicted transcriptional regulator; PFAM: PF02082; PROSITE: PS51197; SUPERFAMILY: SSF46785; HTH-type transcriptional regulator complement(1697195..1697683) Dinoroseobacter shibae DFL 12 = DSM 16493 5712778 YP_001532977.1 CDS Dshi_1634 NC_009952.1 1697855 1698508 D COG: COG2945 - Predicted hydrolase of the alpha/beta superfamily; PFAM: pfam00561; SUPERFAMILY: SSF53474; putative alpha/beta hydrolase 1697855..1698508 Dinoroseobacter shibae DFL 12 = DSM 16493 5712779 YP_001532978.1 CDS Dshi_1635 NC_009952.1 1698511 1698726 D hypothetical protein 1698511..1698726 Dinoroseobacter shibae DFL 12 = DSM 16493 5712780 YP_001532979.1 CDS Dshi_1636 NC_009952.1 1698812 1699540 D PFAM: pfam01988; COG: COG1814 - Uncharacterized membrane protein; hypothetical protein 1698812..1699540 Dinoroseobacter shibae DFL 12 = DSM 16493 5712781 YP_001532980.1 CDS Dshi_1637 NC_009952.1 1699686 1700312 D PFAM: PF02588; COG: COG1284 - Uncharacterized conserved protein; hypothetical protein 1699686..1700312 Dinoroseobacter shibae DFL 12 = DSM 16493 5712782 YP_001532981.1 CDS emrE NC_009952.1 1700339 1700668 D SUPERFAMILY: Multidrug resistance efflux transporter EmrE; SWISSPROT P23895: Multidrug transporter emrE; PFAM: PF00893; SUPERFAMILY: SSF103481; efflux-multidrug resistance protein 1700339..1700668 Dinoroseobacter shibae DFL 12 = DSM 16493 5712783 YP_001532982.1 CDS Dshi_1639 NC_009952.1 1700730 1701272 D hypothetical protein 1700730..1701272 Dinoroseobacter shibae DFL 12 = DSM 16493 5713204 YP_001532983.1 CDS Dshi_1640 NC_009952.1 1701269 1701574 D PROSITE: PS51257; hypothetical protein 1701269..1701574 Dinoroseobacter shibae DFL 12 = DSM 16493 5713205 YP_001532984.1 CDS Dshi_1641 NC_009952.1 1701587 1701880 R PFAM: PF07045; hypothetical protein complement(1701587..1701880) Dinoroseobacter shibae DFL 12 = DSM 16493 5713206 YP_001532985.1 CDS alaS NC_009952.1 1701885 1704548 R 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 complement(1701885..1704548) Dinoroseobacter shibae DFL 12 = DSM 16493 5713207 YP_001532986.1 CDS recA NC_009952.1 1704693 1705760 R 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 complement(1704693..1705760) Dinoroseobacter shibae DFL 12 = DSM 16493 5713208 YP_001532987.1 CDS Dshi_1644 NC_009952.1 1705935 1708274 R COG: COG4191 - Signal transduction histidine kinase regulating C4-dicarboxylate transport system; SMART: SM0009, SM00448, SM00387, SM00388; PROSITE: PS50110, PS50109; PFAM: PF00072, PF02518, PF00512; SPRINTS: PR00344; SUPERFAMILY: SSF55874; histidine kinase complement(1705935..1708274) Dinoroseobacter shibae DFL 12 = DSM 16493 5713209 YP_001532988.1 CDS rsmB2 NC_009952.1 1708348 1709526 R SWISSPROT P36929: Ribosomal RNA small subunit methyltransferas B / rRNA (cytosine-C(5)-)-methyltransferase; PFAM: PF01189; SUPERFAMILY: SSF53335; rRNA (cytosine-C(5)-)-methyltransferase complement(1708348..1709526) Dinoroseobacter shibae DFL 12 = DSM 16493 5713210 YP_001532989.1 CDS guaB NC_009952.1 1709530 1710984 R TIGRFAM: TIGR01302 inosine-5-monophosphate dehydrogenase; COG: COG0516 - IMP dehydrogenase/GMP reductase; PANTHER: INOSINE-5-MONOPHOSPHATE DEHYDROGENASE (PTHR11911:SF6); PFAM: PF00478, PF00571; SMART: SM00116; inosine-5'-monophosphate dehydrogenase complement(1709530..1710984) Dinoroseobacter shibae DFL 12 = DSM 16493 5713211 YP_001532990.1 CDS hpcH NC_009952.1 1711064 1711846 R SWISSPROT Q47098: 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase; PFAM: PF03328; Gene3D: G3DSA:3.20.20.60; SUPERFAMILY: SSF51621; 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase complement(1711064..1711846) Dinoroseobacter shibae DFL 12 = DSM 16493 5713212 YP_001532991.1 CDS malK NC_009952.1 1712121 1713242 R SWISSPROT P68187: Maltose/maltodextrin import ATP-binding protein malK; COG: COG3839 - ABC-type sugar transport systems, ATPase components; PFAM: PF00005, PF08402; SMART: SM00382; SUPERFAMILY: SSF50331; maltose/maltodextrin import ATP-binding protein complement(1712121..1713242) Dinoroseobacter shibae DFL 12 = DSM 16493 5713213 YP_001532992.1 CDS Dshi_1649 NC_009952.1 1713282 1714940 R SWISSPROT Q9Z3R8: Probable alpha-glucosidase; COG: COG0366 - Glycosidases; PFAM: PF00128; SMART: SM00642; SUPERFAMILY: SSF51011, SSF51445; alpha-glucosidase complement(1713282..1714940) Dinoroseobacter shibae DFL 12 = DSM 16493 5713214 YP_001532993.1 CDS Dshi_1650 NC_009952.1 1714954 1716111 R SWISSPROT Q9Z3R7: Alpha-glucoside transport system permease protein aglG, P77716: Inner membrane ABC transporter permease protein ycjP; PFAM: PF00528; PROSITE: PS50928; associated with alpha-glucoside transport system; inner membrane ABC transporter permease complement(1714954..1716111) Dinoroseobacter shibae DFL 12 = DSM 16493 5713215 YP_001532994.1 CDS Dshi_1651 NC_009952.1 1716129 1717133 R SWISSPROT P0AFR7: Inner membrane ABC transporter permease protein ycjO, Q9Z3R6: Alpha-glucoside transport system permease protein aglF; PFAM: PF00528; PROSITE: PS50928; associated with alpha-glucoside transport system; inner membrane ABC transporter permease complement(1716129..1717133) Dinoroseobacter shibae DFL 12 = DSM 16493 5713216 YP_001532995.1 CDS Dshi_1652 NC_009952.1 1717206 1718564 R SWISSPROT Q9Z3R5: Alpha-glucosides-binding periplasmic protein aglE [Precursor]; COG: COG1653 - ABC-type sugar transport system, periplasmic component; PFAM: PF01547; associated with alpha-glucoside transport system; putative solute-binding protein 1 family complement(1717206..1718564) Dinoroseobacter shibae DFL 12 = DSM 16493 5713217 YP_001532996.1 CDS Dshi_1653 NC_009952.1 1718787 1719851 D SWISSPROT Q9Z3R4: HTH-type transcriptional regulator aglR, P21867: HTH-type transcriptional regulator rafR; COG: COG1609 - Transcriptional regulators; PFAM: PF00532; SMART: SM00354; PROSITE: PS50932; HTH-type transcriptional regulator 1718787..1719851 Dinoroseobacter shibae DFL 12 = DSM 16493 5713218 YP_001532997.1 CDS bglA NC_009952.1 1719861 1721168 D SWISSPROT Q08638: Beta-glucosidase A; COG: COG2723 - Beta-glucosidase/6-phospho-beta-glucosidase/beta- galactosidase; PANTHER: GLYCOSIDE HYDROLASES (PTHR10353); PFAM: PF00232; SPRINT: PR00131; PROSITE: PS00572; beta-glucosidase A 1719861..1721168 Dinoroseobacter shibae DFL 12 = DSM 16493 5713219 YP_001532998.1 CDS glk NC_009952.1 1721208 1722179 D SWISSPROT P64254: Glucokinase; TIGRFAM: TIGR00749 glucokinase, proteobacterial type; COG: COG0837; PFAM: PF02685; SUPERFAMILY: SSF53067; glucokinase 1721208..1722179 Dinoroseobacter shibae DFL 12 = DSM 16493 5713220 YP_001532999.1 CDS Dshi_1656 NC_009952.1 1722176 1723027 R SWISSPROT Q55282: Manganese transport system membrane protein mntB, P44660: Probable iron transport system membrane protein HI0359; COG: COG1108 - ABC-type Mn2+/Zn2+ transport systems, permease components; PFAM: pfam00950; SUPERFAMILY: SSF81345; ABC-3 metal transporter complement(1722176..1723027) Dinoroseobacter shibae DFL 12 = DSM 16493 5713221 YP_001533000.1 CDS Dshi_1657 NC_009952.1 1723024 1723923 R SWISSPROT Q55282: Manganese transport system membrane protein mntB, P44661: Probable iron transport system membrane protein HI0360; COG: COG1108 - ABC-type Mn2+/Zn2+ transport systems, permease components; PFAM: pfam00950; SUPERFAMILY: SSF81345; ABC-3 metal transporter complement(1723024..1723923) Dinoroseobacter shibae DFL 12 = DSM 16493 5713222 YP_001533001.1 CDS Dshi_1658 NC_009952.1 1723920 1724816 R SWISSPROT P15031: Iron(III) dicitrate transport ATP-binding protein fecE, Q55281: Manganese transport system ATP-binding protein mntA, P44662: Probable iron transport system ATP-binding protein HI0361; COG: COG1121 - ABC-type Mn/Zn transport systems, ATPase component; PFAM: PF00005; PROSITE: PS00211, PS50893; SMART: SM00382; SUPERFAMILY: SSF52540; Gene3D: G3DSA:3.40.50.300; metal transport system ATP-binding protein complement(1723920..1724816) Dinoroseobacter shibae DFL 12 = DSM 16493 5713223 YP_001533002.1 CDS Dshi_1659 NC_009952.1 1724839 1725729 R SWISSPROT Q57449: Uncharacterized periplasmic iron-binding protein HI0362, P31304: Manganese ABC transporter substrate-binding lipoprotein [Precursor]; COG: COG0803 - ABC-type metal ion transport system, periplasmic component/surface adhesin; PFAM: PF01297; SPRINT: PR00690, PR00691; SUPERFAMILY: SSF53807; Gene3D: G3DSA:3.40.50.1980; metal ABC transporter substrate-binding lipoprotein complement(1724839..1725729) Dinoroseobacter shibae DFL 12 = DSM 16493 5713224 YP_001533003.1 CDS Dshi_1660 NC_009952.1 1725859 1726311 R TIGRFAM: TIGR00738; PFAM: PF02082; SUPERFAMILY: SSF46785; transcriptional regulator complement(1725859..1726311) Dinoroseobacter shibae DFL 12 = DSM 16493 5713225 YP_001533004.1 CDS Dshi_1661 NC_009952.1 1726594 1727178 D COG: COG3707 - Response regulator with putative antiterminator output domain; PFAM: PF00072, PF03861; SUPERFAMILY: SSF52172; transcription antitermination regulatory protein 1726594..1727178 Dinoroseobacter shibae DFL 12 = DSM 16493 5713226 YP_001533005.1 CDS Dshi_1662 NC_009952.1 1727175 1728353 D COG: COG0715 - ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components; SUPERFAMILY: SSF53850; associated with nitrate transport system; periplasmic-binding protein-like II 1727175..1728353 Dinoroseobacter shibae DFL 12 = DSM 16493 5713227 YP_001533006.1 CDS Dshi_1663 NC_009952.1 1728617 1729984 D COG: COG0715 - ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components; SUPERFAMILY: SSF53850; associated with nitrate transport system; periplasmic-binding protein-like II 1728617..1729984 Dinoroseobacter shibae DFL 12 = DSM 16493 5713228 YP_001533007.1 CDS Dshi_1664 NC_009952.1 1730124 1731206 D COG: COG0600 - ABC-type nitrate/sulfonate/bicarbonate transport system, permease component; associated with nitrate transport system; putative ABC transporter permease 1730124..1731206 Dinoroseobacter shibae DFL 12 = DSM 16493 5713229 YP_001533008.1 CDS Dshi_1665 NC_009952.1 1731213 1732898 D TIGRFAM: TIGR01184 nitrate transport ATP-binding subunits C and D; COG: COG1116 - ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component; PFAM: PF00005; SMART: SM00382; SUPERFAMILY: SSF52540; Gene3D: G3DSA:3.40.50.300; nitrate transport ATP binding subunits C and D; ABC transporter 1731213..1732898 Dinoroseobacter shibae DFL 12 = DSM 16493 5713230 YP_001533009.1 CDS Dshi_1666 NC_009952.1 1733027 1733473 D COG: COG1017 - Hemoglobin-like flavoprotein; PFAM: PF00042-Globin; SUPERFAMILY: Globin-like SSF46458; Gene3D: G3DSA:1.10.490.10; SWISSPROT P04252: Bacterial hemoglobin; putative flavohemoglobin 1733027..1733473 Dinoroseobacter shibae DFL 12 = DSM 16493 5713231 YP_001533010.1 CDS nasD NC_009952.1 1733528 1735960 D SWISSPROT P42435: Nitrite reductase [NAD(P)H]; TIGRFAM: TIGR02374 nitrite reductase [NAD(P)H], large subunit; COG: COG1251 - NAD(P)H-nitrite reductase; PFAM: pfam00070, pfam01077, pfam03460, pfam04324; nitrite reductase [NAD(P)H] large subunit 1733528..1735960 Dinoroseobacter shibae DFL 12 = DSM 16493 5713232 YP_001533011.1 CDS nasE NC_009952.1 1735957 1736298 D SWISSPROT P42436: assimilatory nitrite reductase [NAD(P)H], small subunit; TIGRFAM: TIGR02378 nitrite reductase [NAD(P)H], small subunit; COG: COG2146 - Ferredoxin subunits of nitrite reductase and ring-hydroxylating dioxygenases; assimilatory nitrite reductase [NAD(P)H] small subunit 1735957..1736298 Dinoroseobacter shibae DFL 12 = DSM 16493 5713233 YP_001533012.1 CDS nasA NC_009952.1 1736304 1738925 D SWISSPROT Q06457: Nitrate reductase; COG: COG3383 - Uncharacterized anaerobic dehydrogenase; PFAM: pfam00384, pfam01568, pfam04324, pfam04879; nitrate reductase 1736304..1738925 Dinoroseobacter shibae DFL 12 = DSM 16493 5713234 YP_001533013.1 CDS Dshi_1670 NC_009952.1 1738922 1739893 D SWISSPROT Q8R9M6: Anthranilate phosphoribosyltransferase; COG: COG0547 - Anthranilate phosphoribosyltransferase; PFAM: PF02885; Gene3D: G3DSA:3.40.1030.10; SUPERFAMILY: SSF47648, SSF52418; PANTHER: PTHR11922; hypothetical protein 1738922..1739893 Dinoroseobacter shibae DFL 12 = DSM 16493 5713235 YP_001533014.1 CDS cysG NC_009952.1 1739910 1741304 D SWISSPROT P0AEA8: Siroheme synthase; TIGRFAM: TIGR01470, TIGR01469; PFAM: PF00590; Gene3D: G3DSA:3.40.1010.10, G3DSA:3.30.950.10; siroheme synthase 1739910..1741304 Dinoroseobacter shibae DFL 12 = DSM 16493 5713236 YP_001533015.1 CDS Dshi_1672 NC_009952.1 1741348 1742121 R PANTHER: PTHR10920-Ribosomal RNA methyltransferase; PIR: PIRSF005461- 23S riosomal methyltransferase; PFAM: PF01728; ribosomal RNA methyltransferase complement(1741348..1742121) Dinoroseobacter shibae DFL 12 = DSM 16493 5713237 YP_001533016.1 CDS Dshi_1673 NC_009952.1 1742093 1743274 R COG: COG0248 - Exopolyphosphatase; SWISSPROT P25552: Guanosine-5-triphosphate,3-diphosphate pyrophosphatase; PFAM: PF02541; Gene3D: G3DSA:3.30.420.150, G3DSA:3.30.420.40; SUPERFAMILY: SSF53067; phosphatase complement(1742093..1743274) Dinoroseobacter shibae DFL 12 = DSM 16493 5713238 YP_001533017.1 CDS Dshi_1674 NC_009952.1 1743527 1743829 D hypothetical protein 1743527..1743829 Dinoroseobacter shibae DFL 12 = DSM 16493 5713239 YP_001533018.1 CDS Dshi_1675 NC_009952.1 1743856 1744782 D COG:COG0685, Gene3D: G3DSA:3.20.20.220; hypothetical protein 1743856..1744782 Dinoroseobacter shibae DFL 12 = DSM 16493 5713240 YP_001533019.1 CDS Dshi_1676 NC_009952.1 1744794 1745453 D TIGRFAMS: TIGR01509 haloacid dehalogenase superfamily, subfamily IA, variant 3 with third motif having DD or ED; COG: COG0637 - Predicted phosphatase/phosphohexomutase; PFAM: PF00702; SPRINT: PR00413; PROSITE: PS01228; SWISSPROT Q9X0Y1: Phosphorylated carbohydrates phosphatase TM_1254, P77475: Phosphatase yqaB; HAD-like hydrolase 1744794..1745453 Dinoroseobacter shibae DFL 12 = DSM 16493 5713241 YP_001533020.1 CDS Dshi_1677 NC_009952.1 1745450 1746439 D catalyzes the transfer of the N5-methyl group from (6S)-methyl tetrahydrofolate to the cobalt center of a corrinoid iron-sulfur protein; methyltetrahydrofolate:corrinoid/iron-sulfur protein methyltransferase 1745450..1746439 Dinoroseobacter shibae DFL 12 = DSM 16493 5713242 YP_001533021.1 CDS Dshi_1678 NC_009952.1 1746502 1747206 D hypothetical protein 1746502..1747206 Dinoroseobacter shibae DFL 12 = DSM 16493 5713243 YP_001533022.1 CDS Dshi_1679 NC_009952.1 1747369 1747983 D hypothetical protein 1747369..1747983 Dinoroseobacter shibae DFL 12 = DSM 16493 5713244 YP_001533023.1 CDS Dshi_1680 NC_009952.1 1748119 1750191 D COG: COG3894 - Uncharacterized metal-binding protein; PFAM: PF00111; PROSITE: PS51085; similar to ferredoxin; hypothetical protein 1748119..1750191 Dinoroseobacter shibae DFL 12 = DSM 16493 5713245 YP_001533024.1 CDS Dshi_1681 NC_009952.1 1750319 1750810 D COG: COG0824 - Predicted thioesterase; TIGRFAM: TIGR00051-conserved hypothetical protein TIGR00051; PFAM: PF03061; SUPERFAMILY: SSF54637; putative Thioesterase/thiol ester dehydrase-isomerase 1750319..1750810 Dinoroseobacter shibae DFL 12 = DSM 16493 5713247 YP_001533025.1 CDS pgi NC_009952.1 1750801 1752405 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(1750801..1752405) Dinoroseobacter shibae DFL 12 = DSM 16493 5713248 YP_001533026.1 CDS Dshi_1683 NC_009952.1 1752430 1753104 R TIGRFAM: TIGR01198 6-phosphogluconolactonase; COG: COG0363 - 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase; PANTHER: PTHR11054- 6-phosphogluconolactonase; putative 6-phosphogluconolactonase complement(1752430..1753104) Dinoroseobacter shibae DFL 12 = DSM 16493 5713249 YP_001533027.1 CDS zwf NC_009952.1 1753116 1754570 R catalyzes the formation of D-glucono-1,5-lactone 6-phosphate from D-glucose 6-phosphate; glucose-6-phosphate 1-dehydrogenase complement(1753116..1754570) Dinoroseobacter shibae DFL 12 = DSM 16493 5713250 YP_001533028.1 CDS Dshi_1685 NC_009952.1 1754813 1755757 D COG: COG0535 - Predicted Fe-S oxidoreductases; PFAM: PF04055; hypothetical protein 1754813..1755757 Dinoroseobacter shibae DFL 12 = DSM 16493 5713251 YP_001533029.1 CDS Dshi_1686 NC_009952.1 1755768 1756544 R COG: COG1305 - Transglutaminase-like enzymes, putative cysteine proteases; PFAM: pfam01841; SMART: SM00460; SUPERFAMILY: SSF54001; transglutaminase-like; hypothetical protein complement(1755768..1756544) Dinoroseobacter shibae DFL 12 = DSM 16493 5713252 YP_001533030.1 CDS Dshi_1687 NC_009952.1 1756672 1757268 R COG: COG1403 - Restriction endonuclease; PFAM: PF01844-HNH endonuclease; SMART: SM00507-HNH nucleases; putative HNH endonuclease complement(1756672..1757268) Dinoroseobacter shibae DFL 12 = DSM 16493 5713253 YP_001533031.1 CDS Dshi_1688 NC_009952.1 1757458 1758129 R COG: COG0400 - Predicted esterase; PFAM: PF02230; putative phospholipase / carboxylesterase complement(1757458..1758129) Dinoroseobacter shibae DFL 12 = DSM 16493 5713254 YP_001533032.1 CDS Dshi_1689 NC_009952.1 1758126 1758758 R similar to SWISSPROT P04395: DNA-3-methyladenine glycosylase 2, alkylbase DNA glycosidase alkA family member; COG: COG0122 - 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase; PFAM: PF00730; SMART: SM00478; DNA-glycosylase family protein complement(1758126..1758758) Dinoroseobacter shibae DFL 12 = DSM 16493 5713255 YP_001533033.1 CDS cobK NC_009952.1 1758740 1759486 R SWISSPROT P21920: Precorrin-6A reductase; PFAM PF02571: Precorrin-6x reductase CbiJ/CobK; TIGRFAM: TIGR00715; COG: COG2099; precorrin-6A reductase complement(1758740..1759486) Dinoroseobacter shibae DFL 12 = DSM 16493 5713256 YP_001533034.1 CDS cbiD NC_009952.1 1759483 1760532 R PFAM PF01888: CbiD; SUPERFAMILY: CbiD-like; TIGRFAM: TIGR00312 cobalamin biosynthesis protein CbiD; COG: COG1903; SWISSPROT Q2W3X9: putative cobalt-precorrin-6A synthase [deacetylating], belongs to the cbiD-family; cobalamin (vitamin B12) biosynthesis CbiD protein complement(1759483..1760532) Dinoroseobacter shibae DFL 12 = DSM 16493 5713257 YP_001533035.1 CDS cobA1 NC_009952.1 1760630 1761475 D SWISSPROT P21631: Uroporphyrinogen-III C-methyltransferase; TIGRFAM: TIGR01469 uroporphyrin-III C-methyltransferase; COG: COG0007; PFAM: pfam00590; Gene3D: G3DSA:3.30.950.10, G3DSA:3.40.1010.10; PROSITE: PS00840; uroporphyrinogen-III C-methyltransferase 1760630..1761475 Dinoroseobacter shibae DFL 12 = DSM 16493 5713258 YP_001533036.1 CDS cobB NC_009952.1 1761472 1762767 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 1761472..1762767 Dinoroseobacter shibae DFL 12 = DSM 16493 5713259 YP_001533037.1 CDS Dshi_1694 NC_009952.1 1762829 1764055 D PFAM: PF07690; PROSITE: PS50850; major facilitator superfamiy transporter 1762829..1764055 Dinoroseobacter shibae DFL 12 = DSM 16493 5713260 YP_001533038.1 CDS Dshi_1695 NC_009952.1 1764125 1764895 R COG: COG1562 - Phytoene/squalene synthetase; hypothetical protein complement(1764125..1764895) Dinoroseobacter shibae DFL 12 = DSM 16493 5713261 YP_001533039.1 CDS Dshi_1696 NC_009952.1 1764892 1766529 R TIGRFAM: TIGR00977 2-isopropylmalate synthase/homocitrate synthase family protein; COG: COG0119; PFAM: PF00682, PF08502; PROSITE: PS00815, PS00816; SUPERFAMILY: SSF110921, SSF51569; putative alpha-isopropylmalate/homocitrate synthase family transferase complement(1764892..1766529) Dinoroseobacter shibae DFL 12 = DSM 16493 5713262 YP_001533040.1 CDS Dshi_1697 NC_009952.1 1766526 1766948 R hypothetical protein complement(1766526..1766948) Dinoroseobacter shibae DFL 12 = DSM 16493 5713263 YP_001533041.1 CDS cysS NC_009952.1 1767125 1768501 R catalyzes a two-step reaction; charges a cysteine by linking its carboxyl group to the alpha-phosphate of ATP then transfers the aminoacyl-adenylate to its tRNA; cysteinyl-tRNA synthetase complement(1767125..1768501) Dinoroseobacter shibae DFL 12 = DSM 16493 5713264 YP_001533042.1 CDS Dshi_1699 NC_009952.1 1768734 1769330 R COG: COG3637 - Opacity protein and related surface antigens; hypothetical protein complement(1768734..1769330) Dinoroseobacter shibae DFL 12 = DSM 16493 5713265 YP_001533043.1 CDS Dshi_1700 NC_009952.1 1769636 1770391 D PFAM: PF00106-short chain dehydrogenase; PROSITE: PS00061-Short-chain dehydrogenases/reductases family signature; short-chain dehydrogenase/reductase family protein 1769636..1770391 Dinoroseobacter shibae DFL 12 = DSM 16493 5713266 YP_001533044.1 CDS Dshi_1701 NC_009952.1 1770402 1771202 R SWISSPROT P39832: High-affinity zinc uptake system membrane protein znuB; PFAM: PF00950; COG: COG1108 - ABC-type Mn2+/Zn2+ transport systems, permease components; ABC-3 family; znuB; putative high-affinity zinc uptake system membrane protein complement(1770402..1771202) Dinoroseobacter shibae DFL 12 = DSM 16493 5713267 YP_001533045.1 CDS znuC NC_009952.1 1771199 1771942 R SWISSPROT P0A9X1: Zinc import ATP-binding protein znuC; COG: COG1121 - ABC-type Mn/Zn transport systems, ATPase component PFAM: PF00005; SMART: SM00382; SUPERFAMILY: SSF52540; Gene3D: G3DSA:3.40.50.300; zinc import ATP-binding protein complement(1771199..1771942) Dinoroseobacter shibae DFL 12 = DSM 16493 5713268 YP_001533046.1 CDS Dshi_1703 NC_009952.1 1771939 1772436 R SWISSPROT P0AC51: Zinc uptake regulation protein; PRODOM: PD002003; PFAM: pfam01475; zur; putative zinc uptake regulation protein complement(1771939..1772436) Dinoroseobacter shibae DFL 12 = DSM 16493 5713269 YP_001533047.1 CDS Dshi_1704 NC_009952.1 1772514 1773584 D SWISSPROT P39172: High-affinity zinc uptake system protein znuA [Precursor]; COG: COG4531 - ABC-type Zn2+ transport system, periplasmic component/surface adhesin; PFAM: PF01297; znuA; putative high-affinity zinc uptake system protein 1772514..1773584 Dinoroseobacter shibae DFL 12 = DSM 16493 5713270 YP_001533048.1 CDS Dshi_1705 NC_009952.1 1773613 1773951 D hypothetical protein 1773613..1773951 Dinoroseobacter shibae DFL 12 = DSM 16493 5713271 YP_001533049.1 CDS msrB2 NC_009952.1 1773917 1774366 R TIGRFAM: TIGR00357 methionine-R-sulfoxide reductase; COG: COG0229 - Conserved domain frequently associated with peptide methionine sulfoxide reductase; PFAM: pfam01641; peptide methionine sulfoxide reductase complement(1773917..1774366) Dinoroseobacter shibae DFL 12 = DSM 16493 5713272 YP_001533050.1 CDS Dshi_1707 NC_009952.1 1774366 1775166 D SUPERFAMILY: SSF55729; COG: COG3176 - Putative hemolysin; putative acyl-CoA N-acyltransferases (Nat) superfamily protein 1774366..1775166 Dinoroseobacter shibae DFL 12 = DSM 16493 5713273 YP_001533051.1 CDS Dshi_1708 NC_009952.1 1775173 1775952 D PFAM: PF01396, PF08378; SUPERFAMILY: SSF57783; nuclease related; hypothetical protein 1775173..1775952 Dinoroseobacter shibae DFL 12 = DSM 16493 5713274 YP_001533052.1 CDS mscS NC_009952.1 1776333 1777817 R SWISSPROT P0C0S1: Small-conductance mechanosensitive channel; COG: COG0668 - Small-conductance mechanosensitive channel; PFAM: PF00924; SUPERFAMILY: SSF50182, SSF82861, SSF82689; small conductance mechanosensitive channel complement(1776333..1777817) Dinoroseobacter shibae DFL 12 = DSM 16493 5713275 YP_001533053.1 CDS Dshi_1710 NC_009952.1 1778048 1778410 R SWISSPROT P0AC69: Glutaredoxin-4; PFAM: Glutaredoxin; TIGRFAM: TIGR00365 glutaredoxin-related protein; COG: COG0278; putative monothiol glutaredoxin complement(1778048..1778410) Dinoroseobacter shibae DFL 12 = DSM 16493 5713276 YP_001533054.1 CDS Dshi_1711 NC_009952.1 1778403 1778669 R hypothetical protein complement(1778403..1778669) Dinoroseobacter shibae DFL 12 = DSM 16493 5713277 YP_001533055.1 CDS Dshi_1712 NC_009952.1 1778669 1778902 R PFAM: PF01722; PANTHER: PTHR12735; Gene3D: G3DSA:3.30.300.90; COG: COG0271 - Stress-induced morphogen (activity unknown); similar to bolA-like proteins; hypothetical protein complement(1778669..1778902) Dinoroseobacter shibae DFL 12 = DSM 16493 5713278 YP_001533056.1 CDS purL NC_009952.1 1779001 1781172 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(1779001..1781172) Dinoroseobacter shibae DFL 12 = DSM 16493 5713279 YP_001533057.1 CDS Dshi_1714 NC_009952.1 1781528 1783372 D COG: COG0488 - ATPase components of ABC transporters with duplicated ATPase domains; PFAM: PF00005; PROSITE: PS00211, PS50893; SUPERFAMILY: SSF52540; Gene3D: G3DSA:3.40.50.300; ABC transporter ATP-binding protein 1781528..1783372 Dinoroseobacter shibae DFL 12 = DSM 16493 5713280 YP_001533058.1 CDS Dshi_1715 NC_009952.1 1783558 1784403 D SUPERFAMILY: SSF52540; Gene3D: G3DSA:3.40.50.300; PFAM: pfam00685; similar to sulfotransferase; hypothetical protein 1783558..1784403 Dinoroseobacter shibae DFL 12 = DSM 16493 5713281 YP_001533059.1 CDS Dshi_1716 NC_009952.1 1784400 1784858 R COG: COG2913 - Small protein A (tmRNA-binding); hypothetical protein complement(1784400..1784858) Dinoroseobacter shibae DFL 12 = DSM 16493 5713282 YP_001533060.1 CDS Dshi_1717 NC_009952.1 1785059 1785622 D COG: COG1399 - Predicted metal-binding, possibly nucleic acid-binding protein; PFAM: PF02620; hypothetical protein 1785059..1785622 Dinoroseobacter shibae DFL 12 = DSM 16493 5713283 YP_001533061.1 CDS rpmF NC_009952.1 1785846 1786052 D some L32 proteins have zinc finger motifs consisting of CXXC while others do not; 50S ribosomal protein L32 1785846..1786052 Dinoroseobacter shibae DFL 12 = DSM 16493 5713284 YP_001533062.1 CDS plsX NC_009952.1 1786088 1787245 D involved in acylation of glycerol-3-phosphate to form 1-acyl-glycerol-3 phosphate for use in phospholipid biosynthesis; functions with PlsY; putative glycerol-3-phosphate acyltransferase PlsX 1786088..1787245 Dinoroseobacter shibae DFL 12 = DSM 16493 5713285 YP_001533063.1 CDS fabH NC_009952.1 1787238 1788212 D SWISSPROT P0A6R0: 3-oxoacyl-[acyl-carrier-protein] synthase 3. TIGRFAM: TIGR00747 3-oxoacyl-(acyl-carrier-protein) synthase III; COG: COG0332; PFAM: PF08541, PF08545; 3-oxoacyl-ACP synthase 1787238..1788212 Dinoroseobacter shibae DFL 12 = DSM 16493 5713286 YP_001533064.1 CDS ihfA NC_009952.1 1788324 1788629 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 1788324..1788629 Dinoroseobacter shibae DFL 12 = DSM 16493 5713287 YP_001533065.1 CDS Dshi_1722 NC_009952.1 1788669 1789406 D PFAM: PF00376; SMART: SM00422; COG: COG0789 - Predicted transcriptional regulators; similar to MerR family regulatory protein; hypothetical protein 1788669..1789406 Dinoroseobacter shibae DFL 12 = DSM 16493 5713288 YP_001533066.1 CDS Dshi_1723 NC_009952.1 1789628 1790722 D Catalyzes the deamination of dCTP to form dUTP; 2'-deoxycytidine 5'-triphosphate deaminase 1789628..1790722 Dinoroseobacter shibae DFL 12 = DSM 16493 5713290 YP_001533067.1 CDS Dshi_1724 NC_009952.1 1791066 1791755 R TIGRFAM: TIGR00281 segregation and condensation protein B; SWISSPROT Q65HX2: Segregation and condensation protein B; PFAM: PF04079; scpB; putative segregation and condensation protein B complement(1791066..1791755) Dinoroseobacter shibae DFL 12 = DSM 16493 5713291 YP_001533068.1 CDS Dshi_1725 NC_009952.1 1791755 1792549 R SWISSPROT Q87BI4: Segregation and condensation protein A; PFAM: PF02616; scpA; putative Segregation and condensation protein A complement(1791755..1792549) Dinoroseobacter shibae DFL 12 = DSM 16493 5713292 YP_001533069.1 CDS nagZ NC_009952.1 1792572 1793558 R PFAM: PF00933; PROSITE: PS00775; SWISSPROT P75949: Beta-hexosaminidase; COG: COG1472 - Beta-glucosidase-related glycosidases; beta-hexosamidase complement(1792572..1793558) Dinoroseobacter shibae DFL 12 = DSM 16493 5713293 YP_001533070.1 CDS Dshi_1727 NC_009952.1 1793568 1794512 R PFAM: PF05036; related to proteins involved in sporulation and cell division; hypothetical protein complement(1793568..1794512) Dinoroseobacter shibae DFL 12 = DSM 16493 5713294 YP_001533071.1 CDS argS NC_009952.1 1794601 1796346 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(1794601..1796346) Dinoroseobacter shibae DFL 12 = DSM 16493 5713295 YP_001533072.1 CDS Dshi_1729 NC_009952.1 1796409 1797608 R TIGRFAM: TIGR01353 deoxyguanosinetriphosphate triphosphohydrolase, putative, TIGR00277; SWISSPROT P15723: Deoxyguanosinetriphosphate triphosphohydrolase, P63934: Deoxyguanosinetriphosphate triphosphohydrolase-like protein; COG: COG0232 - dGTP triphosphohydrolase; PFAM: pfam01966; putative deoxyguanosinetriphosphate triphosphohydrolase complement(1796409..1797608) Dinoroseobacter shibae DFL 12 = DSM 16493 5713296 YP_001533073.1 CDS Dshi_1730 NC_009952.1 1797652 1797984 D TIGRFAM: TIGR00049 Iron-sulfur cluster assembly accessory protein; PROSITE: PS01152; PFAM: PF01521; iron-sulfur cluster assembly accessory protein 1797652..1797984 Dinoroseobacter shibae DFL 12 = DSM 16493 5713297 YP_001533074.1 CDS Dshi_1731 NC_009952.1 1798047 1798658 R hypothetical protein complement(1798047..1798658) Dinoroseobacter shibae DFL 12 = DSM 16493 5713298 YP_001533075.1 CDS hemK NC_009952.1 1798913 1799737 R SWISSPROT P0ACC1: Protein methyltransferase hemK; TIGRFAM: TIGR00536 HemK family putative methylases; COG: COG2890 - Methylase of polypeptide chain release factors; PFAM: PF08241; PROSITE: PS00092; SUPERFAMILY: SSF53335; putative protein methyltransferase complement(1798913..1799737) Dinoroseobacter shibae DFL 12 = DSM 16493 5713299 YP_001533076.1 CDS prfA NC_009952.1 1799734 1800789 R 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 complement(1799734..1800789) Dinoroseobacter shibae DFL 12 = DSM 16493 5713300 YP_001533077.1 CDS Dshi_1734 NC_009952.1 1801041 1801505 R hypothetical protein complement(1801041..1801505) Dinoroseobacter shibae DFL 12 = DSM 16493 5713301 YP_001533078.1 CDS speB NC_009952.1 1801557 1802531 R catalyzes the formation of putrescine from agmatine; agmatinase complement(1801557..1802531) Dinoroseobacter shibae DFL 12 = DSM 16493 5713302 YP_001533079.1 CDS Dshi_1736 NC_009952.1 1802535 1802939 R PFAM: PF05164- Cell division protein ZapA; putative cell division protein ZapA complement(1802535..1802939) Dinoroseobacter shibae DFL 12 = DSM 16493 5713303 YP_001533080.1 CDS Dshi_1737 NC_009952.1 1802941 1803369 R hypothetical protein complement(1802941..1803369) Dinoroseobacter shibae DFL 12 = DSM 16493 5713304 YP_001533081.1 CDS tktA NC_009952.1 1803674 1805647 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 1803674..1805647 Dinoroseobacter shibae DFL 12 = DSM 16493 5713305 YP_001533082.1 CDS Dshi_1739 NC_009952.1 1805810 1806757 R PFAM: PF05661; COG: COG2354; hypothetical protein complement(1805810..1806757) Dinoroseobacter shibae DFL 12 = DSM 16493 5713306 YP_001533083.1 CDS gap2 NC_009952.1 1807000 1808001 D SWISSPROT P00362: Glyceraldehyde-3-phosphate dehydrogenase; TIGRFAM: TIGR01534 glyceraldehyde-3-phosphate dehydrogenase, type I; COG: COG0057 - Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase; PFAM: pfam02800 pfam00044; glyceraldehyde-3-phosphate dehydrogenase 1807000..1808001 Dinoroseobacter shibae DFL 12 = DSM 16493 5713307 YP_001533084.1 CDS Dshi_1741 NC_009952.1 1808037 1808192 D hypothetical protein 1808037..1808192 Dinoroseobacter shibae DFL 12 = DSM 16493 5713308 YP_001533085.1 CDS gap1 NC_009952.1 1808288 1809310 D SWISSPROT P00362: Glyceraldehyde-3-phosphate dehydrogenase; TIGRFAM: TIGR01534 glyceraldehyde-3-phosphate dehydrogenase, type I; COG: COG0057 - Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase; PFAM: pfam02800 pfam00044; glyceraldehyde-3-phosphate dehydrogenase 1808288..1809310 Dinoroseobacter shibae DFL 12 = DSM 16493 5713309 YP_001533086.1 CDS Dshi_1743 NC_009952.1 1809314 1809916 R PFAM: PF00583; PROSITE: PS51186; related to acetyltransferase, GNAT family; hypothetical protein complement(1809314..1809916) Dinoroseobacter shibae DFL 12 = DSM 16493 5713310 YP_001533087.1 CDS coaD NC_009952.1 1810248 1810763 R Catalyzes the conversion of ATP and pantetheine 4'-phosphate to diphosphate and 3'-dephospho-coA; phosphopantetheine adenylyltransferase complement(1810248..1810763) Dinoroseobacter shibae DFL 12 = DSM 16493 5713311 YP_001533088.1 CDS Dshi_1745 NC_009952.1 1810852 1811286 R PFAM: PF00571; SMART: SM00116; COG: COG2905 - Predicted signal-transduction protein containing cAMP-binding and CBS domains; related to cystathionine beta synthase; hypothetical protein complement(1810852..1811286) Dinoroseobacter shibae DFL 12 = DSM 16493 5713312 YP_001533089.1 CDS Dshi_1746 NC_009952.1 1811339 1812232 R COG: COG0583 - Transcriptional regulator; PFAM: PF00126, PF03466; PROSITE: PS50931; SUPERFAMILY: SSF53850, SSF46785; HTH-type transcriptional regulator complement(1811339..1812232) Dinoroseobacter shibae DFL 12 = DSM 16493 5713313 YP_001533090.1 CDS mmsA NC_009952.1 1812332 1813831 D SWISSPROT P28810: Methylmalonate-semialdehyde dehydrogenase [acylating]; TIGRFAM: TIGR01722 methylmalonic acid semialdehyde dehydrogenase; PANTHER: PTHR11699:SF27; PFAM: PF00171; PROSITE: PS00070; COG: COG1012 - NAD-dependent aldehyde dehydrogenases; acylating methylmalonate-semialdehyde dehydrogenase 1812332..1813831 Dinoroseobacter shibae DFL 12 = DSM 16493 5713314 YP_001533091.1 CDS Dshi_1748 NC_009952.1 1813903 1814532 R hypothetical protein complement(1813903..1814532) Dinoroseobacter shibae DFL 12 = DSM 16493 5713315 YP_001533092.1 CDS Dshi_1749 NC_009952.1 1814843 1815970 D ATP-dependent carboxylate-amine ligase; carboxylate-amine ligase 1814843..1815970 Dinoroseobacter shibae DFL 12 = DSM 16493 5713316 YP_001533093.1 CDS Dshi_1750 NC_009952.1 1816051 1817196 D PFAM: PF00441, PF02770, PF02771; PROSITE: PS00072, PS00073; COG: COG1960 - Acyl-CoA dehydrogenases; acyl-CoA dehydrogenase 1816051..1817196 Dinoroseobacter shibae DFL 12 = DSM 16493 5713317 YP_001533094.1 CDS Dshi_1751 NC_009952.1 1817193 1818239 D COG: COG1024 - Enoyl-CoA hydratase/carnithine racemase; PFAM: PF00378; Gene3D: G3DSA:3.90.226.10; enoyl-CoA hydratase/isomerase family protein 1817193..1818239 Dinoroseobacter shibae DFL 12 = DSM 16493 5713318 YP_001533095.1 CDS mmsB NC_009952.1 1818236 1819111 D TIGRFAM: TIGR01692 3-hydroxyisobutyrate dehydrogenase; PANTHER: PTHR22981; PROSITE: PS00895; PFAM: PF03446; Gene3D: G3DSA:1.10.1040.10; 3-hydroxyisobutyrate dehydrogenase 1818236..1819111 Dinoroseobacter shibae DFL 12 = DSM 16493 5713319 YP_001533096.1 CDS Dshi_1753 NC_009952.1 1819173 1819949 R COG: COG1024 - Enoyl-CoA hydratase/carnithine racemase; PFAM: PF00378; PROSITE: PS00166; enoyl-CoA hydratase complement(1819173..1819949) Dinoroseobacter shibae DFL 12 = DSM 16493 5713320 YP_001533097.1 CDS Dshi_1754 NC_009952.1 1820040 1820456 R hypothetical protein complement(1820040..1820456) Dinoroseobacter shibae DFL 12 = DSM 16493 5713321 YP_001533098.1 CDS Dshi_1755 NC_009952.1 1820449 1820655 R SWISSPROT Q9WZW0: tRNA pseudouridine synthase B; PRODOM: PD012454; similar to tRNA pseudouridine synthase B; putative tRNA pseudouridine synthase B complement(1820449..1820655) Dinoroseobacter shibae DFL 12 = DSM 16493 5713322 YP_001533099.1 CDS Dshi_1756 NC_009952.1 1820645 1821166 R SWISSPROT Q9K197: Carboxylesterase bioH, Q56841: 2-(S)-hydroxypropyl-CoM dehydrogenase; putative carboxylesterase complement(1820645..1821166) Dinoroseobacter shibae DFL 12 = DSM 16493 5713323 YP_001533100.1 CDS Dshi_1757 NC_009952.1 1821157 1821768 R COG: COG3926 - Putative secretion activating protein; PFAM: PF05838; hypothetical protein complement(1821157..1821768) Dinoroseobacter shibae DFL 12 = DSM 16493 5713324 YP_001533101.1 CDS ccmE NC_009952.1 1821878 1822360 R 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 complement(1821878..1822360) Dinoroseobacter shibae DFL 12 = DSM 16493 5713325 YP_001533102.1 CDS argC NC_009952.1 1822376 1823401 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(1822376..1823401) Dinoroseobacter shibae DFL 12 = DSM 16493 5713326 YP_001533103.1 CDS murI NC_009952.1 1823438 1824259 R TIGRFAM: TIGR00067 glutamate racemase; PFAM PF01177: Asp/Glu/Hydantoin racemase; PROSITE: PS00923; COG: COG0796 - Glutamate racemase; glutamate racemase complement(1823438..1824259) Dinoroseobacter shibae DFL 12 = DSM 16493 5713327 YP_001533104.1 CDS Dshi_1761 NC_009952.1 1824259 1825137 R COG: COG3176-Putative hemolysin; PFAM: PF01553; SMART: SM00563; SUPERFAMILY: SSF69593; putative acyltransferase complement(1824259..1825137) Dinoroseobacter shibae DFL 12 = DSM 16493 5713328 YP_001533105.1 CDS Dshi_1762 NC_009952.1 1825196 1828603 R Catalyzes the ferredoxin-dependent oxidative decarboxylation of arylpyruvates; indolepyruvate ferredoxin oxidoreductase complement(1825196..1828603) Dinoroseobacter shibae DFL 12 = DSM 16493 5713329 YP_001533106.1 CDS Dshi_1763 NC_009952.1 1828760 1829662 D SWISSPROT P30846: Uncharacterized HTH-type transcriptional regulator yafC; COG: COG0583 - Transcriptional regulator; PFAM: PF00126, PF03466; PROSITE: PS50931; SUPERFAMILY: SSF53850, SSF46785; HTH-type transcriptional regulator 1828760..1829662 Dinoroseobacter shibae DFL 12 = DSM 16493 5713330 YP_001533107.1 CDS Dshi_1764 NC_009952.1 1829905 1830690 D SUPERFAMILY: SSF53474; PANTHER: PTHR11731; Gene3D: G3DSA:3.40.50.1820; COG: COG0657 - Esterase/lipase; putative hydrolase 1829905..1830690 Dinoroseobacter shibae DFL 12 = DSM 16493 5713331 YP_001533108.1 CDS Dshi_1765 NC_009952.1 1830691 1832526 R SWISSPROT Q99T13: Putative multidrug export ATP-binding/permease protein SAV1866; PROSITE: PS00211, PS50893, PS50929; PFAM: PF00664, PF00005; SMART: SM00382; putative multidrug export ATP-binding/permease complement(1830691..1832526) Dinoroseobacter shibae DFL 12 = DSM 16493 5713332 YP_001533109.1 CDS Dshi_1766 NC_009952.1 1832580 1834175 R PFAM: PF01476; hypothetical protein complement(1832580..1834175) Dinoroseobacter shibae DFL 12 = DSM 16493 5713333 YP_001533110.1 CDS Dshi_1767 NC_009952.1 1834326 1834865 D PFAM: PF03641; TIGRFAM: TIGR00725 conserved hypothetical protein, DprA/Smf-related, family 1, TIGR00730 conserved hypothetical protein, DprA/Smf-related, family 2; SUPERFAMILY SSF102405: putative lysine decarboxylase; putative lysine carboxylase 1834326..1834865 Dinoroseobacter shibae DFL 12 = DSM 16493 5713334 YP_001533111.1 CDS eda NC_009952.1 1835047 1835688 R SWISSPROT P0A955: KHG/KDPG aldolase; PFAM: PF01081; TIGRFAM: TIGR01182; COG: COG0800 - 2-keto-3-deoxy-6-phosphogluconate aldolase; KHG/KDPG aldolase complement(1835047..1835688) Dinoroseobacter shibae DFL 12 = DSM 16493 5713335 YP_001533112.1 CDS edd NC_009952.1 1835700 1837505 R catalyzes the formation of 2-dehydro-3-deoxy-6-phospho-D-gluconate from 6-phospho-D-gluconate; phosphogluconate dehydratase complement(1835700..1837505) Dinoroseobacter shibae DFL 12 = DSM 16493 5713336 YP_001533113.1 CDS Dshi_1770 NC_009952.1 1837632 1837898 D hypothetical protein 1837632..1837898 Dinoroseobacter shibae DFL 12 = DSM 16493 5713337 YP_001533114.1 CDS Dshi_1771 NC_009952.1 1838034 1839236 D COG: COG1092 - Predicted SAM-dependent methyltransferases; PFAM: PF03602; SUPERFAMILY: SSF53335; SWISSPROT P75876: UPF0064 protein yccW; similar to methyltransferase; hypothetical protein 1838034..1839236 Dinoroseobacter shibae DFL 12 = DSM 16493 5713338 YP_001533115.1 CDS Dshi_1772 NC_009952.1 1839233 1839772 D hypothetical protein 1839233..1839772 Dinoroseobacter shibae DFL 12 = DSM 16493 5713339 YP_001533116.1 CDS Dshi_1773 NC_009952.1 1839968 1840660 R SWISSPROT P25894: Uncharacterized metalloprotease yggG; PANTHER: OMA1 HOMOLOG, ZINC METALLOPEPTIDASE (PTHR22726); PFAM: PF01435; putative metalloprotease complement(1839968..1840660) Dinoroseobacter shibae DFL 12 = DSM 16493 5713340 YP_001533117.1 CDS Dshi_1774 NC_009952.1 1840700 1840987 R hypothetical protein complement(1840700..1840987) Dinoroseobacter shibae DFL 12 = DSM 16493 5713341 YP_001533118.1 CDS Dshi_1775 NC_009952.1 1841055 1843865 R PFAM: PF03710; COG: COG1391 - Glutamine synthetase adenylyltransferase; putative glutamate--ammonia ligase adenyltransferase complement(1841055..1843865) Dinoroseobacter shibae DFL 12 = DSM 16493 5713342 YP_001533119.1 CDS Dshi_1776 NC_009952.1 1844200 1844541 D SWISSPROT P0ADU5: Protein ygiW [Precursor]; Gene3D: G3DSA:2.40.50.200; SUPERFAMILY: SSF101756; similar to hypothetical protein ygiW; hypothetical protein 1844200..1844541 Dinoroseobacter shibae DFL 12 = DSM 16493 5713344 YP_001533120.1 CDS lon NC_009952.1 1844619 1847027 R SWISSPROT P0A9M0: ATP-dependent protease La; TIGRFAM: TIGR00763 ATP-dependent protease La, TIGR00764 lon-related putative ATP-dependent protease; COG: COG0466; PFAM: PF02190, PF00004, PF05362; SMART: SM00382; SPRINT: SM00464; ATP-dependent protease La complement(1844619..1847027) Dinoroseobacter shibae DFL 12 = DSM 16493 5713345 YP_001533121.1 CDS Dshi_1778 NC_009952.1 1847401 1848006 D hypothetical protein 1847401..1848006 Dinoroseobacter shibae DFL 12 = DSM 16493 5713346 YP_001533122.1 CDS ilvI NC_009952.1 1848348 1850105 D SWISSPROT P00893: Acetolactate synthase isozyme 3 large subunit; TIGRFAM: TIGR00118 acetolactate synthase, large subunit, biosynthetic type; COG: COG0028 - Thiamine pyrophosphate-requiring enzymes [acetolactate synthase, pyruvate dehydrogenase (cytochrome), glyoxylate carboligase, phosphonopyruvate decarboxylase]; PFAM: PF02775, PF00205, PF02776; acetolactate synthase 3 catalytic subunit 1848348..1850105 Dinoroseobacter shibae DFL 12 = DSM 16493 5713347 YP_001533123.1 CDS Dshi_1780 NC_009952.1 1850105 1850416 D PROSITE: PS51257; hypothetical protein 1850105..1850416 Dinoroseobacter shibae DFL 12 = DSM 16493 5713348 YP_001533124.1 CDS ilvH NC_009952.1 1850474 1851046 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 1850474..1851046 Dinoroseobacter shibae DFL 12 = DSM 16493 5713349 YP_001533125.1 CDS Dshi_1782 NC_009952.1 1851151 1852302 D SWISSPROT P0ABR7: Putative dioxygenase subunit alpha yeaW; PFAM: PF00355; SPRINT: PR00090; putative ring-hydroxylating dioxygenase subunit alpha 1851151..1852302 Dinoroseobacter shibae DFL 12 = DSM 16493 5713350 YP_001533126.1 CDS Dshi_1783 NC_009952.1 1852555 1852800 R PROSITE: PS00018; hypothetical protein complement(1852555..1852800) Dinoroseobacter shibae DFL 12 = DSM 16493 5713351 YP_001533127.1 CDS Dshi_1784 NC_009952.1 1853035 1853577 D TIGRFAM: TIGR02937 RNA polymerase sigma factor, sigma-70 family; COG: COG1595 - DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog; PFAM: PF08281, PF04542; putative RNA polymerase sigma factor 1853035..1853577 Dinoroseobacter shibae DFL 12 = DSM 16493 5713352 YP_001533128.1 CDS nrdJ NC_009952.1 1854290 1857964 R Catalyzes the rate-limiting step in dNTP synthesis; ribonucleotide-diphosphate reductase subunit alpha complement(1854290..1857964) Dinoroseobacter shibae DFL 12 = DSM 16493 5713353 YP_001533129.1 CDS Dshi_1786 NC_009952.1 1858657 1859097 D hypothetical protein 1858657..1859097 Dinoroseobacter shibae DFL 12 = DSM 16493 5713354 YP_001533130.1 CDS Dshi_1787 NC_009952.1 1859391 1859876 R COG: COG1430 - Uncharacterized conserved protein; PFAM: PF02643; hypothetical protein complement(1859391..1859876) Dinoroseobacter shibae DFL 12 = DSM 16493 5713356 YP_001533131.1 CDS Dshi_1788 NC_009952.1 1859873 1860394 R SWISSPROT P32081: Cold shock protein cspB; COG: COG1278 - Cold shock proteins; PFAM: PF00313; SMART: SM00357; SPRINT: PR00050; putative cold shock protein complement(1859873..1860394) Dinoroseobacter shibae DFL 12 = DSM 16493 5713357 YP_001533132.1 CDS pdxH NC_009952.1 1860527 1861132 R TIGRFAM: TIGR00558 pyridoxamine-phosphate oxidase; COG: COG0259; PFAM: PF01243; PROSITE: PS01064; SUPERFAMILY: SSF50475; pyridoxamine 5'-phosphate oxidase complement(1860527..1861132) Dinoroseobacter shibae DFL 12 = DSM 16493 5713358 YP_001533133.1 CDS fabI2 NC_009952.1 1861237 1862055 D SWISSPROT O24990: Enoyl-[acyl-carrier-protein] reductase [NADH]; COG: COG0623 - Enoyl-[acyl-carrier-protein] reductase (NADH); PFAM: PF00106; SPRINT: PR00081; NADH dependent enoyl-[acyl-carrier-protein] reductase 1861237..1862055 Dinoroseobacter shibae DFL 12 = DSM 16493 5713359 YP_001533134.1 CDS Dshi_1791 NC_009952.1 1862057 1862668 D PFAM: PF01810-LysE type translocator; COG: COG1280 - Putative threonine efflux protein; SWISSPROT P0AG38: Threonine efflux protein (rhtC); putative LysE type translocator 1862057..1862668 Dinoroseobacter shibae DFL 12 = DSM 16493 5713360 YP_001533135.1 CDS Dshi_1792 NC_009952.1 1862665 1863276 D PFAM: PF01810-LysE type translocator; COG: COG1280 - Putative threonine efflux protein; SWISSPROT P0AG38: Threonine efflux protein (rhtC); putative LysE type translocator 1862665..1863276 Dinoroseobacter shibae DFL 12 = DSM 16493 5713361 YP_001533136.1 CDS gpt NC_009952.1 1863339 1863842 D catalyzes the conversion of guanine, xanthine and, to a lesser extent, hypoxanthine to GMP, XMP and IMP, respectively; xanthine-guanine phosphoribosyltransferase 1863339..1863842 Dinoroseobacter shibae DFL 12 = DSM 16493 5713362 YP_001533137.1 CDS Dshi_1794 NC_009952.1 1863844 1865025 D COG: COG0436 - Aspartate/tyrosine/aromatic aminotransferase; PFAM: PF00155; SPRINT: PR00753; Gene3D: G3DSA:3.40.640.10; SUPERFAMILY: SSF53383; hypothetical protein 1863844..1865025 Dinoroseobacter shibae DFL 12 = DSM 16493 5713363 YP_001533138.1 CDS Dshi_1795 NC_009952.1 1865219 1867063 D SWISSPROT P0ADY1: Peptidyl-prolyl cis-trans isomerase D; SUPERFAMILY: SSF54534, SSF81827; putative peptidyl-prolyl cis-trans isomerase 1865219..1867063 Dinoroseobacter shibae DFL 12 = DSM 16493 5713364 YP_001533139.1 CDS trpE NC_009952.1 1867111 1868640 D with component II, the glutamine amidotransferase, catalyzes the formation of anthranilate from chorismate and glutamine; anthranilate synthase component I 1867111..1868640 Dinoroseobacter shibae DFL 12 = DSM 16493 5712784 YP_001533140.1 CDS Dshi_1797 NC_009952.1 1868767 1870593 R PFAM: PF04748; hypothetical protein complement(1868767..1870593) Dinoroseobacter shibae DFL 12 = DSM 16493 5712785 YP_001533141.1 CDS trpG NC_009952.1 1870777 1871382 D TrpG; with TrpE catalyzes the formation of anthranilate and glutamate from chorismate and glutamine; TrpG provides the glutamine amidotransferase activity; anthranilate synthase component II 1870777..1871382 Dinoroseobacter shibae DFL 12 = DSM 16493 5712786 YP_001533142.1 CDS trpD NC_009952.1 1871379 1872398 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 1871379..1872398 Dinoroseobacter shibae DFL 12 = DSM 16493 5712787 YP_001533143.1 CDS trpC NC_009952.1 1872395 1873210 D involved in tryptophan biosynthesis; amino acid biosynthesis; converts 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate to C(1)-(3-indolyl)-glycerol 3-phosphate and carbon dioxide and water; Indole-3-glycerol phosphate synthase 1872395..1873210 Dinoroseobacter shibae DFL 12 = DSM 16493 5712788 YP_001533144.1 CDS moaC NC_009952.1 1873207 1873683 D MoaC; along with MoaA is involved in conversion of a guanosine derivative into molybdopterin precursor Z; involved in molybdenum cofactor biosynthesis; molybdenum cofactor biosynthesis protein MoaC 1873207..1873683 Dinoroseobacter shibae DFL 12 = DSM 16493 5712789 YP_001533145.1 CDS moeA1 NC_009952.1 1873680 1874888 D SWISSPROT P12281: Molybdopterin biosynthesis protein moeA; TIGRFAM: TIGR00177; PFAM: pfam03453, pfam00994, pfam03454; COG: COG0303 - Molybdopterin biosynthesis enzyme; molybdopterin biosynthesis protein 1873680..1874888 Dinoroseobacter shibae DFL 12 = DSM 16493 5712790 YP_001533146.1 CDS lexA NC_009952.1 1875043 1875738 D Represses a number of genes involved in the response to DNA damage; LexA repressor 1875043..1875738 Dinoroseobacter shibae DFL 12 = DSM 16493 5712791 YP_001533147.1 CDS Dshi_1804 NC_009952.1 1875927 1878011 R PFAM: PF03772; TIGRFAM: TIGR00360; putative competence protein complement(1875927..1878011) Dinoroseobacter shibae DFL 12 = DSM 16493 5712792 YP_001533148.1 CDS gltX NC_009952.1 1878120 1879535 D Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation; glutamyl-tRNA synthetase 1878120..1879535 Dinoroseobacter shibae DFL 12 = DSM 16493 5712793 YP_001533149.1 CDS gltA2 NC_009952.1 1879651 1880943 D SWISSPROT P0ABH7: Citrate synthase; TIGR01798 citrate synthase I (hexameric type); COG: COG0372; PFAM: PF00285; PROSITE: PS00480; PRINTS: PR00143; citrate synthase 1879651..1880943 Dinoroseobacter shibae DFL 12 = DSM 16493 5712794 YP_001533150.1 CDS Dshi_1807 NC_009952.1 1881214 1881651 D PFAM: PF00582; PRINTS: PR01438; putative universal stress protein 1881214..1881651 Dinoroseobacter shibae DFL 12 = DSM 16493 5712795 YP_001533151.1 CDS Dshi_1808 NC_009952.1 1881663 1883201 D PFAM PF01235: Sodium:alanine symporter family; TIGRFAM: TIGR00835 amino acid carrier protein; COG: COG1115 - Na+/alanine symporter; PRINTS: PR00175; putative sodium:alanine symporter family protein 1881663..1883201 Dinoroseobacter shibae DFL 12 = DSM 16493 5712796 YP_001533152.1 CDS uvrA NC_009952.1 1883361 1886222 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(1883361..1886222) Dinoroseobacter shibae DFL 12 = DSM 16493 5712797 YP_001533153.1 CDS Dshi_1810 NC_009952.1 1886324 1887496 R PFAM PF07690: Major facilitator superfamily; PROSITE: PS50850; putative major facilitator superfamily transport protein complement(1886324..1887496) Dinoroseobacter shibae DFL 12 = DSM 16493 5712798 YP_001533154.1 CDS lpdV NC_009952.1 1887561 1888958 R E3 component of pyruvate complex; catalyzes the oxidation of dihydrolipoamide to lipoamide; dihydrolipoamide dehydrogenase complement(1887561..1888958) Dinoroseobacter shibae DFL 12 = DSM 16493 5712799 YP_001533155.1 CDS Dshi_1812 NC_009952.1 1889023 1889616 R PFAM: PF06041; hypothetical protein complement(1889023..1889616) Dinoroseobacter shibae DFL 12 = DSM 16493 5712800 YP_001533156.1 CDS Dshi_1813 NC_009952.1 1889690 1890979 R PFAM PF07690: Major facilitator superfamily; PROSITE: PS50850; major facilitator superfamiy transporter complement(1889690..1890979) Dinoroseobacter shibae DFL 12 = DSM 16493 5712801 YP_001533157.1 CDS Dshi_1814 NC_009952.1 1891703 1892863 D PROSITE: PS00018; hypothetical protein 1891703..1892863 Dinoroseobacter shibae DFL 12 = DSM 16493 5712804 YP_001533158.1 CDS Dshi_1815 NC_009952.1 1893248 1894045 R PFAM: PF00196, PF03472; SMART: SM00421; PROSITE: PS50043; COG: COG2197 - Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain; HTH type; putative transcriptional regulator complement(1893248..1894045) Dinoroseobacter shibae DFL 12 = DSM 16493 5712805 YP_001533159.1 CDS Dshi_1816 NC_009952.1 1894133 1895479 R COG3264 - Small-conductance mechanosensitive channel; PFAM: PF00924; SUPERFAMILY: SSF50182, SSF82861, SSF82689; mscS family protein complement(1894133..1895479) Dinoroseobacter shibae DFL 12 = DSM 16493 5712806 YP_001533160.1 CDS Dshi_1817 NC_009952.1 1895702 1896640 R COG1741 - Pirin-related protein; PFAM: PF05726, PF02678; pirin-like protein complement(1895702..1896640) Dinoroseobacter shibae DFL 12 = DSM 16493 5712807 YP_001533161.1 CDS Dshi_1818 NC_009952.1 1896712 1896984 R hypothetical protein complement(1896712..1896984) Dinoroseobacter shibae DFL 12 = DSM 16493 5712808 YP_001533162.1 CDS Dshi_1819 NC_009952.1 1897085 1897816 R PFAM: PF00196, PF03472; SMART: SM00421; PROSITE: PS50043; COG: COG2197 - Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain; HTH type; putative transcriptional regulator complement(1897085..1897816) Dinoroseobacter shibae DFL 12 = DSM 16493 5712809 YP_001533163.1 CDS Dshi_1820 NC_009952.1 1898151 1898933 D catalyzes the hydrolysis of mannosyl-3-phosphoglycerate to form the osmolyte mannosylglycerate; mannosyl-3-phosphoglycerate phosphatase 1898151..1898933 Dinoroseobacter shibae DFL 12 = DSM 16493 5712811 YP_001533164.1 CDS Dshi_1821 NC_009952.1 1898926 1900176 D hypothetical protein 1898926..1900176 Dinoroseobacter shibae DFL 12 = DSM 16493 5712812 YP_001533165.1 CDS Dshi_1822 NC_009952.1 1900181 1901206 D TIGRFAM: TIGR00832 arsenical-resistance protein; COG: COG0798 - Arsenite efflux pump ACR3 and related permeases; PFAM: PF01758; putative arsenic resistance protein 1900181..1901206 Dinoroseobacter shibae DFL 12 = DSM 16493 5712813 YP_001533166.1 CDS Dshi_1823 NC_009952.1 1901376 1902356 R hypothetical protein complement(1901376..1902356) Dinoroseobacter shibae DFL 12 = DSM 16493 5712814 YP_001533167.1 CDS Dshi_1824 NC_009952.1 1902502 1904265 R SWISSPROT P76041: Putative sucrose phosphorylase, P10249: Sucrose phosphorylase; COG: COG0366 - Glycosidases; PFAM: PF00128; putative sucrose phosphorylase complement(1902502..1904265) Dinoroseobacter shibae DFL 12 = DSM 16493 5712815 YP_001533168.1 CDS pta1 NC_009952.1 1904769 1905794 R SWISSPROT P39646: Posphate acetyltransferase; TIGRFAM: TIGR00651; COG: COG0280; PFAM: PF01515-Phosphate acetyl/butaryl transferase; phosphate acetyl transferase complement(1904769..1905794) Dinoroseobacter shibae DFL 12 = DSM 16493 5712816 YP_001533169.1 CDS Dshi_1826 NC_009952.1 1905847 1906206 R PFAM: PF05899, SUPERFAMILY: SSF51182; hypothetical protein complement(1905847..1906206) Dinoroseobacter shibae DFL 12 = DSM 16493 5712817 YP_001533170.1 CDS Dshi_1827 NC_009952.1 1906223 1907263 R SWISSPROT Q92UW5: UPF0324 membrane protein; PFAM: PF03601- conserved hypothetical protein 698; TIGRFAM: TIGR00698 conserved hypothetical integral membrane protein; COG: COG2855 - Predicted membrane protein; hypothetical protein complement(1906223..1907263) Dinoroseobacter shibae DFL 12 = DSM 16493 5712818 YP_001533171.1 CDS xcs NC_009952.1 1907402 1909183 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(1907402..1909183) Dinoroseobacter shibae DFL 12 = DSM 16493 5712819 YP_001533172.1 CDS Dshi_1829 NC_009952.1 1909208 1910602 R PFAM: PF01266; COG: COG0665 - Glycine/D-amino acid oxidases (deaminating); putative FAD-dependent oxidoreductase complement(1909208..1910602) Dinoroseobacter shibae DFL 12 = DSM 16493 5712820 YP_001533173.1 CDS Dshi_1830 NC_009952.1 1910630 1911016 R PFAM: PF07366; hypothetical protein complement(1910630..1911016) Dinoroseobacter shibae DFL 12 = DSM 16493 5712821 YP_001533174.1 CDS Dshi_1831 NC_009952.1 1911041 1911544 R PFAM: PF00582; PRINTS: PR01438; COG: COG0589 - Universal stress protein UspA and related nucleotide-binding proteins; putative universal stress protein complement(1911041..1911544) Dinoroseobacter shibae DFL 12 = DSM 16493 5712822 YP_001533175.1 CDS siaT NC_009952.1 1911569 1912909 R SWISSPROT P44543: Sialic acid TRAP transporter permease protein siaT; TIGRFAM: TIGR00786 TRAP transporter, DctM subunit; COG: COG1593 - TRAP-type C4-dicarboxylate transport system, large permease component; PFAM: PF06808-DctM-like transporters; sialic acid TRAP transporter permease complement(1911569..1912909) Dinoroseobacter shibae DFL 12 = DSM 16493 5712823 YP_001533176.1 CDS Dshi_1833 NC_009952.1 1912909 1913475 R PFAM: PF04290; DctQ component; putative TRAP transporter complement(1912909..1913475) Dinoroseobacter shibae DFL 12 = DSM 16493 5712824 YP_001533177.1 CDS Dshi_1834 NC_009952.1 1913539 1914555 R SWISSPROT P44542: Sialic acid-binding periplasmic protein siaP; TIGRFAM: TIGR00787 tripartite ATP-independent periplasmic transporter solute receptor, DctP family; COG: COG1638 - TRAP-type C4-dicarboxylate transport system, periplasmic component; PFAM: PF03480-Bacterial extracellular solute-binding protein, family 7; siaP; putative sialic acid-binding periplasmic protein complement(1913539..1914555) Dinoroseobacter shibae DFL 12 = DSM 16493 5712825 YP_001533178.1 CDS Dshi_1835 NC_009952.1 1914712 1916187 D SWISSPROT P77730: Uncharacterized HTH-type transcriptional repressor ydcR; COG: COG1167 - Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs; PFAM: PF00392, PF00155; SMART: SM00345 ; PROSITE: PS50949; GntR-type; putative transcriptional regulator 1914712..1916187 Dinoroseobacter shibae DFL 12 = DSM 16493 5712826 YP_001533179.1 CDS Dshi_1836 NC_009952.1 1916867 1917976 D PROSITE: PS50817; hypothetical protein 1916867..1917976 Dinoroseobacter shibae DFL 12 = DSM 16493 5712828 YP_001533180.1 CDS Dshi_1837 NC_009952.1 1917978 1919549 R SWISSPROT P31806: Uncharacterized protein yjeF; TIGRFAM: TIGR00197, TIGR00196; PFAM: PF03853, PF01256; COG: COG0063 - Predicted sugar kinase; yjeF-like protein complement(1917978..1919549) Dinoroseobacter shibae DFL 12 = DSM 16493 5712829 YP_001533181.1 CDS Dshi_1838 NC_009952.1 1919720 1920058 D SWISSPROT P0A9Z1: Nitrogen regulation protein PII-1 (glnB); PROSITE: PS00496; PFAM: PF00543; putative nitrogen regulation protein PII 1919720..1920058 Dinoroseobacter shibae DFL 12 = DSM 16493 5712830 YP_001533182.1 CDS glnA NC_009952.1 1920126 1921532 D SWISSPROT P0A9C5: Glutamine synthetase; TIGRFAM: TIGR00653 glutamine synthetase, type I; COG: COG0174; glutamine synthetase 1920126..1921532 Dinoroseobacter shibae DFL 12 = DSM 16493 5712831 YP_001533183.1 CDS Dshi_1840 NC_009952.1 1921699 1922916 D COG: COG1765-Predicted redox protein, regulator or disulfide bond formation. PFAM: pfam02566; SUPERFAMILY: SSF82784; Gene3D: G3DSA:3.30.300.20. No sequence similiarity to protein OsmC from E.coli could be detected with Swiss-Prot BLAST.; hypothetical protein 1921699..1922916 Dinoroseobacter shibae DFL 12 = DSM 16493 5712832 YP_001533184.1 CDS Dshi_1841 NC_009952.1 1923108 1923518 R hypothetical protein complement(1923108..1923518) Dinoroseobacter shibae DFL 12 = DSM 16493 5712833 YP_001533185.1 CDS purB NC_009952.1 1923555 1924907 D Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide; adenylosuccinate lyase 1923555..1924907 Dinoroseobacter shibae DFL 12 = DSM 16493 5712834 YP_001533186.1 CDS Dshi_1843 NC_009952.1 1925007 1925174 D hypothetical protein 1925007..1925174 Dinoroseobacter shibae DFL 12 = DSM 16493 5712835 YP_001533187.1 CDS Dshi_1844 NC_009952.1 1925279 1925812 D PFAM: pfam00515; PROSITE: PS50005, PS50293; related to tetratricopeptide-like; hypothetical protein 1925279..1925812 Dinoroseobacter shibae DFL 12 = DSM 16493 5712836 YP_001533188.1 CDS Dshi_1845 NC_009952.1 1925869 1926918 D SWISSPROT P0ABZ1: Flagellar motor switch protein fliG; COG: COG1536 - Flagellar motor switch protein; PFAM: PF01706; PRINTS: PR00954; putative flagellar motor switch protein fliG 1925869..1926918 Dinoroseobacter shibae DFL 12 = DSM 16493 5712837 YP_001533189.1 CDS Dshi_1846 NC_009952.1 1927300 1927743 D SUPERFAMILY: SSF75169; hypothetical protein 1927300..1927743 Dinoroseobacter shibae DFL 12 = DSM 16493 5712838 YP_001533190.1 CDS Dshi_1847 NC_009952.1 1927842 1928210 D PFAM: PF02211; SUPERFAMILY: SSF50090; similar to nitrile hydratase subunit beta; hypothetical protein 1927842..1928210 Dinoroseobacter shibae DFL 12 = DSM 16493 5712839 YP_001533191.1 CDS Dshi_1848 NC_009952.1 1928185 1928493 D PFAM: PF02211; SUPERFAMILY: SSF50090; similar to nitrile hydratase subunit beta; hypothetical protein 1928185..1928493 Dinoroseobacter shibae DFL 12 = DSM 16493 5712840 YP_001533192.1 CDS nthA NC_009952.1 1928483 1929094 D SWISSPROT Q7SID2: Cobalt-containing nitrile hydratase subunit alpha, P97051: Nitrile hydratase subunit alpha; PFAM: PF02979; PIR: PIRSF001426; nitrile hydratse subunit alpha 1928483..1929094 Dinoroseobacter shibae DFL 12 = DSM 16493 5712841 YP_001533193.1 CDS Dshi_1850 NC_009952.1 1929104 1929808 R PFAM PF06764: Protein of unknown function DUF1223; hypothetical protein complement(1929104..1929808) Dinoroseobacter shibae DFL 12 = DSM 16493 5712842 YP_001533194.1 CDS acnA NC_009952.1 1930031 1932817 D Catalyzes the conversion of citrate to isocitrate; aconitate hydratase 1930031..1932817 Dinoroseobacter shibae DFL 12 = DSM 16493 5712843 YP_001533195.1 CDS Dshi_1852 NC_009952.1 1932907 1933446 R SWISSPROT P0AA86: Thiol:disulfide interchange protein dsbE; TIGRFAM: TIGR00385 periplasmic protein thiol:disulfide oxidoreductases, DsbE subfamily; COG: COG0526 - Thiol-disulfide isomerase and thioredoxins; PFAM: PF08534; PRINTS: PR00421; putative thioredoxin complement(1932907..1933446) Dinoroseobacter shibae DFL 12 = DSM 16493 5712844 YP_001533196.1 CDS ccmC NC_009952.1 1933597 1934328 R SWISSPROT P0ABM1: Heme exporter protein C; TIGRFAM: TIGR01191 heme exporter protein CcmC; COG: COG0755 - ABC-type transport system involved in cytochrome c biogenesis, permease component; PFAM: PF01578; PRINTS: PR01386; heme exporter protein C complement(1933597..1934328) Dinoroseobacter shibae DFL 12 = DSM 16493 5712845 YP_001533197.1 CDS ccmB NC_009952.1 1934384 1935040 R PFAM: PF03379-CcmB protein; TIGRFAM: TIGR01190 heme exporter protein CcmB; COG: COG2386 - ABC-type transport system involved in cytochrome c biogenesis, permease component; PRINTS: PR01414; heme exporter protein B complement(1934384..1935040) Dinoroseobacter shibae DFL 12 = DSM 16493 5712846 YP_001533198.1 CDS ccmA NC_009952.1 1935037 1935654 R ATP-binding protein; required for proper cytochrome c maturation; cytochrome c biogenesis protein CcmA complement(1935037..1935654) Dinoroseobacter shibae DFL 12 = DSM 16493 5712847 YP_001533199.1 CDS Dshi_1856 NC_009952.1 1935699 1936058 R PFAM: Protein of unknown function (DUF498/DUF598); COG: COG3737; hypothetical protein complement(1935699..1936058) Dinoroseobacter shibae DFL 12 = DSM 16493 5712848 YP_001533200.1 CDS Dshi_1857 NC_009952.1 1936069 1936821 R PFAM: PF01925; PROSITE: PS00318; related to DUF81; hypothetical protein complement(1936069..1936821) Dinoroseobacter shibae DFL 12 = DSM 16493 5712849 YP_001533201.1 CDS secF NC_009952.1 1936814 1937776 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(1936814..1937776) Dinoroseobacter shibae DFL 12 = DSM 16493 5712850 YP_001533202.1 CDS secD NC_009952.1 1937778 1939442 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(1937778..1939442) Dinoroseobacter shibae DFL 12 = DSM 16493 5712851 YP_001533203.1 CDS yajC NC_009952.1 1939449 1939766 R SV; Pfam: preprotein translocase subunit, ProDom: YajC preprotein translocase subunit, TIGRFAM: YajC; preprotein translocase subunit complement(1939449..1939766) Dinoroseobacter shibae DFL 12 = DSM 16493 5712852 YP_001533204.1 CDS Dshi_1861 NC_009952.1 1940020 1940709 D hypothetical protein 1940020..1940709 Dinoroseobacter shibae DFL 12 = DSM 16493 5712853 YP_001533205.1 CDS Dshi_1862 NC_009952.1 1940803 1941114 D PFAM: PF00805; COG: COG1357 - Uncharacterized low-complexity proteins; hypothetical protein 1940803..1941114 Dinoroseobacter shibae DFL 12 = DSM 16493 5712854 YP_001533206.1 CDS serS NC_009952.1 1941457 1942752 D 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 1941457..1942752 Dinoroseobacter shibae DFL 12 = DSM 16493 5712855 YP_001533207.1 CDS Dshi_1864 NC_009952.1 1942814 1943926 D TIGRFAM: TIGR02283 lytic murein transglycosylase; COG: COG2951 - Membrane-bound lytic murein transglycosylase B; PFAM: PF01471; Gene3D: G3DSA:1.10.101.10; putative membrane-bound lytic murein transglycosylase 1942814..1943926 Dinoroseobacter shibae DFL 12 = DSM 16493 5712856 YP_001533208.1 CDS Dshi_1865 NC_009952.1 1944045 1944914 R hypothetical protein complement(1944045..1944914) Dinoroseobacter shibae DFL 12 = DSM 16493 5712857 YP_001533209.1 CDS Dshi_1866 NC_009952.1 1945208 1946029 R COG: COG5473 - Predicted integral membrane protein; hypothetical protein complement(1945208..1946029) Dinoroseobacter shibae DFL 12 = DSM 16493 5712858 YP_001533210.1 CDS glnT NC_009952.1 1946164 1947480 R SWISSPROT P31592: Glutamine synthetase 3; COG: COG0174 - Glutamine synthetase; PFAM: PF00120; PROSITE: PS00181; SUPERFAMILY: SSF54368; glutamine synthetase complement(1946164..1947480) Dinoroseobacter shibae DFL 12 = DSM 16493 5712859 YP_001533211.1 CDS Dshi_1868 NC_009952.1 1947542 1948876 R SWISSPROT O87392: Glutamate synthase large subunit-like protein (glxD); PFAM: PF01645; COG: COG0069 - Glutamate synthase domain 2; putative glutamate synthase large subunit-like protein complement(1947542..1948876) Dinoroseobacter shibae DFL 12 = DSM 16493 5712860 YP_001533212.1 CDS Dshi_1869 NC_009952.1 1948897 1949574 R PFAM: PF01493; PIR: PIRSF006519; SWISSPROT O87391: Protein glxC; COG: COG0070 - Glutamate synthase domain 3; fwdC/fmdC family protein; putative glutamate synthase complement(1948897..1949574) Dinoroseobacter shibae DFL 12 = DSM 16493 5712861 YP_001533213.1 CDS Dshi_1870 NC_009952.1 1949574 1950500 R PFAM: PF00310; PROSITE: PS01039; SWISSPROT O87390: Glutamine amidotransferase-like protein glxB; COG: COG0067 - Glutamate synthase domain 1; class II; putative glutamine amidotransferase complement(1949574..1950500) Dinoroseobacter shibae DFL 12 = DSM 16493 5712862 YP_001533214.1 CDS Dshi_1871 NC_009952.1 1950576 1951223 R PFAM: PF01381, PF07883; PROSITE: PS50943; SUPERFAMILY: SSF51182, SSF47413; COG: COG1396 - Predicted transcriptional regulators; putative HTH-type transcriptional regulator complement(1950576..1951223) Dinoroseobacter shibae DFL 12 = DSM 16493 5712863 YP_001533215.1 CDS Dshi_1872 NC_009952.1 1951375 1952643 R SUPERFAMILY: SSF50952; Gene3D: G3DSA:2.120.10.30; COG: COG2133 - Glucose/sorbosone dehydrogenases; putative soluble aldose sugar dehydrogenase complement(1951375..1952643) Dinoroseobacter shibae DFL 12 = DSM 16493 5712864 YP_001533216.1 CDS Dshi_1873 NC_009952.1 1952797 1953105 R SWISSPROT P00105: Cytochrome c-554(548); PFAM: PF00034- cytochrome c; COG: COG2863 - Cytochrome c553; putative cytochrome c complement(1952797..1953105) Dinoroseobacter shibae DFL 12 = DSM 16493 5712865 YP_001533217.1 CDS Dshi_1874 NC_009952.1 1953173 1953769 R PFAM: PF00440; PROSITE: PS50977; SUPERFAMILY: SSF46689, SSF48498; COG: COG1309 - Transcriptional regulator; tetR family; putative regulatory protein complement(1953173..1953769) Dinoroseobacter shibae DFL 12 = DSM 16493 5712866 YP_001533218.1 CDS Dshi_1875 NC_009952.1 1953908 1954423 D PFAM: PF04224-Protein of unknown function, DUF417; COG: Predicted membrane protein; SWISSPROT P75685: Inner membrane protein ykgB; DUF417; putative inner membrane protein 1953908..1954423 Dinoroseobacter shibae DFL 12 = DSM 16493 5712867 YP_001533219.1 CDS Dshi_1876 NC_009952.1 1954483 1954755 D SWISSPROT P0AC62: Glutaredoxin-3; TIGRFAM: TIGR02181 Glutaredoxin, GrxC family; COG: COG0695 - Glutaredoxin and related proteins; PFAM: PF00462-Glutaredoxin; grxC; putative glutaredoxin 3 1954483..1954755 Dinoroseobacter shibae DFL 12 = DSM 16493 5712868 YP_001533220.1 CDS Dshi_1877 NC_009952.1 1954772 1956046 R COG: COG4325 - Predicted membrane protein; hypothetical protein complement(1954772..1956046) Dinoroseobacter shibae DFL 12 = DSM 16493 5712869 YP_001533221.1 CDS Dshi_1878 NC_009952.1 1956140 1957117 R SUPERFAMILY: SSF56784; hypothetical protein complement(1956140..1957117) Dinoroseobacter shibae DFL 12 = DSM 16493 5712870 YP_001533222.1 CDS Dshi_1879 NC_009952.1 1957234 1958421 R COG: COG3825 - Uncharacterized protein conserved in bacteria; hypothetical protein complement(1957234..1958421) Dinoroseobacter shibae DFL 12 = DSM 16493 5712871 YP_001533223.1 CDS Dshi_1880 NC_009952.1 1958425 1958592 R hypothetical protein complement(1958425..1958592) Dinoroseobacter shibae DFL 12 = DSM 16493 5712872 YP_001533224.1 CDS Dshi_1881 NC_009952.1 1958592 1959968 R PROSITE: PS00214, PS51257; hypothetical protein complement(1958592..1959968) Dinoroseobacter shibae DFL 12 = DSM 16493 5712873 YP_001533225.1 CDS Dshi_1882 NC_009952.1 1959965 1960423 R PFAM: PF00583; PROSITE: PS51186; SUPERFAMILY: SSF55729; putative acetyltransferase complement(1959965..1960423) Dinoroseobacter shibae DFL 12 = DSM 16493 5712874 YP_001533226.1 CDS Dshi_1883 NC_009952.1 1960643 1961485 R COG: COG0714 - MoxR-like ATPases; PFAM: PF00004; SMART: SM00382 ; PRITNTS: PR00300; putative clpA/clpB family protein complement(1960643..1961485) Dinoroseobacter shibae DFL 12 = DSM 16493 5712875 YP_001533227.1 CDS Dshi_1884 NC_009952.1 1961615 1962088 D TIGRFAM: TIGR02420 RNA polymerase-binding protein DksA; COG: COG1734 - DnaK suppressor protein; SWISSPROT P0ABS1: DnaK suppressor protein (dksA); PFAM: PF01258; PROSITE: PS01102; putative DnaK suppressor protein 1961615..1962088 Dinoroseobacter shibae DFL 12 = DSM 16493 5712876 YP_001533228.1 CDS Dshi_1885 NC_009952.1 1962221 1963390 D COG: COG0654 - 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases; PFAM: PF01266; PRINTS: PR00420; putative salicylate hydroxylase 1962221..1963390 Dinoroseobacter shibae DFL 12 = DSM 16493 5712877 YP_001533229.1 CDS Dshi_1886 NC_009952.1 1963398 1964177 R TIGRFAM: TIGR00195 exodeoxyribonuclease III, TIGR00633 exodeoxyribonuclease III (xth); COG: COG0708 - Exonuclease III; PFAM: PF03372-Endonuclease/Exonuclease/phosphatase family; PROSITE: PS00726; xthA; putative Exodeoxyribonuclease III complement(1963398..1964177) Dinoroseobacter shibae DFL 12 = DSM 16493 5712878 YP_001533230.1 CDS Dshi_1887 NC_009952.1 1964382 1965539 R TIGRFAM: TIGR01388; COG: COG0349; PFAM: PF01612; SMART: SM00474; PROSITE: PS50967; SUPERFAMILY: SSF53098; rnd; putative ribonuclease D complement(1964382..1965539) Dinoroseobacter shibae DFL 12 = DSM 16493 5712879 YP_001533231.1 CDS purN NC_009952.1 1965637 1966230 R TIGRFAM: TIGR00639 phosphoribosylglycinamide formyltransferase, formyltetrahydrofolate-dependent; COG: COG0299 - Folate-dependent phosphoribosylglycinamide formyltransferase PurN; PFAM PF00551: Formyl transferase; phosphoribosylglycinamide formyltransferase complement(1965637..1966230) Dinoroseobacter shibae DFL 12 = DSM 16493 5712880 YP_001533232.1 CDS purM NC_009952.1 1966227 1967288 R catalyzes the formation of 1-(5-phosphoribosyl)-5-aminoimidazole from 2-(formamido)-N1-(5-phosphoribosyl)acetamidine and ATP in purine biosynthesis; phosphoribosylaminoimidazole synthetase complement(1966227..1967288) Dinoroseobacter shibae DFL 12 = DSM 16493 5712881 YP_001533233.1 CDS Dshi_1890 NC_009952.1 1967456 1968577 R PFAM: PF08238; SMART: SM00671; SUPERFAMILY: SSF81901; hypothetical protein complement(1967456..1968577) Dinoroseobacter shibae DFL 12 = DSM 16493 5712883 YP_001533234.1 CDS Dshi_1891 NC_009952.1 1968779 1969207 D COG: COG1017 - Hemoglobin-like flavoprotein; PFAM: PF00042-Globin; SUPERFAMILY: Globin-like SSF46458; Gene3D: G3DSA:1.10.490.10; SWISSPROT P04252: Bacterial hemoglobin; putative flavohemoglobin 1968779..1969207 Dinoroseobacter shibae DFL 12 = DSM 16493 5712884 YP_001533235.1 CDS Dshi_1892 NC_009952.1 1969284 1970432 D COG: COG3287 - Uncharacterized conserved protein; PFAM: PF08495; hypothetical protein 1969284..1970432 Dinoroseobacter shibae DFL 12 = DSM 16493 5712885 YP_001533236.1 CDS Dshi_1893 NC_009952.1 1970454 1973216 D similar to to known LOV domains (e.g SB1 and SB2 from Pseudomonas putida); highly conserved LOV consensus region including the photoactive Cys. TIGRFAM: TIGR00229 PAS domain S-box; COG: COG0642 - Signal transduction histidine kinase; SMART: SM00091: PAS domain; SM00086: PAC motif, SM00388: Histidine kinase-like ATPases, SM00448 : cheY-homologous receiver domain; PROSITE: PS50112: PAS repeat profile, PS50113: PAC domain profile, PS50110: Response regulatory domain profile, PS50109: Histidine kinase domain profile; PFAM: PF00072: Response regulator receiver domain, PF02518: Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase, PF00512: His Kinase A (phosphoacceptor) domain, PF08447: PAS fold; LOV-regulator, Blue-light sensing 1970454..1973216 Dinoroseobacter shibae DFL 12 = DSM 16493 5712886 YP_001533237.1 CDS Dshi_1894 NC_009952.1 1973228 1973842 D COG: COG2197 - Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain; PFAM: PF00196, PF00072; PROSITE: PS50043, PS50110; SMART: SM00448 ; SUPERFAMILY: SSF52172; putative response regulator receiver protein 1973228..1973842 Dinoroseobacter shibae DFL 12 = DSM 16493 5712887 YP_001533238.1 CDS Dshi_1895 NC_009952.1 1973861 1976413 R PFAM: PF00353; hypothetical protein complement(1973861..1976413) Dinoroseobacter shibae DFL 12 = DSM 16493 5712888 YP_001533239.1 CDS algD NC_009952.1 1976442 1977851 R SWISSPROT P11759: GDP-mannose 6-dehydrogenase; COG: COG1004 - Predicted UDP-glucose 6-dehydrogenase; PROSITE: PS00059; PFAM: PF03721, PF00984, PF03720; GDP-mannose 6-dehydrogenase complement(1976442..1977851) Dinoroseobacter shibae DFL 12 = DSM 16493 5712889 YP_001533240.1 CDS algA NC_009952.1 1978068 1979498 R SWISSPROT P07874: Alginate biosynthesis protein algA; TIGRFAM: TIGR01479 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; COG: COG0836 - Mannose-1-phosphate guanylyltransferase; PFAM: PF01050, PF00483; alginate biosynthesis protein complement(1978068..1979498) Dinoroseobacter shibae DFL 12 = DSM 16493 5712890 YP_001533241.1 CDS Dshi_1898 NC_009952.1 1979617 1981209 R SWISSPROT Q52463: Glycosyltransferase alg8. Possibly a processive enzyme that polymerizes GDP-mannuronic acid. No evidence at protein level but the colocation with algA and algG indicates an involvement in alginate biosynthesis.; putative glycosyltransferase alg8 complement(1979617..1981209) Dinoroseobacter shibae DFL 12 = DSM 16493 5712891 YP_001533242.1 CDS Dshi_1899 NC_009952.1 1981196 1982602 R SWISSPROT P46682: p-hydroxybenzoic acid efflux pump subunit aaeA; related to efflux pump protein; hypothetical protein complement(1981196..1982602) Dinoroseobacter shibae DFL 12 = DSM 16493 5712892 YP_001533243.1 CDS algC NC_009952.1 1982818 1984188 D SWISSPROT P26276: Phosphomannomutase/phosphoglucomutase; COG: COG1109 - Phosphomannomutase; PFAM: PF02880, PF02879, PF02878, PF00408; PROSITE: PS00710; phosphomannomutase 1982818..1984188 Dinoroseobacter shibae DFL 12 = DSM 16493 5712893 YP_001533244.1 CDS Dshi_1901 NC_009952.1 1984363 1984953 D SWISSPROT Q887Q8: alginate biosynthesis protein algF (precursor). No evidence at protein level and low similarity but the colocation with algC, algA and algD indicates an involvement in alginate biosynthesis.; similar to alginate biosynthesis protein algF; hypothetical protein 1984363..1984953 Dinoroseobacter shibae DFL 12 = DSM 16493 5712894 YP_001533245.1 CDS Dshi_1902 NC_009952.1 1984955 1986331 D COG: COG1696 - Predicted membrane protein involved in D-alanine export; PFAM: PF03062; putative poly(beta-D-mannuronate) O-acetylase 1984955..1986331 Dinoroseobacter shibae DFL 12 = DSM 16493 5712895 YP_001533246.1 CDS Dshi_1903 NC_009952.1 1986343 1987356 D SWISSPROT Q51393; putative alginate biosynthesis protein algJ 1986343..1987356 Dinoroseobacter shibae DFL 12 = DSM 16493 5712896 YP_001533247.1 CDS Dshi_1904 NC_009952.1 1987353 1988663 D SWISSPROT Q88NDO; similar to alginate biosynthesis protein algX; hypothetical protein 1987353..1988663 Dinoroseobacter shibae DFL 12 = DSM 16493 5712897 YP_001533248.1 CDS Dshi_1905 NC_009952.1 1989272 1990372 D PFAM: PF00589; Gene3D: G3DSA:1.10.443.10; similar to prophage integrase; hypothetical protein 1989272..1990372 Dinoroseobacter shibae DFL 12 = DSM 16493 5712898 YP_001533249.1 CDS Dshi_1906 NC_009952.1 1990560 1990841 D SUPERFAMILY: SSF46955; PFAM: PF00376; hypothetical protein 1990560..1990841 Dinoroseobacter shibae DFL 12 = DSM 16493 5712899 YP_001533250.1 CDS Dshi_1907 NC_009952.1 1990957 1992414 D PROSITE: PS00039; hypothetical protein 1990957..1992414 Dinoroseobacter shibae DFL 12 = DSM 16493 5712900 YP_001533251.1 CDS Dshi_1908 NC_009952.1 1992667 1993284 D hypothetical protein 1992667..1993284 Dinoroseobacter shibae DFL 12 = DSM 16493 5712901 YP_001533252.1 CDS Dshi_1909 NC_009952.1 1993959 1994612 R hypothetical protein complement(1993959..1994612) Dinoroseobacter shibae DFL 12 = DSM 16493 5712902 YP_001533253.1 CDS Dshi_1910 NC_009952.1 1995268 1995951 D hypothetical protein 1995268..1995951 Dinoroseobacter shibae DFL 12 = DSM 16493 5712903 YP_001533254.1 CDS Dshi_1911 NC_009952.1 1995938 1996333 D PS00527: Ribosomal protein S14 signature.; similar to ribosomal protein; hypothetical protein 1995938..1996333 Dinoroseobacter shibae DFL 12 = DSM 16493 5712904 YP_001533255.1 CDS Dshi_1912 NC_009952.1 1996336 1996743 D hypothetical protein 1996336..1996743 Dinoroseobacter shibae DFL 12 = DSM 16493 5712905 YP_001533256.1 CDS Dshi_1913 NC_009952.1 1996738 1997559 R PFAM: PF00665; PROSITE: PS50994; SUPERFAMILY: SSF53098; COG: COG2801 - Transposase and inactivated derivatives; putative insertion element complement(1996738..1997559) Dinoroseobacter shibae DFL 12 = DSM 16493 5712906 YP_001533257.1 CDS Dshi_1914 NC_009952.1 1997583 1997849 R PFAM: PF01527-Transposase; putative insertion element / transposase complement(1997583..1997849) Dinoroseobacter shibae DFL 12 = DSM 16493 5712907 YP_001533258.1 CDS Dshi_1915 NC_009952.1 1998356 1999138 D hypothetical protein 1998356..1999138 Dinoroseobacter shibae DFL 12 = DSM 16493 5712908 YP_001533259.1 CDS Dshi_1916 NC_009952.1 1999123 1999854 D hypothetical protein 1999123..1999854 Dinoroseobacter shibae DFL 12 = DSM 16493 5712909 YP_001533260.1 CDS Dshi_1917 NC_009952.1 1999930 2001378 D PROSITE: PS00093; PFAM: PF01555; putative modification methylase 1999930..2001378 Dinoroseobacter shibae DFL 12 = DSM 16493 5712910 YP_001533261.1 CDS Dshi_1918 NC_009952.1 2001559 2002620 D PROSITE: PS00093; PFAM: PF01555; putative modification methylase 2001559..2002620 Dinoroseobacter shibae DFL 12 = DSM 16493 5712911 YP_001533262.1 CDS Dshi_1919 NC_009952.1 2002691 2004421 D hypothetical protein 2002691..2004421 Dinoroseobacter shibae DFL 12 = DSM 16493 5712912 YP_001533263.1 CDS Dshi_1920 NC_009952.1 2005076 2005981 R PFAM: PF00753; hypothetical protein complement(2005076..2005981) Dinoroseobacter shibae DFL 12 = DSM 16493 5712914 YP_001533264.1 CDS Dshi_1921 NC_009952.1 2006027 2007346 D COG: COG0642 - Signal transduction histidine kinase; PFAM: PF02518, PF00672, PF00512; histidine kinase 2006027..2007346 Dinoroseobacter shibae DFL 12 = DSM 16493 5712915 YP_001533265.1 CDS Dshi_1922 NC_009952.1 2007318 2007611 R hypothetical protein complement(2007318..2007611) Dinoroseobacter shibae DFL 12 = DSM 16493 5712916 YP_001533266.1 CDS Dshi_1923 NC_009952.1 2007881 2009116 D hypothetical protein 2007881..2009116 Dinoroseobacter shibae DFL 12 = DSM 16493 5712917 YP_001533267.1 CDS Dshi_1924 NC_009952.1 2009151 2010203 D TIGRFAM: TIGR02122 TRAP transporter solute receptor, TAXI family; COG: COG2358 - TRAP-type uncharacterized transport system, periplasmic component; Gene3D: G3DSA:3.40.190.10 ; SUPERFAMIYLY: SSF53850; putative TRAP transporter solute receptor 2009151..2010203 Dinoroseobacter shibae DFL 12 = DSM 16493 5712918 YP_001533268.1 CDS Dshi_1925 NC_009952.1 2010233 2012482 R COG: COG3267 - Type II secretory pathway, component ExeA (predicted ATPase); SMART: SM00382; SUPERFAMILY: SSF52540; putative ATPase complement(2010233..2012482) Dinoroseobacter shibae DFL 12 = DSM 16493 5712919 YP_001533269.1 CDS priA NC_009952.1 2012570 2014753 R binding of PriA to forked DNA starts the assembly of the primosome, also possesses 3'-5' helicase activity; primosome assembly protein PriA complement(2012570..2014753) Dinoroseobacter shibae DFL 12 = DSM 16493 5712920 YP_001533270.1 CDS tal NC_009952.1 2014831 2015484 D similar to novel fructose-6-phosphate aldolase from Escherichia coli; enzyme from Methanocaldococcus janaschii shows transaldolase activity; putative translaldolase 2014831..2015484 Dinoroseobacter shibae DFL 12 = DSM 16493 5712921 YP_001533271.1 CDS Dshi_1928 NC_009952.1 2015542 2016249 D PFAM: PF04340 - Protein of unknown function, DUF484; hypothetical protein 2015542..2016249 Dinoroseobacter shibae DFL 12 = DSM 16493 5712922 YP_003422327.1 CDS xerC NC_009952.1 2016253 2017179 D hypothetical protein 2016253..2017179 Dinoroseobacter shibae DFL 12 = DSM 16493 5712923 YP_001533272.1 CDS Dshi_1930 NC_009952.1 2017199 2018038 R PFAM: PF00892; SUPERFAMILY: SSF103481; hypothetical protein complement(2017199..2018038) Dinoroseobacter shibae DFL 12 = DSM 16493 5712924 YP_001533273.1 CDS Dshi_1931 NC_009952.1 2018101 2018352 R hypothetical protein complement(2018101..2018352) Dinoroseobacter shibae DFL 12 = DSM 16493 5712925 YP_001533274.1 CDS Dshi_1932 NC_009952.1 2018349 2019218 R COG: COG0625 - Glutathione S-transferase; PFAM: PF02798, PF00043; SUPERFAMILY: SSF47616, SSF52833; SWISSPROT Q46845: Uncharacterized GST-like protein yghU; putative glutathione S-transferase family protein complement(2018349..2019218) Dinoroseobacter shibae DFL 12 = DSM 16493 5712926 YP_001533275.1 CDS ileS NC_009952.1 2019318 2022293 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(2019318..2022293) Dinoroseobacter shibae DFL 12 = DSM 16493 5712927 YP_001533276.1 CDS Dshi_1934 NC_009952.1 2022645 2023316 D hypothetical protein 2022645..2023316 Dinoroseobacter shibae DFL 12 = DSM 16493 5712928 YP_001533277.1 CDS Dshi_1935 NC_009952.1 2023345 2024964 R COG: COG0492 - Thioredoxin reductase; PFAM: PF00027, PF00070; PROSITE: PS50042; SMART: SM00100; PRINTS: PR00469, PR00419, PR00368; putative thioredoxin reductase trxB with an additional cyclic nucleotide-monophosphate-binding domain complement(2023345..2024964) Dinoroseobacter shibae DFL 12 = DSM 16493 5712929 YP_001533278.1 CDS Dshi_1936 NC_009952.1 2024978 2025994 R TIGRFAM: TIGR01620 conserved hypothetical protein; COG: COG3768 - Predicted membrane protein; PFAM: pfam05128; family DUF697; hypothetical protein complement(2024978..2025994) Dinoroseobacter shibae DFL 12 = DSM 16493 5712930 YP_001533279.1 CDS Dshi_1937 NC_009952.1 2025991 2027403 R PFAM: PF04317-YcjX-like family, DUF463; SWISSPROT P76046: Uncharacterized protein ycjX; COG: COG3106 - Predicted ATPase; DUF463; YcjX-like family protein complement(2025991..2027403) Dinoroseobacter shibae DFL 12 = DSM 16493 5712931 YP_001533280.1 CDS truA NC_009952.1 2027520 2028293 D mediates pseudouridylation (positions 38, 39, 40) at the tRNA anticodon region which contributes to the structural stability; tRNA pseudouridine synthase A 2027520..2028293 Dinoroseobacter shibae DFL 12 = DSM 16493 5712932 YP_001533281.1 CDS Dshi_1939 NC_009952.1 2028410 2029231 R COG: COG0600 - ABC-type nitrate/sulfonate/bicarbonate transport system, permease component; PFAM: PF00528; PROSITE: PS50928; putative ABC transporter permease complement(2028410..2029231) Dinoroseobacter shibae DFL 12 = DSM 16493 5712933 YP_001533282.1 CDS Dshi_1940 NC_009952.1 2029271 2030071 R COG: COG1116 - ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component; PFAM: PF00005; PROSITE: PS00211, PS50893; SMART: SM00382; ABC transporter ATP-binding protein complement(2029271..2030071) Dinoroseobacter shibae DFL 12 = DSM 16493 5712934 YP_001533283.1 CDS Dshi_1941 NC_009952.1 2030122 2031135 R PFAM: PF09084-NMT1/THI5 like; COG: COG0715 - ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components; NMT1/THI5 family protein complement(2030122..2031135) Dinoroseobacter shibae DFL 12 = DSM 16493 5712935 YP_001533284.1 CDS Dshi_1942 NC_009952.1 2031291 2032652 R PFAM: PF08885; putative GSCFA family protein complement(2031291..2032652) Dinoroseobacter shibae DFL 12 = DSM 16493 5712936 YP_001533285.1 CDS codA NC_009952.1 2032700 2033968 R Catalyzes the deamination of cytosine to uracil and ammonia; cytosine deaminase complement(2032700..2033968) Dinoroseobacter shibae DFL 12 = DSM 16493 5712937 YP_001533286.1 CDS Dshi_1944 NC_009952.1 2033976 2034707 R SUPERFAMILY: S-adenosyl-L-methionine-dependent methyltransferases; PFAM: PF05711 -Macrocin-O-methyltransferase (TylF); putative methyltransferase complement(2033976..2034707) Dinoroseobacter shibae DFL 12 = DSM 16493 5712938 YP_001533287.1 CDS Dshi_1945 NC_009952.1 2034739 2035683 R COG: COG1079 - Uncharacterized ABC-type transport system, permease component; PFAM: PF02653; putative permease of branched-chain amino acid transport system complement(2034739..2035683) Dinoroseobacter shibae DFL 12 = DSM 16493 5712939 YP_001533288.1 CDS Dshi_1946 NC_009952.1 2035685 2036734 R COG4603 - ABC-type uncharacterized transport system, permease component; PFAM: PF02653; branched-chain amino acid ABCtransporter permease complement(2035685..2036734) Dinoroseobacter shibae DFL 12 = DSM 16493 5712940 YP_001533289.1 CDS rbsA4 NC_009952.1 2036724 2038268 R SWISSPROT P04983: Ribose import ATP-binding protein rbsA; COG: COG3845 - ABC-type uncharacterized transport systems, ATPase components; PFAM: PF00005; PROSITE: PS00211, PS50893; SMART: SM00382; ribose import ATP-binding protein complement(2036724..2038268) Dinoroseobacter shibae DFL 12 = DSM 16493 5712941 YP_001533290.1 CDS Dshi_1948 NC_009952.1 2038268 2039287 R COG: COG1744 - Uncharacterized ABC-type transport system, periplasmic component/surface lipoprotein; PFAM: PF02608; PROSITE: PS00024; putative basic membrane protein complement(2038268..2039287) Dinoroseobacter shibae DFL 12 = DSM 16493 5712942 YP_001533291.1 CDS Dshi_1949 NC_009952.1 2039513 2041096 R hypothetical protein complement(2039513..2041096) Dinoroseobacter shibae DFL 12 = DSM 16493 5712943 YP_001533292.1 CDS Dshi_1950 NC_009952.1 2041261 2041860 D SUPERFAMILY: SSF52540; similar to hydrolase; hypothetical protein 2041261..2041860 Dinoroseobacter shibae DFL 12 = DSM 16493 5712944 YP_001533293.1 CDS Dshi_1951 NC_009952.1 2041913 2045206 R PFAM: PF00529; COG: COG1566: Multidrug resistance efflux pump; related to HlyD family secretion proteins; hypothetical protein complement(2041913..2045206) Dinoroseobacter shibae DFL 12 = DSM 16493 5712945 YP_001533294.1 CDS Dshi_1952 NC_009952.1 2045601 2046332 D hypothetical protein 2045601..2046332 Dinoroseobacter shibae DFL 12 = DSM 16493 5712946 YP_001533295.1 CDS Dshi_1953 NC_009952.1 2046386 2047312 D COG: COG3509 - Poly(3-hydroxybutyrate) depolymerase; Gene3D: G3DSA:3.40.50.1820; SUPERFAMILY: SSF53474; putative hydrolase 2046386..2047312 Dinoroseobacter shibae DFL 12 = DSM 16493 5712947 YP_001533296.1 CDS Dshi_1954 NC_009952.1 2047344 2048147 D PFAM: PF00106-short chain dehydrogenase; PRINTS: PR00081; COG: COG0300 - Short-chain dehydrogenases of various substrate specificities; putative short-chain dehydrogenase 2047344..2048147 Dinoroseobacter shibae DFL 12 = DSM 16493 5712948 YP_001533297.1 CDS Dshi_1955 NC_009952.1 2048152 2049948 R PFAM: PF00106, PF01370; PRINTS: PR00081; Gene3D: G3DSA:3.40.50.720; COG: COG1028 - Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases); putative short-chain dehydrogenase complement(2048152..2049948) Dinoroseobacter shibae DFL 12 = DSM 16493 5712949 YP_001533298.1 CDS Dshi_1956 NC_009952.1 2049974 2050936 R PFAM: PF01370; COG: COG0451 - Nucleoside-diphosphate-sugar epimerases; putative NAD-dependent epimerase/dehydratase complement(2049974..2050936) Dinoroseobacter shibae DFL 12 = DSM 16493 5712950 YP_001533299.1 CDS Dshi_1957 NC_009952.1 2051005 2052432 R COG: COG3063 - Tfp pilus assembly protein PilF; PFAM: PF00515 Tetratricopeptide repeat 1, PF07719 Tetratricopeptide repeat 2; PROSITE: PS50005-TPR repeat profile, PS50293-TPR repeat region circular profile; SMART: SM00028-Tetratricopeptide repeats; similar to tetratricopeptide repeat superfamily proteins; hypothetical protein complement(2051005..2052432) Dinoroseobacter shibae DFL 12 = DSM 16493 5712951 YP_001533300.1 CDS Dshi_1958 NC_009952.1 2052491 2055133 R COG: COG0451 - Nucleoside-diphosphate-sugar epimerases; PFAM: PF01370; PROSITE: PS00178, PS00061; Gene3D: G3DSA:3.40.50.720; putative NAD-dependent epimerase/dehydratase complement(2052491..2055133) Dinoroseobacter shibae DFL 12 = DSM 16493 5712952 YP_003422328.1 CDS Dshi_5003 NC_009952.1 2055139 2056056 R hypothetical protein complement(2055139..2056056) Dinoroseobacter shibae DFL 12 = DSM 16493 5712953 YP_001533301.1 CDS Dshi_1960 NC_009952.1 2056060 2057664 R PFAM: PF01663-Type I phosphodiesterase / nucleotide pyrophosphatase; Gene3D: G3DSA:3.40.720.10-Alkaline Phosphatase, subunit A; SUPERFAMILY: Alkaline phosphatase-like; phosphodiesterase/nucleotide pyrophosphatase complement(2056060..2057664) Dinoroseobacter shibae DFL 12 = DSM 16493 5712954 YP_001533302.1 CDS Dshi_1961 NC_009952.1 2057679 2057969 R PROSITE: PS50075; SUPERFAMILY: ACP-like; similar to acyl carrier protein; hypothetical protein complement(2057679..2057969) Dinoroseobacter shibae DFL 12 = DSM 16493 5712955 YP_001533303.1 CDS Dshi_1962 NC_009952.1 2057989 2062884 R SWISSPROT Q03133: Erythronolide synthase, modules 5 and 6; Q03131: Erythronolide synthase, modules 1 and 2; Q03132: Erythronolide synthase, modules 3 and 4; PFAM: PF01648, PF00109, PF02801, PF00698; TIGRFAM: TIGR00556 phosphopantethiene--protein transferase domain; COG: COG3321 - Polyketide synthase modules and related proteins; putative modular PKS system complement(2057989..2062884) Dinoroseobacter shibae DFL 12 = DSM 16493 5712956 YP_001533304.1 CDS Dshi_1963 NC_009952.1 2062881 2070542 R SWISSPROT: Q03131: Erythronolide synthase, modules 1 and 2; Q03132: Erythronolide synthase, modules 3 and 4; PFAM: PF03060, PF08659, PF00109, PF02801, PF00698; TIGRFAM: TIGR02813 polyketide-type polyunsaturated fatty acid synthase PfaA; COG: COG3321 - Polyketide synthase modules and related proteins; putative modular PKS system complement(2062881..2070542) Dinoroseobacter shibae DFL 12 = DSM 16493 5712957 YP_001533305.1 CDS Dshi_1964 NC_009952.1 2071115 2072833 R TIGRFAM: TIGR01681 HAD-superfamily phosphatase, subfamily IIIC; TIGR01686 FkbH-like domain; COG: COG3882 - Predicted enzyme involved in methoxymalonyl-ACP biosynthesis; SUPERFAMILY: SGNH hydrolase, HAD-like; hydrolase / phosphatase related; hypothetical protein complement(2071115..2072833) Dinoroseobacter shibae DFL 12 = DSM 16493 5712958 YP_001533306.1 CDS Dshi_1965 NC_009952.1 2072939 2073871 R SUPERFAMILY: SSF52540; hypothetical protein complement(2072939..2073871) Dinoroseobacter shibae DFL 12 = DSM 16493 5712959 YP_001533307.1 CDS lpdA NC_009952.1 2074131 2075873 R SWISSPROT P0A9P0: Dihydrolipoyl dehydrogenase; PFAM: PF00364, PF00070, PF02852, PF07992; PROSITE: PS50968, PS00189, PS00076; PRINTS: PR00945, PR00411, PR00368; TIGRFAM: TIGR01350 dihydrolipoamide dehydrogenase; COG: COG1249 - Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide dehydrogenase (E3) component, and related enzymes; dihydrolipoyl dehydrogenase complement(2074131..2075873) Dinoroseobacter shibae DFL 12 = DSM 16493 5712960 YP_001533308.1 CDS aceF NC_009952.1 2075886 2077187 R TIGRFAM: TIGR01348 pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form; COG: COG0508 - Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide acyltransferase (E2) component, and related enzymes; PFAM: PF02817; dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex complement(2075886..2077187) Dinoroseobacter shibae DFL 12 = DSM 16493 5712961 YP_001533309.1 CDS aceE NC_009952.1 2077242 2079899 R E1 component; part of pyruvate dehydrogenase; forms a complex with DlaT and LpdC; pyruvate dehydrogenase subunit E1 complement(2077242..2079899) Dinoroseobacter shibae DFL 12 = DSM 16493 5712962 YP_003422329.1 CDS Dshi_5004 NC_009952.1 2080128 2081843 R D-lactate dehydrogenase complement(2080128..2081843) Dinoroseobacter shibae DFL 12 = DSM 16493 5712963 YP_001533310.1 CDS Dshi_1970 NC_009952.1 2081843 2083909 R TIGRFAM: TIGR00786 TRAP transporter, DctM subunit; COG: COG4664 - TRAP-type mannitol/chloroaromatic compound transport system, large permease component; PFAM: PF04290, PF06808; TRAP dicarboxylate transporter complement(2081843..2083909) Dinoroseobacter shibae DFL 12 = DSM 16493 5712964 YP_001533311.1 CDS Dshi_1971 NC_009952.1 2084030 2085007 R PFAM: PF03480-Bacterial extracellular solute-binding protein, family 7; COG: COG4663 - TRAP-type mannitol/chloroaromatic compound transport system, periplasmic component; putative TRAP-transporter extracellular solute-binding protein complement(2084030..2085007) Dinoroseobacter shibae DFL 12 = DSM 16493 5712965 YP_001533312.1 CDS Dshi_1972 NC_009952.1 2085434 2086216 D SWISSPROT P0ACL9: Pyruvate dehydrogenase complex repressor (pdhR); COG: COG2186 - Transcriptional regulators; PFAM: PF07729, PF00392; SMART: SM00345; PROSITE: PS50949; Gene3D: G3DSA:1.10.10.10; SUPERFAMILY: SSF46785; putative pyruvate dehydrogenase complex repressor 2085434..2086216 Dinoroseobacter shibae DFL 12 = DSM 16493 5712966 YP_001533313.1 CDS Dshi_1973 NC_009952.1 2086276 2087394 D PFAM PF07726: ATPase family associated with various cellular activities (AAA); SMART: SM00382; COG: COG0714 - MoxR-like ATPases; related to ATPase (AAA); hypothetical protein 2086276..2087394 Dinoroseobacter shibae DFL 12 = DSM 16493 5712967 YP_001533314.1 CDS Dshi_1974 NC_009952.1 2087391 2088665 D COG: COG3864 - Uncharacterized protein conserved in bacteria; hypothetical protein 2087391..2088665 Dinoroseobacter shibae DFL 12 = DSM 16493 5712968 YP_001533315.1 CDS Dshi_1975 NC_009952.1 2088990 2089682 R hypothetical protein complement(2088990..2089682) Dinoroseobacter shibae DFL 12 = DSM 16493 5712969 YP_001533316.1 CDS Dshi_1976 NC_009952.1 2089743 2090660 R PFAM: PF00294; PRINTS: PR00990; putative ribokinase complement(2089743..2090660) Dinoroseobacter shibae DFL 12 = DSM 16493 5712970 YP_001533317.1 CDS Dshi_1977 NC_009952.1 2090945 2092207 R PFAM: PF01094-Receptor family ligand binding region; PROSITE: PS51257; SWISSPROT P21175: Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein [Precursor] (braC); COG: COG0683 - ABC-type branched-chain amino acid transport systems, periplasmic component; periplasmic-binding protein complement(2090945..2092207) Dinoroseobacter shibae DFL 12 = DSM 16493 5712971 YP_001533318.1 CDS Dshi_1978 NC_009952.1 2092224 2093177 R PFAM: PF02653-Branched-chain amino acid transport system / permease component; COG: COG4177 - ABC-type branched-chain amino acid transport system, permease component; putative branched-chain amino acid transport system / permease complement(2092224..2093177) Dinoroseobacter shibae DFL 12 = DSM 16493 5712972 YP_001533319.1 CDS Dshi_1979 NC_009952.1 2093174 2094091 R SWISSPROT P0AEX7: High-affinity branched-chain amino acid transport system permease protein livH; PFAM: PF02653-Branched-chain amino acid transport system / permease component; COG: COG4177 - ABC-type branched-chain amino acid transport system, permease component; putative branched-chain amino acid transport system / permease complement(2093174..2094091) Dinoroseobacter shibae DFL 12 = DSM 16493 5712973 YP_001533320.1 CDS Dshi_1980 NC_009952.1 2094088 2094810 R SWISSPROT P22731: High-affinity branched-chain amino acid transport ATP-binding protein livF; PFAM: PF00005; PROSITE: PS50893; SMART: SM00382; putative high-affinity branched-chain amino acid transport ATP-binding protein complement(2094088..2094810) Dinoroseobacter shibae DFL 12 = DSM 16493 5712974 YP_001533321.1 CDS Dshi_1981 NC_009952.1 2094803 2095576 R SWISSPROT Q58663: branched-chain amino acid transport ATP-binding protein livG; PFAM: PF00005; PROSITE: PS00211, PS50893; SMART: SM00382; putative branched-chain amino acid transport ATP-binding protein complement(2094803..2095576) Dinoroseobacter shibae DFL 12 = DSM 16493 5712975 YP_001533322.1 CDS Dshi_1982 NC_009952.1 2095569 2096651 R PFAM: PF00248; aldo/keto reductase family protein complement(2095569..2096651) Dinoroseobacter shibae DFL 12 = DSM 16493 5712976 YP_001533323.1 CDS Dshi_1983 NC_009952.1 2096648 2097025 R hypothetical protein complement(2096648..2097025) Dinoroseobacter shibae DFL 12 = DSM 16493 5712977 YP_001533324.1 CDS Dshi_1984 NC_009952.1 2097130 2097777 D SWISSPROT P76114: Uncharacterized HTH-type transcriptional regulator yncC; PFAM: PF07729, PF00392; Gene3D: G3DSA:1.10.10.10; COG: COG1802 - Transcriptional regulators; putative HTH-type transcriptional regulator 2097130..2097777 Dinoroseobacter shibae DFL 12 = DSM 16493 5712978 YP_001533325.1 CDS Dshi_1985 NC_009952.1 2097774 2099216 D COG: COG0667 - Predicted oxidoreductases (related to aryl-alcohol dehydrogenases); PFAM: PF00248, PF01042; PRINTS: PR00069; SUPERFAMILY: SSF51430; aldo/keto reductase family protein 2097774..2099216 Dinoroseobacter shibae DFL 12 = DSM 16493 5712979 YP_001533326.1 CDS icd NC_009952.1 2099648 2101816 D TIGRFAM: TIGR00178 isocitrate dehydrogenase, NADP-dependent, monomeric type; COG: COG2838 - Monomeric isocitrate dehydrogenase; PFAM PF03971: Monomeric isocitrate dehydrogenase; monomeric isocitrate dehydrogenase 2099648..2101816 Dinoroseobacter shibae DFL 12 = DSM 16493 5712980 YP_001533327.1 CDS Dshi_1987 NC_009952.1 2102173 2102721 D similar to molybdenum import ATP-binding protein modC2; hypothetical protein 2102173..2102721 Dinoroseobacter shibae DFL 12 = DSM 16493 5712981 YP_001533328.1 CDS Dshi_1988 NC_009952.1 2102821 2103216 D hypothetical protein 2102821..2103216 Dinoroseobacter shibae DFL 12 = DSM 16493 5712982 YP_001533329.1 CDS Dshi_1989 NC_009952.1 2103220 2104452 D PFAM: PF00529; COG: COG1566: Multidrug resistance efflux pump; related to HlyD family secretion proteins; hypothetical protein 2103220..2104452 Dinoroseobacter shibae DFL 12 = DSM 16493 5712983 YP_001533330.1 CDS Dshi_1990 NC_009952.1 2104752 2106995 R PFAM: PF01636; SUPERFAMILY: SSF56112; COG: COG0510 - Predicted choline kinase involved in LPS biosynthesis; protein kinase-like protein complement(2104752..2106995) Dinoroseobacter shibae DFL 12 = DSM 16493 5712985 YP_001533331.1 CDS Dshi_1991 NC_009952.1 2106982 2108817 R PROSITE: PS50893, PS50929; PFAM: PF00664, PF00005; SMART: SM00382; putative multidrug export ATP-binding/permease complement(2106982..2108817) Dinoroseobacter shibae DFL 12 = DSM 16493 5712986 YP_001533332.1 CDS Dshi_1992 NC_009952.1 2108817 2109965 R PFAM: PF00534; related to glycosyl transferase group 1; hypothetical protein complement(2108817..2109965) Dinoroseobacter shibae DFL 12 = DSM 16493 5712987 YP_001533333.1 CDS Dshi_1993 NC_009952.1 2109965 2111209 R PFAM: PF00534; putative glycosyltransferase complement(2109965..2111209) Dinoroseobacter shibae DFL 12 = DSM 16493 5712988 YP_001533334.1 CDS Dshi_1994 NC_009952.1 2111233 2112393 R COG: COG4671 - Predicted glycosyl transferase; SUPERFAMILY: SSF53756 UDP-Glycosyltransferase/glycogen phosphorylase; Gene3D: G3DSA:3.40.50.2000; putative glycosyltransferase complement(2111233..2112393) Dinoroseobacter shibae DFL 12 = DSM 16493 5712989 YP_001533335.1 CDS Dshi_1995 NC_009952.1 2113662 2114381 D hypothetical protein 2113662..2114381 Dinoroseobacter shibae DFL 12 = DSM 16493 5712990 YP_001533336.1 CDS xylA NC_009952.1 2114512 2115816 R catalyzes the interconversion of D-xylose to D-xylulose; xylose isomerase complement(2114512..2115816) Dinoroseobacter shibae DFL 12 = DSM 16493 5712991 YP_001533337.1 CDS xylB2 NC_009952.1 2115813 2117255 R SWISSPROT P09099: Xylose kinase; PFAM: PF00370, PF02782; TIGRFAM: TIGR01312 D-xylulose kinase; COG: COG1070 - Sugar (pentulose and hexulose) kinases; xylose kinase complement(2115813..2117255) Dinoroseobacter shibae DFL 12 = DSM 16493 5712992 YP_001533338.1 CDS Dshi_1998 NC_009952.1 2117255 2118001 R SWISSPROT P04983: Ribose import ATP-binding protein rbsA; COG: COG1129 - ABC-type sugar transport system, ATPase component, ATPase components; PFAM: PF00005; PROSITE: PS50893; SMART: SM00382; ABC transporter ATP-binding protein complement(2117255..2118001) Dinoroseobacter shibae DFL 12 = DSM 16493 5712993 YP_001533339.1 CDS xylH NC_009952.1 2117998 2119305 R SWISSPROT P0AGI4: Xylose transport system permease protein xylH; COG: COG4214 - ABC-type xylose transport system, permease component; PFAM: PF02653; xylose transport system permease complement(2117998..2119305) Dinoroseobacter shibae DFL 12 = DSM 16493 5712994 YP_001533340.1 CDS Dshi_2000 NC_009952.1 2119423 2120445 R SWISSPROT P37387: D-xylose-binding periplasmic protein [Precursor]; TIGRFAM: TIGR02634 D-xylose ABC transporter, substrate-binding protein; COG: COG4213 - ABC-type xylose transport system, periplasmic component; D-xylose-binding periplasmic protein xylF complement(2119423..2120445) Dinoroseobacter shibae DFL 12 = DSM 16493 5712995 YP_001533341.1 CDS Dshi_2001 NC_009952.1 2120658 2121902 D SWISSPROT Q44406: Xylose repressor xylR. The entry has no evidence at protein level, but the colocation with the xylose operon supports the annotation. COG: COG1940 - Transcriptional regulator/sugar kinase; PFAM: PF00480; putative xylose repressor 2120658..2121902 Dinoroseobacter shibae DFL 12 = DSM 16493 5712996 YP_001533342.1 CDS Dshi_2002 NC_009952.1 2121899 2123377 D SUPERFAMILY: SSF69318; hypothetical protein 2121899..2123377 Dinoroseobacter shibae DFL 12 = DSM 16493 5712997 YP_001533343.1 CDS Dshi_2003 NC_009952.1 2123844 2124359 D TIGRFAM: TIGR01409; hypothetical protein 2123844..2124359 Dinoroseobacter shibae DFL 12 = DSM 16493 5712998 YP_001533344.1 CDS Dshi_2004 NC_009952.1 2124331 2124954 D PFAM: PF01794; hypothetical protein 2124331..2124954 Dinoroseobacter shibae DFL 12 = DSM 16493 5712999 YP_001533345.1 CDS Dshi_2005 NC_009952.1 2125127 2126482 R PFAM: PF03150; Gene3D: G3DSA:1.10.760.10; PROSITE: PS51007; putative cytochrome c peroxidase complement(2125127..2126482) Dinoroseobacter shibae DFL 12 = DSM 16493 5713000 YP_001533346.1 CDS Dshi_2006 NC_009952.1 2126545 2126964 R DK; SWISSPROT O34627: Blue-light photoreceptor; PFAM: PF08447; SMART: SM00086, SM00091; PROSITE: PS50112, PS50113. TD; 1) similar to known LOV domains (e.g SB1 and SB2 from Pseudomonas putida); 2) highly conserved LOV consensus region including the photoactive Cys; putative blue-light photoreceptor complement(2126545..2126964) Dinoroseobacter shibae DFL 12 = DSM 16493 5713001 YP_001533347.1 CDS Dshi_2007 NC_009952.1 2127207 2127674 R PFAM: PF00293; Gene3D: G3DSA:3.90.79.10; SUPERFAMILY: SSF55811; similar to NUDIX hydrolase; hypothetical protein complement(2127207..2127674) Dinoroseobacter shibae DFL 12 = DSM 16493 5713002 YP_001533348.1 CDS Dshi_2008 NC_009952.1 2127799 2128614 D SWISSPROT P0ACL0: Glycerol-3-phosphate regulon repressor; COG: COG1349 - Transcriptional regulators of sugar metabolism; PFAM: PF08220, PF00455; PROSITE: PS00894, PS51000; SMART: SM00420; putative glycerol-3-phosphate regulon repressor 2127799..2128614 Dinoroseobacter shibae DFL 12 = DSM 16493 5713003 YP_001533349.1 CDS Dshi_2009 NC_009952.1 2128649 2129623 D TIGRFAM: TIGR01098 phosphonates-binding periplasmic protein; COG: COG3221 - ABC-type phosphate/phosphonate transport system, periplasmic component; SUPERFAMILY: SSF53850; putative phosphonates-binding periplasmic protein 2128649..2129623 Dinoroseobacter shibae DFL 12 = DSM 16493 5713004 YP_001533350.1 CDS phnC1 NC_009952.1 2129686 2130483 D TIGRFAM: TIGR02315 phosphonate ABC transporter, ATP-binding protein; DK; COG3638 - ABC-type phosphate/phosphonate transport system, ATPase component; PFAM: PF00005; SMART: SM00382; PROSITE: PS00211, PS50893, PS51249; phosphonates import ATP-binding protein 2129686..2130483 Dinoroseobacter shibae DFL 12 = DSM 16493 5713005 YP_001533351.1 CDS Dshi_2011 NC_009952.1 2130480 2131292 D TIGRFAM: TIGR01097 phosphonate ABC transporter, permease protein; COG: COG3639 - ABC-type phosphate/phosphonate transport system, permease component; PFAM: PF00528; PROSITE: PS50928; associated with phosphonates transport system; putative ABC transporter inner membrane component 2130480..2131292 Dinoroseobacter shibae DFL 12 = DSM 16493 5713006 YP_001533352.1 CDS Dshi_2012 NC_009952.1 2131292 2132107 D TIGRFAM: TIGR01097 phosphonate ABC transporter, permease protein; COG: COG3639 - ABC-type phosphate/phosphonate transport system, permease component; PFAM: PF00528; PROSITE: PS50928; associated with phosphonates transport system; putative ABC transporter inner membrane component 2131292..2132107 Dinoroseobacter shibae DFL 12 = DSM 16493 5713007 YP_001533353.1 CDS Dshi_2013 NC_009952.1 2132104 2133009 D PFAM: PF00702; COG: COG0647 - Predicted sugar phosphatases of the HAD superfamily; TIGRFAM: TIGR01459 HAD-superfamily class IIA hydrolase; TIGR01460 Haloacid Dehalogenase Superfamily Class (subfamily) IIA; similar to nagD, associated with phosphonates transport system; hypothetical protein 2132104..2133009 Dinoroseobacter shibae DFL 12 = DSM 16493 5713008 YP_001533354.1 CDS ugpB1 NC_009952.1 2133086 2134387 D SWISSPROT P0AG80: sn-glycerol-3-phosphate-binding periplasmic protein ugpB [Precursor]; COG: COG1653 - ABC-type sugar transport system, periplasmic component; PFAM: PF01547; SUPERFAMILY: SSF53850; Gene3D: G3DSA:3.40.190.10; sn-glycerol-3-phosphate-binding periplasmic protein ugpB 2133086..2134387 Dinoroseobacter shibae DFL 12 = DSM 16493 5713009 YP_001533355.1 CDS ugpA4 NC_009952.1 2134480 2135361 D SWISSPROT P10905: sn-glycerol-3-phosphate transport system permease protein ugpA; PFAM: PF00528; PROSITE: PS50928; COG1175 - ABC-type sugar transport systems, permease components; sn-glycerol-3-phosphate transport system permease 2134480..2135361 Dinoroseobacter shibae DFL 12 = DSM 16493 5713010 YP_001533356.1 CDS ugpE3 NC_009952.1 2135361 2136215 D SWISSPROT P10906: sn-glycerol-3-phosphate transport system permease protein ugpE; PFAM: PF00528; PROSITE: PS50928; COG: COG0395 - ABC-type sugar transport system, permease component; sn-glycerol-3-phosphate transport system permease 2135361..2136215 Dinoroseobacter shibae DFL 12 = DSM 16493 5713011 YP_001533357.1 CDS ugpC4 NC_009952.1 2136216 2137217 D SWISSPROT P10907: sn-glycerol-3-phosphate import ATP-binding protein ugpC; PFAM: PF00005, PF08402; PROSITE: PS00211, PS50893; SMART: SM00382; sn-glycerol-3-phosphate import ATP-binding protein 2136216..2137217 Dinoroseobacter shibae DFL 12 = DSM 16493 5713012 YP_001533358.1 CDS Dshi_2018 NC_009952.1 2137369 2137632 D hypothetical protein 2137369..2137632 Dinoroseobacter shibae DFL 12 = DSM 16493 5713013 YP_001533359.1 CDS Dshi_2019 NC_009952.1 2137715 2139322 R COG: COG0069 - Glutamate synthase domain 2; PFAM: PF01645; Gene3D: G3DSA:3.20.20.70; putative glutamate synthase [NADPH] large chain complement(2137715..2139322) Dinoroseobacter shibae DFL 12 = DSM 16493 5713014 YP_001533360.1 CDS pgm NC_009952.1 2139424 2141055 R catalyzes the interconversion of alpha-D-glucose 1-phosphate to alpha-D-glucose 6-phosphate; phosphoglucomutase complement(2139424..2141055) Dinoroseobacter shibae DFL 12 = DSM 16493 5713015 YP_001533361.1 CDS Dshi_2021 NC_009952.1 2141284 2142312 D SWISSPROT Q9HTX3: Probable binding protein component of ABC iron transporter PA5217 [Precursor]; COG: COG1840 - ABC-type Fe3+ transport system, periplasmic component; PFAM: PF01547; SUPERFAMILY: SSF53850; Gene3D: G3DSA:3.40.190.10; putative-binding protein component of ABC iron transporter 2141284..2142312 Dinoroseobacter shibae DFL 12 = DSM 16493 5713016 YP_001533362.1 CDS Dshi_2022 NC_009952.1 2142399 2142815 D no shine dalgarno sequence, no Swiss-Prot or InterPro Hits, no similar proteins in ncbi database. Probably pseudogene???; hypothetical protein 2142399..2142815 Dinoroseobacter shibae DFL 12 = DSM 16493 5713017 YP_001533363.1 CDS Dshi_2023 NC_009952.1 2142820 2144499 R PFAM: PF00528-Binding-protein-dependent transport system inner membrane component; COG: COG1178 - ABC-type Fe3+ transport system, permease component; PROSITE: PS50928; putative ABC transporter permease complement(2142820..2144499) Dinoroseobacter shibae DFL 12 = DSM 16493 5713018 YP_001533364.1 CDS Dshi_2024 NC_009952.1 2144760 2145515 R PFAM: PF01925; hypothetical protein complement(2144760..2145515) Dinoroseobacter shibae DFL 12 = DSM 16493 5713019 YP_001533365.1 CDS Dshi_2025 NC_009952.1 2145522 2146214 R PFAM: PF07385-Protein of unknown function (DUF1498); COG: COG3822 - ABC-type sugar transport system, auxiliary component; hypothetical protein complement(2145522..2146214) Dinoroseobacter shibae DFL 12 = DSM 16493 5713020 YP_001533366.1 CDS Dshi_2026 NC_009952.1 2146276 2147046 R COG: COG1540 - Uncharacterized proteins, homologs of lactam utilization protein B; PFAM: PF03746; SWISPROT Q5LMA4: UPF0271 protein SPO3659; LamB/YcsF family protein complement(2146276..2147046) Dinoroseobacter shibae DFL 12 = DSM 16493 5713021 YP_001533367.1 CDS Dshi_2027 NC_009952.1 2147043 2148059 R PFAM: PF02626; SMART: SM00797; TIGRFAM: TIGR00724 biotin-dependent carboxylase uncharacterized domain; COG: COG1984 - Allophanate hydrolase subunit 2; putative allophanate hydrolase subunit 2 complement(2147043..2148059) Dinoroseobacter shibae DFL 12 = DSM 16493 5713022 YP_001533368.1 CDS Dshi_2028 NC_009952.1 2148056 2148793 R TIGRFAM: TIGR00370 conserved hypothetical protein TIGR00370; COG: COG2049 - Allophanate hydrolase subunit 1; PFAM: PF02682; SMART: SM00796; putative allophanate hydrolase subunit 1 complement(2148056..2148793) Dinoroseobacter shibae DFL 12 = DSM 16493 5713023 YP_001533369.1 CDS Dshi_2029 NC_009952.1 2149164 2150222 R SWISSPROT P0ACP7: HTH-type transcriptional repressor purR; PFAM: PF00356, PF00532; SMART: SM00354; PROSITE: PS50932; SUPERFAMILY: SSF47413; COG: COG1609 - Transcriptional regulators; HTH-type transcriptional repressor complement(2149164..2150222) Dinoroseobacter shibae DFL 12 = DSM 16493 5713024 YP_001533370.1 CDS Dshi_2030 NC_009952.1 2150383 2150574 D hypothetical protein 2150383..2150574 Dinoroseobacter shibae DFL 12 = DSM 16493 5713025 YP_001533371.1 CDS Dshi_2031 NC_009952.1 2150586 2151734 D PFAM: PF03480; TIGRFAM: TIGR01409; COG: COG1638 - TRAP-type C4-dicarboxylate transport system, periplasmic component; SWISSPROT P37735: C4-dicarboxylate-binding periplasmic protein [Precursor]; putative TRAP-type C4-dicarboxylate transport sytem periplasmic protein 2150586..2151734 Dinoroseobacter shibae DFL 12 = DSM 16493 5713026 YP_001533372.1 CDS Dshi_2032 NC_009952.1 2151852 2152367 D COG: COG3090 - TRAP-type C4-dicarboxylate transport system, small permease component; PFAM: PF04290; PROSITE: PS00430; TRAP transporter permease 2151852..2152367 Dinoroseobacter shibae DFL 12 = DSM 16493 5713027 YP_001533373.1 CDS Dshi_2033 NC_009952.1 2152380 2153708 D PFAM: PF06808-DctM-like transporters; TIGRFAM: TIGR00786 TRAP transporter, DctM subunit; COG: COG1593 - TRAP-type C4-dicarboxylate transport system, large permease component; TRAP dicarboxylate transporter subunit DctM 2152380..2153708 Dinoroseobacter shibae DFL 12 = DSM 16493 5713028 YP_001533374.1 CDS hisD2 NC_009952.1 2153718 2155025 D catalyzes the oxidation of L-histidinol to L-histidinaldehyde and then to L-histidine in histidine biosynthesis; functions as a dimer; histidinol dehydrogenase 2153718..2155025 Dinoroseobacter shibae DFL 12 = DSM 16493 5713029 YP_001533375.1 CDS Dshi_2035 NC_009952.1 2155018 2155782 D COG: COG1028 - Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases); PFAM: PF00106; PROSITE: PS00061; PRINTS: PR00080, PR00081; putative gluconate 5-dehydrogenase 2155018..2155782 Dinoroseobacter shibae DFL 12 = DSM 16493 5713030 YP_001533376.1 CDS Dshi_2036 NC_009952.1 2155779 2156762 D PFAM: PF00107, PF08240; SUPERFAMILY: SSF50129; PANTHER: PTHR11695: Alcohol dehydrogenase related; zinc-containing alcohol dehydrogenase 2155779..2156762 Dinoroseobacter shibae DFL 12 = DSM 16493 5713031 YP_001533377.1 CDS Dshi_2037 NC_009952.1 2156778 2157068 D SWISSPROT P42604: Altronate hydrolase; similar to altronate hydrolase; hypothetical protein 2156778..2157068 Dinoroseobacter shibae DFL 12 = DSM 16493 5713032 YP_001533378.1 CDS Dshi_2038 NC_009952.1 2157081 2158262 D COG: COG2721 - Altronate dehydratase; PFAM: PF04295; putative altronate hydrolase 2157081..2158262 Dinoroseobacter shibae DFL 12 = DSM 16493 5713033 YP_001533379.1 CDS Dshi_2039 NC_009952.1 2158316 2159335 D COG: COG2055 - Malate/L-lactate dehydrogenases; PFAM: PF02615; SUPERFAMILY: SSF89733 L-sulfolactate dehydrogenase-like; malate/L-lactate dehydrogenase family protein 2158316..2159335 Dinoroseobacter shibae DFL 12 = DSM 16493 5713034 YP_001533380.1 CDS Dshi_2040 NC_009952.1 2159382 2159789 D SWISSPROT P37903: Universal stress protein F; PFAM: PF00582 Universal stress protein family; PRINTS: PR01438; SUPERFAMILY: Adenine nucleotide alpha hydrolases-like; COG: COG0589 - Universal stress protein UspA and related nucleotide-binding proteins; putative universal stress protein 2159382..2159789 Dinoroseobacter shibae DFL 12 = DSM 16493 5713035 YP_003422330.1 CDS Dshi_5005 NC_009952.1 2159773 2160468 R hypothetical protein complement(2159773..2160468) Dinoroseobacter shibae DFL 12 = DSM 16493 8130633 YP_001533381.1 CDS tpa NC_009952.1 2160601 2161983 R SWISSPROT Q9APM5: Taurine--pyruvate aminotransferase; COG: COG0161 - Adenosylmethionine-8-amino-7-oxononanoate aminotransferase; PFAM: PF00202; PROSITE: PS00600; taurin--pyruvate aminotransferase complement(2160601..2161983) Dinoroseobacter shibae DFL 12 = DSM 16493 5713037 YP_001533382.1 CDS Dshi_2043 NC_009952.1 2162251 2162490 D hypothetical protein 2162251..2162490 Dinoroseobacter shibae DFL 12 = DSM 16493 5713038 YP_001533383.1 CDS Dshi_2044 NC_009952.1 2162631 2164097 D SWISSPROT P94426: HTH-type transcriptional regulatory protein gabR; COG: COG1167 - Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs; PFAM: PF00392, PF00155; SMART: SM00345; PROSITE: PS50949; HTH-type transcriptional regulator 2162631..2164097 Dinoroseobacter shibae DFL 12 = DSM 16493 5713039 YP_001533384.1 CDS xsc NC_009952.1 2164196 2165974 D catalyzes the formation of acetyl phosphate and sulfite from 2-sulfoacetaldehyde; is active when grown on taurine as a sole carbon source; sulfoacetaldehyde acetyltransferase 2164196..2165974 Dinoroseobacter shibae DFL 12 = DSM 16493 5713040 YP_003422331.1 CDS Dshi_5006 NC_009952.1 2165978 2167135 D hypothetical protein 2165978..2167135 Dinoroseobacter shibae DFL 12 = DSM 16493 5713041 YP_001533385.1 CDS Dshi_2047 NC_009952.1 2167136 2167762 R PROSITE: PS51257; COG: COG3218 - ABC-type uncharacterized transport system, auxiliary component; related to membrane lipoprotein; hypothetical protein complement(2167136..2167762) Dinoroseobacter shibae DFL 12 = DSM 16493 5713042 YP_001533386.1 CDS Dshi_2048 NC_009952.1 2167769 2169508 R PFAM: PF02470; COG: COG1463 - ABC-type transport system involved in resistance to organic solvents, periplasmic component; hypothetical protein complement(2167769..2169508) Dinoroseobacter shibae DFL 12 = DSM 16493 5713043 YP_001533387.1 CDS Dshi_2049 NC_009952.1 2169530 2170309 R COG: COG1127 - ABC-type transport system involved in resistance to organic solvents, ATPase component; PFAM: PF00005; PROSITE: PS00211, PS50893; SMART: SM00382; ABC transporter ATP-binding protein complement(2169530..2170309) Dinoroseobacter shibae DFL 12 = DSM 16493 5713044 YP_001533388.1 CDS Dshi_2050 NC_009952.1 2170309 2171463 R TIGRFAM: TIGR00056 conserved hypothetical integral membrane protein; COG: COG0767 - ABC-type transport system involved in resistance to organic solvents, permease component; PROSITE: PS50801; PFAM: PF02405; SUPERFAMILY: SSF52091; hypothetical protein complement(2170309..2171463) Dinoroseobacter shibae DFL 12 = DSM 16493 5713045 YP_001533389.1 CDS Dshi_2051 NC_009952.1 2171569 2172045 R hypothetical protein complement(2171569..2172045) Dinoroseobacter shibae DFL 12 = DSM 16493 5713046 YP_001533390.1 CDS Dshi_2052 NC_009952.1 2172042 2172206 R COG: COG4256; similar to hemin uptake protein; hypothetical protein complement(2172042..2172206) Dinoroseobacter shibae DFL 12 = DSM 16493 5713047 YP_001533391.1 CDS Dshi_2053 NC_009952.1 2172986 2173456 D hypothetical protein 2172986..2173456 Dinoroseobacter shibae DFL 12 = DSM 16493 5713048 YP_001533392.1 CDS Dshi_2054 NC_009952.1 2173618 2174742 R COG: COG0123 - Deacetylases, including yeast histone deacetylase and acetoin utilization protein; PFAM: PF00850; PRINTS PR01270; histone deacetylase family protein complement(2173618..2174742) Dinoroseobacter shibae DFL 12 = DSM 16493 5713049 YP_001533393.1 CDS Dshi_2055 NC_009952.1 2174739 2175272 R COG: COG0386 - Glutathione peroxidase; SWISSPROT P99097: Glutathione peroxidase homolog bsaA; PFAM: PF00255; PIR: PIRSF000303; PROSITE: PS00460; PRINTS: PR01011; Gene3D: G3DSA:3.40.30.10; putative glutathione peroxidase complement(2174739..2175272) Dinoroseobacter shibae DFL 12 = DSM 16493 5713050 YP_001533394.1 CDS Dshi_2056 NC_009952.1 2175483 2175962 D PFAM: PF00293; PRINTS: PR00502; Gene3D: G3DSA:3.90.79.10; hypothetical protein 2175483..2175962 Dinoroseobacter shibae DFL 12 = DSM 16493 5713051 YP_001533395.1 CDS Dshi_2057 NC_009952.1 2176088 2176564 D COG: COG5319 - Uncharacterized protein conserved in bacteria; PFAM: PF06676-Protein of unknown function (DUF1178); hypothetical protein 2176088..2176564 Dinoroseobacter shibae DFL 12 = DSM 16493 5713052 YP_001533396.1 CDS Dshi_2058 NC_009952.1 2176569 2177234 D COG: COG1028 - Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases); short-chain dehydrogenase 2176569..2177234 Dinoroseobacter shibae DFL 12 = DSM 16493 5713053 YP_001533397.1 CDS Dshi_2059 NC_009952.1 2177212 2177808 D COG: COG0645 - Predicted kinase; similar to adenylyl sulfate kinase; hypothetical protein 2177212..2177808 Dinoroseobacter shibae DFL 12 = DSM 16493 5713054 YP_001533398.1 CDS acnB NC_009952.1 2178310 2181102 D catalyzes the conversion of citrate to isocitrate and the conversion of 2-methylaconitate to 2-methylisocitrate; bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase 2178310..2181102 Dinoroseobacter shibae DFL 12 = DSM 16493 5713055 YP_001533399.1 CDS lysC NC_009952.1 2181413 2182651 D SWISSPROT P26512: Aspartokinase; TIGRFAM: TIGR00656 aspartate kinase, monofunctional class, TIGR00657 aspartate kinase; COG: COG0527 - Aspartokinases; aspartokinase 2181413..2182651 Dinoroseobacter shibae DFL 12 = DSM 16493 5713056 YP_001533400.1 CDS ptsI NC_009952.1 2182811 2185054 D SWISSPROT P08839: Phosphoenolpyruvate-protein phosphotransferase; TIGRFAM: TIGR01417 phosphoenolpyruvate-protein phosphotransferase; COG: COG3605 - Signal transduction protein containing GAF and PtsI domains; PFAM: pfam02896, pfam05524, pfam00391, pfam01590; SMART: SM00065; phosphoenolpyruvate-protein phosphotransferase 2182811..2185054 Dinoroseobacter shibae DFL 12 = DSM 16493 5713057 YP_001533401.1 CDS Dshi_2063 NC_009952.1 2185051 2185806 R PFAM: PF00092; SMART: SM00327; PROSITE: PS50234; PRINTS: PR00453; related to von Willebrand factor type A; hypothetical protein complement(2185051..2185806) Dinoroseobacter shibae DFL 12 = DSM 16493 5713058 YP_001533402.1 CDS Dshi_2064 NC_009952.1 2185839 2186339 R COG: COG3153 - Predicted acetyltransferase; PFAM: PF00583; PROSITE: PS51186; related to acetyltransferase, GNAT family; hypothetical protein complement(2185839..2186339) Dinoroseobacter shibae DFL 12 = DSM 16493 5713059 YP_001533403.1 CDS Dshi_2065 NC_009952.1 2186415 2187020 D COG: COG1853 - Conserved protein/domain typically associated with flavoprotein oxygenases, DIM6/NTAB family; SUPERFAMILY: FMN-binding split barrel; Gene3D: Electron Transport, Fmn-binding Protein; Chain A; hypothetical protein 2186415..2187020 Dinoroseobacter shibae DFL 12 = DSM 16493 5713060 YP_001533404.1 CDS Dshi_2066 NC_009952.1 2187026 2187301 R hypothetical protein complement(2187026..2187301) Dinoroseobacter shibae DFL 12 = DSM 16493 5713061 YP_001533405.1 CDS Dshi_2067 NC_009952.1 2187413 2189017 R SWISSPROT P0AFR2: Putative sulfate transporter ychM; COG: COG0659 - Sulfate permease and related transporters (MFS superfamily); PFAM: PF01740, PF00916; PROSITE: PS50801; sulfate transporter complement(2187413..2189017) Dinoroseobacter shibae DFL 12 = DSM 16493 5713062 YP_001533406.1 CDS Dshi_2068 NC_009952.1 2189203 2190072 D Catalyzes the reversible phosphorolysis of 5'-deoxy-5'- methylthioadenosine (MTA) to adenine and 5-methylthio-D-ribose-1- phosphate; 5'-methylthioadenosine phosphorylase 2189203..2190072 Dinoroseobacter shibae DFL 12 = DSM 16493 5713063 YP_001533407.1 CDS Dshi_2069 NC_009952.1 2190225 2190515 D COG: COG4321 - Uncharacterized protein related to arylsulfate sulfotransferase involved in siderophore biosynthesis; hypothetical protein 2190225..2190515 Dinoroseobacter shibae DFL 12 = DSM 16493 5713064 YP_001533408.1 CDS Dshi_2070 NC_009952.1 2190630 2191025 D TIGRFAM: TIGR00068; COG: COG0346 - Lactoylglutathione lyase and related lyases; PFAM: PF00903-Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; similar to Lactoylglutathione lyase; hypothetical protein 2190630..2191025 Dinoroseobacter shibae DFL 12 = DSM 16493 5713065 YP_001533409.1 CDS Dshi_2071 NC_009952.1 2191066 2191590 D hypothetical protein 2191066..2191590 Dinoroseobacter shibae DFL 12 = DSM 16493 5713066 YP_001533410.1 CDS Dshi_2072 NC_009952.1 2191605 2193176 D COG: COG2303 - Choline dehydrogenase and related flavoproteins; PFAM: PF00732; putative gluconate 2-dehydrogenase flavoprotein 2191605..2193176 Dinoroseobacter shibae DFL 12 = DSM 16493 5713067 YP_001533411.1 CDS Dshi_2073 NC_009952.1 2193621 2194550 R SUPERFAMILY: SSF51101; hypothetical protein complement(2193621..2194550) Dinoroseobacter shibae DFL 12 = DSM 16493 5713068 YP_001533412.1 CDS apt NC_009952.1 2194887 2195426 D catalyzes a salvage reaction resulting in the formation of AMP which is metabolically less costly than a de novo synthesis; adenine phosphoribosyltransferase 2194887..2195426 Dinoroseobacter shibae DFL 12 = DSM 16493 5713069 YP_001533413.1 CDS Dshi_2075 NC_009952.1 2195526 2195978 D COG: COG3439 - Uncharacterized conserved protein; PFAM: PF03625; SUPERFAMILY: TT1751-like; hypothetical protein 2195526..2195978 Dinoroseobacter shibae DFL 12 = DSM 16493 5713070 YP_001533414.1 CDS Dshi_2076 NC_009952.1 2196168 2197586 R COG: COG0277 - FAD/FMN-containing dehydrogenases; PFAM: PF02913, PF01565; FAD-linked oxidase complement(2196168..2197586) Dinoroseobacter shibae DFL 12 = DSM 16493 5713071 YP_001533415.1 CDS Dshi_2077 NC_009952.1 2197642 2198481 R COG: COG2220 - Predicted Zn-dependent hydrolases of the beta-lactamase fold; related to metal-dependent hydrolase/oxidoreductase; hypothetical protein complement(2197642..2198481) Dinoroseobacter shibae DFL 12 = DSM 16493 5713072 YP_001533416.1 CDS tpiA NC_009952.1 2198730 2199473 D TIGRFAM: TIGR00419 triosephosphate isomerase; COG: COG0149; PFAM: PF00121; PROSITE: PS00171; triosephosphate isomerase 2198730..2199473 Dinoroseobacter shibae DFL 12 = DSM 16493 5713073 YP_001533417.1 CDS Dshi_2079 NC_009952.1 2199565 2200521 R COG: COG0583 - Transcriptional regulator; PFAM: PF00126, PF03466; PROSITE: PS50931; SUPERFAMILY: SSF53850, SSF46785; lysR family; HTH-type transcriptional regulator complement(2199565..2200521) Dinoroseobacter shibae DFL 12 = DSM 16493 5713074 YP_001533418.1 CDS metF NC_009952.1 2200594 2201463 D SWISSPROT P0AEZ1: 5,10-methylenetetrahydrofolate reductase; PFAM: PF02219- Methylenetetrahydrofolate reductase; TIGRFAM: TIGR00676 5,10-methylenetetrahydrofolate reductase, prokaryotic form; COG: COG0685 - 5,10-methylenetetrahydrofolate reductase; 5,10-methylenetetrahydrofolate reductase 2200594..2201463 Dinoroseobacter shibae DFL 12 = DSM 16493 5713075 YP_001533419.1 CDS Dshi_2081 NC_009952.1 2201530 2202114 R COG: COG2863 - Cytochrome c553; PROSITE: PS51007; Gene3D: G3DSA:1.10.760.10 ; SUPERFAMILY: SSF46626; putative cytochrome c complement(2201530..2202114) Dinoroseobacter shibae DFL 12 = DSM 16493 5713076 YP_001533420.1 CDS Dshi_2082 NC_009952.1 2202111 2203370 R COG: COG2133 - Glucose/sorbosone dehydrogenases; SUPERFAMILY: Soluble quinoprotein glucose dehydrogenase; Gene3D: G3DSA:2.120.10.30; putative sorbosone/glucose dehydrogenase complement(2202111..2203370) Dinoroseobacter shibae DFL 12 = DSM 16493 5713077 YP_001533421.1 CDS Dshi_2083 NC_009952.1 2203522 2203989 D COG: COG2050 - Uncharacterized protein, possibly involved in aromatic compounds catabolism; PFAM: PF03061; TIGRFAM: TIGR00369; related to thioesterase; hypothetical protein 2203522..2203989 Dinoroseobacter shibae DFL 12 = DSM 16493 5713078 YP_001533422.1 CDS Dshi_2084 NC_009952.1 2204080 2205153 R COG: COG3673 - Uncharacterized conserved protein; PROSITE: PS00120; hypothetical protein complement(2204080..2205153) Dinoroseobacter shibae DFL 12 = DSM 16493 5713079 YP_001533423.1 CDS Dshi_2085 NC_009952.1 2205559 2206308 D TIGRFAM: TIGR02595; hypothetical protein 2205559..2206308 Dinoroseobacter shibae DFL 12 = DSM 16493 5713080 YP_001533424.1 CDS coxL3 NC_009952.1 2206881 2209178 R SWISSPROT P19919: Carbon monoxide dehydrogenase large chain; COG: COG1529 - Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs; PFAM: pfam02738, pfam01315; carbon monoxide dehydrogenase complement(2206881..2209178) Dinoroseobacter shibae DFL 12 = DSM 16493 5713081 YP_001533425.1 CDS valS NC_009952.1 2209300 2212413 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 2209300..2212413 Dinoroseobacter shibae DFL 12 = DSM 16493 5713082 YP_001533426.1 CDS Dshi_2088 NC_009952.1 2212787 2213905 D catalyzes the formation of histidinol phosphate and 2-oxoglutarate from glutamate and imidazole acetol-phosphate; histidinol-phosphate aminotransferase 2212787..2213905 Dinoroseobacter shibae DFL 12 = DSM 16493 5713083 YP_001533427.1 CDS Dshi_2089 NC_009952.1 2213993 2214208 D hypothetical protein 2213993..2214208 Dinoroseobacter shibae DFL 12 = DSM 16493 5713084 YP_001533428.1 CDS Dshi_2090 NC_009952.1 2214205 2215461 R COG: COG0075 - Serine-pyruvate aminotransferase/archaeal aspartate aminotransferase; PFAM: PF00266; putative serine--glyoxylate aminotransferase complement(2214205..2215461) Dinoroseobacter shibae DFL 12 = DSM 16493 5713085 YP_001533429.1 CDS Dshi_2091 NC_009952.1 2215514 2216209 R SUPERFAMILY: SSF53448-Nucleotide-diphospho-sugar transferases; PFAM: PF00535-Glycosyl transferase family 2; COG: COG0463 - Glycosyltransferases involved in cell wall biogenesis; putative glycosyltransferase complement(2215514..2216209) Dinoroseobacter shibae DFL 12 = DSM 16493 5713086 YP_001533430.1 CDS Dshi_2092 NC_009952.1 2216299 2217084 D COG: COG0354 - Predicted aminomethyltransferase related to GcvT; PFAM: PF08669, PF01571; similar to aminomethyltransferase; hypothetical protein 2216299..2217084 Dinoroseobacter shibae DFL 12 = DSM 16493 5713087 YP_001533431.1 CDS Dshi_2093 NC_009952.1 2217100 2217546 R hypothetical protein complement(2217100..2217546) Dinoroseobacter shibae DFL 12 = DSM 16493 5713088 YP_001533432.1 CDS efp NC_009952.1 2217877 2218518 R Involved in peptide bond synthesis; alters the affinity of the ribosome for aminoacyl-tRNA; elongation factor P complement(2217877..2218518) Dinoroseobacter shibae DFL 12 = DSM 16493 5713089 YP_001533433.1 CDS Dshi_2095 NC_009952.1 2218654 2218974 D hypothetical protein 2218654..2218974 Dinoroseobacter shibae DFL 12 = DSM 16493 5713090 YP_001533434.1 CDS cobQ NC_009952.1 2219140 2220600 D catalyzes amidations at positions B, D, E, and G on adenosylcobyrinic A,C-diamide. NH(2) groups are provided by glutamine, and one molecule of ATP is hydrogenolyzed for each amidation; cobyric acid synthase 2219140..2220600 Dinoroseobacter shibae DFL 12 = DSM 16493 5713091 YP_001533435.1 CDS Dshi_2097 NC_009952.1 2220619 2221347 R hypothetical protein complement(2220619..2221347) Dinoroseobacter shibae DFL 12 = DSM 16493 5713092 YP_001533436.1 CDS Dshi_2098 NC_009952.1 2221467 2222837 R SWISSPROT P02930: Outer membrane protein tolC [Precursor]; TIGRFAM: TIGR01844 type I secretion outer membrane protein, TolC family; COG: COG1538 - Outer membrane protein; PFAM: PF02321; putative outer membrane protein tolC complement(2221467..2222837) Dinoroseobacter shibae DFL 12 = DSM 16493 5713093 YP_001533437.1 CDS Dshi_2099 NC_009952.1 2222900 2223553 R TIGRFAM: TIGR00080 protein-L-isoaspartate(D-aspartate) O-methyltransferase; COG: COG2518 - Protein-L-isoaspartate carboxylmethyltransferase; PFAM: PF01135; pcm; putative Protein-L-isoaspartate O-methyltransferase complement(2222900..2223553) Dinoroseobacter shibae DFL 12 = DSM 16493 5713094 YP_001533438.1 CDS Dshi_2100 NC_009952.1 2223872 2225461 D PFAM: PF00589; SUPERFAMILY: SSF56349; Gene3D: G3DSA:1.10.443.10; COG: COG4974 - Site-specific recombinase XerD; putative integrase 2223872..2225461 Dinoroseobacter shibae DFL 12 = DSM 16493 5713096 YP_001533439.1 CDS Dshi_2101 NC_009952.1 2225466 2228060 R SUPERFAMILY: SSF52540; hypothetical protein complement(2225466..2228060) Dinoroseobacter shibae DFL 12 = DSM 16493 5713097 YP_001533440.1 CDS Dshi_2102 NC_009952.1 2228064 2229521 R PFAM: PF01555; related to DNA methylase N4/N6; hypothetical protein complement(2228064..2229521) Dinoroseobacter shibae DFL 12 = DSM 16493 5713098 YP_001533441.1 CDS Dshi_2103 NC_009952.1 2229626 2229892 D PFAM: PF01527-Transposase; putative transposase 2229626..2229892 Dinoroseobacter shibae DFL 12 = DSM 16493 5713099 YP_001533442.1 CDS Dshi_2104 NC_009952.1 2229916 2230737 D COG: COG2801 - Transposase and inactivated derivatives; PFAM: PF00665; PROSITE: PS50994; SUPERFAMILY: SSF53098; putative integrase 2229916..2230737 Dinoroseobacter shibae DFL 12 = DSM 16493 5713100 YP_001533443.1 CDS Dshi_2105 NC_009952.1 2230732 2231412 R PFAM: PF01555; PROSITE: PS00092; SUPERFAMILY: SSF53335; related to DNA methylase N6; hypothetical protein complement(2230732..2231412) Dinoroseobacter shibae DFL 12 = DSM 16493 5713101 YP_001533444.1 CDS Dshi_2106 NC_009952.1 2231752 2232006 R PFAM: PF01381; PROSITE: PS50943; SMART: SM00530; SUPERFAMILY: SSF47413; Gene3D: G3DSA:1.10.260.40; related to HTH-type lambda repressor; hypothetical protein complement(2231752..2232006) Dinoroseobacter shibae DFL 12 = DSM 16493 5713102 YP_001533445.1 CDS Dshi_2107 NC_009952.1 2232133 2232831 D hypothetical protein 2232133..2232831 Dinoroseobacter shibae DFL 12 = DSM 16493 5713103 YP_001533446.1 CDS Dshi_2108 NC_009952.1 2234212 2236719 R COG: COG0025 - NhaP-type Na+/H+ and K+/H+ antiporters; PFAM: PF00027, PF00999; SMART: SM00100; PROSITE: PS50042; related to sodium/hydrogen exchanger; hypothetical protein complement(2234212..2236719) Dinoroseobacter shibae DFL 12 = DSM 16493 5713104 YP_001533447.1 CDS Dshi_2109 NC_009952.1 2236892 2238043 R COG: COG3616 - Predicted amino acid aldolase or racemase; PFAM: PF01168; related to alanine racemase; hypothetical protein complement(2236892..2238043) Dinoroseobacter shibae DFL 12 = DSM 16493 5713105 YP_001533448.1 CDS Dshi_2110 NC_009952.1 2238185 2239102 D PFAM: PF04227- Indigoidine synthase A like protein; SUPERFAMILY SSF110581: Indigoidine synthase A-like; indigoidine synthase A-like protein 2238185..2239102 Dinoroseobacter shibae DFL 12 = DSM 16493 5713106 YP_001533449.1 CDS purU NC_009952.1 2239132 2240037 R SWISSPROT P37051: Formyltetrahydrofolate deformylase; TIGRFAM: TIGR00655; COG: COG0788; PFAM: PF00551, PF01842; PRINTS: PR01575; PIR: PIRSF036480- formyltetrahydrofolate deformylase; formyltetrahydrofolate deformylase complement(2239132..2240037) Dinoroseobacter shibae DFL 12 = DSM 16493 5713107 YP_003422332.1 CDS Dshi_5008 NC_009952.1 2240003 2241415 R L-serine dehydratase complement(2240003..2241415) Dinoroseobacter shibae DFL 12 = DSM 16493 5713108 YP_001533450.1 CDS glyA NC_009952.1 2241420 2242694 R catalyzes the reaction of glycine with 5,10-methylenetetrahydrofolate to form L-serine and tetrahydrofolate; serine hydroxymethyltransferase complement(2241420..2242694) Dinoroseobacter shibae DFL 12 = DSM 16493 5713109 YP_001533451.1 CDS Dshi_2114 NC_009952.1 2242777 2243307 R SWISSPROT O87386: Sarcosine oxidase subunit alpha; TIGRFAM: TIGR01375 sarcosine oxidase, gamma subunit family, heterotetrameric form; COG: COG4583 - Sarcosine oxidase gamma subunit; PFAM: PF04268: SUPERFAMILY: SSF103025; putative sarcosine oxidase subunit gamma complement(2242777..2243307) Dinoroseobacter shibae DFL 12 = DSM 16493 5713110 YP_001533452.1 CDS soxA2 NC_009952.1 2243321 2246323 R SWISSPROT Q46337: Sarcosine oxidase subunit alpha; TIGRFAM: TIGR01372 sarcosine oxidase, alpha subunit family, heterotetrameric form; COG: COG0404 - Glycine cleavage system T protein (aminomethyltransferase); PFAM: PF01571, PF08669, PF07992; sarcosine oxidase subunit alpha complement(2243321..2246323) Dinoroseobacter shibae DFL 12 = DSM 16493 5713111 YP_001533453.1 CDS Dshi_2116 NC_009952.1 2246320 2246619 R SWISSPROT Q46336: Sarcosine oxidase subunit delta; PFAM: Sarcosine oxidase, delta subunit family; TIGRFAM: TIGR01374; COG: COG4311 - Sarcosine oxidase delta subunit; delta subunit (soxD); putative sarcosine oxidase complement(2246320..2246619) Dinoroseobacter shibae DFL 12 = DSM 16493 5713112 YP_001533454.1 CDS soxB NC_009952.1 2246632 2247885 R SWISSPROT P40875: sarcosine oxidase subunit beta; PFAM: PF01266-FAD dependent oxidoreductase; TIGRFAM: TIGR01373-Sarcosine oxidase, beta subunit, heterotetrameric; COG: COG0665 - Glycine/D-amino acid oxidases (deaminating); sarcosine oxidase subunit beta complement(2246632..2247885) Dinoroseobacter shibae DFL 12 = DSM 16493 5713113 YP_001533455.1 CDS Dshi_2118 NC_009952.1 2248012 2248998 D COG: COG4977 - Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain; PFAM: PF00165, PF01965; SMART: SM00342; PROSITE: PS01124; SUPERFAMILY: SSF46689; Gene3D: G3DSA:1.10.10.60; AraC family; HTH-type transcriptional regulator 2248012..2248998 Dinoroseobacter shibae DFL 12 = DSM 16493 5713114 YP_001533456.1 CDS Dshi_2119 NC_009952.1 2249037 2250611 R TIGRFAM: TIGR00842 - choline/carnitine/betaine transport; COG: COG1292 - Choline-glycine betaine transporter; PFAM: PF02028-BCCT family transporter; betaine/carnitine/choline transporter family protein complement(2249037..2250611) Dinoroseobacter shibae DFL 12 = DSM 16493 5713115 YP_001533457.1 CDS potA2 NC_009952.1 2250796 2251926 R SWISSPROT P69874: Spermidine/putrescine import ATP-binding protein potA; COG: COG3842-ABC-type spermidine/putrescine transport systems, ATPase components; PFAM: PF00005, PF08402; PROSITE: PS00211, PS50893; SMART: SM00382; spermidine/putrescine import ATP-binding protein complement(2250796..2251926) Dinoroseobacter shibae DFL 12 = DSM 16493 5713116 YP_001533458.1 CDS Dshi_2121 NC_009952.1 2251923 2252720 R SWISSPROT P0AFK6: Spermidine/putrescine transport system permease protein potC; COG: COG1177 - ABC-type spermidine/putrescine transport system, permease component II; PFAM: PF00528; PROSITE: PS50928; putative spermidine/putrescine transport system permease complement(2251923..2252720) Dinoroseobacter shibae DFL 12 = DSM 16493 5713117 YP_001533459.1 CDS Dshi_2122 NC_009952.1 2252722 2253567 R SWISSPROT P0AFK4: Spermidine/putrescine transport system permease protein potB; COG: COG1176-ABC-type spermidine/putrescine transport system, permease component I; PFAM: pfam00528; PROSITE: PS50928; putative spermidine/putrescine transport system permease complement(2252722..2253567) Dinoroseobacter shibae DFL 12 = DSM 16493 5713118 YP_001533460.1 CDS Dshi_2123 NC_009952.1 2253645 2254763 R COG: COG0687 - Spermidine/putrescine-binding periplasmic protein; PRINTS: PR00909; SWISSPROT P0AFK9: Spermidine/putrescine-binding periplasmic protein [Precursor]; similar to spermidine/putrescine binding periplasmic protein (potD); hypothetical protein complement(2253645..2254763) Dinoroseobacter shibae DFL 12 = DSM 16493 5713119 YP_001533461.1 CDS Dshi_2124 NC_009952.1 2254814 2255617 R PFAM: PF02633; COG: COG1402 - Uncharacterized protein, putative amidase; related to creatininase; hypothetical protein complement(2254814..2255617) Dinoroseobacter shibae DFL 12 = DSM 16493 5713120 YP_001533462.1 CDS Dshi_2125 NC_009952.1 2255710 2256606 D COG: COG0583 - Transcriptional regulator; PFAM: PF00126, PF03466; PROSITE: PS50931; SUPERFAMILY: SSF53850, SSF46785; lysR family; HTH-type transcriptional regulator 2255710..2256606 Dinoroseobacter shibae DFL 12 = DSM 16493 5713121 YP_001533463.1 CDS Dshi_2126 NC_009952.1 2256727 2257959 D SWISSPROT P38488: Creatinase; COG: COG0006 - Xaa-Pro aminopeptidase; PFAM: PF00557, PF01321; creatinase 2256727..2257959 Dinoroseobacter shibae DFL 12 = DSM 16493 5713122 YP_001533464.1 CDS Dshi_2127 NC_009952.1 2258167 2258787 D SUPERFAMILY: SSF51182; hypothetical protein 2258167..2258787 Dinoroseobacter shibae DFL 12 = DSM 16493 5713123 YP_001533465.1 CDS Dshi_2128 NC_009952.1 2258972 2259460 D PFAM PF04403: Paraquat-inducible protein A; similar to paraquat inducible protein A; hypothetical protein 2258972..2259460 Dinoroseobacter shibae DFL 12 = DSM 16493 5713124 YP_001533466.1 CDS Dshi_2129 NC_009952.1 2259500 2260867 D 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 2259500..2260867 Dinoroseobacter shibae DFL 12 = DSM 16493 5713125 YP_001533467.1 CDS Dshi_2130 NC_009952.1 2260890 2261444 D COG: COG1286 - Uncharacterized membrane protein, required for colicin V production; PFAM: PF02674-Colicin V production protein; putative colicin V production protein 2260890..2261444 Dinoroseobacter shibae DFL 12 = DSM 16493 5713126 YP_001533468.1 CDS Dshi_2131 NC_009952.1 2261760 2262230 D no database hits, no shine dalgarno. Pseudogene??; hypothetical protein 2261760..2262230 Dinoroseobacter shibae DFL 12 = DSM 16493 5713127 YP_001533469.1 CDS purF NC_009952.1 2262378 2263904 D Catalyzes first step of the de novo purine nucleotide biosynthetic pathway; amidophosphoribosyltransferase 2262378..2263904 Dinoroseobacter shibae DFL 12 = DSM 16493 5713128 YP_001533470.1 CDS Dshi_2133 NC_009952.1 2263901 2264419 D COG: COG3543 - Uncharacterized conserved protein; PFAM: PF06935-Protein of unknown function; hypothetical protein 2263901..2264419 Dinoroseobacter shibae DFL 12 = DSM 16493 5713129 YP_001533471.1 CDS Dshi_2134 NC_009952.1 2264629 2265222 R COG: COG1268 - Uncharacterized conserved protein; PFAM: PF02632-BioY family; PIR: PIRSF016661- uncharacterized biotin biosynthesis protein, BioY type; putative BioY protein complement(2264629..2265222) Dinoroseobacter shibae DFL 12 = DSM 16493 5713130 YP_001533472.1 CDS Dshi_2135 NC_009952.1 2265345 2266010 D COG: COG4221 - Short-chain alcohol dehydrogenase of unknown specificity; PFAM: PF00106; PRINTS: PR00081; short-chain dehydrogenase 2265345..2266010 Dinoroseobacter shibae DFL 12 = DSM 16493 5713131 YP_001533473.1 CDS surE NC_009952.1 2266110 2266895 D catalyzes the conversion of a phosphate monoester to an alcohol and a phosphate; stationary phase survival protein SurE 2266110..2266895 Dinoroseobacter shibae DFL 12 = DSM 16493 5713132 YP_001533474.1 CDS pcm NC_009952.1 2266892 2267542 D TIGRFAM: TIGR00080 protein-L-isoaspartate(D-aspartate) O-methyltransferase; COG: COG2518 - Protein-L-isoaspartate carboxylmethyltransferase; PFAM: PF01135; PROSITE: PS01279; protein-L-isoaspartate O-methyltransferase 2266892..2267542 Dinoroseobacter shibae DFL 12 = DSM 16493 5713133 YP_001533475.1 CDS Dshi_2138 NC_009952.1 2267574 2268803 D COG: COG0739 - Membrane proteins related to metalloendopeptidases; PFAM: PF01476, PF01551; SMART: SM00257; SUPERFAMILY: SSF51261; related to metalloprotease; hypothetical protein 2267574..2268803 Dinoroseobacter shibae DFL 12 = DSM 16493 5713134 YP_001533476.1 CDS Dshi_2139 NC_009952.1 2268877 2269770 R SWISSPROT P31125: Probable amino-acid metabolite efflux pump; P0ABT8: Uncharacterized inner membrane transporter yiJE; PFAM: PF00892; SUPERFAMILY: SSF103481; related to multidrug resistance efflux transporter; integral membrane protein complement(2268877..2269770) Dinoroseobacter shibae DFL 12 = DSM 16493 5713135 YP_001533477.1 CDS Dshi_2140 NC_009952.1 2269849 2271162 D PFAM: PF00999; COG: COG0025 - NhaP-type Na+/H+ and K+/H+ antiporters; related to sodium/hydrogen exchanger; hypothetical protein 2269849..2271162 Dinoroseobacter shibae DFL 12 = DSM 16493 5713136 YP_001533478.1 CDS Dshi_2141 NC_009952.1 2271249 2271968 D PFAM: PF04391; hypothetical protein 2271249..2271968 Dinoroseobacter shibae DFL 12 = DSM 16493 5713137 YP_001533479.1 CDS Dshi_2142 NC_009952.1 2272078 2272491 D SWISSPROT P0A9A9: Ferric uptake regulation protein (fur); COG: COG0735 - Fe2+/Zn2+ uptake regulation proteins; PFAM: PF01475; SUPERFAMILY: SSF46785; putative ferric uptake regulation protein 2272078..2272491 Dinoroseobacter shibae DFL 12 = DSM 16493 5713138 YP_001533480.1 CDS Dshi_2143 NC_009952.1 2272576 2273487 D COG: COG1741 - Pirin-related protein; PFAM: PF02678, PF05726; SUPERFAMILY: SSF51182; pirin-like protein 2272576..2273487 Dinoroseobacter shibae DFL 12 = DSM 16493 5713139 YP_001533481.1 CDS Dshi_2144 NC_009952.1 2273605 2274639 R SWISSPROT P75823: Low specificity L-threonine aldolase; O07051: L-allo-threonine aldolase COG: COG2008 - Threonine aldolase; PFAM: PF01212; SUPERFAMILY: SSF53383; threonine aldolase complement(2273605..2274639) Dinoroseobacter shibae DFL 12 = DSM 16493 5713140 YP_001533482.1 CDS eno NC_009952.1 2274839 2276113 D enolase; catalyzes the formation of phosphoenolpyruvate from 2-phospho-D-glycerate in glycolysis; phosphopyruvate hydratase 2274839..2276113 Dinoroseobacter shibae DFL 12 = DSM 16493 5713141 YP_001533483.1 CDS Dshi_2146 NC_009952.1 2276189 2276938 R PFAM: PF05239; related to PRC-barrel; hypothetical protein complement(2276189..2276938) Dinoroseobacter shibae DFL 12 = DSM 16493 5713142 YP_001533484.1 CDS Dshi_2147 NC_009952.1 2277080 2277499 R hypothetical protein complement(2277080..2277499) Dinoroseobacter shibae DFL 12 = DSM 16493 5713143 YP_001533485.1 CDS Dshi_2148 NC_009952.1 2277653 2278543 D SWISSPROT Q68XV0: S-adenosylmethionine uptake transporter; PFAM: pfam00892; COG: COG5006 - Predicted permease, DMT superfamily; putative S-adenosylmethionine uptake transporter 2277653..2278543 Dinoroseobacter shibae DFL 12 = DSM 16493 5713144 YP_001533486.1 CDS Dshi_2149 NC_009952.1 2278551 2278991 D COG: COG3542 - Uncharacterized conserved protein; PFAM: PF06172 Cupin superfamily (DUF985); putative cupin 2278551..2278991 Dinoroseobacter shibae DFL 12 = DSM 16493 5713145 YP_001533487.1 CDS anmK NC_009952.1 2279010 2280089 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(2279010..2280089) Dinoroseobacter shibae DFL 12 = DSM 16493 5713146 YP_001533488.1 CDS tyrS NC_009952.1 2280141 2281394 D Swiss-Prot: P0AGJ9-Tyrosyl-tRNA synthetase TIGRFAM: tyrosyl-tRNA synthetase PFAM: aminoacyl-tRNA synthetase class Ib; tyrosyl-tRNA synthetase 2280141..2281394 Dinoroseobacter shibae DFL 12 = DSM 16493 5713147 YP_001533489.1 CDS Dshi_2152 NC_009952.1 2281595 2282566 R -# KEGG: sil:SPO2232 hypothetical protein; hypothetical protein complement(2281595..2282566) Dinoroseobacter shibae DFL 12 = DSM 16493 5713148 YP_001533490.1 CDS Dshi_2153 NC_009952.1 2282789 2283337 R Swiss-Prot: P23869-Peptidyl-prolyl cis-trans isomerase B PFAM: peptidyl-prolyl cis-trans isomerase cyclophilin type; putative peptidyl-prolyl cis-trans isomerase complement(2282789..2283337) Dinoroseobacter shibae DFL 12 = DSM 16493 5713149 YP_001533491.1 CDS Dshi_2154 NC_009952.1 2283330 2283854 R Swiss-Prot: P0AFL3-Peptidyl-prolyl cis-trans isomerase A PFAM: peptidyl-prolyl cis-trans isomerase cyclophilin type; cyclophilin type; putative peptidyl-prolyl cis-trans isomerase complement(2283330..2283854) Dinoroseobacter shibae DFL 12 = DSM 16493 5713150 YP_001533492.1 CDS pgk NC_009952.1 2284018 2285199 D Converts 3-phospho-D-glycerate to 3-phospho-D-glyceroyl phosphate during the glycolysis pathway; phosphoglycerate kinase 2284018..2285199 Dinoroseobacter shibae DFL 12 = DSM 16493 5713151 YP_001533493.1 CDS fda NC_009952.1 2285294 2286178 D catalyzes the formation of glycerone phosphate and D-glyceraldehyde 3-phosphate from D-fructose 1,6-bisphosphate in glycolysis; fructose-1,6-bisphosphate aldolase 2285294..2286178 Dinoroseobacter shibae DFL 12 = DSM 16493 5713152 YP_001533494.1 CDS Dshi_2157 NC_009952.1 2286453 2286755 D PFAM: Septum formation initiator KEGG: jan:Jann_1692 septum formation initiator; similar to septum formation initiator; hypothetical protein 2286453..2286755 Dinoroseobacter shibae DFL 12 = DSM 16493 5713153 YP_001533495.1 CDS pdhA1 NC_009952.1 2286855 2287850 D Swiss-Prot: Q820A6-Pyruvate dehydrogenase E1 component subunit alpha PFAM: dehydrogenase E1 component; pyruvate dehydrogenase E1 component subunit alpha 2286855..2287850 Dinoroseobacter shibae DFL 12 = DSM 16493 5713154 YP_001533496.1 CDS pdhB2 NC_009952.1 2287863 2289218 D 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 2287863..2289218 Dinoroseobacter shibae DFL 12 = DSM 16493 5713155 YP_001533497.1 CDS pdhC1 NC_009952.1 2289232 2290494 D Swiss-Prot: Q9R9N3-Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex 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 2289232..2290494 Dinoroseobacter shibae DFL 12 = DSM 16493 5713156 YP_001533498.1 CDS cysE NC_009952.1 2290509 2291318 R Swiss-Prot: P0A9D4-Serine acetyltransferase TIGRFAM: serine O-acetyltransferase PFAM: transferase hexapeptide repeat containing protein; serine acetyltransferase domain protein; serine O-acetyltransferase complement(2290509..2291318) Dinoroseobacter shibae DFL 12 = DSM 16493 5713157 YP_001533499.1 CDS Dshi_2162 NC_009952.1 2291686 2292393 R hypothetical protein complement(2291686..2292393) Dinoroseobacter shibae DFL 12 = DSM 16493 5713158 YP_001533500.1 CDS Dshi_2163 NC_009952.1 2292386 2296303 R KEGG: sil:SPO2250 hypothetical protein; hypothetical protein complement(2292386..2296303) Dinoroseobacter shibae DFL 12 = DSM 16493 5713159 YP_001533501.1 CDS Dshi_2164 NC_009952.1 2296307 2296747 R TIGRFAM: putative phage cell wall peptidase, NlpC/P60 family PFAM: NLP/P60 protein KEGG: sil:SPO2251 hypothetical protein; similar to phage cell wall peptidase, NlpC/P60 family; hypothetical protein complement(2296307..2296747) Dinoroseobacter shibae DFL 12 = DSM 16493 5713160 YP_001533502.1 CDS Dshi_2165 NC_009952.1 2296744 2297634 R PFAM: conserved hypothetical protein KEGG: rsq:Rsph17025_1087 hypothetical protein; hypothetical protein complement(2296744..2297634) Dinoroseobacter shibae DFL 12 = DSM 16493 5713161 YP_001533503.1 CDS Dshi_2166 NC_009952.1 2297631 2298263 R Conserved hypothetical protein TIGR02217, PFAM: conserved hypothetical protein, KEGG: sil:SPO2253 hypothetical protein; hypothetical protein complement(2297631..2298263) Dinoroseobacter shibae DFL 12 = DSM 16493 5713162 YP_001533504.1 CDS Dshi_2167 NC_009952.1 2298277 2298945 R COG5281, Phage-related minor tail protein [Function unknown].; similar to Phage-related minor tail protein; hypothetical protein complement(2298277..2298945) Dinoroseobacter shibae DFL 12 = DSM 16493 5713163 YP_001533505.1 CDS Dshi_2168 NC_009952.1 2298929 2299144 R TIGR02216# phage conserved hypothetical protein; hypothetical protein complement(2298929..2299144) Dinoroseobacter shibae DFL 12 = DSM 16493 5713164 YP_001533506.1 CDS Dshi_2169 NC_009952.1 2299141 2299470 R KEGG: rsq:Rsph17025_1083 hypothetical protein; hypothetical protein complement(2299141..2299470) Dinoroseobacter shibae DFL 12 = DSM 16493 5713165 YP_001533507.1 CDS Dshi_2170 NC_009952.1 2299476 2299889 R TIGRFAM: phage major tail protein, TP901-1 family KEGG: sit:TM1040_1065 phage major tail protein, TP901-1; similar to Phage major tail protein, TP901-1; hypothetical protein complement(2299476..2299889) Dinoroseobacter shibae DFL 12 = DSM 16493 5713166 YP_001533508.1 CDS Dshi_2171 NC_009952.1 2299911 2300321 R KEGG: sil:SPO2258 hypothetical protein; hypothetical protein complement(2299911..2300321) Dinoroseobacter shibae DFL 12 = DSM 16493 5713167 YP_001533509.1 CDS Dshi_2172 NC_009952.1 2300318 2300656 R TIGR01563# phage head-tail adaptor, putative, SPP1 family; IPR013045 Conserved hypothetical protein 1563; TIGRFAM: phage head-tail adaptor, putative; KEGG: sil:SPO2259 head-tail adaptor, putative; hypothetical protein complement(2300318..2300656) Dinoroseobacter shibae DFL 12 = DSM 16493 5713168 YP_001533510.1 CDS Dshi_2173 NC_009952.1 2300653 2301243 R KEGG: rde:RD1_3027 hypothetical protein, TIGR02215 phage conserved hypothetical protein, phiE125 gp8 family; hypothetical protein complement(2300653..2301243) Dinoroseobacter shibae DFL 12 = DSM 16493 5713826 YP_001533511.1 CDS Dshi_2174 NC_009952.1 2301398 2302615 R TIGRFAM: phage major capsid protein, HK97 family PFAM: major capsid protein HK97 KEGG: jan:Jann_1635 phage major capsid protein, HK97; HK97 family; putative phage major capsid protein complement(2301398..2302615) Dinoroseobacter shibae DFL 12 = DSM 16493 5713827 YP_001533512.1 CDS Dshi_2175 NC_009952.1 2302612 2303229 R TIGRFAM: phage prohead protease, HK97 family PFAM: peptidase U35 phage prohead HK97 KEGG: sil:SPO2262 phage prohead protease, HK97 family; HK97 family; putative phage prohead protease complement(2302612..2303229) Dinoroseobacter shibae DFL 12 = DSM 16493 5713828 YP_001533513.1 CDS Dshi_2176 NC_009952.1 2303242 2303508 R KEGG: jan:Jann_1633 hypothetical protein; hypothetical protein complement(2303242..2303508) Dinoroseobacter shibae DFL 12 = DSM 16493 5713829 YP_001533514.1 CDS Dshi_2177 NC_009952.1 2303499 2304689 R TIGRFAM: phage portal protein, HK97 family PFAM: portal protein KEGG: rde:RD1_3033 phage portal protein, putative; HK97 family; putative phage portal protein complement(2303499..2304689) Dinoroseobacter shibae DFL 12 = DSM 16493 5713830 YP_001533515.1 CDS Dshi_2178 NC_009952.1 2304797 2306155 R PFAM: protein of unknown function DUF264 KEGG: rde:RD1_3034 hypothetical protein; hypothetical protein complement(2304797..2306155) Dinoroseobacter shibae DFL 12 = DSM 16493 5713831 YP_001533516.1 CDS Dshi_2179 NC_009952.1 2306608 2307762 R PFAM: aminodeoxychorismate lyase KEGG: jan:Jann_1630 aminodeoxychorismate lyase; related to aminodeoxychorismate lyase; hypothetical protein complement(2306608..2307762) Dinoroseobacter shibae DFL 12 = DSM 16493 5713832 YP_001533517.1 CDS fabF NC_009952.1 2307762 2309024 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-(acyl carrier protein) synthase II complement(2307762..2309024) Dinoroseobacter shibae DFL 12 = DSM 16493 5713833 YP_001533518.1 CDS acpP NC_009952.1 2309189 2309422 R carries the fatty acid chain in fatty acid biosynthesis; acyl carrier protein complement(2309189..2309422) Dinoroseobacter shibae DFL 12 = DSM 16493 5713834 YP_001533519.1 CDS Dshi_2182 NC_009952.1 2309595 2310332 R Swiss-Prot: P0AEK2- 3-oxoacyl-[acyl-carrier-protein] reductase fabG Swiss-Prot: P72332-Nodulation protein G TIGRFAM: 3-oxoacyl-(acyl-carrier-protein) reductase PFAM: NAD-dependent epimerase/dehydratase; short-chain dehydrogenase/reductase SDR; putative 3-oxoacyl-[acyl-carrier-protein] reductase complement(2309595..2310332) Dinoroseobacter shibae DFL 12 = DSM 16493 5713835 YP_001533520.1 CDS fabD NC_009952.1 2310332 2311279 R Swiss-Prot hit: spP0AAI9 (FABD_ECOLI); TIGR00128# malonyl CoA-acyl carrier protein transacylase PFAM: Acyl transferase KEGG: rsq:Rsph17025_1221 malonyl CoA-acyl carrier protein transacylase; malonyl CoA-acyl carrier protein transacylase complement(2310332..2311279) Dinoroseobacter shibae DFL 12 = DSM 16493 5713836 YP_001533521.1 CDS Dshi_2184 NC_009952.1 2311440 2312642 D PFAM: YceI family protein; cytochrome B561 KEGG: rde:RD1_3041 cytochrome b561, putative; putative cytochrome B561 2311440..2312642 Dinoroseobacter shibae DFL 12 = DSM 16493 5713837 YP_001533522.1 CDS Dshi_2185 NC_009952.1 2312706 2313290 R COG2353 - Uncharacterized conserved protein PFAM: YceI family protein; related to YceI family protein; hypothetical protein complement(2312706..2313290) Dinoroseobacter shibae DFL 12 = DSM 16493 5713838 YP_001533523.1 CDS rpsF NC_009952.1 2313554 2313907 D binds cooperatively with S18 to the S15-16S complex, allowing platform assembly to continue with S11 and S21; 30S ribosomal protein S6 2313554..2313907 Dinoroseobacter shibae DFL 12 = DSM 16493 5713839 YP_001533524.1 CDS rpsR NC_009952.1 2313936 2314163 D 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 2313936..2314163 Dinoroseobacter shibae DFL 12 = DSM 16493 5713840 YP_001533525.1 CDS rplI NC_009952.1 2314176 2314805 D in Escherichia coli this protein is wrapped around the base of the L1 stalk; 50S ribosomal protein L9 2314176..2314805 Dinoroseobacter shibae DFL 12 = DSM 16493 5713841 YP_001533526.1 CDS cpdB NC_009952.1 2314997 2316958 D periplasmic enzyme; functions during ribonucleic acid degradation; 2',3'-cyclic nucleotides are first converted to 3'-nucleotide and then cleaved to yield a ribonucleotide and a phosphate; bifunctional 2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase periplasmic protein 2314997..2316958 Dinoroseobacter shibae DFL 12 = DSM 16493 5713842 YP_001533527.1 CDS tig NC_009952.1 2317027 2318355 R Tig; RopA; peptidyl-prolyl cis/trans isomerase; promotes folding of newly synthesized proteins; binds ribosomal 50S subunit; forms a homodimer; trigger factor complement(2317027..2318355) Dinoroseobacter shibae DFL 12 = DSM 16493 5713843 YP_001533528.1 CDS Dshi_2191 NC_009952.1 2318521 2318832 R PFAM: ETC complex I subunit conserved region KEGG: sit:TM1040_0143 ETC complex I subunit conserved region; putative ETC complex subunit I conserved region complement(2318521..2318832) Dinoroseobacter shibae DFL 12 = DSM 16493 5713844 YP_001533529.1 CDS uvrB NC_009952.1 2319332 2321509 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 2319332..2321509 Dinoroseobacter shibae DFL 12 = DSM 16493 5713845 YP_001533530.1 CDS Dshi_2193 NC_009952.1 2321538 2321693 R hypothetical protein complement(2321538..2321693) Dinoroseobacter shibae DFL 12 = DSM 16493 5713846 YP_001533531.1 CDS Dshi_2194 NC_009952.1 2321854 2322237 D hypothetical protein 2321854..2322237 Dinoroseobacter shibae DFL 12 = DSM 16493 5713847 YP_001533532.1 CDS Dshi_2195 NC_009952.1 2322507 2322644 R PFAM: Entericidin EcnAB; similar to Entericidin EcnAB; hypothetical protein complement(2322507..2322644) Dinoroseobacter shibae DFL 12 = DSM 16493 5713848 YP_001533533.1 CDS Dshi_2196 NC_009952.1 2323007 2324029 R hypothetical protein complement(2323007..2324029) Dinoroseobacter shibae DFL 12 = DSM 16493 5713849 YP_001533534.1 CDS Dshi_2197 NC_009952.1 2324302 2325957 R ChvD; in Agrobacterium tumefaciens, mutations in both Walker boxes were found to affect virulence; putative ABC transporter ATP-binding protein complement(2324302..2325957) Dinoroseobacter shibae DFL 12 = DSM 16493 5713850 YP_001533535.1 CDS Dshi_2198 NC_009952.1 2326037 2326516 D PFAM: MOSC domain containing protein (pfam03473) KEGG: sil:SPO0448 MOSC domain protein; similar to MOCO sulphurase (MOSC domain); hypothetical protein 2326037..2326516 Dinoroseobacter shibae DFL 12 = DSM 16493 5713851 YP_001533536.1 CDS Dshi_2199 NC_009952.1 2326735 2327424 D TIGRFAM: aspartate racemase PFAM: Asp/Glu racemase KEGG: atc:AGR_L_3474 hypothetical protein; aspartate/glutamate racemase family protein 2326735..2327424 Dinoroseobacter shibae DFL 12 = DSM 16493 5713852 YP_001533537.1 CDS Dshi_2200 NC_009952.1 2327502 2328092 R PFAM: regulatory protein TetR KEGG: gvi:gll0188 TetR family transcriptional regulatory protein; putative regulatory protein TetR complement(2327502..2328092) Dinoroseobacter shibae DFL 12 = DSM 16493 5713853 YP_001533538.1 CDS Dshi_2201 NC_009952.1 2328093 2328536 R KEGG: tbd:Tbd_0484 hypothetical protein PFAM: Isoprenylcysteine carboxyl methyltransferase (ICMT) family (pfam04140) COG2020: Putative protein-S-isoprenylcysteine methyltransferase; hypothetical protein complement(2328093..2328536) Dinoroseobacter shibae DFL 12 = DSM 16493 5713854 YP_001533539.1 CDS Dshi_2202 NC_009952.1 2328739 2329656 R hypothetical protein complement(2328739..2329656) Dinoroseobacter shibae DFL 12 = DSM 16493 5713855 YP_001533540.1 CDS nadD NC_009952.1 2329752 2330339 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 2329752..2330339 Dinoroseobacter shibae DFL 12 = DSM 16493 5713856 YP_001533541.1 CDS Dshi_2204 NC_009952.1 2330428 2330763 D hypothetical protein 2330428..2330763 Dinoroseobacter shibae DFL 12 = DSM 16493 5713857 YP_001533542.1 CDS Dshi_2205 NC_009952.1 2330803 2331225 R hypothetical protein complement(2330803..2331225) Dinoroseobacter shibae DFL 12 = DSM 16493 5713858 YP_001533543.1 CDS lysK NC_009952.1 2331348 2333006 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 2331348..2333006 Dinoroseobacter shibae DFL 12 = DSM 16493 5713859 YP_001533544.1 CDS Dshi_2207 NC_009952.1 2333095 2333496 D KEGG:sil:SPO0457 hypothetical protein; hypothetical protein 2333095..2333496 Dinoroseobacter shibae DFL 12 = DSM 16493 5713860 YP_001533545.1 CDS Dshi_2208 NC_009952.1 2333780 2335267 R Swiss-Prot: spP39844, spP45161: Penicillin-binding protein 4 TIGRFAM: D-alanyl-D-alanine carboxypeptidase/D-alanyl-D-alanine-endopeptidase PFAM: peptidase S13 D-Ala-D-Ala carboxypeptidase C KEGG: sit:TM1040_2259 D-alanyl-D-alanine carboxypeptidase/D-alanyl-D-alanine-endopeptidase; putative D-alanyl-D-alanine carboxypeptidase/endopeptidase complement(2333780..2335267) Dinoroseobacter shibae DFL 12 = DSM 16493 5713861 YP_001533546.1 CDS Dshi_2209 NC_009952.1 2335419 2336249 D Swiss-Prot: spQ9ZE70 COG5006: predicted permease, DMT superfamily PFAM: protein of unknown function DUF6 transmembrane KEGG: jan:Jann_3630 protein of unknown function DUF6, transmembrane; associated with drug/metabolite transport; hypothetical protein 2335419..2336249 Dinoroseobacter shibae DFL 12 = DSM 16493 5713862 YP_001533547.1 CDS Dshi_2210 NC_009952.1 2336408 2338699 D KEGG: sil:SPO0459 hypothetical protein; hypothetical protein 2336408..2338699 Dinoroseobacter shibae DFL 12 = DSM 16493 5713863 YP_001533548.1 CDS Dshi_2211 NC_009952.1 2338802 2339278 D PFAM: protein of unknown function DUF427 KEGG: jan:Jann_3615 protein of unknown function DUF427; hypothetical protein 2338802..2339278 Dinoroseobacter shibae DFL 12 = DSM 16493 5713864 YP_001533549.1 CDS Dshi_2212 NC_009952.1 2339288 2339782 R PFAM: pyridoxamine 5-phosphate oxidase-related FMN-binding KEGG: jan:Jann_3613 pyridoxamine 5-phosphate oxidase-related, FMN-binding; related to pyridoxamine 5-phosphate oxidase; hypothetical protein complement(2339288..2339782) Dinoroseobacter shibae DFL 12 = DSM 16493 5713865 YP_001533550.1 CDS Dshi_2213 NC_009952.1 2339879 2340286 D PFAM: UspA domain protein KEGG: rde:RD1_4076 universal stress family protein, putative; putative UspA domain-containing protein 2339879..2340286 Dinoroseobacter shibae DFL 12 = DSM 16493 5713866 YP_001533551.1 CDS Dshi_2214 NC_009952.1 2340335 2340664 D PFAM: Antibiotic biosynthesis monooxygenase KEGG: sil:SPO0462 antibiotic biosynthesis monooxygenase domain protein; related to antibiotic biosynthesis monooxygenase; hypothetical protein 2340335..2340664 Dinoroseobacter shibae DFL 12 = DSM 16493 5713867 YP_001533552.1 CDS Dshi_2215 NC_009952.1 2340674 2341336 R KEGG: rsq:Rsph17025_2878 hypothetical protein; hypothetical protein complement(2340674..2341336) Dinoroseobacter shibae DFL 12 = DSM 16493 5713868 YP_001533553.1 CDS Dshi_2216 NC_009952.1 2341451 2342086 D PFAM: pfam00991 ParA family ATPase COG1192: ATPases involved in chromosome partitioning; associated with ATPases involved in chromosome partitioning; hypothetical protein 2341451..2342086 Dinoroseobacter shibae DFL 12 = DSM 16493 5713869 YP_001533554.1 CDS Dshi_2217 NC_009952.1 2342145 2342387 D COG3809: Uncharacterized protein conserved in bacteria KEGG: rde:RD1_1249 hypothetical protein; hypothetical protein 2342145..2342387 Dinoroseobacter shibae DFL 12 = DSM 16493 5713870 YP_001533555.1 CDS Dshi_2218 NC_009952.1 2343059 2343469 R Swiss-Prot entry: P0A1A1 Acyl-CoA thioester hydrolase yciA COG1607: Acyl-CoA hydrolase PFAM: thioesterase superfamily protein KEGG: sil:SPO0440 thioesterase family protein; putative Acyl-CoA thioester hydrolase complement(2343059..2343469) Dinoroseobacter shibae DFL 12 = DSM 16493 5713871 YP_001533556.1 CDS Dshi_2219 NC_009952.1 2343691 2343897 D PFAM: Cold-shock protein DNA-binding SMART: Cold shock protein KEGG: rde:RD1_1402 cold shock protein CspA-related protein, putative; putative cold-shock DNA-binding domain-containing protein 2343691..2343897 Dinoroseobacter shibae DFL 12 = DSM 16493 5713872 YP_001533557.1 CDS Dshi_2220 NC_009952.1 2343977 2344417 D PFAM: protein of unknown function DUF1332 KEGG: sil:SPO1309 hypothetical protein COG4103: Uncharacterized protein conserved in bacteria; hypothetical protein 2343977..2344417 Dinoroseobacter shibae DFL 12 = DSM 16493 5713873 YP_001533558.1 CDS Dshi_2221 NC_009952.1 2344582 2345361 D COG4598: ABC-type histidine transport system, ATPase component PFAM: ABC transporter related SMART: AAA ATPase KEGG: rde:RD1_1899 amino acid ABC transporter, ATP-binding protein; ATPase subunit; putative amino acid ABC transporter 2344582..2345361 Dinoroseobacter shibae DFL 12 = DSM 16493 5713874 YP_001533559.1 CDS Dshi_2222 NC_009952.1 2345400 2346128 D PFAM: extracellular solute-binding protein family 3 COG0834: ABC-type amino acid transport/signal transduction systems, periplasmic component/domain SMART: ionotropic glutamate receptor KEGG: rde:RD1_1898 periplasmic binding protein, putative; family 3; extracellular solute-binding protein 2345400..2346128 Dinoroseobacter shibae DFL 12 = DSM 16493 5713875 YP_001533560.1 CDS Dshi_2223 NC_009952.1 2346203 2347090 D Swiss-Prot entry: P52094 Histidine transport system permease protein hisQ COG4215: ABC-type arginine transport system, permease component KEGG: sit:TM1040_1713 binding-protein-dependent transport systems inner membrane component; putative amino-acid ABC transporter permease 2346203..2347090 Dinoroseobacter shibae DFL 12 = DSM 16493 5713876 YP_001533561.1 CDS Dshi_2224 NC_009952.1 2347087 2347893 D Swiss-Prot entry: P0A2I7 Histidine transport system permease protein hisM TIGRFAM: polar amino acid ABC transporter, inner membrane subunit PFAM: binding-protein-dependent transport systems inner membrane component KEGG: sit:TM1040_1714 amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine; inner membrane subunit; putative polar amino acid ABC transporter 2347087..2347893 Dinoroseobacter shibae DFL 12 = DSM 16493 5713877 YP_001533562.1 CDS Dshi_2225 NC_009952.1 2347962 2348672 D PFAM: glutamine amidotransferase class-I KEGG: pde:Pden_1396 glutamine amidotransferase class-I COG0518: GMP synthase - Glutamine amidotransferase domain; putative glutamine amidotransferase class-I 2347962..2348672 Dinoroseobacter shibae DFL 12 = DSM 16493 5713878 YP_001533563.1 CDS Dshi_2226 NC_009952.1 2348653 2350023 D Swiss-Prot: P78061-Gamma-glutamylputrescine synthetase / Q9HNI2-Glutamine synthetase PFAM: glutamine synthetase catalytic region KEGG: sil:SPO1300 glutamine synthetase family protein; glutamine synthetase 2348653..2350023 Dinoroseobacter shibae DFL 12 = DSM 16493 5713879 YP_001533564.1 CDS Dshi_2227 NC_009952.1 2350024 2351328 D Swiss-Prot: P37906-Probable oxidoreductase PFAM: FAD dependent oxidoreductase KEGG: sit:TM1040_1839 FAD dependent oxidoreductase; putative FAD dependent oxidoreductase 2350024..2351328 Dinoroseobacter shibae DFL 12 = DSM 16493 5713880 YP_001533565.1 CDS Dshi_2228 NC_009952.1 2351401 2352594 D PFAM: DegT/DnrJ/EryC1/StrS aminotransferase; aromatic amino acid beta-eliminating lyase/threonine aldolase; aminotransferase class I and II KEGG: sil:SPO1295 aminotransferase, DegT/DnrJ/EryC1/StrS family COG0399:Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis; DegT/DnrJ/EryC1/StrS family; putative aminotransferase 2351401..2352594 Dinoroseobacter shibae DFL 12 = DSM 16493 5713881 YP_001533566.1 CDS Dshi_2229 NC_009952.1 2352591 2353535 R PFAM: regulatory protein LysR; LysR substrate-binding Swiss-Prot: P0ACQ4-contains the same pfam domains KEGG: sil:SPO0980 transcriptional regulator, LysR family; LysR family; putative transcriptional regulator complement(2352591..2353535) Dinoroseobacter shibae DFL 12 = DSM 16493 5713882 YP_001533567.1 CDS Dshi_2230 NC_009952.1 2353581 2354141 R TIGRFAM: polyhydroxyalkanoate synthesis repressor PhaR PFAM: PHB accumulation regulatory domain protein; PHA accumulation regulator DNA-binding protein KEGG: rsq:Rsph17025_0856 polyhydroxyalkonate synthesis repressor, PhaR; PhaR; putative polyhydroxyalkonate synthesis repressor complement(2353581..2354141) Dinoroseobacter shibae DFL 12 = DSM 16493 5713883 YP_001533568.1 CDS Dshi_2231 NC_009952.1 2354276 2354704 R NCBI: YP_001043910 - hypothetical protein Rsph17029_2035; hypothetical protein complement(2354276..2354704) Dinoroseobacter shibae DFL 12 = DSM 16493 5713884 YP_001533569.1 CDS Dshi_2232 NC_009952.1 2354912 2355358 R NCBI: YP_682186 - hypothetical protein RD1_1889; hypothetical protein complement(2354912..2355358) Dinoroseobacter shibae DFL 12 = DSM 16493 5713885 YP_001533570.1 CDS phbC NC_009952.1 2355488 2357302 R Swiss-Prot: P50176 - Poly-beta-hydroxybutyrate polymerase TIGRFAM: poly(R)-hydroxyalkanoic acid synthase, class I PFAM: Poly-beta-hydroxybutyrate polymerase domain protein KEGG: rsh:Rsph17029_2036 poly(R)-hydroxyalkanoic acid synthase, class I; poly-beta-hydroxybutyrate polymerase complement(2355488..2357302) Dinoroseobacter shibae DFL 12 = DSM 16493 5713886 YP_001533571.1 CDS Dshi_2234 NC_009952.1 2357406 2358683 D TIGRFAM: polyhydroxyalkanoate depolymerase, intracellular PFAM: PHB de-polymerase domain protein KEGG: sil:SPO1291 polyhydroxyalkanoate depolymerase, intracellular; intracellular; putative polyhydroxyalkanoate depolymerase 2357406..2358683 Dinoroseobacter shibae DFL 12 = DSM 16493 5713887 YP_001533572.1 CDS Dshi_2235 NC_009952.1 2358775 2359911 R COG0620: Methionine synthase II (cobalamin-independent) PFAM: Methionine synthase vitamin-B12 independent KEGG: jan:Jann_1114 methionine synthase, vitamin-B12 independent; putative methionine synthase vitamin-B12 independent complement(2358775..2359911) Dinoroseobacter shibae DFL 12 = DSM 16493 5713888 YP_001533573.1 CDS Dshi_2236 NC_009952.1 2359966 2360964 R hypothetical protein complement(2359966..2360964) Dinoroseobacter shibae DFL 12 = DSM 16493 5713889 YP_001533574.1 CDS Dshi_2237 NC_009952.1 2361020 2362003 R PFAM: protein of unknown function DUF1486 KEGG: rde:RD1_3943 hypothetical protein; hypothetical protein complement(2361020..2362003) Dinoroseobacter shibae DFL 12 = DSM 16493 5713890 YP_001533575.1 CDS Dshi_2238 NC_009952.1 2361990 2363024 R Swiss-Prot: P0ACP7-HTH-type transcriptional repressor purR KEGG: rde:RD1_3944 transcriptional regulatory protein, LacI family, putative PFAM: periplasmic binding protein/LacI transcriptional regulator SMART: regulatory protein LacI; LacI family; transcriptional regulator complement(2361990..2363024) Dinoroseobacter shibae DFL 12 = DSM 16493 5713891 YP_001533576.1 CDS Dshi_2239 NC_009952.1 2363027 2363779 R Swiss-Prot: P50199 Gluconate 5-dehydrogenase (SDR family protein) PFAM: short-chain dehydrogenase/reductase SDR; KR domain protein KEGG: jan:Jann_1106 short-chain dehydrogenase/reductase SDR; short-chain dehydrogenase/reductase SDR complement(2363027..2363779) Dinoroseobacter shibae DFL 12 = DSM 16493 5713892 YP_001533577.1 CDS Dshi_2240 NC_009952.1 2363849 2364484 R hypothetical protein complement(2363849..2364484) Dinoroseobacter shibae DFL 12 = DSM 16493 5713893 YP_001533578.1 CDS Dshi_2241 NC_009952.1 2364498 2365532 R PFAM: protein of unknown function DUF1486 KEGG: rde:RD1_3946 hypothetical protein; hypothetical protein complement(2364498..2365532) Dinoroseobacter shibae DFL 12 = DSM 16493 5713894 YP_001533579.1 CDS hisD3 NC_009952.1 2365495 2366820 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(2365495..2366820) Dinoroseobacter shibae DFL 12 = DSM 16493 5713895 YP_001533580.1 CDS Dshi_2243 NC_009952.1 2366910 2367665 R PFAM: alpha/beta hydrolase fold KEGG: rsp:RSP_0384 hypothetical protein; hypothetical protein complement(2366910..2367665) Dinoroseobacter shibae DFL 12 = DSM 16493 5713896 YP_001533581.1 CDS Dshi_2244 NC_009952.1 2367721 2368161 R PFAM: protein of unknown function DUF1052 KEGG: jan:Jann_3406 protein of unknown function DUF1052; hypothetical protein complement(2367721..2368161) Dinoroseobacter shibae DFL 12 = DSM 16493 5713897 YP_001533582.1 CDS Dshi_2245 NC_009952.1 2368423 2368770 R KEGG: rsq:Rsph17025_0423 hypothetical protein; hypothetical protein complement(2368423..2368770) Dinoroseobacter shibae DFL 12 = DSM 16493 5713898 YP_001533583.1 CDS Dshi_2246 NC_009952.1 2369013 2369543 R COG3335: Transposase and inactivated derivatives PFAM: Integrase core domain; related to transposase and inactivated derivatives; hypothetical protein complement(2369013..2369543) Dinoroseobacter shibae DFL 12 = DSM 16493 5713899 YP_001533584.1 CDS Dshi_2247 NC_009952.1 2369605 2369967 R COG3415 Transposase and inactivated derivatives; related to transposase and inactivated derivatives; hypothetical protein complement(2369605..2369967) Dinoroseobacter shibae DFL 12 = DSM 16493 5713900 YP_001533585.1 CDS Dshi_2248 NC_009952.1 2370080 2370526 D hypothetical protein 2370080..2370526 Dinoroseobacter shibae DFL 12 = DSM 16493 5713901 YP_001533586.1 CDS nusB NC_009952.1 2370535 2371014 R Swiss-Prot: Q0APG4-N utilization substance protein B homolog TIGRFAM: transcription antitermination factor NusB PFAM: NusB/RsmB/TIM44; N utilization substance protein B-like protein complement(2370535..2371014) Dinoroseobacter shibae DFL 12 = DSM 16493 5713902 YP_001533587.1 CDS ribH NC_009952.1 2371011 2371562 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(2371011..2371562) Dinoroseobacter shibae DFL 12 = DSM 16493 5713903 YP_001533588.1 CDS ribB NC_009952.1 2371565 2372680 R Swiss-Prot: P0A7J0 3,4-dihydroxy-2-butanone 4-phosphate synthase (DHBP synthase) TIGRFAM: 3,4-dihydroxy-2-butanone 4-phosphate synthase PFAM: 34-dihydroxy-2-butanone 4-phosphate synthase; GTP cyclohydrolase II; 3,4-dihydroxy-2-butanone 4-phosphate synthase complement(2371565..2372680) Dinoroseobacter shibae DFL 12 = DSM 16493 5713904 YP_001533589.1 CDS ribC NC_009952.1 2372819 2373421 R catalyzes the formation of riboflavin from 6,7-dimethyl-8-(1-D-ribityl)lumazine; riboflavin synthase subunit alpha complement(2372819..2373421) Dinoroseobacter shibae DFL 12 = DSM 16493 5713905 YP_001533590.1 CDS Dshi_2253 NC_009952.1 2373608 2374894 D Swiss-Prot: P42218 - Capsule polysaccharide export protein kpsS PFAM: Capsule polysaccharide biosynthesis protein KEGG: jan:Jann_3418 capsule polysaccharide biosynthesis; putative capsule polysaccharide export protein 2373608..2374894 Dinoroseobacter shibae DFL 12 = DSM 16493 5713906 YP_001533591.1 CDS Dshi_2254 NC_009952.1 2375007 2376164 D Swiss-Prot: P0A932 - Putative polysaccharide export protein yccZ [Precursor] PFAM: polysaccharide export protein KEGG: sil:SPO1756 polysaccharide biosynthesis/export protein; putative polysaccharide export protein 2375007..2376164 Dinoroseobacter shibae DFL 12 = DSM 16493 5713907 YP_001533592.1 CDS Dshi_2255 NC_009952.1 2376242 2378218 D Swiss-Prot: P42217 - Capsule polysaccharide export protein kpsC PFAM: Capsule polysaccharide biosynthesis protein KEGG: sil:SPO1755 capsular polysaccharide export protein KpsC; putative capsule polysaccharide export protein 2376242..2378218 Dinoroseobacter shibae DFL 12 = DSM 16493 5713908 YP_001533593.1 CDS ribD NC_009952.1 2378215 2379312 R Swiss-Prot: P25539 - Riboflavin biosynthesis protein ribD (includes: EC:1.1.1.193 - 5-amino-6-(5-phosphoribosylamino)uracil reductase EC:3.5.4.26 - Diaminohydroxyphosphoribosylaminopyrimidine deaminase) TIGRFAM: riboflavin biosynthesis protein RibD; riboflavin biosynthesis protein complement(2378215..2379312) Dinoroseobacter shibae DFL 12 = DSM 16493 5713909 YP_001533594.1 CDS nrdR NC_009952.1 2379314 2379781 R Swiss-Prot: Q1GEP8 and P0A8D0 - Transcriptional repressor nrdR PFAM: ATP-cone domain protein KEGG: rsq:Rsph17025_0843 ATP-cone domain protein; transcriptional regulator NrdR complement(2379314..2379781) Dinoroseobacter shibae DFL 12 = DSM 16493 5713910 YP_001533595.1 CDS Dshi_2258 NC_009952.1 2379941 2380360 R PFAM: protein of unknown function UPF0047 KEGG: sit:TM1040_2137 protein of unknown function UPF0047; hypothetical protein complement(2379941..2380360) Dinoroseobacter shibae DFL 12 = DSM 16493 5713911 YP_001533596.1 CDS Dshi_2259 NC_009952.1 2380410 2380916 R hypothetical protein complement(2380410..2380916) Dinoroseobacter shibae DFL 12 = DSM 16493 5713912 YP_001533597.1 CDS Dshi_2260 NC_009952.1 2381127 2381549 R hypothetical protein complement(2381127..2381549) Dinoroseobacter shibae DFL 12 = DSM 16493 5713913 YP_001533598.1 CDS rpoD NC_009952.1 2381601 2383595 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(2381601..2383595) Dinoroseobacter shibae DFL 12 = DSM 16493 5713914 YP_001533599.1 CDS dnaG NC_009952.1 2383717 2385669 R synthesizes RNA primers at the replication forks; DNA primase complement(2383717..2385669) Dinoroseobacter shibae DFL 12 = DSM 16493 5713915 YP_001533600.1 CDS Dshi_2263 NC_009952.1 2385725 2386303 R Swiss-Prot: Q46338 - Sarcosine oxidase subunit gamma TIGR01375# sarcosine oxidase, gamma subunit family, heterotetrameric form; gamma subunit; putative sarcosine oxidase complement(2385725..2386303) Dinoroseobacter shibae DFL 12 = DSM 16493 5713916 YP_001533601.1 CDS Dshi_2264 NC_009952.1 2386296 2389238 R TIGRFAM: sarcosine oxidase, alpha subunit family (TIGR01372) Swiss-Prot: O87386 - Sarcosine oxidase subunit alpha PFAM: glycine cleavage T protein (aminomethyl transferase); FAD-dependent pyridine nucleotide-disulphide oxidoreductase; Glycine cleavage T-protein barrel; alpha subunit family; putative sarcosine oxidase complement(2386296..2389238) Dinoroseobacter shibae DFL 12 = DSM 16493 5713917 YP_001533602.1 CDS Dshi_2265 NC_009952.1 2389235 2389498 R Swiss-Prot: O87387 - Sarcosine oxidase subunit delta PFAM: Sarcosine oxidase delta subunit heterotetrameric KEGG: sil:SPO1745 sarcosine oxidase, delta subunit family; delta subunit heterotetrameric; putative sarcosine oxidase complement(2389235..2389498) Dinoroseobacter shibae DFL 12 = DSM 16493 5713918 YP_001533603.1 CDS Dshi_2266 NC_009952.1 2389926 2391176 R Swiss-Prot: O87388 - Sarcosine oxidase subunit beta TIGRFAM: sarcosine oxidase, beta subunit family PFAM: FAD dependent oxidoreductase KEGG: jan:Jann_3445 sarcosine oxidase, beta subunit family; putative sarcosine oxidase subunit beta complement(2389926..2391176) Dinoroseobacter shibae DFL 12 = DSM 16493 5713919 YP_001533604.1 CDS Dshi_2267 NC_009952.1 2391484 2393145 D IPR002035: von Willebrand factor, type A; hypothetical protein 2391484..2393145 Dinoroseobacter shibae DFL 12 = DSM 16493 5713920 YP_001533605.1 CDS Dshi_2268 NC_009952.1 2393142 2393666 D PFAM: TadE family protein KEGG: rsh:Rsph17029_2053 hypothetical protein; associated with TadE-like protein family; hypothetical protein 2393142..2393666 Dinoroseobacter shibae DFL 12 = DSM 16493 5713921 YP_001533606.1 CDS Dshi_2269 NC_009952.1 2393676 2394230 D KEGG: rde:RD1_2616 hypothetical protein; hypothetical protein 2393676..2394230 Dinoroseobacter shibae DFL 12 = DSM 16493 5713922 YP_001533607.1 CDS Dshi_2270 NC_009952.1 2394227 2394736 R KEGG: sil:SPO1739 hypothetical protein; hypothetical protein complement(2394227..2394736) Dinoroseobacter shibae DFL 12 = DSM 16493 5713923 YP_001533608.1 CDS Dshi_2271 NC_009952.1 2394736 2395365 R PFAM: regulatory protein TetR KEGG: rsq:Rsph17025_0835 transcriptional regulator, TetR family; TetR-related; transcriptional regulator complement(2394736..2395365) Dinoroseobacter shibae DFL 12 = DSM 16493 5713924 YP_001533609.1 CDS Dshi_2272 NC_009952.1 2395380 2395685 D hypothetical protein 2395380..2395685 Dinoroseobacter shibae DFL 12 = DSM 16493 5713925 YP_001533610.1 CDS Dshi_2273 NC_009952.1 2395765 2397051 D catalyzes the formation of L-aspartate 4-semialdehyde from L-homoserine; homoserine dehydrogenase 2395765..2397051 Dinoroseobacter shibae DFL 12 = DSM 16493 5713926 YP_001533611.1 CDS glpX NC_009952.1 2397177 2398148 D type II fructose 1,6-bisphosphatae; in Escherichia coli this protein forms a dimer and binds manganese; fructose 1,6-bisphosphatase II 2397177..2398148 Dinoroseobacter shibae DFL 12 = DSM 16493 5713927 YP_001533612.1 CDS recJ NC_009952.1 2398150 2399907 D Swiss-Prot: P21893 - Single-stranded-DNA-specific exonuclease recJ TIGRFAM: single-stranded-DNA-specific exonuclease RecJ PFAM: phosphoesterase RecJ domain protein; phosphoesterase DHHA1 KEGG: sit:TM1040_2166 single-stranded-DNA-specific exonuclease RecJ; single-stranded-DNA-specific exonuclease 2398150..2399907 Dinoroseobacter shibae DFL 12 = DSM 16493 5713928 YP_001533613.1 CDS Dshi_2276 NC_009952.1 2400364 2400894 R hypothetical protein complement(2400364..2400894) Dinoroseobacter shibae DFL 12 = DSM 16493 5713930 YP_001533614.1 CDS moeA2 NC_009952.1 2400891 2402162 R Swiss-Prot: P12281 - Molybdopterin biosynthesis protein TIGRFAM: molybdenum cofactor synthesis domain PFAM: molybdopterin binding domain; MoeA domain protein domain I and II; MoeA domain protein domain IV; molybdopterin biosynthesis protein complement(2400891..2402162) Dinoroseobacter shibae DFL 12 = DSM 16493 5713931 YP_001533615.1 CDS dmsA1 NC_009952.1 2402247 2404919 R Swiss-Prot: Q57366 - Dimethyl sulfoxide reductase [Precursor] PFAM: molybdopterin oxidoreductase; molydopterin dinucleotide-binding region KEGG: rde:RD1_3664 dimethyl sulfoxide reductase; dimethyl sulfoxide reductase complement(2402247..2404919) Dinoroseobacter shibae DFL 12 = DSM 16493 5713932 YP_001533616.1 CDS Dshi_2279 NC_009952.1 2405034 2405738 D differing Swiss-Prot hits: P0A9Q1-Aerobic respiration control protein arcA; P0AA16-Transcriptional regulatory protein ompR; P38684-TorCAD operon transcriptional regulatory protein torR; putative arcA, ompR or torR protein; two component transcriptional regulator 2405034..2405738 Dinoroseobacter shibae DFL 12 = DSM 16493 5713933 YP_001533617.1 CDS Dshi_2280 NC_009952.1 2405708 2408494 R differing Swiss-Prot hits: P0AEC3-Aerobic respiration control sensor protein arcB P39453-Sensor protein torS PFAM: response regulator receiver; ATP-binding region ATPase domain protein; histidine kinase HAMP region domain protein; histidine kinase A domain protein; Hpt domain protein; signal transduction histidine kinase complement(2405708..2408494) Dinoroseobacter shibae DFL 12 = DSM 16493 5713934 YP_001533618.1 CDS Dshi_2281 NC_009952.1 2408517 2409482 D periplasmic sensory protein associated with the TorRS two-component regulatory system; TMAO reductase system periplasmic protein TorT 2408517..2409482 Dinoroseobacter shibae DFL 12 = DSM 16493 5713935 YP_001533619.1 CDS Dshi_2282 NC_009952.1 2409776 2410660 D PFAM: helix-turn-helix- domain containing protein AraC type COG4977: Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain KEGG: mva:Mvan_3996 helix-turn-helix-domain containing protein, AraC type; AraC family; putative transcriptional regulator 2409776..2410660 Dinoroseobacter shibae DFL 12 = DSM 16493 5713936 YP_001533620.1 CDS pamO NC_009952.1 2410872 2412536 D Swiss-Prot: Q47PU3-Phenylacetone monooxygenase pfam00743: Flavin-binding monooxygenase-like KEGG: rha:RHA1_ro08185 monooxygenase; phenylacetone monooxygenase 2410872..2412536 Dinoroseobacter shibae DFL 12 = DSM 16493 5713937 YP_001533621.1 CDS Dshi_2284 NC_009952.1 2412606 2413793 D Swiss-Prot: Q11037-Uncharacterized protein Rv1367c/MT1414 PFAM: beta-lactamase COG1680: Beta-lactamase class C and other penicillin binding proteins; related to beta-lactamase; hypothetical protein 2412606..2413793 Dinoroseobacter shibae DFL 12 = DSM 16493 5713938 YP_001533622.1 CDS Dshi_2285 NC_009952.1 2413857 2414513 R hypothetical protein complement(2413857..2414513) Dinoroseobacter shibae DFL 12 = DSM 16493 5713939 YP_001533623.1 CDS Dshi_2286 NC_009952.1 2414815 2415318 D COG1846: Transcriptional regulators PFAM: regulatory protein MarR KEGG: reu:Reut_B5322 regulatory protein, MarR; associated with transcriptional regulators, marR family; hypothetical protein 2414815..2415318 Dinoroseobacter shibae DFL 12 = DSM 16493 5713940 YP_001533624.1 CDS Dshi_2287 NC_009952.1 2415315 2417234 D TIGRFAM: TRAP transporter, 4TM/12TM fusion protein PFAM: TRAP C4-dicarboxylate transport system permease DctM subunit KEGG: rde:RD1_3648 hypothetical protein; 4TM/12TM fusion protein; putative TRAP transporter 2415315..2417234 Dinoroseobacter shibae DFL 12 = DSM 16493 5713941 YP_001533625.1 CDS Dshi_2288 NC_009952.1 2417255 2418247 D TIGRFAM: TRAP transporter solute receptor, TAXI family KEGG: rde:RD1_3647 TRAP-type transporter, periplasmic component , putative; TAXI family; putative TRAP transporter solute receptor 2417255..2418247 Dinoroseobacter shibae DFL 12 = DSM 16493 5713942 YP_001533626.1 CDS Dshi_2289 NC_009952.1 2418278 2419648 D PFAM: amidohydrolase; Amidohydrolase 3 KEGG: slo:Shew_0983 amidohydrolase; amidohydrolase 2418278..2419648 Dinoroseobacter shibae DFL 12 = DSM 16493 5713943 YP_001533627.1 CDS Dshi_2290 NC_009952.1 2419657 2420955 D probably associated with sugar transport; PFAM: Carbohydrate-selective porin OprB KEGG: cps:CPS_0267 hypothetical protein; hypothetical protein 2419657..2420955 Dinoroseobacter shibae DFL 12 = DSM 16493 5713944 YP_001533628.1 CDS Dshi_2291 NC_009952.1 2420989 2421627 D PFAM: protein of unknown function DUF306 Meta and HslJ; hypothetical protein 2420989..2421627 Dinoroseobacter shibae DFL 12 = DSM 16493 5713945 YP_001533629.1 CDS Dshi_2292 NC_009952.1 2421771 2422820 R pfam05976: DUF893; hypothetical protein complement(2421771..2422820) Dinoroseobacter shibae DFL 12 = DSM 16493 5713946 YP_001533630.1 CDS Dshi_2293 NC_009952.1 2422831 2423928 R PFAM: secretion protein HlyD family protein KEGG: rde:RD1_3593 multidrug resistance efflux pump, putative; HlyD family; secretion protein complement(2422831..2423928) Dinoroseobacter shibae DFL 12 = DSM 16493 5713947 YP_001533631.1 CDS Dshi_2294 NC_009952.1 2423982 2426291 R PFAM: Pyrrolo-quinoline quinone KEGG: pfl:PFL_5668 quinate/shikimate dehydrogenase, putative COG4993: Glucose dehydrogenase; PQQ dehydrogenase family protein complement(2423982..2426291) Dinoroseobacter shibae DFL 12 = DSM 16493 5713948 YP_001533632.1 CDS Dshi_2295 NC_009952.1 2426408 2427880 R PFAM: amidohydrolase; Amidohydrolase 3 COG1228: Imidazolonepropionase and related amidohydrolases KEGG: sus:Acid_5787 amidohydrolase; putative amidohydrolase complement(2426408..2427880) Dinoroseobacter shibae DFL 12 = DSM 16493 5713949 YP_001533633.1 CDS Dshi_2296 NC_009952.1 2427999 2428427 R PFAM: transposase IS4 family protein COG3293: Transposase and inactivated derivatives KEGG: pde:Pden_3333 transposase, IS4 family protein; transposase complement(2427999..2428427) Dinoroseobacter shibae DFL 12 = DSM 16493 5713950 YP_001533634.1 CDS Dshi_2297 NC_009952.1 2428514 2428810 R COG3293: Transposase and inactivated derivatives KEGG: sit:TM1040_0173 transposase orfA IS5 family element; associated with replication, recombination and repair; hypothetical protein complement(2428514..2428810) Dinoroseobacter shibae DFL 12 = DSM 16493 5713951 YP_001533635.1 CDS Dshi_2298 NC_009952.1 2429143 2430264 R COG3457: Predicted amino acid racemase PFAM: alanine racemase domain protein, N-terminal domain; no C-terminal domain; putative amino acid racemase complement(2429143..2430264) Dinoroseobacter shibae DFL 12 = DSM 16493 5713952 YP_001533636.1 CDS Dshi_2299 NC_009952.1 2430261 2431439 R IPR011669: protein of unknown function DUF1611; hypothetical protein complement(2430261..2431439) Dinoroseobacter shibae DFL 12 = DSM 16493 5713953 YP_001533637.1 CDS Dshi_2300 NC_009952.1 2431492 2432319 R hypothetical protein complement(2431492..2432319) Dinoroseobacter shibae DFL 12 = DSM 16493 5713954 YP_001533638.1 CDS Dshi_2301 NC_009952.1 2432309 2432662 R hypothetical protein complement(2432309..2432662) Dinoroseobacter shibae DFL 12 = DSM 16493 5713955 YP_001533639.1 CDS Dshi_2302 NC_009952.1 2433069 2433371 R hypothetical protein complement(2433069..2433371) Dinoroseobacter shibae DFL 12 = DSM 16493 5713956 YP_001533640.1 CDS Dshi_2303 NC_009952.1 2433393 2434691 R PFAM: NnrS family protein COG3213: Uncharacterized protein involved in response to NO KEGG: rde:RD1_1694 NnrS protein, putative; associated with NO response; hypothetical protein complement(2433393..2434691) Dinoroseobacter shibae DFL 12 = DSM 16493 5713957 YP_001533641.1 CDS Dshi_2304 NC_009952.1 2434878 2435366 R Swiss-Prot: P69506-Regulator of cell morphogenesis and NO signaling COG2846: Regulator of cell morphogenesis and NO signaling PFAM: Hemerythrin HHE cation binding domain protein; putative regulator of cell morphogenesis and NO signaling complement(2434878..2435366) Dinoroseobacter shibae DFL 12 = DSM 16493 5713958 YP_001533642.1 CDS Dshi_2305 NC_009952.1 2435382 2435837 R PFAM: globin KEGG: hne:HNE_1540 protozoan/cyanobacterial globin family protein COG2346: truncated hemoglobins; similar to bacterial-like globin; hypothetical protein complement(2435382..2435837) Dinoroseobacter shibae DFL 12 = DSM 16493 5713959 YP_001533643.1 CDS Dshi_2306 NC_009952.1 2435930 2436349 D Swiss-Prot: P0AF63-HTH-type transcriptional repressor nsrR TIGR00738: rrf2 family protein (putative transcriptional regulator) PS51197: Rrf2-type HTH domain profile; BadM/Rrf2 family; putative transcriptional regulator 2435930..2436349 Dinoroseobacter shibae DFL 12 = DSM 16493 5713960 YP_001533644.1 CDS Dshi_2307 NC_009952.1 2436374 2436607 D hypothetical protein 2436374..2436607 Dinoroseobacter shibae DFL 12 = DSM 16493 5713961 YP_001533645.1 CDS Dshi_2308 NC_009952.1 2436607 2436873 D hypothetical protein 2436607..2436873 Dinoroseobacter shibae DFL 12 = DSM 16493 5713962 YP_001533646.1 CDS Dshi_2309 NC_009952.1 2437551 2438477 D Swiss-Prot: P39138-Arginase TIGRFAM: arginase PFAM: Arginase/agmatinase/formiminoglutamase COG0010: Arginase/agmatinase/formimionoglutamate hydrolase, arginase family KEGG: rde:RD1_1416 arginase; arginase 2437551..2438477 Dinoroseobacter shibae DFL 12 = DSM 16493 5713963 YP_001533647.1 CDS Dshi_2310 NC_009952.1 2438486 2439559 D catalyzes the formation of L-proline from L-ornithine; ornithine cyclodeaminase 2438486..2439559 Dinoroseobacter shibae DFL 12 = DSM 16493 5713964 YP_001533648.1 CDS putA NC_009952.1 2439747 2443412 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 2439747..2443412 Dinoroseobacter shibae DFL 12 = DSM 16493 5713965 YP_001533649.1 CDS Dshi_2312 NC_009952.1 2443877 2444392 D hypothetical protein 2443877..2444392 Dinoroseobacter shibae DFL 12 = DSM 16493 5713966 YP_001533650.1 CDS Dshi_2313 NC_009952.1 2444714 2445433 R PROSITE: PS50860-Aminoacyl-transfer RNA synthetases class-II profiles PFAM: Threonyl/alanyl tRNA synthetase SAD KEGG: rsh:Rsph17029_0823 threonyl/alanyl tRNA synthetase, SAD; aminoacyl-tRNA synthetase complement(2444714..2445433) Dinoroseobacter shibae DFL 12 = DSM 16493 5713968 YP_001533651.1 CDS Dshi_2314 NC_009952.1 2445430 2446467 R Swiss-Prot: P0ABK5-Cysteine synthase A PFAM: Pyridoxal-5-phosphate-dependent protein beta subunit COG0031: Cysteine synthase IMG Term; putative cysteine synthase A complement(2445430..2446467) Dinoroseobacter shibae DFL 12 = DSM 16493 5713969 YP_001533652.1 CDS Dshi_2315 NC_009952.1 2446520 2447656 R PFAM: NUDIX hydrolase; AIG2 family protein KEGG: jan:Jann_1992 nucleoside diphosphate pyrophosphatase; NUDIX hydrolase complement(2446520..2447656) Dinoroseobacter shibae DFL 12 = DSM 16493 5713970 YP_001533653.1 CDS Dshi_2316 NC_009952.1 2447670 2448110 R hypothetical protein complement(2447670..2448110) Dinoroseobacter shibae DFL 12 = DSM 16493 5713971 YP_001533654.1 CDS cfa NC_009952.1 2448130 2449374 R Swiss-Prot: P0A9H7-Cyclopropane-fatty-acyl-phospholipid synthase PFAM: Cyclopropane-fatty-acyl-phospholipid synthase; Methyltransferase type 11; Methyltransferase type 12; cyclopropane-fatty-acyl-phospholipid synthase complement(2448130..2449374) Dinoroseobacter shibae DFL 12 = DSM 16493 5713972 YP_001533655.1 CDS phrB NC_009952.1 2449473 2450903 R Swiss-Prot: P00914-deoxyribodipyrimidine photo-lyase phrB PFAM: DNA photolyase FAD-binding; DNA photolyase domain protein; deoxyribodipyrimidine photo-lyase complement(2449473..2450903) Dinoroseobacter shibae DFL 12 = DSM 16493 5713973 YP_001533656.1 CDS Dshi_2319 NC_009952.1 2451184 2452170 R Swiss-Prot: P26646-Protein yhdH TIGRFAM: Quinone oxidoreductase putative YhdH/YhfP PFAM: Alcohol dehydrogenase zinc-binding domain protein; Alcohol dehydrogenase GroES domain protein; YhdH; putative quinone oxidoreductase complement(2451184..2452170) Dinoroseobacter shibae DFL 12 = DSM 16493 5713974 YP_001533657.1 CDS dmdA NC_009952.1 2452182 2453288 R DmdA; DMSP demethylase; in Silicibacter knockout of this gene results in an inability to convert DMSP to methanethiol which is restored with a cloned copy of the gene; putative dimethyl sulfoniopropionate demethylase complement(2452182..2453288) Dinoroseobacter shibae DFL 12 = DSM 16493 5713975 YP_001533658.1 CDS Dshi_2321 NC_009952.1 2453285 2453764 R Swiss-Prot: Q02886-Protein dinB PFAM: DinB family protein KEGG: acr:Acry_1562 DinB family protein COG2318: Uncharacterized protein conserved in bacteria; associated with DNA damage-inducible (din) genes; hypothetical protein complement(2453285..2453764) Dinoroseobacter shibae DFL 12 = DSM 16493 5713976 YP_001533659.1 CDS Dshi_2322 NC_009952.1 2453788 2454489 R PFAM: protein of unknown function DUF1326 KEGG: rde:RD1_2286 hypothetical protein; hypothetical protein complement(2453788..2454489) Dinoroseobacter shibae DFL 12 = DSM 16493 5713977 YP_001533660.1 CDS Dshi_2323 NC_009952.1 2454501 2455259 R hypothetical protein complement(2454501..2455259) Dinoroseobacter shibae DFL 12 = DSM 16493 5713978 YP_001533661.1 CDS Dshi_2324 NC_009952.1 2455350 2456078 D PFAM: regulatory protein GntR HTH; GntR domain protein KEGG: rde:RD1_2283 transcriptional regulator, GntR family, putative; GntR HTH; regulatory protein 2455350..2456078 Dinoroseobacter shibae DFL 12 = DSM 16493 5713979 YP_001533662.1 CDS Dshi_2325 NC_009952.1 2456174 2457220 D Swiss-Prot: P31133-Putrescine-binding periplasmic protein [Precursor] SSF53850: Periplasmic binding protein-like II superfamily; putative periplasmic-binding protein 2456174..2457220 Dinoroseobacter shibae DFL 12 = DSM 16493 5713980 YP_001533663.1 CDS Dshi_2326 NC_009952.1 2457262 2457699 D hypothetical protein 2457262..2457699 Dinoroseobacter shibae DFL 12 = DSM 16493 5713981 YP_001533664.1 CDS Dshi_2327 NC_009952.1 2458342 2459106 D hypothetical protein 2458342..2459106 Dinoroseobacter shibae DFL 12 = DSM 16493 5713982 YP_001533665.1 CDS Dshi_2328 NC_009952.1 2459215 2459814 D SSF88874: Receptor-binding domain of short tail fibre protein gp12 superfamily PFAM: Tail Collar domain protein; hypothetical protein 2459215..2459814 Dinoroseobacter shibae DFL 12 = DSM 16493 5713983 YP_001533666.1 CDS Dshi_2329 NC_009952.1 2459914 2460507 D PFAM: Tail Collar domain protein; hypothetical protein 2459914..2460507 Dinoroseobacter shibae DFL 12 = DSM 16493 5713984 YP_001533667.1 CDS Dshi_2330 NC_009952.1 2460588 2461223 D PFAM: protein of unknown function DUF1194 KEGG: rsq:Rsph17025_0723 protein of unknown function DUF1194; hypothetical protein 2460588..2461223 Dinoroseobacter shibae DFL 12 = DSM 16493 5713985 YP_001533668.1 CDS Dshi_2331 NC_009952.1 2461236 2461580 D PFAM: Antibiotic biosynthesis monooxygenase COG2329: Uncharacterized enzyme involved in biosynthesis of extracellular polysaccharides KEGG: reu:Reut_B5114 antibiotic biosynthesis monooxygenase; similar to antibiotic biosynthesis monooxygenase; hypothetical protein 2461236..2461580 Dinoroseobacter shibae DFL 12 = DSM 16493 5713986 YP_001533669.1 CDS Dshi_2332 NC_009952.1 2461615 2462868 D Swiss-Prot: Q55027-Probable chromate transport protein TIGRFAM: chromate transporter, chromate ion transporter (CHR) family PFAM: Chromate transporter KEGG: jan:Jann_1226 chromate transporter; putative chromate transport protein 2461615..2462868 Dinoroseobacter shibae DFL 12 = DSM 16493 5713987 YP_001533670.1 CDS Dshi_2333 NC_009952.1 2462966 2463493 D COG3814: Uncharacterized protein conserved in bacteria PFAM: protein of unknown function DUF1321 KEGG: sit:TM1040_1450 protein of unknown function DUF1321; hypothetical protein 2462966..2463493 Dinoroseobacter shibae DFL 12 = DSM 16493 5713988 YP_001533671.1 CDS fumC NC_009952.1 2463610 2465007 D 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 2463610..2465007 Dinoroseobacter shibae DFL 12 = DSM 16493 5713989 YP_001533672.1 CDS Dshi_2335 NC_009952.1 2465235 2465534 D PFAM: Ribbon-helix-helix protein, copG family COG4321:Uncharacterized protein related to arylsulfate sulfotransferase involved in siderophore biosynthesis; hypothetical protein 2465235..2465534 Dinoroseobacter shibae DFL 12 = DSM 16493 5713990 YP_001533673.1 CDS Dshi_2336 NC_009952.1 2465612 2465803 D KEGG: jan:Jann_3588 hypothetical protein; hypothetical protein 2465612..2465803 Dinoroseobacter shibae DFL 12 = DSM 16493 5713991 YP_001533674.1 CDS Dshi_2337 NC_009952.1 2465843 2467219 R PFAM: cytochrome P450 KEGG: jan:Jann_2396 cytochrome P450; cytochrome P450 complement(2465843..2467219) Dinoroseobacter shibae DFL 12 = DSM 16493 5713992 YP_001533675.1 CDS Dshi_2338 NC_009952.1 2467216 2468406 R KEGG: sil:SPO1897 hypothetical protein; hypothetical protein complement(2467216..2468406) Dinoroseobacter shibae DFL 12 = DSM 16493 5713993 YP_001533676.1 CDS Dshi_2339 NC_009952.1 2468530 2468757 D PFAM: SirA family protein KEGG: sil:SPO1895 SirA family protein Swiss-Prot: Q2NWX1-Sulfurtransferase tusA; SirA family protein 2468530..2468757 Dinoroseobacter shibae DFL 12 = DSM 16493 5713994 YP_001533677.1 CDS Dshi_2340 NC_009952.1 2468813 2471893 R Swiss-Prot: P21513-Ribonuclease E TIGRFAM: ribonuclease, Rne/Rng family KEGG: sit:TM1040_1459 ribonuclease, Rne/Rng family; Rne/Rng family; ribonuclease complement(2468813..2471893) Dinoroseobacter shibae DFL 12 = DSM 16493 5713995 YP_001533678.1 CDS Dshi_2341 NC_009952.1 2472393 2474747 R PFAM: TRAP C4-dicarboxylate transport system permease DctM subunit Swiss-Prot: P44483-Putative TRAP transporter large permease protein HI0050 TIGR00786: TRAP transporter, DctM subunit KEGG: sil:SPO2571 TRAP transporter, DctM subunit, putative; DctM subunit; putative TRAP C4-dicarboxylate transport system permease complement(2472393..2474747) Dinoroseobacter shibae DFL 12 = DSM 16493 5713996 YP_001533679.1 CDS Dshi_2342 NC_009952.1 2474765 2475718 R PFAM: Tripartite ATP-independent periplasmic transporters, DctQ component COG4665: TRAP-type mannitol/chloroaromatic compound transport system, small permease component; associated with TRAP transporters, DctQ component; hypothetical protein complement(2474765..2475718) Dinoroseobacter shibae DFL 12 = DSM 16493 5713997 YP_001533680.1 CDS Dshi_2343 NC_009952.1 2475833 2476918 R PFAM: TRAP dicarboxylate transporter- DctP subunit COG4663: TRAP-type mannitol/chloroaromatic compound transport system, periplasmic component; associated with TRAP dicarboxylate transporter, DctP subunit; hypothetical protein complement(2475833..2476918) Dinoroseobacter shibae DFL 12 = DSM 16493 5713998 YP_001533681.1 CDS Dshi_2344 NC_009952.1 2477127 2478569 D PFAM: ATP-binding region ATPase domain protein; histidine kinase dimerisation and phosphoacceptor region; Cache type 2 domain protein Swiss-Prot: P09835-Sensor protein uhpB; colocated with two component transcriptional regulator; integral membrane sensor signal transduction histidine kinase 2477127..2478569 Dinoroseobacter shibae DFL 12 = DSM 16493 5713999 YP_001533682.1 CDS Dshi_2345 NC_009952.1 2478566 2479228 D PFAM: regulatory protein LuxR; response regulator receiver COG2197: Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain Swiss-Prot: P0AF28-Nitrate/nitrite response regulator protein narL; colocated with histidine kinase; LuxR family; two component transcriptional regulator 2478566..2479228 Dinoroseobacter shibae DFL 12 = DSM 16493 5714000 YP_001533683.1 CDS tgt NC_009952.1 2479455 2480585 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(2479455..2480585) Dinoroseobacter shibae DFL 12 = DSM 16493 5714001 YP_001533684.1 CDS Dshi_2347 NC_009952.1 2481051 2482004 D PFAM: regulatory protein LysR; LysR substrate-binding COG0583: transcriptional regulator Swiss-Prot: P55700-nodulation protein D 2 (Represses the expression of the nodABCIJ-nolO-noeI operon); LysR family transcriptional regulator 2481051..2482004 Dinoroseobacter shibae DFL 12 = DSM 16493 5714002 YP_001533685.1 CDS Dshi_2348 NC_009952.1 2482067 2482429 D PFAM: protein of unknown function DUF59; hypothetical protein 2482067..2482429 Dinoroseobacter shibae DFL 12 = DSM 16493 5714003 YP_001533686.1 CDS Dshi_2349 NC_009952.1 2482501 2482866 D Swiss-Prot: P0AAC8-Iron-binding protein iscA TIGRFAM: iron-sulfur cluster assembly accessory protein PFAM: HesB/YadR/YfhF-family protein; putative iron-binding protein iscA 2482501..2482866 Dinoroseobacter shibae DFL 12 = DSM 16493 5714004 YP_001533687.1 CDS Dshi_2350 NC_009952.1 2482885 2483898 R Swiss-Prot: Q58296-Putative molybdopterin biosynthesis protein MJ0886 PFAM: molybdopterin binding domain COG0303: Molybdopterin biosynthesis enzyme; putative molybdopterin biosynthesis protein complement(2482885..2483898) Dinoroseobacter shibae DFL 12 = DSM 16493 5714005 YP_001533688.1 CDS Dshi_2351 NC_009952.1 2483895 2484884 R IPR003777 / pfam02625 XdhC and CoxI family protein COG1975: Xanthine and CO dehydrogenases maturation factor, XdhC/CoxF family; related to XdhC and CoxI family; hypothetical protein complement(2483895..2484884) Dinoroseobacter shibae DFL 12 = DSM 16493 5714006 YP_001533689.1 CDS Dshi_2352 NC_009952.1 2485055 2486401 D PFAM: Protein of unknown function DUF1800 COG5267: Uncharacterized protein conserved in bacteria; hypothetical protein 2485055..2486401 Dinoroseobacter shibae DFL 12 = DSM 16493 5714007 YP_001533690.1 CDS Dshi_2353 NC_009952.1 2486413 2487582 D PFAM: protein of unknown function DUF1501 COG4102: Uncharacterized protein conserved in bacteria; hypothetical protein 2486413..2487582 Dinoroseobacter shibae DFL 12 = DSM 16493 5714008 YP_001533691.1 CDS Dshi_2354 NC_009952.1 2487671 2488822 D PFAM: major facilitator superfamily MFS_1 KEGG: reu:Reut_A3422 major facilitator superfamily MFS_1 Swiss-Prot: P77389-Inner membrane transport protein; MFS transporter 2487671..2488822 Dinoroseobacter shibae DFL 12 = DSM 16493 5714009 YP_001533692.1 CDS Dshi_2355 NC_009952.1 2488833 2490095 R PFAM: VWA containing CoxE family protein KEGG: jan:Jann_1760 VWA containing CoxE-like; hypothetical protein complement(2488833..2490095) Dinoroseobacter shibae DFL 12 = DSM 16493 5714010 YP_001533693.1 CDS Dshi_2356 NC_009952.1 2490196 2491107 R PFAM: ATPase associated with various cellular activities AAA_5 KEGG: sil:SPO2646 hypothetical protein Swiss-Prot: Q4L6B6-Uncharacterized protein SH1500; hypothetical protein complement(2490196..2491107) Dinoroseobacter shibae DFL 12 = DSM 16493 5714011 YP_001533694.1 CDS Dshi_2357 NC_009952.1 2491250 2492470 D COG1960: Acyl-CoA dehydrogenases PFAM: Acyl-CoA dehydrogenase; acyl-CoA dehydrogenase 2491250..2492470 Dinoroseobacter shibae DFL 12 = DSM 16493 5714012 YP_001533695.1 CDS Dshi_2358 NC_009952.1 2492678 2493325 D PFAM: Lysine exporter protein (LYSE/YGGA) KEGG: jan:Jann_3206 lysine exporter protein (LysE/YggA); putative lysine exporter protein 2492678..2493325 Dinoroseobacter shibae DFL 12 = DSM 16493 5714013 YP_001533696.1 CDS Dshi_2359 NC_009952.1 2493841 2495091 D hypothetical protein 2493841..2495091 Dinoroseobacter shibae DFL 12 = DSM 16493 5714014 YP_001533697.1 CDS ureG NC_009952.1 2495217 2495825 R Swiss-Prot: Q03287-Urease accessory protein ureG TIGRFAM: urease accessory protein UreG PFAM: cobalamin synthesis protein P47K KEGG: rsq:Rsph17025_0992 urease accessory protein UreG; urease accessory protein complement(2495217..2495825) Dinoroseobacter shibae DFL 12 = DSM 16493 5714015 YP_001533698.1 CDS Dshi_2361 NC_009952.1 2495818 2496201 R COG0599: Uncharacterized homolog of gamma-carboxymuconolactone decarboxylase subunit Swiss-Prot: P29911-Uncharacterized 13.8 kDa protein in nqo9-nqo10 intergenic region PFAM: Carboxymuconolactone decarboxylase; related to carboxymuconolactone decarboxylase; hypothetical protein complement(2495818..2496201) Dinoroseobacter shibae DFL 12 = DSM 16493 5714016 YP_001533699.1 CDS ureF NC_009952.1 2496198 2496830 R Swiss-Prot: Q9HUS1-Urease accessory protein ureF PFAM: Urease accessory protein UreF COG0830: Urease accessory protein UreF; putative urease accessory protein complement(2496198..2496830) Dinoroseobacter shibae DFL 12 = DSM 16493 5714017 YP_001533700.1 CDS ureE NC_009952.1 2496832 2497314 R PFAM: UreE urease accessory domain protein PIRSF036402: urease accessory protein UreE (nickel metallochaperone) Swiss-Prot: Q9AQT2-Urease accessory protein ureE; urease accessory domain-containing protein complement(2496832..2497314) Dinoroseobacter shibae DFL 12 = DSM 16493 5714018 YP_001533701.1 CDS Dshi_2364 NC_009952.1 2497676 2497882 R hypothetical protein complement(2497676..2497882) Dinoroseobacter shibae DFL 12 = DSM 16493 5714019 YP_001533702.1 CDS ureC NC_009952.1 2498640 2500349 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(2498640..2500349) Dinoroseobacter shibae DFL 12 = DSM 16493 5714020 YP_001533703.1 CDS Dshi_2366 NC_009952.1 2500485 2500814 R hypothetical protein complement(2500485..2500814) Dinoroseobacter shibae DFL 12 = DSM 16493 5714021 YP_001533704.1 CDS Dshi_2367 NC_009952.1 2500927 2501649 R hypothetical protein complement(2500927..2501649) Dinoroseobacter shibae DFL 12 = DSM 16493 5714022 YP_001533705.1 CDS ureB NC_009952.1 2501649 2501954 R Swiss-Prot: Q28RJ8-Urease subunit beta ureB TIGRFAM: urease, beta subunit PFAM: Urease beta subunit; urease subunit beta complement(2501649..2501954) Dinoroseobacter shibae DFL 12 = DSM 16493 5714023 YP_001533706.1 CDS ureA NC_009952.1 2502086 2502388 R UreA, with UreB and UreC catalyzes the hydrolysis of urea into ammonia and carbon dioxide; nickel metalloenzyme; accessory proteins UreD, UreE, UreF, and UreG are necessary for assembly of the metallocenter; urease subunit gamma complement(2502086..2502388) Dinoroseobacter shibae DFL 12 = DSM 16493 5714024 YP_001533707.1 CDS ureD NC_009952.1 2502483 2503328 R Swiss-Prot: P42888-Urease accessory protein ureD PFAM: Urease accessory protein UreD KEGG: rsh:Rsph17029_1955 urease accessory protein UreD; urease accessory protein complement(2502483..2503328) Dinoroseobacter shibae DFL 12 = DSM 16493 5714025 YP_001533708.1 CDS pyrC2 NC_009952.1 2503566 2504603 D catalyzes the formation of N-carbamoyl-L-aspartate from (S)-dihydroorotate in pyrimidine biosynthesis; dihydroorotase 2503566..2504603 Dinoroseobacter shibae DFL 12 = DSM 16493 5714026 YP_001533709.1 CDS pyrE NC_009952.1 2504743 2505423 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 2504743..2505423 Dinoroseobacter shibae DFL 12 = DSM 16493 5714027 YP_001533710.1 CDS dnaB NC_009952.1 2505654 2507174 D unwinds double stranded DNA; replicative DNA helicase 2505654..2507174 Dinoroseobacter shibae DFL 12 = DSM 16493 5714028 YP_001533711.1 CDS Dshi_2374 NC_009952.1 2507462 2508685 D PFAM: histidine kinase HAMP region domain protein KEGG: rde:RD1_0232 HAMP domain protein, putative; hypothetical protein 2507462..2508685 Dinoroseobacter shibae DFL 12 = DSM 16493 5714029 YP_001533712.1 CDS Dshi_2375 NC_009952.1 2508782 2509588 D PFAM: protein of unknown function DUF1194 KEGG: mes:Meso_1299 protein of unknown function DUF1194; hypothetical protein 2508782..2509588 Dinoroseobacter shibae DFL 12 = DSM 16493 5714030 YP_001533713.1 CDS Dshi_2376 NC_009952.1 2509613 2510089 R hypothetical protein complement(2509613..2510089) Dinoroseobacter shibae DFL 12 = DSM 16493 5714031 YP_001533714.1 CDS Dshi_2377 NC_009952.1 2510218 2512242 R PFAM: protein of unknown function DUF839 KEGG: rde:RD1_0767 hypothetical protein COG3211: Predicted phosphatase; hypothetical protein complement(2510218..2512242) Dinoroseobacter shibae DFL 12 = DSM 16493 5714032 YP_001533715.1 CDS alr NC_009952.1 2512525 2513574 D Swiss-Prot: Q92R07-Alanine racemase alr TIGRFAM: alanine racemase PFAM: alanine racemase domain protein; alanine racemase 2512525..2513574 Dinoroseobacter shibae DFL 12 = DSM 16493 5714033 YP_001533716.1 CDS Dshi_2379 NC_009952.1 2513571 2514347 D Swiss-Prot: P64606-UPF0393 inner membrane protein yrbE TIGR00056: conserved hypothetical integral membrane protein PFAM: protein of unknown function DUF140 COG0767: ABC-type transport system involved in resistance to organic solvents, permease component; similar to UPF0393 inner membrane protein yrbE; hypothetical protein 2513571..2514347 Dinoroseobacter shibae DFL 12 = DSM 16493 5714034 YP_001533717.1 CDS Dshi_2380 NC_009952.1 2514344 2515117 D Swiss-Prot: P63386-Uncharacterized ABC transporter ATP-binding protein yrbF COG1127: ABC-type transport system involved in resistance to organic solvents, ATPase component; ABC transporter 2514344..2515117 Dinoroseobacter shibae DFL 12 = DSM 16493 5714035 YP_001533718.1 CDS lipB NC_009952.1 2515483 2516145 D lipoyl/octanoyltransferase; catalyzes the transfer of the lipoyl/octanoyl moiety of lipoyl/octanoyl-ACP onto lipoate-dependent enzymes like pyruvate dehydrogenase and the glycine cleavage system H protein; lipoate-protein ligase B 2515483..2516145 Dinoroseobacter shibae DFL 12 = DSM 16493 5714037 YP_001533719.1 CDS Dshi_2382 NC_009952.1 2516182 2516721 D hypothetical protein 2516182..2516721 Dinoroseobacter shibae DFL 12 = DSM 16493 5714038 YP_001533720.1 CDS ctaD NC_009952.1 2517133 2518809 D Swiss-Prot: P33517- Cytochrome c oxidase subunit 1 ctaD TIGRFAM: Cytochrome c oxidase subunit I type PFAM: cytochrome c oxidase subunit I; cytochrome c oxidase subunit 1 2517133..2518809 Dinoroseobacter shibae DFL 12 = DSM 16493 5714039 YP_001533721.1 CDS Dshi_2384 NC_009952.1 2518819 2519340 D hypothetical protein 2518819..2519340 Dinoroseobacter shibae DFL 12 = DSM 16493 5714040 YP_001533722.1 CDS Dshi_2385 NC_009952.1 2519748 2520101 R Swiss-Prot:P0ABS1-DnaK suppressor protein dksA COG1734: DnaK suppressor protein; related to DnaK suppressor protein; hypothetical protein complement(2519748..2520101) Dinoroseobacter shibae DFL 12 = DSM 16493 5714041 YP_001533723.1 CDS Dshi_2386 NC_009952.1 2520173 2520634 R COG1610: Uncharacterized conserved protein Swiss-Prot: P54464-Uncharacterized protein yqeY; hypothetical protein complement(2520173..2520634) Dinoroseobacter shibae DFL 12 = DSM 16493 5714042 YP_001533724.1 CDS carA NC_009952.1 2520801 2521970 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 2520801..2521970 Dinoroseobacter shibae DFL 12 = DSM 16493 5714043 YP_001533725.1 CDS Dshi_2388 NC_009952.1 2522050 2523957 D PFAM: glycosyl transferase family 2 Swiss-Prot: P75905-Biofilm PGA synthesis N-glycosyltransferase pgaC COG1215: Glycosyltransferases, probably involved in cell wall biogenesis; family 2; glycosyl transferase family protein 2522050..2523957 Dinoroseobacter shibae DFL 12 = DSM 16493 5714044 YP_001533726.1 CDS Dshi_2389 NC_009952.1 2523970 2524611 R Swiss-Prot: P76114-Uncharacterized HTH-type transcriptional regulator PFAM: regulatory protein GntR HTH; GntR domain protein KEGG: sil:SPO1375 transcriptional regulator, GntR family; GntR family; putative transcriptional regulator complement(2523970..2524611) Dinoroseobacter shibae DFL 12 = DSM 16493 5714045 YP_001533727.1 CDS Dshi_2390 NC_009952.1 2524704 2525351 D TIGRFAM: HAD-superfamily hydrolase, subfamily IA, variant 3; pyrimidine 5-nucleotidase PFAM: Haloacid dehalogenase domain protein hydrolase KEGG: sil:SPO1374 pyrimidine 5-nucleotidase; putative pyrimidine 5'-nucleotidase 2524704..2525351 Dinoroseobacter shibae DFL 12 = DSM 16493 5714046 YP_001533728.1 CDS Dshi_2391 NC_009952.1 2525481 2525726 D hypothetical protein 2525481..2525726 Dinoroseobacter shibae DFL 12 = DSM 16493 5714047 YP_001533729.1 CDS Dshi_2392 NC_009952.1 2525802 2527001 D Swiss-Prot: P75728-2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase, ubiF TIGRFAM: Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family PFAM: monooxygenase FAD-binding; FAD dependent oxidoreductase KEGG: sil:SPO1371 2-octaprenyl-6-methoxyphenol hydroxylase, putative; ubiF; 2-octaprenyl-6-methoxyphenyl hydroxylase 2525802..2527001 Dinoroseobacter shibae DFL 12 = DSM 16493 5714048 YP_001533730.1 CDS Dshi_2393 NC_009952.1 2527234 2528364 R PFAM: Aminotransferase class-V KEGG: rde:RD1_1957 aminotransferase family protein, putative COG0075: Serine-pyruvate aminotransferase/archaeal aspartate aminotransferase; class 5; aminotransferase complement(2527234..2528364) Dinoroseobacter shibae DFL 12 = DSM 16493 5714049 YP_001533731.1 CDS Dshi_2394 NC_009952.1 2528605 2529063 R PFAM: regulatory protein AsnC/Lrp family; regulatory protein ArsR KEGG: sil:SPO1368 transcriptional regulator, AsnC family COG1522: Transcriptional regulators; AsnC family; transcriptional regulator complement(2528605..2529063) Dinoroseobacter shibae DFL 12 = DSM 16493 5714050 YP_001533732.1 CDS Dshi_2395 NC_009952.1 2529060 2529518 R Swiss-Prot: P0ACJ5-Uncharacterized HTH-type transcriptional regulator ybaO PFAM: regulatory protein AsnC/Lrp family KEGG: sil:SPO1367 transcriptional regulator, AsnC family; AsnC family; transcriptional regulator complement(2529060..2529518) Dinoroseobacter shibae DFL 12 = DSM 16493 5714051 YP_001533733.1 CDS ilvC NC_009952.1 2529653 2530675 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 2529653..2530675 Dinoroseobacter shibae DFL 12 = DSM 16493 5714052 YP_001533734.1 CDS glmM NC_009952.1 2531044 2532387 R catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate; phosphoglucosamine mutase complement(2531044..2532387) Dinoroseobacter shibae DFL 12 = DSM 16493 5714053 YP_001533735.1 CDS folP NC_009952.1 2532406 2533419 R Swiss-Prot: P0AC13-Dihydropteroate synthase folP TIGRFAM: dihydropteroate synthase PFAM: dihydropteroate synthase DHPS; dihydropteroate synthase complement(2532406..2533419) Dinoroseobacter shibae DFL 12 = DSM 16493 5714054 YP_001533736.1 CDS Dshi_2399 NC_009952.1 2533430 2534281 R Swiss-Prot: Q9X8I0-Dihydroneopterin aldolase folB PFAM: dihydroneopterin aldolase TIGR00525: dihydroneopterin aldolase TIGR00526: FolB domain; putative dihydroneopterin aldolase complement(2533430..2534281) Dinoroseobacter shibae DFL 12 = DSM 16493 5714055 YP_001533737.1 CDS Dshi_2400 NC_009952.1 2534372 2535064 R PFAM: cell wall hydrolase SleB KEGG: sit:TM1040_2308 cell wall hydrolase, SleB COG3773: Cell wall hydrolyses involved in spore germination; related to cell wall hydrolase; hypothetical protein complement(2534372..2535064) Dinoroseobacter shibae DFL 12 = DSM 16493 5714056 YP_001533738.1 CDS Dshi_2401 NC_009952.1 2535240 2537828 R catalyzes the formation of phosphoenolpyruvate from pyruvate; pyruvate phosphate dikinase complement(2535240..2537828) Dinoroseobacter shibae DFL 12 = DSM 16493 5714057 YP_001533739.1 CDS glyS NC_009952.1 2537985 2540147 R Swiss-Prot: Q986B5-Glycyl-tRNA synthetase beta chain glyS TIGRFAM: glycyl-tRNA synthetase, beta subunit; glycyl-tRNA synthetase subunit beta complement(2537985..2540147) Dinoroseobacter shibae DFL 12 = DSM 16493 5714058 YP_001533740.1 CDS Dshi_2403 NC_009952.1 2540151 2540627 R hypothetical protein complement(2540151..2540627) Dinoroseobacter shibae DFL 12 = DSM 16493 5714059 YP_001533741.1 CDS glyQ NC_009952.1 2540624 2541607 R 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 complement(2540624..2541607) Dinoroseobacter shibae DFL 12 = DSM 16493 5714060 YP_001533742.1 CDS Dshi_2405 NC_009952.1 2541693 2543423 D Swiss-Prot: P55377-Uncharacterized protein y4bJ; hypothetical protein 2541693..2543423 Dinoroseobacter shibae DFL 12 = DSM 16493 5714061 YP_001533743.1 CDS trkG NC_009952.1 2543430 2544878 R Swiss-Prot: P23849-Trk system potassium uptake protein trkG PFAM: cation transporter KEGG: rde:RD1_1942 trk system potassium uptake protein COG0168: Trk-type K+ transport systems, membrane components; Trk system potassium uptake protein complement(2543430..2544878) Dinoroseobacter shibae DFL 12 = DSM 16493 5714062 YP_001533744.1 CDS Dshi_2407 NC_009952.1 2544924 2545631 R Swiss-Prot: P77526-Uncharacterized GST-like protein PFAM: Glutathione S-transferase domain KEGG: rde:RD1_1937 glutathione S-transferase, putative; putative glutathione S-transferase complement(2544924..2545631) Dinoroseobacter shibae DFL 12 = DSM 16493 5714063 YP_001533745.1 CDS Dshi_2410 NC_009952.1 2546843 2548021 D Swiss-Prot: P55218-O-succinylhomoserine sulfhydrylase P00935-Cystathionine gamma-synthase TIGRFAM: O-succinylhomoserine sulfhydrylase PFAM: Cys/Met metabolism PLP-dependent enzyme; trans-sulfuration enzyme family protein 2546843..2548021 Dinoroseobacter shibae DFL 12 = DSM 16493 5714066 YP_001533746.1 CDS Dshi_2411 NC_009952.1 2548194 2549297 D similar protein in Methanocaldococcus converts GTP to 7,8-dihydro-D-neopterin 2',3'-cyclic phosphate as the first step in methanopterin biosynthesis; putative GTP cyclohydrolase 2548194..2549297 Dinoroseobacter shibae DFL 12 = DSM 16493 5714067 YP_001533747.1 CDS Dshi_2412 NC_009952.1 2549412 2551100 R Swiss-Prot: Q8XTT4-Putative chloride channel protein clcB-like / P76175-Voltage-gated ClC-type chloride channel, clcB PFAM: Chloride channel core KEGG: jan:Jann_2746 Cl-channel, voltage gated; clcB-like; putative chloride channel protein complement(2549412..2551100) Dinoroseobacter shibae DFL 12 = DSM 16493 5714068 YP_001533748.1 CDS recN NC_009952.1 2551263 2552924 R Swiss-Prot: P05824-DNA repair protein recN TIGRFAM: DNA repair protein RecN PFAM: SMC domain protein KEGG: sil:SPO1207 DNA repair protein RecN; DNA repair protein complement(2551263..2552924) Dinoroseobacter shibae DFL 12 = DSM 16493 5714069 YP_001533749.1 CDS Dshi_2414 NC_009952.1 2553013 2553852 R Swiss-Prot: P0AC02-UPF0169 lipoprotein yfiO [Precursor]; hypothetical protein complement(2553013..2553852) Dinoroseobacter shibae DFL 12 = DSM 16493 5714070 YP_001533750.1 CDS lpxC NC_009952.1 2553954 2554874 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(2553954..2554874) Dinoroseobacter shibae DFL 12 = DSM 16493 5714071 YP_001533751.1 CDS ftsZ NC_009952.1 2555094 2556689 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(2555094..2556689) Dinoroseobacter shibae DFL 12 = DSM 16493 5714072 YP_001533752.1 CDS ftsA NC_009952.1 2557114 2558451 R Swiss-Prot: P0ABH0-Cell division protein ftsA TIGR01174: cell division protein FtsA; colocated with ftsZ and ftsQ; cell division protein complement(2557114..2558451) Dinoroseobacter shibae DFL 12 = DSM 16493 5714073 YP_001533753.1 CDS Dshi_2418 NC_009952.1 2558448 2559341 R Swiss-Prot: Q9X5H9-Cell division protein ftsQ homolog PFAM: cell division protein FtsQ KEGG: sil:SPO1202 cell division protein FtsQ COG1589: Cell division septal protein; colocated with ftsZ and ftsA; putative cell division protein FtsQ complement(2558448..2559341) Dinoroseobacter shibae DFL 12 = DSM 16493 5714074 YP_001533754.1 CDS ddl NC_009952.1 2559329 2560255 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(2559329..2560255) Dinoroseobacter shibae DFL 12 = DSM 16493 5714075 YP_001533755.1 CDS murB NC_009952.1 2560320 2561243 R catalyzes the reduction of UDP-N-acetylglucosamine enolpyruvate to form UDP-N-acetylmuramate in peptidoglycan biosynthesis; UDP-N-acetylenolpyruvoylglucosamine reductase complement(2560320..2561243) Dinoroseobacter shibae DFL 12 = DSM 16493 5714076 YP_001533756.1 CDS Dshi_2421 NC_009952.1 2561240 2561506 R hypothetical protein complement(2561240..2561506) Dinoroseobacter shibae DFL 12 = DSM 16493 5714077 YP_001533757.1 CDS murC NC_009952.1 2561559 2562971 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(2561559..2562971) Dinoroseobacter shibae DFL 12 = DSM 16493 5714078 YP_001533758.1 CDS murG NC_009952.1 2562998 2564107 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; undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase complement(2562998..2564107) Dinoroseobacter shibae DFL 12 = DSM 16493 5714079 YP_001533759.1 CDS Dshi_2424 NC_009952.1 2564111 2565277 R Swiss-Prot: P0ABG4-Cell division protein ftsW TIGRFAM: cell division protein FtsW PFAM: cell cycle protein; colocated with ftsA,ftsZ and (putative)ftsQ; putative cell division protein ftsW complement(2564111..2565277) Dinoroseobacter shibae DFL 12 = DSM 16493 5714080 YP_001533760.1 CDS Dshi_2425 NC_009952.1 2565692 2567371 D PFAM: Hemolysin-type calcium-binding region; hypothetical protein 2565692..2567371 Dinoroseobacter shibae DFL 12 = DSM 16493 5714081 YP_001533761.1 CDS Dshi_2426 NC_009952.1 2567452 2568609 R PFAM: peptidase S8 / subtilase family KEGG: rde:RD1_4002 subtilisin carlsberg precursor, putative PTHR10795: subtilisin-related serine protease; related to subtilase; hypothetical protein complement(2567452..2568609) Dinoroseobacter shibae DFL 12 = DSM 16493 5714082 YP_001533762.1 CDS Dshi_2427 NC_009952.1 2568795 2569361 D KEGG: rde:RD1_4000 hypothetical protein; hypothetical protein 2568795..2569361 Dinoroseobacter shibae DFL 12 = DSM 16493 5714083 YP_001533763.1 CDS Dshi_2428 NC_009952.1 2569367 2569903 R Swiss-Prot: P0AGB6-RNA polymerase sigma-E factor rpoE TIGRFAM: RNA polymerase sigma-70 PFAM: sigma-70 region 2 domain protein; sigma-70 region 4 domain protein; Sigma-70 region 4 type 2; sigma-24 subunit, ECF subfamily; RNA polymerase complement(2569367..2569903) Dinoroseobacter shibae DFL 12 = DSM 16493 5714084 YP_001533764.1 CDS Dshi_2429 NC_009952.1 2570227 2571612 R Swiss-Prot: P11553- L-fuculokinase fucK PFAM: carbohydrate kinase FGGY KEGG: rde:RD1_3075 carbohydrate kinases, putative COG1070: Sugar (pentulose and hexulose) kinases; FGGY family; carbohydrate kinase complement(2570227..2571612) Dinoroseobacter shibae DFL 12 = DSM 16493 5714085 YP_001533765.1 CDS Dshi_2430 NC_009952.1 2571609 2571947 R TIGRFAM: L-rhamnose 1-epimerase PFAM: protein of unknown function DUF718 KEGG: jan:Jann_2598 protein of unknown function DUF718; hypothetical protein complement(2571609..2571947) Dinoroseobacter shibae DFL 12 = DSM 16493 5714086 YP_001533766.1 CDS Dshi_2431 NC_009952.1 2571923 2572909 R Swiss-Prot: P0AE26- L-arabinose transport system permease protein araH PFAM: inner-membrane translocator KEGG: jan:Jann_2597 inner-membrane translocator; (monosaccharide) transport system permease complement(2571923..2572909) Dinoroseobacter shibae DFL 12 = DSM 16493 5714087 YP_001533767.1 CDS Dshi_2432 NC_009952.1 2572906 2573889 R Swiss-Prot: P77672-Inner membrane ABC transporter permease protein ydeY PFAM: inner-membrane translocator KEGG: rde:RD1_3078 ribose ABC transporter, permease protein; putative-binding-protein-dependent transport system permease complement(2572906..2573889) Dinoroseobacter shibae DFL 12 = DSM 16493 5714088 YP_001533768.1 CDS rbsA1 NC_009952.1 2573902 2575434 R Swiss-Prot: P04983-Ribose import ATP-binding protein rbsA COG1129: ABC-type sugar transport system, ATPase component PFAM: ABC transporter related SMART: AAA ATPase; ribose import ATP-binding protein complement(2573902..2575434) Dinoroseobacter shibae DFL 12 = DSM 16493 5714089 YP_001533769.1 CDS Dshi_2434 NC_009952.1 2575507 2576508 R TIGRFAM: rhamnose ABC transporter, periplasmic rhamnose-binding protein KEGG: rde:RD1_3080 sugar ABC transporter, ATP binding protein, putative COG1879: ABC-type sugar transport system, periplasmic component; putative periplasmic-binding abc transporter protein complement(2575507..2576508) Dinoroseobacter shibae DFL 12 = DSM 16493 5714090 YP_001533770.1 CDS Dshi_2435 NC_009952.1 2576547 2577401 R Swiss-Prot: P0A9W0-HTH-type transcriptional regulator PFAM: regulatory protein DeoR KEGG: jan:Jann_2593 transcriptional regulator, DeoR family COG1349: Transcriptional regulators of sugar metabolism; colocated with sugar transport system; DeoR family; transcriptional regulator complement(2576547..2577401) Dinoroseobacter shibae DFL 12 = DSM 16493 5714091 YP_001533771.1 CDS Dshi_2436 NC_009952.1 2577535 2579637 D Swiss-Prot: P40747-Uncharacterized oxidoreductase yuxG TIGRFAM: rhamnulose-1-phosphate aldolase/alcohol dehydrogenase PFAM: short-chain dehydrogenase/reductase SDR; KR domain protein KEGG: jan:Jann_2592 short-chain dehydrogenase/reductase SDR COG3347: Uncharacterized conserved protein; short chain dehydrogenase 2577535..2579637 Dinoroseobacter shibae DFL 12 = DSM 16493 5714092 YP_001533772.1 CDS rhaA NC_009952.1 2579647 2580885 D catalyzes the formation of L-rhamnulose from L-rhamnose; L-rhamnose isomerase 2579647..2580885 Dinoroseobacter shibae DFL 12 = DSM 16493 5714093 YP_001533773.1 CDS Dshi_2438 NC_009952.1 2580993 2581871 R PFAM: amidohydrolase 2 KEGG: pau:PA14_36110 putative hydrolase COG3618: Predicted metal-dependent hydrolase of the TIM-barrel fold; putative amidohydrolase 2 complement(2580993..2581871) Dinoroseobacter shibae DFL 12 = DSM 16493 5714094 YP_001533774.1 CDS Dshi_2439 NC_009952.1 2581868 2583352 R PFAM: protein of unknown function DUF112 transmembrane COG3333: Uncharacterized protein conserved in bacteria; hypothetical protein complement(2581868..2583352) Dinoroseobacter shibae DFL 12 = DSM 16493 5714095 YP_001533775.1 CDS Dshi_2440 NC_009952.1 2583349 2583807 R hypothetical protein complement(2583349..2583807) Dinoroseobacter shibae DFL 12 = DSM 16493 5714096 YP_001533776.1 CDS Dshi_2441 NC_009952.1 2583868 2584830 R Swiss-Prot: P0A177-UPF0065 protein in clcB-clcD intergenic region [Precursor] PFAM: Bordetella uptake gene (bug) product COG3181: Uncharacterized protein conserved in bacteria; similar to UPF0065 protein; hypothetical protein complement(2583868..2584830) Dinoroseobacter shibae DFL 12 = DSM 16493 5714097 YP_001533777.1 CDS aldH1 NC_009952.1 2584873 2586378 R Swiss-Prot: Q56694-NADP-dependent fatty aldehyde dehydrogenase aldH PFAM: aldehyde dehydrogenase KEGG: pde:Pden_4865 aldehyde dehydrogenase; NADP-dependent fatty aldehyde dehydrogenase complement(2584873..2586378) Dinoroseobacter shibae DFL 12 = DSM 16493 5714098 YP_001533778.1 CDS Dshi_2443 NC_009952.1 2586430 2587299 R PTHR22981: 3-hydroxyisobutyrate dehydrogenase-related COG2084: 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases KEGG: sil:SPO2416 3-hydroxyisobutyrate dehydrogenase family protein; no well-defined Swiss-Prot hits: P0ABQ2, P28811, O34948; 3-hydroxyisobutyrate dehydrogenase complement(2586430..2587299) Dinoroseobacter shibae DFL 12 = DSM 16493 5714099 YP_001533779.1 CDS pdxA NC_009952.1 2587296 2588300 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(2587296..2588300) Dinoroseobacter shibae DFL 12 = DSM 16493 5714100 YP_001533780.1 CDS Dshi_2445 NC_009952.1 2588300 2589013 R PFAM: regulatory protein GntR HTH; GntR domain protein KEGG: sil:SPO2434 transcriptional regulator, GntR family COG1802: Transcriptional regulators; GntR family; transcriptional regulator complement(2588300..2589013) Dinoroseobacter shibae DFL 12 = DSM 16493 5714101 YP_001533781.1 CDS Dshi_2446 NC_009952.1 2589015 2589926 R PFAM: dihydrodipicolinate synthetase Swiss-Prot: O69782-Dihydrodipicolinate synthase KEGG: sil:SPOA0244 dihydrodipicolinate synthase family protein; dihydrodipicolinate synthase complement(2589015..2589926) Dinoroseobacter shibae DFL 12 = DSM 16493 5714102 YP_001533782.1 CDS Dshi_2447 NC_009952.1 2589923 2591098 R PFAM: Mandelate racemase/muconate lactonizing protein PTHR13794: enolase superfamily, mandelate racemase; putative mandelate racemase/muconate lactonizing protein complement(2589923..2591098) Dinoroseobacter shibae DFL 12 = DSM 16493 5714103 YP_001533783.1 CDS Dshi_2448 NC_009952.1 2591102 2592598 R PFAM: protein of unknown function DUF112 transmembrane KEGG: jan:Jann_1159 protein of unknown function DUF112, transmembrane COG3333: Uncharacterized protein conserved in bacteria; hypothetical protein complement(2591102..2592598) Dinoroseobacter shibae DFL 12 = DSM 16493 5714104 YP_001533784.1 CDS Dshi_2449 NC_009952.1 2592604 2593044 R hypothetical protein complement(2592604..2593044) Dinoroseobacter shibae DFL 12 = DSM 16493 5714105 YP_001533785.1 CDS Dshi_2450 NC_009952.1 2593114 2594058 R PFAM: conserved hypothetical protein KEGG: ecp:ECP_4043 hypothetical protein; similar to UPF0065 protein; hypothetical protein complement(2593114..2594058) Dinoroseobacter shibae DFL 12 = DSM 16493 5714106 YP_001533786.1 CDS murD NC_009952.1 2594434 2595828 R 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 complement(2594434..2595828) Dinoroseobacter shibae DFL 12 = DSM 16493 5714107 YP_001533787.1 CDS Dshi_2452 NC_009952.1 2596056 2596997 R PFAM: glycoside hydrolase family 25 KEGG: nha:Nham_3711 glycoside hydrolase, family 25 COG3757: Lyzozyme M1 (1,4-beta-N-acetylmuramidase); associated with glycoside hydrolase; hypothetical protein complement(2596056..2596997) Dinoroseobacter shibae DFL 12 = DSM 16493 5714108 YP_001533788.1 CDS Dshi_2453 NC_009952.1 2597049 2598080 R hypothetical protein complement(2597049..2598080) Dinoroseobacter shibae DFL 12 = DSM 16493 5714109 YP_001533789.1 CDS Dshi_2454 NC_009952.1 2598124 2598690 R hypothetical protein complement(2598124..2598690) Dinoroseobacter shibae DFL 12 = DSM 16493 5714110 YP_001533790.1 CDS Dshi_2455 NC_009952.1 2598687 2600012 R PFAM: AAA ATPase central domain protein SMART: AAA ATPase KEGG: ppd:Ppro_0362 AAA ATPase, central domain protein; AAA family; putative ATPase complement(2598687..2600012) Dinoroseobacter shibae DFL 12 = DSM 16493 5714111 YP_001533791.1 CDS Dshi_2456 NC_009952.1 2600009 2604343 R hypothetical protein complement(2600009..2604343) Dinoroseobacter shibae DFL 12 = DSM 16493 5714112 YP_001533792.1 CDS Dshi_2457 NC_009952.1 2604619 2607219 R hypothetical protein complement(2604619..2607219) Dinoroseobacter shibae DFL 12 = DSM 16493 5714113 YP_001533793.1 CDS Dshi_2458 NC_009952.1 2607235 2608275 R hypothetical protein complement(2607235..2608275) Dinoroseobacter shibae DFL 12 = DSM 16493 5714114 YP_001533794.1 CDS Dshi_2459 NC_009952.1 2608289 2612149 R KEGG: ppd:Ppro_0366 hypothetical protein; hypothetical protein complement(2608289..2612149) Dinoroseobacter shibae DFL 12 = DSM 16493 5714115 YP_001533795.1 CDS Dshi_2460 NC_009952.1 2612167 2612616 R PFAM: GPW/gp25 family protein KEGG: ppd:Ppro_0367 gpW/GP25 family protein COG3628: Phage baseplate assembly protein W; related to gene 25-like lysozyme; hypothetical protein complement(2612167..2612616) Dinoroseobacter shibae DFL 12 = DSM 16493 5714116 YP_001533796.1 CDS Dshi_2461 NC_009952.1 2612621 2612920 R PFAM: PAAR repeat-containing protein KEGG: sdn:Sden_3002 PaaR COG4104: Uncharacterized conserved protein; hypothetical protein complement(2612621..2612920) Dinoroseobacter shibae DFL 12 = DSM 16493 5714117 YP_001533797.1 CDS Dshi_2462 NC_009952.1 2612931 2614718 R PFAM: Rhs element Vgr protein KEGG: ppd:Ppro_0369 rhs element Vgr protein TIGR01646: Rhs element Vgr protein; related to phage late control gene D; hypothetical protein complement(2612931..2614718) Dinoroseobacter shibae DFL 12 = DSM 16493 5714118 YP_001533798.1 CDS Dshi_2463 NC_009952.1 2614711 2615373 R hypothetical protein complement(2614711..2615373) Dinoroseobacter shibae DFL 12 = DSM 16493 5714119 YP_001533799.1 CDS Dshi_2464 NC_009952.1 2615591 2616073 R TIGRFAM: conserved hypothetical phage tail protein (TIGR02241) PFAM: conserved hypothetical protein KEGG: rde:RD1_4219 hypothetical protein; phage tail region protein; hypothetical protein complement(2615591..2616073) Dinoroseobacter shibae DFL 12 = DSM 16493 5714120 YP_001533800.1 CDS Dshi_2465 NC_009952.1 2616086 2616544 R TIGRFAM: conserved hypothetical phage tail protein (TIGR02241) PFAM: conserved hypothetical protein KEGG: ppd:Ppro_0372 conserved hypothetical phage tail protein; phage tail region protein; hypothetical protein complement(2616086..2616544) Dinoroseobacter shibae DFL 12 = DSM 16493 5714121 YP_001533801.1 CDS Dshi_2466 NC_009952.1 2616568 2618061 R PFAM:Phage tail sheath protein KEGG: sdn:Sden_3007 hypothetical protein; related to phage tail sheath protein; hypothetical protein complement(2616568..2618061) Dinoroseobacter shibae DFL 12 = DSM 16493 5714122 YP_001533802.1 CDS Dshi_2467 NC_009952.1 2618145 2619143 R hypothetical protein complement(2618145..2619143) Dinoroseobacter shibae DFL 12 = DSM 16493 5714123 YP_001533803.1 CDS Dshi_2468 NC_009952.1 2619421 2620425 D hypothetical protein 2619421..2620425 Dinoroseobacter shibae DFL 12 = DSM 16493 5714124 YP_001533804.1 CDS mraY NC_009952.1 2620435 2621520 R First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan; phospho-N-acetylmuramoyl-pentapeptide- transferase complement(2620435..2621520) Dinoroseobacter shibae DFL 12 = DSM 16493 5713365 YP_001533805.1 CDS murF NC_009952.1 2621533 2622972 R Swiss-Prot: P11880- UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase murF TIGRFAM: UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate--D-alanyl-D-alanyl ligase PFAM: cytoplasmic peptidoglycan synthetase domain protein; Mur ligase middle domain protein; UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D- alanine ligase complement(2621533..2622972) Dinoroseobacter shibae DFL 12 = DSM 16493 5713366 YP_001533806.1 CDS murE NC_009952.1 2622969 2624450 R 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 complement(2622969..2624450) Dinoroseobacter shibae DFL 12 = DSM 16493 5713367 YP_001533807.1 CDS ftsI2 NC_009952.1 2624468 2626261 R Swiss-Prot: P0AD68-Peptidoglycan synthetase ftsI [Precursor] PFAM: penicillin-binding protein transpeptidase; Penicillin-binding protein dimerisation domain COG0768: Cell division protein FtsI/penicillin-binding protein 2; peptidoglycan synthetase ftsI complement(2624468..2626261) Dinoroseobacter shibae DFL 12 = DSM 16493 5713368 YP_001533808.1 CDS Dshi_2473 NC_009952.1 2626258 2626614 R hypothetical protein complement(2626258..2626614) Dinoroseobacter shibae DFL 12 = DSM 16493 5713369 YP_001533809.1 CDS mraW NC_009952.1 2626611 2627612 R Swiss-Prot: P60390- S-adenosyl-L-methionine-dependent methyltransferase mraW TIGRFAM: S-adenosyl-methyltransferase MraW PFAM: methyltransferase KEGG: rsq:Rsph17025_0683 S-adenosyl-methyltransferase MraW; S-adenosyl-methyltransferase MraW complement(2626611..2627612) Dinoroseobacter shibae DFL 12 = DSM 16493 5713370 YP_001533810.1 CDS Dshi_2475 NC_009952.1 2627617 2628129 R MraZ; UPF0040; crystal structure shows similarity to AbrB; cell division protein MraZ complement(2627617..2628129) Dinoroseobacter shibae DFL 12 = DSM 16493 5713371 YP_001533811.1 CDS Dshi_2476 NC_009952.1 2628776 2629864 R Swiss-Prot: P0AF08-Protein mrp COG0489: ATPases involved in chromosome partitioning; related to protein mrp; hypothetical protein complement(2628776..2629864) Dinoroseobacter shibae DFL 12 = DSM 16493 5713372 YP_001533812.1 CDS Dshi_2477 NC_009952.1 2630248 2630712 R Swiss-Prot: P0ACJ0- Leucine-responsive regulatory protein PFAM: regulatory protein AsnC/Lrp family KEGG: sil:SPO3612 transcriptional regulator, AsnC family; putative leucine-responsive regulatory protein complement(2630248..2630712) Dinoroseobacter shibae DFL 12 = DSM 16493 5713373 YP_001533813.1 CDS Dshi_2478 NC_009952.1 2630776 2631372 D Swiss-Prot: P38101-Inner membrane protein yfiK PFAM: Lysine exporter protein (LYSE/YGGA) KEGG: sil:SPO3613 transporter, LysE family; similar to inner membrane protein yfiK; hypothetical protein 2630776..2631372 Dinoroseobacter shibae DFL 12 = DSM 16493 5713374 YP_001533814.1 CDS Dshi_2479 NC_009952.1 2631379 2632347 R Swiss-Prot:P30864-Uncharacterized HTH-type transcriptional regulator yafC PFAM: regulatory protein LysR; LysR substrate-binding; LysR family; transcriptional regulator complement(2631379..2632347) Dinoroseobacter shibae DFL 12 = DSM 16493 5713375 YP_001533815.1 CDS Dshi_2480 NC_009952.1 2632408 2633268 D PFAM: short-chain dehydrogenase/reductase SDR COG1028: Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases); short-chain dehydrogenase/reductase SDR 2632408..2633268 Dinoroseobacter shibae DFL 12 = DSM 16493 5713376 YP_001533816.1 CDS Dshi_2481 NC_009952.1 2633360 2633482 D hypothetical protein 2633360..2633482 Dinoroseobacter shibae DFL 12 = DSM 16493 5713377 YP_001533817.1 CDS Dshi_2482 NC_009952.1 2633707 2634015 D TIGRFAM / PFAM: Ethyl tert-butyl ether degradation EthD; similar to EthD protein; hypothetical protein 2633707..2634015 Dinoroseobacter shibae DFL 12 = DSM 16493 5713378 YP_001533818.1 CDS uvrD NC_009952.1 2634052 2636475 R Swiss-Prot: P03018-DNA helicase II PFAM: UvrD/REP helicase KEGG: jan:Jann_2777 UvrD/REP helicase; DNA helicase II complement(2634052..2636475) Dinoroseobacter shibae DFL 12 = DSM 16493 5713379 YP_001533819.1 CDS lldD1 NC_009952.1 2636566 2637735 D Swiss-Prot: P33232- L-lactate dehydrogenase [cytochrome] lldD PFAM: FMN-dependent alpha-hydroxy acid dehydrogenase KEGG: sit:TM1040_2026 L-lactate dehydrogenase (cytochrome); cytochrome containing L-lactate dehydrogenase 2636566..2637735 Dinoroseobacter shibae DFL 12 = DSM 16493 5713380 YP_001533820.1 CDS Dshi_2485 NC_009952.1 2637777 2641214 D biotin-containing enzyme that catalyzes a two step carboxylation of pyruvate to oxaloacetate; pyruvate carboxylase 2637777..2641214 Dinoroseobacter shibae DFL 12 = DSM 16493 5713381 YP_001533821.1 CDS Dshi_2486 NC_009952.1 2641492 2642133 R PFAM: Protein of unknown function DUF1826 KEGG: rde:RD1_1857 hypothetical protein; hypothetical protein complement(2641492..2642133) Dinoroseobacter shibae DFL 12 = DSM 16493 5713382 YP_001533822.1 CDS Dshi_2487 NC_009952.1 2642133 2643338 R Swiss-Prot: P31521- 47 kDa protein; PFAM: cobalamin synthesis protein P47K; cobalamin synthesis CobW domain protein; putative 47 kDa protein complement(2642133..2643338) Dinoroseobacter shibae DFL 12 = DSM 16493 5713383 YP_001533823.1 CDS Dshi_2488 NC_009952.1 2643636 2645039 R PFAM: helix-turn-helix domain protein; protein of unknown function DUF955 KEGG: rde:RD1_2203 transcriptional regulator, putative; associated with regulation of transcription; hypothetical protein complement(2643636..2645039) Dinoroseobacter shibae DFL 12 = DSM 16493 5713385 YP_001533824.1 CDS Dshi_2489 NC_009952.1 2645177 2646379 D Swiss-Prot: O08374- Serine--glyoxylate aminotransferase (Inferred from homology) PFAM: aminotransferase class V KEGG: sme:SMa2139 probable SgaA serine-glyoxylate aminotransferase (SgaT); putative serine--glyoxylate aminotransferase 2645177..2646379 Dinoroseobacter shibae DFL 12 = DSM 16493 5713386 YP_001533825.1 CDS citE1 NC_009952.1 2646434 2647366 D Swiss-Prot: P0A9I1-Citrate lyase subunit beta PIRSF015582: citrate lyase, beta subunit [Validated]; subunit beta; citrate lyase 2646434..2647366 Dinoroseobacter shibae DFL 12 = DSM 16493 5713387 YP_001533826.1 CDS sucC2 NC_009952.1 2647390 2648568 D catalyzes the formation of malyl-CoA from malate and CoA; malate--CoA ligase subunit beta 2647390..2648568 Dinoroseobacter shibae DFL 12 = DSM 16493 5713388 YP_001533827.1 CDS sucD2 NC_009952.1 2648581 2649480 D Catalyzes the only substrate-level phosphorylation in the TCA cycle; succinyl-CoA synthetase subunit alpha 2648581..2649480 Dinoroseobacter shibae DFL 12 = DSM 16493 5713389 YP_001533828.1 CDS Dshi_2493 NC_009952.1 2649470 2650336 D KEGG: pde:Pden_4111 hypothetical protein; hypothetical protein 2649470..2650336 Dinoroseobacter shibae DFL 12 = DSM 16493 5713390 YP_001533829.1 CDS Dshi_2494 NC_009952.1 2650338 2651579 D IPR003673: CoA-transferase family III KEGG: rrs:RoseRS_4174 acyl-CoA transferase/carnitine dehydratase-like protei; CoA-transferase 2650338..2651579 Dinoroseobacter shibae DFL 12 = DSM 16493 5713391 YP_001533830.1 CDS Dshi_2495 NC_009952.1 2651711 2652277 R Swiss-Prot: P75925-Cytochrome b561 homolog 2 PFAM: cytochrome B561; putative cytochrome B561 complement(2651711..2652277) Dinoroseobacter shibae DFL 12 = DSM 16493 5713392 YP_001533831.1 CDS Dshi_2496 NC_009952.1 2652382 2652942 R PFAM: EF hand IPR002048: Calcium-binding EF-hand KEGG: rsh:Rsph17029_2073 putative signal transduction protein with EFhand domain; associated with signal transduction; hypothetical protein complement(2652382..2652942) Dinoroseobacter shibae DFL 12 = DSM 16493 5713393 YP_001533832.1 CDS Dshi_2497 NC_009952.1 2653184 2653903 D Swiss-Prot: P0AA16-Transcriptional regulatory protein (ompR) PFAM: response regulator receiver; transcriptional regulator domain protein KEGG: rpe:RPE_4561 two component transcriptional regulator, winged helix family; colocated with histidin kinase; winged helix family; two component transcriptional regulator 2653184..2653903 Dinoroseobacter shibae DFL 12 = DSM 16493 5713394 YP_001533833.1 CDS Dshi_2498 NC_009952.1 2653900 2655261 D Swiss-Prot: P0AEJ4-Osmolarity sensor protein (envZ) PFAM: ATP-binding region ATPase domain protein; histidine kinase HAMP region domain protein; histidine kinase A domain protein KEGG: sil:SPOA0358 sensor histidine kinase; colocated with response regulator; integral membrane sensor signal transduction histidine kinase 2653900..2655261 Dinoroseobacter shibae DFL 12 = DSM 16493 5713395 YP_001533834.1 CDS Dshi_2499 NC_009952.1 2655477 2656199 R Swiss-Prot: P0A0V3-Outer membrane protein class 4 [Precursor] PFAM: OmpA/MotB domain protein KEGG: rde:RD1_1126 OmpA family domain protein COG2885: Outer membrane protein and related peptidoglycan-associated (lipo)proteins; related to outer membrane protein (ompA); hypothetical protein complement(2655477..2656199) Dinoroseobacter shibae DFL 12 = DSM 16493 5713396 YP_001533835.1 CDS Dshi_2501 NC_009952.1 2657746 2659947 D Swiss-Prot: P18770-Cyclolysin secretion/processing ATP-binding protein cyaB; P26760-Toxin RTX-I translocation ATP-binding protein PFAM: ABC transporter transmembrane region; ABC transporter related SMART: AAA ATPase KEGG: rde:RD1_1124 toxin secretion ABC transporter, ATP-binding component, putative; colocated with secretion protein (HylD family); associated with toxin excretion; ABC transporter 2657746..2659947 Dinoroseobacter shibae DFL 12 = DSM 16493 5713398 YP_001533836.1 CDS Dshi_2502 NC_009952.1 2659944 2661263 D Swiss-Prot: Q03025-Alkaline protease secretion protein aprE TIGRFAM: type I secretion membrane fusion protein, HlyD family PFAM: secretion protein HlyD family protein KEGG: rde:RD1_1123 HlyD family secretion protein, putative; colocated with ABC transporter; HlyD family; secretion protein 2659944..2661263 Dinoroseobacter shibae DFL 12 = DSM 16493 5713399 YP_001533837.1 CDS Dshi_2503 NC_009952.1 2661268 2668737 R hypothetical protein complement(2661268..2668737) Dinoroseobacter shibae DFL 12 = DSM 16493 5713400 YP_001533838.1 CDS Dshi_2504 NC_009952.1 2668891 2670234 D KEGG: jan:Jann_0233 hypothetical protein; hypothetical protein 2668891..2670234 Dinoroseobacter shibae DFL 12 = DSM 16493 5713401 YP_001533839.1 CDS Dshi_2505 NC_009952.1 2670313 2670798 R hypothetical protein complement(2670313..2670798) Dinoroseobacter shibae DFL 12 = DSM 16493 5713402 YP_001533840.1 CDS Dshi_2506 NC_009952.1 2670795 2671211 R hypothetical protein complement(2670795..2671211) Dinoroseobacter shibae DFL 12 = DSM 16493 5713403 YP_001533841.1 CDS Dshi_2507 NC_009952.1 2672204 2672470 D Swiss-Prot: P17985-Insertion element ISR1 uncharacterized 10 kDa protein A3 IPR002514: Transposase IS3/IS911 PFAM: transposase IS3/IS911 family protein KEGG: rde:RD1_3450 inverted repeat region; transposase 2672204..2672470 Dinoroseobacter shibae DFL 12 = DSM 16493 5713404 YP_001533842.1 CDS Dshi_2508 NC_009952.1 2672494 2673315 D Swiss-Prot: P25438-Insertion element IS476 uncharacterized 39.2 kDa protein PFAM: Integrase catalytic region KEGG: rde:RD1_3449 integrase, catalytic domain, putativ; catalytic region; integrase 2672494..2673315 Dinoroseobacter shibae DFL 12 = DSM 16493 5713405 YP_001533843.1 CDS Dshi_2509 NC_009952.1 2673339 2674034 R Swiss-Prot: P25438-Insertion element IS476 uncharacterized 39.2 kDa protein PFAM: Integrase catalytic region KEGG: bbt:BBta_7691 integrase, catalytic domain; catalytic region; integrase complement(2673339..2674034) Dinoroseobacter shibae DFL 12 = DSM 16493 5713406 YP_001533844.1 CDS Dshi_2510 NC_009952.1 2674058 2674324 R Swiss-Prot: P17985-Insertion element ISR1 uncharacterized 10 kDa protein A3 PFAM: transposase IS3/IS911 family protein KEGG: mag:amb0646 insertion element ISR1 hypothetical 10 kDa protein A3; transposase complement(2674058..2674324) Dinoroseobacter shibae DFL 12 = DSM 16493 5713407 YP_001533845.1 CDS Dshi_2511 NC_009952.1 2675127 2675798 R hypothetical protein complement(2675127..2675798) Dinoroseobacter shibae DFL 12 = DSM 16493 5713408 YP_001533846.1 CDS dusA NC_009952.1 2676018 2677034 D Swiss-Prot: Q87L85- tRNA-dihydrouridine synthase A PIRSF006621-tRNA-dihydrouridine synthase TIGRFAM: TIM-barrel protein, yjbN family PFAM: dihydrouridine synthase DuS; tRNA-dihydrouridine synthase A 2676018..2677034 Dinoroseobacter shibae DFL 12 = DSM 16493 5713409 YP_001533847.1 CDS Dshi_2513 NC_009952.1 2677050 2677463 R KEGG: sil:SPO1770 hypothetical protein; hypothetical protein complement(2677050..2677463) Dinoroseobacter shibae DFL 12 = DSM 16493 5713410 YP_001533848.1 CDS Dshi_2514 NC_009952.1 2677548 2678540 D KEGG: sil:SPO1769 hypothetical protein; hypothetical protein 2677548..2678540 Dinoroseobacter shibae DFL 12 = DSM 16493 5713411 YP_001533849.1 CDS Dshi_2515 NC_009952.1 2678672 2680408 R Swiss-Prot: P0AFR2-Putative sulfate transporter ychM TIGRFAM: sulfate transporter PFAM: Sulfate transporter/antisigma-factor antagonist STAS; sulphate transporter KEGG: sit:TM1040_3648 sulfate permease; putative sulfate transporter complement(2678672..2680408) Dinoroseobacter shibae DFL 12 = DSM 16493 5713412 YP_001533850.1 CDS Dshi_2516 NC_009952.1 2680474 2680680 D hypothetical protein 2680474..2680680 Dinoroseobacter shibae DFL 12 = DSM 16493 5713413 YP_001533851.1 CDS Dshi_2517 NC_009952.1 2680792 2681676 R Swiss-Prot: Q8UAA9-Beta-lactamase hydrolase-like protein PFAM: beta-lactamase domain protein KEGG: rde:RD1_0785 metallo-beta-lactamase family protein; related to beta-lactamase hydrolase-like protein; hypothetical protein complement(2680792..2681676) Dinoroseobacter shibae DFL 12 = DSM 16493 5713414 YP_001533852.1 CDS Dshi_2518 NC_009952.1 2681705 2682142 R Swiss-Prot: Q87AD3-UPF0394 membrane protein PD_1893 PFAM: protein of unknown function DUF395 YeeE/YedE KEGG: sit:TM1040_3646 protein of unknown function DUF395, YeeE/YedE; hypothetical protein complement(2681705..2682142) Dinoroseobacter shibae DFL 12 = DSM 16493 5713415 YP_001533853.1 CDS Dshi_2519 NC_009952.1 2682147 2682581 R PFAM: protein of unknown function DUF395 YeeE/YedE KEGG: jan:Jann_2818 protein of unknown function DUF395, YeeE/YedE; hypothetical protein complement(2682147..2682581) Dinoroseobacter shibae DFL 12 = DSM 16493 5713416 YP_001533854.1 CDS Dshi_2520 NC_009952.1 2682578 2682790 R KEGG: rde:RD1_0788 hypothetical protein; hypothetical protein complement(2682578..2682790) Dinoroseobacter shibae DFL 12 = DSM 16493 5713417 YP_001533855.1 CDS Dshi_2521 NC_009952.1 2682892 2683569 R Swiss-Prot: P0ACJ8-Catabolite gene activator crp PFAM: cyclic nucleotide-binding SMART: regulatory protein Crp KEGG: sil:SPO1615 cyclic nucleotide-binding protein; Crp/Fnr family; transcriptional regulator complement(2682892..2683569) Dinoroseobacter shibae DFL 12 = DSM 16493 5713418 YP_001533856.1 CDS Dshi_2522 NC_009952.1 2683654 2684346 R Swiss-Prot: Q8PYP6-Probable peroxiredoxin PFAM: alkyl hydroperoxide reductase/ Thiol specific antioxidant/ Mal allergen; Redoxin domain protein; putative peroxiredoxin complement(2683654..2684346) Dinoroseobacter shibae DFL 12 = DSM 16493 5713419 YP_001533857.1 CDS Dshi_2523 NC_009952.1 2684418 2685335 D Swiss-Prot: P0ACQ4-Hydrogen peroxide-inducible genes activator oxyR PFAM: regulatory protein LysR; LysR substrate-binding KEGG: rpb:RPB_4602 transcriptional regulator, LysR family; putative hydrogen peroxide-inducible genes activator 2684418..2685335 Dinoroseobacter shibae DFL 12 = DSM 16493 5713420 YP_001533858.1 CDS Dshi_2524 NC_009952.1 2685358 2686335 R TIGR00816: C4-dicarboxylate transporter/malic acid transport protein PFAM: C4-dicarboxylate transporter/malic acid transport protein KEGG: jan:Jann_2959 C4-dicarboxylate transporter/malic acid transport protein Swiss-Prot: P25396-Tellurite resistance protein tehA; putative C4-dicarboxylate transporter / malic acid transport protein complement(2685358..2686335) Dinoroseobacter shibae DFL 12 = DSM 16493 5713421 YP_001533859.1 CDS Dshi_2525 NC_009952.1 2686607 2686975 R KEGG: sil:SPO1613 hypothetical protein; hypothetical protein complement(2686607..2686975) Dinoroseobacter shibae DFL 12 = DSM 16493 5713422 YP_001533860.1 CDS Dshi_2526 NC_009952.1 2686988 2688289 R PTHR10632: Sulfide quinone-reductase PFAM: FAD-dependent pyridine nucleotide-disulphide oxidoreductase; putative sulfide quinone-rductase complement(2686988..2688289) Dinoroseobacter shibae DFL 12 = DSM 16493 5713423 YP_001533861.1 CDS Dshi_2527 NC_009952.1 2688731 2689123 R hypothetical protein complement(2688731..2689123) Dinoroseobacter shibae DFL 12 = DSM 16493 5713424 YP_001533862.1 CDS Dshi_2528 NC_009952.1 2689216 2689971 R PFAM: Bacterial regulatory proteins, crp family KEGG: rru:Rru_A1245 transcriptional regulator, Crp/Fnr family; Crp/Fnr family; putative transcriptional regulator complement(2689216..2689971) Dinoroseobacter shibae DFL 12 = DSM 16493 5713425 YP_001533863.1 CDS Dshi_2529 NC_009952.1 2689949 2691163 R KEGG: sil:SPO1611 hypothetical protein; hypothetical protein complement(2689949..2691163) Dinoroseobacter shibae DFL 12 = DSM 16493 5713426 YP_001533864.1 CDS Dshi_2530 NC_009952.1 2691359 2691556 R hypothetical protein complement(2691359..2691556) Dinoroseobacter shibae DFL 12 = DSM 16493 5713427 YP_001533865.1 CDS Dshi_2531 NC_009952.1 2691653 2691925 R hypothetical protein complement(2691653..2691925) Dinoroseobacter shibae DFL 12 = DSM 16493 5713428 YP_001533866.1 CDS Dshi_2532 NC_009952.1 2692195 2692497 R hypothetical protein complement(2692195..2692497) Dinoroseobacter shibae DFL 12 = DSM 16493 5713429 YP_001533867.1 CDS Dshi_2533 NC_009952.1 2692835 2693023 R hypothetical protein complement(2692835..2693023) Dinoroseobacter shibae DFL 12 = DSM 16493 5713430 YP_001533868.1 CDS Dshi_2534 NC_009952.1 2693038 2693469 R PFAM: Integral membrane protein DUF112 COG3333: Uncharacterized protein conserved in bacteria; hypothetical protein complement(2693038..2693469) Dinoroseobacter shibae DFL 12 = DSM 16493 5713431 YP_001533869.1 CDS Dshi_2535 NC_009952.1 2693658 2693837 R hypothetical protein complement(2693658..2693837) Dinoroseobacter shibae DFL 12 = DSM 16493 5713432 YP_001533870.1 CDS Dshi_2536 NC_009952.1 2693913 2694260 R hypothetical protein complement(2693913..2694260) Dinoroseobacter shibae DFL 12 = DSM 16493 5713433 YP_001533871.1 CDS Dshi_2537 NC_009952.1 2694263 2695291 R Swiss-Prot: Q59727- 4,5-dihydroxyphthalate decarboxylase [predicted]; putative 4,5-dihydroxyphthalate decarboxylase complement(2694263..2695291) Dinoroseobacter shibae DFL 12 = DSM 16493 5713434 YP_001533872.1 CDS Dshi_2538 NC_009952.1 2695338 2696024 R Swiss-Prot: P76004-Uncharacterized protein ycgM PFAM: fumarylacetoacetate (FAA) hydrolase KEGG: rsh:Rsph17029_0213 fumarylacetoacetate (FAA) hydrolase; related to fumarylacetoacetate (FAA) hydrolase; hypothetical protein complement(2695338..2696024) Dinoroseobacter shibae DFL 12 = DSM 16493 5713435 YP_001533873.1 CDS Dshi_2539 NC_009952.1 2696193 2696882 D Swiss-Prot: P39161-Uxu operon transcriptional regulator PFAM: regulatory protein GntR HTH; GntR domain protein KEGG: ent:Ent638_0750 GntR domain protein; gntR family; transcriptional regulator 2696193..2696882 Dinoroseobacter shibae DFL 12 = DSM 16493 5713436 YP_001533874.1 CDS Dshi_2540 NC_009952.1 2696948 2697499 D hypothetical protein 2696948..2697499 Dinoroseobacter shibae DFL 12 = DSM 16493 5713437 YP_001533875.1 CDS Dshi_2541 NC_009952.1 2697654 2698334 R Swiss-Prot: P0ACL7- Putative L-lactate dehydrogenase operon regulatory protein PFAM: regulatory protein GntR HTH; GntR domain protein KEGG: rle:RL4574 putative GntR family transcriptional regulator; gntR family; transcriptional regulator complement(2697654..2698334) Dinoroseobacter shibae DFL 12 = DSM 16493 5713438 YP_001533876.1 CDS Dshi_2542 NC_009952.1 2698518 2699444 D Swiss-Prot: P76004-Uncharacterized protein ycgM PFAM: fumarylacetoacetate (FAA) hydrolase KEGG: bxe:Bxe_A3618 putative hydrolase; related to fumarylacetoacetate (FAA) hydrolase; hypothetical protein 2698518..2699444 Dinoroseobacter shibae DFL 12 = DSM 16493 5713439 YP_001533877.1 CDS Dshi_2543 NC_009952.1 2699475 2700533 D Swiss-Prot: P40400-Putative aliphatic sulfonates-binding protein [Precursor] PFAM: NMT1/THI5 like domain protein; putative-binding protein 2699475..2700533 Dinoroseobacter shibae DFL 12 = DSM 16493 5713440 YP_001533878.1 CDS Dshi_2544 NC_009952.1 2700533 2701342 D Swiss-Prot: Q57855-Uncharacterized ABC transporter ATP-binding protein MJ0412 PFAM: ABC transporter related SMART: AAA ATPase KEGG: rsh:Rsph17029_3905 ABC transporter related; ATP-binding protein; ABC transporter 2700533..2701342 Dinoroseobacter shibae DFL 12 = DSM 16493 5713441 YP_001533879.1 CDS Dshi_2545 NC_009952.1 2701339 2702202 D Swiss-Prot: P40401-Putative aliphatic sulfonates transport permease protein PFAM: binding-protein-dependent transport systems inner membrane component; inner membrane component; binding-protein-dependent transport system protein 2701339..2702202 Dinoroseobacter shibae DFL 12 = DSM 16493 5713442 YP_001533880.1 CDS Dshi_2546 NC_009952.1 2702195 2703250 D Swiss-Prot: O34736-Uncharacterized oxidoreductase yjmC PFAM: Malate/L-lactate dehydrogenase KEGG: tth:TT_P0035 dehydrogenase; dehydrogenase 2702195..2703250 Dinoroseobacter shibae DFL 12 = DSM 16493 5713443 YP_001533881.1 CDS Dshi_2547 NC_009952.1 2703342 2703722 R hypothetical protein complement(2703342..2703722) Dinoroseobacter shibae DFL 12 = DSM 16493 5713444 YP_001533882.1 CDS Dshi_2548 NC_009952.1 2703739 2707950 R COG5412: Phage-related protein; hypothetical protein complement(2703739..2707950) Dinoroseobacter shibae DFL 12 = DSM 16493 5713445 YP_001533883.1 CDS Dshi_2549 NC_009952.1 2707954 2709441 R PFAM: cell surface receptor IPT/TIG domain protein KEGG: rrs:RoseRS_1653 hypothetical protein; hypothetical protein complement(2707954..2709441) Dinoroseobacter shibae DFL 12 = DSM 16493 5713446 YP_001533884.1 CDS Dshi_2550 NC_009952.1 2709454 2713869 R PFAM: impB/mucB/samB family SSF50969: quinoprotein amine dehydrogenase, beta chain-like KEGG: gme:Gmet_1144 hypothetical protein; hypothetical protein complement(2709454..2713869) Dinoroseobacter shibae DFL 12 = DSM 16493 5713447 YP_001533885.1 CDS Dshi_2551 NC_009952.1 2713924 2715474 R KEGG: gme:Gmet_1142 hypothetical protein; hypothetical protein complement(2713924..2715474) Dinoroseobacter shibae DFL 12 = DSM 16493 5713448 YP_001533886.1 CDS Dshi_2552 NC_009952.1 2715478 2718297 R TIGR02243: conserved hypothetical protein, phage tail-like region KEGG: aeh:Mlg_1745 hypothetical protein; hypothetical protein complement(2715478..2718297) Dinoroseobacter shibae DFL 12 = DSM 16493 5713449 YP_001533887.1 CDS Dshi_2553 NC_009952.1 2718294 2719487 R hypothetical protein complement(2718294..2719487) Dinoroseobacter shibae DFL 12 = DSM 16493 5713450 YP_001533888.1 CDS Dshi_2554 NC_009952.1 2719489 2719884 R PFAM: Gene 25-like lysozyme KEGG: aeh:Mlg_1747 hypothetical protein; related to gene 25-like lysozyme; hypothetical protein complement(2719489..2719884) Dinoroseobacter shibae DFL 12 = DSM 16493 5713451 YP_001533889.1 CDS Dshi_2555 NC_009952.1 2719895 2720716 R PFAM: Protein of unknown function, DUF586 COG3501: Uncharacterized protein conserved in bacteria; hypothetical protein complement(2719895..2720716) Dinoroseobacter shibae DFL 12 = DSM 16493 5713452 YP_001533890.1 CDS Dshi_2556 NC_009952.1 2720713 2721852 R PFAM: Phage late control gene D protein KEGG: gme:Gmet_1137 hypothetical protein COG3500: Phage protein D; hypothetical protein complement(2720713..2721852) Dinoroseobacter shibae DFL 12 = DSM 16493 5713453 YP_001533891.1 CDS Dshi_2557 NC_009952.1 2721857 2722219 R hypothetical protein complement(2721857..2722219) Dinoroseobacter shibae DFL 12 = DSM 16493 5713454 YP_001533892.1 CDS Dshi_2558 NC_009952.1 2722223 2722885 R hypothetical protein complement(2722223..2722885) Dinoroseobacter shibae DFL 12 = DSM 16493 5713455 YP_001533893.1 CDS Dshi_2559 NC_009952.1 2723112 2724446 R Swiss-Prot: P55530-Uncharacterized AAA family ATPase y4kL PFAM: AAA ATPase central domain protein SMART: AAA ATPase KEGG: gme:Gmet_1133 AAA ATPase, central region; central domain protein; AAA ATPase complement(2723112..2724446) Dinoroseobacter shibae DFL 12 = DSM 16493 5713456 YP_001533894.1 CDS Dshi_2560 NC_009952.1 2724452 2725531 R ##; hypothetical protein complement(2724452..2725531) Dinoroseobacter shibae DFL 12 = DSM 16493 5713457 YP_001533895.1 CDS Dshi_2561 NC_009952.1 2725535 2726218 R hypothetical protein complement(2725535..2726218) Dinoroseobacter shibae DFL 12 = DSM 16493 5713458 YP_001533896.1 CDS Dshi_2562 NC_009952.1 2726402 2727220 R hypothetical protein complement(2726402..2727220) Dinoroseobacter shibae DFL 12 = DSM 16493 5713459 YP_001533897.1 CDS Dshi_2563 NC_009952.1 2727217 2727726 R TIGRFAM: conserved hypothetical phage tail protein PFAM: conserved hypothetical protein KEGG: aeh:Mlg_1757 conserved hypothetical phage tail protein; phage tail region; hypothetical protein complement(2727217..2727726) Dinoroseobacter shibae DFL 12 = DSM 16493 5713460 YP_001533898.1 CDS Dshi_2564 NC_009952.1 2727753 2730098 R PFAM: tail sheath protein KEGG: gme:Gmet_1128 phage tail sheath protein; related to phage tail sheath protein; hypothetical protein complement(2727753..2730098) Dinoroseobacter shibae DFL 12 = DSM 16493 5713461 YP_001533899.1 CDS Dshi_2565 NC_009952.1 2730319 2730960 R Swiss-Prot: O32197-Sensory transduction protein PFAM: regulatory protein LuxR; response regulator receiver KEGG: sen:SACE_5003 two component transcriptional regulator, LuxR family; colocated with histidine kinase; response regulator protein complement(2730319..2730960) Dinoroseobacter shibae DFL 12 = DSM 16493 5713462 YP_001533900.1 CDS Dshi_2566 NC_009952.1 2731137 2733368 D PFAM: dehydrogenase E1 component; Transketolase central region; Transketolase domain protein; transketolase / dehydrogenase; putative bifunctional enzyme 2731137..2733368 Dinoroseobacter shibae DFL 12 = DSM 16493 5713463 YP_001533901.1 CDS Dshi_2567 NC_009952.1 2733766 2736072 D Swiss-Prot: P26489-Sensor protein fixL TIGRFAM: PAS sensor protein PFAM: ATP-binding region ATPase domain protein; histidine kinase A domain protein; Cache domain protein; PAS fold-3 domain protein; PAS fold-4 domain protein SMART: PAS domain containing protein, colocated with response regulator; multi-sensor signal transduction histidine kinase 2733766..2736072 Dinoroseobacter shibae DFL 12 = DSM 16493 5713464 YP_001533902.1 CDS Dshi_2568 NC_009952.1 2736065 2736709 D Swiss-Prot: P10958-Transcriptional regulatory protein fixJ PFAM: regulatory protein LuxR; response regulator receiver KEGG: rde:RD1_3086 transcriptional regulatory protein FixJ, putative; colocated with histidine kinase; response regulator protein 2736065..2736709 Dinoroseobacter shibae DFL 12 = DSM 16493 5713465 YP_001533903.1 CDS Dshi_2569 NC_009952.1 2736718 2737746 R Swiss-Prot: P75747-Protein abrB (multi-pass membrane protein / probably involved in gene regulation) PFAM: putative ammonia monooxygenase KEGG: rde:RD1_2159 hypothetical protein; similar to Protein abrB; hypothetical protein complement(2736718..2737746) Dinoroseobacter shibae DFL 12 = DSM 16493 5713466 YP_001533904.1 CDS Dshi_2570 NC_009952.1 2737743 2738384 R Swiss-Prot: P76114-Uncharacterized HTH-type transcriptional regulator yncC PFAM: regulatory protein GntR HTH; GntR domain protein KEGG: bja:bll2319 transcriptional regulatory protein; GntR family; transcriptional regulator complement(2737743..2738384) Dinoroseobacter shibae DFL 12 = DSM 16493 5713467 YP_001533905.1 CDS Dshi_2571 NC_009952.1 2738741 2739532 D Swiss-Prot: P63177- 23S rRNA (guanosine-2-O-)-methyltransferase rlmB 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; TrmH family, group 3; RNA methyltransferase 2738741..2739532 Dinoroseobacter shibae DFL 12 = DSM 16493 5713469 YP_001533906.1 CDS Dshi_2572 NC_009952.1 2739576 2739908 D KEGG: jan:Jann_2800 hypothetical protein; hypothetical protein 2739576..2739908 Dinoroseobacter shibae DFL 12 = DSM 16493 5713470 YP_001533907.1 CDS Dshi_2573 NC_009952.1 2740015 2740470 D KEGG: rde:RD1_2147 hypothetical protein; hypothetical protein 2740015..2740470 Dinoroseobacter shibae DFL 12 = DSM 16493 5713471 YP_001533908.1 CDS Dshi_2574 NC_009952.1 2740741 2741226 D PFAM: CoA-binding domain protein KEGG: sil:SPO1153 CoA-binding domain protein; hypothetical protein 2740741..2741226 Dinoroseobacter shibae DFL 12 = DSM 16493 5713472 YP_001533909.1 CDS hisE NC_009952.1 2741315 2741623 R catalyzes the formation of 1-(5-phosphoribosyl)-AMP from 1-(5-phosphoribolsyl)-ATP in histidine biosynthesis; phosphoribosyl-ATP pyrophosphatase complement(2741315..2741623) Dinoroseobacter shibae DFL 12 = DSM 16493 5713473 YP_001533910.1 CDS hisF NC_009952.1 2741620 2742381 R 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 complement(2741620..2742381) Dinoroseobacter shibae DFL 12 = DSM 16493 5713474 YP_001533911.1 CDS Dshi_2577 NC_009952.1 2742482 2743606 D PFAM: putative RNA methylase KEGG: pde:Pden_2378 putative RNA methylase; putative RNA methylase 2742482..2743606 Dinoroseobacter shibae DFL 12 = DSM 16493 5713475 YP_001533912.1 CDS hisA NC_009952.1 2743867 2744589 R 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 complement(2743867..2744589) Dinoroseobacter shibae DFL 12 = DSM 16493 5713476 YP_001533913.1 CDS Dshi_2579 NC_009952.1 2744733 2745137 D COG4731: Uncharacterized protein conserved in bacteria; hypothetical protein 2744733..2745137 Dinoroseobacter shibae DFL 12 = DSM 16493 5713477 YP_001533914.1 CDS hrpB NC_009952.1 2745303 2747807 R Swiss-Prot: P37024- ATP-dependent RNA helicase hrpB TIGRFAM: ATP-dependent helicase HrpB PFAM: helicase domain protein; helicase-associated domain protein; DEAD/DEAH box helicase domain protein; Helicase ATP-dependent domain protein SMART: DEAD-like helicases; ATP-dependent RNA helicase complement(2745303..2747807) Dinoroseobacter shibae DFL 12 = DSM 16493 5713478 YP_001533915.1 CDS Dshi_2581 NC_009952.1 2747856 2748656 R hypothetical protein complement(2747856..2748656) Dinoroseobacter shibae DFL 12 = DSM 16493 5713479 YP_001533916.1 CDS Dshi_2582 NC_009952.1 2748739 2749815 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 2748739..2749815 Dinoroseobacter shibae DFL 12 = DSM 16493 5713480 YP_001533917.1 CDS rpmB NC_009952.1 2749939 2750226 D required for 70S ribosome assembly; 50S ribosomal protein L28 2749939..2750226 Dinoroseobacter shibae DFL 12 = DSM 16493 5713481 YP_001533918.1 CDS Dshi_2584 NC_009952.1 2750551 2750907 D KEGG: rsq:Rsph17025_3115 hypothetical protein; hypothetical protein 2750551..2750907 Dinoroseobacter shibae DFL 12 = DSM 16493 5713482 YP_001533919.1 CDS Dshi_2585 NC_009952.1 2750951 2751463 D PFAM: protein of unknown function DUF461 KEGG: rde:RD1_1682 hypothetical protein COG2847: Uncharacterized protein conserved in bacteria; hypothetical protein 2750951..2751463 Dinoroseobacter shibae DFL 12 = DSM 16493 5713483 YP_001533920.1 CDS Dshi_2586 NC_009952.1 2751482 2752237 R PFAM: HpcH/HpaI aldolase KEGG: jan:Jann_2691 HpcH/HpaI aldolase; HpcH/HpaI aldolase complement(2751482..2752237) Dinoroseobacter shibae DFL 12 = DSM 16493 5713484 YP_001533921.1 CDS Dshi_2587 NC_009952.1 2752527 2753555 D PFAM: Metallo-beta-lactamase superfamily COG1236: Predicted exonuclease of the beta-lactamase fold involved in RNA processing; related to beta-lactamases; hypothetical protein 2752527..2753555 Dinoroseobacter shibae DFL 12 = DSM 16493 5713485 YP_001533922.1 CDS Dshi_2588 NC_009952.1 2753552 2754448 D PFAM: Alpha/beta hydrolase fold-3 domain protein COG0657: Esterase/lipase; putative esterase/lipase 2753552..2754448 Dinoroseobacter shibae DFL 12 = DSM 16493 5713486 YP_001533923.1 CDS Dshi_2589 NC_009952.1 2754445 2756049 D catalyzes the ATP-dependent formation of a phosphodiester at the site of a single strand break in duplex DNA; ATP-dependent DNA ligase 2754445..2756049 Dinoroseobacter shibae DFL 12 = DSM 16493 5713487 YP_001533924.1 CDS Dshi_2590 NC_009952.1 2756272 2756904 D PFAM: integrase family protein KEGG: rsh:Rsph17029_2267 phage integrase family protein; related to phage integrase; hypothetical protein 2756272..2756904 Dinoroseobacter shibae DFL 12 = DSM 16493 5713488 YP_001533925.1 CDS Dshi_2591 NC_009952.1 2757021 2757491 R TIGRFAM: putative transcriptional regulator, Rrf2 family PFAM: protein of unknown function UPF0074 KEGG: rde:RD1_1855 transcriptional regulator, rrf2 family, putative; transcriptional regulator complement(2757021..2757491) Dinoroseobacter shibae DFL 12 = DSM 16493 5713489 YP_001533926.1 CDS Dshi_2592 NC_009952.1 2757530 2758741 D Swiss-Prot: P31521- 47 kDa protein; PFAM: cobalamin synthesis protein P47K COG0523: Putative GTPases (G3E family); putative 47 kDa protein 2757530..2758741 Dinoroseobacter shibae DFL 12 = DSM 16493 5713490 YP_001533927.1 CDS Dshi_2593 NC_009952.1 2758738 2759373 D PFAM: Protein of unknown function DUF1826 KEGG: rde:RD1_1857 hypothetical protein; hypothetical protein 2758738..2759373 Dinoroseobacter shibae DFL 12 = DSM 16493 5713491 YP_001533928.1 CDS Dshi_2594 NC_009952.1 2759370 2759642 D hypothetical protein 2759370..2759642 Dinoroseobacter shibae DFL 12 = DSM 16493 5713492 YP_001533929.1 CDS Dshi_2595 NC_009952.1 2759653 2761176 D PFAM: extracellular solute-binding protein family Swiss-Prot: P76128-Putative ABC transporter periplasmic-binding protein yddS [Precursor]; putative extracellular solute-binding protein 2759653..2761176 Dinoroseobacter shibae DFL 12 = DSM 16493 5713493 YP_001533930.1 CDS Dshi_2596 NC_009952.1 2761173 2761856 D PFAM: ABC transporter related SMART: AAA ATPase Swiss-Prot: P33593-Nickel import ATP-binding protein nikD COG0444:ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component; ATPase component; ABC transporter 2761173..2761856 Dinoroseobacter shibae DFL 12 = DSM 16493 5713494 YP_001533931.1 CDS Dshi_2597 NC_009952.1 2761850 2762575 D PFAM: ABC transporter related SMART: AAA ATPase Swiss-Prot: P77622-Uncharacterized ABC transporter ATP-binding protein yddO COG1124: ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component; ATPase component; ABC transporter 2761850..2762575 Dinoroseobacter shibae DFL 12 = DSM 16493 5713495 YP_001533932.1 CDS Dshi_2598 NC_009952.1 2762572 2763510 D PFAM: binding-protein-dependent transport systems inner membrane component Swiss-Prot: P75798-Glutathione transport system permease protein gsiC COG0601: ABC-type dipeptide/oligopeptide/nickel transport systems, permease components; binding-protein-dependent transport system permease 2762572..2763510 Dinoroseobacter shibae DFL 12 = DSM 16493 5713496 YP_001533933.1 CDS Dshi_2599 NC_009952.1 2763494 2764297 D PFAM: binding-protein-dependent transport systems inner membrane component Swiss-Prot: P0AFA9-Nickel transport system permease protein nikC COG0601: ABC-type dipeptide/oligopeptide/nickel transport systems, permease components; binding-protein-dependent transport system permease 2763494..2764297 Dinoroseobacter shibae DFL 12 = DSM 16493 5713497 YP_001533934.1 CDS Dshi_2600 NC_009952.1 2764294 2765190 D PFAM: protein of unknown function DUF6 transmembrane KEGG: rde:RD1_1864 integral membrane protein, putative; hypothetical protein 2764294..2765190 Dinoroseobacter shibae DFL 12 = DSM 16493 5713498 YP_001533935.1 CDS Dshi_2601 NC_009952.1 2765180 2766208 D PFAM: helix-turn-helix- domain containing protein AraC type KEGG: rde:RD1_0249 transcriptional regulator, AraC family, putative; putative transcriptional regulator 2765180..2766208 Dinoroseobacter shibae DFL 12 = DSM 16493 5713499 YP_001533936.1 CDS Dshi_2602 NC_009952.1 2766389 2767594 D Swiss-Prot: Q06319-Acyl-CoA dehydrogenase, short-chain specific PFAM: acyl-CoA dehydrogenase domain protein; Acyl-CoA dehydrogenase type 2 domain KEGG: rde:RD1_0250 acyl-CoA dehydrogenase, putative; acyl-CoA dehydrogenase 2766389..2767594 Dinoroseobacter shibae DFL 12 = DSM 16493 5713500 YP_001533937.1 CDS Dshi_2603 NC_009952.1 2767996 2769831 D Swiss-Prot: O31605-Oligoendopeptidase F homolog TIGRFAM: oligoendopeptidase, pepF/M3 family PFAM: peptidase M3A and M3B thimet/oligopeptidase F; Oligopeptidase F; pepF/M3 family; oligoendopeptidase 2767996..2769831 Dinoroseobacter shibae DFL 12 = DSM 16493 5713501 YP_001533938.1 CDS Dshi_2604 NC_009952.1 2769916 2770317 R Swiss-Prot: P64590-Inner membrane protein yhaH PFAM: protein of unknown function DUF805; similar to inner membrane protein yhaH; hypothetical protein complement(2769916..2770317) Dinoroseobacter shibae DFL 12 = DSM 16493 5713502 YP_001533939.1 CDS Dshi_2605 NC_009952.1 2770330 2770554 R hypothetical protein complement(2770330..2770554) Dinoroseobacter shibae DFL 12 = DSM 16493 5713503 YP_001533940.1 CDS Dshi_2606 NC_009952.1 2770620 2770862 R SMART: zinc finger CDGSH-type domain protein KEGG: rde:RD1_1658 hypothetical protein; hypothetical protein complement(2770620..2770862) Dinoroseobacter shibae DFL 12 = DSM 16493 5713504 YP_001533941.1 CDS Dshi_2607 NC_009952.1 2770982 2771284 R KEGG: sil:SPO0456 hypothetical protein; hypothetical protein complement(2770982..2771284) Dinoroseobacter shibae DFL 12 = DSM 16493 5713505 YP_001533942.1 CDS Dshi_2608 NC_009952.1 2771502 2772488 R Swiss-Prot: P49305-Putative oxidoreductase ORF334 / Q07982-Glucose--fructose oxidoreductase [Precursor] PFAM: oxidoreductase domain protein; Oxidoreductase domain KEGG: sit:TM1040_0565 oxidoreductase-like; putative oxidoreductase complement(2771502..2772488) Dinoroseobacter shibae DFL 12 = DSM 16493 5713506 YP_001533943.1 CDS rpoH2 NC_009952.1 2772541 2773437 R 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 complement(2772541..2773437) Dinoroseobacter shibae DFL 12 = DSM 16493 5713507 YP_001533944.1 CDS rluD NC_009952.1 2773631 2774674 R Swiss-Prot: P33643-Ribosomal large subunit pseudouridine synthase D TIGR00005: pseudouridine synthase, RluA family; ribosomal large subunit pseudouridine synthase D complement(2773631..2774674) Dinoroseobacter shibae DFL 12 = DSM 16493 5713508 YP_001533945.1 CDS Dshi_2611 NC_009952.1 2774718 2775005 D hypothetical protein 2774718..2775005 Dinoroseobacter shibae DFL 12 = DSM 16493 5713509 YP_001533946.1 CDS npdA NC_009952.1 2775209 2775895 R Modulates the activities of several enzymes which are inactive in their acetylated form; NAD-dependent deacetylase complement(2775209..2775895) Dinoroseobacter shibae DFL 12 = DSM 16493 5713510 YP_001533947.1 CDS Dshi_2613 NC_009952.1 2775951 2776406 D Swiss-Prot: O35016-Low molecular weight protein-tyrosine-phosphatase PFAM: low molecular weight phosphotyrosine protein phosphatase KEGG: sil:SPO0979 low molecular weight phosphotyrosine protein phosphatase; low molecular weight protein-tyrosine-phosphatase 2775951..2776406 Dinoroseobacter shibae DFL 12 = DSM 16493 5713511 YP_001533948.1 CDS Dshi_2614 NC_009952.1 2776403 2776708 R KEGG: sit:TM1040_0677 hypothetical protein; hypothetical protein complement(2776403..2776708) Dinoroseobacter shibae DFL 12 = DSM 16493 5713512 YP_001533949.1 CDS Dshi_2615 NC_009952.1 2776824 2777627 R Swiss-Prot: P0AFN6-Inner membrane transport permease yadH PFAM: ABC-2 type transporter KEGG: sil:SPO0957 ABC transporter, permease protein COG1682 : ABC-type polysaccharide/polyol phosphate export systems, permease component; permease component; ABC transporter complement(2776824..2777627) Dinoroseobacter shibae DFL 12 = DSM 16493 5713513 YP_001533950.1 CDS Dshi_2616 NC_009952.1 2777782 2778405 D PFAM: GcrA cell cycle regulator KEGG: jan:Jann_1020 GcrA cell cycle regulator; putative gcrA cell cycle regulator 2777782..2778405 Dinoroseobacter shibae DFL 12 = DSM 16493 5713514 YP_001533951.1 CDS Dshi_2617 NC_009952.1 2778606 2779247 R KEGG: sde:Sde_2877 hypothetical protein; hypothetical protein complement(2778606..2779247) Dinoroseobacter shibae DFL 12 = DSM 16493 5713515 YP_001533952.1 CDS rimO NC_009952.1 2779585 2780955 D catalyzes the methylthiolation of an aspartic acid residue of the S12 protein of the 30S ribosomal subunit; 30S ribosomal protein S12 methylthiotransferase 2779585..2780955 Dinoroseobacter shibae DFL 12 = DSM 16493 5713516 YP_001533953.1 CDS cutA NC_009952.1 2781030 2781365 D Swiss-Prot: P69488-Divalent-cation tolerance protein cutA PFAM: CutA1 divalent ion tolerance protein; putative divalent-cation tolerance protein 2781030..2781365 Dinoroseobacter shibae DFL 12 = DSM 16493 5713517 YP_001533954.1 CDS Dshi_2620 NC_009952.1 2781369 2781725 R KEGG: rde:RD1_3491 hypothetical protein; hypothetical protein complement(2781369..2781725) Dinoroseobacter shibae DFL 12 = DSM 16493 5713518 YP_001533955.1 CDS Dshi_2621 NC_009952.1 2781735 2782070 R KEGG: sil:SPO0942 hypothetical protein; hypothetical protein complement(2781735..2782070) Dinoroseobacter shibae DFL 12 = DSM 16493 5713519 YP_001533956.1 CDS Dshi_2622 NC_009952.1 2782124 2782372 R KEGG: sil:SPO0941 hypothetical protein; hypothetical protein complement(2782124..2782372) Dinoroseobacter shibae DFL 12 = DSM 16493 5713520 YP_001533957.1 CDS Dshi_2623 NC_009952.1 2782469 2783221 R PFAM: peptidase M48 Ste24p KEGG: rde:RD1_1656 peptidase, M48 family, putative; Ste24p; peptidase M48 complement(2782469..2783221) Dinoroseobacter shibae DFL 12 = DSM 16493 5713521 YP_001533958.1 CDS Dshi_2624 NC_009952.1 2783358 2783780 D KEGG: rde:RD1_1657 hypothetical protein; hypothetical protein 2783358..2783780 Dinoroseobacter shibae DFL 12 = DSM 16493 5713522 YP_001533959.1 CDS Dshi_2625 NC_009952.1 2783790 2784044 D KEGG: sil:SPO0938 hypothetical protein; hypothetical protein 2783790..2784044 Dinoroseobacter shibae DFL 12 = DSM 16493 5713523 YP_001533960.1 CDS Dshi_2626 NC_009952.1 2784148 2785326 D Swiss-Prot: P55682-Uncharacterized transporter y4wD PFAM: major facilitator superfamily MFS_1; putative major facilitator superfamily transporter 2784148..2785326 Dinoroseobacter shibae DFL 12 = DSM 16493 5713524 YP_001533961.1 CDS Dshi_2627 NC_009952.1 2785328 2785978 D Swiss-Prot: P0ACY1-Protein ydjA PFAM: nitroreductase KEGG: rsq:Rsph17025_0371 nitroreductase; related to nitroreductase; hypothetical protein 2785328..2785978 Dinoroseobacter shibae DFL 12 = DSM 16493 5713525 YP_001533962.1 CDS Dshi_2628 NC_009952.1 2785975 2786685 D PFAM: Protein of unknown function (DUF540); hypothetical protein 2785975..2786685 Dinoroseobacter shibae DFL 12 = DSM 16493 5713526 YP_001533963.1 CDS Dshi_2629 NC_009952.1 2786713 2787000 R PFAM: protein of unknown function DUF1467 KEGG: sil:SPO0933 hypothetical protein; hypothetical protein complement(2786713..2787000) Dinoroseobacter shibae DFL 12 = DSM 16493 5713527 YP_001533964.1 CDS Dshi_2630 NC_009952.1 2787004 2787408 R PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase Swiss-Prot: P54540-Uncharacterized protein yqjC; putative glyoxalase complement(2787004..2787408) Dinoroseobacter shibae DFL 12 = DSM 16493 5713528 YP_001533965.1 CDS Dshi_2631 NC_009952.1 2787540 2788244 D PFAM: response regulator receiver KEGG: rde:RD1_1178 response regulator, putative; putative response regulator 2787540..2788244 Dinoroseobacter shibae DFL 12 = DSM 16493 5713529 YP_001533966.1 CDS Dshi_2632 NC_009952.1 2788411 2788605 D hypothetical protein 2788411..2788605 Dinoroseobacter shibae DFL 12 = DSM 16493 5713530 YP_001533967.1 CDS aspS NC_009952.1 2788656 2790428 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(2788656..2790428) Dinoroseobacter shibae DFL 12 = DSM 16493 5713531 YP_001533968.1 CDS Dshi_2634 NC_009952.1 2790528 2790977 R hypothetical protein complement(2790528..2790977) Dinoroseobacter shibae DFL 12 = DSM 16493 5713532 YP_001533969.1 CDS Dshi_2635 NC_009952.1 2791005 2791742 D PFAM: pentapeptide repeat protein; hypothetical protein 2791005..2791742 Dinoroseobacter shibae DFL 12 = DSM 16493 5713533 YP_001533970.1 CDS Dshi_2636 NC_009952.1 2791785 2792408 R Swiss-Prot: Q9Z5D7-Bacteriochlorophyll synthase 23 kDa chain (4-vinyl reductase) TIGRFAM: bacteriochlorophyll 4-vinyl reductase PFAM: 4-vinyl reductase 4VR; bacteriochlorophyll synthase complement(2791785..2792408) Dinoroseobacter shibae DFL 12 = DSM 16493 5713534 YP_001533971.1 CDS Dshi_2637 NC_009952.1 2792408 2794051 R Swiss-Prot: Q7X2C7-Anaerobic magnesium-protoporphyrin IX monomethyl ester [oxidative] cyclase (bchE) TIGRFAM: magnesium-protoporphyrin IX monomethyl ester anaerobic oxidative cyclase PFAM: cobalamin B12-binding domain protein; Radical SAM domain protein SMART: Elongator protein 3/MiaB/NifB; putative anaerobic magnesium-protoporphyrin IX monomethyl ester [oxidative] cyclase complement(2792408..2794051) Dinoroseobacter shibae DFL 12 = DSM 16493 5713535 YP_001533972.1 CDS Dshi_2638 NC_009952.1 2794120 2794332 R hypothetical protein complement(2794120..2794332) Dinoroseobacter shibae DFL 12 = DSM 16493 5713536 YP_001533973.1 CDS carB NC_009952.1 2794515 2797832 D 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 2794515..2797832 Dinoroseobacter shibae DFL 12 = DSM 16493 5713537 YP_001533974.1 CDS Dshi_2640 NC_009952.1 2797947 2798738 R hypothetical protein complement(2797947..2798738) Dinoroseobacter shibae DFL 12 = DSM 16493 5713538 YP_001533975.1 CDS tdk NC_009952.1 2798852 2799451 D catalyzes the formation of thymidine 5'-phosphate from thymidine; thymidine kinase 2798852..2799451 Dinoroseobacter shibae DFL 12 = DSM 16493 5713539 YP_001533976.1 CDS Dshi_2642 NC_009952.1 2799448 2800284 R hypothetical protein complement(2799448..2800284) Dinoroseobacter shibae DFL 12 = DSM 16493 5713540 YP_001533977.1 CDS Dshi_2643 NC_009952.1 2800367 2801317 R Swiss-Prot: P36234-Glycerate dehydrogenase; putative glycerate dehydrogenase complement(2800367..2801317) Dinoroseobacter shibae DFL 12 = DSM 16493 5713541 YP_001533978.1 CDS Dshi_2644 NC_009952.1 2801317 2801655 R Swiss-Prot: P37584-Protein csaA TIGRFAM: export-related chaperone CsaA PFAM: t-RNA-binding domain protein; putative export-like chaperone complement(2801317..2801655) Dinoroseobacter shibae DFL 12 = DSM 16493 5713542 YP_001533979.1 CDS proC NC_009952.1 2801659 2802480 R catalyzes the formation of L-proline from pyrroline-5-carboxylate; pyrroline-5-carboxylate reductase complement(2801659..2802480) Dinoroseobacter shibae DFL 12 = DSM 16493 5713543 YP_001533980.1 CDS Dshi_2646 NC_009952.1 2802512 2803042 R PFAM: Protein of unknown function DUF1790 COG5465: Uncharacterized conserved protein; hypothetical protein complement(2802512..2803042) Dinoroseobacter shibae DFL 12 = DSM 16493 5713544 YP_001533981.1 CDS Dshi_2647 NC_009952.1 2803326 2804246 D hypothetical protein 2803326..2804246 Dinoroseobacter shibae DFL 12 = DSM 16493 5713545 YP_001533982.1 CDS Dshi_2648 NC_009952.1 2804249 2804491 R PFAM: protein of unknown function DUF526 COG2960: Uncharacterized protein conserved in bacteria; hypothetical protein complement(2804249..2804491) Dinoroseobacter shibae DFL 12 = DSM 16493 5713546 YP_001533983.1 CDS lgt NC_009952.1 2804601 2805491 D transfers the N-acyl diglyceride moiety to the prospective N-terminal cysteine in prolipoprotein; prolipoprotein diacylglyceryl transferase 2804601..2805491 Dinoroseobacter shibae DFL 12 = DSM 16493 5713547 YP_001533984.1 CDS Dshi_2650 NC_009952.1 2805488 2806579 D PFAM: protein of unknown function DUF185 COG1565: Uncharacterized conserved protein; hypothetical protein 2805488..2806579 Dinoroseobacter shibae DFL 12 = DSM 16493 5713548 YP_001533985.1 CDS Dshi_2651 NC_009952.1 2806576 2807334 D PFAM: protein of unknown function DUF152 TIGR00726: conserved hypothetical protein TIGR00726; hypothetical protein 2806576..2807334 Dinoroseobacter shibae DFL 12 = DSM 16493 5713549 YP_001533986.1 CDS Dshi_2652 NC_009952.1 2807834 2808538 D KEGG: sil:SPO0905 hypothetical protein; hypothetical protein 2807834..2808538 Dinoroseobacter shibae DFL 12 = DSM 16493 5713550 YP_001533987.1 CDS Dshi_2653 NC_009952.1 2808558 2809058 R Swiss-Prot: P0ACJ0-Leucine-responsive regulatory protein PFAM: regulatory protein AsnC/Lrp family KEGG: rsq:Rsph17025_0257 putative transcriptional regulator, AsnC family; putative leucine-responsive regulatory protein complement(2808558..2809058) Dinoroseobacter shibae DFL 12 = DSM 16493 5713551 YP_001533988.1 CDS trxB NC_009952.1 2809223 2810221 D Swiss-Prot: P0A9P4-Thioredoxin reductase TIGRFAM: thioredoxin reductase PFAM: FAD-dependent pyridine nucleotide-disulphide oxidoreductase; glucose-inhibited division protein A; thioredoxin reductase 2809223..2810221 Dinoroseobacter shibae DFL 12 = DSM 16493 5713552 YP_001533989.1 CDS ccpA NC_009952.1 2810268 2811320 R Swiss-Prot: P14532-Cytochrome c551 peroxidase [Precursor] PFAM: Di-haem cytochrome c peroxidase KEGG: sil:SPO0330 cytochrome c peroxidase COG1858: Cytochrome c peroxidase; cytochrome-c peroxidase complement(2810268..2811320) Dinoroseobacter shibae DFL 12 = DSM 16493 5713553 YP_001533990.1 CDS Dshi_2656 NC_009952.1 2811577 2813652 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 2811577..2813652 Dinoroseobacter shibae DFL 12 = DSM 16493 5713554 YP_001533991.1 CDS Dshi_2657 NC_009952.1 2813746 2814336 R hypothetical protein complement(2813746..2814336) Dinoroseobacter shibae DFL 12 = DSM 16493 5713555 YP_001533992.1 CDS Dshi_2658 NC_009952.1 2814514 2815302 R Swiss-Prot: P19920-Carbon monoxide dehydrogenase medium chain coxM; PFAM: molybdopterin dehydrogenase FAD-binding COG1319: Aerobic-type carbon monoxide dehydrogenase, middle subunit CoxM/CutM homologs; medium chain; putative carbon monoxide dehydrogenase complement(2814514..2815302) Dinoroseobacter shibae DFL 12 = DSM 16493 5713556 YP_001533993.1 CDS coxL1 NC_009952.1 2815351 2817726 R Swiss-Prot: P19919-Carbon monoxide dehydrogenase large chain coxL TIGR02416: carbon-monoxide dehydrogenase, large subunit PFAM: aldehyde oxidase and xanthine dehydrogenase a/b hammerhead; aldehyde oxidase and xanthine dehydrogenase molybdopterin binding COG1529: Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs; carbon monoxide dehydrogenase complement(2815351..2817726) Dinoroseobacter shibae DFL 12 = DSM 16493 5713557 YP_001533994.1 CDS Dshi_2660 NC_009952.1 2817800 2818288 R Swiss-Prot: P19921-Carbon monoxide dehydrogenase small chain coxS PFAM: ferredoxin; [2Fe-2S]-binding domain protein COG2080: Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs; small chain; putative carbon monoxide dehydrogenase complement(2817800..2818288) Dinoroseobacter shibae DFL 12 = DSM 16493 5713558 YP_001533995.1 CDS Dshi_2661 NC_009952.1 2818337 2818867 R PFAM: carbon monoxide dehydrogenase subunit G COG3427: Uncharacterized conserved protein; subunit G; putative carbon monoxide dehydrogenase complement(2818337..2818867) Dinoroseobacter shibae DFL 12 = DSM 16493 5713559 YP_001533996.1 CDS Dshi_2662 NC_009952.1 2818944 2819846 R PFAM: Bacterial extracellular solute-binding proteins, family 3 SMART: extracellular solute-binding protein family; similar to extracellular solute-binding protein (family 3); hypothetical protein complement(2818944..2819846) Dinoroseobacter shibae DFL 12 = DSM 16493 5713560 YP_001533997.1 CDS Dshi_2663 NC_009952.1 2819920 2820594 R PS51007: CYTC SSF46626: Cytochrome_c KEGG: sil:SPO1515 cytochrome c550, putative; related to cytochrome c; hypothetical protein complement(2819920..2820594) Dinoroseobacter shibae DFL 12 = DSM 16493 5713561 YP_001533998.1 CDS Dshi_2664 NC_009952.1 2820907 2822067 D KEGG: sil:SPO1514 hypothetical protein; hypothetical protein 2820907..2822067 Dinoroseobacter shibae DFL 12 = DSM 16493 5713562 YP_001533999.1 CDS Dshi_2665 NC_009952.1 2822130 2823107 D TIGRFAM: 40-residue YVTN family beta-propeller repeat protein KEGG: sil:SPO1513 hypothetical protein; hypothetical protein 2822130..2823107 Dinoroseobacter shibae DFL 12 = DSM 16493 5713563 YP_001534000.1 CDS Dshi_2666 NC_009952.1 2823214 2823660 D hypothetical protein 2823214..2823660 Dinoroseobacter shibae DFL 12 = DSM 16493 5713564 YP_001534001.1 CDS Dshi_2667 NC_009952.1 2823667 2824386 D Swiss-Prot: P0A9U1-Uncharacterized ABC transporter ATP-binding protein ybhF PFAM: ABC transporter related SMART: AAA ATPase; ATP-binding protein; ABC transporter 2823667..2824386 Dinoroseobacter shibae DFL 12 = DSM 16493 5713565 YP_001534002.1 CDS Dshi_2668 NC_009952.1 2824868 2825659 D PFAM: ABC-2 type transporter Swiss-Prot: P0AFP9-Inner membrane transport permease ybhR KEGG: sil:SPO1510 efflux ABC transporter, permease protein; permease component; putative ABC-2 type transporter 2824868..2825659 Dinoroseobacter shibae DFL 12 = DSM 16493 5713566 YP_001534003.1 CDS Dshi_2669 NC_009952.1 2825706 2826251 D hypothetical protein 2825706..2826251 Dinoroseobacter shibae DFL 12 = DSM 16493 5713567 YP_001534004.1 CDS Dshi_2670 NC_009952.1 2826191 2826901 R PFAM: ABC transporter related SMART: AAA ATPase Swiss-Prot: Q47538-Taurine import ATP-binding protein tauB / P0AAI1-Aliphatic sulfonates import ATP-binding protein ssuB; COG1116: ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component; ATP-binding protein; ABC transporter complement(2826191..2826901) Dinoroseobacter shibae DFL 12 = DSM 16493 5713568 YP_001534005.1 CDS Dshi_2671 NC_009952.1 2826918 2827889 R SSF53850: Periplasmic binding protein-like II COG0715: ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components; similar to periplasmic binding protein; hypothetical protein complement(2826918..2827889) Dinoroseobacter shibae DFL 12 = DSM 16493 5713569 YP_001534006.1 CDS Dshi_2672 NC_009952.1 2828064 2828483 D PFAM: cytochrome c class I KEGG: sil:SPO1509 cytochrome c family protein; cytochrome c class I; hypothetical protein 2828064..2828483 Dinoroseobacter shibae DFL 12 = DSM 16493 5713570 YP_001534007.1 CDS exaA NC_009952.1 2828781 2830547 D Swiss-Prot: Q9Z4J7-Quinoprotein ethanol dehydrogenase [Precursor] PFAM: Pyrrolo-quinoline quinone SSF50998: Quinonprotein alcohol dehydrogenase-like KEGG: sil:SPO1508 quinoprotein ethanol dehydrogenase; quinoprotein ethanol dehydrogenase 2828781..2830547 Dinoroseobacter shibae DFL 12 = DSM 16493 5713571 YP_001534008.1 CDS Dshi_2674 NC_009952.1 2830905 2831591 D PFAM: regulatory protein LuxR; response regulator receiver KEGG: rsp:RSP_2882 two component transcriptional regulator, LuxR family Swiss-Prot: P0AF28-Nitrate/nitrite response regulator protein narL; LuxR family; two component transcriptional regulator 2830905..2831591 Dinoroseobacter shibae DFL 12 = DSM 16493 5713572 YP_001534009.1 CDS Dshi_2675 NC_009952.1 2831646 2832845 D PFAM: domain of unknown function DUF1745 COG3287- Uncharacterized conserved protein; hypothetical protein 2831646..2832845 Dinoroseobacter shibae DFL 12 = DSM 16493 5713573 YP_001534010.1 CDS Dshi_2676 NC_009952.1 2832817 2834847 D PFAM: response regulator receiver; ATP-binding region ATPase domain protein; histidine kinase A domain protein; histidine kinase 2832817..2834847 Dinoroseobacter shibae DFL 12 = DSM 16493 5713574 YP_001534011.1 CDS Dshi_2677 NC_009952.1 2834844 2835545 R PFAM: lipolytic protein G-D-S-L family; G-D-S-L family; lipolytic protein complement(2834844..2835545) Dinoroseobacter shibae DFL 12 = DSM 16493 5713575 YP_001534012.1 CDS Dshi_2678 NC_009952.1 2835568 2836272 D Swiss-Prot: P0A9T8-Uncharacterized ABC transporter ATP-binding protein ybbA PFAM: ABC transporter related SMART: AAA ATPase; ATP-binding protein; ABC transporter 2835568..2836272 Dinoroseobacter shibae DFL 12 = DSM 16493 5713576 YP_001534013.1 CDS Dshi_2679 NC_009952.1 2836269 2838797 D PFAM: protein of unknown function DUF214 COG3127: Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component Swiss-Prot: P77504-Uncharacterized ABC transporter permease ybbP; putative ABC transporter permease 2836269..2838797 Dinoroseobacter shibae DFL 12 = DSM 16493 5713577 YP_001534014.1 CDS gcvP NC_009952.1 2839208 2842072 R acts in conjunction with GvcH to form H-protein-S-aminomethyldihydrolipoyllysine from glycine; glycine dehydrogenase complement(2839208..2842072) Dinoroseobacter shibae DFL 12 = DSM 16493 5713578 YP_001534015.1 CDS gcvH NC_009952.1 2842164 2842532 R part of multienzyme complex composed of H, L, P, and T proteins which catalyzes oxidation of glycine to yield carbon dioxide, ammonia, 5,10-CH2-H4folate and a reduced pyridine nucleotide; protein H is involved in transfer of methylamine group from the P to T protein; covalently bound to a lipoyl cofactor; glycine cleavage system protein H complement(2842164..2842532) Dinoroseobacter shibae DFL 12 = DSM 16493 5713579 YP_001534016.1 CDS gcvT2 NC_009952.1 2842546 2843631 R Swiss-Prot: P54378-Aminomethyltransferase TIGRFAM: glycine cleavage system T protein PFAM: glycine cleavage T protein (aminomethyl transferase); Glycine cleavage T-protein barrel; aminomethyltransferase, glycine cleavage system T protein complement(2842546..2843631) Dinoroseobacter shibae DFL 12 = DSM 16493 5713580 YP_001534017.1 CDS mro NC_009952.1 2843824 2844828 D Swiss-Prot: P05149-aldose 1-epimerase [Precursor] PFAM: Aldose 1-epimerase; aldose 1-epimerase 2843824..2844828 Dinoroseobacter shibae DFL 12 = DSM 16493 5713581 YP_001534018.1 CDS Dshi_2684 NC_009952.1 2844910 2845275 R Swiss-Prot: Q92UG5-Putative transthyretin-like protein RB1166 TIGRFAM: Hydroxyisourate hydrolase PFAM: Transthyretin; putative transthyretin-like protein complement(2844910..2845275) Dinoroseobacter shibae DFL 12 = DSM 16493 5713582 YP_001534019.1 CDS gap3 NC_009952.1 2845670 2846659 R Swiss-Prot: P09124-Glyceraldehyde-3-phosphate dehydrogenase 1 PFAM: glyceraldehyde 3-phosphate dehydrogenase TIGR01534 glyceraldehyde-3-phosphate dehydrogenase, type I; phosphorylating; glyceraldehyde-3-phosphate dehydrogenase complement(2845670..2846659) Dinoroseobacter shibae DFL 12 = DSM 16493 5713583 YP_001534020.1 CDS Dshi_2686 NC_009952.1 2846962 2847378 D Swiss-Prot: P37903-Universal stress protein F PFAM: UspA domain protein KEGG: sit:TM1040_2126 UspA; universal stress protein 2846962..2847378 Dinoroseobacter shibae DFL 12 = DSM 16493 5713584 YP_001534021.1 CDS Dshi_2687 NC_009952.1 2847605 2848090 D Swiss-Prot: P19567-Pseudoazurin [Precursor] TIGR02375# pseudoazurin; putative pseudoazurin 2847605..2848090 Dinoroseobacter shibae DFL 12 = DSM 16493 5713585 YP_001534022.1 CDS appC NC_009952.1 2848368 2849762 D Swiss-Prot: P26459-Cytochrome bd-II oxidase subunit 1 PFAM: cytochrome bd ubiquinol oxidase subunit I; cytochrome bd-II oxidase subunit 1 2848368..2849762 Dinoroseobacter shibae DFL 12 = DSM 16493 5713586 YP_001534023.1 CDS cydB NC_009952.1 2849767 2850780 D Swiss-Prot: P0ABK2-Cytochrome d ubiquinol oxidase subunit 2 TIGR00203: cytochrome d oxidase, subunit II (cydB) PFAM: cytochrome bd ubiquinol oxidase subunit II; cytochrome bd-I oxidase subunit II 2849767..2850780 Dinoroseobacter shibae DFL 12 = DSM 16493 5713587 YP_001534024.1 CDS Dshi_2690 NC_009952.1 2850801 2851355 R KEGG: jan:Jann_3427 hypothetical protein; hypothetical protein complement(2850801..2851355) Dinoroseobacter shibae DFL 12 = DSM 16493 5713588 YP_001534025.1 CDS Dshi_2691 NC_009952.1 2851499 2852269 D Swiss-Prot: P0AC84-Probable hydroxyacylglutathione hydrolase ( Glyoxalase II) PFAM: beta-lactamase domain protein KEGG: mlo:mlr3546 putative glyoxalase II; putative hydroxyacylglutathione hydrolase 2851499..2852269 Dinoroseobacter shibae DFL 12 = DSM 16493 5713589 YP_001534026.1 CDS Dshi_2692 NC_009952.1 2852282 2853010 R PFAM: protein of unknown function DUF1194; hypothetical protein complement(2852282..2853010) Dinoroseobacter shibae DFL 12 = DSM 16493 5713590 YP_001534027.1 CDS Dshi_2693 NC_009952.1 2853046 2853459 R PFAM: protein of unknown function DUF606 COG3238: Uncharacterized protein conserved in bacteria; hypothetical protein complement(2853046..2853459) Dinoroseobacter shibae DFL 12 = DSM 16493 5713591 YP_001534028.1 CDS Dshi_2694 NC_009952.1 2853623 2854024 D SSF46626: Cytochrome c superfamily PS51007: CYTC (Cytochrome c family profile); putative cytochrome c family protein 2853623..2854024 Dinoroseobacter shibae DFL 12 = DSM 16493 5713592 YP_001534029.1 CDS Dshi_2695 NC_009952.1 2854595 2855953 D Swiss-Prot: P27017-Aliphatic amidase expression-regulating protein amiC COG0683: ABC-type branched-chain amino acid transport systems, periplasmic component SSF53822: Periplasmic binding protein-like I superfamily; putative aliphatic amidase expression-regulating protein 2854595..2855953 Dinoroseobacter shibae DFL 12 = DSM 16493 5713594 YP_001534030.1 CDS Dshi_2696 NC_009952.1 2856015 2857679 D Swiss-Prot: P0AEX7-High-affinity branched-chain amino acid transport system permease protein livH PFAM: inner-membrane translocator SMART: PBS lyase HEAT domain protein repeat-containing protein; inner-membrane translocator 2856015..2857679 Dinoroseobacter shibae DFL 12 = DSM 16493 5713595 YP_001534031.1 CDS Dshi_2697 NC_009952.1 2857981 2859084 D Swiss-Prot: P22729-High-affinity branched-chain amino acid transport system permease protein livM PFAM: inner-membrane translocator; permease protein; putative high-affinity branched-chain amino acid transport system 2857981..2859084 Dinoroseobacter shibae DFL 12 = DSM 16493 5713596 YP_001534032.1 CDS Dshi_2698 NC_009952.1 2859081 2859818 D Swiss-Prot: P0A9S7-High-affinity branched-chain amino acid transport ATP-binding protein livG PFAM: ABC transporter related SMART: AAA ATPase COG4674: Uncharacterized ABC-type transport system, ATPase component; putative high-affinity branched-chain amino acid transport ATP-binding protein 2859081..2859818 Dinoroseobacter shibae DFL 12 = DSM 16493 5713597 YP_001534033.1 CDS Dshi_2699 NC_009952.1 2859820 2860515 D Swiss-Prot: P22731-High-affinity branched-chain amino acid transport ATP-binding protein livF PFAM: ABC transporter related SMART: AAA ATPase COG0410: ABC-type branched-chain amino acid transport systems, ATPase component; putative high-affinity branched-chain amino acid transport ATP-binding protein 2859820..2860515 Dinoroseobacter shibae DFL 12 = DSM 16493 5713598 YP_001534034.1 CDS dhlB NC_009952.1 2860992 2861681 D Swiss-Prot: Q60099-(S)-2-haloacid dehalogenase TIGRFAM: haloacid dehalogenase, type II; HAD-superfamily hydrolase, subfamily IA, variant 2 (HAD-like) PFAM: Haloacid dehalogenase domain protein hydrolase; (S)-2-haloacid dehalogenase 2860992..2861681 Dinoroseobacter shibae DFL 12 = DSM 16493 5713599 YP_001534035.1 CDS Dshi_2701 NC_009952.1 2861681 2862505 D PFAM: alpha/beta hydrolase fold KEGG: rsh:Rsph17029_0927 alpha/beta hydrolase fold; alpha/beta hydrolase superfamily; putative hydrolase / acyltransferase 2861681..2862505 Dinoroseobacter shibae DFL 12 = DSM 16493 5713600 YP_001534036.1 CDS Dshi_2702 NC_009952.1 2862502 2863494 D Swiss-Prot: P0AGF6-Threonine dehydratase catabolic tdcB PFAM: Pyridoxal-5-phosphate-dependent protein beta subunit; catabolic; putative threonine dehydratase 2862502..2863494 Dinoroseobacter shibae DFL 12 = DSM 16493 5713601 YP_001534037.1 CDS Dshi_2703 NC_009952.1 2863568 2863975 R KEGG: rde:RD1_0908 hypothetical protein; hypothetical protein complement(2863568..2863975) Dinoroseobacter shibae DFL 12 = DSM 16493 5713602 YP_001534038.1 CDS hemC NC_009952.1 2864136 2865179 R transformation of porphobilinogen to hydroxymethylbilane in porphyrin biosynthesis; porphobilinogen deaminase complement(2864136..2865179) Dinoroseobacter shibae DFL 12 = DSM 16493 5713603 YP_001534039.1 CDS hemE NC_009952.1 2865197 2866231 D catalyzes the formation of coproporphyrinogen from uroporphyrinogen III; uroporphyrinogen decarboxylase 2865197..2866231 Dinoroseobacter shibae DFL 12 = DSM 16493 5713604 YP_001534040.1 CDS Dshi_2706 NC_009952.1 2866405 2867619 D Swiss-Prot: P21503-Uncharacterized MFS-type transporter ycaD PFAM: major facilitator superfamily MFS_1; putative major facilitator superfamily transporter 2866405..2867619 Dinoroseobacter shibae DFL 12 = DSM 16493 5713605 YP_001534041.1 CDS metG NC_009952.1 2867674 2869392 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 2867674..2869392 Dinoroseobacter shibae DFL 12 = DSM 16493 5713606 YP_001534042.1 CDS Dshi_2708 NC_009952.1 2869501 2871093 D TIGRFAM: PAS sensor protein PFAM: response regulator receiver; ATP-binding region ATPase domain protein; histidine kinase A domain protein; PAS fold-3 domain protein; PAS fold-4 domain protein; PAS fold domain protein SMART: PAS domain containing protein; sensor hybrid histidine kinase 2869501..2871093 Dinoroseobacter shibae DFL 12 = DSM 16493 5713607 YP_001534043.1 CDS msrB1 NC_009952.1 2871102 2871578 R Swiss-Prot: Q92RA4-Peptide methionine sulfoxide reductase msrB 1 TIGRFAM: methionine-R-sulfoxide reductase PFAM: Methionine sulfoxide reductase B; peptide methionine sulfoxide reductase complement(2871102..2871578) Dinoroseobacter shibae DFL 12 = DSM 16493 5713608 YP_001534044.1 CDS Dshi_2710 NC_009952.1 2871715 2872920 D PFAM: HI0933 family protein; FAD dependent oxidoreductase TIGR00275: conserved hypothetical protein SSF51905: FAD/NAD(P)-binding domain superfamily; hypothetical protein 2871715..2872920 Dinoroseobacter shibae DFL 12 = DSM 16493 5713609 YP_001534045.1 CDS cobS2 NC_009952.1 2873040 2874023 D Swiss-Prot: P29933-Aerobic cobaltochelatase subunit cobS TIGRFAM: cobalt chelatase, pCobS small subunit PFAM: ATPase associated with various cellular activities AAA_5; aerobic cobaltochelatase subunit cobS 2873040..2874023 Dinoroseobacter shibae DFL 12 = DSM 16493 5713610 YP_001534046.1 CDS Dshi_2712 NC_009952.1 2874084 2874764 R Swiss-Prot: Q05197-Phosphatidylethanolamine N-methyltransferase [predicted] PFAM: UbiE/COQ5 methyltransferase; Methyltransferase type 11; Methyltransferase type 12; putative phosphatidylethanolamine N-methyltransferase complement(2874084..2874764) Dinoroseobacter shibae DFL 12 = DSM 16493 5713611 YP_001534047.1 CDS Dshi_2713 NC_009952.1 2874781 2875530 R Swiss-Prot: Q9ZBM2- CDP-diacylglycerol--serine O-phosphatidyltransferase TIGRFAM: CDP-diacylglycerol--serine O-phosphatidyltransferase PFAM: CDP-alcohol phosphatidyltransferase; putative CDP-diacylglycerol--serine O-phosphatidyltransferase complement(2874781..2875530) Dinoroseobacter shibae DFL 12 = DSM 16493 5713612 YP_001534048.1 CDS psd NC_009952.1 2875527 2876204 R catalyzes the decarboxylaton of phospatidyl-L-sering to phosphatidylethanolamine; phosphatidylserine decarboxylase complement(2875527..2876204) Dinoroseobacter shibae DFL 12 = DSM 16493 5713613 YP_001534049.1 CDS Dshi_2715 NC_009952.1 2876659 2877963 D Swiss-Prot: P25888-Putative ATP-dependent RNA helicase rhlE PFAM: helicase domain protein; DEAD/DEAH box helicase domain protein SMART: DEAD-like helicases; putative ATP-dependent RNA helicase 2876659..2877963 Dinoroseobacter shibae DFL 12 = DSM 16493 5713614 YP_001534050.1 CDS Dshi_2716 NC_009952.1 2878109 2878555 R hypothetical protein complement(2878109..2878555) Dinoroseobacter shibae DFL 12 = DSM 16493 5713615 YP_001534051.1 CDS Dshi_2717 NC_009952.1 2878689 2879210 D hypothetical protein 2878689..2879210 Dinoroseobacter shibae DFL 12 = DSM 16493 5713616 YP_001534052.1 CDS Dshi_2718 NC_009952.1 2879224 2879460 D SMART: Helix-turn-helix XRE-family like proteins; XRE family; putative transcriptional regulator 2879224..2879460 Dinoroseobacter shibae DFL 12 = DSM 16493 5713617 YP_001534053.1 CDS cobT1 NC_009952.1 2879516 2881390 D Swiss-Prot: P29934-Aerobic cobaltochelatase subunit cobT TIGR01651: cobaltochelatase, CobT subunit PFAM: Cobalt chelatase CobT subunit SMART: von Willebrand factor type A; aerobic cobaltochelatase subunit cobT 2879516..2881390 Dinoroseobacter shibae DFL 12 = DSM 16493 5713618 YP_001534054.1 CDS Dshi_2720 NC_009952.1 2881448 2882575 D PFAM: Endonuclease/exonuclease/phosphatase; putative endonuclease/exonuclease/phosphatase 2881448..2882575 Dinoroseobacter shibae DFL 12 = DSM 16493 5713619 YP_001534055.1 CDS Dshi_2721 NC_009952.1 2882651 2884507 D PFAM: creatinase; peptidase M24; putative metallopeptidase 2882651..2884507 Dinoroseobacter shibae DFL 12 = DSM 16493 5713620 YP_001534056.1 CDS Dshi_2722 NC_009952.1 2884592 2884933 D PFAM: protein of unknown function DUF427 COG2343: Uncharacterized protein conserved in bacteria; hypothetical protein 2884592..2884933 Dinoroseobacter shibae DFL 12 = DSM 16493 5713621 YP_001534057.1 CDS Dshi_2723 NC_009952.1 2885147 2885776 R TIGR00997: intracellular septation protein A PFAM: Intracellular septation protein A; intracellular septation protein A complement(2885147..2885776) Dinoroseobacter shibae DFL 12 = DSM 16493 5713622 YP_001534058.1 CDS Dshi_2724 NC_009952.1 2885773 2886675 R PFAM: protein of unknown function DUF6 transmembrane; hypothetical protein complement(2885773..2886675) Dinoroseobacter shibae DFL 12 = DSM 16493 5713623 YP_001534059.1 CDS Dshi_2725 NC_009952.1 2886699 2888198 R Swiss-Prot: P10121-Cell division protein ftsY TIGRFAM: signal recognition particle-docking protein FtsY PFAM: GTP-binding signal recognition particle SRP54 G- domain SMART: AAA ATPase; related to cell division protein ftsY; hypothetical protein complement(2886699..2888198) Dinoroseobacter shibae DFL 12 = DSM 16493 5713624 YP_001534060.1 CDS Dshi_2726 NC_009952.1 2888326 2888730 D hypothetical protein 2888326..2888730 Dinoroseobacter shibae DFL 12 = DSM 16493 5713625 YP_001534061.1 CDS xseA NC_009952.1 2888799 2890370 R Swiss-Prot: Q1GF88-Exodeoxyribonuclease 7 large subunit; exodeoxyribonuclease 7 large subunit complement(2888799..2890370) Dinoroseobacter shibae DFL 12 = DSM 16493 5713626 YP_001534062.1 CDS purD NC_009952.1 2890448 2891710 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 2890448..2891710 Dinoroseobacter shibae DFL 12 = DSM 16493 5713627 YP_001534063.1 CDS Dshi_2729 NC_009952.1 2891789 2892655 D PFAM: Ion transport 2 domain protein; putative ion transport protein 2891789..2892655 Dinoroseobacter shibae DFL 12 = DSM 16493 5713628 YP_001534064.1 CDS Dshi_2730 NC_009952.1 2892698 2893456 R hypothetical protein complement(2892698..2893456) Dinoroseobacter shibae DFL 12 = DSM 16493 5713629 YP_001534065.1 CDS Dshi_2731 NC_009952.1 2893456 2893779 R Swiss-Prot: P80306-Ferredoxin-6 PFAM: ferredoxin; ferredoxin complement(2893456..2893779) Dinoroseobacter shibae DFL 12 = DSM 16493 5713630 YP_001534066.1 CDS Dshi_2732 NC_009952.1 2893851 2894264 D PFAM: nucleic acid binding OB-fold tRNA/helicase-type COG0587: DNA polymerase III, alpha subunit; associated with nucleic acid binding; hypothetical protein 2893851..2894264 Dinoroseobacter shibae DFL 12 = DSM 16493 5713631 YP_001534067.1 CDS degP NC_009952.1 2894377 2895882 R Swiss-Prot: P0C0V0-Protease do [Precursor] TIGR02037: periplasmic serine protease, Do/DeqQ family PFAM: peptidase S1 and S6 chymotrypsin/Hap; PDZ/DHR/GLGF domain protein; protease do complement(2894377..2895882) Dinoroseobacter shibae DFL 12 = DSM 16493 5713632 YP_001534068.1 CDS Dshi_2734 NC_009952.1 2896047 2896241 R hypothetical protein complement(2896047..2896241) Dinoroseobacter shibae DFL 12 = DSM 16493 5713633 YP_001534069.1 CDS hflC NC_009952.1 2896241 2897134 R Swiss-Prot: P0ABC3-Protein hflC TIGRFAM: HflC protein PFAM: band 7 protein; colocated with hflK; protein hflC complement(2896241..2897134) Dinoroseobacter shibae DFL 12 = DSM 16493 5713634 YP_001534070.1 CDS hflK NC_009952.1 2897134 2898282 R Swiss-Prot: P0ABC7-Protein hflK TIGRFAM: HflK protein; colocated with hflC; Protein HflK complement(2897134..2898282) Dinoroseobacter shibae DFL 12 = DSM 16493 5713635 YP_001534071.1 CDS gor NC_009952.1 2898349 2899800 R Swiss-Prot: P06715-Glutathione reductase PFAM: FAD-dependent pyridine nucleotide-disulphide oxidoreductase; pyridine nucleotide-disulphide oxidoreductase dimerisation region; glutathione reductase complement(2898349..2899800) Dinoroseobacter shibae DFL 12 = DSM 16493 5713636 YP_001534072.1 CDS rpiA NC_009952.1 2899846 2900628 R Catalyzes D-ribose 5-phosphate --> D-ribulose 5-phosphate in the nonoxidative branch of the pentose phosphate pathway; ribose-5-phosphate isomerase A complement(2899846..2900628) Dinoroseobacter shibae DFL 12 = DSM 16493 5713637 YP_001534073.1 CDS Dshi_2739 NC_009952.1 2900734 2901423 R TIGRFAM: thiamine pyrophosphokinase PFAM: Thiamin pyrophosphokinase catalytic region; putative thiamine pyrophosphokinase complement(2900734..2901423) Dinoroseobacter shibae DFL 12 = DSM 16493 5713638 YP_001534074.1 CDS Dshi_2740 NC_009952.1 2901566 2903512 D PFAM: herpesvirus transcription activation factor; related to transactivator; hypothetical protein 2901566..2903512 Dinoroseobacter shibae DFL 12 = DSM 16493 5713639 YP_001534075.1 CDS Dshi_2741 NC_009952.1 2903555 2903791 R Swiss-Prot: P45566-Uncharacterized protein yhdT; hypothetical protein complement(2903555..2903791) Dinoroseobacter shibae DFL 12 = DSM 16493 5713640 YP_001534076.1 CDS purA NC_009952.1 2903816 2905111 R catalyzes the formation of N6-(1,2,-dicarboxyethyl)-AMP from L-aspartate, inosine monophosphate and GTP in AMP biosynthesis; adenylosuccinate synthetase complement(2903816..2905111) Dinoroseobacter shibae DFL 12 = DSM 16493 5713641 YP_001534077.1 CDS secG NC_009952.1 2905312 2905680 D TIGRFAM: preprotein translocase, SecG subunit PFAM: Preprotein translocase SecG subunit; SecG subunit; preprotein translocase subunit SecG 2905312..2905680 Dinoroseobacter shibae DFL 12 = DSM 16493 5713642 YP_001534078.1 CDS pyrG NC_009952.1 2905872 2907515 D 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 2905872..2907515 Dinoroseobacter shibae DFL 12 = DSM 16493 5713643 YP_001534079.1 CDS Dshi_2745 NC_009952.1 2907576 2908436 D Swiss-Prot: P37757-Uncharacterized isomerase yddE TIGRFAM: phenazine biosynthesis protein PhzF family PFAM: Phenazine biosynthesis PhzC/PhzF protein; isomerase 2907576..2908436 Dinoroseobacter shibae DFL 12 = DSM 16493 5713644 YP_001534080.1 CDS Dshi_2746 NC_009952.1 2908468 2908728 R KEGG: rde:RD1_1231 hypothetical protein; hypothetical protein complement(2908468..2908728) Dinoroseobacter shibae DFL 12 = DSM 16493 5713645 YP_001534081.1 CDS Dshi_2747 NC_009952.1 2908850 2909440 D KEGG: sil:SPO0431 hypothetical protein; hypothetical protein 2908850..2909440 Dinoroseobacter shibae DFL 12 = DSM 16493 5713646 YP_001534082.1 CDS gltX NC_009952.1 2909448 2910770 R Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation; glutamyl-tRNA synthetase complement(2909448..2910770) Dinoroseobacter shibae DFL 12 = DSM 16493 5713647 YP_001534083.1 CDS Dshi_2749 NC_009952.1 2910830 2912143 R Swiss-Prot: PFAM: Di-haem cytochrome c peroxidase COG1858: Cytochrome c peroxidase Swiss-Prot: [predicted] Q51658-Methylamine utilization protein mauG [Precursor] P37197-Probable cytochrome c peroxidase; putative cytochrome c peroxidase complement(2910830..2912143) Dinoroseobacter shibae DFL 12 = DSM 16493 5713648 YP_001534084.1 CDS Dshi_2750 NC_009952.1 2912622 2913089 D hypothetical protein 2912622..2913089 Dinoroseobacter shibae DFL 12 = DSM 16493 5713649 YP_001534085.1 CDS Dshi_2751 NC_009952.1 2913448 2913789 R hypothetical protein complement(2913448..2913789) Dinoroseobacter shibae DFL 12 = DSM 16493 5713650 YP_001534086.1 CDS Dshi_2752 NC_009952.1 2913824 2914882 R Swiss-Prot: P44542-Sialic acid-binding periplasmic protein siaP [Precursor] PFAM: TRAP dicarboxylate transporter- DctP subunit COG1638: TRAP-type C4-dicarboxylate transport system, periplasmic component; colocated with DctQ & DctM subunits; DctP subunit; TRAP dicarboxylate transporter complement(2913824..2914882) Dinoroseobacter shibae DFL 12 = DSM 16493 5713651 YP_001534087.1 CDS Dshi_2753 NC_009952.1 2914929 2916218 R Swiss-Prot: P44543-Sialic acid TRAP transporter permease protein TIGRFAM: TRAP dicarboxylate transporter, DctM subunit PFAM: Citrate transporter; TRAP C4-dicarboxylate transport system permease DctM subunit; colocated with DctQ & DctP subunit; DctM subunit; TRAP dicarboxylate transporter complement(2914929..2916218) Dinoroseobacter shibae DFL 12 = DSM 16493 5713652 YP_001534088.1 CDS Dshi_2754 NC_009952.1 2916220 2916810 R Swiss-Prot: P44994-Putative TRAP transporter small permease protein HI1030 PFAM: Tripartite ATP-independent periplasmic transporter DctQ component; colocated with DctM & DctP subunits; DctQ component; tripartite ATP-independent periplasmic transporter complement(2916220..2916810) Dinoroseobacter shibae DFL 12 = DSM 16493 5713653 YP_001534089.1 CDS Dshi_2755 NC_009952.1 2916877 2917410 R Swiss-Prot: P54990-Nitrilotriacetate monooxygenase component B PFAM: flavin reductase domain protein FMN-binding; FMN-binding; flavin reductase domain-containing protein complement(2916877..2917410) Dinoroseobacter shibae DFL 12 = DSM 16493 5713654 YP_001534090.1 CDS Dshi_2756 NC_009952.1 2917412 2918302 R Swiss-Prot: P42972-Uncharacterized oxidoreductase ycsN PFAM: aldo/keto reductase COG4989: Predicted oxidoreductase; aldo/keto reductase complement(2917412..2918302) Dinoroseobacter shibae DFL 12 = DSM 16493 5713655 YP_001534091.1 CDS ssuD NC_009952.1 2918302 2919456 R Swiss-Prot: P80645-Alkanesulfonate monooxygenase PFAM: luciferase family protein; alkanesulfonate monooxygenase complement(2918302..2919456) Dinoroseobacter shibae DFL 12 = DSM 16493 5713656 YP_001534092.1 CDS Dshi_2758 NC_009952.1 2919558 2920268 D PFAM: regulatory protein GntR HTH; UbiC transcription regulator-associated domain protein; GntR family; transcriptional regulator 2919558..2920268 Dinoroseobacter shibae DFL 12 = DSM 16493 5713657 YP_001534093.1 CDS Dshi_2759 NC_009952.1 2920265 2921386 D Swiss-Prot: O05389-Putative oxidoreductase yrbE PFAM: oxidoreductase domain protein; Oxidoreductase domain COG0673: Predicted dehydrogenases and related proteins; putative oxidoreductase 2920265..2921386 Dinoroseobacter shibae DFL 12 = DSM 16493 5713658 YP_001534094.1 CDS Dshi_2760 NC_009952.1 2921376 2922041 R Swiss-Prot: P32662-Phosphoglycolate phosphatase TIGRFAM: phosphoglycolate phosphatase ; HAD-superfamily hydrolase, subfamily IA, variant 3; HAD-superfamily hydrolase, subfamily IA, variant 1 PFAM: Haloacid dehalogenase domain protein hydrolase; putative phosphoglycolate phosphatase complement(2921376..2922041) Dinoroseobacter shibae DFL 12 = DSM 16493 5713659 YP_001534095.1 CDS Dshi_2761 NC_009952.1 2922178 2923956 R Swiss-Prot: P0AFU2-Uncharacterized transporter yfbS PFAM: Citrate transporter; TrkA-C domain protein; transporter complement(2922178..2923956) Dinoroseobacter shibae DFL 12 = DSM 16493 5713660 YP_001534096.1 CDS Dshi_2762 NC_009952.1 2924076 2924816 D Swiss-Prot: P0A8A0-UPF0082 protein yebC TIGR01033 conserved hypothetical protein COG0217: Uncharacterized conserved protein; hypothetical protein 2924076..2924816 Dinoroseobacter shibae DFL 12 = DSM 16493 5713661 YP_001534097.1 CDS Dshi_2763 NC_009952.1 2924884 2926548 R Swiss-Prot: P09983-Hemolysin, chromosomal PFAM: Hemolysin-type calcium-binding region; related to hemolysin; hypothetical protein complement(2924884..2926548) Dinoroseobacter shibae DFL 12 = DSM 16493 5713662 YP_001534098.1 CDS Dshi_2764 NC_009952.1 2926666 2927010 R hypothetical protein complement(2926666..2927010) Dinoroseobacter shibae DFL 12 = DSM 16493 5713663 YP_001534099.1 CDS Dshi_2765 NC_009952.1 2927040 2927444 R hypothetical protein complement(2927040..2927444) Dinoroseobacter shibae DFL 12 = DSM 16493 5713664 YP_001534100.1 CDS Dshi_2766 NC_009952.1 2927535 2929334 R Swiss-Prot: P72958-Uncharacterized transporter sll0640 PFAM: Citrate transporter; TrkA-C domain protein; TRAP C4-dicarboxylate transport system permease DctM subunit; transporter complement(2927535..2929334) Dinoroseobacter shibae DFL 12 = DSM 16493 5713665 YP_001534101.1 CDS Dshi_2767 NC_009952.1 2929331 2930296 R PFAM: protein of unknown function DUF6 transmembrane; hypothetical protein complement(2929331..2930296) Dinoroseobacter shibae DFL 12 = DSM 16493 5713666 YP_001534102.1 CDS Dshi_2768 NC_009952.1 2930293 2931126 R Swiss-Prot: P75429-Uncharacterized protein MG246 homolog TIGR00282# conserved hypothetical protein COG1692: Uncharacterized protein conserved in bacteria; hypothetical protein complement(2930293..2931126) Dinoroseobacter shibae DFL 12 = DSM 16493 5713667 YP_001534103.1 CDS Dshi_2769 NC_009952.1 2931169 2931762 R Swiss-Prot: P0AC28-Uncharacterized protein ygfA PFAM: 5-formyltetrahydrofolate cyclo-ligase TIGR02727: 5,10-methenyltetrahydrofolate synthetase; related to 5-formyltetrahydrofolate cyclo-ligase; hypothetical protein complement(2931169..2931762) Dinoroseobacter shibae DFL 12 = DSM 16493 5713668 YP_001534104.1 CDS Dshi_2770 NC_009952.1 2931759 2933141 R TIGR00400: Mg2+ transporter (mgtE) PFAM: CBS domain containing protein; MgtE integral membrane region; MgtE intracellular region COG2239: Mg/Co/Ni transporter MgtE (contains CBS domain); putative magnesium transporter complement(2931759..2933141) Dinoroseobacter shibae DFL 12 = DSM 16493 5713669 YP_001534105.1 CDS guaD NC_009952.1 2933279 2934565 D Catalyzes the deamination of guanine; guanine deaminase 2933279..2934565 Dinoroseobacter shibae DFL 12 = DSM 16493 5713670 YP_001534106.1 CDS Dshi_2772 NC_009952.1 2934712 2935170 R Swiss-Prot: PFAM: SCP-like extracellular COG2340: Uncharacterized protein with SCP/PR1 domains; related to SCP-like extracellular protein; hypothetical protein complement(2934712..2935170) Dinoroseobacter shibae DFL 12 = DSM 16493 5713671 YP_001534107.1 CDS Dshi_2773 NC_009952.1 2935167 2936507 R catalyzes the transformation of hydroxyatrazine to N-isopropylammelide and ethylamine in the atrazine degradation pathway.; hydroxydechloroatrazine ethylaminohydrolase complement(2935167..2936507) Dinoroseobacter shibae DFL 12 = DSM 16493 5713672 YP_001534108.1 CDS Dshi_2774 NC_009952.1 2936504 2937325 R Swiss-Prot: P0ADG4-Inositol-1-monophosphatase suhB TIGRFAM: histidinol-phosphate phosphatase, putative PFAM: inositol monophosphatase; putative inositol-1-monophosphatase complement(2936504..2937325) Dinoroseobacter shibae DFL 12 = DSM 16493 5713673 YP_001534109.1 CDS Dshi_2775 NC_009952.1 2937384 2937755 R Swiss-Prot:Q52911-Uncharacterized HTH-type transcriptional regulator R00410 PFAM: helix-turn-helix domain protein COG1396: Predicted transcriptional regulators SM00530: Helix-turn-helix XRE-family like proteins; XRE family; putative transcriptional regulator complement(2937384..2937755) Dinoroseobacter shibae DFL 12 = DSM 16493 5713674 YP_001534110.1 CDS Dshi_2776 NC_009952.1 2938108 2939067 D Swiss-Prot: P12311-Alcohol dehydrogenase PFAM: Alcohol dehydrogenase zinc-binding domain protein; Alcohol dehydrogenase GroES domain protein; putative alcohol dehydrogenase 2938108..2939067 Dinoroseobacter shibae DFL 12 = DSM 16493 5713675 YP_001534111.1 CDS Dshi_2777 NC_009952.1 2939244 2940098 R Swiss-Prot:P36771-Probable HTH-type transcriptional regulator lrhA PFAM: regulatory protein LysR; LysR substrate-binding; LysR family; putative transcriptional regulator complement(2939244..2940098) Dinoroseobacter shibae DFL 12 = DSM 16493 5713676 YP_001534112.1 CDS Dshi_2778 NC_009952.1 2940224 2940442 D hypothetical protein 2940224..2940442 Dinoroseobacter shibae DFL 12 = DSM 16493 5713677 YP_001534113.1 CDS Dshi_2779 NC_009952.1 2940622 2941344 D Swiss-Prot: P0AAC4-Inner membrane protein ybhL PFAM: protein of unknown function UPF0005; hypothetical protein 2940622..2941344 Dinoroseobacter shibae DFL 12 = DSM 16493 5713678 YP_001534114.1 CDS Dshi_2780 NC_009952.1 2941414 2941887 R hypothetical protein complement(2941414..2941887) Dinoroseobacter shibae DFL 12 = DSM 16493 5713679 YP_001534115.1 CDS rpmG NC_009952.1 2942214 2942381 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(2942214..2942381) Dinoroseobacter shibae DFL 12 = DSM 16493 5713680 YP_001534116.1 CDS Dshi_2782 NC_009952.1 2942514 2943002 R hypothetical protein complement(2942514..2943002) Dinoroseobacter shibae DFL 12 = DSM 16493 5713681 YP_001534117.1 CDS Dshi_2783 NC_009952.1 2943475 2944113 R Swiss-Prot: P75820-N-acetylmuramoyl-L-alanine amidase amiD [Precursor] PFAM: N-acetylmuramoyl-L-alanine amidase family 2; similar to N-acetylmuramoyl-L-alanine amidase; hypothetical protein complement(2943475..2944113) Dinoroseobacter shibae DFL 12 = DSM 16493 5713683 YP_001534118.1 CDS Dshi_2784 NC_009952.1 2944167 2944769 R hypothetical protein complement(2944167..2944769) Dinoroseobacter shibae DFL 12 = DSM 16493 5713684 YP_001534119.1 CDS gatA NC_009952.1 2944803 2946290 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 A complement(2944803..2946290) Dinoroseobacter shibae DFL 12 = DSM 16493 5713685 YP_001534120.1 CDS gatC NC_009952.1 2946295 2946582 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; some Mycoplasma proteins contain an N-terminal fusion to an unknown domain; aspartyl/glutamyl-tRNA amidotransferase subunit C complement(2946295..2946582) Dinoroseobacter shibae DFL 12 = DSM 16493 5713686 YP_001534121.1 CDS Dshi_2787 NC_009952.1 2946619 2947284 R hypothetical protein complement(2946619..2947284) Dinoroseobacter shibae DFL 12 = DSM 16493 5713687 YP_001534122.1 CDS Dshi_2788 NC_009952.1 2947338 2948030 D Swiss-Prot:Q98M91- UPF0173 metal-dependent hydrolase PFAM:beta-lactamase domain protein COG2220: Predicted Zn-dependent hydrolases of the beta-lactamase fold; hypothetical protein 2947338..2948030 Dinoroseobacter shibae DFL 12 = DSM 16493 5713688 YP_001534123.1 CDS Dshi_2789 NC_009952.1 2948196 2948651 R Swiss-Prot: P68398- tRNA-specific adenosine deaminase tadA PFAM: CMP/dCMP deaminase zinc-binding PTHR11079: cytidine / deoxycytidylate deaminase-related; related to cytidine / deoxycytidylate deaminase; hypothetical protein complement(2948196..2948651) Dinoroseobacter shibae DFL 12 = DSM 16493 5713689 YP_001534124.1 CDS Dshi_2790 NC_009952.1 2948736 2949704 D Swiss-Prot: Q4UL59-Uncharacterized RNA pseudouridine synthase RF_0863 TIGR00093: pseudouridine synthase family COG1187:16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases; RNA pseudouridine synthase 2948736..2949704 Dinoroseobacter shibae DFL 12 = DSM 16493 5713690 YP_001534125.1 CDS Dshi_2791 NC_009952.1 2950066 2950944 D KEGG: sil:SPO2985 hypothetical protein; hypothetical protein 2950066..2950944 Dinoroseobacter shibae DFL 12 = DSM 16493 5713691 YP_001534126.1 CDS Dshi_2792 NC_009952.1 2950980 2952173 D PFAM: toxic anion resistance family protein Swiss-Prot: Q2YY12- TelA-like protein SAB1262 COG3853: Uncharacterized protein involved in tellurite resistance; related to toxic anion resistance protein (TelA); hypothetical protein 2950980..2952173 Dinoroseobacter shibae DFL 12 = DSM 16493 5713692 YP_001534127.1 CDS Dshi_2793 NC_009952.1 2952170 2953117 D hypothetical protein 2952170..2953117 Dinoroseobacter shibae DFL 12 = DSM 16493 5713693 YP_001534128.1 CDS Dshi_2794 NC_009952.1 2953140 2954270 D hypothetical protein 2953140..2954270 Dinoroseobacter shibae DFL 12 = DSM 16493 5713694 YP_001534129.1 CDS Dshi_2795 NC_009952.1 2954277 2955392 D hypothetical protein 2954277..2955392 Dinoroseobacter shibae DFL 12 = DSM 16493 5713695 YP_001534130.1 CDS Dshi_2796 NC_009952.1 2955399 2955857 R PFAM: heat shock protein Hsp20 SSF49764: HSP20-like chaperones superfamily; Hsp20; heat shock protein complement(2955399..2955857) Dinoroseobacter shibae DFL 12 = DSM 16493 5713696 YP_001534131.1 CDS Dshi_2797 NC_009952.1 2955983 2956909 D PFAM: PfkB domain protein COG0524: Sugar kinases, ribokinase family PTHR10584: sugar kinase related; pfkB family; carbohydrate kinase 2955983..2956909 Dinoroseobacter shibae DFL 12 = DSM 16493 5713697 YP_001534132.1 CDS dtd NC_009952.1 2956906 2957343 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 2956906..2957343 Dinoroseobacter shibae DFL 12 = DSM 16493 5713698 YP_001534133.1 CDS fccB NC_009952.1 2957464 2958732 R Swiss-Prot: Q06530- Sulfide dehydrogenase [flavocytochrome c] flavoprotein chain [Precursor] PFAM: FAD-dependent pyridine nucleotide-disulphide oxidoreductase; Flavocytochrome c sulphide dehydrogenase flavin-binding; sulfide dehydrogenase [flavocytochrome c] flavoprotein chain complement(2957464..2958732) Dinoroseobacter shibae DFL 12 = DSM 16493 5713699 YP_001534134.1 CDS Dshi_2800 NC_009952.1 2958766 2959473 R Swiss-Prot: P00082-Cytochrome c2 PFAM: cytochrome c class I; cytochrome c complement(2958766..2959473) Dinoroseobacter shibae DFL 12 = DSM 16493 5713700 YP_001534135.1 CDS Dshi_2801 NC_009952.1 2959478 2960506 R Swiss-Prot: P00081-Cytochrome c2 PFAM: cytochrome c class I; cytochrome c complement(2959478..2960506) Dinoroseobacter shibae DFL 12 = DSM 16493 5713701 YP_001534136.1 CDS Dshi_2802 NC_009952.1 2960490 2961767 R Swiss-Prot: PFAM: oxidoreductase molybdopterin binding; Mo-co oxidoreductase dimerisation domain; molybdopterin binding; oxidoreductase complement(2960490..2961767) Dinoroseobacter shibae DFL 12 = DSM 16493 5713702 YP_001534137.1 CDS Dshi_2803 NC_009952.1 2961826 2963520 R PFAM: metallophosphoesterase; 5-Nucleotidase domain protein Swiss-Prot:P07024-Protein ushA [Precursor] COG0737: 5-nucleotidase/2,3-cyclic phosphodiesterase and related esterases; putative 5'-nucleotidase complement(2961826..2963520) Dinoroseobacter shibae DFL 12 = DSM 16493 5713703 YP_001534138.1 CDS soxA1 NC_009952.1 2963655 2964509 R Swiss-Prot: Q939U1-Diheme cytochrome c GENE3D / SSF46626: Cytochrome c, monohaem PS51008: Multihaem cytochrome; diheme cytochrome c complement(2963655..2964509) Dinoroseobacter shibae DFL 12 = DSM 16493 5713704 YP_001534139.1 CDS Dshi_2805 NC_009952.1 2964559 2964888 R PFAM: Sulphur oxidation protein SoxZ Swiss-Prot: Q939U2- SoxZ [predicted]; soxZ; putative sulfur oxidation protein complement(2964559..2964888) Dinoroseobacter shibae DFL 12 = DSM 16493 5713705 YP_001534140.1 CDS Dshi_2806 NC_009952.1 2964907 2965323 R with SoxZ catalyzes the oxidation of sulfur compounds; sulfur oxidation protein SoxY complement(2964907..2965323) Dinoroseobacter shibae DFL 12 = DSM 16493 5713706 YP_001534141.1 CDS Dshi_2807 NC_009952.1 2965359 2965841 R PFAM: cytochrome c SSF46626 / PS51007 / G3DSA:1.10.760.10: Cytochrome c, monohaem Swiss-Prot: A3W521- Monoheme cytochrome c SoxX [predicted]; monohaem; cytochrome c complement(2965359..2965841) Dinoroseobacter shibae DFL 12 = DSM 16493 5713707 YP_001534142.1 CDS Dshi_2808 NC_009952.1 2965958 2966524 R SSF52833: Thioredoxin-like superfamily COG2143: Thioredoxin-related protein Swiss-Prot: Q16A50-Thioredoxin SoxW [predicted]; putative thioredoxin complement(2965958..2966524) Dinoroseobacter shibae DFL 12 = DSM 16493 5710659 YP_001534143.1 CDS Dshi_2809 NC_009952.1 2966552 2967286 R PFAM: cytochrome c biogenesis protein transmembrane region COG0785: Cytochrome c biogenesis protein; transmembrane region; cytochrome c biogenesis protein complement(2966552..2967286) Dinoroseobacter shibae DFL 12 = DSM 16493 5710660 YP_001534144.1 CDS Dshi_2810 NC_009952.1 2967368 2967775 D hypothetical protein 2967368..2967775 Dinoroseobacter shibae DFL 12 = DSM 16493 5710661 YP_001534145.1 CDS Dshi_2811 NC_009952.1 2967772 2968284 D PFAM: protein of unknown function DUF336; hypothetical protein 2967772..2968284 Dinoroseobacter shibae DFL 12 = DSM 16493 5710662 YP_001534146.1 CDS Dshi_2812 NC_009952.1 2968306 2968641 D PFAM: regulatory protein ArsR; ArsR family; transcriptional regulator 2968306..2968641 Dinoroseobacter shibae DFL 12 = DSM 16493 5710663 YP_001534147.1 CDS Dshi_2813 NC_009952.1 2968662 2969750 D PFAM: protein of unknown function DUF395 YeeE/YedE; hypothetical protein 2968662..2969750 Dinoroseobacter shibae DFL 12 = DSM 16493 5710664 YP_001534148.1 CDS Dshi_2814 NC_009952.1 2969763 2970803 R TIGRFAM: diguanylate cyclase (GGDEF) domain PFAM: GGDEF domain containing protein; hypothetical protein complement(2969763..2970803) Dinoroseobacter shibae DFL 12 = DSM 16493 5710665 YP_001534149.1 CDS Dshi_2815 NC_009952.1 2970800 2971384 R PFAM: Heme NO binding domain protein; hypothetical protein complement(2970800..2971384) Dinoroseobacter shibae DFL 12 = DSM 16493 5710666 YP_001534150.1 CDS Dshi_2816 NC_009952.1 2971486 2973201 R hypothetical protein complement(2971486..2973201) Dinoroseobacter shibae DFL 12 = DSM 16493 5710667 YP_001534151.1 CDS Dshi_2817 NC_009952.1 2973240 2974799 R Swiss-Prot: PFAM: trimethylamine methyltransferase PIRSF037567: trimethylamine methyltransferase, MttB type; trimethylamine methyltransferase complement(2973240..2974799) Dinoroseobacter shibae DFL 12 = DSM 16493 5710668 YP_001534152.1 CDS Dshi_2818 NC_009952.1 2974910 2975632 R Swiss-Prot: P32662-Phosphoglycolate phosphatase TIGRFAM: HAD-superfamily hydrolase, subfamily IA, variant 3; HAD-superfamily hydrolase, subfamily IA, variant 1 PFAM: Haloacid dehalogenase domain protein hydrolase; HAD-like hydrolase complement(2974910..2975632) Dinoroseobacter shibae DFL 12 = DSM 16493 5710669 YP_001534153.1 CDS Dshi_2819 NC_009952.1 2976015 2976293 R KEGG: sil:SPO2752 hypothetical protein; hypothetical protein complement(2976015..2976293) Dinoroseobacter shibae DFL 12 = DSM 16493 5710670 YP_001534154.1 CDS Dshi_2820 NC_009952.1 2976378 2977766 D Swiss-Prot: Q9A5I5-Response regulator pleD (part of a signal transduction pathway controlling cell differentiation in the swarmer-to-stalked cell transition) TIGR00254: diguanylate cyclase (GGDEF) domain PFAM: GGDEF domain containing protein; response regulator receiver; response regulator 2976378..2977766 Dinoroseobacter shibae DFL 12 = DSM 16493 5710671 YP_001534155.1 CDS Dshi_2821 NC_009952.1 2977988 2978386 D PFAM: protein of unknown function DUF983 COG5349: Uncharacterized protein conserved in bacteria; hypothetical protein 2977988..2978386 Dinoroseobacter shibae DFL 12 = DSM 16493 5710672 YP_001534156.1 CDS Dshi_2822 NC_009952.1 2978410 2979087 D Swiss-Prot: PFAM: NUDIX hydrolase; NUDIX hydrolase 2978410..2979087 Dinoroseobacter shibae DFL 12 = DSM 16493 5710673 YP_001534157.1 CDS Dshi_2823 NC_009952.1 2979098 2980144 R PFAM: aldo/keto reductase IPR001395: Aldo/keto reductase; aldo/keto reductase complement(2979098..2980144) Dinoroseobacter shibae DFL 12 = DSM 16493 5710674 YP_001534158.1 CDS Dshi_2824 NC_009952.1 2980248 2981147 D hypothetical protein 2980248..2981147 Dinoroseobacter shibae DFL 12 = DSM 16493 5710675 YP_001534159.1 CDS Dshi_2825 NC_009952.1 2981199 2982374 D PFAM: 3-hydroxyacyl-CoA dehydrogenase NAD-binding COG1250: 3-hydroxyacyl-CoA dehydrogenase; related to 3-hydroxyacyl-CoA dehydrogenase; hypothetical protein 2981199..2982374 Dinoroseobacter shibae DFL 12 = DSM 16493 5710676 YP_001534160.1 CDS Dshi_2826 NC_009952.1 2982421 2983074 D KEGG: rde:RD1_2519 hypothetical protein COG4544: Uncharacterized conserved protein; hypothetical protein 2982421..2983074 Dinoroseobacter shibae DFL 12 = DSM 16493 5710677 YP_001534161.1 CDS Dshi_2827 NC_009952.1 2983112 2983675 D Swiss-Prot: P0A8X2-Protein yceI [Precursor] PFAM: YceI family protein COG2353: Uncharacterized conserved protein; similar to protein yceI [Precursor]; hypothetical protein 2983112..2983675 Dinoroseobacter shibae DFL 12 = DSM 16493 5710678 YP_001534162.1 CDS Dshi_2828 NC_009952.1 2983768 2985282 D Swiss-Prot: TIGRFAM: Mg chelatase, subunit ChlI PFAM: magnesium chelatase ChlI subunit; ATPase associated with various cellular activities AAA_5 SMART: AAA ATPase; related to Mg chelatase; hypothetical protein 2983768..2985282 Dinoroseobacter shibae DFL 12 = DSM 16493 5710679 YP_001534163.1 CDS gshB NC_009952.1 2985279 2986226 R catalyzes the second step in the glutathione biosynthesis pathway, where it synthesizes ATP + gamma-L-glutamyl-L-cysteine + glycine = ADP + phosphate + glutathione; glutathione synthetase complement(2985279..2986226) Dinoroseobacter shibae DFL 12 = DSM 16493 5710680 YP_001534164.1 CDS Dshi_2830 NC_009952.1 2986303 2986707 R TIGR00252 conserved hypothetical protein PFAM: protein of unknown function UPF0102; hypothetical protein complement(2986303..2986707) Dinoroseobacter shibae DFL 12 = DSM 16493 5710681 YP_001534165.1 CDS Dshi_2831 NC_009952.1 2986732 2987586 R Swiss-Prot: P67087-UPF0011 protein yraL TIGR00096: conserved hypothetical protein TIGR00096 PFAM: Uroporphyrin-III C/tetrapyrrole (Corrin/Porphyrin) methyltransferase; hypothetical protein complement(2986732..2987586) Dinoroseobacter shibae DFL 12 = DSM 16493 5710682 YP_001534166.1 CDS Dshi_2832 NC_009952.1 2987697 2988881 D SSF53822: Periplasmic binding protein-like I superfamily PS51257: Prokaryotic membrane lipoprotein lipid attachment site profile; hypothetical protein 2987697..2988881 Dinoroseobacter shibae DFL 12 = DSM 16493 5710683 YP_001534167.1 CDS glnD NC_009952.1 2988886 2991717 D catalyzes the uridylylation or deuridylylation of the PII nitrogen regulatory protein; PII uridylyl-transferase 2988886..2991717 Dinoroseobacter shibae DFL 12 = DSM 16493 5710684 YP_001534168.1 CDS Dshi_2834 NC_009952.1 2991755 2993359 D Swiss-Prot: O05467-Virulence factor mviN homolog TIGRFAM: integral membrane protein MviN PFAM: virulence factor MVIN family protein COG072: Uncharacterized membrane protein, putative virulence factor; mviN homolog; putative virulence factor 2991755..2993359 Dinoroseobacter shibae DFL 12 = DSM 16493 5710685 YP_001534169.1 CDS Dshi_2835 NC_009952.1 2993548 2994231 R PFAM: Rhomboid family protein KEGG: sit:TM1040_0444 rhomboid-like protein COG0705: Uncharacterized membrane protein (homolog of Drosophila rhomboid); related to rhomboid family protein; hypothetical protein complement(2993548..2994231) Dinoroseobacter shibae DFL 12 = DSM 16493 5710686 YP_001534170.1 CDS trpS NC_009952.1 2994331 2995356 D 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 2994331..2995356 Dinoroseobacter shibae DFL 12 = DSM 16493 5710687 YP_001534171.1 CDS Dshi_2837 NC_009952.1 2995862 2996722 D Swiss-Prot: P0AB80-Branched-chain-amino-acid aminotransferase PFAM: aminotransferase class IV; class IV; aminotransferase 2995862..2996722 Dinoroseobacter shibae DFL 12 = DSM 16493 5710688 YP_001534172.1 CDS Dshi_2838 NC_009952.1 2996802 2997257 D PFAM: UspA domain protein COG0589: Universal stress protein UspA and related nucleotide-binding proteins; related to universal stress protein; hypothetical protein 2996802..2997257 Dinoroseobacter shibae DFL 12 = DSM 16493 5710689 YP_001534173.1 CDS Dshi_2839 NC_009952.1 2997347 2997910 D PFAM: nitrogen-fixing NifU domain protein; Scaffold protein Nfu/NifU Swiss-Prot: P33179-Nitrogen fixation protein nifU [Fragment] (inferred from homology); related to nitrogen fixation protein; hypothetical protein 2997347..2997910 Dinoroseobacter shibae DFL 12 = DSM 16493 5710690 YP_001534174.1 CDS Dshi_2840 NC_009952.1 2997915 2998571 D PFAM: peptidase M22 glycoprotease; glycoprotease; peptidase M22 2997915..2998571 Dinoroseobacter shibae DFL 12 = DSM 16493 5710691 YP_001534175.1 CDS Dshi_2841 NC_009952.1 2998568 2998987 D TIGRFAM: ribosomal-protein-alanine acetyltransferase Swiss-Prot: P0A947-Ribosomal-protein-alanine acetyltransferase [inferred from homology] PFAM: GCN5-related N-acetyltransferase; putative ribosomal-protein-alanine acetyltransferase 2998568..2998987 Dinoroseobacter shibae DFL 12 = DSM 16493 5710692 YP_001534176.1 CDS Dshi_2842 NC_009952.1 2999169 3000158 D PFAM: basic membrane lipoprotein SSF53822: Periplasmic binding protein-like I superfamily; putative lipoprotein 2999169..3000158 Dinoroseobacter shibae DFL 12 = DSM 16493 5710693 YP_001534177.1 CDS rbsA2 NC_009952.1 3000182 3001828 D Swiss-Prot: P04983-Ribose import ATP-binding protein rbsA; ribose import ATP-binding protein 3000182..3001828 Dinoroseobacter shibae DFL 12 = DSM 16493 5710694 YP_001534178.1 CDS Dshi_2844 NC_009952.1 3001828 3002946 D Swiss-Prot: P0AGI1-Ribose transport system permease protein rbsC PFAM: inner-membrane translocator; similar to ribose transport system permease protein; integral inner-membrane protein 3001828..3002946 Dinoroseobacter shibae DFL 12 = DSM 16493 5710695 YP_001534179.1 CDS Dshi_2845 NC_009952.1 3002943 3003572 D PFAM: Lysine exporter protein (LYSE/YGGA) Swiss-Prot: P75693-Uncharacterized membrane protein yahN; related to LysE type translocator; hypothetical protein 3002943..3003572 Dinoroseobacter shibae DFL 12 = DSM 16493 5710696 YP_001534180.1 CDS Dshi_2846 NC_009952.1 3003577 3004542 D PFAM: inner-membrane translocator COG1079: Uncharacterized ABC-type transport system, permease component; inner-membrane translocator 3003577..3004542 Dinoroseobacter shibae DFL 12 = DSM 16493 5710697 YP_001534181.1 CDS Dshi_2847 NC_009952.1 3004600 3005520 D Swiss-Prot: PFAM: protein of unknown function DUF81 KEGG: sil:SPO0375 membrane protein; hypothetical protein 3004600..3005520 Dinoroseobacter shibae DFL 12 = DSM 16493 5710698 YP_001534182.1 CDS Dshi_2848 NC_009952.1 3005517 3006275 D TIGR02186# conserved hypothetical protein; hypothetical protein 3005517..3006275 Dinoroseobacter shibae DFL 12 = DSM 16493 5710699 YP_001534183.1 CDS Dshi_2849 NC_009952.1 3006406 3007137 R Swiss-Prot: Q9KWN1-Serine 3-dehydrogenase PFAM: NAD-dependent epimerase/dehydratase; short-chain dehydrogenase/reductase SDR COG4221: Short-chain alcohol dehydrogenase of unknown specificity; short-chain dehydrogenase/reductase complement(3006406..3007137) Dinoroseobacter shibae DFL 12 = DSM 16493 5710700 YP_001534184.1 CDS Dshi_2850 NC_009952.1 3007134 3008669 R SMART 00382: AAA - ATPases associated with a variety of cellular activities; AAA family; putative ATPase complement(3007134..3008669) Dinoroseobacter shibae DFL 12 = DSM 16493 5710701 YP_001534185.1 CDS Dshi_2851 NC_009952.1 3008719 3009339 R Swiss-Prot: P33883-Autoinducer synthesis protein lasI PFAM: autoinducer synthesis protein; autoinducer synthetase complement(3008719..3009339) Dinoroseobacter shibae DFL 12 = DSM 16493 5710702 YP_001534186.1 CDS Dshi_2852 NC_009952.1 3009442 3010152 R ibu, PFAM: regulatory protein LuxR; Autoinducer-binding domain protein KEGG: sil:SPO0371 autoinducer-binding transcriptional regulator LuxR, Autoinducer binding domain pfam03472, HTH-LuxR domain pfam00196; LuxR family; transcriptional regulator complement(3009442..3010152) Dinoroseobacter shibae DFL 12 = DSM 16493 5710703 YP_001534187.1 CDS Dshi_2853 NC_009952.1 3010523 3011815 R TIGRFAM: crotonyl-CoA reductase PFAM: Alcohol dehydrogenase zinc-binding domain protein; Alcohol dehydrogenase GroES domain protein Swiss-Prot: P42328-Alcohol dehydrogenase; alcohol dehydrogenase complement(3010523..3011815) Dinoroseobacter shibae DFL 12 = DSM 16493 5710704 YP_001534188.1 CDS Dshi_2854 NC_009952.1 3011938 3013380 R Swiss-Prot: P0A7A7-Glycerol-3-phosphate acyltransferase PFAM: phospholipid/glycerol acyltransferase; putative glycerol-3-phosphate acyltransferase complement(3011938..3013380) Dinoroseobacter shibae DFL 12 = DSM 16493 5710705 YP_001534189.1 CDS mutB NC_009952.1 3013589 3015562 D Swiss-Prot: PFAM: methylmalonyl-CoA mutase; cobalamin B12-binding domain protein TIGR00640: methylmalonyl-CoA mutase C-terminal domain TIGR00641: methylmalonyl-CoA mutase N-terminal domain; methylmalonyl-CoA mutase 3013589..3015562 Dinoroseobacter shibae DFL 12 = DSM 16493 5710706 YP_001534190.1 CDS Dshi_2856 NC_009952.1 3015677 3016192 R hypothetical protein complement(3015677..3016192) Dinoroseobacter shibae DFL 12 = DSM 16493 5710707 YP_001534191.1 CDS Dshi_2857 NC_009952.1 3016278 3016748 D hypothetical protein 3016278..3016748 Dinoroseobacter shibae DFL 12 = DSM 16493 5710708 YP_001534192.1 CDS deoD NC_009952.1 3016895 3017599 D catalyzes the reversible phosphorolysis of ribonucleosides and 2'- deoxyribonucleosides to the free base and (2'-deoxy)ribose-1- phosphate; purine nucleoside phosphorylase 3016895..3017599 Dinoroseobacter shibae DFL 12 = DSM 16493 5710709 YP_001534193.1 CDS Dshi_2859 NC_009952.1 3017596 3018039 D hypothetical protein 3017596..3018039 Dinoroseobacter shibae DFL 12 = DSM 16493 5710710 YP_001534194.1 CDS Dshi_2860 NC_009952.1 3018036 3018221 R hypothetical protein complement(3018036..3018221) Dinoroseobacter shibae DFL 12 = DSM 16493 5710711 YP_001534195.1 CDS sdhB NC_009952.1 3018314 3019093 R 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 complement(3018314..3019093) Dinoroseobacter shibae DFL 12 = DSM 16493 5710712 YP_001534196.1 CDS Dshi_2862 NC_009952.1 3019123 3019902 R hypothetical protein complement(3019123..3019902) Dinoroseobacter shibae DFL 12 = DSM 16493 5710713 YP_001534197.1 CDS Dshi_2863 NC_009952.1 3019899 3020720 R hypothetical protein complement(3019899..3020720) Dinoroseobacter shibae DFL 12 = DSM 16493 5710714 YP_001534198.1 CDS Dshi_2864 NC_009952.1 3020723 3021550 R hypothetical protein complement(3020723..3021550) Dinoroseobacter shibae DFL 12 = DSM 16493 5710715 YP_001534199.1 CDS sdhA NC_009952.1 3021696 3023498 R 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 complement(3021696..3023498) Dinoroseobacter shibae DFL 12 = DSM 16493 5710716 YP_001534200.1 CDS Dshi_2866 NC_009952.1 3023515 3023886 R TIGRFAM: TIGR02968 succinate dehydrogenase, hydrophobic membrane anchor protein; COG: COG2142 - Succinate dehydrogenase, hydrophobic anchor subunit; similar to succinate dehydrogenase; hypothetical protein complement(3023515..3023886) Dinoroseobacter shibae DFL 12 = DSM 16493 5710717 YP_001534201.1 CDS Dshi_2867 NC_009952.1 3023898 3024281 R SWISSPROT P69054: Succinate dehydrogenase cytochrome b556 subunit sdhC; TIGRFAM: TIGR02970 succinate dehydrogenase, cytochrome b556 subunit; COG: COG2009 - Succinate dehydrogenase/fumarate reductase, cytochrome b subunit; PFAM: PF01127 - Succinate dehydrogenase cytochrome b subunit; PIR: PIRSF000178 - succinate dehydrogenase, cytochrome b560 subunit; PROSITE: PS01001; putative succinate dehydrogenase cytochrome subunit B complement(3023898..3024281) Dinoroseobacter shibae DFL 12 = DSM 16493 5710718 YP_001534202.1 CDS Dshi_2868 NC_009952.1 3024581 3025060 D SWISSPROT Q3J2P2: Cytochrome c-554 [Precursor] cycF; COG: COG3909 - Cytochrome c556; PFAM: PF01322; PIR: PIRSF000027; PRINTS: PR00608; PROSITE: PS51009; Gene3D: G3DSA:1.20.120.10; cytochrome c 3024581..3025060 Dinoroseobacter shibae DFL 12 = DSM 16493 5710719 YP_001534203.1 CDS Dshi_2869 NC_009952.1 3025070 3025948 D SWISSPROT P0A388: Alcohol dehydrogenase cytochrome c subunit [Precursor] adhB; COG: COG2010 - Cytochrome c, mono- and diheme variants; PROSITE: PS51007; SUPERFAMILY: SSF46626; putative alcohol dehydrogenase cytochrome subunit C 3025070..3025948 Dinoroseobacter shibae DFL 12 = DSM 16493 5710720 YP_001534204.1 CDS Dshi_2870 NC_009952.1 3026023 3026229 D hypothetical protein 3026023..3026229 Dinoroseobacter shibae DFL 12 = DSM 16493 5710721 YP_001534205.1 CDS Dshi_2871 NC_009952.1 3026266 3027297 R COG: COG2030 - Acyl dehydratase; PIR: PIRSF021494; SUPERFAMILY: SSF54637; putative thiol ester dehydrase/isomerase complement(3026266..3027297) Dinoroseobacter shibae DFL 12 = DSM 16493 5710722 YP_001534206.1 CDS Dshi_2872 NC_009952.1 3027297 3027500 R COG: COG5515 - Uncharacterized conserved small protein; hypothetical protein complement(3027297..3027500) Dinoroseobacter shibae DFL 12 = DSM 16493 5710723 YP_001534207.1 CDS Dshi_2873 NC_009952.1 3027513 3028076 R COG: COG4094 - Predicted membrane protein; PFAM: PF07298 - NnrU protein; putative NnrU protein complement(3027513..3028076) Dinoroseobacter shibae DFL 12 = DSM 16493 5710724 YP_001534208.1 CDS Dshi_2874 NC_009952.1 3028080 3028967 R PIR: PIRSF015582 - citrate lyase, beta subunit; PFAM: PF03328; COG: COG2301 - Citrate lyase beta subunit; Gene3D: G3DSA:3.20.20.60; putative citrate lyase subunit beta complement(3028080..3028967) Dinoroseobacter shibae DFL 12 = DSM 16493 5710725 YP_001534209.1 CDS Dshi_2875 NC_009952.1 3029274 3029597 D hypothetical protein 3029274..3029597 Dinoroseobacter shibae DFL 12 = DSM 16493 5710726 YP_001534210.1 CDS mdh NC_009952.1 3029964 3030926 D Catalyzes the reversible oxidation of malate to oxaloacetate; malate dehydrogenase 3029964..3030926 Dinoroseobacter shibae DFL 12 = DSM 16493 5710727 YP_001534211.1 CDS Dshi_2877 NC_009952.1 3031039 3032007 D hypothetical protein 3031039..3032007 Dinoroseobacter shibae DFL 12 = DSM 16493 5710728 YP_001534212.1 CDS sucC NC_009952.1 3032211 3033404 D catalyzes the interconversion of succinyl-CoA and succinate; succinyl-CoA synthetase subunit beta 3032211..3033404 Dinoroseobacter shibae DFL 12 = DSM 16493 5710729 YP_001534213.1 CDS Dshi_2879 NC_009952.1 3033534 3034235 D hypothetical protein 3033534..3034235 Dinoroseobacter shibae DFL 12 = DSM 16493 5710730 YP_001534214.1 CDS Dshi_2880 NC_009952.1 3034232 3034780 D hypothetical protein 3034232..3034780 Dinoroseobacter shibae DFL 12 = DSM 16493 5710731 YP_001534215.1 CDS Dshi_2881 NC_009952.1 3034840 3035316 D hypothetical protein 3034840..3035316 Dinoroseobacter shibae DFL 12 = DSM 16493 5710732 YP_001534216.1 CDS sucD1 NC_009952.1 3035436 3036317 D SWISSPROT P0AGE9: Succinyl-CoA ligase [ADP-forming] subunit alpha; PIR: PIRSF001553 - succinyl-CoA synthetase, alpha subunit; TIGRFAM: TIGR01019 succinyl-CoA synthetase, alpha subunit; COG: COG0074; PFAM: PF02629, PF00549; PROSITE: PS00399, PS01216; PRINTS: PR01798; succinyl-CoA ligase [ADP-forming] subunit alpha 3035436..3036317 Dinoroseobacter shibae DFL 12 = DSM 16493 5710733 YP_001534217.1 CDS sucA NC_009952.1 3036507 3039470 D 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 component 3036507..3039470 Dinoroseobacter shibae DFL 12 = DSM 16493 5710734 YP_001534218.1 CDS sucB NC_009952.1 3039475 3040965 D component of 2-oxoglutarate dehydrogenase complex; catalyzes the transfer of succinyl coenzyme A to form succinyl CoA as part of the conversion of 2-oxoglutarate to succinyl-CoA; dihydrolipoamide succinyltransferase 3039475..3040965 Dinoroseobacter shibae DFL 12 = DSM 16493 5710735 YP_001534219.1 CDS Dshi_2885 NC_009952.1 3041239 3041628 D COG: COG3686 - Predicted membrane protein; hypothetical protein 3041239..3041628 Dinoroseobacter shibae DFL 12 = DSM 16493 5710736 YP_001534220.1 CDS lpd NC_009952.1 3041719 3043113 D SWISSPROT P14218: Dihydrolipoyl dehydrogenase; TIGRFAM: TIGR01350 dihydrolipoamide dehydrogenase; COG: COG1249 - Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide dehydrogenase (E3) component, and related enzymes; PFAM: PF00070, PF02852, PF07992; PRINTS: PR00945, PR00411, PR00368; dihydrolipoyl dehydrogenase 3041719..3043113 Dinoroseobacter shibae DFL 12 = DSM 16493 5710737 YP_001534221.1 CDS gabD NC_009952.1 3043208 3044686 R TIGRFAM: TIGR01780 succinic semialdehyde dehydrogenase; COG: COG1012 - NAD-dependent aldehyde dehydrogenases; PFAM: PF00171; PROSITE: PS00070, PS00687; NADP(+) dependentsuccinate-semialdehyde dehydrogenase complement(3043208..3044686) Dinoroseobacter shibae DFL 12 = DSM 16493 5710738 YP_001534222.1 CDS Dshi_2888 NC_009952.1 3044761 3045534 D SUPERFAMILY: SSF53474; Gene3D: G3DSA:3.40.50.1820; COG: COG0657 - Esterase/lipase; putative alpha/beta hydrolase 3044761..3045534 Dinoroseobacter shibae DFL 12 = DSM 16493 5710739 YP_001534223.1 CDS Dshi_2889 NC_009952.1 3045531 3046514 R COG: COG3191 - L-aminopeptidase/D-esterase; putative peptidase complement(3045531..3046514) Dinoroseobacter shibae DFL 12 = DSM 16493 5710740 YP_001534224.1 CDS Dshi_2890 NC_009952.1 3046511 3046822 R hypothetical protein complement(3046511..3046822) Dinoroseobacter shibae DFL 12 = DSM 16493 5710741 YP_001534225.1 CDS fabG NC_009952.1 3046819 3047547 R Catalyzes the first of the two reduction steps in the elongation cycle of fatty acid synthesis; 3-ketoacyl-ACP reductase complement(3046819..3047547) Dinoroseobacter shibae DFL 12 = DSM 16493 5710742 YP_001534226.1 CDS Dshi_2892 NC_009952.1 3047660 3048118 R SWISSPROT P0C054: Small heat shock protein ibpA; PFAM: PF00011; PROSITE: PS01031; SUPERFAMILY: SSF49764; COG: COG0071 - Molecular chaperone (small heat shock protein); putative small heat shock (HSP20) protein complement(3047660..3048118) Dinoroseobacter shibae DFL 12 = DSM 16493 5710743 YP_001534227.1 CDS Dshi_2893 NC_009952.1 3048258 3049076 R COG: COG3591 - V8-like Glu-specific endopeptidase; PFAM: PF00089; SMART: SM00020; PROSITE: PS00134, PS50240; PRINTS: PR00722; similar to serine protease; hypothetical protein complement(3048258..3049076) Dinoroseobacter shibae DFL 12 = DSM 16493 5710744 YP_001534228.1 CDS Dshi_2894 NC_009952.1 3049140 3050444 R COG: COG0247 - Fe-S oxidoreductase; PFAM: PF00037, PF02754; PROSITE: PS00198; SWISSPROT P52074: Glycolate oxidase iron-sulfur subunit; similar to glycolate oxidase iron-sulfur subunit; hypothetical protein complement(3049140..3050444) Dinoroseobacter shibae DFL 12 = DSM 16493 5710745 YP_001534229.1 CDS Dshi_2895 NC_009952.1 3050467 3051603 R COG: COG0277 - FAD/FMN-containing dehydrogenases; PFAM: PF01565; similar to glycolate oxidase subunit glcE; hypothetical protein complement(3050467..3051603) Dinoroseobacter shibae DFL 12 = DSM 16493 5710746 YP_001534230.1 CDS Dshi_2896 NC_009952.1 3051689 3053131 R TIGRFAM: TIGR00387 glycolate oxidase, subunit GlcD; COG: COG0277 - FAD/FMN-containing dehydrogenases; PFAM: PF01565, PF02913; SWISSPROT P0AEP9: Glycolate oxidase subunit glcD; similar to glycolate oxidase subunit glcD; FAD-binding oxidoreductase/transferase complement(3051689..3053131) Dinoroseobacter shibae DFL 12 = DSM 16493 5710747 YP_001534231.1 CDS Dshi_2897 NC_009952.1 3053287 3053973 R SWISSPROT P23461: Protein pucD; associated with puc operon, related to protein pucD; hypothetical protein complement(3053287..3053973) Dinoroseobacter shibae DFL 12 = DSM 16493 5710748 YP_001534232.1 CDS pucC1 NC_009952.1 3054022 3055425 R SWISSPROT P23462: Protein pucC; PFAM: PF03209; PucC protein complement(3054022..3055425) Dinoroseobacter shibae DFL 12 = DSM 16493 5710749 YP_001534233.1 CDS Dshi_2899 NC_009952.1 3055496 3055837 R SWISSPROT P95655: Light-harvesting protein B-800/850 alpha chain; PFAM: PF00556; PRINTS: PR00673; PROSITE: PS00968; pucA; putative light-harvesting protein B-800/850 subunit alpha complement(3055496..3055837) Dinoroseobacter shibae DFL 12 = DSM 16493 5710750 YP_001534234.1 CDS pucB NC_009952.1 3055850 3056005 R SWISSPROT P07368: Light-harvesting protein B-800/850 beta chain; PFAM: PF00556; PRINTS: PR00674; PROSITE: PS00969; light-harvesting protein B-800/850 subunit beta complement(3055850..3056005) Dinoroseobacter shibae DFL 12 = DSM 16493 5710751 YP_001534235.1 CDS Dshi_2901 NC_009952.1 3056406 3058565 R hypothetical protein complement(3056406..3058565) Dinoroseobacter shibae DFL 12 = DSM 16493 5710752 YP_001534236.1 CDS Dshi_2902 NC_009952.1 3058709 3059089 D hypothetical protein 3058709..3059089 Dinoroseobacter shibae DFL 12 = DSM 16493 5710753 YP_001534237.1 CDS Dshi_2903 NC_009952.1 3059093 3061177 R hypothetical protein complement(3059093..3061177) Dinoroseobacter shibae DFL 12 = DSM 16493 5710754 YP_001534238.1 CDS Dshi_2904 NC_009952.1 3061174 3063948 R TIGRFAM: TIGR02226; hypothetical protein complement(3061174..3063948) Dinoroseobacter shibae DFL 12 = DSM 16493 5710755 YP_001534239.1 CDS Dshi_2905 NC_009952.1 3063948 3064850 R PFAM: PF01882; COG: COG1721 - Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain); related to DUF58; hypothetical protein complement(3063948..3064850) Dinoroseobacter shibae DFL 12 = DSM 16493 5710756 YP_001534240.1 CDS Dshi_2906 NC_009952.1 3064847 3065854 R COG: COG0714 - MoxR-like ATPases; PFAM: PF07726; SMART: SM00382; related to AAA ATPase; hypothetical protein complement(3064847..3065854) Dinoroseobacter shibae DFL 12 = DSM 16493 5710757 YP_001534241.1 CDS Dshi_2907 NC_009952.1 3065916 3066521 D COG: COG3816 - Uncharacterized protein conserved in bacteria; PFAM: PF06938 - Protein of unknown function (DUF1285); hypothetical protein 3065916..3066521 Dinoroseobacter shibae DFL 12 = DSM 16493 5710758 YP_001534242.1 CDS rluE NC_009952.1 3066582 3067118 R SWISSPROT P75966: Ribosomal large subunit pseudouridine synthase E; TIGRFAM: TIGR00093 pseudouridine synthase family; COG: COG1187 - 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases; PFAM: PF00849 - RNA pseudouridylate synthase; PROSITE: PS01149; ribosomal large subunit pseudouridine synthase E complement(3066582..3067118) Dinoroseobacter shibae DFL 12 = DSM 16493 5710759 YP_001534243.1 CDS polA NC_009952.1 3067301 3070099 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(3067301..3070099) Dinoroseobacter shibae DFL 12 = DSM 16493 5710760 YP_001534244.1 CDS Dshi_2910 NC_009952.1 3070163 3070828 R TIGRFAM: TIGR01065 channel protein, hemolysin III family; COG: COG1272 - Predicted membrane protein, hemolysin III homolog; PFAM: PF03006; related to haemolysin-III family protein; hypothetical protein complement(3070163..3070828) Dinoroseobacter shibae DFL 12 = DSM 16493 5710761 YP_001534245.1 CDS Dshi_2911 NC_009952.1 3070889 3071575 R TIGRFAM: TIGR02117 conserved hypothetical protein; hypothetical protein complement(3070889..3071575) Dinoroseobacter shibae DFL 12 = DSM 16493 5710762 YP_001534246.1 CDS Dshi_2912 NC_009952.1 3071600 3071788 R COG: COG4391 - Uncharacterized protein conserved in bacteria; hypothetical protein complement(3071600..3071788) Dinoroseobacter shibae DFL 12 = DSM 16493 5710763 YP_001534247.1 CDS Dshi_2913 NC_009952.1 3071922 3072887 D SWISSPROT P36879: Uncharacterized ABC transporter ATP-binding protein yadG; PFAM: PF00005; PROSITE: PS00211, PS50893; ABC transporter ATP-binding protein 3071922..3072887 Dinoroseobacter shibae DFL 12 = DSM 16493 5710764 YP_001534248.1 CDS Dshi_2914 NC_009952.1 3072942 3073709 R COG: COG1075 - Predicted acetyltransferases and hydrolases with the alpha/beta hydrolase fold; PROSITE: PS51257; SUPERFAMILY: SSF53474; putative alpha/beta hydrolase complement(3072942..3073709) Dinoroseobacter shibae DFL 12 = DSM 16493 5710765 YP_001534249.1 CDS Dshi_2915 NC_009952.1 3073785 3074231 D SWISSPROT Q58549: ADP-ribose pyrophosphatase; COG: COG1051 - ADP-ribose pyrophosphatase PFAM: PF00293; PRINTS: PR00502; Gene3D: G3DSA:3.90.79.10; related to ADP-ribose pyrophosphatase; hypothetical protein 3073785..3074231 Dinoroseobacter shibae DFL 12 = DSM 16493 5710766 YP_001534250.1 CDS Dshi_2916 NC_009952.1 3074228 3075076 R PFAM: PF00892 - integral membrane protein DUF6; COG: COG5006 - Predicted permease, DMT superfamily; similar to integral membrane protein DUF6; hypothetical protein complement(3074228..3075076) Dinoroseobacter shibae DFL 12 = DSM 16493 5710767 YP_001534251.1 CDS Dshi_2917 NC_009952.1 3075327 3076484 R TIGRFAM: TIGR02318 phosphonate metabolism protein PhnM; COG: COG3454 - Metal-dependent hydrolase involved in phosphonate metabolism; PFAM: PF01979 - Amidohydrolase family; similar to amidohydrolase; hypothetical protein complement(3075327..3076484) Dinoroseobacter shibae DFL 12 = DSM 16493 5710768 YP_001534252.1 CDS Dshi_2918 NC_009952.1 3076513 3077004 R PFAM: Acetyltransferase (GNAT) family; PROSITE: PS51186; COG: COG3153 - Predicted acetyltransferase; similar to acetyltransferase (GNAT); hypothetical protein complement(3076513..3077004) Dinoroseobacter shibae DFL 12 = DSM 16493 5710769 YP_001534253.1 CDS groEL NC_009952.1 3077174 3078817 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; chaperonin GroEL complement(3077174..3078817) Dinoroseobacter shibae DFL 12 = DSM 16493 5710770 YP_001534254.1 CDS Dshi_2920 NC_009952.1 3078861 3079172 R COG: COG0234 - Co-chaperonin GroES (HSP10); PFAM: PF00166; PROSITE: PS00681; PRINTS: PR00297; chaperonin 10 Kd subunit complement(3078861..3079172) Dinoroseobacter shibae DFL 12 = DSM 16493 5710771 YP_001534255.1 CDS Dshi_2921 NC_009952.1 3079549 3080532 D hypothetical protein 3079549..3080532 Dinoroseobacter shibae DFL 12 = DSM 16493 5710772 YP_001534256.1 CDS Dshi_2922 NC_009952.1 3080559 3081224 R COG: COG5482 - Uncharacterized conserved protein; hypothetical protein complement(3080559..3081224) Dinoroseobacter shibae DFL 12 = DSM 16493 5710773 YP_001534257.1 CDS Dshi_2923 NC_009952.1 3081428 3082663 D PFAM: PF07694; related to 5TMR of 5TMR-LYT; hypothetical protein 3081428..3082663 Dinoroseobacter shibae DFL 12 = DSM 16493 5710774 YP_001534258.1 CDS ppaC NC_009952.1 3082742 3083743 D catalyzes the hydrolysis of pyrophosphate to phosphate; putative manganese-dependent inorganic pyrophosphatase 3082742..3083743 Dinoroseobacter shibae DFL 12 = DSM 16493 5710775 YP_001534259.1 CDS Dshi_2925 NC_009952.1 3084036 3084908 D TIGRFAM: TIGR01459 HAD-superfamily class IIA hydrolase, TIGR01459 TIGR01460 Haloacid Dehalogenase Superfamily Class (subfamily) IIA; COG: COG0647 - Predicted sugar phosphatases of the HAD superfamily; PFAM: PF00702; putative Haloacid dehalogenase-like hydrolase 3084036..3084908 Dinoroseobacter shibae DFL 12 = DSM 16493 5710776 YP_001534260.1 CDS Dshi_2926 NC_009952.1 3085029 3085472 D SWISSPROT P77455: Protein maoC; PFAM: PF01575; COG: COG2030 - Acyl dehydratase; putative MaoC-like dehydratase 3085029..3085472 Dinoroseobacter shibae DFL 12 = DSM 16493 5710777 YP_001534261.1 CDS ribF NC_009952.1 3085522 3086475 D SWISSPROT P0AG40: Riboflavin biosynthesis protein; TIGRFAM: TIGR00083 riboflavin kinase/FMN adenylyltransferase; COG: COG0196 - FAD synthase; PFAM: PF06574; Gene3D: G3DSA:3.40.50.620; riboflavin biosynthesis protein 3085522..3086475 Dinoroseobacter shibae DFL 12 = DSM 16493 5710778 YP_001534262.1 CDS Dshi_2928 NC_009952.1 3086472 3086963 D COG: COG2983 - Uncharacterized conserved protein; PFAM: PF03692 - Uncharacterized protein family (UPF0153); hypothetical protein 3086472..3086963 Dinoroseobacter shibae DFL 12 = DSM 16493 5710779 YP_001534263.1 CDS Dshi_2929 NC_009952.1 3086930 3087763 R COG: COG0596 - Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily); PFAM: PF00561; PRINTS: PR00412, PR00111; PROSITE: PS00120; putative alpha/beta hydrolase complement(3086930..3087763) Dinoroseobacter shibae DFL 12 = DSM 16493 5710780 YP_001534264.1 CDS Dshi_2930 NC_009952.1 3087763 3088362 R COG: COG3917 - 2-hydroxychromene-2-carboxylate isomerase; SWISSPROT Q51948: 2-hydroxychromene-2-carboxylate isomerase nahD; putative 2-hydroxychromene-2-carboxylate isomerase complement(3087763..3088362) Dinoroseobacter shibae DFL 12 = DSM 16493 5710781 YP_001534265.1 CDS prs NC_009952.1 3088497 3089519 D SWISSPROT P0A717: ribose-phosphate pyrophosphokinase; TIGRFAM: TIGR01251 ribose-phosphate pyrophosphokinase; COG: COG0462 - Phosphoribosylpyrophosphate synthetase; PFAM: PF00156; PROSITE: PS00114; ribose-phosphate pyrophosphokinase 3088497..3089519 Dinoroseobacter shibae DFL 12 = DSM 16493 5710782 YP_001534266.1 CDS Dshi_2932 NC_009952.1 3089529 3089879 R associated with ATP synthase gene cluster; hypothetical protein complement(3089529..3089879) Dinoroseobacter shibae DFL 12 = DSM 16493 5710783 YP_001534267.1 CDS atpC1 NC_009952.1 3089986 3090381 R PFAM: PF02823; TIGRFAM: TIGR01216 ATP synthase, F1 epsilon subunit (delta in mitochondria); COG: COG0355 - F0F1-type ATP synthase, epsilon subunit (mitochondrial delta subunit); ATP synhtase epsilon chain complement(3089986..3090381) Dinoroseobacter shibae DFL 12 = DSM 16493 5710784 YP_001534268.1 CDS atpD2 NC_009952.1 3090391 3091815 R 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 complement(3090391..3091815) Dinoroseobacter shibae DFL 12 = DSM 16493 5710785 YP_001534269.1 CDS atpG2 NC_009952.1 3091833 3092705 R 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 complement(3091833..3092705) Dinoroseobacter shibae DFL 12 = DSM 16493 5710786 YP_001534270.1 CDS atpA1 NC_009952.1 3092718 3094256 R 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 complement(3092718..3094256) Dinoroseobacter shibae DFL 12 = DSM 16493 5710787 YP_001534271.1 CDS atpH NC_009952.1 3094257 3094817 R SWISSPROT P72244: ATP synthase delta chain; TIGRFAM: TIGR01145 ATP synthase, F1 delta subunit; COG: COG0712 - F0F1-type ATP synthase, delta subunit (mitochondrial oligomycin sensitivity protein); PFAM: PF00213; PROSITE: PS00389; ATP synthase subunit delta complement(3094257..3094817) Dinoroseobacter shibae DFL 12 = DSM 16493 5710788 YP_001534272.1 CDS Dshi_2938 NC_009952.1 3095104 3095874 R hypothetical protein complement(3095104..3095874) Dinoroseobacter shibae DFL 12 = DSM 16493 5710789 YP_001534273.1 CDS clpA NC_009952.1 3096331 3098658 D SWISSPROT P0ABH9: ATP-dependent Clp protease ATP-binding subunit; TIGRFAM: TIGR02639 ATP-dependent Clp protease ATP-binding subunit clpA; COG: COG0542 - ATPases with chaperone activity, ATP-binding subunit; PFAM: PF00004, PF02861, PF07724; ATP-dependent Clp protease ATP-binding subunit 3096331..3098658 Dinoroseobacter shibae DFL 12 = DSM 16493 5710790 YP_001534274.1 CDS Dshi_2940 NC_009952.1 3098707 3100653 R COG: COG1360 - Flagellar motor protein; PFAM: PF00691; PROSITE: PS51123; related to OmpA; hypothetical protein complement(3098707..3100653) Dinoroseobacter shibae DFL 12 = DSM 16493 5710791 YP_001534275.1 CDS Dshi_2941 NC_009952.1 3100657 3101940 R hypothetical protein complement(3100657..3101940) Dinoroseobacter shibae DFL 12 = DSM 16493 5710792 YP_001534276.1 CDS Dshi_2942 NC_009952.1 3102031 3102573 R PFAM: PF04752 - ChaC-like protein; SWISSPROT P39163: Cation transport protein chaC; COG: COG3703 - Uncharacterized protein involved in cation transport; putative cation transport protein complement(3102031..3102573) Dinoroseobacter shibae DFL 12 = DSM 16493 5710793 YP_001534277.1 CDS Dshi_2943 NC_009952.1 3102640 3103638 D hypothetical protein 3102640..3103638 Dinoroseobacter shibae DFL 12 = DSM 16493 5710794 YP_001534278.1 CDS Dshi_2944 NC_009952.1 3103635 3104450 R COG: COG3921 - Uncharacterized protein conserved in bacteria; PFAM: PF06904; related to extensin; hypothetical protein complement(3103635..3104450) Dinoroseobacter shibae DFL 12 = DSM 16493 5710795 YP_001534279.1 CDS tyrC NC_009952.1 3104447 3105388 R dual function enzyme catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate and the formation of tyrosine from arogenate; cyclohexadienyl dehydrogenase complement(3104447..3105388) Dinoroseobacter shibae DFL 12 = DSM 16493 5710796 YP_001534280.1 CDS hisC NC_009952.1 3105385 3106470 R catalyzes the formation of L-histidinol phosphate from imidazole-acetol phosphate and glutamate in histidine biosynthesis; histidinol-phosphate aminotransferase complement(3105385..3106470) Dinoroseobacter shibae DFL 12 = DSM 16493 5710797 YP_001534281.1 CDS hss NC_009952.1 3106547 3107965 R SWISSPROT O32323: Homospermidine synthase; PFAM: PF06408 - Homospermidine synthase; COG: COG5310 - Homospermidine synthase; homospermidine synthase complement(3106547..3107965) Dinoroseobacter shibae DFL 12 = DSM 16493 5710798 YP_001534282.1 CDS rpsD NC_009952.1 3108054 3108674 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(3108054..3108674) Dinoroseobacter shibae DFL 12 = DSM 16493 5710799 YP_001534283.1 CDS Dshi_2949 NC_009952.1 3109029 3111326 R TIGRFAM: TIGR02504 ribonucleoside-diphosphate reductase, adenosylcobalamin-dependent; COG: COG0209 - Ribonucleotide reductase, alpha subunit; putative Vitamin B12-dependent ribonucleotide reductase complement(3109029..3111326) Dinoroseobacter shibae DFL 12 = DSM 16493 5710800 YP_001534284.1 CDS Dshi_2950 NC_009952.1 3111468 3111923 D PFAM: PF07370 - Protein of unknown function (DUF1489); COG: COG5458 - Uncharacterized conserved protein; hypothetical protein 3111468..3111923 Dinoroseobacter shibae DFL 12 = DSM 16493 5710801 YP_001534285.1 CDS Dshi_2951 NC_009952.1 3112137 3113279 R COG: COG0031 - Cysteine synthase; PFAM: PF00291; PROSITE: PS00216; similar to cysteine synthase; hypothetical protein complement(3112137..3113279) Dinoroseobacter shibae DFL 12 = DSM 16493 5710802 YP_001534286.1 CDS panC NC_009952.1 3113286 3114131 R TIGRFAM: TIGR00018 pantoate--beta-alanine ligase; COG: COG0414 - Panthothenate synthetase; PFAM: PF02569 - Pantoate-beta-alanine ligase; pantothenate synthase complement(3113286..3114131) Dinoroseobacter shibae DFL 12 = DSM 16493 5710803 YP_001534287.1 CDS hisG NC_009952.1 3114128 3114847 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 catalytic subunit complement(3114128..3114847) Dinoroseobacter shibae DFL 12 = DSM 16493 5710804 YP_001534288.1 CDS hisZ NC_009952.1 3114844 3115950 R May allow the feedback regulation of ATP phosphoribosyltransferase activity by histidine; ATP phosphoribosyltransferase regulatory subunit complement(3114844..3115950) Dinoroseobacter shibae DFL 12 = DSM 16493 5710805 YP_001534289.1 CDS hisS NC_009952.1 3115954 3117447 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(3115954..3117447) Dinoroseobacter shibae DFL 12 = DSM 16493 5710806 YP_001534290.1 CDS Dshi_2956 NC_009952.1 3117536 3117745 D PFAM: PF04102- SlyX; similar to slyX; hypothetical protein 3117536..3117745 Dinoroseobacter shibae DFL 12 = DSM 16493 5710807 YP_001534291.1 CDS dnaE NC_009952.1 3117972 3121466 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(3117972..3121466) Dinoroseobacter shibae DFL 12 = DSM 16493 5710808 YP_001534292.1 CDS xghB NC_009952.1 3121712 3123163 D PFAM: PF00111, PF00941, PF01799, PF03450; TIGRFAM: TIGR02963 xanthine dehydrogenase, small subunit; COG: COG4630 - Xanthine dehydrogenase, iron-sulfur cluster and FAD-binding subunit A; iron-sulfur-binding subunit and FAD-binding subunit; putative xanthine dehydrogenase 3121712..3123163 Dinoroseobacter shibae DFL 12 = DSM 16493 5710809 YP_001534293.1 CDS xdhA NC_009952.1 3123160 3125505 D SWISSPROT Q46799: Xanthine dehydrogenase molybdenum-binding subunit; TIGRFAM: TIGR02965 xanthine dehydrogenase, molybdopterin binding subunit; COG: COG4631 - Xanthine dehydrogenase, molybdopterin-binding subunit B; xanthine dehydrogenase molybdenum-binding subunit 3123160..3125505 Dinoroseobacter shibae DFL 12 = DSM 16493 5710810 YP_001534294.1 CDS xdhC NC_009952.1 3125502 3126464 D TIGRFAM: TIGR02964 xanthine dehydrogenase accessory protein XdhC; PFAM: PF02625; COG: COG1975 - Xanthine and CO dehydrogenases maturation factor, XdhC/CoxF family; putative xanthine dehydrogenase accessory protein 3125502..3126464 Dinoroseobacter shibae DFL 12 = DSM 16493 5710811 YP_001534295.1 CDS Dshi_2961 NC_009952.1 3126461 3127996 D COG: COG3845 - ABC-type uncharacterized transport systems, ATPase components; PFAM: PF00005; PROSITE: PS00211, PS50893; SMART: SM00382; ABC transporter ATP-binding protein 3126461..3127996 Dinoroseobacter shibae DFL 12 = DSM 16493 5710812 YP_001534296.1 CDS Dshi_2962 NC_009952.1 3128219 3129304 D COG: COG4603 - ABC-type uncharacterized transport system, permease component; PFAM: PF02653-Branched-chain amino acid transport system / permease component; permease component; putative ABC type branched chain amino acid transport system 3128219..3129304 Dinoroseobacter shibae DFL 12 = DSM 16493 5710813 YP_001534297.1 CDS Dshi_2963 NC_009952.1 3129327 3130253 D COG: COG1079 - Uncharacterized ABC-type transport system, permease component; PFAM: PF02653-Branched-chain amino acid transport system / permease component; permease component; putative ABC type branched chain amino acid transport system 3129327..3130253 Dinoroseobacter shibae DFL 12 = DSM 16493 5710814 YP_001534298.1 CDS Dshi_2964 NC_009952.1 3130346 3131509 D PFAM: PF02608; SUPERFAMILY: SSF53822; putative basic membrane protein 3130346..3131509 Dinoroseobacter shibae DFL 12 = DSM 16493 5710815 YP_001534299.1 CDS Dshi_2965 NC_009952.1 3131594 3131788 R hypothetical protein complement(3131594..3131788) Dinoroseobacter shibae DFL 12 = DSM 16493 5710816 YP_001534300.1 CDS panB NC_009952.1 3131957 3132778 R TIGRFAM: TIGR00222 3-methyl-2-oxobutanoate hydroxymethyltransferase; COG: COG0413 - Ketopantoate hydroxymethyltransferase; PFAM: PF02548 Ketopantoate hydroxymethyltransferase; 3-methyl-2-oxobutanoate hydroxymethyltransferase complement(3131957..3132778) Dinoroseobacter shibae DFL 12 = DSM 16493 5710817 YP_001534301.1 CDS Dshi_2967 NC_009952.1 3133015 3135510 D COG: COG0404 - Glycine cleavage system T protein (aminomethyltransferase); PFAM: PF01266, PF01571, PF08669; bifunctional enzyme involved in glycine degradation 3133015..3135510 Dinoroseobacter shibae DFL 12 = DSM 16493 5710818 YP_001534302.1 CDS Dshi_2968 NC_009952.1 3135780 3136373 D hypothetical protein 3135780..3136373 Dinoroseobacter shibae DFL 12 = DSM 16493 5710819 YP_001534303.1 CDS Dshi_2969 NC_009952.1 3136386 3136724 R COG: COG0599 - Uncharacterized homolog of gamma-carboxymuconolactone decarboxylase subunit; TIGRFAM: TIGR00778; PFAM: PF02627; SUPERFAMILY: SSF69118; Gene3D: G3DSA:1.20.1290.10; related to alkylhydroxyperoxidase; hypothetical protein complement(3136386..3136724) Dinoroseobacter shibae DFL 12 = DSM 16493 5710820 YP_001534304.1 CDS gyaR NC_009952.1 3136810 3137796 R COG: COG1052 - Lactate dehydrogenase and related dehydrogenases; PFAM: PF00389, PF02826; PROSITE: PS00065, PS00671; glyoxylate reductase complement(3136810..3137796) Dinoroseobacter shibae DFL 12 = DSM 16493 5710821 YP_001534305.1 CDS Dshi_2971 NC_009952.1 3137930 3138544 D PFAM: PF06347; COG: COG3807 - Uncharacterized protein conserved in bacteria; hypothetical protein 3137930..3138544 Dinoroseobacter shibae DFL 12 = DSM 16493 5710822 YP_001534306.1 CDS Dshi_2972 NC_009952.1 3138517 3139428 R PFAM: PF00989, PROSITE: PS50112, SMART: SM00091; hypothetical protein complement(3138517..3139428) Dinoroseobacter shibae DFL 12 = DSM 16493 5710823 YP_001534307.1 CDS dcp NC_009952.1 3139524 3141545 R SWISSPROT P27236: Peptidyl-dipeptidase dcp; COG: COG0339 - Zn-dependent oligopeptidases; PFAM: PF01432; PROSITE: PS00142; peptidyl-dipeptidase complement(3139524..3141545) Dinoroseobacter shibae DFL 12 = DSM 16493 5710824 YP_001534308.1 CDS moeB NC_009952.1 3141645 3142685 R SWISSPROT P12282: Molybdopterin biosynthesis protein moeB; COG: COG0476 - Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 2; PFAM: PF00899, PF05237; molydopterin biosynthesis protein complement(3141645..3142685) Dinoroseobacter shibae DFL 12 = DSM 16493 5710825 YP_001534309.1 CDS dut NC_009952.1 3142690 3143157 R PFAM: PF00692- dUTPase; TIGRFAM: TIGR00576 deoxyuridine 5-triphosphate nucleotidohydrolase (dut); COG: COG0756 - dUTPase; deoxyuridine 5'-triphosphate nucleotidohydrolase complement(3142690..3143157) Dinoroseobacter shibae DFL 12 = DSM 16493 5710826 YP_001534310.1 CDS coaBC NC_009952.1 3143154 3144347 R 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 complement(3143154..3144347) Dinoroseobacter shibae DFL 12 = DSM 16493 5710827 YP_001534311.1 CDS Dshi_2977 NC_009952.1 3144414 3145166 R PFAM: PF04187 - Protein of unknown function DUF399; COG: COG3016 - Uncharacterized iron-regulated protein; hypothetical protein complement(3144414..3145166) Dinoroseobacter shibae DFL 12 = DSM 16493 5710828 YP_001534312.1 CDS rpoH2 NC_009952.1 3145214 3146095 R binds with the catalytic core of RNA polymerase to produce the holoenzyme; sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released; sigma-32 is responsible for the expression of heat shock promoters; there are paralogs in Rhizobium and Sinorhizobium; the proteins in this cluster act as secondary heat shock sigma factors; the Rhizobium sigma-32 factor may also be involved in exopolysaccharide production; RNA polymerase factor sigma-32 complement(3145214..3146095) Dinoroseobacter shibae DFL 12 = DSM 16493 5710829 YP_001534313.1 CDS Dshi_2979 NC_009952.1 3146213 3146737 D SWISSPROT P29931: Bifunctional adenosylcobalamin biosynthesis protein cobP; PFAM: PF02283 - Cobinamide kinase / cobinamide phosphate guanyltransferase; PIR: PIRSF006135 - bifunctional cobinamide kinase/cobinamide phosphate guanyltransferase; COG: COG2087 - Adenosyl cobinamide kinase/adenosyl cobinamide phosphate guanylyltransferase; putative bifunctional adenosylcobalamin biosynthesis protein 3146213..3146737 Dinoroseobacter shibae DFL 12 = DSM 16493 5710830 YP_001534314.1 CDS Dshi_2980 NC_009952.1 3146734 3147306 D PFAM: PF00300; related to phosphoglycerate mutase; hypothetical protein 3146734..3147306 Dinoroseobacter shibae DFL 12 = DSM 16493 5710831 YP_001534315.1 CDS Dshi_2981 NC_009952.1 3147482 3148744 D COG: COG2041 - Sulfite oxidase and related enzymes; PFAM: PF00174, PF03404; PRINTS: PR00407; SUPERFAMILY: SSF56524, SSF81296; putative molydopterin-binding oxidoreductase 3147482..3148744 Dinoroseobacter shibae DFL 12 = DSM 16493 5710832 YP_001534316.1 CDS Dshi_2982 NC_009952.1 3148819 3149169 D PROSITE: PS51257; SUPERFAMILY: SSF46626; related to cytochrome c; hypothetical protein 3148819..3149169 Dinoroseobacter shibae DFL 12 = DSM 16493 5710833 YP_001534317.1 CDS Dshi_2983 NC_009952.1 3149233 3150231 D COG:COG2130 - Putative NADP-dependent oxidoreductases; PFAM: PF00107; SUPERFAMILY: SSF50129; PANTHER: Alcohol dehydrogenase related; related to zinc-binding dehydrogenase; hypothetical protein 3149233..3150231 Dinoroseobacter shibae DFL 12 = DSM 16493 5710834 YP_001534318.1 CDS Dshi_2984 NC_009952.1 3150311 3151009 D COG: COG0625 - Glutathione S-transferase; SUPERFAMILY: SSF52833, SSF47616; Gene3D: G3DSA:3.40.30.10; similar to glutathione S-transferase; hypothetical protein 3150311..3151009 Dinoroseobacter shibae DFL 12 = DSM 16493 5710835 YP_001534319.1 CDS Dshi_2985 NC_009952.1 3151506 3152165 R COG: COG1802 - Transcriptional regulators; PFAM: PF00392, PF07729; PROSITE: PS50949; Gene3D: G3DSA:1.10.10.10; GntR type; HTH-type transcriptional regulator complement(3151506..3152165) Dinoroseobacter shibae DFL 12 = DSM 16493 5710836 YP_001534320.1 CDS Dshi_2986 NC_009952.1 3152197 3152889 R COG: COG1451 - Predicted metal-dependent hydrolase; PFAM: PF01863 - Protein of unknown function DUF45; PROSITE: PS00142; hypothetical protein complement(3152197..3152889) Dinoroseobacter shibae DFL 12 = DSM 16493 5710837 YP_001534321.1 CDS Dshi_2987 NC_009952.1 3152992 3153318 D TIGRFAM: TIGR02300 conserved hypothetical protein; PROSITE: PS00018; hypothetical protein 3152992..3153318 Dinoroseobacter shibae DFL 12 = DSM 16493 5710838 YP_001534322.1 CDS Dshi_2988 NC_009952.1 3153753 3154094 D PFAM: PF01906; COG: COG0393 - Uncharacterized conserved protein; hypothetical protein 3153753..3154094 Dinoroseobacter shibae DFL 12 = DSM 16493 5710840 YP_001534323.1 CDS Dshi_2989 NC_009952.1 3154359 3154565 R PROSITE: PS51257; related to membrane lipoprotein; hypothetical protein complement(3154359..3154565) Dinoroseobacter shibae DFL 12 = DSM 16493 5710841 YP_001534324.1 CDS Dshi_2990 NC_009952.1 3154721 3155620 D COG: COG4333 - Uncharacterized protein conserved in bacteria; PFAM: PF00126, PF03466; PROSITE: PS5093; Gene3D: G3DSA:1.10.10.10; LysR family; HTH-type transcriptional regulator 3154721..3155620 Dinoroseobacter shibae DFL 12 = DSM 16493 5710842 YP_001534325.1 CDS Dshi_2991 NC_009952.1 3155748 3156266 D PFAM: PF07799-Protein of unknown function (DUF1643); COG: COG4333 - Uncharacterized protein conserved in bacteria; hypothetical protein 3155748..3156266 Dinoroseobacter shibae DFL 12 = DSM 16493 5710843 YP_001534326.1 CDS dehH NC_009952.1 3156259 3157146 D SWISSPROT Q01398: Haloacetate dehalogenase H-1; COG: COG0596 - Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily); PFAM: PF00561; PRINTS: PR00412, PR00111; Haloacetate dehalogenase H-1 3156259..3157146 Dinoroseobacter shibae DFL 12 = DSM 16493 5710844 YP_001534327.1 CDS Dshi_2993 NC_009952.1 3157143 3157856 R hypothetical protein complement(3157143..3157856) Dinoroseobacter shibae DFL 12 = DSM 16493 5710845 YP_001534328.1 CDS rpsO NC_009952.1 3158099 3158368 D 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 3158099..3158368 Dinoroseobacter shibae DFL 12 = DSM 16493 5710846 YP_001534329.1 CDS Dshi_2995 NC_009952.1 3158467 3158823 R hypothetical protein complement(3158467..3158823) Dinoroseobacter shibae DFL 12 = DSM 16493 5710847 YP_001534330.1 CDS Dshi_2996 NC_009952.1 3158863 3159771 R COG: COG3568 - Metal-dependent hydrolase; PFAM: PF03372; PROSITE: PS51257; SUPERFAMILY: SSF56219; similar to Endonuclease/Exonuclease/Phosphatase family; hypothetical protein complement(3158863..3159771) Dinoroseobacter shibae DFL 12 = DSM 16493 5710848 YP_001534331.1 CDS pnp NC_009952.1 3159996 3162131 D SWISSPROT P05055: Polyribonucleotide nucleotidyltransferase; COG: COG1185 - Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase); PFAM: PF01138, PF00575, PF00013, PF03725, PF03726; SMART: SM00322; polynucleotide phosphorylase/polyadenylase 3159996..3162131 Dinoroseobacter shibae DFL 12 = DSM 16493 5710849 YP_001534332.1 CDS Dshi_2998 NC_009952.1 3162333 3164813 D COG: COG0668 - Small-conductance mechanosensitive channel; PFAM: PF00924; SUPERFAMILY: SSF82689, SSF82861, SSF50182; putative mechanosensitive ion channel 3162333..3164813 Dinoroseobacter shibae DFL 12 = DSM 16493 5710850 YP_001534333.1 CDS fadD1 NC_009952.1 3164958 3166478 R catalyzes the formation of malonyl-CoA from malonate and CoA; malonyl-CoA synthase complement(3164958..3166478) Dinoroseobacter shibae DFL 12 = DSM 16493 5710851 YP_001534334.1 CDS mcd NC_009952.1 3166482 3167735 R PFAM: Malonyl-CoA decarboxylase KEGG: rde:RD1_1475 malonyl-CoA decarboxylase. Good Pfam hit, good BLAST hit to several Roseobacter species, RBS 10nt upstream; malonyl-CoA decarboxylase complement(3166482..3167735) Dinoroseobacter shibae DFL 12 = DSM 16493 5710852 YP_001534335.1 CDS dctM2 NC_009952.1 3167732 3169048 R TIGRFAM: TRAP dicarboxylate transporter, DctM subunit PFAM: Citrate transporter; TRAP C4-dicarboxylate transport system permease DctM subunit KEGG: rde:RD1_1476 TrapT family, DctM subunit, putative. Good BLAST hit to Rhodobacterales, gene cluster; TRAP dicarboxylate transporter subunit DctM complement(3167732..3169048) Dinoroseobacter shibae DFL 12 = DSM 16493 5710853 YP_001534336.1 CDS dctQ4 NC_009952.1 3169048 3169599 R PFAM: Tripartite ATP-independent periplasmic transporter DctQ component . BLAST hit to Proteobacteria; TRAP dicarboxylate transporter subunit DctQ complement(3169048..3169599) Dinoroseobacter shibae DFL 12 = DSM 16493 5710854 YP_001534337.1 CDS dctP4 NC_009952.1 3169667 3170650 R PFAM: TRAP dicarboxylate transporter- DctP subunit KEGG: rde:RD1_1478 C4-dicarboxylate transport system C4-dicarboxylate-binding protein, putative. BLAST hit, good RBS 6nt upstream; TRAP dicarboxylate transporter subunit DctP complement(3169667..3170650) Dinoroseobacter shibae DFL 12 = DSM 16493 5710855 YP_001534338.1 CDS Dshi_3004 NC_009952.1 3170785 3171441 D PFAM: regulatory protein GntR HTH; GntR domain protein KEGG: rde:RD1_1479 GntR-family transcription regulator, putative; GntR family; transcriptional regulator 3170785..3171441 Dinoroseobacter shibae DFL 12 = DSM 16493 5710856 YP_001534339.1 CDS Dshi_3005 NC_009952.1 3171549 3171857 D hypothetical protein 3171549..3171857 Dinoroseobacter shibae DFL 12 = DSM 16493 5710857 YP_001534340.1 CDS rpe NC_009952.1 3171858 3172556 R PFAM: ribulose-phosphate 3-epimerase KEGG: rsp:RSP_2864 pentose-5-phosphate-3-epimerase; ribulose-phosphate 3-epimerase complement(3171858..3172556) Dinoroseobacter shibae DFL 12 = DSM 16493 5710858 YP_001534341.1 CDS ybgG NC_009952.1 3172670 3175837 R PFAM: glycoside hydrolase family 38; glycosyl hydrolase 38 domain protein; Glycoside hydrolase family 38 central region KEGG: jan:Jann_2057 alpha-mannosidase; alpha-mannosidase complement(3172670..3175837) Dinoroseobacter shibae DFL 12 = DSM 16493 5710859 YP_001534342.1 CDS Dshi_3008 NC_009952.1 3175881 3177611 R PFAM: ABC transporter related; Oligopeptide/dipeptide ABC transporter domain protein SMART: AAA ATPase KEGG: jan:Jann_2056 ABC transporter related. Contain duplicated ATPase; ATPase subunit; ABC transporter-like protein complement(3175881..3177611) Dinoroseobacter shibae DFL 12 = DSM 16493 5710860 YP_001534343.1 CDS Dshi_3009 NC_009952.1 3177623 3178567 R contain signal peptide und Transmembrane Helices; MSD; ABC transporter-like protein complement(3177623..3178567) Dinoroseobacter shibae DFL 12 = DSM 16493 5710861 YP_001534344.1 CDS Dshi_3010 NC_009952.1 3178564 3179583 R contain signal peptide und Transmembrane Helices; MSD; ABC transporter-like protein complement(3178564..3179583) Dinoroseobacter shibae DFL 12 = DSM 16493 5710862 YP_001534345.1 CDS Dshi_3011 NC_009952.1 3179758 3181491 R contain signal peptide, RBS 5nt upstream; periplasmic component; ABC transporter-like protein complement(3179758..3181491) Dinoroseobacter shibae DFL 12 = DSM 16493 5710863 YP_001534346.1 CDS Dshi_3012 NC_009952.1 3181609 3182298 R KEGG: jan:Jann_2052 Zn-dependent hydrolase of the beta-lactamase fold; putative Zn-dependent hydrolase of the beta-lactamase fold family complement(3181609..3182298) Dinoroseobacter shibae DFL 12 = DSM 16493 5710864 YP_001534347.1 CDS Dshi_3013 NC_009952.1 3182474 3182914 D PFAM: protein of unknown function DUF606 KEGG: jan:Jann_1137 protein of unknown function DUF606 ; TMH; hypothetical protein 3182474..3182914 Dinoroseobacter shibae DFL 12 = DSM 16493 5710865 YP_001534348.1 CDS Dshi_3014 NC_009952.1 3182924 3183751 R PFAM: Phytanoyl-CoA dioxygenase KEGG: jan:Jann_2051 phytanoyl-CoA dioxygenase; phytanoyl-CoA dioxygenase complement(3182924..3183751) Dinoroseobacter shibae DFL 12 = DSM 16493 5710866 YP_001534349.1 CDS Dshi_3015 NC_009952.1 3183841 3184692 D PFAM: helix-turn-helix- domain containing protein AraC type; AraC protein arabinose-binding/dimerisation KEGG: jan:Jann_2050 transcriptional regulator, AraC family; AraC family; transcriptional regulator 3183841..3184692 Dinoroseobacter shibae DFL 12 = DSM 16493 5710867 YP_001534350.1 CDS deoC NC_009952.1 3184761 3185780 D KEGG: jan:Jann_0789 deoxyribose-phosphate aldolase TIGRFAM: deoxyribose-phosphate aldolase PFAM: deoxyribose-phosphate aldolase/phospho-2-dehydro-3-deoxyheptonate aldolase; DERA; Deoxyriboaldolase; deoxyribose-phosphate aldolase 3184761..3185780 Dinoroseobacter shibae DFL 12 = DSM 16493 5710868 YP_001534351.1 CDS ald NC_009952.1 3185825 3188167 D PFAM: aldehyde dehydrogenase KEGG: sil:SPO3368 aldehyde dehydrogenase family protein; aldehyde dehydrogenase 3185825..3188167 Dinoroseobacter shibae DFL 12 = DSM 16493 5710869 YP_001534352.1 CDS Dshi_3018 NC_009952.1 3188327 3188980 R PFAM: protein of unknown function DUF1523; hypothetical protein complement(3188327..3188980) Dinoroseobacter shibae DFL 12 = DSM 16493 5710870 YP_001534353.1 CDS Dshi_3019 NC_009952.1 3188982 3189224 R hypothetical protein complement(3188982..3189224) Dinoroseobacter shibae DFL 12 = DSM 16493 5710871 YP_001534354.1 CDS dapE2 NC_009952.1 3189351 3190646 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 3189351..3190646 Dinoroseobacter shibae DFL 12 = DSM 16493 5710872 YP_001534355.1 CDS puuC NC_009952.1 3190673 3192130 D PFAM: aldehyde dehydrogenase KEGG: sil:SPO0097 aldehyde dehydrogenase family protein; Gamma-Glu-gamma-aminobutyraldehyde dehydrogenase; gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase 3190673..3192130 Dinoroseobacter shibae DFL 12 = DSM 16493 5710873 YP_001534356.1 CDS Dshi_3022 NC_009952.1 3192313 3193314 R PFAM: PfkB domain protein KEGG: jan:Jann_1671 PfkB; rde:RD1_0962 PfkB family kinase, putative; PfkB domain-containing protein complement(3192313..3193314) Dinoroseobacter shibae DFL 12 = DSM 16493 5710874 YP_001534357.1 CDS nth NC_009952.1 3193311 3193955 R KEGG: sil:SPO3581 endonuclease III TIGRFAM: endonuclease III PFAM: helix-hairpin-helix motif; HhH-GPD family protein SMART: iron-sulfur cluster loop; endonuclease III complement(3193311..3193955) Dinoroseobacter shibae DFL 12 = DSM 16493 5710875 YP_001534358.1 CDS ada NC_009952.1 3194067 3194930 D TIGRFAM: methylated-DNA--protein-cysteine methyltransferase PFAM: helix-turn-helix- domain containing protein AraC type; Methylated-DNA-[protein]-cysteine S-methyltransferase DNA binding KEGG: sil:SPO3578 ADA regulatory protein; ADA regulatory protein 3194067..3194930 Dinoroseobacter shibae DFL 12 = DSM 16493 5710876 YP_001534359.1 CDS Dshi_3025 NC_009952.1 3195037 3195663 D PFAM: OmpA/MotB domain protein; 17 kDa surface antigen KEGG: rsq:Rsph17025_0195 OmpA/MotB domain protein; OmpA/MotB domain-containing protein 3195037..3195663 Dinoroseobacter shibae DFL 12 = DSM 16493 5710877 YP_001534360.1 CDS pdhR NC_009952.1 3195719 3196486 D PFAM: regulatory protein GntR HTH; GntR domain protein KEGG: rde:RD1_1326 pdhR; pyruvate dehydrogenase complex repressor; pyruvate dehydrogenase complex repressor 3195719..3196486 Dinoroseobacter shibae DFL 12 = DSM 16493 5710878 YP_001534361.1 CDS atpF2 NC_009952.1 3196549 3197109 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(3196549..3197109) Dinoroseobacter shibae DFL 12 = DSM 16493 5710879 YP_001534362.1 CDS atpX NC_009952.1 3197114 3197638 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(3197114..3197638) Dinoroseobacter shibae DFL 12 = DSM 16493 5710880 YP_001534363.1 CDS atpE2 NC_009952.1 3197716 3197940 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(3197716..3197940) Dinoroseobacter shibae DFL 12 = DSM 16493 5710881 YP_001534364.1 CDS atpB1 NC_009952.1 3198004 3198750 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(3198004..3198750) Dinoroseobacter shibae DFL 12 = DSM 16493 5710882 YP_001534365.1 CDS atpI NC_009952.1 3198754 3199086 R KEGG: rde:RD1_1321 ATP synthase F0, subunit I; I subunit; ATP synthase F0 complement(3198754..3199086) Dinoroseobacter shibae DFL 12 = DSM 16493 5710883 YP_001534366.1 CDS Dshi_3032 NC_009952.1 3199429 3201147 R PFAM: Heparinase II/III family protein KEGG: rde:RD1_0654 hypothetical protein; sit:TM1040_0090 heparinase II/III-like; heparinase II/III family protein complement(3199429..3201147) Dinoroseobacter shibae DFL 12 = DSM 16493 5710884 YP_001534367.1 CDS rsmB1 NC_009952.1 3201216 3202547 R PFAM: Fmu (Sun) domain protein; NusB/RsmB/TIM44; methyltransferase small; Methyltransferase type 11 KEGG: rsh:Rsph17029_2765 Fmu (Sun) domain protein; 16S rRNA m5C967 methyltransferase; rRNA (cytosine-C(5)-)-methyltransferase; ribosomal RNA small subunit methyltransferase B complement(3201216..3202547) Dinoroseobacter shibae DFL 12 = DSM 16493 5710885 YP_001534368.1 CDS Dshi_3034 NC_009952.1 3202651 3202875 D PFAM: protein of unknown function DUF1674; hypothetical protein 3202651..3202875 Dinoroseobacter shibae DFL 12 = DSM 16493 5710886 YP_001534369.1 CDS Dshi_3035 NC_009952.1 3202894 3203289 R KEGG: jan:Jann_4038 hypothetical protein; hypothetical protein complement(3202894..3203289) Dinoroseobacter shibae DFL 12 = DSM 16493 5710887 YP_001534370.1 CDS Dshi_3036 NC_009952.1 3203392 3206619 R colocated with MFP subunit; pfam00873,; RND family, RND subunit; efflux transporter complement(3203392..3206619) Dinoroseobacter shibae DFL 12 = DSM 16493 5710888 YP_001534371.1 CDS Dshi_3037 NC_009952.1 3206616 3207824 R colocated with RND subunit; TIGRFAM: efflux transporter, RND family, MFP subunit PFAM: secretion protein HlyD family protein KEGG: jan:Jann_1310 secretion protein HlyD; RND family, MFP subunit; efflux transporter complement(3206616..3207824) Dinoroseobacter shibae DFL 12 = DSM 16493 5710889 YP_001534372.1 CDS Dshi_3038 NC_009952.1 3207941 3208633 D PFAM: regulatory protein TetR KEGG: rpb:RPB_3412 transcriptional regulator, TetR family; TetR family; transcriptional regulator 3207941..3208633 Dinoroseobacter shibae DFL 12 = DSM 16493 5710890 YP_001534373.1 CDS Dshi_3039 NC_009952.1 3208637 3209044 R PFAM: BLUF domain protein KEGG: rpe:RPE_3231 BLUF domain protein. Good BLAST hit to several Rhodobacteraceae species, pfam04940, RBS 10nt upstream; BLUF domain-containing protein complement(3208637..3209044) Dinoroseobacter shibae DFL 12 = DSM 16493 5710891 YP_001534374.1 CDS dapB NC_009952.1 3209163 3209972 R catalyzes the reduction of 2,3-dihydrodipicolinate to 2,3,4,5-tetrahydrodipicolinate in lysine and diaminopimelate biosynthesis; dihydrodipicolinate reductase complement(3209163..3209972) Dinoroseobacter shibae DFL 12 = DSM 16493 5710892 YP_001534375.1 CDS rbfA NC_009952.1 3210091 3210498 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 3210091..3210498 Dinoroseobacter shibae DFL 12 = DSM 16493 5710893 YP_001534376.1 CDS truB NC_009952.1 3210502 3211416 D catalyzes isomerization of specific uridines in RNA to pseudouridine; responsible for residues in T loops of many tRNAs; tRNA pseudouridine synthase B 3210502..3211416 Dinoroseobacter shibae DFL 12 = DSM 16493 5710894 YP_001534377.1 CDS Dshi_3043 NC_009952.1 3211416 3211694 D PFAM: protein of unknown function DUF1294 KEGG: ret:RHE_CH01861 putative inner membrane protein, predicted 3TMH; hypothetical protein 3211416..3211694 Dinoroseobacter shibae DFL 12 = DSM 16493 5710895 YP_001534378.1 CDS Dshi_3044 NC_009952.1 3211817 3213247 D PFAM: Tannase and feruloyl esterase KEGG: psa:PST_1665 tannase precursor; BLAST hit to Rhodobacteraceae, RBS 5nt upstream; feruloyl esterase 3211817..3213247 Dinoroseobacter shibae DFL 12 = DSM 16493 5710896 YP_001534379.1 CDS Dshi_3045 NC_009952.1 3213310 3214326 D PFAM: glycosyl transferase family 2 KEGG: rde:RD1_0635 glycosyl transferase, putative; putative glycosyl transferase 3213310..3214326 Dinoroseobacter shibae DFL 12 = DSM 16493 5710897 YP_001534380.1 CDS ttuD NC_009952.1 3214330 3215577 R PFAM: MOFRL domain protein KEGG: rso:RSp1449 probable hydroxypyruvate reductase oxidoreductase protein; hydroxypyruvate reductase complement(3214330..3215577) Dinoroseobacter shibae DFL 12 = DSM 16493 5710898 YP_001534381.1 CDS glxR NC_009952.1 3215574 3216458 R COG2084 MmsB - 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases PFAM: oxidoreductase domain protein; 6-phosphogluconate dehydrogenase NAD-binding KEGG: jan:Jann_3485 3-hydroxyisobutyrate dehydrogenase; TSAR; Tartronate semialdehyde reductase; 2-hydroxy-3-oxopropionate reductase complement(3215574..3216458) Dinoroseobacter shibae DFL 12 = DSM 16493 5710899 YP_001534382.1 CDS Dshi_3048 NC_009952.1 3216579 3217361 D PFAM: regulatory protein GntR HTH; GntR domain protein KEGG: bbr:BB2654 GntR-family transcriptional regulator COG2186:FadR, PRK10225 ; GntR domain protein KEGG: bbr:BB2654 GntR-family transcriptional regulator; GntR family transcriptional regulator 3216579..3217361 Dinoroseobacter shibae DFL 12 = DSM 16493 5710900 YP_001534383.1 CDS Dshi_3049 NC_009952.1 3217365 3218309 R RBS 7nt upstream PFAM: NAD-dependent epimerase/dehydratase; short-chain dehydrogenase/reductase SDR; 3-beta hydroxysteroid dehydrogenase/isomerase; dTDP-4-dehydrorhamnose reductase KEGG: acr:Acry_2399 NAD-dependent epimerase/dehydratase; NAD-dependent epimerase/dehydratase complement(3217365..3218309) Dinoroseobacter shibae DFL 12 = DSM 16493 5710901 YP_001534384.1 CDS citE2 NC_009952.1 3218553 3219509 R PFAM: HpcH/HpaI aldolase KEGG: rsq:Rsph17025_2481 citrate (pro-3S)-lyase; citrate lyase subunit beta complement(3218553..3219509) Dinoroseobacter shibae DFL 12 = DSM 16493 5710902 YP_001534385.1 CDS Dshi_3051 NC_009952.1 3219781 3220143 R hypothetical protein complement(3219781..3220143) Dinoroseobacter shibae DFL 12 = DSM 16493 5710903 YP_001534386.1 CDS Dshi_3052 NC_009952.1 3220290 3220997 R N-terminal elongation? Mu phage related?; Mu-like prophage I protein complement(3220290..3220997) Dinoroseobacter shibae DFL 12 = DSM 16493 5710904 YP_001534387.1 CDS Dshi_3053 NC_009952.1 3221433 3222143 R rde:RD1_0339 transposase, putative; putative transposase complement(3221433..3222143) Dinoroseobacter shibae DFL 12 = DSM 16493 5710905 YP_001534388.1 CDS Dshi_3054 NC_009952.1 3222427 3223182 R PFAM: phospholipid/glycerol acyltransferase KEGG: sit:TM1040_3500 phospholipid/glycerol acyltransferas,COG0204; phospholipid/glycerol acyltransferase complement(3222427..3223182) Dinoroseobacter shibae DFL 12 = DSM 16493 5710906 YP_001534389.1 CDS Dshi_3055 NC_009952.1 3223182 3224075 R SY, PFAM: protein of unknown function DUF214 KEGG: rsh:Rsph17029_2388 protein of unknown function DUF214 , COG2177, conserved neighborhood regions (with COG2884 and COG0204); hypothetical protein complement(3223182..3224075) Dinoroseobacter shibae DFL 12 = DSM 16493 5710907 YP_001534390.1 CDS ftsE NC_009952.1 3224072 3224743 R PFAM: ABC transporter related SMART: AAA ATPase KEGG: rde:RD1_1599 ftsE; cell division ATP-binding protein, putative; ABC transporter-like protein complement(3224072..3224743) Dinoroseobacter shibae DFL 12 = DSM 16493 5710908 YP_001534391.1 CDS Dshi_3057 NC_009952.1 3224908 3225654 D TIGRFAM: MJ0042 family finger-like protein KEGG: sil:SPO0336 hypothetical protein, Bad blast, but this protein contains a CXXCX(19)CXXC motif suggestive of MJ0042 family; hypothetical protein 3224908..3225654 Dinoroseobacter shibae DFL 12 = DSM 16493 5710909 YP_001534392.1 CDS Dshi_3058 NC_009952.1 3225943 3228627 R TIGRFAM: conserved hypothetical protein TIGR02302 KEGG: sil:SPO0335 hypothetical protein; hypothetical protein complement(3225943..3228627) Dinoroseobacter shibae DFL 12 = DSM 16493 5710910 YP_001534393.1 CDS lysA NC_009952.1 3228631 3229926 R TIGRFAM: diaminopimelate decarboxylase PFAM: Orn/DAP/Arg decarboxylase 2 KEGG: jan:Jann_0481 diaminopimelate decarboxylase; DAP decarboxylase; diaminopimelate decarboxylase complement(3228631..3229926) Dinoroseobacter shibae DFL 12 = DSM 16493 5710911 YP_001534394.1 CDS Dshi_3060 NC_009952.1 3230005 3230340 R KEGG: rsq:Rsph17025_2447 hypothetical protein, RBS; hypothetical protein complement(3230005..3230340) Dinoroseobacter shibae DFL 12 = DSM 16493 5710912 YP_001534395.1 CDS Dshi_3061 NC_009952.1 3230492 3230662 R hypothetical protein complement(3230492..3230662) Dinoroseobacter shibae DFL 12 = DSM 16493 5710913 YP_001534396.1 CDS argH NC_009952.1 3230659 3232050 R catalyzes the formation of arginine from (N-L-arginino)succinate; argininosuccinate lyase complement(3230659..3232050) Dinoroseobacter shibae DFL 12 = DSM 16493 5710914 YP_001534397.1 CDS tlpA NC_009952.1 3232085 3232660 D PFAM: alkyl hydroperoxide reductase/ Thiol specific antioxidant/ Mal allergen; Redoxin domain protein Swissprot: Thiol:disulfide interchange protein tlpA (Cytochrome c biogenesis protein tlpA); Cytochrome c biogenesis protein TlpA; Thiol:disulfide interchange protein TlpA 3232085..3232660 Dinoroseobacter shibae DFL 12 = DSM 16493 5710915 YP_001534398.1 CDS tag NC_009952.1 3232657 3233226 R KEGG: rsq:Rsph17025_2464 DNA-3-methyladenine glycosylase I TIGRFAM: DNA-3-methyladenine glycosylase I PFAM: methyladenine glycosylase; DNA-3-methyladenine glycosylase 1 complement(3232657..3233226) Dinoroseobacter shibae DFL 12 = DSM 16493 5710916 YP_001534399.1 CDS Dshi_3065 NC_009952.1 3233338 3234183 D PFAM: EAL domain protein KEGG: pde:Pden_2025 diguanylate phosphodiesterase , DUF2; EAL domain-containing protein 3233338..3234183 Dinoroseobacter shibae DFL 12 = DSM 16493 5710917 YP_001534400.1 CDS atoB NC_009952.1 3234503 3235678 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 3234503..3235678 Dinoroseobacter shibae DFL 12 = DSM 16493 5710918 YP_001534401.1 CDS fabG1 NC_009952.1 3235779 3236501 D TIGRFAM: acetoacetyl-CoA reductase PFAM: NAD-dependent epimerase/dehydratase; short-chain dehydrogenase/reductase SDR; KR domain protein KEGG: jan:Jann_0492 acetoacetyl-CoA reductase; 3-ketoacyl-acyl carrier protein reductase; 3-oxoacyl-[acyl-carrier-protein] reductase; acetoacetyl-CoA reductase 3235779..3236501 Dinoroseobacter shibae DFL 12 = DSM 16493 5710919 YP_001534402.1 CDS Dshi_3068 NC_009952.1 3236804 3237751 D Glycine cleavage system transcriptional activator; activates the gcvTHP operon in the presence of glycine and represses the operon in its absence; DNA-binding transcriptional activator GcvA 3236804..3237751 Dinoroseobacter shibae DFL 12 = DSM 16493 5710920 YP_001534403.1 CDS Dshi_3069 NC_009952.1 3237811 3237978 R PFAM: protein of unknown function DUF465 KEGG: pde:Pden_2028 protein of unknown function DUF465, COG5570; hypothetical protein complement(3237811..3237978) Dinoroseobacter shibae DFL 12 = DSM 16493 5710921 YP_001534404.1 CDS Dshi_3070 NC_009952.1 3238074 3238844 R KEGG: rsp:RSP_0748 N-6 adenine-specific DNA methylase ;pfam05175 MTS Methyltransferase small domain; COG4123 Predicted O-methyltransferase; type 11 methyltransferase complement(3238074..3238844) Dinoroseobacter shibae DFL 12 = DSM 16493 5710922 YP_001534405.1 CDS Dshi_3071 NC_009952.1 3238844 3239071 R pfam09413 Protein of unknown function (DUF2007) KEGG: rde:RD1_3400 hypothetical protein; hypothetical protein complement(3238844..3239071) Dinoroseobacter shibae DFL 12 = DSM 16493 5710923 YP_001534406.1 CDS ispB NC_009952.1 3239127 3240131 D PFAM: Polyprenyl synthetase KEGG: rsh:Rsph17029_2406 trans-hexaprenyltranstransferase; octaprenyl-diphosphate synthase 3239127..3240131 Dinoroseobacter shibae DFL 12 = DSM 16493 5710924 YP_001534407.1 CDS ispE NC_009952.1 3240124 3240987 R An essential enzyme in the nonmevalonate pathway of isopentenyl diphosphate and dimethylallyl diphosphate biosynthesis; 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase complement(3240124..3240987) Dinoroseobacter shibae DFL 12 = DSM 16493 5710925 YP_001534408.1 CDS Dshi_3074 NC_009952.1 3240971 3242725 R PFAM: TPR repeat-containing protein; Tetratricopeptide TPR_4; Tetratricopeptide TPR_2 repeat protein SMART: Tetratricopeptide domain protein KEGG: sil:SPO0317 TPR domain protein. Annotation was derived from R. denitrificans; hypothetical protein complement(3240971..3242725) Dinoroseobacter shibae DFL 12 = DSM 16493 5710926 YP_001534409.1 CDS ydiS NC_009952.1 3242821 3244470 R pfam05187 FAD dependent oxidoreductase; electron transfer flavoprotein-ubiquinone oxidoreductase KEGG: rde:RD1_3404 electron transfer flavoprotein-ubiquinone oxidoreductase, putative COG0644; Electron-transferring-flavoprotein dehydrogenase; ETF dehydrogenase; ETF-ubiquinone oxidoreductase; ETF-QO; electron transfer flavoprotein-ubiquinone oxidoreductase complement(3242821..3244470) Dinoroseobacter shibae DFL 12 = DSM 16493 5710927 YP_001534410.1 CDS greA NC_009952.1 3244630 3245145 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 3244630..3245145 Dinoroseobacter shibae DFL 12 = DSM 16493 5710928 YP_001534411.1 CDS Dshi_3077 NC_009952.1 3245223 3246209 D KEGG: sil:SPO0311 hypothetical protein; hypothetical protein 3245223..3246209 Dinoroseobacter shibae DFL 12 = DSM 16493 5710929 YP_001534412.1 CDS Dshi_3078 NC_009952.1 3246273 3246977 D PFAM: AzlC family protein KEGG: rsq:Rsph17025_2457 AzlC family protein; AzlC family protein 3246273..3246977 Dinoroseobacter shibae DFL 12 = DSM 16493 5710930 YP_001534413.1 CDS Dshi_3079 NC_009952.1 3246974 3247306 D PFAM: branched-chain amino acid transport pfam05437AzlDKEGG: rde:RD1_3412 hypothetical protein ; Neighborhood with AzlC family protein ; predicted TMH; AzlD branched-chain amino acid transport 3246974..3247306 Dinoroseobacter shibae DFL 12 = DSM 16493 5710931 YP_001534414.1 CDS Dshi_3080 NC_009952.1 3247400 3248863 D colocated with RND subunit; TIGRFAM: efflux transporter, RND family, MFP subunit PFAM: secretion protein HlyD family protein KEGG: jan:Jann_1310 secretion protein HlyD; RND family, MFP subunit; efflux transporter 3247400..3248863 Dinoroseobacter shibae DFL 12 = DSM 16493 5710932 YP_001534415.1 CDS Dshi_3081 NC_009952.1 3248865 3252272 D colocated with MFP subunit; pfam00873,; RND family, RND subunit; efflux transporter 3248865..3252272 Dinoroseobacter shibae DFL 12 = DSM 16493 5710933 YP_001534416.1 CDS Dshi_3082 NC_009952.1 3252382 3253191 R KEGG: rsh:Rsph17029_2660 hypothetical protein ,COG4233; hypothetical protein complement(3252382..3253191) Dinoroseobacter shibae DFL 12 = DSM 16493 5710934 YP_001534417.1 CDS Dshi_3083 NC_009952.1 3253311 3253889 D pfam02622,DUF179,COG1678 Putative transcriptional regulator; KEGG: rde:RD1_3419 hypothetical protein; hypothetical protein 3253311..3253889 Dinoroseobacter shibae DFL 12 = DSM 16493 5710935 YP_001534418.1 CDS Dshi_3084 NC_009952.1 3253947 3254924 R TIGRFAM: Sua5/YciO/YrdC/YwlC family protein PFAM: SUA5 domain protein; SUA5/yciO/yrdC domain KEGG: pde:Pden_0435 SUA5/YciO/YrdC/YwlC family protein; Sua5/YciO/YrdC/YwlC family protein complement(3253947..3254924) Dinoroseobacter shibae DFL 12 = DSM 16493 5710936 YP_001534419.1 CDS Dshi_3085 NC_009952.1 3255050 3256765 D PFAM: acyl-CoA dehydrogenase domain protein; Acyl-CoA dehydrogenase type 2 domain KEGG: sil:SPO0298 acyl-CoA dehydrogenase family protein; rde:RD1_3417 putative acyl-CoA; putative acyl-CoA dehydrogenase family protein 3255050..3256765 Dinoroseobacter shibae DFL 12 = DSM 16493 5710937 YP_001534420.1 CDS Dshi_3086 NC_009952.1 3256765 3257814 D PFAM: beta-lactamase domain protein KEGG: rsh:Rsph17029_2397 beta-lactamase domain protein; metallo-beta-lactamase family protein 3256765..3257814 Dinoroseobacter shibae DFL 12 = DSM 16493 5710938 YP_001534421.1 CDS Dshi_3087 NC_009952.1 3257905 3258042 D 45aa protein PFAM: aa3 type cytochrome c oxidase subunit IV; hypothetical protein 3257905..3258042 Dinoroseobacter shibae DFL 12 = DSM 16493 5710939 YP_001534422.1 CDS Dshi_3088 NC_009952.1 3258055 3258663 D KEGG: rsh:Rsph17029_2395 hypothetical protein; hypothetical protein 3258055..3258663 Dinoroseobacter shibae DFL 12 = DSM 16493 5710940 YP_001534423.1 CDS moaB NC_009952.1 3258688 3259230 R TIGRFAM: molybdenum cofactor synthesis domain; molybdenum cofactor biosynthesis protein B PFAM: molybdopterin binding domain KEGG: sil:SPO0291 molybdenum cofactor biosynthesis protein B; molybdenum cofactor biosynthesis protein B complement(3258688..3259230) Dinoroseobacter shibae DFL 12 = DSM 16493 5710941 YP_001534424.1 CDS udgA NC_009952.1 3259227 3260024 R TIGRFAM: phage SPO1 DNA polymerase-related protein PFAM: Uracil-DNA glycosylase superfamily KEGG: sil:SPO0288 uracil-DNA glycosylase; rde:RD1_3425 udgA; uracil-DNA glycosylase, C-terminal; uracil-DNA glycosylase complement(3259227..3260024) Dinoroseobacter shibae DFL 12 = DSM 16493 5710942 YP_001534425.1 CDS pyrB NC_009952.1 3260134 3261084 D catalyzes the transfer of the carbamoyl moiety from carbamoyl phosphate to L- aspartate in pyrimidine biosynthesis; aspartate carbamoyltransferase catalytic subunit 3260134..3261084 Dinoroseobacter shibae DFL 12 = DSM 16493 5710943 YP_001534426.1 CDS Dshi_3092 NC_009952.1 3261081 3261506 D hypothetical protein 3261081..3261506 Dinoroseobacter shibae DFL 12 = DSM 16493 5710944 YP_001534427.1 CDS Dshi_3093 NC_009952.1 3261503 3262081 D hypothetical protein 3261503..3262081 Dinoroseobacter shibae DFL 12 = DSM 16493 5710945 YP_001534428.1 CDS pyrC1 NC_009952.1 3262081 3263379 D KEGG: rsh:Rsph17029_2663 dihydroorotase, multifunctional complex type TIGRFAM: dihydroorotase, multifunctional complex type PFAM: amidohydrolase; DHOase; dihydroorotase 3262081..3263379 Dinoroseobacter shibae DFL 12 = DSM 16493 5710946 YP_001534429.1 CDS Dshi_3095 NC_009952.1 3263379 3263990 D PFAM: protein of unknown function DUF205 KEGG: jan:Jann_3906 protein of unknown function DUF205 , COG0344, COG0344; hypothetical protein 3263379..3263990 Dinoroseobacter shibae DFL 12 = DSM 16493 5710947 YP_001534430.1 CDS Dshi_3096 NC_009952.1 3263993 3264499 D PFAM: protein of unknown function DUF805 KEGG: jan:Jann_3908 protein of unknown function DUF805,COG3152 - Predicted membrane protein; hypothetical protein 3263993..3264499 Dinoroseobacter shibae DFL 12 = DSM 16493 5710948 YP_001534431.1 CDS gsh NC_009952.1 3264516 3265886 R KEGG: sil:SPO3626 glutamate-cysteine ligase TIGRFAM: glutamate--cysteine ligase PFAM: glutamate--cysteine ligase GCS2; glutamate--cysteine ligase complement(3264516..3265886) Dinoroseobacter shibae DFL 12 = DSM 16493 5710949 YP_001534432.1 CDS Dshi_3098 NC_009952.1 3265922 3266470 R hypothetical protein complement(3265922..3266470) Dinoroseobacter shibae DFL 12 = DSM 16493 5710950 YP_001534433.1 CDS Dshi_3099 NC_009952.1 3266467 3267216 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(3266467..3267216) Dinoroseobacter shibae DFL 12 = DSM 16493 5710951 YP_001534434.1 CDS ubiA NC_009952.1 3267233 3268201 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 3267233..3268201 Dinoroseobacter shibae DFL 12 = DSM 16493 5710952 YP_001534435.1 CDS Dshi_3101 NC_009952.1 3268262 3270115 D PFAM: OmpA/MotB domain protein KEGG: sit:TM1040_3081 OmpA/MotB. Annotation was derived from R. denitrificans; OmpA domain-containing protein 3268262..3270115 Dinoroseobacter shibae DFL 12 = DSM 16493 5710953 YP_001534436.1 CDS Dshi_3102 NC_009952.1 3270112 3270444 D KEGG: rsh:Rsph17029_2670 hypothetical protein; hypothetical protein 3270112..3270444 Dinoroseobacter shibae DFL 12 = DSM 16493 5710954 YP_001534437.1 CDS moaE NC_009952.1 3270452 3270895 R PFAM: molybdopterin biosynthesis MoaE protein KEGG: sil:SPO3633 molybdopterin converting factor, subunit 2; Molybdopterin-converting factor large subunit; Molybdenum cofactor biosynthesis protein E; Molybdopterin synthase subunit 2; MPT synthase subunit 2; molybdopterin-converting factor subunit 2 complement(3270452..3270895) Dinoroseobacter shibae DFL 12 = DSM 16493 5710955 YP_001534438.1 CDS moaD NC_009952.1 3270897 3271148 R TIGRFAM: molybdopterin converting factor, subunit 1 PFAM: thiamineS protein KEGG: rsp:RSP_1072 putative molybdopterin MPT converting factor, subunit 1 protein; Neigbhorhood; Molybdopterin-converting factor small subunit; Molybdenum cofactor biosynthesis protein D; Molybdopterin synthase subunit 1; MPT synthase subunit 1; molybdopterin-converting factor subunit 1 complement(3270897..3271148) Dinoroseobacter shibae DFL 12 = DSM 16493 5710956 YP_001534439.1 CDS pgsA NC_009952.1 3271145 3271810 R TIGRFAM: CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase PFAM: CDP-alcohol phosphatidyltransferase KEGG: rsh:Rsph17029_2734 CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase; PGP synthase; Phosphatidylglycerophosphate synthase; CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase complement(3271145..3271810) Dinoroseobacter shibae DFL 12 = DSM 16493 5710957 YP_001534440.1 CDS rluA NC_009952.1 3272254 3272913 R pfam00849 PseudoU_synth_2, COG0564 -Pseudouridylate synthases, 23S RNA-specific, TIGR00005 pseudouridine synthase, RluA family, good blast hit to swissprot.; rRNA pseudouridylate synthase A; rRNA-uridine isomerase A; ribosomal large subunit pseudouridine synthase A complement(3272254..3272913) Dinoroseobacter shibae DFL 12 = DSM 16493 5710958 YP_001534441.1 CDS rhtB NC_009952.1 3273004 3273621 D PFAM: Lysine exporter protein (LYSE/YGGA) KEGG: sit:TM1040_0069 lysine exporter protein (LysE/YggA), good blast hit to R. denitrificans; homoserine/homoserine lactone efflux protein 3273004..3273621 Dinoroseobacter shibae DFL 12 = DSM 16493 5710959 YP_001534442.1 CDS Dshi_3108 NC_009952.1 3273755 3274522 D PFAM: DSBA oxidoreductase KEGG: rde:RD1_0191 protein-disulfide isomerase, putative; putative protein-disulfide isomerase 3273755..3274522 Dinoroseobacter shibae DFL 12 = DSM 16493 5710960 YP_001534443.1 CDS Dshi_3109 NC_009952.1 3274527 3276476 R KEGG: rde:RD1_0522 hypothetical protein; hypothetical protein complement(3274527..3276476) Dinoroseobacter shibae DFL 12 = DSM 16493 5710961 YP_001534444.1 CDS Dshi_3110 NC_009952.1 3276494 3277162 R PFAM: cyclic nucleotide-binding KEGG: rsq:Rsph17025_3179 hypothetical protein; cyclic nucleotide-binding protein complement(3276494..3277162) Dinoroseobacter shibae DFL 12 = DSM 16493 5710962 YP_001534445.1 CDS aslA NC_009952.1 3277491 3279092 D PFAM: sulfatase KEGG: rde:RD1_0531 arylsulfatase; Aryl-sulfate sulphohydrolase; AS; arylsulfatase 3277491..3279092 Dinoroseobacter shibae DFL 12 = DSM 16493 5710963 YP_001534446.1 CDS Dshi_3112 NC_009952.1 3279170 3280126 D KEGG: rde:RD1_0530 nonspecific acid phosphatase; nonspecific acid phosphatase 3279170..3280126 Dinoroseobacter shibae DFL 12 = DSM 16493 5710964 YP_001534447.1 CDS Dshi_3113 NC_009952.1 3280195 3281160 D PFAM: ATPase associated with various cellular activities AAA_3; ATPase associated with various cellular activities AAA_5 KEGG: rde:RD1_0529 MoxR-like ATPase, putative; putative MoxR-like ATPase 3280195..3281160 Dinoroseobacter shibae DFL 12 = DSM 16493 5710965 YP_001534448.1 CDS Dshi_3114 NC_009952.1 3281172 3282107 D PFAM: protein of unknown function DUF58 KEGG: rde:RD1_0528 hypothetical protein, COG1721; hypothetical protein 3281172..3282107 Dinoroseobacter shibae DFL 12 = DSM 16493 5710966 YP_001534449.1 CDS Dshi_3115 NC_009952.1 3282104 3282577 D KEGG: rde:RD1_0527 hypothetical protein; hypothetical protein 3282104..3282577 Dinoroseobacter shibae DFL 12 = DSM 16493 5710967 YP_001534450.1 CDS Dshi_3116 NC_009952.1 3282574 3283560 D PFAM:VWA von Willebrand factor type A domain KEGG: rde:RD1_0526 hypothetical protein,TMH; von Willebrand factor type A domain-containing protein 3282574..3283560 Dinoroseobacter shibae DFL 12 = DSM 16493 5710968 YP_001534451.1 CDS Dshi_3117 NC_009952.1 3283557 3285068 D KEGG: rde:RD1_0525 hypothetical protein; hypothetical protein 3283557..3285068 Dinoroseobacter shibae DFL 12 = DSM 16493 5710969 YP_001534452.1 CDS Dshi_3118 NC_009952.1 3285065 3286309 D KEGG: rde:RD1_0524 hypothetical protein; hypothetical protein 3285065..3286309 Dinoroseobacter shibae DFL 12 = DSM 16493 5710970 YP_001534453.1 CDS gltA1 NC_009952.1 3286328 3287092 R KEGG: sit:TM1040_2728 citrate synthase; citrate synthase complement(3286328..3287092) Dinoroseobacter shibae DFL 12 = DSM 16493 5710971 YP_001534454.1 CDS yfdW2 NC_009952.1 3287089 3288279 R PFAM: CoA-transferase family III PRK05398 formyl-coenzyme A transferase KEGG: sit:TM1040_2729 L-carnitine dehydratase/bile acid-inducible protein F; Formyl-CoA transferase; formyl-coenzyme A transferase complement(3287089..3288279) Dinoroseobacter shibae DFL 12 = DSM 16493 5710972 YP_001534455.1 CDS Dshi_3121 NC_009952.1 3288269 3289786 R PFAM: protein of unknown function DUF112 transmembrane COG3333 - Uncharacterized protein conserved in bacteria; hypothetical protein complement(3288269..3289786) Dinoroseobacter shibae DFL 12 = DSM 16493 5710973 YP_001534456.1 CDS Dshi_3122 NC_009952.1 3289790 3290278 R KEGG: rde:RD1_2947 hypothetical protein; hypothetical protein complement(3289790..3290278) Dinoroseobacter shibae DFL 12 = DSM 16493 5710974 YP_001534457.1 CDS Dshi_3123 NC_009952.1 3290359 3291339 R COG3181 Uncharacterized protein conserved in bacteria KEGG: rde:RD1_2946 hypothetical protein; hypothetical protein complement(3290359..3291339) Dinoroseobacter shibae DFL 12 = DSM 16493 5710975 YP_001534458.1 CDS qseB NC_009952.1 3291441 3292106 D PFAM: response regulator receiver; transcriptional regulator domain protein KEGG: sit:TM1040_2733 two component transcriptional regulator, winged helix family COG0745 - Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain; transcriptional regulatory protein QseB 3291441..3292106 Dinoroseobacter shibae DFL 12 = DSM 16493 5710976 YP_001534459.1 CDS qseC NC_009952.1 3292103 3293476 D PFAM:HATPase_c Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase ,2CSK_N Two-component sensor kinase N-terminal KEGG: sit:TM1040_2734 periplasmic sensor signal transduction histidine kinase; sensor protein QseC 3292103..3293476 Dinoroseobacter shibae DFL 12 = DSM 16493 5710977 YP_001534460.1 CDS Dshi_3126 NC_009952.1 3293446 3294447 D KEGG: sil:SPO0189 putative iron(III) transport system substrate-binding protein. Annotation was derived from R. denitrificans; putative periplasmic iron-binding protein 3293446..3294447 Dinoroseobacter shibae DFL 12 = DSM 16493 5710978 YP_001534461.1 CDS ugpB2 NC_009952.1 3294602 3296341 D PFAM: extracellular solute-binding protein family 1 KEGG: rde:RD1_4122 sugar ABC transporter, periplasmic sugar-binding protein, putative; periplasmic sugar-binding protein, putative; sugar ABC transporter 3294602..3296341 Dinoroseobacter shibae DFL 12 = DSM 16493 5710979 YP_001534462.1 CDS ugpC5 NC_009952.1 3296414 3297475 D PFAM: ABC transporter related; Transport-associated OB domain protein pfam00005,SMART: AAA ATPase KEGG: rde:RD1_4120 SN-glycerol-3-phosphate transport ATP-binding protein; ATP-binding protein (sn-glycerol-3-phosphate import ATP-binding protein ugpC); sugar ABC transporter 3296414..3297475 Dinoroseobacter shibae DFL 12 = DSM 16493 5710980 YP_001534463.1 CDS ugpC1 NC_009952.1 3297477 3298550 D PFAM: ABC transporter related; pfam00005, Transport-associated OB domain protein SMART: AAA ATPase KEGG: rde:RD1_4119 sugar ABC transporter, ATP-binding protein, putative; ATP-binding protein (sn-glycerol-3-phosphate import ATP-binding protein ugpC); sugar ABC transporter 3297477..3298550 Dinoroseobacter shibae DFL 12 = DSM 16493 5710981 YP_001534464.1 CDS ugpA2 NC_009952.1 3298547 3299410 D PFAM: binding-protein-dependent transport systems inner membrane component KEGG: rde:RD1_4118 sugar ABC transporter, permease protein, putative COG1175 - ABC-type sugar transport systems, permease components ,TMH; permease protein, putative (MSD); sugar ABC transporter 3298547..3299410 Dinoroseobacter shibae DFL 12 = DSM 16493 5710982 YP_001534465.1 CDS ugpE1 NC_009952.1 3299407 3300204 D PFAM: binding-protein-dependent transport systems inner membrane component KEGG: jan:Jann_4088 binding-protein-dependent transport systems inner membrane component COG0395 - ABC-type sugar transport system, permease component , TMH; permease protein, putative (MSD); sugar ABC transporter 3299407..3300204 Dinoroseobacter shibae DFL 12 = DSM 16493 5710983 YP_001534466.1 CDS Dshi_3132 NC_009952.1 3300204 3300602 D TMH; hypothetical protein 3300204..3300602 Dinoroseobacter shibae DFL 12 = DSM 16493 5710984 YP_001534467.1 CDS Dshi_3133 NC_009952.1 3300641 3301048 D PFAM: Penicillinase repressor KEGG: rde:RD1_4115 transcriptional regulator, putative; putative transcriptional regulator 3300641..3301048 Dinoroseobacter shibae DFL 12 = DSM 16493 5710985 YP_001534468.1 CDS Dshi_3134 NC_009952.1 3301023 3302168 D PFAM: peptidase M56 BlaR1 KEGG: rde:RD1_4114 BlaR1 peptidase M56 domain protein; Motif HEXXH; BlaR1 peptidase M56 domain-containing protein 3301023..3302168 Dinoroseobacter shibae DFL 12 = DSM 16493 5710986 YP_001534469.1 CDS Dshi_3135 NC_009952.1 3302652 3303122 D hypothetical protein 3302652..3303122 Dinoroseobacter shibae DFL 12 = DSM 16493 5710987 YP_001534470.1 CDS Dshi_3136 NC_009952.1 3303263 3304162 D LipoP1.0 KEGG: jan:Jann_1313 lipoprotein, putative; putative lipoprotein 3303263..3304162 Dinoroseobacter shibae DFL 12 = DSM 16493 5710988 YP_001534471.1 CDS Dshi_3137 NC_009952.1 3304170 3304880 R hypothetical protein complement(3304170..3304880) Dinoroseobacter shibae DFL 12 = DSM 16493 5710989 YP_001534472.1 CDS Dshi_3138 NC_009952.1 3304846 3305598 R KEGG: smd:Smed_4297 alpha/beta hydrolase fold; hypothetical protein complement(3304846..3305598) Dinoroseobacter shibae DFL 12 = DSM 16493 5710990 YP_001534473.1 CDS Dshi_3139 NC_009952.1 3305602 3306732 R KEGG: jan:Jann_1112 cupin 2 protein; cupin domain-containing protein complement(3305602..3306732) Dinoroseobacter shibae DFL 12 = DSM 16493 5712195 YP_001534474.1 CDS Dshi_3140 NC_009952.1 3306735 3307787 R PFAM: regulatory protein LacI; periplasmic binding protein/LacI transcriptional regulator KEGG: rde:RD1_3944 transcriptional regulatory protein, LacI family, putative; LacI family; transcriptional regulator complement(3306735..3307787) Dinoroseobacter shibae DFL 12 = DSM 16493 5712196 YP_001534475.1 CDS ugpC3 NC_009952.1 3307792 3308850 R PFAM: ABC transporter related; Transport-associated OB domain protein pfam00005,SMART: AAA ATPase KEGG: jan:Jann_4087 ABC transporter related; ATP-binding protein (sn-glycerol-3-phosphate import ATP-binding protein ugpC); sugar ABC transporter complement(3307792..3308850) Dinoroseobacter shibae DFL 12 = DSM 16493 5712197 YP_001534476.1 CDS ugpE2 NC_009952.1 3308891 3309718 R PFAM: binding-protein-dependent transport systems inner membrane component KEGG: jan:Jann_4088 binding-protein-dependent transport systems inner membrane component COG0395 - ABC-type sugar transport system, permease component ,TMH; permease protein, putative (MSD); sugar ABC transporter complement(3308891..3309718) Dinoroseobacter shibae DFL 12 = DSM 16493 5712198 YP_001534477.1 CDS ugpA3 NC_009952.1 3309722 3310594 R PFAM: binding-protein-dependent transport systems inner membrane component KEGG: jan:Jann_4089 binding-protein-dependent transport systems inner membrane component ;COG1175 - ABC-type sugar transport systems, permease components ,TMH; permease protein, putative (MSD); sugar ABC transporter complement(3309722..3310594) Dinoroseobacter shibae DFL 12 = DSM 16493 5712199 YP_001534478.1 CDS ugpB3 NC_009952.1 3310655 3312037 R PFAM: extracellular solute-binding protein family 1 COG1653 - ABC-type sugar transport system, periplasmic component; sugar ABC transporter periplasmic sugar-binding protein complement(3310655..3312037) Dinoroseobacter shibae DFL 12 = DSM 16493 5712200 YP_001534479.1 CDS garL NC_009952.1 3312119 3312880 D PFAM: HpcH/HpaI aldolase KEGG: mpt:Mpe_A0974 2-dehydro-3-deoxyglucarate aldolase ,COG3836 - 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase ,good sp-hit; KDGlucA; 5-keto-4-deoxy-D-glucarate aldolase; DDG aldolase; 2-dehydro-3-deoxygalactarate aldolase; 2-keto-3-deoxyglucarate aldolase; 2-dehydro-3-deoxyglucarate aldolase 3312119..3312880 Dinoroseobacter shibae DFL 12 = DSM 16493 5712201 YP_001534480.1 CDS accA NC_009952.1 3312960 3313922 D 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 3312960..3313922 Dinoroseobacter shibae DFL 12 = DSM 16493 5712202 YP_001534481.1 CDS Dshi_3147 NC_009952.1 3313957 3314697 D PFAM: protein of unknown function DUF306 Meta and HslJ KEGG: sil:SPO2951 hypothetical protein COG3126 - Uncharacterized protein conserved in bacteria ;good GC-Frame Plot; hypothetical protein 3313957..3314697 Dinoroseobacter shibae DFL 12 = DSM 16493 5712203 YP_001534482.1 CDS Dshi_3148 NC_009952.1 3314700 3315176 R hypothetical protein complement(3314700..3315176) Dinoroseobacter shibae DFL 12 = DSM 16493 5712204 YP_001534483.1 CDS ddpX NC_009952.1 3315173 3315985 R PFAM: peptidase M15D vanX D-ala-D-ala dipeptidase KEGG: nmc:NMC1731 ddpX; putative D-alanyl-D-alanine dipeptidase; putative D-alanyl-d-alanine dipeptidase complement(3315173..3315985) Dinoroseobacter shibae DFL 12 = DSM 16493 5712205 YP_001534484.1 CDS dat NC_009952.1 3316090 3316944 D TIGR01121D-amino acid aminotransferase PFAM: aminotransferase class IV KEGG: jan:Jann_0363 aminotransferase, class IV ;good blast hit; DAAT; D-amino acid transaminase; D-amino acid aminotransferase; D-aspartate aminotransferase; D-alanine aminotransferase 3316090..3316944 Dinoroseobacter shibae DFL 12 = DSM 16493 5712206 YP_001534485.1 CDS Dshi_3151 NC_009952.1 3316985 3317893 D PFAM: regulatory protein LysR; LysR substrate-binding KEGG: sil:SPO1110 transcriptional regulator, LysR family COG0583 - Transcriptional regulator; LysR family; transcriptional regulator 3316985..3317893 Dinoroseobacter shibae DFL 12 = DSM 16493 5712207 YP_001534486.1 CDS Dshi_3152 NC_009952.1 3317939 3318841 D PFAM: protein of unknown function DUF1445 KEGG: sil:SPO1111 hypothetical protein; hypothetical protein 3317939..3318841 Dinoroseobacter shibae DFL 12 = DSM 16493 5712208 YP_001534487.1 CDS Dshi_3153 NC_009952.1 3318825 3319859 D PFAM: TRAP dicarboxylate transporter- DctP subunit KEGG: sil:SPO1112 TRAP transporter, periplasmic protein; TRAP dicarboxylate transporter subunit DctP 3318825..3319859 Dinoroseobacter shibae DFL 12 = DSM 16493 5712209 YP_001534488.1 CDS Dshi_3154 NC_009952.1 3319882 3320430 D KEGG: sil:SPO1113 TRAP transporter, transmembrane protein, putative,TMH; TRAP dicarboxylate transporter subunit DctQ 3319882..3320430 Dinoroseobacter shibae DFL 12 = DSM 16493 5712210 YP_001534489.1 CDS Dshi_3155 NC_009952.1 3320427 3321716 D TIGRFAM: TRAP dicarboxylate transporter, DctM subunit PFAM: TRAP C4-dicarboxylate transport system permease DctM subunit KEGG: sil:SPO1114 TRAP dicarboxylate transporter, DctM subunit,TMH; TRAP dicarboxylate transporter subunit DctM 3320427..3321716 Dinoroseobacter shibae DFL 12 = DSM 16493 5712211 YP_001534490.1 CDS Dshi_3156 NC_009952.1 3321720 3322373 D hypothetical protein 3321720..3322373 Dinoroseobacter shibae DFL 12 = DSM 16493 5712212 YP_001534491.1 CDS Dshi_3157 NC_009952.1 3322458 3323468 D PFAM: TRAP dicarboxylate transporter- DctP subunit KEGG: csa:Csal_2479 TRAP dicarboxylate transporter, DctP subunit; TRAP dicarboxylate transporter subunit DctP 3322458..3323468 Dinoroseobacter shibae DFL 12 = DSM 16493 5712213 YP_001534492.1 CDS Dshi_3158 NC_009952.1 3323471 3323968 D PFAM: Tripartite ATP-independent periplasmic transporter DctQ component KEGG: rsq:Rsph17025_2045 tripartite ATP-independent periplasmic transporter, DctQ component,TMH; TRAP dicarboxylate transporter subunit DctQ 3323471..3323968 Dinoroseobacter shibae DFL 12 = DSM 16493 5712214 YP_001534493.1 CDS Dshi_3159 NC_009952.1 3323968 3325263 D TIGRFAM: TRAP dicarboxylate transporter, DctM subunit PFAM: TRAP C4-dicarboxylate transport system permease DctM subunit KEGG: bbr:BB0721 hypothetical protein,TMH; TRAP dicarboxylate transporter subunit DctM 3323968..3325263 Dinoroseobacter shibae DFL 12 = DSM 16493 5712215 YP_001534494.1 CDS Dshi_3160 NC_009952.1 3325448 3325705 R TMH; hypothetical protein complement(3325448..3325705) Dinoroseobacter shibae DFL 12 = DSM 16493 5712216 YP_001534495.1 CDS napC NC_009952.1 3325753 3326466 R PFAM: NapC/NirT cytochrome c domain protein KEGG: rsq:Rsph17025_3218 4Fe-4S ferredoxin, iron-sulfur binding domain protein; cytochrome c-type protein NapC complement(3325753..3326466) Dinoroseobacter shibae DFL 12 = DSM 16493 5712217 YP_001534496.1 CDS napB NC_009952.1 3326494 3326937 R PFAM: Nitrate reductase cytochrome c-type subunit (NapB) KEGG: rsq:Rsph17025_3219 polyferredoxin-like protein; cytochrome c-type protein NapB complement(3326494..3326937) Dinoroseobacter shibae DFL 12 = DSM 16493 5712218 YP_001534497.1 CDS napH NC_009952.1 3326957 3327865 R part of NapHG quinol dehydrogenase; couples electron transfer from ubiquinone-ubiquinol couple via NapC/B to NapA; quinol dehydrogenase membrane component complement(3326957..3327865) Dinoroseobacter shibae DFL 12 = DSM 16493 5712219 YP_001534498.1 CDS napG NC_009952.1 3327862 3328674 R TIGRFAM: MauM/NapG family ferredoxin-type protein PFAM: 4Fe-4S ferredoxin iron-sulfur binding domain protein KEGG: dar:Daro_3839 napG; MauM/NapG ferredoxin-type protein; ferredoxin-type protein NapG complement(3327862..3328674) Dinoroseobacter shibae DFL 12 = DSM 16493 5712220 YP_001534499.1 CDS napA NC_009952.1 3328696 3331191 R periplasmic; catalytic subunit; with NapBC catalyzes the reduction of nitrate to nitrite; NapAB receives electrons from NapC; nitrate reductase catalytic subunit complement(3328696..3331191) Dinoroseobacter shibae DFL 12 = DSM 16493 5712221 YP_001534500.1 CDS napD NC_009952.1 3331178 3331480 R PFAM: NapD family protein KEGG: rsq:Rsph17025_3223 hypothetical protein; periplasmic nitrate reductase NapD complement(3331178..3331480) Dinoroseobacter shibae DFL 12 = DSM 16493 5712222 YP_001534501.1 CDS napF NC_009952.1 3331477 3331989 R TIGRFAM: ferredoxin-type protein NapF PFAM: 4Fe-4S ferredoxin iron-sulfur binding domain protein KEGG: sbl:Sbal_1481 ferredoxin-type protein NapF; ferredoxin-type protein napF complement(3331477..3331989) Dinoroseobacter shibae DFL 12 = DSM 16493 5712223 YP_001534502.1 CDS apbE1 NC_009952.1 3332404 3333345 D PFAM: ApbE family lipoprotein KEGG: pde:Pden_2485 ApbE family lipoprotein; ApbE family lipoprotein 3332404..3333345 Dinoroseobacter shibae DFL 12 = DSM 16493 5712224 YP_001534503.1 CDS cycA1 NC_009952.1 3333379 3333759 D PFAM: cytochrome c class I KEGG: sil:SPOA0055 cytochrome c family protein; cytochrome c2 3333379..3333759 Dinoroseobacter shibae DFL 12 = DSM 16493 5712225 YP_001534504.1 CDS Dshi_3170 NC_009952.1 3333779 3334027 R hypothetical protein complement(3333779..3334027) Dinoroseobacter shibae DFL 12 = DSM 16493 5712226 YP_001534505.1 CDS cbiX1 NC_009952.1 3334024 3334740 R PFAM: cobalamin (vitamin B12) biosynthesis CbiX protein KEGG: rde:RD1_1574 cbiX; CbiX protein, putative; cobalamin (vitamin B12) biosynthesis CbiX protein complement(3334024..3334740) Dinoroseobacter shibae DFL 12 = DSM 16493 5712227 YP_001534506.1 CDS nirN NC_009952.1 3334742 3336295 R PFAM: cytochrome d1 heme region KEGG: sil:SPOA0228 nitrite reductase protein N; nitrite reductase protein N complement(3334742..3336295) Dinoroseobacter shibae DFL 12 = DSM 16493 5712228 YP_001534507.1 CDS nirJ NC_009952.1 3336270 3337484 R PFAM: Radical SAM domain protein SMART: Elongator protein 3/MiaB/NifB KEGG: sil:SPOA0227 nitrite reductase heme biosynthesis J protein; putative nitrite reductase heme biosynthesis J protein complement(3336270..3337484) Dinoroseobacter shibae DFL 12 = DSM 16493 5712229 YP_001534508.1 CDS nirH NC_009952.1 3337486 3337971 R KEGG: sil:SPOA0226 nitrite reductase heme biosynthesis H protein, COG1522 - Transcriptional regulators; putative nitrite reductase heme biosynthesis H protein complement(3337486..3337971) Dinoroseobacter shibae DFL 12 = DSM 16493 5712230 YP_001534509.1 CDS nirG NC_009952.1 3337968 3338417 R SMART: regulatory protein AsnC/Lrp family KEGG: rde:RD1_1570 nitrite reductase heme biosynthesis G; nitrite reductase heme biosynthesis G complement(3337968..3338417) Dinoroseobacter shibae DFL 12 = DSM 16493 5712231 YP_001534510.1 CDS nirD NC_009952.1 3338414 3339409 R KEGG: sil:SPOA0224 nitrite reductase heme biosynthesis D/L protein, putative; nitrite reductase heme biosynthesis D protein complement(3338414..3339409) Dinoroseobacter shibae DFL 12 = DSM 16493 5712232 YP_001534511.1 CDS nirF NC_009952.1 3339414 3340580 R PFAM: cytochrome d1 heme region KEGG: rde:RD1_1568 cytochrome cd1; cytochrome cd1 complement(3339414..3340580) Dinoroseobacter shibae DFL 12 = DSM 16493 5712233 YP_001534512.1 CDS nirC NC_009952.1 3340585 3340896 R KEGG: sil:SPOA0222 cytochrome c55X , neighborhood; c55X; putative cytochrome c complement(3340585..3340896) Dinoroseobacter shibae DFL 12 = DSM 16493 5712234 YP_001534513.1 CDS nirE NC_009952.1 3340889 3341683 R TIGRFAM: uroporphyrin-III C-methyltransferase PFAM: Uroporphyrin-III C/tetrapyrrole (Corrin/Porphyrin) methyltransferase KEGG: sil:SPOA0221 nitrite reductase heme biosynthesis E protein rde:RD1_1566 nirE; uroporphyrin-III C-methyltransferase; Urogen III methylase; uroporphyrinogen-III C-methyltransferase complement(3340889..3341683) Dinoroseobacter shibae DFL 12 = DSM 16493 5712235 YP_001534514.1 CDS nirS NC_009952.1 3341772 3343523 R PFAM: cytochrome d1 heme region KEGG: rde:RD1_1565 nitrite reductase; Hydroxylamine reductase; Cytochrome oxidase; Cytochrome cd1; nitrite reductase complement(3341772..3343523) Dinoroseobacter shibae DFL 12 = DSM 16493 5712236 YP_001534515.1 CDS nosR2 NC_009952.1 3343637 3345700 D PFAM: FMN-binding domain protein KEGG: pde:Pden_2486 FMN-binding domain protein; nitrous oxide reductase regulatory protein NosR 3343637..3345700 Dinoroseobacter shibae DFL 12 = DSM 16493 5712237 YP_001534516.1 CDS Dshi_3182 NC_009952.1 3345697 3346887 D PFAM: NnrS family protein KEGG: sil:SPOA0219 NnrS, putative; NnrS family protein 3345697..3346887 Dinoroseobacter shibae DFL 12 = DSM 16493 5712238 YP_001534517.1 CDS norC NC_009952.1 3346997 3347449 D KEGG: sil:SPOA0217 nitric oxide reductase, small subunit; NOR small subunit; Nitric oxide reductase cytochrome c subunit; nitric-oxide reductase subunit C 3346997..3347449 Dinoroseobacter shibae DFL 12 = DSM 16493 5712239 YP_001534518.1 CDS norB NC_009952.1 3347463 3348842 D KEGG: sil:SPOA0216 nitric oxide reductase, large subunit rde:RD1_1561 norB; nitric-oxide reductase subunit B; nitric oxide reductase subunit B 3347463..3348842 Dinoroseobacter shibae DFL 12 = DSM 16493 5712240 YP_001534519.1 CDS norQ NC_009952.1 3348848 3349654 D KEGG: sil:SPOA0215 nitric oxide reductase Q protein; nitric oxide reductase Q protein 3348848..3349654 Dinoroseobacter shibae DFL 12 = DSM 16493 5712241 YP_001534520.1 CDS norD NC_009952.1 3349663 3351597 D PFAM: von Willebrand factor type A KEGG: sil:SPOA0214 nitric oxide reductase D protein pde:Pden_2481 von Willebrand factor, type A; nitric oxide reductase D protein 3349663..3351597 Dinoroseobacter shibae DFL 12 = DSM 16493 5712242 YP_001534521.1 CDS norE NC_009952.1 3351594 3352148 D PFAM: cytochrome c oxidase subunit III KEGG:rde:RD1_1558 norE; NorE protein; nitric oxide reductase E protein 3351594..3352148 Dinoroseobacter shibae DFL 12 = DSM 16493 5712243 YP_001534522.1 CDS Dshi_3188 NC_009952.1 3352145 3352414 D hypothetical protein 3352145..3352414 Dinoroseobacter shibae DFL 12 = DSM 16493 5712244 YP_001534523.1 CDS Dshi_3189 NC_009952.1 3352427 3353137 R PFAM: cyclic nucleotide-binding KEGG: sil:SPOA0323 cyclic nucleotide-binding protein; similar to DnrD; transcriptional regulator complement(3352427..3353137) Dinoroseobacter shibae DFL 12 = DSM 16493 5712245 YP_001534524.1 CDS hemA3 NC_009952.1 3353217 3354440 R catalyzes the formation of 5-aminolevulinate from succinyl-CoA and glycine; 5-aminolevulinate synthase complement(3353217..3354440) Dinoroseobacter shibae DFL 12 = DSM 16493 5712246 YP_001534525.1 CDS dnr NC_009952.1 3354578 3355261 D PFAM: cyclic nucleotide-binding SMART: regulatory protein Crp KEGG: sil:SPOA0323 cyclic nucleotide-binding protein; transcriptional regulator Dnr 3354578..3355261 Dinoroseobacter shibae DFL 12 = DSM 16493 5712247 YP_001534526.1 CDS Dshi_3192 NC_009952.1 3355274 3355933 D hypothetical protein 3355274..3355933 Dinoroseobacter shibae DFL 12 = DSM 16493 5712248 YP_001534527.1 CDS nosR3 NC_009952.1 3355930 3358116 D KEGG:rde:RD1_1546 nosR; nitrous-oxide reductase regulatory protein NosR PFAM: FMN-binding domain protein; nitrous oxide reductase regulatory protein NosR 3355930..3358116 Dinoroseobacter shibae DFL 12 = DSM 16493 5712249 YP_001534528.1 CDS nosZ NC_009952.1 3358128 3360071 D reduces nitrous oxide to nitrogen; nitrous-oxide reductase 3358128..3360071 Dinoroseobacter shibae DFL 12 = DSM 16493 5712250 YP_001534529.1 CDS nosD NC_009952.1 3360074 3361411 D PFAM: periplasmic copper-binding NosD SMART: Parallel beta-helix repeat; Carbohydrate-binding and sugar hydrolysis KEGG: rde:RD1_1548 nosD; nitrous oxide maturation protein; pde:Pden_4218 periplasmic copper-binding; nitrous oxide maturation protein 3360074..3361411 Dinoroseobacter shibae DFL 12 = DSM 16493 5712251 YP_001534530.1 CDS nosF NC_009952.1 3361377 3362273 D PFAM: ABC transporter related SMART: AAA ATPase KEGG: rde:RD1_1549 nosF; copper transport ATP-binding protein NosF; copper transport ATP-binding protein NosF 3361377..3362273 Dinoroseobacter shibae DFL 12 = DSM 16493 5712252 YP_001534531.1 CDS nosY NC_009952.1 3362270 3363094 D KEGG: pde:Pden_4216 nitrous oxide maturation protein NosY; nitrous oxide maturation protein NosY 3362270..3363094 Dinoroseobacter shibae DFL 12 = DSM 16493 5712253 YP_001534532.1 CDS nosL NC_009952.1 3363091 3363660 D PFAM: NosL family protein KEGG: pde:Pden_4215 NosL family protein; nitrous oxide reductase accessory protein NosL 3363091..3363660 Dinoroseobacter shibae DFL 12 = DSM 16493 5712254 YP_001534533.1 CDS nosX NC_009952.1 3363665 3364573 D PFAM: ApbE family lipoprotein KEGG: pde:Pden_4214 ApbE family lipoprotein rde:RD1_1552 nosX; nitrous-oxide reductase protein NosX; putative nitrous-oxide reductase protein NosX 3363665..3364573 Dinoroseobacter shibae DFL 12 = DSM 16493 5712255 YP_001534534.1 CDS Dshi_3200 NC_009952.1 3364993 3365862 D PFAM: protein of unknown function DUF861 cupin_3; Cupin 2 conserved barrel domain protein KEGG: jan:Jann_2601 protein of unknown function DUF861, cupin_3; hypothetical protein 3364993..3365862 Dinoroseobacter shibae DFL 12 = DSM 16493 5712256 YP_001534535.1 CDS Dshi_3201 NC_009952.1 3366067 3366408 D PFAM: Endoribonuclease L-PSP KEGG: rde:RD1_1044 endoribonuclease L-PSP family protein, putative; endoribonuclease L-PSP 3366067..3366408 Dinoroseobacter shibae DFL 12 = DSM 16493 5712257 YP_001534536.1 CDS uraA NC_009952.1 3366483 3367907 R TIGRFAM: uracil-xanthine permease PFAM: Xanthine/uracil/vitamin C permease KEGG: rde:RD1_4153 xanthine/uracil permease, putative,10xTHM; Uracil transporter; uracil permease complement(3366483..3367907) Dinoroseobacter shibae DFL 12 = DSM 16493 5712258 YP_001534537.1 CDS allA NC_009952.1 3367958 3368452 R PFAM: Ureidoglycolate hydrolase KEGG: rsh:Rsph17029_0204 ureidoglycolate hydrolase; ureidoglycolatehydrolase complement(3367958..3368452) Dinoroseobacter shibae DFL 12 = DSM 16493 5712259 YP_001534538.1 CDS Dshi_3204 NC_009952.1 3368449 3369861 R PFAM: polysaccharide deacetylase; pfam09349, OHCU_decarbox, OHCU decarboxylase. KEGG: jan:Jann_2608 polysaccharide deacetylase; polysaccharide deacetylase complement(3368449..3369861) Dinoroseobacter shibae DFL 12 = DSM 16493 5712260 YP_001534539.1 CDS Dshi_3205 NC_009952.1 3370012 3370365 D TIGRFAM: Hydroxyisourate hydrolase PFAM: Transthyretin KEGG: rde:RD1_4150 hypothetical protein; hydroxyisourate hydrolase 3370012..3370365 Dinoroseobacter shibae DFL 12 = DSM 16493 5712261 YP_001534540.1 CDS Dshi_3206 NC_009952.1 3370362 3371345 R PFAM: regulatory protein LysR; LysR substrate-binding ;HTH_1 pfam00126 Bacterial regulatory helix-turn-helix protein, lysR family KEGG: rde:RD1_4149 transcriptional regulator, LysR family, putative; LysR family; transcriptional regulator complement(3370362..3371345) Dinoroseobacter shibae DFL 12 = DSM 16493 5712262 YP_001534541.1 CDS Dshi_3207 NC_009952.1 3371394 3372626 D PFAM: protein of unknown function DUF989 KEGG: rde:RD1_4148 hypothetical protein; hypothetical protein 3371394..3372626 Dinoroseobacter shibae DFL 12 = DSM 16493 5712263 YP_001534542.1 CDS Dshi_3208 NC_009952.1 3372902 3374383 D hypothetical protein 3372902..3374383 Dinoroseobacter shibae DFL 12 = DSM 16493 5712264 YP_001534543.1 CDS Dshi_3209 NC_009952.1 3374380 3375372 R hypothetical protein complement(3374380..3375372) Dinoroseobacter shibae DFL 12 = DSM 16493 5712265 YP_001534544.1 CDS ymdC NC_009952.1 3375531 3377120 D PFAM: phospholipase D/Transphosphatidylase KEGG: bpe:BP3092 putative phospholipase D protein; putative phospholipase D protein 3375531..3377120 Dinoroseobacter shibae DFL 12 = DSM 16493 5712266 YP_001534545.1 CDS Dshi_3211 NC_009952.1 3377373 3377993 R KEGG: mpt:Mpe_A0912 putative sulfite oxidase cytochrome subunit; putative sulfite oxidase cytochrome subunit complement(3377373..3377993) Dinoroseobacter shibae DFL 12 = DSM 16493 5712267 YP_001534546.1 CDS Dshi_3212 NC_009952.1 3377980 3379251 R PFAM: oxidoreductase molybdopterin binding; Mo-co oxidoreductase dimerisation domain KEGG: mpt:Mpe_A0911 putative sulfite oxidase;nwi:Nwi_2988 oxidoreductase, molybdopterin binding; molybdopterin-binding oxidoreductase complement(3377980..3379251) Dinoroseobacter shibae DFL 12 = DSM 16493 5712268 YP_001534547.1 CDS Dshi_3213 NC_009952.1 3379874 3381040 D PFAM: integrase family protein KEGG: nwi:Nwi_0831 phage integrase; integrase family protein 3379874..3381040 Dinoroseobacter shibae DFL 12 = DSM 16493 5712269 YP_001534548.1 CDS cas3 NC_009952.1 3381532 3384105 R KEGG: rru:Rru_A0340 CRISPR-associated helicase Cas3, core TIGRFAM: CRISPR-associated helicase Cas3 PFAM: helicase domain protein SMART: DEAD-like helicases; CRISPR-associated protein Cas3 complement(3381532..3384105) Dinoroseobacter shibae DFL 12 = DSM 16493 5712270 YP_001534549.1 CDS cse1 NC_009952.1 3384277 3385797 D TIGRFAM: CRISPR-associated protein, Cse1 family KEGG: rru:Rru_A0341 hypothetical protein;aeh:Mlg_0954 CRISPR-associated protein, CSE1 family; Cse1 family CRISPR-associated protein 3384277..3385797 Dinoroseobacter shibae DFL 12 = DSM 16493 5712271 YP_001534550.1 CDS Dshi_3216 NC_009952.1 3385790 3386365 D hypothetical protein 3385790..3386365 Dinoroseobacter shibae DFL 12 = DSM 16493 5712272 YP_001534551.1 CDS cse3 NC_009952.1 3386358 3387479 D TIGRFAM: CRISPR-associated protein, Cse4 family PFAM: CRISPR-associated protein CT1975 KEGG: rru:Rru_A0344 CRISPR-associated CT1975 family protein; Cse4 family; CRISPR-associated protein 3386358..3387479 Dinoroseobacter shibae DFL 12 = DSM 16493 5712273 YP_001534552.1 CDS cas5 NC_009952.1 3387476 3388162 D TIGRFAM: CRISPR-associated protein Cas5 family; CRISPR-associated protein Cas5 KEGG: rru:Rru_A0345 CRISPR-associated CT1976 family protein; Cas5 family CRISPR-associated protein 3387476..3388162 Dinoroseobacter shibae DFL 12 = DSM 16493 5712274 YP_001534553.1 CDS cse2 NC_009952.1 3388159 3388950 D PFAM: CRISPR-associated protein CT1974 KEGG: rru:Rru_A0346 CRISPR-associated CT1974 family protein TIGR01907 CRISPR-associated protein, Cse3 family; Cse3 family; CRISPR-associated protein 3388159..3388950 Dinoroseobacter shibae DFL 12 = DSM 16493 5712275 YP_001534554.1 CDS cas1 NC_009952.1 3388955 3389830 D TIGRFAM: CRISPR-associated protein Cas1 KEGG: mca:MCA0930 CRISPR-associated protein Cas1; CRISPR-associated protein Cas1 3388955..3389830 Dinoroseobacter shibae DFL 12 = DSM 16493 5712276 YP_001534555.1 CDS cas2 NC_009952.1 3389862 3390155 D TIGRFAM: CRISPR-associated protein Cas2 KEGG: rru:Rru_A0348 CRISPR-associated protein, Cas2; CRISPR-associated protein Cas2 3389862..3390155 Dinoroseobacter shibae DFL 12 = DSM 16493 5712277 YP_001534556.1 CDS Dshi_3222 NC_009952.1 3392485 3392688 D hypothetical protein 3392485..3392688 Dinoroseobacter shibae DFL 12 = DSM 16493 5712278 YP_001534557.1 CDS Dshi_3223 NC_009952.1 3392688 3393194 D TIGRFAM: DNA binding domain, excisionase family KEGG: she:Shewmr4_2783 hypothetical protein; hypothetical protein 3392688..3393194 Dinoroseobacter shibae DFL 12 = DSM 16493 5712279 YP_001534558.1 CDS Dshi_3224 NC_009952.1 3393172 3394230 D PFAM: integrase family protein KEGG: mpt:Mpe_A3816 site-specific recombinase XerD-like protein; integrase family protein 3393172..3394230 Dinoroseobacter shibae DFL 12 = DSM 16493 5712280 YP_001534559.1 CDS Dshi_3225 NC_009952.1 3394234 3395673 R hypothetical protein complement(3394234..3395673) Dinoroseobacter shibae DFL 12 = DSM 16493 5712281 YP_001534560.1 CDS Dshi_3226 NC_009952.1 3395713 3395988 R hypothetical protein complement(3395713..3395988) Dinoroseobacter shibae DFL 12 = DSM 16493 5712282 YP_001534561.1 CDS Dshi_3227 NC_009952.1 3396008 3396778 R hypothetical protein complement(3396008..3396778) Dinoroseobacter shibae DFL 12 = DSM 16493 5712283 YP_001534562.1 CDS dapF NC_009952.1 3397087 3397935 D PFAM: diaminopimelate epimerase KEGG: sil:SPO0278 diaminopimelate epimerase; DAP epimerase; diaminopimelate epimerase 3397087..3397935 Dinoroseobacter shibae DFL 12 = DSM 16493 5712285 YP_001534563.1 CDS Dshi_3229 NC_009952.1 3397932 3399182 D KEGG: pde:Pden_0396 MiaB-like tRNA modifying enzyme TIGRFAM: RNA modification enzyme, MiaB family; MiaB-like tRNA modifying enzyme PFAM: Radical SAM domain protein; Protein of unknown function UPF0004 SMART: Elongator protein 3/MiaB/NifB; MiaB-like tRNA modifying enzyme 3397932..3399182 Dinoroseobacter shibae DFL 12 = DSM 16493 5712286 YP_001534564.1 CDS Dshi_3230 NC_009952.1 3399206 3399451 D hypothetical protein 3399206..3399451 Dinoroseobacter shibae DFL 12 = DSM 16493 5712287 YP_001534565.1 CDS Dshi_3231 NC_009952.1 3399663 3401321 D rsp:RSP_1458 putative DNA repair enzyme; putative DNA repair enzyme 3399663..3401321 Dinoroseobacter shibae DFL 12 = DSM 16493 5712288 YP_001534566.1 CDS Dshi_3232 NC_009952.1 3401706 3402056 D KEGG: sil:SPO3807 hypothetical protein; hypothetical protein 3401706..3402056 Dinoroseobacter shibae DFL 12 = DSM 16493 5712289 YP_001534567.1 CDS Dshi_3233 NC_009952.1 3402060 3402899 R PFAM: NLP/P60 protein KEGG: jan:Jann_0105 NLP/P60; NLP/P60 protein complement(3402060..3402899) Dinoroseobacter shibae DFL 12 = DSM 16493 5712290 YP_001534568.1 CDS pepA2 NC_009952.1 3402896 3404287 R PFAM: peptidase M17 leucyl aminopeptidase domain protein KEGG: sil:SPO3717 cytosol aminopeptidase family protein; (LAP) (Leucyl aminopeptidase); leucine aminopeptidase complement(3402896..3404287) Dinoroseobacter shibae DFL 12 = DSM 16493 5712291 YP_001534569.1 CDS Dshi_3235 NC_009952.1 3404838 3405260 R hypothetical protein complement(3404838..3405260) Dinoroseobacter shibae DFL 12 = DSM 16493 5712292 YP_001534570.1 CDS cynT NC_009952.1 3405407 3406057 D PFAM: carbonic anhydrase KEGG: sil:SPO3715 carbonic anhydrase, putative ; rde:RD1_0312 cynT; carbonate anhydratase; carbonate anhydratase 3405407..3406057 Dinoroseobacter shibae DFL 12 = DSM 16493 5712293 YP_001534571.1 CDS Dshi_3237 NC_009952.1 3406143 3407117 D PFAM: protein of unknown function DUF897 KEGG: jan:Jann_0109 protein of unknown function DUF897; hypothetical protein 3406143..3407117 Dinoroseobacter shibae DFL 12 = DSM 16493 5712294 YP_001534572.1 CDS Dshi_3238 NC_009952.1 3407128 3407439 D KEGG: jan:Jann_0110 hypothetical protein; hypothetical protein 3407128..3407439 Dinoroseobacter shibae DFL 12 = DSM 16493 5712295 YP_001534573.1 CDS Dshi_3239 NC_009952.1 3407481 3407954 D KEGG: sil:SPO3714 hypothetical protein; hypothetical protein 3407481..3407954 Dinoroseobacter shibae DFL 12 = DSM 16493 5712296 YP_001534574.1 CDS asd NC_009952.1 3407961 3408983 R catalyzes the formation of 4-aspartyl phosphate from aspartate 4-semialdehyde; aspartate-semialdehyde dehydrogenase complement(3407961..3408983) Dinoroseobacter shibae DFL 12 = DSM 16493 5712297 YP_001534575.1 CDS lpcC NC_009952.1 3409201 3410250 R PFAM: glycosyl transferase group 1 KEGG: pde:Pden_2773 glycosyl transferase, group 1;rde:RD1_3309 lpcC;lipopolysaccharide core biosynthesis mannosyltransferase; lipopolysaccharide core biosynthesis mannosyltransferase complement(3409201..3410250) Dinoroseobacter shibae DFL 12 = DSM 16493 5712298 YP_001534576.1 CDS Dshi_3242 NC_009952.1 3410436 3411863 D PFAM: protein of unknown function DUF404; protein of unknown function DUF407 KEGG: sit:TM1040_2114 protein of unknown function DUF404; DUF407; hypothetical protein 3410436..3411863 Dinoroseobacter shibae DFL 12 = DSM 16493 5712299 YP_001534577.1 CDS Dshi_3243 NC_009952.1 3411868 3412809 D PFAM: protein of unknown function DUF403 KEGG: jan:Jann_2677 protein of unknown function DUF403; hypothetical protein 3411868..3412809 Dinoroseobacter shibae DFL 12 = DSM 16493 5712300 YP_001534578.1 CDS Dshi_3244 NC_009952.1 3412814 3413650 D PFAM: transglutaminase domain protein; transglutaminase domain protein KEGG: hne:HNE_2679 transglutaminase family protein; putative transglutaminase-like superfamily protein 3412814..3413650 Dinoroseobacter shibae DFL 12 = DSM 16493 5712301 YP_001534579.1 CDS Dshi_3245 NC_009952.1 3413789 3414574 D PFAM: 20S proteasome A and B subunits KEGG: rde:RD1_4009 proteasome-type protease, putative; putative proteasome-type protease 3413789..3414574 Dinoroseobacter shibae DFL 12 = DSM 16493 5712302 YP_001534580.1 CDS fliI NC_009952.1 3414677 3416029 R KEGG: rsq:Rsph17025_2599 ATPase, FliI/YscN family TIGRFAM: ATPase, FliI/YscN family PFAM: H+transporting two-sector ATPase alpha/beta subunit central region; flagellum-specific ATP synthase complement(3414677..3416029) Dinoroseobacter shibae DFL 12 = DSM 16493 5712303 YP_001534581.1 CDS flgB NC_009952.1 3416124 3416504 D with FlgF and C makes up the proximal portion of the flagellar basal body rod; flagellar basal body rod protein FlgB 3416124..3416504 Dinoroseobacter shibae DFL 12 = DSM 16493 5712304 YP_001534582.1 CDS flgC NC_009952.1 3416511 3416903 D with FlgF and B makes up the proximal portion of the flagellar basal body rod; flagellar basal body rod protein FlgC 3416511..3416903 Dinoroseobacter shibae DFL 12 = DSM 16493 5712305 YP_001534583.1 CDS fliE NC_009952.1 3416918 3417196 D forms a junction between the M-ring and FlgB during flagella biosynthesis; Bradyrhizobium has one thick flagellum and several thin flagella; the protein in this cluster is associated with the thin flagella; flagellar hook-basal body protein FliE 3416918..3417196 Dinoroseobacter shibae DFL 12 = DSM 16493 5712306 YP_001534584.1 CDS fliQ NC_009952.1 3417196 3417462 D Swissprot: P74931 Flagellar biosynthetic protein fliQ PFAM: export protein FliQ family 3 KEGG: pde:Pden_2113 export protein FliQ, family 3; flagellar biosynthetic protein FliQ 3417196..3417462 Dinoroseobacter shibae DFL 12 = DSM 16493 5712307 YP_001534585.1 CDS flgF NC_009952.1 3417469 3418185 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 3417469..3418185 Dinoroseobacter shibae DFL 12 = DSM 16493 5712308 YP_001534586.1 CDS flgG NC_009952.1 3418207 3418992 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 3418207..3418992 Dinoroseobacter shibae DFL 12 = DSM 16493 5712309 YP_001534587.1 CDS flgA NC_009952.1 3418989 3419414 D required for the assembly of the flagellar basal body P-ring; flagellar basal body P-ring biosynthesis protein FlgA 3418989..3419414 Dinoroseobacter shibae DFL 12 = DSM 16493 5712310 YP_001534588.1 CDS flgH NC_009952.1 3419427 3420155 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 3419427..3420155 Dinoroseobacter shibae DFL 12 = DSM 16493 5712311 YP_001534589.1 CDS fliL1 NC_009952.1 3420164 3420655 D PFAM: flagellar basal body-associated protein FliL; flagellar basal body-associated protein FliL 3420164..3420655 Dinoroseobacter shibae DFL 12 = DSM 16493 5712312 YP_001534590.1 CDS flhB NC_009952.1 3421032 3422120 R membrane protein responsible for substrate specificity switching from rod/hook-type export to filament-type export; flagellar biosynthesis protein FlhB complement(3421032..3422120) Dinoroseobacter shibae DFL 12 = DSM 16493 5712313 YP_001534591.1 CDS fliR NC_009952.1 3422117 3422890 R PFAM: type III secretion system inner membrane R protein KEGG: jan:Jann_4187 flagellar biosynthetic protein FliR; flagellar biosynthesis protein FliR complement(3422117..3422890) Dinoroseobacter shibae DFL 12 = DSM 16493 5712314 YP_001534592.1 CDS flhA NC_009952.1 3422887 3424983 R membrane protein involved in the flagellar export apparatus; flagellar biosynthesis protein FlhA complement(3422887..3424983) Dinoroseobacter shibae DFL 12 = DSM 16493 5712315 YP_001534593.1 CDS Dshi_3259 NC_009952.1 3424994 3426859 R KEGG: rsh:Rsph17029_2977 hypothetical protein; hypothetical protein complement(3424994..3426859) Dinoroseobacter shibae DFL 12 = DSM 16493 5712316 YP_001534594.1 CDS motA NC_009952.1 3426856 3427725 R With MotB forms the ion channels that couple flagellar rotation to proton/sodium motive force across the membrane and forms the stator elements of the rotary flagellar machine; flagellar motor protein MotA complement(3426856..3427725) Dinoroseobacter shibae DFL 12 = DSM 16493 5712317 YP_001534595.1 CDS Dshi_3261 NC_009952.1 3427775 3428380 R KEGG: rsh:Rsph17029_2975 hypothetical protein; hypothetical protein complement(3427775..3428380) Dinoroseobacter shibae DFL 12 = DSM 16493 5712318 YP_001534596.1 CDS Dshi_3262 NC_009952.1 3428380 3428760 R KEGG: rde:RD1_0271 hypothetical protein; hypothetical protein complement(3428380..3428760) Dinoroseobacter shibae DFL 12 = DSM 16493 5712319 YP_001534597.1 CDS fliL2 NC_009952.1 3428769 3429269 R PFAM: flagellar basal body-associated protein FliL KEGG: rsh:Rsph17029_2973 flagellar basal body-associated protein FliL; flagellar basal body-associated protein FliL complement(3428769..3429269) Dinoroseobacter shibae DFL 12 = DSM 16493 5712320 YP_001534598.1 CDS fliF NC_009952.1 3429384 3431060 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 3429384..3431060 Dinoroseobacter shibae DFL 12 = DSM 16493 5712321 YP_001534599.1 CDS fliH NC_009952.1 3431060 3431665 D COG: FliH, Flagellar biosynthesis/type III secretory pathway protein PRK: fliH, flagellar assembly protein H KEGG: rsh:Rsph17029_2971 putative flagellar biosynthesis/type III secretory pathway protein; flagellar biosynthesis protein FliH 3431060..3431665 Dinoroseobacter shibae DFL 12 = DSM 16493 5712322 YP_001534600.1 CDS fliN NC_009952.1 3431658 3431927 D Swissprot: Q03593 Flagellar motor switch protein fliN COG: Flagellar motor switch/type III secretory pathway protein; flagellar motor switch protein FliN 3431658..3431927 Dinoroseobacter shibae DFL 12 = DSM 16493 5712323 YP_001534601.1 CDS fliP NC_009952.1 3431930 3432658 D FliP, with proteins FliQ and FliR, forms the core of the central channel in the flagella export apparatus; flagellar biosynthesis protein FliP 3431930..3432658 Dinoroseobacter shibae DFL 12 = DSM 16493 5712324 YP_001534602.1 CDS Dshi_3268 NC_009952.1 3432733 3433962 D PFAM: coenzyme F420 hydrogenase/dehydrogenase beta subunit domain protein KEGG: rpe:RPE_1300 coenzyme F420 hydrogenase/dehydrogenase beta subunit domain protein; beta subunit; putative coenzyme F420 hydrogenase 3432733..3433962 Dinoroseobacter shibae DFL 12 = DSM 16493 5712325 YP_001534603.1 CDS Dshi_3269 NC_009952.1 3433959 3435065 R PFAM: L-carnitine dehydratase/bile acid-inducible protein F KEGG: sit:TM1040_0389 L-carnitine dehydratase/bile acid-inducible protein F; L-carnitine dehydratase/bile acid-inducible protein F complement(3433959..3435065) Dinoroseobacter shibae DFL 12 = DSM 16493 5712326 YP_001534604.1 CDS Dshi_3270 NC_009952.1 3435120 3435839 R hypothetical protein complement(3435120..3435839) Dinoroseobacter shibae DFL 12 = DSM 16493 5712327 YP_001534605.1 CDS Dshi_3271 NC_009952.1 3435991 3437064 R PFAM: protein of unknown function DUF59 KEGG: rde:RD1_2906 hypothetical protein; hypothetical protein complement(3435991..3437064) Dinoroseobacter shibae DFL 12 = DSM 16493 5712328 YP_001534606.1 CDS Dshi_3272 NC_009952.1 3437061 3437258 R KEGG: rde:RD1_2905 hypothetical protein; hypothetical protein complement(3437061..3437258) Dinoroseobacter shibae DFL 12 = DSM 16493 5712329 YP_001534607.1 CDS Dshi_3273 NC_009952.1 3437544 3438491 D hypothetical protein 3437544..3438491 Dinoroseobacter shibae DFL 12 = DSM 16493 5712330 YP_001534608.1 CDS Dshi_3274 NC_009952.1 3438585 3439571 D hypothetical protein 3438585..3439571 Dinoroseobacter shibae DFL 12 = DSM 16493 5712331 YP_001534609.1 CDS aroC NC_009952.1 3439739 3440842 R catalyzes the formation of chorismate from 5-O-(1-carboxyvinyl)-3-phosphoshikimate in aromatic amino acid biosynthesis; chorismate synthase complement(3439739..3440842) Dinoroseobacter shibae DFL 12 = DSM 16493 5712332 YP_001534610.1 CDS petC NC_009952.1 3441060 3441854 R PFAM: cytochrome c1 KEGG: rde:RD1_0565 cytochrome c1; cytochrome c1 complement(3441060..3441854) Dinoroseobacter shibae DFL 12 = DSM 16493 5712333 YP_001534611.1 CDS petB NC_009952.1 3441879 3443228 R PFAM: Cytochrome b/b6 domain KEGG: jan:Jann_0326 cytochrome b/b6-like; cytochrome b complement(3441879..3443228) Dinoroseobacter shibae DFL 12 = DSM 16493 5712334 YP_001534612.1 CDS petA NC_009952.1 3443243 3443800 R 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; iron-sulfur subunit; ubiquinol-cytochrome c reductase complement(3443243..3443800) Dinoroseobacter shibae DFL 12 = DSM 16493 5712335 YP_001534613.1 CDS Dshi_3279 NC_009952.1 3444069 3444680 R PFAM: Glutathione S-transferase domain KEGG: rsp:RSP_1397 glutathione S-transferase; putative glutathione S-transferase family protein complement(3444069..3444680) Dinoroseobacter shibae DFL 12 = DSM 16493 5712336 YP_001534614.1 CDS Dshi_3280 NC_009952.1 3444680 3444967 R KEGG: rsq:Rsph17025_2805 hypothetical protein; hypothetical protein complement(3444680..3444967) Dinoroseobacter shibae DFL 12 = DSM 16493 5712337 YP_001534615.1 CDS Dshi_3281 NC_009952.1 3445107 3448478 R PFAM: nucleic acid binding OB-fold tRNA/helicase-type; Endonuclease/exonuclease/phosphatase KEGG: syn:sll0656 extracellular nuclease; putative endonuclease/exonuclease/phosphatase complement(3445107..3448478) Dinoroseobacter shibae DFL 12 = DSM 16493 5712338 YP_001534616.1 CDS fdhD NC_009952.1 3448790 3449674 D TIGR00129 formate dehydrogenase family accessory protein FdhD PFAM: formate dehydrogenase subunit FdhD KEGG: sil:SPO0306 formate dehydrogenase accessory protein FdhD; putative formate dehydrogenase accessory protein FdhD 3448790..3449674 Dinoroseobacter shibae DFL 12 = DSM 16493 5712339 YP_001534617.1 CDS mobA NC_009952.1 3449671 3450306 D in Escherichia coli MobA links a guanosine 5'-phosphate to molydopterin to form molybdopterin guanine dinucleotide during molybdenum cofactor biosynthesis; molybdopterin-guanine dinucleotide biosynthesis protein MobA 3449671..3450306 Dinoroseobacter shibae DFL 12 = DSM 16493 5712340 YP_001534618.1 CDS moeA3 NC_009952.1 3450303 3452075 D TIGRFAM: molybdenum cofactor synthesis domain; molybdopterin-guanine dinucleotide biosynthesis protein B PFAM: molybdopterin binding domain; molybdopterin-guanine dinucleotide biosynthesis MobB region; MoeA domain protein domain I and II; MoeA domain protein domain IV KEGG: sil:SPO0310 molybdopterin biosynthesis protein MoeA rde:RD1_3407 moeA; molybdopterin biosynthesis protein, putative; putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobB/MoeA 3450303..3452075 Dinoroseobacter shibae DFL 12 = DSM 16493 5712341 YP_001534619.1 CDS trx NC_009952.1 3452072 3452488 R PFAM: Thioredoxin domain KEGG: rde:RD1_0213 thioredoxin, putative; putative thioredoxin complement(3452072..3452488) Dinoroseobacter shibae DFL 12 = DSM 16493 5712342 YP_001534620.1 CDS ccdA NC_009952.1 3452504 3453217 R PFAM: cytochrome c biogenesis protein transmembrane region KEGG: rde:RD1_0214 cytochrome c biogenesis protein; cytochrome c biogenesis protein complement(3452504..3453217) Dinoroseobacter shibae DFL 12 = DSM 16493 5712343 YP_001534621.1 CDS Dshi_3287 NC_009952.1 3453276 3454142 R PFAM: protein of unknown function DUF6 transmembrane KEGG: sit:TM1040_2802 protein of unknown function DUF6, transmembrane ; rde:RD1_0601 hypothetical protein ; TMH; 2x DUF6; hypothetical protein complement(3453276..3454142) Dinoroseobacter shibae DFL 12 = DSM 16493 5712344 YP_001534622.1 CDS hup NC_009952.1 3454254 3454544 R PFAM: histone family protein DNA-binding protein KEGG: rde:RD1_0603 DNA-binding protein HU; DNA-binding protein HU complement(3454254..3454544) Dinoroseobacter shibae DFL 12 = DSM 16493 5712345 YP_001534623.1 CDS amn NC_009952.1 3455298 3456767 R Catalyzes the hydrolysis of AMP to form adenine and ribose 5-phosphate using water as the nucleophile; AMP nucleosidase complement(3455298..3456767) Dinoroseobacter shibae DFL 12 = DSM 16493 5712346 YP_001534624.1 CDS Dshi_3290 NC_009952.1 3456894 3457313 D KEGG: sil:SPO3747 hypothetical protein; hypothetical protein 3456894..3457313 Dinoroseobacter shibae DFL 12 = DSM 16493 5712347 YP_001534625.1 CDS Dshi_3291 NC_009952.1 3457352 3458224 D KEGG: jan:Jann_0273 NAD-dependent epimerase/dehydratase rde:RD1_0614 hypothetical protein; hypothetical protein 3457352..3458224 Dinoroseobacter shibae DFL 12 = DSM 16493 5712348 YP_001534626.1 CDS Dshi_3292 NC_009952.1 3458254 3459135 R hypothetical protein complement(3458254..3459135) Dinoroseobacter shibae DFL 12 = DSM 16493 5712349 YP_001534627.1 CDS Dshi_3293 NC_009952.1 3459141 3459959 R hypothetical protein complement(3459141..3459959) Dinoroseobacter shibae DFL 12 = DSM 16493 5712350 YP_001534628.1 CDS dxs1 NC_009952.1 3459972 3461903 R catalyzes the formation of 1-deoxy-D-xylulose 5-phosphate from pyruvate and D-glyceraldehyde 3-phosphate; 1-deoxy-D-xylulose-5-phosphate synthase complement(3459972..3461903) Dinoroseobacter shibae DFL 12 = DSM 16493 5712351 YP_001534629.1 CDS ispA NC_009952.1 3461924 3462799 R PFAM: Polyprenyl synthetase KEGG: rde:RD1_0549 ispA; geranyltranstransferase; FPP synthase; Farnesyl-diphosphate synthase; geranyltranstransferase complement(3461924..3462799) Dinoroseobacter shibae DFL 12 = DSM 16493 5712352 YP_001534630.1 CDS xseB NC_009952.1 3462803 3463045 R PFAM: histone deacetylase superfamily KEGG: rsp:RSP_1137 histone deacetylase family protein; Exonuclease VII small subunit; exodeoxyribonuclease 7 small subunit complement(3462803..3463045) Dinoroseobacter shibae DFL 12 = DSM 16493 5712353 YP_001534631.1 CDS Dshi_3297 NC_009952.1 3463042 3463983 R PFAM: histone deacetylase superfamily KEGG: rsp:RSP_1137 histone deacetylase family protein; histone deacetylase family protein complement(3463042..3463983) Dinoroseobacter shibae DFL 12 = DSM 16493 5712354 YP_001534632.1 CDS Dshi_3298 NC_009952.1 3464011 3464559 D KEGG: mlo:mlr2044 hypothetical protein; hypothetical protein 3464011..3464559 Dinoroseobacter shibae DFL 12 = DSM 16493 5712355 YP_001534633.1 CDS petR NC_009952.1 3464567 3465280 R Swissprot: Protein petR PFAM: response regulator receiver; transcriptional regulator domain protein; DNA-binding response regulator PetR complement(3464567..3465280) Dinoroseobacter shibae DFL 12 = DSM 16493 5712356 YP_001534634.1 CDS Dshi_3300 NC_009952.1 3465280 3465786 R PFAM: regulatory protein MarR KEGG: rde:RD1_0552 transcriptional regulator, MarR family; MarR family; transcriptional regulator complement(3465280..3465786) Dinoroseobacter shibae DFL 12 = DSM 16493 5712357 YP_001534635.1 CDS ilvE NC_009952.1 3465947 3466816 D catalyzes the transamination of the branched-chain amino acids to their respective alpha-keto acids; branched-chain amino acid aminotransferase 3465947..3466816 Dinoroseobacter shibae DFL 12 = DSM 16493 5712358 YP_001534636.1 CDS Dshi_3302 NC_009952.1 3467100 3467408 D KEGG: atc:AGR_L_2414 hypothetical protein; hypothetical protein 3467100..3467408 Dinoroseobacter shibae DFL 12 = DSM 16493 5712359 YP_001534637.1 CDS Dshi_3303 NC_009952.1 3467405 3468508 R REFSEQ: ref|ZP_01012112.1 membrane protein, putative [Rhodobacterale bacterium]; hypothetical protein complement(3467405..3468508) Dinoroseobacter shibae DFL 12 = DSM 16493 5712360 YP_001534638.1 CDS Dshi_3304 NC_009952.1 3468555 3469358 D KEGG: sil:SPO2058 hypothetical protein; hypothetical protein 3468555..3469358 Dinoroseobacter shibae DFL 12 = DSM 16493 5712361 YP_001534639.1 CDS Dshi_3305 NC_009952.1 3469362 3470303 R PFAM: integral membrane protein DUF6 KEGG: jan:Jann_3870 protein of unknown function DUF6, transmembrane; transmembrane; hypothetical protein complement(3469362..3470303) Dinoroseobacter shibae DFL 12 = DSM 16493 5712362 YP_001534640.1 CDS Dshi_3306 NC_009952.1 3470332 3470643 R hypothetical protein complement(3470332..3470643) Dinoroseobacter shibae DFL 12 = DSM 16493 5712363 YP_001534641.1 CDS Dshi_3307 NC_009952.1 3470805 3471839 R TIGRFAM: iron-sulfur cluster binding protein, putative PFAM: domain of unknown function DUF1730 KEGG: jan:Jann_0274 4Fe-4S ferredoxin, iron-sulfur binding; (protein of unknown function DUF1730); putative 4Fe-4S-binding domain-containing protein complement(3470805..3471839) Dinoroseobacter shibae DFL 12 = DSM 16493 5712364 YP_001534642.1 CDS gst1 NC_009952.1 3471836 3472501 R PFAM: Glutathione S-transferase domain KEGG: rsq:Rsph17025_2783 glutathione S-transferase, N-terminal domain; glutathione S-transferase complement(3471836..3472501) Dinoroseobacter shibae DFL 12 = DSM 16493 5712365 YP_001534643.1 CDS mtgA NC_009952.1 3472552 3473298 R TIGRFAM: monofunctional biosynthetic peptidoglycan transglycosylase PFAM: glycosyl transferase family 51 KEGG: rsh:Rsph17029_2806 monofunctional biosynthetic peptidoglycan transglycosylase; monofunctional biosynthetic peptidoglycan transglycosylase complement(3472552..3473298) Dinoroseobacter shibae DFL 12 = DSM 16493 5712366 YP_001534644.1 CDS rssA NC_009952.1 3473352 3474155 R COG: RssA, Predicted esterase of the alpha-beta hydrolase superfamily PFAM: Patatin-like phospholipase; patatin-like phospholipase complement(3473352..3474155) Dinoroseobacter shibae DFL 12 = DSM 16493 5712367 YP_001534645.1 CDS Dshi_3311 NC_009952.1 3474155 3475375 R TIGRFAM: radical SAM enzyme, Cfr family PFAM: Radical SAM domain protein KEGG: rsq:Rsph17025_0041 radical SAM enzyme, Cfr family; Cfr family; radical SAM protein complement(3474155..3475375) Dinoroseobacter shibae DFL 12 = DSM 16493 5712368 YP_001534646.1 CDS Dshi_3312 NC_009952.1 3475522 3476199 D KEGG: jan:Jann_2393 hypothetical protein; hypothetical protein 3475522..3476199 Dinoroseobacter shibae DFL 12 = DSM 16493 5712369 YP_001534647.1 CDS Dshi_3313 NC_009952.1 3476196 3476906 R KEGG: rsh:Rsph17029_0081 hypothetical protein; hypothetical protein complement(3476196..3476906) Dinoroseobacter shibae DFL 12 = DSM 16493 5712370 YP_001534648.1 CDS Dshi_3314 NC_009952.1 3477352 3477885 R KEGG: rde:RD1_0193 hypothetical protein; hypothetical protein complement(3477352..3477885) Dinoroseobacter shibae DFL 12 = DSM 16493 5712371 YP_001534649.1 CDS Dshi_3315 NC_009952.1 3478272 3478583 D hypothetical protein 3478272..3478583 Dinoroseobacter shibae DFL 12 = DSM 16493 5712372 YP_001534650.1 CDS serB NC_009952.1 3478598 3479476 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 complement(3478598..3479476) Dinoroseobacter shibae DFL 12 = DSM 16493 5712373 YP_001534651.1 CDS serC NC_009952.1 3479701 3480855 D catalyzes the formation of 3-phosphonooxypyruvate and glutamate from O-phospho-L-serine and 2-oxoglutarate; phosphoserine aminotransferase 3479701..3480855 Dinoroseobacter shibae DFL 12 = DSM 16493 5712374 YP_001534652.1 CDS serA1 NC_009952.1 3481012 3482607 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 3481012..3482607 Dinoroseobacter shibae DFL 12 = DSM 16493 5712375 YP_001534653.1 CDS Dshi_3319 NC_009952.1 3482662 3483396 D PFAM: metallophosphoesterase KEGG: rsq:Rsph17025_0011 metallophosphoesterase; metallophosphoesterase 3482662..3483396 Dinoroseobacter shibae DFL 12 = DSM 16493 5712376 YP_001534654.1 CDS Dshi_3320 NC_009952.1 3483410 3483616 R KEGG: rde:RD1_1295 hypothetical protein; hypothetical protein complement(3483410..3483616) Dinoroseobacter shibae DFL 12 = DSM 16493 5712377 YP_001534655.1 CDS Dshi_3321 NC_009952.1 3483814 3484269 D PFAM: CreA family protein KEGG: rsh:Rsph17029_1167 CreA family protein; CreA family protein 3483814..3484269 Dinoroseobacter shibae DFL 12 = DSM 16493 5712378 YP_001534656.1 CDS Dshi_3322 NC_009952.1 3484266 3485303 R PFAM: regulatory protein LacI; periplasmic binding protein/LacI transcriptional regulator KEGG: sil:SPO3684 transcriptional regulator, LacI family; LacI family; transcriptional regulator complement(3484266..3485303) Dinoroseobacter shibae DFL 12 = DSM 16493 5712379 YP_001534657.1 CDS Dshi_3323 NC_009952.1 3485578 3486258 R PFAM: regulatory protein GntR HTH; GntR domain protein KEGG: jan:Jann_1164 transcriptional regulator, GntR family; GntR family; transcriptional regulator complement(3485578..3486258) Dinoroseobacter shibae DFL 12 = DSM 16493 5712380 YP_001534658.1 CDS dld2 NC_009952.1 3486236 3489157 R PFAM: FAD binding domain, FAD linked oxidases KEGG: jan:Jann_1163 D-lactate dehydrogenase (cytochrome); D-lactate dehydrogenase complement(3486236..3489157) Dinoroseobacter shibae DFL 12 = DSM 16493 5712381 YP_001534659.1 CDS sgaA1 NC_009952.1 3489205 3490473 D Swissprot: Q56YA5 Serine--glyoxylate aminotransferase PFAM: aminotransferase class V; aromatic amino acid beta-eliminating lyase/threonine aldolase KEGG: jan:Jann_1162 aminotransferase, class V; Serine--pyruvate aminotransferase; AGT; Alanine--glyoxylate aminotransferase; serine--glyoxylate aminotransferase 3489205..3490473 Dinoroseobacter shibae DFL 12 = DSM 16493 5712382 YP_001534660.1 CDS dctP3 NC_009952.1 3490512 3491489 D TIGRFAM: TRAP dicarboxylate transporter, DctP subunit PFAM: TRAP dicarboxylate transporter- DctP subunit KEGG: pmu:PM1651 hypothetical E.coli; precursor; TRAP dicarboxylate transporter subunit DctP 3490512..3491489 Dinoroseobacter shibae DFL 12 = DSM 16493 5712383 YP_001534661.1 CDS dctQ1 NC_009952.1 3491612 3492154 D PFAM: Tripartite ATP-independent periplasmic transporter DctQ component; TRAP dicarboxylate transporter subunit DctQ 3491612..3492154 Dinoroseobacter shibae DFL 12 = DSM 16493 5712384 YP_001534662.1 CDS dctM4 NC_009952.1 3492154 3493434 D TIGRFAM: TRAP dicarboxylate transporter, DctM subunit PFAM: TRAP C4-dicarboxylate transport system permease DctM subunit; TRAP dicarboxylate transporter subunit DctM 3492154..3493434 Dinoroseobacter shibae DFL 12 = DSM 16493 5712385 YP_001534663.1 CDS Dshi_3329 NC_009952.1 3493431 3494204 D Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA; enoyl-CoA hydratase 3493431..3494204 Dinoroseobacter shibae DFL 12 = DSM 16493 5712386 YP_001534664.1 CDS yfdW1 NC_009952.1 3494201 3495436 D PFAM: CoA-transferase family III PRK: formyl-coenzyme A transferase; formyl-CoA transferase 3494201..3495436 Dinoroseobacter shibae DFL 12 = DSM 16493 5712387 YP_001534665.1 CDS bktB NC_009952.1 3495749 3496933 D catalyzes the formation of beta-ketovaleryl-CoA from acetyl-CoA and propionyl-CoA; beta-ketothiolase 3495749..3496933 Dinoroseobacter shibae DFL 12 = DSM 16493 5712389 YP_001534666.1 CDS Dshi_3332 NC_009952.1 3497022 3499481 D PFAM: response regulator receiver; ATP-binding region ATPase domain protein; histidine kinase A domain protein KEGG: rde:RD1_0357 hybrid sensory histidine kinase, putative; sensor histidine kinase/response regulator 3497022..3499481 Dinoroseobacter shibae DFL 12 = DSM 16493 5712390 YP_001534667.1 CDS Dshi_3333 NC_009952.1 3499478 3500281 R PFAM: protein of unknown function DUF328 KEGG: sil:SPO0106 hypothetical protein; hypothetical protein complement(3499478..3500281) Dinoroseobacter shibae DFL 12 = DSM 16493 5712391 YP_001534668.1 CDS recQ NC_009952.1 3500340 3502379 R KEGG: rde:RD1_0359 ATP-dependent DNA helicase RecQ TIGRFAM: ATP-dependent DNA helicase RecQ PFAM: helicase domain protein; HRDC domain protein; DEAD/DEAH box helicase domain protein; Helicase superfamily 1 and 2 ATP-binding SMART: DEAD-like helicases; ATP-dependent DNA helicase RecQ complement(3500340..3502379) Dinoroseobacter shibae DFL 12 = DSM 16493 5712392 YP_001534669.1 CDS Dshi_3335 NC_009952.1 3502462 3502749 R PFAM: protein of unknown function YGGT KEGG: sil:SPO0122 YGGT family protein; transmembrane; hypothetical protein complement(3502462..3502749) Dinoroseobacter shibae DFL 12 = DSM 16493 5712393 YP_001534670.1 CDS Dshi_3336 NC_009952.1 3502874 3503410 D KEGG: sit:TM1040_2661 hypothetical protein; hypothetical protein 3502874..3503410 Dinoroseobacter shibae DFL 12 = DSM 16493 5712394 YP_001534671.1 CDS Dshi_3337 NC_009952.1 3503472 3504803 D PFAM: major facilitator superfamily MFS_1 KEGG: jan:Jann_0343 major facilitator superfamily MFS_1; major facilitator superfamily (MFS) transporter 3503472..3504803 Dinoroseobacter shibae DFL 12 = DSM 16493 5712395 YP_001534672.1 CDS mepA NC_009952.1 3504800 3505690 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 3504800..3505690 Dinoroseobacter shibae DFL 12 = DSM 16493 5712396 YP_001534673.1 CDS Dshi_3339 NC_009952.1 3505663 3506544 D KEGG: rsq:Rsph17025_0022 hypothetical protein; hypothetical protein 3505663..3506544 Dinoroseobacter shibae DFL 12 = DSM 16493 5712397 YP_001534674.1 CDS Dshi_3340 NC_009952.1 3506634 3507257 D TIGRFAM: conserved hypothetical integral membrane protein PFAM: protein of unknown function DUF165 KEGG: sit:TM1040_2665 protein of unknown function DUF165; hypothetical protein 3506634..3507257 Dinoroseobacter shibae DFL 12 = DSM 16493 5712398 YP_001534675.1 CDS rimK NC_009952.1 3507600 3509015 D TIGRFAM: alpha-L-glutamate ligase, RimK family PFAM: RimK domain protein ATP-grasp KEGG: rde:RD1_2956 ribosomal protein S6 modification protein (C terminal domain); ribosomal protein S6 modification protein 3507600..3509015 Dinoroseobacter shibae DFL 12 = DSM 16493 5712399 YP_001534676.1 CDS Dshi_3342 NC_009952.1 3509061 3509483 D PFAM: Class I peptide chain release factor KEGG: rde:RD1_0366 peptidyl-tRNA hydrolase, putative; peptidyl-tRNA hydrolase domain-containing protein 3509061..3509483 Dinoroseobacter shibae DFL 12 = DSM 16493 5712400 YP_001534677.1 CDS Dshi_3343 NC_009952.1 3509480 3510721 D PFAM: aminotransferase class-III KEGG: sil:SPOA0354 aminotransferase, class III; class III aminotransferase 3509480..3510721 Dinoroseobacter shibae DFL 12 = DSM 16493 5712401 YP_001534678.1 CDS Dshi_3344 NC_009952.1 3510709 3511665 D PFAM: aminoglycoside phosphotransferase; aminoglycoside phosphotransferase 3510709..3511665 Dinoroseobacter shibae DFL 12 = DSM 16493 5712402 YP_001534679.1 CDS pncB NC_009952.1 3511662 3512954 R catalyzes the formation of nictonate and 5-phospho-alpha-D-ribose 1-diphosphate from nicotinate D-ribonucleotide and diphosphate; nicotinate phosphoribosyltransferase complement(3511662..3512954) Dinoroseobacter shibae DFL 12 = DSM 16493 5712403 YP_001534680.1 CDS Dshi_3346 NC_009952.1 3513033 3515378 R KEGG: sil:SPO0094 sensory box sensor histidine kinase/response regulator TIGRFAM: PAS sensor protein PFAM: response regulator receiver; ATP-binding region ATPase domain protein; histidine kinase A domain protein; PAS fold-3 domain protein; PAS fold-4 domain protein; PAS fold domain protein SMART: PAS domain containing protein; PAC repeat-containing protein; multi-sensor hybrid histidine kinase complement(3513033..3515378) Dinoroseobacter shibae DFL 12 = DSM 16493 5712404 YP_001534681.1 CDS pncA NC_009952.1 3515388 3515990 R KEGG: jan:Jann_0014 nicotinamidase; nicotinamidase complement(3515388..3515990) Dinoroseobacter shibae DFL 12 = DSM 16493 5712405 YP_001534682.1 CDS Dshi_3348 NC_009952.1 3516052 3516993 D PFAM: Rhodanese domain protein KEGG: pde:Pden_0850 rhodanese domain protein; rhodanese domain-containing protein 3516052..3516993 Dinoroseobacter shibae DFL 12 = DSM 16493 5712406 YP_001534683.1 CDS ybbB NC_009952.1 3517036 3518097 D PRK tRNA 2-selenouridine synthase; tRNA 2-selenouridine synthase 3517036..3518097 Dinoroseobacter shibae DFL 12 = DSM 16493 5712407 YP_001534684.1 CDS selD NC_009952.1 3518104 3520233 R TIGRFAM: selenium donor protein PFAM: AIR synthase related protein domain protein KEGG: sil:SPO2899 selenide,water dikinase, putative; (Selenophosphate synthetase) (Selenium donor protein); selenide, water dikinase complement(3518104..3520233) Dinoroseobacter shibae DFL 12 = DSM 16493 5712408 YP_001534685.1 CDS Dshi_3351 NC_009952.1 3520331 3521806 D KEGG: bbt:BBta_2726 putative membrane protein of unknown function; hypothetical protein 3520331..3521806 Dinoroseobacter shibae DFL 12 = DSM 16493 5712409 YP_001534686.1 CDS Dshi_3352 NC_009952.1 3522370 3523434 R KEGG: jan:Jann_0255 hypothetical protein; hypothetical protein complement(3522370..3523434) Dinoroseobacter shibae DFL 12 = DSM 16493 5712410 YP_001534687.1 CDS Dshi_3353 NC_009952.1 3523424 3525826 R PFAM: Predicted permease KEGG: rsq:Rsph17025_3021 protein of unknown function DUF214; protein of unknown function DUF214; putative permease FtsX complement(3523424..3525826) Dinoroseobacter shibae DFL 12 = DSM 16493 5712411 YP_001534688.1 CDS Dshi_3354 NC_009952.1 3525826 3526482 R PFAM: FtsE, Predicted ATPase involved in cell division; putative ATPase involved in cell division FtsE complement(3525826..3526482) Dinoroseobacter shibae DFL 12 = DSM 16493 5712412 YP_001534689.1 CDS gyrB NC_009952.1 3526685 3529102 D negatively supercoils closed circular double-stranded DNA; DNA gyrase subunit B 3526685..3529102 Dinoroseobacter shibae DFL 12 = DSM 16493 5712413 YP_001534690.1 CDS Dshi_3356 NC_009952.1 3530095 3530361 D PFAM: Transposase KEGG: mag:amb0646 insertion element ISR1 hypothetical 10 kDa protein A3; insertion element ISR1 10 kDa protein A3 3530095..3530361 Dinoroseobacter shibae DFL 12 = DSM 16493 5712414 YP_001534691.1 CDS Dshi_3357 NC_009952.1 3530385 3531194 D PFAM: Integrase catalytic region KEGG: bbt:BBta_7691 integrase, catalytic domain; integrase catalytic subunit 3530385..3531194 Dinoroseobacter shibae DFL 12 = DSM 16493 5712415 YP_001534692.1 CDS Dshi_3358 NC_009952.1 3531547 3532338 R PFAM: protein of unknown function DUF1217 KEGG: sil:SPO3456 flagellar protein, putative; hypothetical protein complement(3531547..3532338) Dinoroseobacter shibae DFL 12 = DSM 16493 5712416 YP_001534693.1 CDS flbT NC_009952.1 3532338 3532739 R post-transcriptional repressor of flagellum biosynthesis; promotes degradation of fljK mRNA: Bradyrhizobium has one thick flagellum and several thin flagella; the protein in this cluster is associated with the thin flagella; flagellar biosynthesis repressor FlbT complement(3532338..3532739) Dinoroseobacter shibae DFL 12 = DSM 16493 5712417 YP_001534694.1 CDS flaF NC_009952.1 3532736 3533107 R acts as an activator of flagellin translation and may be required for filament secretion or assembly; Bradyrhizobium has one thick flagellum and several thin flagella; the Bradyrhizobium protein in this cluster is associated with the thick flagellum; flagellar biosynthesis regulatory protein FlaF complement(3532736..3533107) Dinoroseobacter shibae DFL 12 = DSM 16493 5712418 YP_001534695.1 CDS fliC NC_009952.1 3533170 3534720 R PFAM: flagellin domain protein KEGG: jan:Jann_4203 flagellin-like; flagellin complement(3533170..3534720) Dinoroseobacter shibae DFL 12 = DSM 16493 5712419 YP_001534696.1 CDS Dshi_3362 NC_009952.1 3534911 3535219 R hypothetical protein complement(3534911..3535219) Dinoroseobacter shibae DFL 12 = DSM 16493 5712420 YP_001534697.1 CDS Dshi_3363 NC_009952.1 3535242 3535544 R PRK: flgJ, peptidoglycan hydrolase KEGG: sit:TM1040_2976 flagellar protein FlgJ, putative; putative flagellar protein FlgJ complement(3535242..3535544) Dinoroseobacter shibae DFL 12 = DSM 16493 5712421 YP_001534698.1 CDS Dshi_3364 NC_009952.1 3535667 3538003 D PFAM: flagellar hook-length control protein; putative flagellar hook-length control protein 3535667..3538003 Dinoroseobacter shibae DFL 12 = DSM 16493 5712422 YP_001534699.1 CDS flgD NC_009952.1 3538012 3538674 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 3538012..3538674 Dinoroseobacter shibae DFL 12 = DSM 16493 5712423 YP_001534700.1 CDS Dshi_3366 NC_009952.1 3538823 3539614 D PFAM: Phosphotransferase enzyme family Genbank: gb|ABF65711.1 aminoglycoside phosphotransferase (Silicibacter sp.); putative aminoglycoside phosphotransferase 3538823..3539614 Dinoroseobacter shibae DFL 12 = DSM 16493 5712424 YP_001534701.1 CDS ubiB NC_009952.1 3539582 3541111 R TIGRFAM: 2-polyprenylphenol 6-hydroxylase PFAM: ABC-1 domain protein KEGG: rde:RD1_0202 ubiquinone biosynthesis protein UbiB; 2-polyprenylphenol 6-hydroxylase complement(3539582..3541111) Dinoroseobacter shibae DFL 12 = DSM 16493 5712425 YP_001534702.1 CDS ubiE NC_009952.1 3541114 3541866 R TIGRFAM: ubiquinone biosynthesis methyltransferase PFAM: UbiE/COQ5 methyltransferase; Methyltransferase type 11; Methyltransferase type 12 KEGG: jan:Jann_4209 ubiquinone/menaquinone biosynthesis methyltransferases PMID: 9045837; 2-polyprenylmethoxybenozoquinol methylase complement(3541114..3541866) Dinoroseobacter shibae DFL 12 = DSM 16493 5712426 YP_001534703.1 CDS mutM NC_009952.1 3541951 3542805 D Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases; formamidopyrimidine-DNA glycosylase 3541951..3542805 Dinoroseobacter shibae DFL 12 = DSM 16493 5712427 YP_001534704.1 CDS Dshi_3370 NC_009952.1 3542870 3543646 D PFAM: Enoyl-CoA hydratase/isomerase KEGG: rsh:Rsph17029_0009 enoyl-CoA hydratase/isomerase; enoyl-CoA hydratase/isomerase 3542870..3543646 Dinoroseobacter shibae DFL 12 = DSM 16493 5712428 YP_001534705.1 CDS rpsT NC_009952.1 3543739 3544005 D binds directly to the 16S rRNA and is involved in post-translational inhibition of arginine and ornithine decarboxylase; 30S ribosomal protein S20 3543739..3544005 Dinoroseobacter shibae DFL 12 = DSM 16493 5712429 YP_001534706.1 CDS yibN NC_009952.1 3544233 3544682 D PFAM: Rhodanese Homology Domain superfamily, subgroup 1 COG: PspE, Rhodanese-related sulfurtransferase; rhodanese-like sulfurtransferase 3544233..3544682 Dinoroseobacter shibae DFL 12 = DSM 16493 5712430 YP_001534707.1 CDS dnaA NC_009952.1 3544704 3546086 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 3544704..3546086 Dinoroseobacter shibae DFL 12 = DSM 16493 5712431 YP_001534708.1 CDS dnaN NC_009952.1 3546223 3547341 D binds the polymerase to DNA and acts as a sliding clamp; DNA polymerase III subunit beta 3546223..3547341 Dinoroseobacter shibae DFL 12 = DSM 16493 5712432 YP_001534709.1 CDS recF NC_009952.1 3547348 3548433 D Required for DNA replication; binds preferentially to single-stranded, linear DNA; recombination protein F 3547348..3548433 Dinoroseobacter shibae DFL 12 = DSM 16493 5712433 YP_001534710.1 CDS flgI NC_009952.1 3548430 3549533 R 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 protein complement(3548430..3549533) Dinoroseobacter shibae DFL 12 = DSM 16493 5712434 YP_001534711.1 CDS flgL NC_009952.1 3549530 3550540 R PFAM: Putative flagellar hook-associated protein 3 (HAP3) KEGG: sil:SPO0194 flagellar hook-associated protein FlgL family protein; flagellar hook-associated protein FlgL complement(3549530..3550540) Dinoroseobacter shibae DFL 12 = DSM 16493 5712435 YP_001534712.1 CDS flgK NC_009952.1 3550543 3552000 R with FlgL acts as a hook filament junction protein to join the flagellar filament to the hook; flagellar hook-associated protein FlgK complement(3550543..3552000) Dinoroseobacter shibae DFL 12 = DSM 16493 5712436 YP_001534713.1 CDS flgE NC_009952.1 3552016 3553320 R PFAM: flagellar basal body rod protein; protein of unknown function DUF1078 domain protein Swissprot: Flagellar hook protein flgE; flagellar hook protein FlgE complement(3552016..3553320) Dinoroseobacter shibae DFL 12 = DSM 16493 5712437 YP_001534714.1 CDS motB NC_009952.1 3553404 3554222 R PRK: motB, flagellar motor protein MotB COG: MotB, Flagellar motor protein REFSEQ: chemotaxis protein MotB; chemotaxis protein MotB complement(3553404..3554222) Dinoroseobacter shibae DFL 12 = DSM 16493 5712438 YP_001534715.1 CDS Dshi_3381 NC_009952.1 3554408 3556192 D PFAM: surface antigen (D15); surface antigen variable number repeat protein KEGG: rde:RD1_2329 outer membrane protein, putative; hypothetical protein 3554408..3556192 Dinoroseobacter shibae DFL 12 = DSM 16493 5712439 YP_001534716.1 CDS Dshi_3382 NC_009952.1 3556189 3559443 D PFAM: protein of unknown function DUF490 KEGG: jan:Jann_0244 protein of unknown function DUF490; hypothetical protein 3556189..3559443 Dinoroseobacter shibae DFL 12 = DSM 16493 5712440 YP_001534717.1 CDS Dshi_3383 NC_009952.1 3559437 3560141 R PFAM: Rhomboid family protein KEGG: jan:Jann_4233 rhomboid-like protein; rhomboid family protein complement(3559437..3560141) Dinoroseobacter shibae DFL 12 = DSM 16493 5712441 YP_001534718.1 CDS epsH NC_009952.1 3560203 3561804 R TIGRFAM: eight transmembrane protein EpsH; Methanolan biosynthesis EpsI KEGG: jan:Jann_4271 hypothetical protein; transmembrane exosortase complement(3560203..3561804) Dinoroseobacter shibae DFL 12 = DSM 16493 5712442 YP_001534719.1 CDS Dshi_3385 NC_009952.1 3561914 3564349 R PFAM: Tetratricopeptide TPR_4; Tetratricopeptide TPR_2 repeat protein SMART: Tetratricopeptide domain protein KEGG: jan:Jann_4236 tetratricopeptide TPR_2; tetratricopeptide complement(3561914..3564349) Dinoroseobacter shibae DFL 12 = DSM 16493 5712443 YP_001534720.1 CDS wcaJ NC_009952.1 3564483 3564998 R PFAM: sugar transferase KEGG: rde:RD1_B0024 bacterial sugar transferase; Galactosyl-P-P-undecaprenol synthetase; undecaprenyl-phosphate galactose phosphotransferase complement(3564483..3564998) Dinoroseobacter shibae DFL 12 = DSM 16493 5712444 YP_001534721.1 CDS exeA NC_009952.1 3565730 3566584 D REFSEQ: general secretion pathway protein A [Roseobacter denitrificans] COG: Type II secretory pathway, component ExeA (predicted ATPase) SMART: AAA ATPase KEGG: jan:Jann_4238 ATPase; component ExeA (predicted ATPase); Type II secretory pathway 3565730..3566584 Dinoroseobacter shibae DFL 12 = DSM 16493 5712445 YP_001534722.1 CDS Dshi_3388 NC_009952.1 3566584 3568110 D TIGRFAM: polysaccharide chain length determinant protein, PEP-CTERM locus subfamily PFAM: lipopolysaccharide biosynthesis protein KEGG: jan:Jann_4239 lipopolysaccharide biosynthesis; PEP-CTERM locus subfamily; polysaccharide chain length determinant protein 3566584..3568110 Dinoroseobacter shibae DFL 12 = DSM 16493 5712446 YP_001534723.1 CDS Dshi_3389 NC_009952.1 3568158 3568988 D KEGG: jan:Jann_4240 ATPases involved in chromosome partitioning-like; chromosome partitioning ATPase 3568158..3568988 Dinoroseobacter shibae DFL 12 = DSM 16493 5712447 YP_001534724.1 CDS Dshi_3390 NC_009952.1 3568985 3569746 R PFAM: metallophosphoesterase KEGG: jan:Jann_3688 metallophosphoesterase; metallophosphoesterase complement(3568985..3569746) Dinoroseobacter shibae DFL 12 = DSM 16493 5712448 YP_001534725.1 CDS Dshi_3391 NC_009952.1 3569750 3570550 R PFAM: beta-lactamase domain protein KEGG: rde:RD1_3791 metallo-beta-lactamase family protein, putative; putative metallo-beta-lactamase family protein complement(3569750..3570550) Dinoroseobacter shibae DFL 12 = DSM 16493 5712449 YP_001534726.1 CDS Dshi_3392 NC_009952.1 3570547 3570837 R PFAM: Antibiotic biosynthesis monooxygenase KEGG: rde:RD1_3790 hypothetical protein; hypothetical protein complement(3570547..3570837) Dinoroseobacter shibae DFL 12 = DSM 16493 5712450 YP_001534727.1 CDS leuB NC_009952.1 3570952 3572025 D PFAM: isocitrate/isopropylmalate dehydrogenase KEGG: rde:RD1_3789 3-isopropylmalate dehydrogenase; 3-IPM-DH; IMDH; Beta-IPM dehydrogenase; 3-isopropylmalate dehydrogenase 3570952..3572025 Dinoroseobacter shibae DFL 12 = DSM 16493 5712451 YP_001534728.1 CDS Dshi_3394 NC_009952.1 3572022 3573032 D PFAM: oxidoreductase domain protein; Oxidoreductase domain; homoserine dehydrogenase NAD-binding KEGG: rde:RD1_3788 probable NADH-dependent dyhydrogenase; oxidoreductase domain-containing protein 3572022..3573032 Dinoroseobacter shibae DFL 12 = DSM 16493 5712452 YP_001534729.1 CDS dctM3 NC_009952.1 3573085 3574533 R PFAM: Citrate transporter; TRAP C4-dicarboxylate transport system permease DctM subunit KEGG: cps:CPS_1266 putative C4-dicarboxylate transporter family protein, DctM subunit; TRAP dicarboxylate transporter subunit DctM complement(3573085..3574533) Dinoroseobacter shibae DFL 12 = DSM 16493 5712453 YP_001534730.1 CDS dctQ2 NC_009952.1 3574537 3575340 R PFAM: Tripartite ATP-independent periplasmic transporter DctQ component KEGG: maq:Maqu_0086 tripartite ATP-independent periplasmic transporter, DctQ component; TRAP dicarboxylate transporter subunit DctQ complement(3574537..3575340) Dinoroseobacter shibae DFL 12 = DSM 16493 5712454 YP_001534731.1 CDS dctP2 NC_009952.1 3575429 3576475 R PFAM: TRAP dicarboxylate transporter- DctP subunit KEGG: cps:CPS_1264 extracellular solute-binding protein, family 7; precursor; TRAP dicarboxylate transporter subunit DctP complement(3575429..3576475) Dinoroseobacter shibae DFL 12 = DSM 16493 5712455 YP_001534732.1 CDS orfB NC_009952.1 3576583 3577113 R KEGG: nha:Nham_4013 ISSpo6, transposase OrfB; transposase OrfB; ISSpo6 complement(3576583..3577113) Dinoroseobacter shibae DFL 12 = DSM 16493 5712456 YP_001534733.1 CDS orfA NC_009952.1 3577175 3577537 R KEGG: nha:Nham_4014 ISSpo6, transposase orf A; transposase OrfA; ISSpo6 complement(3577175..3577537) Dinoroseobacter shibae DFL 12 = DSM 16493 5712457 YP_001534734.1 CDS ubiG2 NC_009952.1 3577798 3578496 R KEGG: rde:RD1_0737 3-demethylubiquinone-9 3-methyltransferase TIGRFAM: ubiquinone biosynthesis O-methyltransferase PFAM: Methyltransferase type 11; Methyltransferase type 12; (3,4-dihydroxy-5-hexaprenylbenzoate methyltransferase) (DHHB methyltransferase); 3-demethylubiquinone-9 3-methyltransferase complement(3577798..3578496) Dinoroseobacter shibae DFL 12 = DSM 16493 5712458 YP_001534735.1 CDS Dshi_3401 NC_009952.1 3578510 3579325 R KEGG: rde:RD1_0738 hypothetical protein; hypothetical protein complement(3578510..3579325) Dinoroseobacter shibae DFL 12 = DSM 16493 5712459 YP_001534736.1 CDS Dshi_3402 NC_009952.1 3579372 3580727 R KEGG: rsp:RSP_0230 neutral zinc metallopeptidase CD: Zinc-dependent metalloprotease, serralysin_like subfamily; neutral zinc metallopeptidase complement(3579372..3580727) Dinoroseobacter shibae DFL 12 = DSM 16493 5712460 YP_001534737.1 CDS Dshi_3403 NC_009952.1 3580985 3582724 R PFAM: AMP-dependent synthetase and ligase KEGG: rde:RD1_1106 putative long chain fatty acid acyl-CoA ligase; acyl-CoA synthetase complement(3580985..3582724) Dinoroseobacter shibae DFL 12 = DSM 16493 5712461 YP_001534738.1 CDS Dshi_3404 NC_009952.1 3582924 3583157 D KEGG: mpt:Mpe_A3536 hypothetical protein; hypothetical protein 3582924..3583157 Dinoroseobacter shibae DFL 12 = DSM 16493 5712462 YP_001534739.1 CDS dsbA2 NC_009952.1 3583162 3583923 R PFAM: DSBA oxidoreductase; thiol:disulfide interchange protein DsbA complement(3583162..3583923) Dinoroseobacter shibae DFL 12 = DSM 16493 5712463 YP_001534740.1 CDS Dshi_3406 NC_009952.1 3584144 3584692 D PFAM: ErfK/YbiS/YcfS/YnhG family protein KEGG: mes:Meso_4112 ErfK/YbiS/YcfS/YnhG; ErfK/YbiS/YcfS/YnhG family protein 3584144..3584692 Dinoroseobacter shibae DFL 12 = DSM 16493 5712464 YP_001534741.1 CDS dsbD NC_009952.1 3584847 3586958 D KEGG: mag:amb3382 thiol:disulfide interchange protein DsbD 1 precursor; thiol:disulfide interchange protein DsbD 3584847..3586958 Dinoroseobacter shibae DFL 12 = DSM 16493 5712465 YP_001534742.1 CDS cycH NC_009952.1 3586961 3588142 R PFAM: TPR repeat-containing protein SMART: Tetratricopeptide domain protein KEGG: ret:RHE_CH01289 cytochrome-C-type biogenesis protein; cytochrome c-type biogenesis protein CycH complement(3586961..3588142) Dinoroseobacter shibae DFL 12 = DSM 16493 5712466 YP_001534743.1 CDS cycL NC_009952.1 3588139 3588624 R PFAM: cytochrome C biogenesis protein KEGG: rsh:Rsph17029_1291 cytochrome c biogenesis protein; cytochrome c-type biogenesis protein CycL complement(3588139..3588624) Dinoroseobacter shibae DFL 12 = DSM 16493 5712467 YP_001534744.1 CDS dsbE NC_009952.1 3588621 3589190 R TIGRFAM: periplasmic protein thiol--disulphide oxidoreductase DsbE PFAM: alkyl hydroperoxide reductase/ Thiol specific antioxidant/ Mal allergen; Redoxin domain protein KEGG: mes:Meso_3362 periplasmic protein thiol--disulphide oxidoreductase DsbE; thiol:disulfide interchange protein DsbE complement(3588621..3589190) Dinoroseobacter shibae DFL 12 = DSM 16493 5712468 YP_001534745.1 CDS cycK NC_009952.1 3589195 3591189 R TIGRFAM: cytochrome c-type biogenesis protein CcmF PFAM: cytochrome c assembly protein KEGG: mag:amb4200 cytochrome c biogenesis factor; cytochrome c-type biogenesis protein CycK complement(3589195..3591189) Dinoroseobacter shibae DFL 12 = DSM 16493 5712469 YP_001534746.1 CDS Dshi_3412 NC_009952.1 3591397 3591816 R PFAM: protein of unknown function DUF55; hypothetical protein complement(3591397..3591816) Dinoroseobacter shibae DFL 12 = DSM 16493 5712470 YP_001534747.1 CDS Dshi_3413 NC_009952.1 3591816 3592088 R PFAM: YCII-related KEGG: rde:RD1_0468 YCII-related domain protein; YCII-like domain-containing protein complement(3591816..3592088) Dinoroseobacter shibae DFL 12 = DSM 16493 5712471 YP_001534748.1 CDS gpsA NC_009952.1 3592090 3593052 R catalyzes the NAD(P)H-dependent reduction of glycerol 3-phosphate to glycerone phosphate; NAD(P)H-dependent glycerol-3-phosphate dehydrogenase complement(3592090..3593052) Dinoroseobacter shibae DFL 12 = DSM 16493 5712472 YP_001534749.1 CDS gcp NC_009952.1 3593049 3594119 R 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; putative DNA-binding/iron metalloprotein/AP endonuclease complement(3593049..3594119) Dinoroseobacter shibae DFL 12 = DSM 16493 5712473 YP_001534750.1 CDS hemD NC_009952.1 3594171 3594887 D PFAM: Uroporphyrinogen III synthase HEM4 KEGG: rsq:Rsph17025_2913 uroporphyrinogen III synthase HEM4; Hydroxymethylbilane hydrolyase [cyclizing]; Uroporphyrinogen-III cosynthetase; UROS; uroporphyrinogen-III synthase 3594171..3594887 Dinoroseobacter shibae DFL 12 = DSM 16493 5712474 YP_001534751.1 CDS Dshi_3417 NC_009952.1 3594961 3596388 D KEGG: jan:Jann_4082 hypothetical protein; hypothetical protein 3594961..3596388 Dinoroseobacter shibae DFL 12 = DSM 16493 5712475 YP_001534752.1 CDS Dshi_3418 NC_009952.1 3596399 3597907 D PFAM: HemY domain protein; hypothetical protein 3596399..3597907 Dinoroseobacter shibae DFL 12 = DSM 16493 5712476 YP_001534753.1 CDS Dshi_3419 NC_009952.1 3597982 3599307 R PFAM: Amidase KEGG: rsq:Rsph17025_3870 2-alkenal reductase; amidase complement(3597982..3599307) Dinoroseobacter shibae DFL 12 = DSM 16493 5712477 YP_001534754.1 CDS glpK NC_009952.1 3599365 3600924 D TIGRFAM: glycerol kinase PFAM: carbohydrate kinase FGGY KEGG: rde:RD1_2883 glycerol kinase; GK; Glycerokinase; ATP:glycerol 3-phosphotransferase; glycerol kinase 3599365..3600924 Dinoroseobacter shibae DFL 12 = DSM 16493 5712478 YP_001534755.1 CDS apr NC_009952.1 3601513 3603003 R Hydrolysis of proteins with broad specificity for peptide bonds, and a preference for a large uncharged residue in P1. Hydrolyses peptide amides; subtilisin DY complement(3601513..3603003) Dinoroseobacter shibae DFL 12 = DSM 16493 5712479 YP_001534756.1 CDS Dshi_3422 NC_009952.1 3603000 3603596 R no hits to other proteins; hypothetical protein complement(3603000..3603596) Dinoroseobacter shibae DFL 12 = DSM 16493 5712480 YP_001534757.1 CDS rpoE1 NC_009952.1 3603596 3604171 R TIGRFAM: RNA polymerase sigma-70 PFAM: sigma-70 region 2 domain protein; sigma-70 region 4 domain protein; Sigma-70 region 4 type 2; (sigma-70 factor family, ECF subfamily); RNA polymerase sigma factor complement(3603596..3604171) Dinoroseobacter shibae DFL 12 = DSM 16493 5712481 YP_001534758.1 CDS Dshi_3424 NC_009952.1 3604171 3605991 R no significant BLAST hits, GC frame plot ok; hypothetical protein complement(3604171..3605991) Dinoroseobacter shibae DFL 12 = DSM 16493 5712482 YP_001534759.1 CDS Dshi_3425 NC_009952.1 3606501 3606842 R KEGG: sil:SPO3859 hypothetical protein; hypothetical protein complement(3606501..3606842) Dinoroseobacter shibae DFL 12 = DSM 16493 5712483 YP_001534760.1 CDS ahcY NC_009952.1 3607055 3608443 R catalyzes the formation of L-homocysteine from S-adenosyl-L-homocysteine; S-adenosyl-L-homocysteine hydrolase complement(3607055..3608443) Dinoroseobacter shibae DFL 12 = DSM 16493 5712484 YP_001534761.1 CDS rafI NC_009952.1 3608567 3609595 D PFAM: glycosyl transferase family 8 KEGG: rde:RD1_0464 lipopolysaccharide 1,3-galactosyltransferase, putative; 3-galactosyltransferase, (Lipopolysaccharide 3-alpha-galactosyltransferase); lipopolysaccharide 1 3608567..3609595 Dinoroseobacter shibae DFL 12 = DSM 16493 5712485 YP_001534762.1 CDS Dshi_3428 NC_009952.1 3609608 3609898 R no hits to other proteins; hypothetical protein complement(3609608..3609898) Dinoroseobacter shibae DFL 12 = DSM 16493 5712486 YP_001534763.1 CDS Dshi_3429 NC_009952.1 3610138 3610746 D PFAM: HD domain KEGG: sit:TM1040_2836 metal dependent phosphohydrolase; metal dependent phosphohydrolase 3610138..3610746 Dinoroseobacter shibae DFL 12 = DSM 16493 5712487 YP_001534764.1 CDS regA NC_009952.1 3610863 3611417 R PFAM: response regulator receiver KEGG: sil:SPO3865 photosynthetic apparatus regulatory protein RegA; Response regulator PrrA; photosynthetic apparatus regulatory protein RegA complement(3610863..3611417) Dinoroseobacter shibae DFL 12 = DSM 16493 5712488 YP_001534765.1 CDS senC NC_009952.1 3611501 3612121 R PFAM: electron transport protein SCO1/SenC KEGG: sit:TM1040_2839 electron transport protein SCO1/SenC; regulatory protein SenC complement(3611501..3612121) Dinoroseobacter shibae DFL 12 = DSM 16493 5712489 YP_001534766.1 CDS regB NC_009952.1 3612224 3613615 D PFAM: ATP-binding region ATPase domain protein; histidine kinase A domain protein KEGG: sil:SPO3867 sensor histidine kinase RegB; Protein PrrB; sensor histidine kinase RegB 3612224..3613615 Dinoroseobacter shibae DFL 12 = DSM 16493 5712490 YP_001534767.1 CDS Dshi_3433 NC_009952.1 3613670 3614974 D TIGRFAM: PAS domain S-box REFSEQ: PAS domain containing protein; putative PAS/PAC sensor protein 3613670..3614974 Dinoroseobacter shibae DFL 12 = DSM 16493 5712491 YP_001534768.1 CDS Dshi_3434 NC_009952.1 3615034 3615531 D PFAM: protein of unknown function UPF0079 KEGG: rsq:Rsph17025_2955 protein of unknown function UPF0079; hypothetical protein 3615034..3615531 Dinoroseobacter shibae DFL 12 = DSM 16493 5712492 YP_001534769.1 CDS Dshi_3435 NC_009952.1 3615528 3616526 D PFAM: aminoglycoside phosphotransferase KEGG: rsh:Rsph17029_0175 aminoglycoside phosphotransferase; aminoglycoside phosphotransferase 3615528..3616526 Dinoroseobacter shibae DFL 12 = DSM 16493 5712493 YP_001534770.1 CDS Dshi_3436 NC_009952.1 3616511 3617194 D PFAM: Nucleotidyl transferase KEGG: pde:Pden_2796 nucleotidyl transferase; nucleotidyl transferase 3616511..3617194 Dinoroseobacter shibae DFL 12 = DSM 16493 5712494 YP_001534771.1 CDS addB NC_009952.1 3617191 3620157 D TIGRFAM: Double-strand break repair protein AddB KEGG: rsq:Rsph17025_2952 RecB family exonuclease-like protein PMID: 15547262; double-strand break repair helicase AddB 3617191..3620157 Dinoroseobacter shibae DFL 12 = DSM 16493 5712495 YP_001534772.1 CDS addA NC_009952.1 3620154 3623531 D TIGRFAM: Double-strand break repair helicase AddA PFAM: UvrD/REP helicase KEGG: rsp:RSP_1527 helicase, UvrD/Rep family PMID: 15547262; double-strand break repair helicase AddA 3620154..3623531 Dinoroseobacter shibae DFL 12 = DSM 16493 5712496 YP_001534773.1 CDS trxA1 NC_009952.1 3623597 3623917 D TIGRFAM: thioredoxin PFAM: Thioredoxin domain KEGG: rde:RD1_0451 thioredoxin; Trx; thioredoxin 3623597..3623917 Dinoroseobacter shibae DFL 12 = DSM 16493 5712497 YP_001534774.1 CDS hslV NC_009952.1 3624024 3624581 D heat shock protein involved in degradation of misfolded proteins; ATP-dependent protease peptidase subunit 3624024..3624581 Dinoroseobacter shibae DFL 12 = DSM 16493 5712498 YP_001534775.1 CDS hslU NC_009952.1 3624650 3625963 D heat shock protein involved in degradation of misfolded proteins; ATP-dependent protease ATP-binding subunit HslU 3624650..3625963 Dinoroseobacter shibae DFL 12 = DSM 16493 5712499 YP_001534776.1 CDS Dshi_3442 NC_009952.1 3626001 3627206 D PFAM: major facilitator superfamily MFS_1 KEGG: sit:TM1040_0930 major facilitator superfamily MFS_1; major facilitator superfamily (MFS) transporter 3626001..3627206 Dinoroseobacter shibae DFL 12 = DSM 16493 5712500 YP_001534777.1 CDS Dshi_3443 NC_009952.1 3627203 3627796 R PFAM: Smr protein/MutS2 KEGG: rde:RD1_0446 Smr domain protein; Smr protein/MutS2 complement(3627203..3627796) Dinoroseobacter shibae DFL 12 = DSM 16493 5712501 YP_001534778.1 CDS mltA NC_009952.1 3627798 3628826 R PFAM: MltA domain protein; 3D domain protein KEGG: jan:Jann_0190 MltA; membrane-bound lytic murein transglycosylase A complement(3627798..3628826) Dinoroseobacter shibae DFL 12 = DSM 16493 5712502 YP_001534779.1 CDS Dshi_3445 NC_009952.1 3628823 3629488 R PFAM: import inner membrane translocase subunit Tim44 KEGG: jan:Jann_0191 import inner membrane translocase, subunit Tim44; subunit Tim44; import inner membrane translocase complement(3628823..3629488) Dinoroseobacter shibae DFL 12 = DSM 16493 5712503 YP_001534780.1 CDS fxsA NC_009952.1 3629595 3630086 D PFAM: FxsA cytoplasmic membrane protein KEGG: sil:SPO3887 FxsA; FxsA cytoplasmic membrane protein 3629595..3630086 Dinoroseobacter shibae DFL 12 = DSM 16493 5712504 YP_001534781.1 CDS secB NC_009952.1 3630144 3630662 D 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 3630144..3630662 Dinoroseobacter shibae DFL 12 = DSM 16493 5712505 YP_001534782.1 CDS dnaQ1 NC_009952.1 3630667 3631359 R KEGG: rsq:Rsph17025_2673 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 complement(3630667..3631359) Dinoroseobacter shibae DFL 12 = DSM 16493 5712506 YP_001534783.1 CDS coaE NC_009952.1 3631352 3631948 R KEGG: pde:Pden_2814 dephospho-CoA kinase TIGRFAM: dephospho-CoA kinase PFAM: Dephospho-CoA kinase; Dephosphocoenzyme A kinase; dephospho-CoA kinase complement(3631352..3631948) Dinoroseobacter shibae DFL 12 = DSM 16493 5712507 YP_001534784.1 CDS aroE NC_009952.1 3631945 3632781 R AroE; catalyzes the conversion of shikimate to 3-dehydroshikimate; shikimate 5-dehydrogenase complement(3631945..3632781) Dinoroseobacter shibae DFL 12 = DSM 16493 5712508 YP_001534785.1 CDS maf NC_009952.1 3632778 3633374 R TIGRFAM: maf protein PFAM: Maf family protein KEGG: sil:SPO3892 Maf; septum formation protein complement(3632778..3633374) Dinoroseobacter shibae DFL 12 = DSM 16493 5712509 YP_001534786.1 CDS Dshi_3452 NC_009952.1 3633757 3634194 D PFAM: Uncharacterized protein family (UPF0093) Swissprot: UPF0093 membrane protein; hypothetical protein 3633757..3634194 Dinoroseobacter shibae DFL 12 = DSM 16493 5712510 YP_001534787.1 CDS rho NC_009952.1 3634311 3635582 D An RNA-DNA helicase that actively releases nascent mRNAs from paused transcription complexes; transcription termination factor Rho 3634311..3635582 Dinoroseobacter shibae DFL 12 = DSM 16493 5712511 YP_001534788.1 CDS trmE NC_009952.1 3635603 3636892 D in Escherichia coli this protein is involved in the biosynthesis of the hypermodified nucleoside 5-methylaminomethyl-2-thiouridine, which is found in the wobble position of some tRNAs and affects ribosomal frameshifting; shows potassium-dependent dimerization and GTP hydrolysis; also involved in regulation of glutamate-dependent acid resistance and activation of gadE; tRNA modification GTPase TrmE 3635603..3636892 Dinoroseobacter shibae DFL 12 = DSM 16493 5712512 YP_001534789.1 CDS gidA NC_009952.1 3636905 3638764 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 3636905..3638764 Dinoroseobacter shibae DFL 12 = DSM 16493 5712513 YP_001534790.1 CDS gidB NC_009952.1 3638775 3639362 D TIGRFAM: methyltransferase GidB PFAM: glucose inhibited division protein KEGG: acr:Acry_2405 methyltransferase GidB; Glucose-inhibited division protein B; methyltransferase GidB 3638775..3639362 Dinoroseobacter shibae DFL 12 = DSM 16493 5712514 YP_001534791.1 CDS parA1 NC_009952.1 3639355 3640161 D PFAM: ParA family ATPase; chromosome partitioning protein ParA 3639355..3640161 Dinoroseobacter shibae DFL 12 = DSM 16493 5712515 YP_001534792.1 CDS parB NC_009952.1 3640179 3641078 D TIGRFAM: parB-like partition protein PFAM: ParB domain protein nuclease KEGG: rsp:RSP_1225 ParB-like partition protein; chromosome partitioning protein parB 3640179..3641078 Dinoroseobacter shibae DFL 12 = DSM 16493 5712516 YP_001534793.1 CDS Dshi_3459 NC_009952.1 3641075 3641428 R PFAM: protein of unknown function DUF454 KEGG: rsh:Rsph17029_2886 protein of unknown function DUF454; hypothetical protein complement(3641075..3641428) Dinoroseobacter shibae DFL 12 = DSM 16493 5712517 YP_001534794.1 CDS hemN3 NC_009952.1 3641425 3642588 R catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III; coproporphyrinogen III oxidase complement(3641425..3642588) Dinoroseobacter shibae DFL 12 = DSM 16493 5712518 YP_001534795.1 CDS Dshi_3461 NC_009952.1 3642591 3642968 R PFAM: Endoribonuclease L-PSP KEGG: rsp:RSP_1223 putative translation initiation inhibitor, YjgF family / putative endoribonuclease L-PSP; endoribonuclease L-PSP complement(3642591..3642968) Dinoroseobacter shibae DFL 12 = DSM 16493 5712519 YP_001534796.1 CDS ham1 NC_009952.1 3642968 3643582 R HAM1-like protein; Rec-dependent growth; RgdB; yggV; it is suspected that this protein functions to remove misincorporated bases such as xanthine or hypoxanthine; putative deoxyribonucleotide triphosphate pyrophosphatase complement(3642968..3643582) Dinoroseobacter shibae DFL 12 = DSM 16493 5712520 YP_001534797.1 CDS rph NC_009952.1 3643582 3644295 R 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 complement(3643582..3644295) Dinoroseobacter shibae DFL 12 = DSM 16493 5712521 YP_001534798.1 CDS hrcA NC_009952.1 3644431 3645495 D 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 3644431..3645495 Dinoroseobacter shibae DFL 12 = DSM 16493 5712522 YP_001534799.1 CDS grpE NC_009952.1 3645508 3646101 D PFAM: GrpE protein KEGG: jan:Jann_0208 GrpE protein; HSP-70 cofactor; protein GrpE 3645508..3646101 Dinoroseobacter shibae DFL 12 = DSM 16493 5712523 YP_001534800.1 CDS mutS NC_009952.1 3646135 3648768 R This protein performs the mismatch recognition step during the DNA repair process; DNA mismatch repair protein MutS complement(3646135..3648768) Dinoroseobacter shibae DFL 12 = DSM 16493 5712524 YP_001534801.1 CDS maeB NC_009952.1 3648901 3651159 D NADP-dependent; catalyzes the oxidative decarboxylation of malate to form pyruvate; decarboxylates oxaloacetate; malic enzyme 3648901..3651159 Dinoroseobacter shibae DFL 12 = DSM 16493 5712525 YP_001534802.1 CDS msrA1 NC_009952.1 3651291 3651971 R TIGRFAM: peptide methionine sulfoxide reductase PFAM: Methionine sulfoxide reductase A KEGG: rde:RD1_0419 methionine-S-sulfoxide reductase, putative; peptide methionine sulfoxide reductase complement(3651291..3651971) Dinoroseobacter shibae DFL 12 = DSM 16493 5712526 YP_001534803.1 CDS Dshi_3469 NC_009952.1 3652180 3652893 D REFSEQ: putative branched-chain amino acid aminotransferase; putative branched-chain amino acid aminotransferase 3652180..3652893 Dinoroseobacter shibae DFL 12 = DSM 16493 5712527 YP_001534804.1 CDS Dshi_3470 NC_009952.1 3652890 3653921 R PFAM: peptidase M48 Ste24p; peptidase M48 Ste24p complement(3652890..3653921) Dinoroseobacter shibae DFL 12 = DSM 16493 5712528 YP_001534805.1 CDS Dshi_3471 NC_009952.1 3653928 3654965 R PFAM: protein of unknown function DUF898 transmembrane KEGG: sme:SMc00782 hypothetical protein; hypothetical protein complement(3653928..3654965) Dinoroseobacter shibae DFL 12 = DSM 16493 5712529 YP_001534806.1 CDS argG NC_009952.1 3655044 3656264 R catalyzes the formation of 2-N(omega)-(L-arginino)succinate from L-citrulline and L-aspartate in arginine biosynthesis, AMP-forming; argininosuccinate synthase complement(3655044..3656264) Dinoroseobacter shibae DFL 12 = DSM 16493 5712530 YP_001534807.1 CDS ilvA NC_009952.1 3656372 3657613 D catalyzes the formation of 2-oxobutanoate from L-threonine; biosynthetic; threonine dehydratase 3656372..3657613 Dinoroseobacter shibae DFL 12 = DSM 16493 5712531 YP_001534808.1 CDS pcaB NC_009952.1 3657613 3658659 D Catalyzes the cycloisomerization of cis,cis-muconate; 3-carboxy-cis,cis-muconate cycloisomerase 3657613..3658659 Dinoroseobacter shibae DFL 12 = DSM 16493 5712532 YP_001534809.1 CDS Dshi_3475 NC_009952.1 3658656 3659495 R PFAM: protein of unknown function DUF849 KEGG: jan:Jann_4165 protein of unknown function DUF849; hypothetical protein complement(3658656..3659495) Dinoroseobacter shibae DFL 12 = DSM 16493 5712533 YP_001534810.1 CDS pcaG NC_009952.1 3659505 3660119 R KEGG: bmb:BruAb2_0580 protocatechuate 3,4-dioxygenase, alpha subunit TIGRFAM: protocatechuate 3,4-dioxygenase, alpha subunit PFAM: intradiol ring-cleavage dioxygenase; (3,4-PCD); protocatechuate 3,4-dioxygenase subunit alpha complement(3659505..3660119) Dinoroseobacter shibae DFL 12 = DSM 16493 5712534 YP_001534811.1 CDS pcaH NC_009952.1 3660122 3660859 R TIGRFAM: protocatechuate 3,4-dioxygenase, beta subunit PFAM: intradiol ring-cleavage dioxygenase KEGG: sit:TM1040_0558 protocatechuate 3,4-dioxygenase, beta subunit; (3,4-PCD); protocatechuate 3,4-dioxygenase subunit beta complement(3660122..3660859) Dinoroseobacter shibae DFL 12 = DSM 16493 5712535 YP_001534812.1 CDS pcaC NC_009952.1 3660856 3661242 R TIGRFAM: 4-carboxymuconolactone decarboxylase PFAM: Carboxymuconolactone decarboxylase KEGG: sit:TM1040_0559 4-carboxymuconolactone decarboxylase; CMD; 4-carboxymuconolactone decarboxylase complement(3660856..3661242) Dinoroseobacter shibae DFL 12 = DSM 16493 5713709 YP_001534813.1 CDS pobA NC_009952.1 3661252 3662421 R catalyzes the formation of protocatechuate from 4-hydroxybenzoate; 4-hydroxybenzoate 3-monooxygenase complement(3661252..3662421) Dinoroseobacter shibae DFL 12 = DSM 16493 5713710 YP_001534814.1 CDS modE NC_009952.1 3662578 3662931 D PFAM: regulatory protein LysR KEGG: pde:Pden_2664 putative transcriptional regulator, ModE family PMID 8550508; transcriptional regulator ModE 3662578..3662931 Dinoroseobacter shibae DFL 12 = DSM 16493 5713711 YP_001534815.1 CDS modA NC_009952.1 3662924 3663676 D TIGRFAM: molybdenum ABC transporter, periplasmic molybdate-binding protein PFAM: extracellular solute-binding protein family 1 KEGG: rsp:RSP_3871 ABC molybdate transporter, periplasmic binding protein ModA; molybdate-binding periplasmic protein 3662924..3663676 Dinoroseobacter shibae DFL 12 = DSM 16493 5713712 YP_001534816.1 CDS modB NC_009952.1 3663669 3664367 D part of ModCBA molybdate transporter; member of ABC superfamily; inner membrane component; regulated by repressor protein ModE; molybdate ABC transporter permease 3663669..3664367 Dinoroseobacter shibae DFL 12 = DSM 16493 5713713 YP_001534817.1 CDS modC NC_009952.1 3664364 3665446 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; molybdenum import ATP-binding protein modC 3664364..3665446 Dinoroseobacter shibae DFL 12 = DSM 16493 5713714 YP_001534818.1 CDS Dshi_3484 NC_009952.1 3665477 3665809 R PFAM: Hpt domain protein KEGG: sit:TM1040_2886 Hpt protein; Hpt domain-containing protein complement(3665477..3665809) Dinoroseobacter shibae DFL 12 = DSM 16493 5713715 YP_001534819.1 CDS Dshi_3485 NC_009952.1 3665965 3667233 D PFAM: response regulator receiver; Stage II sporulation E family protein SMART: protein phosphatase 2C domain protein KEGG: rde:RD1_0413 response regulator; response regulator 3665965..3667233 Dinoroseobacter shibae DFL 12 = DSM 16493 5713716 YP_001534820.1 CDS Dshi_3486 NC_009952.1 3667262 3667714 R PFAM: NUDIX hydrolase KEGG: rsp:RSP_1208 NUDIX hydrolase; NUDIX hydrolase complement(3667262..3667714) Dinoroseobacter shibae DFL 12 = DSM 16493 5713717 YP_001534821.1 CDS hslO NC_009952.1 3667814 3668812 D PFAM: Hsp33 protein KEGG: jan:Jann_0079 HSP33 protein; HSP33; 33 kDa chaperonin 3667814..3668812 Dinoroseobacter shibae DFL 12 = DSM 16493 5713718 YP_001534822.1 CDS Dshi_3488 NC_009952.1 3668799 3669398 D PFAM: NUDIX hydrolase KEGG: sit:TM1040_2890 NUDIX hydrolase; NUDIX hydrolase 3668799..3669398 Dinoroseobacter shibae DFL 12 = DSM 16493 5713719 YP_001534823.1 CDS cca NC_009952.1 3669395 3670543 D PFAM: Polynucleotide adenylyltransferase region KEGG: sil:SPO0026 polyA polymerase family protein; tRNA-NT; tRNA CCA-pyrophosphorylase; tRNA adenylyl-/cytidylyl-transferase; tRNA nucleotidyltransferase; CCA-adding enzyme 3669395..3670543 Dinoroseobacter shibae DFL 12 = DSM 16493 5713720 YP_001534824.1 CDS Dshi_3490 NC_009952.1 3670604 3672448 D PFAM: ABC transporter related SMART: AAA ATPase KEGG: sil:SPO0027 ABC transporter, transmembrane ATP-binding protein; ATPase 3670604..3672448 Dinoroseobacter shibae DFL 12 = DSM 16493 5713721 YP_001534825.1 CDS Dshi_3491 NC_009952.1 3672445 3674289 D PFAM: ABC transporter transmembrane region; ABC transporter related SMART: AAA ATPase KEGG: rsq:Rsph17025_2641 ABC transporter related; ATPase 3672445..3674289 Dinoroseobacter shibae DFL 12 = DSM 16493 5713722 YP_001534826.1 CDS rumA NC_009952.1 3674330 3675574 D PFAM: (Uracil-5)-methyltransferase KEGG: sil:SPO0029 23S rRNA (uracil-5-)-methyltransferase RumA; 23S rRNA (uracil-5-)-methyltransferase RumA 3674330..3675574 Dinoroseobacter shibae DFL 12 = DSM 16493 5713723 YP_001534827.1 CDS Dshi_3493 NC_009952.1 3675591 3676379 D PFAM: Ion transport protein KEGG: rsq:Rsph17025_2848 ion transport protein REFSEQ: ref|ZP_01055369.1 voltage-gated sodium channel; voltage-gated sodium channel 3675591..3676379 Dinoroseobacter shibae DFL 12 = DSM 16493 5713724 YP_001534828.1 CDS Dshi_3494 NC_009952.1 3676456 3676956 D PFAM: ErfK/YbiS/YcfS/YnhG family protein KEGG: sil:SPO0031 ErfK/YbiS/YcfS/YnhG family protein PMID: 17098896; ErfK/YbiS/YcfS/YnhG family protein 3676456..3676956 Dinoroseobacter shibae DFL 12 = DSM 16493 5713725 YP_001534829.1 CDS Dshi_3495 NC_009952.1 3676961 3677491 R PFAM: SCP-like extracellular KEGG: rsh:Rsph17029_2861 allergen V5/TPX-1 family protein; putative SCP-like extracellular protein complement(3676961..3677491) Dinoroseobacter shibae DFL 12 = DSM 16493 5713726 YP_001534830.1 CDS Dshi_3496 NC_009952.1 3677660 3678262 D PFAM: ErfK/YbiS/YcfS/YnhG family protein KEGG: rde:RD1_0402 ErfK/YbiS/YcfS/YnhG family protein PMID: 17098896; ErfK/YbiS/YcfS/YnhG family protein 3677660..3678262 Dinoroseobacter shibae DFL 12 = DSM 16493 5713727 YP_001534832.1 CDS hemH NC_009952.1 3678932 3680020 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(3678932..3680020) Dinoroseobacter shibae DFL 12 = DSM 16493 5713729 YP_001534833.1 CDS Dshi_3499 NC_009952.1 3680013 3680882 R KEGG: jan:Jann_0294 hypothetical protein PFAM Methyltransferase domain PMID: 17098896; SAM-dependent methyltransferase complement(3680013..3680882) Dinoroseobacter shibae DFL 12 = DSM 16493 5713730 YP_001534834.1 CDS comF NC_009952.1 3680913 3681689 D KEGG: sil:SPO0071 competence protein F, putative TIGR00201 comF family protein PMID 17098896; competence protein F 3680913..3681689 Dinoroseobacter shibae DFL 12 = DSM 16493 5713731 YP_001534835.1 CDS crtA NC_009952.1 3681743 3682489 D KEGG: rde:RD1_0121 spheroidene monooxygenase PMID: 17098896; spheroidene monooxygenase 3681743..3682489 Dinoroseobacter shibae DFL 12 = DSM 16493 5713732 YP_001534836.1 CDS bchI NC_009952.1 3682486 3683490 D involved in chelation of magnesium into protoporphyrin IX; involved in bacteriochlorophyll biosynthesis; part of a complex with BchI, BchD, and BchH; magnesium chelatase subunit I 3682486..3683490 Dinoroseobacter shibae DFL 12 = DSM 16493 5713733 YP_001534837.1 CDS bchD NC_009952.1 3683499 3685220 D involved in chelation of magnesium into protoporphyrin IX; involved in bacteriochlorophyll biosynthesis; part of a complex with BchI, BchD, and BchH; magnesium chelatase subunit D 3683499..3685220 Dinoroseobacter shibae DFL 12 = DSM 16493 5713734 YP_001534838.1 CDS bchO NC_009952.1 3685217 3686125 D PFAM: alpha/beta hydrolase fold; Thioesterase; phospholipase/Carboxylesterase KEGG: rsh:Rsph17029_1918 alpha/beta hydrolase fold Swissprot: P26174 Magnesium-chelatase 30 kDa subunit PMID: 17098896; Mg-protoporphyrin IX chelatase; magnesium-chelatase 30 kDa subunit 3685217..3686125 Dinoroseobacter shibae DFL 12 = DSM 16493 5713735 YP_001534839.1 CDS Dshi_3505 NC_009952.1 3686122 3686574 R PFAM: regulatory protein MarR KEGG: rsh:Rsph17029_2853 transcriptional regulator, MarR family; MarR family; transcriptional regulator complement(3686122..3686574) Dinoroseobacter shibae DFL 12 = DSM 16493 5713736 YP_001534840.1 CDS Dshi_3506 NC_009952.1 3686571 3687404 R PFAM: Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase KEGG: sil:SPO0069 hydrolase, carbon-nitrogen family; nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase complement(3686571..3687404) Dinoroseobacter shibae DFL 12 = DSM 16493 5713737 YP_001534841.1 CDS grxC NC_009952.1 3687404 3687661 R TIGRFAM: glutaredoxin 3 PFAM: glutaredoxin KEGG: sil:SPO0070 glutaredoxin; Grx3; glutaredoxin-3 complement(3687404..3687661) Dinoroseobacter shibae DFL 12 = DSM 16493 5713738 YP_001534842.1 CDS crtI NC_009952.1 3687777 3689351 D TIGRFAM: Zeta-phytoene desaturase PFAM: amine oxidase; FAD dependent oxidoreductase KEGG: rde:RD1_0120 phytoene dehydrogenase PMID: 17098896; Phytoene desaturase; phytoene dehydrogenase 3687777..3689351 Dinoroseobacter shibae DFL 12 = DSM 16493 5713739 YP_001534843.1 CDS crtB NC_009952.1 3689348 3690433 D PFAM: Squalene/phytoene synthase KEGG: rde:RD1_0119 phytoene synthase PMID: 17098896; phytoene synthase 3689348..3690433 Dinoroseobacter shibae DFL 12 = DSM 16493 5713740 YP_001534844.1 CDS tspO NC_009952.1 3690440 3690922 D PFAM: TspO/MBR family protein KEGG: jan:Jann_0035 TspO and MBR like proteins PMID: 17098896; 10648776; tryptophan rich sensory protein 3690440..3690922 Dinoroseobacter shibae DFL 12 = DSM 16493 5713741 YP_001534845.1 CDS Dshi_3511 NC_009952.1 3690919 3691104 R KEGG: rsh:Rsph17029_2919 hypothetical protein; hypothetical protein complement(3690919..3691104) Dinoroseobacter shibae DFL 12 = DSM 16493 5713742 YP_001534846.1 CDS crtC NC_009952.1 3691117 3691875 R PFAM: hydroxyneurosporene synthase KEGG: rde:RD1_0116 hydroxyneurosporene dehydrogenase PMID: 17098896; hydroxyneurosporene dehydrogenase complement(3691117..3691875) Dinoroseobacter shibae DFL 12 = DSM 16493 5713743 YP_001534847.1 CDS crtD NC_009952.1 3691944 3693542 R TIGRFAM: Zeta-phytoene desaturase PFAM: amine oxidase; FAD dependent oxidoreductase KEGG: jan:Jann_0183 amine oxidase Swissprot: P17059 PMID: 17098896; methoxyneurosporene dehydrogenase complement(3691944..3693542) Dinoroseobacter shibae DFL 12 = DSM 16493 5713744 YP_001534848.1 CDS crtE NC_009952.1 3693641 3694519 D PFAM: Polyprenyl synthetase KEGG: jan:Jann_0182 polyprenyl synthetase COG0142 PMID: 17098896; Farnesyltranstransferase; GGPP synthetase; geranylgeranyl pyrophosphate synthetase 3693641..3694519 Dinoroseobacter shibae DFL 12 = DSM 16493 5713745 YP_001534849.1 CDS crtF NC_009952.1 3694523 3695653 D PFAM: O-methyltransferase family 2; Methyltransferase type 12 KEGG: jan:Jann_0181 O-methyltransferase, family 2 PMID: 17098896; O-methylase; hydroxyneurosporene methyltransferase 3694523..3695653 Dinoroseobacter shibae DFL 12 = DSM 16493 5713746 YP_001534850.1 CDS bchC NC_009952.1 3695777 3696715 D TIGRFAM: chlorophyll synthesis pathway, BchC PFAM: Alcohol dehydrogenase GroES domain protein KEGG: jan:Jann_0180 chlorophyll synthesis pathway, BchC PMID: 17098896; 2-desacetyl-2-hydroxyethyl bacteriochlorophyllide A dehydrogenase 3695777..3696715 Dinoroseobacter shibae DFL 12 = DSM 16493 5713747 YP_001534851.1 CDS bchX NC_009952.1 3696712 3697719 D KEGG: jan:Jann_0179 chlorophyllide reductase iron protein subunit X TIGRFAM: chlorophyllide reductase iron protein subunit X PFAM: NifH/frxC-family protein PMID: 17098896; 10648776; 8468299; bacteriachlorophyllide reductase iron protein subunit X 3696712..3697719 Dinoroseobacter shibae DFL 12 = DSM 16493 5713748 YP_001534852.1 CDS bchY NC_009952.1 3697755 3699359 D TIGRFAM: chlorophyllide reductase subunit Y KEGG: jan:Jann_0178 chlorophyllide reductase subunit Y PMID: 17098896; 10648776; 8468299; bacteriachlorophyllide reductase iron protein subunit Y 3697755..3699359 Dinoroseobacter shibae DFL 12 = DSM 16493 5713749 YP_001534853.1 CDS bchZ NC_009952.1 3699577 3701043 D TIGRFAM: chlorophyllide reductase subunit Z PFAM: oxidoreductase/nitrogenase component 1; protein of unknown function DUF1197 KEGG: jan:Jann_0177 chlorophyllide reductase subunit Z PMID: 17098896; 10648776; 8468299; bacteriachlorophyllide reductase iron protein subunit Z 3699577..3701043 Dinoroseobacter shibae DFL 12 = DSM 16493 5713750 YP_001534854.1 CDS pufQ NC_009952.1 3701062 3701286 D PFAM: PufQ cytochrome subunit KEGG: rde:RD1_0108 protein PufQ PMID: 17098896; protein pufQ 3701062..3701286 Dinoroseobacter shibae DFL 12 = DSM 16493 5713751 YP_001534855.1 CDS pufB NC_009952.1 3701410 3701559 D PFAM: antenna complex alpha/beta subunit KEGG: rsq:Rsph17025_2032 antenna complex, alpha/beta subunit PMID: 17098896; 15879238; Antenna pigment protein beta chain; LH-1; light-harvesting protein B-870 subunit beta 3701410..3701559 Dinoroseobacter shibae DFL 12 = DSM 16493 5713752 YP_001534856.1 CDS pufA NC_009952.1 3701573 3701734 D PFAM: antenna complex alpha/beta subunit KEGG: rsh:Rsph17029_1901 antenna complex, alpha/beta subunit PMID: 17098896; 15879238; Antenna pigment protein alpha chain; LH-1; light-harvesting protein B-870 subunit alpha 3701573..3701734 Dinoroseobacter shibae DFL 12 = DSM 16493 5713753 YP_001534857.1 CDS pufL NC_009952.1 3701883 3702722 D TIGRFAM: photosynthetic reaction center L subunit PFAM: photosynthetic reaction centre protein KEGG: rde:RD1_0104 photosynthetic reaction center L subunit PMID: 17098896; Photosynthetic reaction center L subunit; photosynthetic reaction center subunit L 3701883..3702722 Dinoroseobacter shibae DFL 12 = DSM 16493 5713754 YP_001534858.1 CDS pufM NC_009952.1 3702726 3703718 D TIGRFAM: photosynthetic reaction center, M subunit PFAM: photosynthetic reaction centre protein KEGG: jan:Jann_0172 photosynthetic reaction center M subunit PMID: 17098896; Photosynthetic reaction center M subunit; photosynthetic reaction center subunit M 3702726..3703718 Dinoroseobacter shibae DFL 12 = DSM 16493 5713755 YP_001534859.1 CDS pufC NC_009952.1 3703718 3704800 D PFAM: photosynthetic reaction centre cytochrome c subunit KEGG: rde:RD1_0102 photosynthetic reaction center cytochrome c subunit PMID: 17098896; photosynthetic reaction center cytochrome subunit C 3703718..3704800 Dinoroseobacter shibae DFL 12 = DSM 16493 5713756 YP_001534860.1 CDS dxs2 NC_009952.1 3704933 3706909 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 3704933..3706909 Dinoroseobacter shibae DFL 12 = DSM 16493 5713757 YP_001534861.1 CDS idi NC_009952.1 3707023 3707553 R KEGG: rsq:Rsph17025_1019 isopentenyl-diphosphate delta-isomerase, type 1 TIGRFAM: isopentenyl-diphosphate delta-isomerase, type 1 PFAM: NUDIX hydrolase PMID: 17098896; IPP:DMAPP isomerase; Isopentenyl pyrophosphate isomerase; IPP isomerase; isopentenyl-diphosphate Delta-isomerase complement(3707023..3707553) Dinoroseobacter shibae DFL 12 = DSM 16493 5713758 YP_001534862.1 CDS bchP NC_009952.1 3707550 3708734 R TIGRFAM: geranylgeranyl reductase PFAM: monooxygenase FAD-binding; FAD dependent oxidoreductase; Lycopene beta and epsilon cyclase KEGG: jan:Jann_0167 geranylgeranyl reductase PMID: 10572128; 17098896; geranylgeranyl reductase complement(3707550..3708734) Dinoroseobacter shibae DFL 12 = DSM 16493 5713759 YP_001534863.1 CDS pucC2 NC_009952.1 3708748 3710049 R PFAM: PUCC protein; major facilitator superfamily MFS_1 KEGG: rsp:RSP_0278 putative light-harvesting 1 (B870) complex assembly protein PucC PMID: 17098896; PucC protein complement(3708748..3710049) Dinoroseobacter shibae DFL 12 = DSM 16493 5713760 YP_001534864.1 CDS bchG NC_009952.1 3710051 3710956 R TIGRFAM: bacteriochlorophyll/chlorophyll synthetase PFAM: UbiA prenyltransferase KEGG: jan:Jann_0165 bacteriochlorophyll/chlorophyll synthetase PMID: 17098896; bacteriochlorophyll/chlorophyll a synthase complement(3710051..3710956) Dinoroseobacter shibae DFL 12 = DSM 16493 5713761 YP_001534865.1 CDS ppsR NC_009952.1 3711054 3712484 R TIGRFAM: PAS sensor protein; transcriptional regulator PpsR PMID: 10735869; 17098896; transcriptional regulator PpsR complement(3711054..3712484) Dinoroseobacter shibae DFL 12 = DSM 16493 5713762 YP_001534866.1 CDS ppaA NC_009952.1 3712527 3713387 R REFSEQ: ref|ZP_01034604.1 regulatory protein PpaA PMID: 17098896; regulatory protein PpaA complement(3712527..3713387) Dinoroseobacter shibae DFL 12 = DSM 16493 5713763 YP_001534867.1 CDS bchF NC_009952.1 3713645 3714133 D PFAM: 2-vinyl bacteriochlorophyllide hydratase KEGG: rsh:Rsph17029_1927 2-vinyl bacteriochlorophyllide hydratase PMID: 17098896; 2-oxoglutarate synthase subunit, 2-oxoacid-ferredoxin oxidoreductase subunit CD 3713645..3714133 Dinoroseobacter shibae DFL 12 = DSM 16493 5713764 YP_001534868.1 CDS bchN NC_009952.1 3714130 3715413 D light-independent reduction of protochlorophyllide to form chlorophyllide a; light-independent protochlorophyllide reductase subunit N 3714130..3715413 Dinoroseobacter shibae DFL 12 = DSM 16493 5713765 YP_001534869.1 CDS bchB NC_009952.1 3715410 3716996 D light-independent reduction of protochlorophyllide to form chlorophyllide a; light-independent protochlorophyllide reductase subunit B 3715410..3716996 Dinoroseobacter shibae DFL 12 = DSM 16493 5713766 YP_001534870.1 CDS bchH NC_009952.1 3716986 3720570 D involved in chelation of magnesium into protoporphyrin IX; involved in bacteriochlorophyll biosynthesis; the enzyme from Rhodobacter capsulatus contains an Fe-S cluster; part of a complex with BchI, BchD, and BchH; magnesium chelatase subunit H 3716986..3720570 Dinoroseobacter shibae DFL 12 = DSM 16493 5713767 YP_001534871.1 CDS chlL NC_009952.1 3720602 3721501 D light-independent; with chlN(bchN) and chlB(bchB) reduces ring D of protochlorophyllide to form chlorophyllide a in chlorophyll/bacteriochlorophyll production; protochlorophyllide reductase iron-sulfur ATP-binding protein 3720602..3721501 Dinoroseobacter shibae DFL 12 = DSM 16493 5713768 YP_001534872.1 CDS bchM NC_009952.1 3721548 3722231 D catalyzes the formation of Mg-protoporphyrin IX methyl ester and S-adenosyl-L-homocysteine from Mg-protoporphyrin IX and S-adenosyl-L-methionine; Mg-protoporphyrin IX methyl transferase 3721548..3722231 Dinoroseobacter shibae DFL 12 = DSM 16493 5713769 YP_001534873.1 CDS lhaA NC_009952.1 3722228 3723673 D PFAM: PUCC protein; major facilitator superfamily MFS_1 KEGG: rde:RD1_0134 LhaA protein PMID: 17098896; PucC protein 3722228..3723673 Dinoroseobacter shibae DFL 12 = DSM 16493 5713770 YP_001534874.1 CDS puhA NC_009952.1 3723698 3724468 D TIGRFAM: photosynthetic reaction center H subunit PFAM: PRC-barrel domain protein; Photosynthetic reaction centre H subunit KEGG: rde:RD1_0133 photosynthetic reaction center H subunit PMID: 17098896; reaction center protein H chain 3723698..3724468 Dinoroseobacter shibae DFL 12 = DSM 16493 5713771 YP_001534875.1 CDS puhB NC_009952.1 3724493 3725170 D KEGG: rde:RD1_0132 possible photosynthetic co REFSEQ: ref|ZP_01879036.1 putative photosynthetic complex assembly protein PMID: 17098896; putative photosynthetic complex assembly protein 3724493..3725170 Dinoroseobacter shibae DFL 12 = DSM 16493 5713772 YP_001534876.1 CDS puhC NC_009952.1 3725184 3725663 D KEGG: rde:RD1_0131 REFSEQ: ref|YP_680552.1 PuhC Protein PMID: 17098896; 17098896; PuhC protein 3725184..3725663 Dinoroseobacter shibae DFL 12 = DSM 16493 5713773 YP_001534877.1 CDS Dshi_3543 NC_009952.1 3725667 3725963 D KEGG: rde:RD1_0130 hypothetical protein; hypothetical protein 3725667..3725963 Dinoroseobacter shibae DFL 12 = DSM 16493 5713774 YP_001534878.1 CDS acsF NC_009952.1 3725960 3727081 D oxidative; catalyzes the formation of divinylprotochlorophyllide from magnesium-protoporphyrin IX 13-monomethyl ester in isocyclic ring formation in chlorophyll biosynthesis; magnesium-protoporphyrin IX monomethyl ester cyclase 3725960..3727081 Dinoroseobacter shibae DFL 12 = DSM 16493 5713775 YP_001534879.1 CDS puhE NC_009952.1 3727081 3727878 D KEGG: rde:RD1_0128 REFSEQ: ref|YP_680549.1 PuhE Protein PMID: 17098896; PuhE protein 3727081..3727878 Dinoroseobacter shibae DFL 12 = DSM 16493 5713776 YP_001534880.1 CDS hemA1 NC_009952.1 3728081 3729295 D catalyzes the formation of 5-aminolevulinate from succinyl-CoA and glycine; 5-aminolevulinate synthase 3728081..3729295 Dinoroseobacter shibae DFL 12 = DSM 16493 5713777 YP_001534881.1 CDS cycA2 NC_009952.1 3729391 3729831 D JTo: PFAM: cytochrome c class I KEGG: jan:Jann_0148 cytochrome c, class I Swiss-Prot: cytochrome c class I, SignalP: signal peptide cleavage between VLA-DD, PSORT: inner membrane PMID: 8611557, 17098896; cytochrome c2 3729391..3729831 Dinoroseobacter shibae DFL 12 = DSM 16493 5713778 YP_001534882.1 CDS Dshi_3548 NC_009952.1 3729973 3731778 D PFAM: ABC transporter transmembrane region; ABC transporter related SMART: AAA ATPase KEGG: jan:Jann_4278 ABC transporter related; ATPase 3729973..3731778 Dinoroseobacter shibae DFL 12 = DSM 16493 5713779 YP_001534883.1 CDS glpQ NC_009952.1 3731871 3733085 D PFAM: glycerophosphoryl diester phosphodiesterase KEGG: rde:RD1_1698 glycerophosphoryl diester phosphodiesterase family protein, putative PRK: glpQ; periplasmic; glycerophosphoryl diester phosphodiesterase 3731871..3733085 Dinoroseobacter shibae DFL 12 = DSM 16493 5713780 YP_001534884.1 CDS ubiG1 NC_009952.1 3733252 3733998 R Involved in ubiquinone biosynthesis; 3-demethylubiquinone-9 3-methyltransferase complement(3733252..3733998) Dinoroseobacter shibae DFL 12 = DSM 16493 5713781 YP_001534885.1 CDS pip NC_009952.1 3734063 3735049 D KEGG: sil:SPO0066 proline iminopeptidase TIGRFAM: proline iminopeptidase PFAM: alpha/beta hydrolase fold; PAP; Prolyl aminopeptidase; PIP; proline iminopeptidase 3734063..3735049 Dinoroseobacter shibae DFL 12 = DSM 16493 5713782 YP_001534886.1 CDS Dshi_3552 NC_009952.1 3735027 3736508 D PFAM: extracellular solute-binding protein family 5; family 5 extracellular solute-binding protein 3735027..3736508 Dinoroseobacter shibae DFL 12 = DSM 16493 5713783 YP_001534887.1 CDS acs NC_009952.1 3736896 3738872 D TIGRFAM: acetate--CoA ligase PFAM: AMP-dependent synthetase and ligase KEGG: rde:RD1_2332 acetyl-coenzyme A synthetase; Acyl-activating enzyme; Acetate--CoA ligase; acetyl-coenzyme A synthetase 3736896..3738872 Dinoroseobacter shibae DFL 12 = DSM 16493 5713784 YP_001534888.1 CDS adk1 NC_009952.1 3738878 3739567 D PFAM: adenylate kinase; adenylate kinase lid domain protein KEGG: sil:SPO1812 adenylate kinase; ATP-AMP transphosphorylase; adenylate kinase 3738878..3739567 Dinoroseobacter shibae DFL 12 = DSM 16493 5713785 YP_001534889.1 CDS Dshi_3555 NC_009952.1 3739687 3739944 D KEGG: psa:PST_3903 hypothetical protein; hypothetical protein 3739687..3739944 Dinoroseobacter shibae DFL 12 = DSM 16493 5713786 YP_001534890.1 CDS Dshi_3556 NC_009952.1 3739962 3741758 D PFAM: Na+/solute symporter KEGG: sil:SPO1810 sodium/solute symporter family protein; sodium/solute symporter family protein 3739962..3741758 Dinoroseobacter shibae DFL 12 = DSM 16493 5713787 YP_001534891.1 CDS Dshi_3557 NC_009952.1 3741883 3743700 D PFAM: cyclic nucleotide-binding; CBS domain containing protein; protein of unknown function DUF294 nucleotidyltransferase putative KEGG: sil:SPO1809 nucleotidyltransferase/CBS/cyclic nucleotide-binding domain protein; putative CBS domain and cyclic nucleotide-regulated nucleotidyltransferase 3741883..3743700 Dinoroseobacter shibae DFL 12 = DSM 16493 5713788 YP_001534892.1 CDS Dshi_3558 NC_009952.1 3743713 3744228 D KEGG: sil:SPO1808 hypothetical protein; hypothetical protein 3743713..3744228 Dinoroseobacter shibae DFL 12 = DSM 16493 5713789 YP_001534893.1 CDS dnaQ2 NC_009952.1 3744249 3745706 D KEGG: sil:SPO1807 exonuclease, DNA polymerase III, epsilon subunit family TIGRFAM: DNA polymerase III, epsilon subunit PFAM: Exonuclease RNase T and DNA polymerase III SMART: Exonuclease COG0847; DNA polymerase III subunit epsilon 3744249..3745706 Dinoroseobacter shibae DFL 12 = DSM 16493 5713790 YP_001534894.1 CDS Dshi_3560 NC_009952.1 3745860 3746450 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 3745860..3746450 Dinoroseobacter shibae DFL 12 = DSM 16493 5713791 YP_001534895.1 CDS nusA NC_009952.1 3746464 3748098 D modifies transcription through interactions with RNA polymerase affecting elongation, readthrough, termination, and antitermination; transcription elongation factor NusA 3746464..3748098 Dinoroseobacter shibae DFL 12 = DSM 16493 5713792 YP_001534896.1 CDS Dshi_3562 NC_009952.1 3748122 3748760 D PFAM: protein of unknown function DUF448; hypothetical protein 3748122..3748760 Dinoroseobacter shibae DFL 12 = DSM 16493 5713793 YP_001534897.1 CDS infB NC_009952.1 3748757 3751255 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 3748757..3751255 Dinoroseobacter shibae DFL 12 = DSM 16493 5713794 YP_001534898.1 CDS mutT NC_009952.1 3751598 3751996 R TIGRFAM: mutator MutT protein PFAM: NUDIX hydrolase KEGG: sil:SPO0060 mutator MutT protein; mutator MutT protein complement(3751598..3751996) Dinoroseobacter shibae DFL 12 = DSM 16493 5713795 YP_001534899.1 CDS argJ NC_009952.1 3751993 3753216 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(3751993..3753216) Dinoroseobacter shibae DFL 12 = DSM 16493 5713796 YP_001534900.1 CDS ppiC NC_009952.1 3753294 3754136 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(3753294..3754136) Dinoroseobacter shibae DFL 12 = DSM 16493 5713797 YP_001534901.1 CDS secA NC_009952.1 3754364 3757090 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 3754364..3757090 Dinoroseobacter shibae DFL 12 = DSM 16493 5713798 YP_001534902.1 CDS Dshi_3568 NC_009952.1 3757069 3758595 D no domains found, significant blast hits only to JGI projects, good GC frame plot; hypothetical protein 3757069..3758595 Dinoroseobacter shibae DFL 12 = DSM 16493 5713799 YP_001534903.1 CDS radC NC_009952.1 3758567 3759331 R TIGRFAM: DNA repair protein radc PFAM: DNA repair protein RadC KEGG: pde:Pden_2304 DNA repair protein RadC; DNA repair protein RadC complement(3758567..3759331) Dinoroseobacter shibae DFL 12 = DSM 16493 5713800 YP_001534904.1 CDS dnaJ NC_009952.1 3759367 3760518 R 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; chaperone protein DnaJ complement(3759367..3760518) Dinoroseobacter shibae DFL 12 = DSM 16493 5713801 YP_001534905.1 CDS dnaK NC_009952.1 3760594 3762513 R 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 complement(3760594..3762513) Dinoroseobacter shibae DFL 12 = DSM 16493 5713802 YP_001534906.1 CDS alkB2 NC_009952.1 3762679 3763314 D KEGG: rde:RD1_0377 alkylated DNA repair protein TIGRFAM: DNA alkylation damage repair protein AlkB, COG: Alkylated DNA repair protein; Alkylated DNA repair protein alkB; alpha-ketoglutarate-dependent dioxygenase alkB 3762679..3763314 Dinoroseobacter shibae DFL 12 = DSM 16493 5713803 YP_001534907.1 CDS Dshi_3573 NC_009952.1 3763345 3764166 R PFAM: ABC-2 type transporter KEGG: sil:SPO0040 ABC transporter, permease protein; putative ABC-2 type transporter complement(3763345..3764166) Dinoroseobacter shibae DFL 12 = DSM 16493 5713804 YP_001534908.1 CDS cysQ NC_009952.1 3764320 3765117 D TIGRFAM: 3(2),5-bisphosphate nucleotidase PFAM: inositol monophosphatase KEGG: sil:SPO0039 3(2),5-bisphosphate nucleotidase; 3'(2'),5'-bisphosphate nucleotidase 3764320..3765117 Dinoroseobacter shibae DFL 12 = DSM 16493 5713805 YP_001534909.1 CDS kdsB NC_009952.1 3765117 3765917 D 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 3765117..3765917 Dinoroseobacter shibae DFL 12 = DSM 16493 5713806 YP_001534910.1 CDS Dshi_3576 NC_009952.1 3765914 3767146 D PFAM: glycosyl transferase family 2 KEGG: pde:Pden_2298 glycosyl transferase, family 2; family 2; glycosyl transferase family protein 3765914..3767146 Dinoroseobacter shibae DFL 12 = DSM 16493 5713807 YP_001534911.1 CDS galU NC_009952.1 3767288 3768184 D TIGRFAM: UTP-glucose-1-phosphate uridylyltransferase PFAM: Nucleotidyl transferase KEGG: jan:Jann_0218 UTP-glucose-1-phosphate uridylyltransferase,PMID:4284510; UTP-glucose-1-phosphate uridylyltransferase 3767288..3768184 Dinoroseobacter shibae DFL 12 = DSM 16493 5713808 YP_001534912.1 CDS Dshi_3578 NC_009952.1 3768197 3769435 D PFAM: glycosyl transferase group 1 KEGG: pde:Pden_2295 glycosyl transferase, group 1, COG0438 - Glycosyltransferase; group 1; glycosyl transferase family protein 3768197..3769435 Dinoroseobacter shibae DFL 12 = DSM 16493 5713809 YP_001534913.1 CDS Dshi_3579 NC_009952.1 3769483 3770499 D KEGG: sil:SPO0036 hypothetical protein; hypothetical protein 3769483..3770499 Dinoroseobacter shibae DFL 12 = DSM 16493 5713810 YP_001534914.1 CDS Dshi_3580 NC_009952.1 3770718 3772205 D KEGG: sil:SPO0035 core-2/I-branching enzyme family protein; core-2/I-branching enzyme family protein 3770718..3772205 Dinoroseobacter shibae DFL 12 = DSM 16493 5713811 YP_001534915.1 CDS Dshi_3581 NC_009952.1 3772212 3773648 D KEGG: jan:Jann_0222 hypothetical protein; hypothetical protein 3772212..3773648 Dinoroseobacter shibae DFL 12 = DSM 16493 5713812 YP_001534916.1 CDS ptsN NC_009952.1 3773660 3774124 R PFAM: phosphoenolpyruvate-dependent sugar phosphotransferase system EIIA 2 KEGG: rsq:Rsph17025_2769 PTS IIA-like nitrogen-regulatory protein PtsN, COG1762 - Phosphotransferase system mannitol/fructose-specific IIA domain (Ntr-type); PTS transporter subunit IIA-like nitrogen-regulatory protein PtsN complement(3773660..3774124) Dinoroseobacter shibae DFL 12 = DSM 16493 5713813 YP_001534917.1 CDS Dshi_3583 NC_009952.1 3774163 3774738 R TIGRFAM: ribosomal subunit interface protein PFAM: sigma 54 modulation protein/ribosomal protein S30EA KEGG: rde:RD1_0372 sigma-54 modulation protein, putative; 30S ribosomal protein S30 complement(3774163..3774738) Dinoroseobacter shibae DFL 12 = DSM 16493 5713814 YP_001534918.1 CDS rpoN NC_009952.1 3774813 3776129 R TIGRFAM: RNA polymerase sigma-54 factor, RpoN PFAM: sigma-54 factor; sigma-54 factor core-binding region; sigma-54 DNA-binding domain protein KEGG: rsh:Rsph17029_2179 RNA polymerase, sigma 54 subunit, RpoN; RNA polymerase sigma-54 factor complement(3774813..3776129) Dinoroseobacter shibae DFL 12 = DSM 16493 5713815 YP_001534919.1 CDS Dshi_3585 NC_009952.1 3776138 3776902 R pfam00005: ABC_tran, COG1137 - ABC-type (unclassified) transport system, ATPase component, BLAST hits to several ABC transporter, ATP-binding protein; ATPase complement(3776138..3776902) Dinoroseobacter shibae DFL 12 = DSM 16493 5713816 YP_001534920.1 CDS Dshi_3586 NC_009952.1 3776899 3777411 R PFAM: OstA family protein KEGG: rsh:Rsph17029_2816 OstA family protein, COG1934 - Uncharacterized protein conserved in bacteria; OstA family protein complement(3776899..3777411) Dinoroseobacter shibae DFL 12 = DSM 16493 5713817 YP_001534921.1 CDS Dshi_3587 NC_009952.1 3777425 3778027 R similar hit in Roseovarius, not conserved throughout many species; hypothetical protein complement(3777425..3778027) Dinoroseobacter shibae DFL 12 = DSM 16493 5713818 YP_001534922.1 CDS yrbH NC_009952.1 3778031 3778993 R KEGG: rde:RD1_0368 arabinose 5-phosphate isomerase TIGRFAM: KpsF/GutQ family protein PFAM: CBS domain containing protein; sugar isomerase (SIS); arabinose-5-phosphate isomerase complement(3778031..3778993) Dinoroseobacter shibae DFL 12 = DSM 16493 5713819 YP_001534923.1 CDS Dshi_3589 NC_009952.1 3779003 3779614 R PFAM: 3-5 exonuclease; 3'-5' exonuclease complement(3779003..3779614) Dinoroseobacter shibae DFL 12 = DSM 16493 5713820 YP_001534924.1 CDS Dshi_3590 NC_009952.1 3780019 3781002 D pfam07993: NAD_binding_4 domain, COG0702 - Predicted nucleoside-diphosphate-sugar epimerases; ubiquinone dependent NADH dehydrogenase 3780019..3781002 Dinoroseobacter shibae DFL 12 = DSM 16493 5713822 YP_001534925.1 CDS Dshi_3591 NC_009952.1 3781025 3782716 R domain hit: Abi, transmembrane helices predicted, weak BLAST hits; CAAX amino terminal protease family protein complement(3781025..3782716) Dinoroseobacter shibae DFL 12 = DSM 16493 5713823 YP_001534926.1 CDS Dshi_3592 NC_009952.1 3783102 3788285 R no domain hits, no BLAST hit, good GC frame plot over whole length; hypothetical protein complement(3783102..3788285) Dinoroseobacter shibae DFL 12 = DSM 16493 5713824 YP_001534927.1 CDS uppP NC_009952.1 3788688 3789491 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(3788688..3789491) Dinoroseobacter shibae DFL 12 = DSM 16493 5713825 YP_001541808.1 CDS Dshi_3594 NC_009955.1 8 844 R PFAM: protein of unknown function DUF305; KEGG: rsh:Rsph17029_3677 protein of unknown function DUF305; hypothetical protein complement(8..844) Dinoroseobacter shibae DFL 12 = DSM 16493 5714321 YP_001541809.1 CDS Dshi_3595 NC_009955.1 1024 1605 D PFAM: ErfK/YbiS/YcfS/YnhG family protein; KEGG: mes:Meso_4112 ErfK/YbiS/YcfS/YnhG; ErfK/YbiS/YcfS/YnhG family protein 1024..1605 Dinoroseobacter shibae DFL 12 = DSM 16493 5714125 YP_001541810.1 CDS Dshi_3596 NC_009955.1 1689 2993 D PFAM: multicopper oxidase type 1; multicopper oxidase type 2; multicopper oxidase type 3; KEGG: sit:TM1040_0289 multicopper oxidase, type 3; multicopper oxidase type 3 1689..2993 Dinoroseobacter shibae DFL 12 = DSM 16493 5714126 YP_001541811.1 CDS Dshi_3597 NC_009955.1 3107 3619 D KEGG: sit:TM1040_1167 disulphide bond formation protein DsbB; disulfide bond formation protein DsbB 3107..3619 Dinoroseobacter shibae DFL 12 = DSM 16493 5714127 YP_001541812.1 CDS Dshi_3598 NC_009955.1 3662 4327 D PFAM: ErfK/YbiS/YcfS/YnhG family protein; KEGG: rde:RD1_0492 ErfK/YbiS/YcfS/YnhG family protein; ErfK/YbiS/YcfS/YnhG family protein 3662..4327 Dinoroseobacter shibae DFL 12 = DSM 16493 5714128 YP_001541813.1 CDS Dshi_3599 NC_009955.1 4404 4961 R KEGG: sil:SPO0304 lipoprotein, putative; putative lipoprotein complement(4404..4961) Dinoroseobacter shibae DFL 12 = DSM 16493 5714129 YP_001541814.1 CDS Dshi_3600 NC_009955.1 5359 5967 D SMART: Calcium-binding EF-hand-containing protein; KEGG: rpb:RPB_2375 calcium-binding EF-hand protein; calcium-binding EF-hand-containing protein 5359..5967 Dinoroseobacter shibae DFL 12 = DSM 16493 5714130 YP_001541815.1 CDS Dshi_3601 NC_009955.1 6108 6494 D PFAM: protein of unknown function DUF302; KEGG: mmr:Mmar10_2335 protein of unknown function DUF302; hypothetical protein 6108..6494 Dinoroseobacter shibae DFL 12 = DSM 16493 5714131 YP_001541816.1 CDS Dshi_3602 NC_009955.1 6600 7520 D transfers the N-acyl diglyceride moiety to the prospective N-terminal cysteine in prolipoprotein; prolipoprotein diacylglyceryl transferase 6600..7520 Dinoroseobacter shibae DFL 12 = DSM 16493 5714132 YP_001541817.1 CDS Dshi_3603 NC_009955.1 7599 9944 D 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; E1-E2 ATPase-associated domain protein; KEGG: sil:SPOA0365 copper-translocating P-type ATPase; heavy metal translocating P-type ATPase 7599..9944 Dinoroseobacter shibae DFL 12 = DSM 16493 5714133 YP_001541818.1 CDS Dshi_3604 NC_009955.1 9993 11330 D PFAM: amino acid permease-associated region; KEGG: sil:SPOA0366 amino acid permease; amino acid permease 9993..11330 Dinoroseobacter shibae DFL 12 = DSM 16493 5714134 YP_001541819.1 CDS Dshi_3605 NC_009955.1 11338 11982 R hypothetical protein complement(11338..11982) Dinoroseobacter shibae DFL 12 = DSM 16493 5714135 YP_001541820.1 CDS Dshi_3606 NC_009955.1 12199 12921 D PFAM: cytochrome c biogenesis protein transmembrane region; KEGG: maq:Maqu_3250 cytochrome c biogenesis protein, transmembrane region; cytochrome c biogenesis protein transmembrane region 12199..12921 Dinoroseobacter shibae DFL 12 = DSM 16493 5714136 YP_001541821.1 CDS Dshi_3607 NC_009955.1 13115 13780 D PFAM: ErfK/YbiS/YcfS/YnhG family protein; KEGG: rde:RD1_0492 ErfK/YbiS/YcfS/YnhG family protein; ErfK/YbiS/YcfS/YnhG family protein 13115..13780 Dinoroseobacter shibae DFL 12 = DSM 16493 5714137 YP_001541822.1 CDS Dshi_3608 NC_009955.1 13828 14100 R KEGG: rde:RD1_0491 hypothetical protein; hypothetical protein complement(13828..14100) Dinoroseobacter shibae DFL 12 = DSM 16493 5714138 YP_001541823.1 CDS Dshi_3609 NC_009955.1 14461 16647 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: mes:Meso_4212 heavy metal translocating P-type ATPase; heavy metal translocating P-type ATPase 14461..16647 Dinoroseobacter shibae DFL 12 = DSM 16493 5714139 YP_001541824.1 CDS Dshi_3610 NC_009955.1 16641 16916 R hypothetical protein complement(16641..16916) Dinoroseobacter shibae DFL 12 = DSM 16493 5714140 YP_001541825.1 CDS Dshi_3611 NC_009955.1 17014 17472 D PFAM: regulatory protein MarR; iron dependent repressor; SMART: regulatory protein Crp; KEGG: mlo:mll2499 hypothetical protein; DtxR family iron dependent repressor 17014..17472 Dinoroseobacter shibae DFL 12 = DSM 16493 5714141 YP_001541826.1 CDS Dshi_3612 NC_009955.1 17567 17734 R KEGG: sil:SPO2514 hypothetical protein; hypothetical protein complement(17567..17734) Dinoroseobacter shibae DFL 12 = DSM 16493 5714142 YP_001541827.1 CDS Dshi_3613 NC_009955.1 17734 19305 R TIGRFAM: apolipoprotein N-acyltransferase; PFAM: Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase; KEGG: nha:Nham_0025 apolipoprotein N-acyltransferase; apolipoprotein N-acyltransferase complement(17734..19305) Dinoroseobacter shibae DFL 12 = DSM 16493 5714143 YP_001541828.1 CDS Dshi_3614 NC_009955.1 19302 19775 R TIGRFAM: lipoprotein signal peptidase; PFAM: peptidase A8 signal peptidase II; KEGG: eli:ELI_04470 putative lipoprotein signal peptidase; lipoprotein signal peptidase complement(19302..19775) Dinoroseobacter shibae DFL 12 = DSM 16493 5714144 YP_001541829.1 CDS Dshi_3615 NC_009955.1 19780 20562 R PFAM: zinc/iron permease; KEGG: gvi:glr4280 zinc transporter, ZIP family; zinc/iron permease complement(19780..20562) Dinoroseobacter shibae DFL 12 = DSM 16493 5714145 YP_001541830.1 CDS Dshi_3616 NC_009955.1 20585 21043 R PFAM: protein of unknown function DUF411; KEGG: aav:Aave_1809 protein of unknown function DUF411; hypothetical protein complement(20585..21043) Dinoroseobacter shibae DFL 12 = DSM 16493 5714146 YP_001541831.1 CDS Dshi_3617 NC_009955.1 21047 22420 R PFAM: peptidase M23B; KEGG: hch:HCH_06239 membrane protein related to metalloendopeptidase; peptidase M23B complement(21047..22420) Dinoroseobacter shibae DFL 12 = DSM 16493 5714147 YP_001541832.1 CDS Dshi_3618 NC_009955.1 22417 23043 R PFAM: electron transport protein SCO1/SenC; KEGG: ccr:CC_3503 SCO1/2 family protein; electron transport protein SCO1/SenC complement(22417..23043) Dinoroseobacter shibae DFL 12 = DSM 16493 5714148 YP_001541833.1 CDS Dshi_3619 NC_009955.1 23043 23513 R PFAM: protein of unknown function DUF461; KEGG: bra:BRADO4160 conserved hypothetical protein; putative signal peptide; hypothetical protein complement(23043..23513) Dinoroseobacter shibae DFL 12 = DSM 16493 5714149 YP_001541834.1 CDS Dshi_3620 NC_009955.1 23536 24195 R PFAM: DSBA oxidoreductase; KEGG: mes:Meso_4133 DsbA oxidoreductase; DSBA oxidoreductase complement(23536..24195) Dinoroseobacter shibae DFL 12 = DSM 16493 5714150 YP_001541835.1 CDS Dshi_3621 NC_009955.1 24192 24614 R PFAM: Disulphide bond formation protein DsbB; KEGG: psa:PST_0576 disulfide bond formation protein; disulfide bond formation protein DsbB complement(24192..24614) Dinoroseobacter shibae DFL 12 = DSM 16493 5714151 YP_001541836.1 CDS Dshi_3622 NC_009955.1 24620 25222 R PFAM: electron transport protein SCO1/SenC; KEGG: mag:amb0517 uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems; electron transport protein SCO1/SenC complement(24620..25222) Dinoroseobacter shibae DFL 12 = DSM 16493 5714152 YP_001541837.1 CDS Dshi_3623 NC_009955.1 25400 25828 D PFAM: regulatory protein MerR; Transcription regulator MerR DNA binding; KEGG: sil:SPOA0389 transcriptional regulator, MerR family; MerR family transcriptional regulator 25400..25828 Dinoroseobacter shibae DFL 12 = DSM 16493 5714153 YP_001541838.1 CDS Dshi_3624 NC_009955.1 25911 26531 D PFAM: cation efflux protein; KEGG: mes:Meso_4424 cation efflux protein; cation efflux protein 25911..26531 Dinoroseobacter shibae DFL 12 = DSM 16493 5714154 YP_001541839.1 CDS Dshi_3625 NC_009955.1 26601 27164 D KEGG: ajs:Ajs_1334 hypothetical protein; hypothetical protein 26601..27164 Dinoroseobacter shibae DFL 12 = DSM 16493 5714155 YP_001541840.1 CDS Dshi_3626 NC_009955.1 27154 28119 D TIGRFAM: cation diffusion facilitator family transporter; PFAM: cation efflux protein; KEGG: maq:Maqu_3275 cation diffusion facilitator family transporter; cation diffusion facilitator family transporter 27154..28119 Dinoroseobacter shibae DFL 12 = DSM 16493 5714156 YP_001541841.1 CDS Dshi_3627 NC_009955.1 28091 28402 D KEGG: gfo:GFO_1210 hypothetical protein; hypothetical protein 28091..28402 Dinoroseobacter shibae DFL 12 = DSM 16493 5714157 YP_001541842.1 CDS Dshi_3628 NC_009955.1 28756 29451 D KEGG: sit:TM1040_3830 hypothetical protein; hypothetical protein 28756..29451 Dinoroseobacter shibae DFL 12 = DSM 16493 5714158 YP_001541843.1 CDS Dshi_3629 NC_009955.1 29691 30563 D PFAM: integrase family protein; integrase domain protein SAM domain protein; KEGG: acr:Acry_2348 phage integrase family protein; integrase family protein 29691..30563 Dinoroseobacter shibae DFL 12 = DSM 16493 5714159 YP_001541844.1 CDS Dshi_3630 NC_009955.1 30576 31778 D PFAM: putative transposase; KEGG: sal:Sala_0067 putative transposase; putative transposase 30576..31778 Dinoroseobacter shibae DFL 12 = DSM 16493 5714160 YP_001541845.1 CDS Dshi_3631 NC_009955.1 32223 33164 R PFAM: helix-turn-helix- domain containing protein AraC type; ThiJ/PfpI domain protein; KEGG: sil:SPO1704 transcriptional regulator, AraC family; AraC family transcriptional regulator complement(32223..33164) Dinoroseobacter shibae DFL 12 = DSM 16493 5714161 YP_001541846.1 CDS Dshi_3632 NC_009955.1 33247 35727 D PFAM: L-carnitine dehydratase/bile acid-inducible protein F; KEGG: sil:SPO1703 CaiB/BaiF family protein; L-carnitine dehydratase/bile acid-inducible protein F 33247..35727 Dinoroseobacter shibae DFL 12 = DSM 16493 5714162 YP_001541847.1 CDS Dshi_3633 NC_009955.1 35746 37389 D KEGG: sil:SPO1702 hypothetical protein; hypothetical protein 35746..37389 Dinoroseobacter shibae DFL 12 = DSM 16493 5714163 YP_001541848.1 CDS Dshi_3634 NC_009955.1 37539 37766 R KEGG: sit:TM1040_3826 hypothetical protein; hypothetical protein complement(37539..37766) Dinoroseobacter shibae DFL 12 = DSM 16493 5714164 YP_001541849.1 CDS Dshi_3635 NC_009955.1 37936 38193 R PFAM: helix-turn-helix domain protein; KEGG: rsq:Rsph17025_0810 putative transcriptional regulator, XRE family; XRE family transcriptional regulator complement(37936..38193) Dinoroseobacter shibae DFL 12 = DSM 16493 5714165 YP_001541850.1 CDS Dshi_3636 NC_009955.1 38318 38611 R KEGG: sit:TM1040_3824 hypothetical protein; hypothetical protein complement(38318..38611) Dinoroseobacter shibae DFL 12 = DSM 16493 5714166 YP_001541851.1 CDS Dshi_3637 NC_009955.1 38780 39133 D KEGG: sit:TM1040_3823 hypothetical protein; hypothetical protein 38780..39133 Dinoroseobacter shibae DFL 12 = DSM 16493 5714167 YP_001541852.1 CDS Dshi_3638 NC_009955.1 39177 39797 D PFAM: Lytic transglycosylase catalytic; KEGG: sit:TM1040_3822 lytic transglycosylase, catalytic; lytic transglycosylase 39177..39797 Dinoroseobacter shibae DFL 12 = DSM 16493 5714168 YP_001541853.1 CDS Dshi_3639 NC_009955.1 39794 40087 D PFAM: Conjugal transfer protein TrbC; KEGG: sit:TM1040_3821 VirB2 type IV secretion; conjugal transfer protein TrbC 39794..40087 Dinoroseobacter shibae DFL 12 = DSM 16493 5714169 YP_001541854.1 CDS Dshi_3640 NC_009955.1 40080 40358 D PFAM: type IV secretory pathway VirB3 family protein; KEGG: sit:TM1040_3820 type IV secretory pathway, VirB3-like; type IV secretory pathway VirB3 family protein 40080..40358 Dinoroseobacter shibae DFL 12 = DSM 16493 5714170 YP_001541855.1 CDS Dshi_3641 NC_009955.1 40348 42723 D PFAM: CagE TrbE VirB component of type IV transporter system; SMART: AAA ATPase; KEGG: sit:TM1040_3819 CagE, TrbE, VirB component of type IV transporter system; CagE TrbE VirB component of type IV transporter system 40348..42723 Dinoroseobacter shibae DFL 12 = DSM 16493 5714171 YP_001541856.1 CDS Dshi_3642 NC_009955.1 42720 42887 D KEGG: sit:TM1040_3818 hypothetical protein; hypothetical protein 42720..42887 Dinoroseobacter shibae DFL 12 = DSM 16493 5714172 YP_001541857.1 CDS Dshi_3643 NC_009955.1 42877 44031 D PFAM: Lytic transglycosylase catalytic; KEGG: sit:TM1040_3817 lytic transglycosylase, catalytic; lytic transglycosylase catalytic 42877..44031 Dinoroseobacter shibae DFL 12 = DSM 16493 5714173 YP_001541858.1 CDS Dshi_3644 NC_009955.1 44031 44840 D KEGG: sit:TM1040_3816 hypothetical protein; hypothetical protein 44031..44840 Dinoroseobacter shibae DFL 12 = DSM 16493 5714174 YP_001541859.1 CDS Dshi_3645 NC_009955.1 44855 45511 D PFAM: VirB8 family protein; KEGG: sit:TM1040_3815 VirB8; VirB8 family protein 44855..45511 Dinoroseobacter shibae DFL 12 = DSM 16493 5714175 YP_001541860.1 CDS Dshi_3646 NC_009955.1 45513 46208 D PFAM: Conjugal transfer protein TrbG/VirB9/CagX; KEGG: sit:TM1040_3814 conjugal transfer protein TrbG/VirB9/CagX; conjugal transfer protein TrbG/VirB9/CagX 45513..46208 Dinoroseobacter shibae DFL 12 = DSM 16493 5714176 YP_001541861.1 CDS Dshi_3647 NC_009955.1 46205 47584 D PFAM: conjugation TrbI family protein; KEGG: sit:TM1040_3813 conjugation TrbI-like protein; conjugation TrbI family protein 46205..47584 Dinoroseobacter shibae DFL 12 = DSM 16493 5714177 YP_001541862.1 CDS Dshi_3648 NC_009955.1 47589 48575 D PFAM: type II secretion system protein E; KEGG: sit:TM1040_3812 type II secretion system protein E; type II secretion system protein E 47589..48575 Dinoroseobacter shibae DFL 12 = DSM 16493 5714178 YP_001541863.1 CDS Dshi_3649 NC_009955.1 48572 48766 D KEGG: sit:TM1040_3811 hypothetical protein; hypothetical protein 48572..48766 Dinoroseobacter shibae DFL 12 = DSM 16493 5714179 YP_001541864.1 CDS Dshi_3650 NC_009955.1 48763 49173 D KEGG: sit:TM1040_3810 hypothetical protein; hypothetical protein 48763..49173 Dinoroseobacter shibae DFL 12 = DSM 16493 5714180 YP_001541865.1 CDS Dshi_3651 NC_009955.1 49186 50262 D PFAM: TrbL/VirB6 plasmid conjugal transfer protein; KEGG: sit:TM1040_3809 TrbL/VirB6 plasmid conjugal transfer protein; TrbL/VirB6 plasmid conjugal transfer protein 49186..50262 Dinoroseobacter shibae DFL 12 = DSM 16493 5714181 YP_001541866.1 CDS Dshi_3652 NC_009955.1 50623 51540 D KEGG: mes:Meso_4413 hypothetical protein; hypothetical protein 50623..51540 Dinoroseobacter shibae DFL 12 = DSM 16493 5714182 YP_001541867.1 CDS Dshi_3653 NC_009955.1 51856 53406 R PFAM: DNA-directed DNA polymerase; KEGG: psp:PSPPH_4219 DNA polymerase I domain protein; DNA-directed DNA polymerase complement(51856..53406) Dinoroseobacter shibae DFL 12 = DSM 16493 5714183 YP_001541868.1 CDS Dshi_3654 NC_009955.1 53399 55099 R KEGG: pna:Pnap_3925 hypothetical protein; hypothetical protein complement(53399..55099) Dinoroseobacter shibae DFL 12 = DSM 16493 5714184 YP_001541869.1 CDS Dshi_3655 NC_009955.1 55361 57364 R PFAM: TRAG family protein; KEGG: sit:TM1040_3794 TraG protein; TRAG family protein complement(55361..57364) Dinoroseobacter shibae DFL 12 = DSM 16493 5714185 YP_001541870.1 CDS Dshi_3656 NC_009955.1 57373 59706 R PFAM: Relaxase/mobilization nuclease family protein; KEGG: sit:TM1040_3793 relaxase/mobilization nuclease domain; relaxase/mobilization nuclease family protein complement(57373..59706) Dinoroseobacter shibae DFL 12 = DSM 16493 5714186 YP_001541871.1 CDS Dshi_3657 NC_009955.1 59693 60274 R PFAM: transposase IS3/IS911 family protein; KEGG: sit:TM1040_3792 hypothetical protein; transposase IS3/IS911 family protein complement(59693..60274) Dinoroseobacter shibae DFL 12 = DSM 16493 5714187 YP_001541872.1 CDS Dshi_3658 NC_009955.1 60838 61044 R KEGG: sit:TM1040_3791 hypothetical protein; hypothetical protein complement(60838..61044) Dinoroseobacter shibae DFL 12 = DSM 16493 5714188 YP_001541873.1 CDS Dshi_3659 NC_009955.1 61245 61547 R hypothetical protein complement(61245..61547) Dinoroseobacter shibae DFL 12 = DSM 16493 5714189 YP_001541874.1 CDS Dshi_3660 NC_009955.1 61583 62512 R KEGG: mes:Meso_4225 hypothetical protein; hypothetical protein complement(61583..62512) Dinoroseobacter shibae DFL 12 = DSM 16493 5714190 YP_001541875.1 CDS Dshi_3661 NC_009955.1 63298 64170 D PFAM: integrase family protein; integrase domain protein SAM domain protein; KEGG: acr:Acry_2348 phage integrase family protein; integrase family protein 63298..64170 Dinoroseobacter shibae DFL 12 = DSM 16493 5714191 YP_001541876.1 CDS Dshi_3662 NC_009955.1 64183 65385 D PFAM: putative transposase; KEGG: sal:Sala_0067 putative transposase; putative transposase 64183..65385 Dinoroseobacter shibae DFL 12 = DSM 16493 5714192 YP_001541877.1 CDS Dshi_3663 NC_009955.1 65753 66727 R KEGG: bbt:BBta_1126 putative membrane protein of unknown function; hypothetical protein complement(65753..66727) Dinoroseobacter shibae DFL 12 = DSM 16493 5714193 YP_001541878.1 CDS Dshi_3664 NC_009955.1 67147 67365 D KEGG: acr:Acry_3183 hypothetical protein; hypothetical protein 67147..67365 Dinoroseobacter shibae DFL 12 = DSM 16493 5714194 YP_001541879.1 CDS Dshi_3665 NC_009955.1 67356 67688 D KEGG: gox:GOX2735 PemK-like protein; transcriptional modulator of MazE/toxin MazF 67356..67688 Dinoroseobacter shibae DFL 12 = DSM 16493 5714195 YP_001541880.1 CDS Dshi_3666 NC_009955.1 68206 68370 R KEGG: rde:RD1_3456 hypothetical protein; hypothetical protein complement(68206..68370) Dinoroseobacter shibae DFL 12 = DSM 16493 5714196 YP_001541881.1 CDS Dshi_3667 NC_009955.1 68732 69094 R KEGG: reh:H16_B1492 hypothetical protein; hypothetical protein complement(68732..69094) Dinoroseobacter shibae DFL 12 = DSM 16493 5714197 YP_001541882.1 CDS Dshi_3668 NC_009955.1 69101 69835 R PFAM: protein of unknown function UPF0005; KEGG: rsh:Rsph17029_3820 protein of unknown function UPF0005; hypothetical protein complement(69101..69835) Dinoroseobacter shibae DFL 12 = DSM 16493 5714198 YP_001541883.1 CDS Dshi_3669 NC_009955.1 70079 70657 R PFAM: Exopolysaccharide synthesis ExoD; KEGG: jan:Jann_0449 exopolysaccharide synthesis, ExoD; exopolysaccharide synthesis ExoD complement(70079..70657) Dinoroseobacter shibae DFL 12 = DSM 16493 5714199 YP_001541884.1 CDS Dshi_3670 NC_009955.1 70773 71738 R TIGRFAM: Na+/Ca+ antiporter, CaCA family; PFAM: sodium/calcium exchanger membrane region; KEGG: sil:SPO0535 K+-dependent Na+/Ca+ exchanger related-protein; CaCA family Na(+)/Ca(+) antiporter complement(70773..71738) Dinoroseobacter shibae DFL 12 = DSM 16493 5714200 YP_001541885.1 CDS Dshi_3671 NC_009955.1 71864 72325 R PFAM: pentapeptide repeat protein; KEGG: tel:tlr0822 hypothetical protein; pentapeptide repeat-containing protein complement(71864..72325) Dinoroseobacter shibae DFL 12 = DSM 16493 5714201 YP_001541886.1 CDS Dshi_3672 NC_009955.1 72650 73927 R PFAM: CBS domain containing protein; protein of unknown function DUF21; transporter-associated region; KEGG: pde:Pden_0723 protein of unknown function DUF21; hypothetical protein complement(72650..73927) Dinoroseobacter shibae DFL 12 = DSM 16493 5714202 YP_001541887.1 CDS Dshi_3673 NC_009955.1 74023 74991 R KEGG: rsp:RSP_0408 hypothetical protein; hypothetical protein complement(74023..74991) Dinoroseobacter shibae DFL 12 = DSM 16493 5714203 YP_001541888.1 CDS Dshi_3674 NC_009955.1 75225 77591 R PFAM: cyclic nucleotide-binding; sodium/hydrogen exchanger; KEGG: rde:RD1_3698 sodium/hydrogen exchanger family, putative; cyclic nucleotide-binding protein complement(75225..77591) Dinoroseobacter shibae DFL 12 = DSM 16493 5714204 YP_001541889.1 CDS Dshi_3675 NC_009955.1 77607 77891 R KEGG: rde:RD1_3698 sodium/hydrogen exchanger family, putative; hypothetical protein complement(77607..77891) Dinoroseobacter shibae DFL 12 = DSM 16493 5714205 YP_001541890.1 CDS Dshi_3676 NC_009955.1 78020 80338 R PFAM: transposase Tn3 family protein; KEGG: psb:Psyr_2667 transposase Tn3; transposase Tn3 family protein complement(78020..80338) Dinoroseobacter shibae DFL 12 = DSM 16493 5714206 YP_001541891.1 CDS Dshi_3677 NC_009955.1 80378 80902 R KEGG: rsq:Rsph17025_4307 hypothetical protein; hypothetical protein complement(80378..80902) Dinoroseobacter shibae DFL 12 = DSM 16493 5714207 YP_001541892.1 CDS Dshi_3678 NC_009955.1 81019 81843 R KEGG: art:Arth_4384 ATP-binding protein; ATP-binding protein complement(81019..81843) Dinoroseobacter shibae DFL 12 = DSM 16493 5714208 YP_001541893.1 CDS Dshi_3679 NC_009955.1 81840 83333 R PFAM: Integrase catalytic region; Transposase-like Mu; KEGG: art:Arth_4385 integrase, catalytic region; integrase catalytic region complement(81840..83333) Dinoroseobacter shibae DFL 12 = DSM 16493 5714209 YP_001541894.1 CDS Dshi_3680 NC_009955.1 83472 84071 D PFAM: Resolvase domain; Resolvase helix-turn-helix domain protein; KEGG: gox:GOX2646 DNA integration/recombination/invertion protein; resolvase domain-containing protein 83472..84071 Dinoroseobacter shibae DFL 12 = DSM 16493 5714210 YP_001541895.1 CDS Dshi_3681 NC_009955.1 84592 86400 D required for the synthesis of the hydromethylpyrimidine moiety of thiamine; thiamine biosynthesis protein ThiC 84592..86400 Dinoroseobacter shibae DFL 12 = DSM 16493 5714211 YP_001541896.1 CDS Dshi_3682 NC_009955.1 86804 88186 R PFAM: transposase IS4 family protein; KEGG: rde:RD1_3444 transposase, putative; transposase IS4 family protein complement(86804..88186) Dinoroseobacter shibae DFL 12 = DSM 16493 5714212 YP_001541897.1 CDS Dshi_3683 NC_009955.1 88435 89082 D PFAM: Resolvase domain; KEGG: psb:Psyr_2668 helix-turn-helix, fis-type; resolvase domain-containing protein 88435..89082 Dinoroseobacter shibae DFL 12 = DSM 16493 5714213 YP_001541898.1 CDS Dshi_3684 NC_009955.1 89186 90118 D KEGG: pfl:PFL_2489 hypothetical protein; hypothetical protein 89186..90118 Dinoroseobacter shibae DFL 12 = DSM 16493 5714214 YP_001541899.1 CDS Dshi_3685 NC_009955.1 90129 90698 D PFAM: BioY protein; KEGG: bbk:BARBAKC583_1193 biotin transport protein BioY; BioY protein 90129..90698 Dinoroseobacter shibae DFL 12 = DSM 16493 5714215 YP_001541900.1 CDS Dshi_3686 NC_009955.1 90714 91379 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sit:TM1040_3661 ABC transporter related; ABC transporter 90714..91379 Dinoroseobacter shibae DFL 12 = DSM 16493 5714216 YP_001541901.1 CDS Dshi_3687 NC_009955.1 91376 91969 D PFAM: cobalt transport protein; KEGG: sit:TM1040_3660 cobalt transport protein; cobalt transport protein 91376..91969 Dinoroseobacter shibae DFL 12 = DSM 16493 5714217 YP_001541902.1 CDS Dshi_3688 NC_009955.1 92394 92966 R PFAM: BioY protein; KEGG: mlo:mlr7429 bioY protein; BioY protein complement(92394..92966) Dinoroseobacter shibae DFL 12 = DSM 16493 5714218 YP_001541903.1 CDS Dshi_3689 NC_009955.1 93160 93360 D KEGG: psb:Psyr_2668 helix-turn-helix, fis-type; hypothetical protein 93160..93360 Dinoroseobacter shibae DFL 12 = DSM 16493 5714219 YP_001541904.1 CDS Dshi_3690 NC_009955.1 93569 94297 R KEGG: jan:Jann_4220 ParB-like nuclease; ParB-like nuclease complement(93569..94297) Dinoroseobacter shibae DFL 12 = DSM 16493 5714220 YP_001541905.1 CDS Dshi_3691 NC_009955.1 94422 94724 R hypothetical protein complement(94422..94724) Dinoroseobacter shibae DFL 12 = DSM 16493 5714221 YP_001541906.1 CDS Dshi_3692 NC_009955.1 94825 95286 R KEGG: bbt:BBta_7341 hypothetical protein; hypothetical protein complement(94825..95286) Dinoroseobacter shibae DFL 12 = DSM 16493 5714222 YP_001541907.1 CDS Dshi_3693 NC_009955.1 95288 95674 R KEGG: sal:Sala_2657 hypothetical protein; hypothetical protein complement(95288..95674) Dinoroseobacter shibae DFL 12 = DSM 16493 5714223 YP_001541908.1 CDS Dshi_3694 NC_009955.1 95796 97667 R KEGG: ana:alr7089 hypothetical protein; hypothetical protein complement(95796..97667) Dinoroseobacter shibae DFL 12 = DSM 16493 5714224 YP_001541909.1 CDS Dshi_3695 NC_009955.1 97825 100266 D PFAM: DNA primase small subunit; type III restriction protein res subunit; DEAD/DEAH box helicase domain protein; SMART: DEAD-like helicases; KEGG: sfu:Sfum_3271 type III restriction enzyme, res subunit; type III restriction protein res subunit 97825..100266 Dinoroseobacter shibae DFL 12 = DSM 16493 5714225 YP_001541910.1 CDS Dshi_3696 NC_009955.1 100305 101309 R PFAM: integrase family protein; integrase domain protein SAM domain protein; KEGG: sal:Sala_0440 phage integrase; integrase family protein complement(100305..101309) Dinoroseobacter shibae DFL 12 = DSM 16493 5714226 YP_001541911.1 CDS Dshi_3697 NC_009955.1 101306 102217 R PFAM: integrase family protein; KEGG: sal:Sala_0439 phage integrase; integrase family protein complement(101306..102217) Dinoroseobacter shibae DFL 12 = DSM 16493 5714227 YP_001541912.1 CDS Dshi_3698 NC_009955.1 102214 103740 R PFAM: integrase family protein; integrase domain protein SAM domain protein; KEGG: sal:Sala_0438 phage integrase; integrase family protein complement(102214..103740) Dinoroseobacter shibae DFL 12 = DSM 16493 5714228 YP_001541913.1 CDS Dshi_3699 NC_009955.1 103864 106374 R KEGG: nar:Saro_2208 putative methylase/helicase; putative methylase/helicase complement(103864..106374) Dinoroseobacter shibae DFL 12 = DSM 16493 5714229 YP_001541914.1 CDS Dshi_3700 NC_009955.1 107197 108084 D PFAM: integrase family protein; integrase domain protein SAM domain protein; KEGG: nha:Nham_0858 phage integrase; integrase family protein 107197..108084 Dinoroseobacter shibae DFL 12 = DSM 16493 5714230 YP_001541915.1 CDS Dshi_3701 NC_009955.1 108097 109296 D PFAM: putative transposase; KEGG: sal:Sala_0067 putative transposase; putative transposase 108097..109296 Dinoroseobacter shibae DFL 12 = DSM 16493 5714231 YP_001541916.1 CDS Dshi_3702 NC_009955.1 109817 110656 R PFAM: fatty acid hydroxylase; KEGG: pol:Bpro_3325 hypothetical protein; fatty acid hydroxylase complement(109817..110656) Dinoroseobacter shibae DFL 12 = DSM 16493 5714232 YP_001541917.1 CDS Dshi_3705 NC_009955.1 112171 113076 R PFAM: Integrase catalytic region; KEGG: pde:Pden_3846 integrase, catalytic region; integrase catalytic region complement(112171..113076) Dinoroseobacter shibae DFL 12 = DSM 16493 5714234 YP_001541918.1 CDS Dshi_3706 NC_009955.1 113073 113405 R PFAM: transposase IS3/IS911 family protein; KEGG: psp:PSPPH_A0090 ISPsy21, transposase orfA; transposase IS3/IS911 family protein complement(113073..113405) Dinoroseobacter shibae DFL 12 = DSM 16493 5714235 YP_001541919.1 CDS Dshi_3707 NC_009955.1 113417 113626 R KEGG: acr:Acry_0097 transposase, IS4 family protein; transposase, IS4 family protein complement(113417..113626) Dinoroseobacter shibae DFL 12 = DSM 16493 5714236 YP_001541920.1 CDS Dshi_3708 NC_009955.1 113772 114608 D PFAM: helix-turn-helix- domain containing protein AraC type; AraC protein arabinose-binding/dimerisation; KEGG: rpc:RPC_0847 transcriptional regulator, AraC family; AraC family transcriptional regulator 113772..114608 Dinoroseobacter shibae DFL 12 = DSM 16493 5714237 YP_001541921.1 CDS Dshi_3709 NC_009955.1 114610 115872 R TIGRFAM: TRAP dicarboxylate transporter, DctM subunit; PFAM: TRAP C4-dicarboxylate transport system permease DctM subunit; KEGG: jan:Jann_1450 TRAP dicarboxylate transporter-DctM subunit; TRAP dicarboxylate transporter, DctM subunit complement(114610..115872) Dinoroseobacter shibae DFL 12 = DSM 16493 5714238 YP_001541922.1 CDS Dshi_3710 NC_009955.1 115872 116441 R PFAM: Tripartite ATP-independent periplasmic transporter DctQ component; KEGG: jan:Jann_1449 tripartite ATP-independent periplasmic transporter, DctQ component; tripartite ATP-independent periplasmic transporter DctQ complement(115872..116441) Dinoroseobacter shibae DFL 12 = DSM 16493 5714239 YP_001541923.1 CDS Dshi_3711 NC_009955.1 116503 117483 R PFAM: TRAP dicarboxylate transporter- DctP subunit; KEGG: sit:TM1040_1591 TRAP dicarboxylate transporter-DctP subunit; TRAP dicarboxylate transporter- DctP subunit complement(116503..117483) Dinoroseobacter shibae DFL 12 = DSM 16493 5714240 YP_001541924.1 CDS Dshi_3712 NC_009955.1 117527 118285 R PFAM: short-chain dehydrogenase/reductase SDR; KR domain protein; KEGG: swi:Swit_3068 short-chain dehydrogenase/reductase SDR; short-chain dehydrogenase/reductase SDR complement(117527..118285) Dinoroseobacter shibae DFL 12 = DSM 16493 5714241 YP_001541925.1 CDS Dshi_3713 NC_009955.1 118469 118945 D PFAM: conserved hypothetical protein; KEGG: ccr:CC_3289 hypothetical protein; hypothetical protein 118469..118945 Dinoroseobacter shibae DFL 12 = DSM 16493 5714242 YP_001541926.1 CDS Dshi_3714 NC_009955.1 118926 119519 R TIGRFAM: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; PFAM: flavoprotein; KEGG: rpc:RPC_0842 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; 3-octaprenyl-4-hydroxybenzoate carboxy-lyase complement(118926..119519) Dinoroseobacter shibae DFL 12 = DSM 16493 5714243 YP_001541927.1 CDS Dshi_3715 NC_009955.1 119636 120550 R PFAM: regulatory protein LysR; LysR substrate-binding; KEGG: bxe:Bxe_A2070 transcriptional regulator, LysR family; LysR family transcriptional regulator complement(119636..120550) Dinoroseobacter shibae DFL 12 = DSM 16493 5714244 YP_001541928.1 CDS Dshi_3716 NC_009955.1 120678 122087 D TIGRFAM: UbiD family decarboxylase; PFAM: Carboxylyase-related protein; KEGG: bja:blr3531 hypothetical protein; UbiD family decarboxylase 120678..122087 Dinoroseobacter shibae DFL 12 = DSM 16493 5714245 YP_001541929.1 CDS Dshi_3717 NC_009955.1 122126 123583 D PFAM: aldehyde dehydrogenase; KEGG: rpc:RPC_0853 aldehyde dehydrogenase; aldehyde dehydrogenase 122126..123583 Dinoroseobacter shibae DFL 12 = DSM 16493 5714246 YP_001541930.1 CDS Dshi_3718 NC_009955.1 123637 124554 D SMART: helix-turn-helix- domain containing protein AraC type; KEGG: rpc:RPC_0847 transcriptional regulator, AraC family; AraC family transcriptional regulator 123637..124554 Dinoroseobacter shibae DFL 12 = DSM 16493 5714247 YP_001541931.1 CDS Dshi_3719 NC_009955.1 124654 127605 D PFAM: aldehyde oxidase and xanthine dehydrogenase a/b hammerhead; cyclase/dehydrase; aldehyde oxidase and xanthine dehydrogenase molybdopterin binding; carbon monoxide dehydrogenase subunit G; KEGG: rpc:RPC_0848 carbon-monoxide dehydrogenase; molybdopterin binding aldehyde oxidase and xanthine dehydrogenase 124654..127605 Dinoroseobacter shibae DFL 12 = DSM 16493 5714248 YP_001541932.1 CDS Dshi_3720 NC_009955.1 127602 128429 D PFAM: molybdopterin dehydrogenase FAD-binding; KEGG: acr:Acry_0669 molybdopterin dehydrogenase, FAD-binding; molybdopterin dehydrogenase FAD-binding 127602..128429 Dinoroseobacter shibae DFL 12 = DSM 16493 5714249 YP_001541933.1 CDS Dshi_3721 NC_009955.1 128417 128926 D PFAM: ferredoxin; [2Fe-2S]-binding domain protein; KEGG: rpc:RPC_0850 (2Fe-2S)-binding; 2Fe-2S iron-sulfur cluster binding domain-containing protein 128417..128926 Dinoroseobacter shibae DFL 12 = DSM 16493 5714250 YP_001541934.1 CDS Dshi_3722 NC_009955.1 128919 130454 D PFAM: AMP-dependent synthetase and ligase; KEGG: rpc:RPC_0851 AMP-dependent synthetase and ligase; AMP-dependent synthetase and ligase 128919..130454 Dinoroseobacter shibae DFL 12 = DSM 16493 5714251 YP_001541935.1 CDS Dshi_3723 NC_009955.1 130481 131284 D PFAM: Enoyl-CoA hydratase/isomerase; KEGG: acr:Acry_0672 enoyl-CoA hydratase/isomerase; enoyl-CoA hydratase/isomerase 130481..131284 Dinoroseobacter shibae DFL 12 = DSM 16493 5714252 YP_001541936.1 CDS Dshi_3724 NC_009955.1 131326 132480 D PFAM: Extracellular ligand-binding receptor; KEGG: rpc:RPC_0836 extracellular ligand-binding receptor; extracellular ligand-binding receptor 131326..132480 Dinoroseobacter shibae DFL 12 = DSM 16493 5714253 YP_001541937.1 CDS Dshi_3725 NC_009955.1 132501 133385 D PFAM: inner-membrane translocator; KEGG: rpc:RPC_0837 inner-membrane translocator; inner-membrane translocator 132501..133385 Dinoroseobacter shibae DFL 12 = DSM 16493 5714254 YP_001541938.1 CDS Dshi_3726 NC_009955.1 133378 134406 D PFAM: inner-membrane translocator; KEGG: rpc:RPC_0838 inner-membrane translocator; inner-membrane translocator 133378..134406 Dinoroseobacter shibae DFL 12 = DSM 16493 5714255 YP_001541939.1 CDS Dshi_3727 NC_009955.1 134403 135143 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rpc:RPC_0839 ABC transporter related; ABC transporter 134403..135143 Dinoroseobacter shibae DFL 12 = DSM 16493 5714256 YP_001541940.1 CDS Dshi_3728 NC_009955.1 135136 135846 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rpc:RPC_0840 ABC transporter related; ABC transporter 135136..135846 Dinoroseobacter shibae DFL 12 = DSM 16493 5714257 YP_001541941.1 CDS Dshi_3729 NC_009955.1 136657 137175 R KEGG: psa:PST_3459 hypothetical protein; hypothetical protein complement(136657..137175) Dinoroseobacter shibae DFL 12 = DSM 16493 5714258 YP_001541942.1 CDS Dshi_3730 NC_009955.1 137172 137498 R SohA; PrlF; involved in protein secretion; when overproduced or mutated, it induces growth defect and increased export of a reporter protein; a PrlF mutation induces the activity of the Lon protease, and a Lon-deficient strain suppresses the phenotype conferred by the PrlF mutation; putative regulator PrlF complement(137172..137498) Dinoroseobacter shibae DFL 12 = DSM 16493 5714259 YP_001541943.1 CDS Dshi_3731 NC_009955.1 137625 138278 R KEGG: rde:RD1_A0106 RC187; hypothetical protein complement(137625..138278) Dinoroseobacter shibae DFL 12 = DSM 16493 5714260 YP_001541944.1 CDS Dshi_3732 NC_009955.1 138278 138871 R hypothetical protein complement(138278..138871) Dinoroseobacter shibae DFL 12 = DSM 16493 5714261 YP_001541945.1 CDS Dshi_3733 NC_009955.1 138944 140926 R TIGRFAM: parB-like partition protein; PFAM: ParB domain protein nuclease; KEGG: rde:RD1_A0072 plasmid stabilization protein, putative; parB-like partition protein complement(138944..140926) Dinoroseobacter shibae DFL 12 = DSM 16493 5714262 YP_001541946.1 CDS Dshi_3734 NC_009955.1 141254 142120 D KEGG: swi:Swit_5197 transposase IS116/IS110/IS902 family protein; transposase IS116/IS110/IS902 family protein 141254..142120 Dinoroseobacter shibae DFL 12 = DSM 16493 5714263 YP_001541947.1 CDS Dshi_3736 NC_009955.1 142349 143254 R PFAM: Integrase catalytic region; KEGG: pde:Pden_3846 integrase, catalytic region; integrase catalytic region complement(142349..143254) Dinoroseobacter shibae DFL 12 = DSM 16493 5714265 YP_001541948.1 CDS Dshi_3737 NC_009955.1 143251 143583 R PFAM: transposase IS3/IS911 family protein; KEGG: psp:PSPPH_A0090 ISPsy21, transposase orfA; transposase IS3/IS911 family protein complement(143251..143583) Dinoroseobacter shibae DFL 12 = DSM 16493 5714266 YP_001541949.1 CDS Dshi_3738 NC_009955.1 143895 145256 D PFAM: transposase IS116/IS110/IS902 family protein; KEGG: cph:Cpha266_0024 transposase; transposase IS116/IS110/IS902 family protein 143895..145256 Dinoroseobacter shibae DFL 12 = DSM 16493 5714267 YP_001541950.1 CDS Dshi_3739 NC_009955.1 145289 146146 D PFAM: Integrase catalytic region; KEGG: bms:BRA1116 IS3 family element, transposase orfB; integrase catalytic region 145289..146146 Dinoroseobacter shibae DFL 12 = DSM 16493 5714268 YP_001541951.1 CDS Dshi_3740 NC_009955.1 147054 147263 R hypothetical protein complement(147054..147263) Dinoroseobacter shibae DFL 12 = DSM 16493 5714269 YP_001541952.1 CDS Dshi_3741 NC_009955.1 147287 148219 R PFAM: domain of unknown function DUF1738; KEGG: nha:Nham_4029 peptidase M, neutral zinc metallopeptidases, zinc-binding site; hypothetical protein complement(147287..148219) Dinoroseobacter shibae DFL 12 = DSM 16493 5714270 YP_001541953.1 CDS Dshi_3742 NC_009955.1 148260 148730 R hypothetical protein complement(148260..148730) Dinoroseobacter shibae DFL 12 = DSM 16493 5714271 YP_001541954.1 CDS Dshi_3743 NC_009955.1 149105 150385 R PFAM: replication protein C; KEGG: rde:RD1_A0024 replication protein C; replication protein C complement(149105..150385) Dinoroseobacter shibae DFL 12 = DSM 16493 5714272 YP_001541955.1 CDS Dshi_3744 NC_009955.1 150613 151635 R KEGG: rde:RD1_A0023 RC101; hypothetical protein complement(150613..151635) Dinoroseobacter shibae DFL 12 = DSM 16493 5714273 YP_001541956.1 CDS Dshi_3745 NC_009955.1 151632 152987 R KEGG: rde:RD1_A0021 RC102; hypothetical protein complement(151632..152987) Dinoroseobacter shibae DFL 12 = DSM 16493 5714274 YP_001541957.1 CDS Dshi_3746 NC_009955.1 153227 153460 D hypothetical protein 153227..153460 Dinoroseobacter shibae DFL 12 = DSM 16493 5714275 YP_001541958.1 CDS Dshi_3747 NC_009955.1 153767 154930 R KEGG: mlo:mlr9349 hypothetical protein; hypothetical protein complement(153767..154930) Dinoroseobacter shibae DFL 12 = DSM 16493 5714276 YP_001541959.1 CDS Dshi_3748 NC_009955.1 155050 155931 R PFAM: Resolvase domain; KEGG: rsp:RSP_2482 TonB-dependent receptor protein; resolvase domain-containing protein complement(155050..155931) Dinoroseobacter shibae DFL 12 = DSM 16493 5714277 YP_001541960.1 CDS Dshi_3749 NC_009955.1 156052 156297 D TIGRFAM: putative addiction module antidote protein, CC2985 family; PFAM: CopG domain protein DNA-binding domain protein; KEGG: nwi:Nwi_3093 helix-turn-helix protein, CopG; CopG/Arc/MetJ family addiction module antidote protein 156052..156297 Dinoroseobacter shibae DFL 12 = DSM 16493 5714278 YP_001541961.1 CDS Dshi_3750 NC_009955.1 156284 156592 D PFAM: plasmid stabilization system; KEGG: nwi:Nwi_3092 plasmid stabilization system; plasmid stabilization system protein 156284..156592 Dinoroseobacter shibae DFL 12 = DSM 16493 5714279 YP_001541962.1 CDS Dshi_3751 NC_009955.1 156596 157705 R PFAM: integrase family protein; KEGG: rsq:Rsph17025_4239 hypothetical protein; integrase family protein complement(156596..157705) Dinoroseobacter shibae DFL 12 = DSM 16493 5714280 YP_001541963.1 CDS Dshi_3752 NC_009955.1 157819 158703 D PFAM: protein of unknown function DUF1403; KEGG: sit:TM1040_3403 protein of unknown function DUF1403; hypothetical protein 157819..158703 Dinoroseobacter shibae DFL 12 = DSM 16493 5714281 YP_001541964.1 CDS Dshi_3753 NC_009955.1 158706 159323 D PFAM: chromosome segregation and condensation protein ScpB; KEGG: rsq:Rsph17025_4232 hypothetical protein; chromosome segregation and condensation protein ScpB 158706..159323 Dinoroseobacter shibae DFL 12 = DSM 16493 5714282 YP_001541965.1 CDS Dshi_3754 NC_009955.1 159373 159636 D PFAM: WGR domain protein; KEGG: mlo:msl9076 hypothetical protein; WGR domain-containing protein 159373..159636 Dinoroseobacter shibae DFL 12 = DSM 16493 5714283 YP_001541966.1 CDS Dshi_3755 NC_009955.1 159706 160824 D PFAM: filamentation induced by cAMP protein Fic; KEGG: atc:AGR_pAT_503 hypothetical protein; filamentation induced by cAMP protein fic 159706..160824 Dinoroseobacter shibae DFL 12 = DSM 16493 5714284 YP_001541967.1 CDS Dshi_3756 NC_009955.1 160821 161543 R hypothetical protein complement(160821..161543) Dinoroseobacter shibae DFL 12 = DSM 16493 5714285 YP_001541968.1 CDS Dshi_3757 NC_009955.1 161654 162001 D KEGG: pde:Pden_2059 transposase orfA IS5 family element; IS5 family transposase OrfA 161654..162001 Dinoroseobacter shibae DFL 12 = DSM 16493 5714286 YP_001541969.1 CDS Dshi_3758 NC_009955.1 162022 162411 D PFAM: transposase IS4 family protein; KEGG: pde:Pden_3333 transposase, IS4 family protein; transposase IS4 family protein 162022..162411 Dinoroseobacter shibae DFL 12 = DSM 16493 5714287 YP_001541970.1 CDS Dshi_3759 NC_009955.1 162514 163542 D PFAM: transposase IS116/IS110/IS902 family protein; KEGG: rru:Rru_A0676 transposase IS116/IS110/IS902; transposase IS116/IS110/IS902 family protein 162514..163542 Dinoroseobacter shibae DFL 12 = DSM 16493 5714288 YP_001541971.1 CDS Dshi_3760 NC_009955.1 163896 164078 R KEGG: rsq:Rsph17025_2803 ubiquinol-cytochrome c reductase, iron-sulfur subunit; hypothetical protein complement(163896..164078) Dinoroseobacter shibae DFL 12 = DSM 16493 5714289 YP_001541972.1 CDS Dshi_3761 NC_009955.1 164408 164770 D KEGG: nha:Nham_4014 ISSpo6, transposase orf A; ISSpo6, transposase orf A 164408..164770 Dinoroseobacter shibae DFL 12 = DSM 16493 5714290 YP_001541973.1 CDS Dshi_3762 NC_009955.1 164832 165362 D KEGG: nha:Nham_4013 ISSpo6, transposase OrfB; ISSpo6, transposase OrfB 164832..165362 Dinoroseobacter shibae DFL 12 = DSM 16493 5714291 YP_001541974.1 CDS Dshi_3763 NC_009955.1 165334 165762 R KEGG: sru:SRU_1982 hypothetical protein; hypothetical protein complement(165334..165762) Dinoroseobacter shibae DFL 12 = DSM 16493 5714292 YP_001541975.1 CDS Dshi_3764 NC_009955.1 165838 166404 D PFAM: cyclic nucleotide-binding; KEGG: reh:H16_A1838 transcriptional regulator, NNR like; cyclic nucleotide-binding protein 165838..166404 Dinoroseobacter shibae DFL 12 = DSM 16493 5714293 YP_001541976.1 CDS Dshi_3765 NC_009955.1 166410 166862 R PFAM: protein of unknown function DUF411; KEGG: rde:RD1_2307 hypothetical protein; hypothetical protein complement(166410..166862) Dinoroseobacter shibae DFL 12 = DSM 16493 5714294 YP_001541977.1 CDS Dshi_3766 NC_009955.1 166777 167769 R PFAM: fatty acid hydroxylase; KEGG: aeh:Mlg_0287 sterol desaturase-like protein; fatty acid hydroxylase complement(166777..167769) Dinoroseobacter shibae DFL 12 = DSM 16493 5714295 YP_001541978.1 CDS Dshi_3767 NC_009955.1 167776 168762 R TIGRFAM: cation diffusion facilitator family transporter; PFAM: cation efflux protein; KEGG: dge:Dgeo_0215 cation diffusion facilitator family transporter; cation diffusion facilitator family transporter complement(167776..168762) Dinoroseobacter shibae DFL 12 = DSM 16493 5714296 YP_001541979.1 CDS Dshi_3768 NC_009955.1 168764 169426 R PFAM: SNARE associated Golgi protein; KEGG: sil:SPOA0363 hypothetical protein; SNARE associated Golgi protein complement(168764..169426) Dinoroseobacter shibae DFL 12 = DSM 16493 5714297 YP_001541980.1 CDS Dshi_3769 NC_009955.1 169430 169879 R KEGG: ddi:DDBDRAFT_0184550 hypothetical protein; hypothetical protein complement(169430..169879) Dinoroseobacter shibae DFL 12 = DSM 16493 5714298 YP_001541981.1 CDS Dshi_3770 NC_009955.1 170041 170478 R KEGG: maq:Maqu_0306 ion transport 2 domain protein; ion transport 2 domain-containing protein complement(170041..170478) Dinoroseobacter shibae DFL 12 = DSM 16493 5714299 YP_001541982.1 CDS Dshi_3771 NC_009955.1 170567 171040 R KEGG: rde:RD1_1666 hypothetical protein; hypothetical protein complement(170567..171040) Dinoroseobacter shibae DFL 12 = DSM 16493 5714300 YP_001541983.1 CDS Dshi_3772 NC_009955.1 171229 171951 D PFAM: response regulator receiver; transcriptional regulator domain protein; KEGG: sil:SPOA0357 DNA-binding response regulator; two component transcriptional regulator 171229..171951 Dinoroseobacter shibae DFL 12 = DSM 16493 5714301 YP_001541984.1 CDS Dshi_3773 NC_009955.1 171951 173417 D PFAM: ATP-binding region ATPase domain protein; histidine kinase HAMP region domain protein; histidine kinase A domain protein; KEGG: sil:SPOA0358 sensor histidine kinase; integral membrane sensor signal transduction histidine kinase 171951..173417 Dinoroseobacter shibae DFL 12 = DSM 16493 5714302 YP_001541985.1 CDS Dshi_3774 NC_009955.1 173467 173658 D KEGG: aeh:Mlg_1384 hypothetical protein; hypothetical protein 173467..173658 Dinoroseobacter shibae DFL 12 = DSM 16493 5714303 YP_001541986.1 CDS Dshi_3775 NC_009955.1 173724 175724 D TIGRFAM: cytochrome c-type biogenesis protein CcmF; PFAM: cytochrome c assembly protein; KEGG: mag:amb4200 cytochrome c biogenesis factor; cytochrome c-type biogenesis protein CcmF 173724..175724 Dinoroseobacter shibae DFL 12 = DSM 16493 5714304 YP_001541987.1 CDS Dshi_3776 NC_009955.1 175733 176299 D TIGRFAM: periplasmic protein thiol--disulphide oxidoreductase DsbE; PFAM: alkyl hydroperoxide reductase/ Thiol specific antioxidant/ Mal allergen; Redoxin domain protein; KEGG: mlo:mll4330 cytochrome c biogenesis protein CycX; periplasmic protein thiol--disulfide oxidoreductase DsbE 175733..176299 Dinoroseobacter shibae DFL 12 = DSM 16493 5714305 YP_001541988.1 CDS Dshi_3777 NC_009955.1 176296 176769 D PFAM: cytochrome C biogenesis protein; KEGG: atc:AGR_C_1789 cytochrome C-type biogenesis protein; cytochrome C biogenesis protein 176296..176769 Dinoroseobacter shibae DFL 12 = DSM 16493 5714306 YP_001541989.1 CDS Dshi_3778 NC_009955.1 176766 177917 D PFAM: TPR repeat-containing protein; Tetratricopeptide TPR_2 repeat protein; SMART: Tetratricopeptide domain protein; KEGG: smd:Smed_0633 cytochrome c-type biogenesis transmembrane protein; hypothetical protein 176766..177917 Dinoroseobacter shibae DFL 12 = DSM 16493 5714307 YP_001541990.1 CDS Dshi_3779 NC_009955.1 177946 180075 R KEGG: mag:amb3382 thiol:disulfide interchange protein DsbD 1 precursor; thiol:disulfide interchange protein DsbD 1 precursor complement(177946..180075) Dinoroseobacter shibae DFL 12 = DSM 16493 5714308 YP_001541991.1 CDS Dshi_3780 NC_009955.1 180359 180661 R hypothetical protein complement(180359..180661) Dinoroseobacter shibae DFL 12 = DSM 16493 5714309 YP_001541992.1 CDS Dshi_3781 NC_009955.1 180817 181377 D PFAM: ErfK/YbiS/YcfS/YnhG family protein; KEGG: sil:SPO2205 ErfK/YbiS/YcfS/YnhG family protein; ErfK/YbiS/YcfS/YnhG family protein 180817..181377 Dinoroseobacter shibae DFL 12 = DSM 16493 5714310 YP_001541993.1 CDS Dshi_3782 NC_009955.1 181406 181864 D PFAM: cytochrome c class I; KEGG: sil:SPOA0359 cytochrome c family protein; cytochrome c class I 181406..181864 Dinoroseobacter shibae DFL 12 = DSM 16493 5714311 YP_001541994.1 CDS Dshi_3783 NC_009955.1 182234 182827 D KEGG: ret:RHE_CH02511 putative cytochrome c-like protein; putative cytochrome c-like protein 182234..182827 Dinoroseobacter shibae DFL 12 = DSM 16493 5714312 YP_001541995.1 CDS Dshi_3784 NC_009955.1 182830 183747 D KEGG: psa:PST_0453 cytochrome c family protein; gluconate 2-dehydrogenase (acceptor) 182830..183747 Dinoroseobacter shibae DFL 12 = DSM 16493 5714313 YP_001541996.1 CDS Dshi_3785 NC_009955.1 183791 185185 D PFAM: multicopper oxidase type 1; multicopper oxidase type 2; multicopper oxidase type 3; KEGG: sil:SPOA0360 multicopper oxidase, putative; multicopper oxidase type 3 183791..185185 Dinoroseobacter shibae DFL 12 = DSM 16493 5714314 YP_001541997.1 CDS Dshi_3786 NC_009955.1 185182 185664 D PFAM: cytochrome c class I; KEGG: sil:SPOA0361 cytochrome c family protein; cytochrome c class I 185182..185664 Dinoroseobacter shibae DFL 12 = DSM 16493 5714315 YP_001541998.1 CDS Dshi_3787 NC_009955.1 185666 186397 D PFAM: DSBA oxidoreductase; KEGG: sil:SPOA0362 27kDa outer membrane protein; DSBA oxidoreductase 185666..186397 Dinoroseobacter shibae DFL 12 = DSM 16493 5714316 YP_001541999.1 CDS Dshi_3788 NC_009955.1 186440 186640 R PFAM: Heavy metal transport/detoxification protein; KEGG: pen:PSEEN0671 copper-binding protein; heavy metal transport/detoxification protein complement(186440..186640) Dinoroseobacter shibae DFL 12 = DSM 16493 5714317 YP_001542000.1 CDS Dshi_3789 NC_009955.1 186794 189304 D 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 186794..189304 Dinoroseobacter shibae DFL 12 = DSM 16493 5714318 YP_001542001.1 CDS Dshi_3790 NC_009955.1 189317 189715 D TIGRFAM: Cu(I)-responsive transcriptional regulator; PFAM: regulatory protein MerR; Transcription regulator MerR DNA binding; KEGG: sit:TM1040_0537 transcriptional regulator, MerR family; MerR family transcriptional regulator 189317..189715 Dinoroseobacter shibae DFL 12 = DSM 16493 5714319 YP_001542002.1 CDS Dshi_3791 NC_009955.1 189737 190501 R PFAM: glutaredoxin; KEGG: eli:ELI_04570 hypothetical protein; glutaredoxin complement(189737..190501) Dinoroseobacter shibae DFL 12 = DSM 16493 5714320 YP_001542003.1 CDS Dshi_3792 NC_009956.1 167 1822 D PFAM: extracellular solute-binding protein family 5; KEGG: rme:Rmet_1932 extracellular solute-binding protein, family 5; extracellular solute-binding protein 167..1822 Dinoroseobacter shibae DFL 12 = DSM 16493 5714460 YP_001542004.1 CDS Dshi_3793 NC_009956.1 1905 2858 D PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: pol:Bpro_0381 binding-protein-dependent transport systems inner membrane component; binding-protein-dependent transport systems inner membrane component 1905..2858 Dinoroseobacter shibae DFL 12 = DSM 16493 5714322 YP_001542005.1 CDS Dshi_3794 NC_009956.1 2862 3749 D PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: pol:Bpro_0382 binding-protein-dependent transport systems inner membrane component; binding-protein-dependent transport systems inner membrane component 2862..3749 Dinoroseobacter shibae DFL 12 = DSM 16493 5714323 YP_001542006.1 CDS Dshi_3795 NC_009956.1 3746 4741 D KEGG: pol:Bpro_0383 oligopeptide/dipeptide ABC transporter, ATP-binding protein-like; TIGRFAM: oligopeptide/dipeptide ABC transporter, ATPase subunit; PFAM: ABC transporter related; Oligopeptide/dipeptide ABC transporter domain protein; SMART: AAA ATPase; oligopeptide/dipeptide ABC transporter, ATPase subunit 3746..4741 Dinoroseobacter shibae DFL 12 = DSM 16493 5714324 YP_001542007.1 CDS Dshi_3796 NC_009956.1 4738 5739 D KEGG: rpa:RPA0755 putative oligopeptide ABC transporter, ATP-binding component; TIGRFAM: oligopeptide/dipeptide ABC transporter, ATPase subunit; PFAM: ABC transporter related; Oligopeptide/dipeptide ABC transporter domain protein; SMART: AAA ATPase; oligopeptide/dipeptide ABC transporter, ATPase subunit 4738..5739 Dinoroseobacter shibae DFL 12 = DSM 16493 5714325 YP_001542008.1 CDS Dshi_3797 NC_009956.1 5736 6419 D PFAM: Asp/Glu racemase; KEGG: rsq:Rsph17025_3633 hypothetical protein; Asp/Glu racemase 5736..6419 Dinoroseobacter shibae DFL 12 = DSM 16493 5714326 YP_001542009.1 CDS Dshi_3798 NC_009956.1 6416 6958 R PFAM: NADH:ubiquinone oxidoreductase complex I intermediate-associated protein 30; KEGG: rde:RD1_3877 hypothetical protein; NADH:ubiquinone oxidoreductase complex I intermediate-associated protein 30 complement(6416..6958) Dinoroseobacter shibae DFL 12 = DSM 16493 5714327 YP_001542010.1 CDS Dshi_3799 NC_009956.1 7084 7680 D PFAM: HupE/UreJ protein; KEGG: bra:BRADO6336 conserved hypothetical protein; putative [NiFe]-hydrogenase/urease accessory HupE/UreJ family protein; HupE/UreJ protein 7084..7680 Dinoroseobacter shibae DFL 12 = DSM 16493 5714328 YP_001542011.1 CDS Dshi_3800 NC_009956.1 7685 8299 D KEGG: bbt:BBta_1289 putative membrane protein of unknown function; hypothetical protein 7685..8299 Dinoroseobacter shibae DFL 12 = DSM 16493 5714329 YP_001542012.1 CDS Dshi_3801 NC_009956.1 8358 10535 R TIGRFAM: catalase/peroxidase HPI; PFAM: Haem peroxidase; KEGG: rde:RD1_2195 catalase-peroxidase; catalase/peroxidase HPI complement(8358..10535) Dinoroseobacter shibae DFL 12 = DSM 16493 5714330 YP_001542013.1 CDS Dshi_3802 NC_009956.1 10649 11578 D PFAM: regulatory protein LysR; LysR substrate-binding; KEGG: rde:RD1_2194 oxidative stress transcription regulator, OxyR, putative; LysR family transcriptional regulator 10649..11578 Dinoroseobacter shibae DFL 12 = DSM 16493 5714331 YP_001542014.1 CDS Dshi_3803 NC_009956.1 11636 11827 D hypothetical protein 11636..11827 Dinoroseobacter shibae DFL 12 = DSM 16493 5714332 YP_001542015.1 CDS Dshi_3804 NC_009956.1 11802 12791 D PFAM: regulatory protein LuxR; KEGG: rle:RL1113 putative transcriptional regulator; LuxR family transcriptional regulator 11802..12791 Dinoroseobacter shibae DFL 12 = DSM 16493 5714333 YP_001542016.1 CDS Dshi_3805 NC_009956.1 12918 15827 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+; putative monovalent cation/H+ antiporter subunit A 12918..15827 Dinoroseobacter shibae DFL 12 = DSM 16493 5714334 YP_001542017.1 CDS Dshi_3806 NC_009956.1 15829 16182 D subunit C of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; putative monovalent cation/H+ antiporter subunit C 15829..16182 Dinoroseobacter shibae DFL 12 = DSM 16493 5714335 YP_001542018.1 CDS Dshi_3807 NC_009956.1 16179 17699 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; putative monovalent cation/H+ antiporter subunit D 16179..17699 Dinoroseobacter shibae DFL 12 = DSM 16493 5714336 YP_001542019.1 CDS Dshi_3808 NC_009956.1 17704 18195 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; putative monovalent cation/H+ antiporter subunit E 17704..18195 Dinoroseobacter shibae DFL 12 = DSM 16493 5714337 YP_001542020.1 CDS Dshi_3809 NC_009956.1 18192 18461 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 18192..18461 Dinoroseobacter shibae DFL 12 = DSM 16493 5714338 YP_001542021.1 CDS Dshi_3810 NC_009956.1 18469 18858 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, MnhG/PhaG subunit 18469..18858 Dinoroseobacter shibae DFL 12 = DSM 16493 5714339 YP_001542022.1 CDS Dshi_3811 NC_009956.1 18901 20142 R KEGG: sit:TM1040_2622 fumarylacetoacetase; TIGRFAM: fumarylacetoacetase; PFAM: fumarylacetoacetate (FAA) hydrolase; Domain of unknown function DUF1969; fumarylacetoacetase complement(18901..20142) Dinoroseobacter shibae DFL 12 = DSM 16493 5714340 YP_001542023.1 CDS Dshi_3812 NC_009956.1 20139 21494 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(20139..21494) Dinoroseobacter shibae DFL 12 = DSM 16493 5714341 YP_001542024.1 CDS Dshi_3813 NC_009956.1 21527 21970 R PFAM: regulatory protein MarR; KEGG: pde:Pden_3546 transcriptional regulator, MarR family; MarR family transcriptional regulator complement(21527..21970) Dinoroseobacter shibae DFL 12 = DSM 16493 5714342 YP_001542025.1 CDS Dshi_3814 NC_009956.1 22097 23047 D PFAM: beta-lactamase domain protein; KEGG: sil:SPO0683 metallo-beta-lactamase family protein; beta-lactamase domain-containing protein 22097..23047 Dinoroseobacter shibae DFL 12 = DSM 16493 5714343 YP_001542026.1 CDS Dshi_3815 NC_009956.1 23077 24702 D PFAM: monooxygenase FAD-binding; FAD dependent oxidoreductase; KEGG: sil:SPO0682 monooxygenase family protein; FAD-dependent oxidoreductase 23077..24702 Dinoroseobacter shibae DFL 12 = DSM 16493 5714344 YP_001542027.1 CDS Dshi_3816 NC_009956.1 24705 24890 D KEGG: sil:SPO0681 hypothetical protein; hypothetical protein 24705..24890 Dinoroseobacter shibae DFL 12 = DSM 16493 5714345 YP_001542028.1 CDS Dshi_3817 NC_009956.1 25016 26218 D KEGG: sil:SPO0758 acetyl-CoA acetyltransferase; TIGRFAM: acetyl-CoA acetyltransferase; beta-ketoadipyl CoA thiolase; PFAM: Thiolase; beta-ketoadipyl CoA thiolase 25016..26218 Dinoroseobacter shibae DFL 12 = DSM 16493 5714346 YP_001542029.1 CDS paaA NC_009956.1 26236 27213 D with PaaBCDE catalyzes the hydroxylation of phenylacetyl-CoA; phenylacetate-CoA oxygenase subunit PaaA 26236..27213 Dinoroseobacter shibae DFL 12 = DSM 16493 5714347 YP_001542030.1 CDS paaB NC_009956.1 27210 27542 D with PaaBCDE catalyzes the hydroxylation of phenylacetyl-CoA; involved in phenylacetate degradation; phenylacetate-CoA oxygenase subunit PaaB 27210..27542 Dinoroseobacter shibae DFL 12 = DSM 16493 5714348 YP_001542031.1 CDS Dshi_3820 NC_009956.1 27542 28309 D TIGRFAM: phenylacetate-CoA oxygenase, PaaI subunit; PFAM: phenylacetic acid catabolic family protein; KEGG: sit:TM1040_3726 phenylacetate-CoA oxygenase, PaaI subunit; phenylacetate-CoA oxygenase, PaaI subunit 27542..28309 Dinoroseobacter shibae DFL 12 = DSM 16493 5714349 YP_001542032.1 CDS Dshi_3821 NC_009956.1 28311 28769 D TIGRFAM: phenylacetate-CoA oxygenase, PaaJ subunit; PFAM: protein of unknown function DUF59; KEGG: jan:Jann_0652 phenylacetate-CoA oxygenase, PaaJ subunit; phenylacetate-CoA oxygenase, PaaJ subunit 28311..28769 Dinoroseobacter shibae DFL 12 = DSM 16493 5714350 YP_001542033.1 CDS Dshi_3822 NC_009956.1 28782 29852 D TIGRFAM: phenylacetate-CoA oxygenase/reductase, PaaK subunit; PFAM: ferredoxin; oxidoreductase FAD/NAD(P)-binding domain protein; Oxidoreductase FAD-binding domain protein; KEGG: sil:SPO0753 phenylacetic acid degradation oxidoreductase PaaK; phenylacetate-CoA oxygenase/reductase, PaaK subunit 28782..29852 Dinoroseobacter shibae DFL 12 = DSM 16493 5714351 YP_001542034.1 CDS Dshi_3823 NC_009956.1 29860 30456 R PFAM: regulatory protein TetR; KEGG: sil:SPO0743 transcriptional regulator, TetR family; TetR family transcriptional regulator complement(29860..30456) Dinoroseobacter shibae DFL 12 = DSM 16493 5714352 YP_001542035.1 CDS Dshi_3824 NC_009956.1 30459 31769 R TIGRFAM: phenylacetate-CoA ligase; KEGG: sil:SPO0742 phenylacetate-CoA ligase; phenylacetate-CoA ligase complement(30459..31769) Dinoroseobacter shibae DFL 12 = DSM 16493 5714353 YP_001542036.1 CDS Dshi_3825 NC_009956.1 31792 32217 R TIGRFAM: phenylacetic acid degradation protein PaaD; PFAM: thioesterase superfamily protein; KEGG: sil:SPO0741 phenylacetic acid degradation protein PaaD; phenylacetic acid degradation protein PaaD complement(31792..32217) Dinoroseobacter shibae DFL 12 = DSM 16493 5714354 YP_001542037.1 CDS Dshi_3826 NC_009956.1 32430 34451 D PFAM: Enoyl-CoA hydratase/isomerase; 3-hydroxyacyl-CoA dehydrogenase domain protein; 3-hydroxyacyl-CoA dehydrogenase NAD-binding; KEGG: sil:SPO0739 enoyl-CoA hydratase/isomerase/3-hydroxyacyl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase 32430..34451 Dinoroseobacter shibae DFL 12 = DSM 16493 5714355 YP_001542038.1 CDS Dshi_3827 NC_009956.1 34493 36529 D catalyzes the ring cleavage reaction in phenylacetate degradation and the formation of 3-hydroxyacyl-CoA from crotonyl-CoA; bifunctional aldehyde dehydrogenase/enoyl-CoA hydratase 34493..36529 Dinoroseobacter shibae DFL 12 = DSM 16493 5714356 YP_001542039.1 CDS Dshi_3828 NC_009956.1 36567 37361 D PFAM: PaaX domain protein; KEGG: sil:SPO0734 PaaX domain protein; PaaX family transcriptional regulator 36567..37361 Dinoroseobacter shibae DFL 12 = DSM 16493 5714357 YP_001542040.1 CDS Dshi_3829 NC_009956.1 37489 37941 D hypothetical protein 37489..37941 Dinoroseobacter shibae DFL 12 = DSM 16493 5714358 YP_001542041.1 CDS Dshi_3830 NC_009956.1 38247 39386 D PFAM: NAD-dependent glycerol-3-phosphate dehydrogenase domain protein; Ketopantoate reductase ApbA/PanE domain protein; KEGG: mlo:mlr4225 glycerol-3-phosphate dehydrogenase; glycerol-3-phosphate dehydrogenase (NAD(P)(+)) 38247..39386 Dinoroseobacter shibae DFL 12 = DSM 16493 5714359 YP_001542042.1 CDS Dshi_3831 NC_009956.1 39383 40162 D PFAM: sucrose-6F-phosphate phosphohydrolase; Haloacid dehalogenase domain protein hydrolase type 3; KEGG: tbd:Tbd_2627 alpha,alpha-trehalose-phosphate synthase; sucrose-6F-phosphate phosphohydrolase 39383..40162 Dinoroseobacter shibae DFL 12 = DSM 16493 5714360 YP_001542043.1 CDS Dshi_3832 NC_009956.1 40174 41664 D KEGG: tbd:Tbd_2626 glucosyl-glycerol-phosphate synthase; TIGRFAM: glucosylglycerol-phosphate synthase; PFAM: glycosyl transferase family 20; glucosylglycerol-phosphate synthase 40174..41664 Dinoroseobacter shibae DFL 12 = DSM 16493 5714361 YP_001542044.1 CDS Dshi_3833 NC_009956.1 41763 43181 R PFAM: phospholipase D/Transphosphatidylase; KEGG: rde:RD1_2477 phospholipase D, putative; phospholipase D/transphosphatidylase complement(41763..43181) Dinoroseobacter shibae DFL 12 = DSM 16493 5714362 YP_001542045.1 CDS Dshi_3834 NC_009956.1 43171 44907 R PFAM: histidine kinase HAMP region domain protein; histidine kinase dimerisation/phosphoacceptor; KEGG: jan:Jann_3564 signal transduction histidine kinase; signal transduction histidine kinase complement(43171..44907) Dinoroseobacter shibae DFL 12 = DSM 16493 5714363 YP_001542046.1 CDS Dshi_3835 NC_009956.1 44882 45445 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(44882..45445) Dinoroseobacter shibae DFL 12 = DSM 16493 5714364 YP_001542047.1 CDS Dshi_3836 NC_009956.1 45442 45621 R hypothetical protein complement(45442..45621) Dinoroseobacter shibae DFL 12 = DSM 16493 5714365 YP_001542048.1 CDS Dshi_3837 NC_009956.1 45758 46573 D in Caulobacter crescentus, CC3477 is differentially expressed in minimal salts media with glucose as compared to complex media; two-component response regulator 45758..46573 Dinoroseobacter shibae DFL 12 = DSM 16493 5714366 YP_001542049.1 CDS Dshi_3838 NC_009956.1 46686 48080 R KEGG: rde:RD1_4211 hypothetical protein; hypothetical protein complement(46686..48080) Dinoroseobacter shibae DFL 12 = DSM 16493 5714367 YP_001542050.1 CDS Dshi_3839 NC_009956.1 48216 48713 R PFAM: Ferritin Dps family protein; KEGG: sit:TM1040_2721 ferritin and Dps; Ferritin Dps family protein complement(48216..48713) Dinoroseobacter shibae DFL 12 = DSM 16493 5714368 YP_001542051.1 CDS Dshi_3840 NC_009956.1 48774 50414 R PFAM: thiamine pyrophosphate protein domain protein TPP-binding; thiamine pyrophosphate protein central region; thiamine pyrophosphate protein TPP binding domain protein; KEGG: rde:RD1_2449 acetolactate synthase; thiamine pyrophosphate binding domain-containing protein complement(48774..50414) Dinoroseobacter shibae DFL 12 = DSM 16493 5714369 YP_001542052.1 CDS Dshi_3841 NC_009956.1 50414 51757 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(50414..51757) Dinoroseobacter shibae DFL 12 = DSM 16493 5714370 YP_001542053.1 CDS Dshi_3842 NC_009956.1 51857 52027 R PFAM: protein of unknown function DUF1328; KEGG: rso:RS02225 probable transmembrane protein; hypothetical protein complement(51857..52027) Dinoroseobacter shibae DFL 12 = DSM 16493 5714371 YP_001542054.1 CDS Dshi_3843 NC_009956.1 52170 52586 R hypothetical protein complement(52170..52586) Dinoroseobacter shibae DFL 12 = DSM 16493 5714372 YP_001542055.1 CDS Dshi_3844 NC_009956.1 52616 53344 D PFAM: cyclic nucleotide-binding; KEGG: rde:RD1_2451 nitrogen fixation regulatory protein FixK , putative; cyclic nucleotide-binding protein 52616..53344 Dinoroseobacter shibae DFL 12 = DSM 16493 5714373 YP_001542056.1 CDS Dshi_3847 NC_009956.1 54662 55786 D SMART: ParB domain protein nuclease; KEGG: pde:Pden_2912 replication protein, putative; nuclease 54662..55786 Dinoroseobacter shibae DFL 12 = DSM 16493 5714376 YP_001542057.1 CDS Dshi_3848 NC_009956.1 55886 56080 R KEGG: rsh:Rsph17029_2919 hypothetical protein; hypothetical protein complement(55886..56080) Dinoroseobacter shibae DFL 12 = DSM 16493 5714377 YP_001542058.1 CDS Dshi_3849 NC_009956.1 56108 56320 R KEGG: jan:Jann_2179 hypothetical protein; hypothetical protein complement(56108..56320) Dinoroseobacter shibae DFL 12 = DSM 16493 5714378 YP_001542059.1 CDS Dshi_3850 NC_009956.1 56328 56588 R KEGG: gfo:GFO_0298 hypothetical protein; hypothetical protein complement(56328..56588) Dinoroseobacter shibae DFL 12 = DSM 16493 5714379 YP_001542060.1 CDS Dshi_3851 NC_009956.1 56652 56915 R hypothetical protein complement(56652..56915) Dinoroseobacter shibae DFL 12 = DSM 16493 5714380 YP_001542061.1 CDS Dshi_3852 NC_009956.1 57076 58143 R KEGG: rsq:Rsph17025_2741 hypothetical protein; hypothetical protein complement(57076..58143) Dinoroseobacter shibae DFL 12 = DSM 16493 5714381 YP_001542062.1 CDS Dshi_3853 NC_009956.1 58283 59263 D PFAM: Resolvase domain; KEGG: rsp:RSP_2482 TonB-dependent receptor protein; resolvase domain-containing protein 58283..59263 Dinoroseobacter shibae DFL 12 = DSM 16493 5714382 YP_001542063.1 CDS Dshi_3854 NC_009956.1 59311 60357 R KEGG: sit:TM1040_3772 RepA; hypothetical protein complement(59311..60357) Dinoroseobacter shibae DFL 12 = DSM 16493 5714383 YP_001542064.1 CDS Dshi_3855 NC_009956.1 60736 62127 D PFAM: Cobyrinic acid ac-diamide synthase; KEGG: sit:TM1040_3773 cobyrinic acid a,c-diamide synthase; cobyrinic acid ac-diamide synthase 60736..62127 Dinoroseobacter shibae DFL 12 = DSM 16493 5714384 YP_001542065.1 CDS Dshi_3856 NC_009956.1 62250 63425 D SMART: ParB domain protein nuclease; KEGG: rsp:RSP_7084 ParB-like nuclease; nuclease 62250..63425 Dinoroseobacter shibae DFL 12 = DSM 16493 5714385 YP_001542066.1 CDS Dshi_3857 NC_009956.1 63834 65726 D 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 domain; KEGG: rsh:Rsph17029_2850 polysaccharide biosynthesis protein CapD; polysaccharide biosynthesis protein CapD 63834..65726 Dinoroseobacter shibae DFL 12 = DSM 16493 5714386 YP_001542067.1 CDS Dshi_3858 NC_009956.1 66007 68247 D PFAM: protein of unknown function DUF940 membrane lipoprotein putative; KEGG: rsp:RSP_1187 hypothetical protein; hypothetical protein 66007..68247 Dinoroseobacter shibae DFL 12 = DSM 16493 5714387 YP_001542068.1 CDS Dshi_3859 NC_009956.1 68244 69005 D KEGG: rsh:Rsph17029_2848 hypothetical protein; hypothetical protein 68244..69005 Dinoroseobacter shibae DFL 12 = DSM 16493 5714388 YP_001542069.1 CDS Dshi_3860 NC_009956.1 69139 69381 D hypothetical protein 69139..69381 Dinoroseobacter shibae DFL 12 = DSM 16493 5714389 YP_001542070.1 CDS Dshi_3861 NC_009956.1 69562 70758 D PFAM: UDP-glucose/GDP-mannose dehydrogenase; NAD-dependent glycerol-3-phosphate dehydrogenase domain protein; UDP-glucose/GDP-mannose dehydrogenase dimerisation; UDP-glucose/GDP-mannose dehydrogenase; KEGG: xcv:XCV3705 UDP-glucose dehydrogenase; UDP-glucose 6-dehydrogenase 69562..70758 Dinoroseobacter shibae DFL 12 = DSM 16493 5714390 YP_001542071.1 CDS Dshi_3862 NC_009956.1 70763 72700 D hypothetical protein 70763..72700 Dinoroseobacter shibae DFL 12 = DSM 16493 5714391 YP_001542072.1 CDS Dshi_3863 NC_009956.1 72755 73885 R KEGG: ter:Tery_3237 hypothetical protein; hypothetical protein complement(72755..73885) Dinoroseobacter shibae DFL 12 = DSM 16493 5714392 YP_001542073.1 CDS Dshi_3864 NC_009956.1 73902 74681 R PFAM: sulfotransferase; KEGG: rsh:Rsph17029_4075 sulfotransferase; sulfotransferase complement(73902..74681) Dinoroseobacter shibae DFL 12 = DSM 16493 5714393 YP_001542074.1 CDS Dshi_3865 NC_009956.1 74804 75793 R KEGG: ter:Tery_4433 hypothetical protein; hypothetical protein complement(74804..75793) Dinoroseobacter shibae DFL 12 = DSM 16493 5714394 YP_001542075.1 CDS Dshi_3866 NC_009956.1 75905 79813 R PFAM: glycosyl transferase group 1; KEGG: jan:Jann_4244 glycosyl transferase, group 1; glycosyl transferase group 1 complement(75905..79813) Dinoroseobacter shibae DFL 12 = DSM 16493 5714395 YP_001542076.1 CDS Dshi_3867 NC_009956.1 79818 80708 R KEGG: nar:Saro_0725 chromosome segregation ATPases-like; hypothetical protein complement(79818..80708) Dinoroseobacter shibae DFL 12 = DSM 16493 5714396 YP_001542077.1 CDS Dshi_3868 NC_009956.1 80804 81883 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; Male sterility domain; KEGG: mpt:Mpe_A1914 UDP-glucose 4-epimerase; UDP-glucose 4-epimerase complement(80804..81883) Dinoroseobacter shibae DFL 12 = DSM 16493 5714397 YP_001542078.1 CDS Dshi_3869 NC_009956.1 81946 83121 R KEGG: ter:Tery_3237 hypothetical protein; hypothetical protein complement(81946..83121) Dinoroseobacter shibae DFL 12 = DSM 16493 5714398 YP_001542079.1 CDS Dshi_3870 NC_009956.1 83556 84359 R PFAM: peptidase S1 and S6 chymotrypsin/Hap; KEGG: rru:Rru_A0562 peptidase S1 and S6, chymotrypsin/Hap; peptidase S1 and S6 chymotrypsin/Hap complement(83556..84359) Dinoroseobacter shibae DFL 12 = DSM 16493 5714399 YP_001542080.1 CDS Dshi_3871 NC_009956.1 84768 88262 D KEGG: pde:Pden_2124 hemolysin-type calcium-binding region; RTX toxins and related Ca2+-binding protein-like protein 84768..88262 Dinoroseobacter shibae DFL 12 = DSM 16493 5714400 YP_001542081.1 CDS Dshi_3872 NC_009956.1 88354 94041 D PFAM: Hemolysin-type calcium-binding region; KEGG: rde:RD1_A0054 iron-regulated protein FrpC, putative; hemolysin-type calcium-binding region 88354..94041 Dinoroseobacter shibae DFL 12 = DSM 16493 5714401 YP_001542082.1 CDS Dshi_3873 NC_009956.1 94097 94681 R KEGG: sil:SPOA0441 hypothetical protein; hypothetical protein complement(94097..94681) Dinoroseobacter shibae DFL 12 = DSM 16493 5714402 YP_001542083.1 CDS Dshi_3874 NC_009956.1 94737 95561 R KEGG: art:Arth_4384 ATP-binding protein; ATP-binding protein complement(94737..95561) Dinoroseobacter shibae DFL 12 = DSM 16493 5714403 YP_001542084.1 CDS Dshi_3875 NC_009956.1 95558 97051 R PFAM: Integrase catalytic region; Transposase-like Mu; KEGG: art:Arth_4385 integrase, catalytic region; integrase catalytic region complement(95558..97051) Dinoroseobacter shibae DFL 12 = DSM 16493 5714404 YP_001542085.1 CDS Dshi_3876 NC_009956.1 97190 97789 D PFAM: Resolvase domain; Resolvase helix-turn-helix domain protein; KEGG: gox:GOX2646 DNA integration/recombination/invertion protein; resolvase domain-containing protein 97190..97789 Dinoroseobacter shibae DFL 12 = DSM 16493 5714405 YP_001542086.1 CDS Dshi_3877 NC_009956.1 98310 100118 D required for the synthesis of the hydromethylpyrimidine moiety of thiamine; thiamine biosynthesis protein ThiC 98310..100118 Dinoroseobacter shibae DFL 12 = DSM 16493 5714406 YP_001542087.1 CDS Dshi_3878 NC_009956.1 100522 101904 R PFAM: transposase IS4 family protein; KEGG: rde:RD1_3444 transposase, putative; transposase IS4 family protein complement(100522..101904) Dinoroseobacter shibae DFL 12 = DSM 16493 5714407 YP_001542088.1 CDS Dshi_3879 NC_009956.1 102305 103117 D hypothetical protein 102305..103117 Dinoroseobacter shibae DFL 12 = DSM 16493 5714408 YP_001542089.1 CDS Dshi_3880 NC_009956.1 103401 103925 D hypothetical protein 103401..103925 Dinoroseobacter shibae DFL 12 = DSM 16493 5714409 YP_001542090.1 CDS Dshi_3881 NC_009956.1 104842 105309 D hypothetical protein 104842..105309 Dinoroseobacter shibae DFL 12 = DSM 16493 5714410 YP_001542091.1 CDS Dshi_3882 NC_009956.1 105261 105971 D KEGG: rde:RD1_A0058 transposase, putative; transposase, putative 105261..105971 Dinoroseobacter shibae DFL 12 = DSM 16493 5714411 YP_001542092.1 CDS Dshi_3883 NC_009956.1 106070 106648 R KEGG: pat:Patl_4083 hypothetical protein; hypothetical protein complement(106070..106648) Dinoroseobacter shibae DFL 12 = DSM 16493 5714412 YP_001542093.1 CDS Dshi_3884 NC_009956.1 106635 108044 R PFAM: multi antimicrobial extrusion protein MatE; polysaccharide biosynthesis protein; KEGG: rde:RD1_2470 MatE efflux family protein; multi anti extrusion protein MatE complement(106635..108044) Dinoroseobacter shibae DFL 12 = DSM 16493 5714413 YP_001542094.1 CDS Dshi_3885 NC_009956.1 108221 109795 D PFAM: phospholipase D/Transphosphatidylase; KEGG: rde:RD1_2477 phospholipase D, putative; phospholipase D/transphosphatidylase 108221..109795 Dinoroseobacter shibae DFL 12 = DSM 16493 5714414 YP_001542095.1 CDS Dshi_3886 NC_009956.1 110041 110658 D KEGG: rpd:RPD_2508 hypothetical protein; hypothetical protein 110041..110658 Dinoroseobacter shibae DFL 12 = DSM 16493 5714415 YP_001542096.1 CDS Dshi_3887 NC_009956.1 110663 111094 R PFAM: cytochrome c class I; KEGG: psa:PST_1611 cytochrome c6; cytochrome c class I complement(110663..111094) Dinoroseobacter shibae DFL 12 = DSM 16493 5714416 YP_001542097.1 CDS Dshi_3888 NC_009956.1 111091 112716 R PFAM: amine oxidase; KEGG: psa:PST_1610 flavin monoamine oxidase-related protein; L-amino-acid oxidase complement(111091..112716) Dinoroseobacter shibae DFL 12 = DSM 16493 5714417 YP_001542098.1 CDS Dshi_3889 NC_009956.1 112739 113458 R KEGG: nwi:Nwi_2311 hypothetical protein; hypothetical protein complement(112739..113458) Dinoroseobacter shibae DFL 12 = DSM 16493 5714418 YP_001542099.1 CDS Dshi_3890 NC_009956.1 113475 113804 R hypothetical protein complement(113475..113804) Dinoroseobacter shibae DFL 12 = DSM 16493 5714419 YP_001542100.1 CDS Dshi_3891 NC_009956.1 113801 116362 R TIGRFAM: Cytochrome c oxidase subunit I type; PFAM: cytochrome c oxidase subunit I; KEGG: eba:ebA156 putative cytochrome c oxidase subunit I; cytochrome c oxidase subunit I type complement(113801..116362) Dinoroseobacter shibae DFL 12 = DSM 16493 5714420 YP_001542101.1 CDS Dshi_3892 NC_009956.1 116359 117396 R TIGRFAM: Cytochrome c oxidase subunit II; PFAM: cytochrome c oxidase subunit II; cytochrome c class I; KEGG: mes:Meso_2792 cytochrome c oxidase, subunit II; cytochrome c oxidase subunit II complement(116359..117396) Dinoroseobacter shibae DFL 12 = DSM 16493 5714421 YP_001542102.1 CDS Dshi_3893 NC_009956.1 117396 117893 R PFAM: cytochrome c class I; KEGG: eba:ebA4540 cytochrome c1, probably related to cytocrome c oxidase function; cytochrome c class I complement(117396..117893) Dinoroseobacter shibae DFL 12 = DSM 16493 5714422 YP_001542103.1 CDS Dshi_3894 NC_009956.1 117901 118716 R KEGG: psa:PST_2844 cytochrome c type protein; cytochrome c553-like protein complement(117901..118716) Dinoroseobacter shibae DFL 12 = DSM 16493 5714423 YP_001542104.1 CDS Dshi_3895 NC_009956.1 118732 120516 R PFAM: FAD dependent oxidoreductase; KEGG: nha:Nham_4244 putative gluconate dehydrogenase; gluconate 2-dehydrogenase (acceptor) complement(118732..120516) Dinoroseobacter shibae DFL 12 = DSM 16493 5714424 YP_001542105.1 CDS Dshi_3896 NC_009956.1 120509 121231 R KEGG: bvi:Bcep1808_4793 hypothetical protein; hypothetical protein complement(120509..121231) Dinoroseobacter shibae DFL 12 = DSM 16493 5714425 YP_001542106.1 CDS Dshi_3897 NC_009956.1 121309 121845 R PFAM: MgtC/SapB transporter; KEGG: mes:Meso_3446 MgtC/SapB transporter; MgtC/SapB transporter complement(121309..121845) Dinoroseobacter shibae DFL 12 = DSM 16493 5714426 YP_001542107.1 CDS Dshi_3898 NC_009956.1 121824 123404 R PFAM: alpha amylase catalytic region; SMART: alpha amylase catalytic sub domain; KEGG: xcb:XC_1642 alpha-glucosidase; alpha amylase complement(121824..123404) Dinoroseobacter shibae DFL 12 = DSM 16493 5714427 YP_001542108.1 CDS Dshi_3899 NC_009956.1 123407 124261 R PFAM: short-chain dehydrogenase/reductase SDR; KR domain protein; KEGG: rru:Rru_A3667 short-chain dehydrogenase/reductase SDR; short-chain dehydrogenase/reductase SDR complement(123407..124261) Dinoroseobacter shibae DFL 12 = DSM 16493 5714428 YP_001542109.1 CDS Dshi_3900 NC_009956.1 124299 125282 R PFAM: short-chain dehydrogenase/reductase SDR; KR domain protein; KEGG: psa:PST_3887 probable short-chain dehydrogenase; short-chain dehydrogenase/reductase SDR complement(124299..125282) Dinoroseobacter shibae DFL 12 = DSM 16493 5714429 YP_001542110.1 CDS Dshi_3901 NC_009956.1 125343 128468 R PFAM: acriflavin resistance protein; KEGG: sru:SRU_0473 multidrug efflux transporter, AcrB/AcrD/AcrF family; acriflavin resistance protein complement(125343..128468) Dinoroseobacter shibae DFL 12 = DSM 16493 5714430 YP_001542111.1 CDS Dshi_3902 NC_009956.1 128472 129650 R TIGRFAM: efflux transporter, RND family, MFP subunit; PFAM: secretion protein HlyD family protein; KEGG: vpa:VPA0343 putative membrane fusion protein; RND family efflux transporter MFP subunit complement(128472..129650) Dinoroseobacter shibae DFL 12 = DSM 16493 5714431 YP_001542112.1 CDS Dshi_3903 NC_009956.1 129663 130460 R PFAM: short-chain dehydrogenase/reductase SDR; KR domain protein; KEGG: cmi:CMM_2063 short chain dehydrogenase/oxidoreductase; short-chain dehydrogenase/reductase SDR complement(129663..130460) Dinoroseobacter shibae DFL 12 = DSM 16493 5714432 YP_001542113.1 CDS Dshi_3904 NC_009956.1 130573 132153 R TIGRFAM: SSS sodium solute transporter superfamily; PFAM: Na+/solute symporter; KEGG: sru:SRU_0355 sodium/glucose cotransporter 2; SSS family solute/sodium (Na+) symporter complement(130573..132153) Dinoroseobacter shibae DFL 12 = DSM 16493 5714433 YP_001542114.1 CDS Dshi_3905 NC_009956.1 132871 133992 R PFAM: MscS Mechanosensitive ion channel; KEGG: bra:BRADO5370 conserved hypothetical protein; putative membrane protein; putative small-conductance mechanosensitive channel; MscS mechanosensitive ion channel complement(132871..133992) Dinoroseobacter shibae DFL 12 = DSM 16493 5714434 YP_001542115.1 CDS Dshi_3906 NC_009956.1 133997 135598 R TIGRFAM: SSS sodium solute transporter superfamily; PFAM: Na+/solute symporter; KEGG: sru:SRU_0355 sodium/glucose cotransporter 2; SSS family solute/sodium (Na+) symporter complement(133997..135598) Dinoroseobacter shibae DFL 12 = DSM 16493 5714435 YP_001542116.1 CDS Dshi_3907 NC_009956.1 135680 136705 R PFAM: sodium/calcium exchanger membrane region; KEGG: eli:ELI_06950 cation antiporter (Na+/Ca2+); sodium/calcium exchanger membrane region complement(135680..136705) Dinoroseobacter shibae DFL 12 = DSM 16493 5714436 YP_001542117.1 CDS Dshi_3908 NC_009956.1 136970 138121 D PFAM: protein of unknown function UPF0118; KEGG: cps:CPS_2311 hypothetical protein; hypothetical protein 136970..138121 Dinoroseobacter shibae DFL 12 = DSM 16493 5714437 YP_001542118.1 CDS Dshi_3909 NC_009956.1 138124 138396 R KEGG: tcx:Tcr_1058 hypothetical protein; hypothetical protein complement(138124..138396) Dinoroseobacter shibae DFL 12 = DSM 16493 5714438 YP_001542119.1 CDS Dshi_3910 NC_009956.1 138528 138908 R hypothetical protein complement(138528..138908) Dinoroseobacter shibae DFL 12 = DSM 16493 5714439 YP_001542120.1 CDS Dshi_3911 NC_009956.1 139092 140549 D KEGG: rpe:RPE_2181 protease Do; TIGRFAM: protease Do; PFAM: peptidase S1 and S6 chymotrypsin/Hap; PDZ/DHR/GLGF domain protein; protease Do 139092..140549 Dinoroseobacter shibae DFL 12 = DSM 16493 5714440 YP_001542121.1 CDS Dshi_3912 NC_009956.1 140779 141261 R PFAM: Ferritin Dps family protein; KEGG: pcr:Pcryo_0735 ferritin and Dps; Ferritin Dps family protein complement(140779..141261) Dinoroseobacter shibae DFL 12 = DSM 16493 5714441 YP_001542122.1 CDS Dshi_3913 NC_009956.1 141452 142111 R PFAM: TrkA-N domain protein; TrkA-C domain protein; KEGG: rde:RD1_2464 trk potassium uptake system protein; TrkA domain-containing protein complement(141452..142111) Dinoroseobacter shibae DFL 12 = DSM 16493 5714442 YP_001542123.1 CDS Dshi_3914 NC_009956.1 142116 143591 R PFAM: cation transporter; KEGG: rde:RD1_2465 trk potassium uptake system protein, transmembrane component; cation transporter complement(142116..143591) Dinoroseobacter shibae DFL 12 = DSM 16493 5714443 YP_001542124.1 CDS Dshi_3915 NC_009956.1 143779 143946 D PFAM: protein of unknown function UPF0057; KEGG: rxy:Rxyl_0694 protein of unknown function UPF0057; hypothetical protein 143779..143946 Dinoroseobacter shibae DFL 12 = DSM 16493 5714444 YP_001542125.1 CDS Dshi_3916 NC_009956.1 143909 144319 D KEGG: rde:RD1_2473 hypothetical protein; hypothetical protein 143909..144319 Dinoroseobacter shibae DFL 12 = DSM 16493 5714445 YP_001542126.1 CDS Dshi_3917 NC_009956.1 144427 144894 D KEGG: mlo:mlr3233 hypothetical protein; hypothetical protein 144427..144894 Dinoroseobacter shibae DFL 12 = DSM 16493 5714446 YP_001542127.1 CDS Dshi_3918 NC_009956.1 145009 145482 R KEGG: sde:Sde_3869 hypothetical protein; hypothetical protein complement(145009..145482) Dinoroseobacter shibae DFL 12 = DSM 16493 5714447 YP_001542128.1 CDS Dshi_3919 NC_009956.1 145798 146166 D PFAM: transposase IS3/IS911 family protein; KEGG: xac:XAC4322 ISxac3 transposase; transposase IS3/IS911 family protein 145798..146166 Dinoroseobacter shibae DFL 12 = DSM 16493 5714448 YP_001542129.1 CDS Dshi_3920 NC_009956.1 146299 146496 D KEGG: ajs:Ajs_1844 integrase, catalytic region; integrase, catalytic region 146299..146496 Dinoroseobacter shibae DFL 12 = DSM 16493 5714449 YP_001542130.1 CDS Dshi_3921 NC_009956.1 146523 146837 D PFAM: Integrase catalytic region; KEGG: sfv:SFV_0556 ISEhe3 orfB; integrase catalytic region 146523..146837 Dinoroseobacter shibae DFL 12 = DSM 16493 5714450 YP_001542131.1 CDS Dshi_3922 NC_009956.1 147270 148109 D KEGG: rde:RD1_2466 transport protein, putative; transport protein, putative 147270..148109 Dinoroseobacter shibae DFL 12 = DSM 16493 5714451 YP_001542132.1 CDS Dshi_3923 NC_009956.1 148170 148334 R KEGG: rde:RD1_2471 hypothetical protein; hypothetical protein complement(148170..148334) Dinoroseobacter shibae DFL 12 = DSM 16493 5714452 YP_001542133.1 CDS Dshi_3924 NC_009956.1 148360 148554 R hypothetical protein complement(148360..148554) Dinoroseobacter shibae DFL 12 = DSM 16493 5714453 YP_001542134.1 CDS Dshi_3925 NC_009956.1 148620 149342 R PFAM: glutamine amidotransferase class-I; peptidase C26; KEGG: csa:Csal_1160 peptidase C26; peptidase C26 complement(148620..149342) Dinoroseobacter shibae DFL 12 = DSM 16493 5714454 YP_001542135.1 CDS Dshi_3926 NC_009956.1 149344 150306 R KEGG: ilo:IL1070 hypothetical protein; hypothetical protein complement(149344..150306) Dinoroseobacter shibae DFL 12 = DSM 16493 5714455 YP_001542136.1 CDS Dshi_3927 NC_009956.1 150369 150764 R KEGG: pnu:Pnuc_1656 hypothetical protein; hypothetical protein complement(150369..150764) Dinoroseobacter shibae DFL 12 = DSM 16493 5714456 YP_001542137.1 CDS Dshi_3928 NC_009956.1 150931 151857 D PFAM: homocysteine S-methyltransferase; KEGG: sil:SPO3398 homocysteine S-methyltransferase family protein; homocysteine S-methyltransferase 150931..151857 Dinoroseobacter shibae DFL 12 = DSM 16493 5714457 YP_001542138.1 CDS Dshi_3929 NC_009956.1 151908 152129 D KEGG: pna:Pnap_3267 hypothetical protein; hypothetical protein 151908..152129 Dinoroseobacter shibae DFL 12 = DSM 16493 5714458 YP_001542139.1 CDS Dshi_3930 NC_009956.1 152139 152852 R PFAM: regulatory protein GntR HTH; GntR domain protein; KEGG: rsp:RSP_3339 transcriptional regulator, GntR family; GntR family transcriptional regulator complement(152139..152852) Dinoroseobacter shibae DFL 12 = DSM 16493 5714459 YP_001542140.1 CDS Dshi_3931 NC_009957.1 12 776 R PFAM: glutaredoxin; KEGG: eli:ELI_04570 hypothetical protein; glutaredoxin complement(12..776) Dinoroseobacter shibae DFL 12 = DSM 16493 5714596 YP_001542141.1 CDS Dshi_3932 NC_009957.1 789 1625 R PFAM: protein of unknown function DUF305; KEGG: rsh:Rsph17029_3677 protein of unknown function DUF305; hypothetical protein complement(789..1625) Dinoroseobacter shibae DFL 12 = DSM 16493 5714461 YP_001542142.1 CDS Dshi_3933 NC_009957.1 1805 2386 D PFAM: ErfK/YbiS/YcfS/YnhG family protein; KEGG: mes:Meso_4112 ErfK/YbiS/YcfS/YnhG; ErfK/YbiS/YcfS/YnhG family protein 1805..2386 Dinoroseobacter shibae DFL 12 = DSM 16493 5714462 YP_001542143.1 CDS Dshi_3934 NC_009957.1 2470 3774 D PFAM: multicopper oxidase type 1; multicopper oxidase type 2; multicopper oxidase type 3; KEGG: sit:TM1040_0289 multicopper oxidase, type 3; multicopper oxidase type 3 2470..3774 Dinoroseobacter shibae DFL 12 = DSM 16493 5714463 YP_001542144.1 CDS Dshi_3935 NC_009957.1 3888 4400 D KEGG: sit:TM1040_1167 disulphide bond formation protein DsbB; disulphide bond formation protein DsbB 3888..4400 Dinoroseobacter shibae DFL 12 = DSM 16493 5714464 YP_001542145.1 CDS Dshi_3936 NC_009957.1 4443 5108 D PFAM: ErfK/YbiS/YcfS/YnhG family protein; KEGG: rde:RD1_0492 ErfK/YbiS/YcfS/YnhG family protein; ErfK/YbiS/YcfS/YnhG family protein 4443..5108 Dinoroseobacter shibae DFL 12 = DSM 16493 5714465 YP_001542146.1 CDS Dshi_3937 NC_009957.1 5185 5742 R KEGG: sil:SPO0304 lipoprotein, putative; putative lipoprotein complement(5185..5742) Dinoroseobacter shibae DFL 12 = DSM 16493 5714466 YP_001542147.1 CDS Dshi_3938 NC_009957.1 6140 6748 D SMART: Calcium-binding EF-hand-containing protein; KEGG: rpb:RPB_2375 calcium-binding EF-hand protein; calcium-binding EF-hand-containing protein 6140..6748 Dinoroseobacter shibae DFL 12 = DSM 16493 5714467 YP_001542148.1 CDS Dshi_3939 NC_009957.1 6889 7275 D PFAM: protein of unknown function DUF302; KEGG: mmr:Mmar10_2335 protein of unknown function DUF302; hypothetical protein 6889..7275 Dinoroseobacter shibae DFL 12 = DSM 16493 5714468 YP_001542149.1 CDS Dshi_3940 NC_009957.1 7381 8301 D transfers the N-acyl diglyceride moiety to the prospective N-terminal cysteine in prolipoprotein; prolipoprotein diacylglyceryl transferase 7381..8301 Dinoroseobacter shibae DFL 12 = DSM 16493 5714469 YP_001542150.1 CDS Dshi_3941 NC_009957.1 8380 10725 D 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; E1-E2 ATPase-associated domain protein; KEGG: sil:SPOA0365 copper-translocating P-type ATPase; heavy metal translocating P-type ATPase 8380..10725 Dinoroseobacter shibae DFL 12 = DSM 16493 5714470 YP_001542151.1 CDS Dshi_3942 NC_009957.1 10774 12111 D PFAM: amino acid permease-associated region; KEGG: sil:SPOA0366 amino acid permease; amino acid permease 10774..12111 Dinoroseobacter shibae DFL 12 = DSM 16493 5714471 YP_001542152.1 CDS Dshi_3943 NC_009957.1 12119 12763 R hypothetical protein complement(12119..12763) Dinoroseobacter shibae DFL 12 = DSM 16493 5714472 YP_001542153.1 CDS Dshi_3944 NC_009957.1 12980 13702 D PFAM: cytochrome c biogenesis protein transmembrane region; KEGG: maq:Maqu_3250 cytochrome c biogenesis protein, transmembrane region; cytochrome c biogenesis protein transmembrane region 12980..13702 Dinoroseobacter shibae DFL 12 = DSM 16493 5714473 YP_001542154.1 CDS Dshi_3945 NC_009957.1 13896 14561 D PFAM: ErfK/YbiS/YcfS/YnhG family protein; KEGG: rde:RD1_0492 ErfK/YbiS/YcfS/YnhG family protein; ErfK/YbiS/YcfS/YnhG family protein 13896..14561 Dinoroseobacter shibae DFL 12 = DSM 16493 5714474 YP_001542155.1 CDS Dshi_3946 NC_009957.1 14609 14881 R KEGG: rde:RD1_0491 hypothetical protein; hypothetical protein complement(14609..14881) Dinoroseobacter shibae DFL 12 = DSM 16493 5714475 YP_001542156.1 CDS Dshi_3947 NC_009957.1 15242 17428 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: mes:Meso_4212 heavy metal translocating P-type ATPase; heavy metal translocating P-type ATPase 15242..17428 Dinoroseobacter shibae DFL 12 = DSM 16493 5714476 YP_001542157.1 CDS Dshi_3948 NC_009957.1 17422 17697 R hypothetical protein complement(17422..17697) Dinoroseobacter shibae DFL 12 = DSM 16493 5714477 YP_001542158.1 CDS Dshi_3949 NC_009957.1 17795 18253 D PFAM: regulatory protein MarR; iron dependent repressor; SMART: regulatory protein Crp; KEGG: mlo:mll2499 hypothetical protein; DtxR family iron dependent repressor 17795..18253 Dinoroseobacter shibae DFL 12 = DSM 16493 5714478 YP_001542159.1 CDS Dshi_3950 NC_009957.1 18348 18515 R KEGG: sil:SPO2514 hypothetical protein; hypothetical protein complement(18348..18515) Dinoroseobacter shibae DFL 12 = DSM 16493 5714479 YP_001542160.1 CDS Dshi_3951 NC_009957.1 18515 20086 R TIGRFAM: apolipoprotein N-acyltransferase; PFAM: Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase; KEGG: nha:Nham_0025 apolipoprotein N-acyltransferase; apolipoprotein N-acyltransferase complement(18515..20086) Dinoroseobacter shibae DFL 12 = DSM 16493 5714480 YP_001542161.1 CDS Dshi_3952 NC_009957.1 20083 20556 R TIGRFAM: lipoprotein signal peptidase; PFAM: peptidase A8 signal peptidase II; KEGG: eli:ELI_04470 putative lipoprotein signal peptidase; lipoprotein signal peptidase complement(20083..20556) Dinoroseobacter shibae DFL 12 = DSM 16493 5714481 YP_001542162.1 CDS Dshi_3953 NC_009957.1 20561 21343 R PFAM: zinc/iron permease; KEGG: gvi:glr4280 zinc transporter, ZIP family; zinc/iron permease complement(20561..21343) Dinoroseobacter shibae DFL 12 = DSM 16493 5714482 YP_001542163.1 CDS Dshi_3954 NC_009957.1 21366 21824 R PFAM: protein of unknown function DUF411; KEGG: aav:Aave_1809 protein of unknown function DUF411; hypothetical protein complement(21366..21824) Dinoroseobacter shibae DFL 12 = DSM 16493 5714483 YP_001542164.1 CDS Dshi_3955 NC_009957.1 21828 23201 R PFAM: peptidase M23B; KEGG: hch:HCH_06239 membrane protein related to metalloendopeptidase; peptidase M23B complement(21828..23201) Dinoroseobacter shibae DFL 12 = DSM 16493 5714484 YP_001542165.1 CDS Dshi_3956 NC_009957.1 23198 23824 R PFAM: electron transport protein SCO1/SenC; KEGG: ccr:CC_3503 SCO1/2 family protein; electron transport protein SCO1/SenC complement(23198..23824) Dinoroseobacter shibae DFL 12 = DSM 16493 5714485 YP_001542166.1 CDS Dshi_3957 NC_009957.1 23824 24294 R PFAM: protein of unknown function DUF461; KEGG: bra:BRADO4160 conserved hypothetical protein; putative signal peptide; hypothetical protein complement(23824..24294) Dinoroseobacter shibae DFL 12 = DSM 16493 5714486 YP_001542167.1 CDS Dshi_3958 NC_009957.1 24317 24976 R PFAM: DSBA oxidoreductase; KEGG: mes:Meso_4133 DsbA oxidoreductase; DSBA oxidoreductase complement(24317..24976) Dinoroseobacter shibae DFL 12 = DSM 16493 5714487 YP_001542168.1 CDS Dshi_3959 NC_009957.1 24973 25395 R PFAM: Disulphide bond formation protein DsbB; KEGG: psa:PST_0576 disulfide bond formation protein; disulphide bond formation protein DsbB complement(24973..25395) Dinoroseobacter shibae DFL 12 = DSM 16493 5714488 YP_001542169.1 CDS Dshi_3960 NC_009957.1 25401 26003 R PFAM: electron transport protein SCO1/SenC; KEGG: mag:amb0517 uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems; electron transport protein SCO1/SenC complement(25401..26003) Dinoroseobacter shibae DFL 12 = DSM 16493 5714489 YP_001542170.1 CDS Dshi_3961 NC_009957.1 26181 26609 D PFAM: regulatory protein MerR; Transcription regulator MerR DNA binding; KEGG: sil:SPOA0389 transcriptional regulator, MerR family; MerR family transcriptional regulator 26181..26609 Dinoroseobacter shibae DFL 12 = DSM 16493 5714490 YP_001542171.1 CDS Dshi_3962 NC_009957.1 26692 27312 D PFAM: cation efflux protein; KEGG: mes:Meso_4424 cation efflux protein; cation efflux protein 26692..27312 Dinoroseobacter shibae DFL 12 = DSM 16493 5714491 YP_001542172.1 CDS Dshi_3963 NC_009957.1 27382 27945 D KEGG: ajs:Ajs_1334 hypothetical protein; hypothetical protein 27382..27945 Dinoroseobacter shibae DFL 12 = DSM 16493 5714492 YP_001542173.1 CDS Dshi_3964 NC_009957.1 27935 28900 D TIGRFAM: cation diffusion facilitator family transporter; PFAM: cation efflux protein; KEGG: maq:Maqu_3275 cation diffusion facilitator family transporter; cation diffusion facilitator family transporter 27935..28900 Dinoroseobacter shibae DFL 12 = DSM 16493 5714493 YP_001542174.1 CDS Dshi_3965 NC_009957.1 28872 29183 D KEGG: gfo:GFO_1210 hypothetical protein; hypothetical protein 28872..29183 Dinoroseobacter shibae DFL 12 = DSM 16493 5714494 YP_001542175.1 CDS Dshi_3966 NC_009957.1 29536 30282 D KEGG: sit:TM1040_3830 hypothetical protein; hypothetical protein 29536..30282 Dinoroseobacter shibae DFL 12 = DSM 16493 5714495 YP_001542176.1 CDS Dshi_3967 NC_009957.1 30471 30821 R PFAM: regulatory protein ArsR; KEGG: mkm:Mkms_5742 regulatory protein, ArsR; ArsR family transcriptional regulator complement(30471..30821) Dinoroseobacter shibae DFL 12 = DSM 16493 5714496 YP_001542177.1 CDS Dshi_3968 NC_009957.1 30885 31736 D PFAM: cation efflux protein; KEGG: sal:Sala_2560 hypothetical protein; cation efflux protein 30885..31736 Dinoroseobacter shibae DFL 12 = DSM 16493 5714497 YP_001542178.1 CDS Dshi_3969 NC_009957.1 31897 32124 R KEGG: sit:TM1040_3826 hypothetical protein; hypothetical protein complement(31897..32124) Dinoroseobacter shibae DFL 12 = DSM 16493 5714498 YP_001542179.1 CDS Dshi_3970 NC_009957.1 32292 32549 R PFAM: helix-turn-helix domain protein; KEGG: rsq:Rsph17025_0810 putative transcriptional regulator, XRE family; XRE family transcriptional regulator complement(32292..32549) Dinoroseobacter shibae DFL 12 = DSM 16493 5714499 YP_001542180.1 CDS Dshi_3971 NC_009957.1 32674 32994 R KEGG: sit:TM1040_3824 hypothetical protein; hypothetical protein complement(32674..32994) Dinoroseobacter shibae DFL 12 = DSM 16493 5714500 YP_001542181.1 CDS Dshi_3972 NC_009957.1 33138 33491 D KEGG: sit:TM1040_3823 hypothetical protein; hypothetical protein 33138..33491 Dinoroseobacter shibae DFL 12 = DSM 16493 5714501 YP_001542182.1 CDS Dshi_3973 NC_009957.1 33535 34149 D PFAM: Lytic transglycosylase catalytic; KEGG: sit:TM1040_3822 lytic transglycosylase, catalytic; lytic transglycosylase 33535..34149 Dinoroseobacter shibae DFL 12 = DSM 16493 5714502 YP_001542183.1 CDS Dshi_3974 NC_009957.1 34146 34439 D PFAM: Conjugal transfer protein TrbC; KEGG: sit:TM1040_3821 VirB2 type IV secretion; conjugal transfer protein TrbC 34146..34439 Dinoroseobacter shibae DFL 12 = DSM 16493 5714503 YP_001542184.1 CDS Dshi_3975 NC_009957.1 34432 34710 D PFAM: type IV secretory pathway VirB3 family protein; KEGG: sit:TM1040_3820 type IV secretory pathway, VirB3-like; type IV secretory pathway VirB3 family protein 34432..34710 Dinoroseobacter shibae DFL 12 = DSM 16493 5714504 YP_001542185.1 CDS Dshi_3976 NC_009957.1 34700 37063 D PFAM: CagE TrbE VirB component of type IV transporter system; SMART: AAA ATPase; KEGG: sit:TM1040_3819 CagE, TrbE, VirB component of type IV transporter system; CagE TrbE VirB component of type IV transporter system 34700..37063 Dinoroseobacter shibae DFL 12 = DSM 16493 5714505 YP_001542186.1 CDS Dshi_3977 NC_009957.1 37060 37227 D KEGG: sit:TM1040_3818 hypothetical protein; hypothetical protein 37060..37227 Dinoroseobacter shibae DFL 12 = DSM 16493 5714506 YP_001542187.1 CDS Dshi_3978 NC_009957.1 37217 38371 D PFAM: Lytic transglycosylase catalytic; KEGG: sit:TM1040_3817 lytic transglycosylase, catalytic; lytic transglycosylase catalytic 37217..38371 Dinoroseobacter shibae DFL 12 = DSM 16493 5714507 YP_001542188.1 CDS Dshi_3979 NC_009957.1 38371 39180 D KEGG: sit:TM1040_3816 hypothetical protein; hypothetical protein 38371..39180 Dinoroseobacter shibae DFL 12 = DSM 16493 5714508 YP_001542189.1 CDS Dshi_3980 NC_009957.1 39197 39850 D PFAM: VirB8 family protein; KEGG: sit:TM1040_3815 VirB8; VirB8 family protein 39197..39850 Dinoroseobacter shibae DFL 12 = DSM 16493 5714509 YP_001542190.1 CDS Dshi_3981 NC_009957.1 39853 40548 D PFAM: Conjugal transfer protein TrbG/VirB9/CagX; KEGG: sit:TM1040_3814 conjugal transfer protein TrbG/VirB9/CagX; conjugal transfer protein TrbG/VirB9/CagX 39853..40548 Dinoroseobacter shibae DFL 12 = DSM 16493 5714510 YP_001542191.1 CDS Dshi_3982 NC_009957.1 40545 41924 D PFAM: conjugation TrbI family protein; KEGG: sit:TM1040_3813 conjugation TrbI-like protein; conjugation TrbI family protein 40545..41924 Dinoroseobacter shibae DFL 12 = DSM 16493 5714511 YP_001542192.1 CDS Dshi_3983 NC_009957.1 41929 42915 D PFAM: type II secretion system protein E; KEGG: sit:TM1040_3812 type II secretion system protein E; type II secretion system protein E 41929..42915 Dinoroseobacter shibae DFL 12 = DSM 16493 5714512 YP_001542193.1 CDS Dshi_3984 NC_009957.1 43103 43513 D KEGG: sit:TM1040_3810 hypothetical protein; hypothetical protein 43103..43513 Dinoroseobacter shibae DFL 12 = DSM 16493 5714513 YP_001542194.1 CDS Dshi_3985 NC_009957.1 43526 44602 D PFAM: TrbL/VirB6 plasmid conjugal transfer protein; KEGG: sit:TM1040_3809 TrbL/VirB6 plasmid conjugal transfer protein; TrbL/VirB6 plasmid conjugal transfer protein 43526..44602 Dinoroseobacter shibae DFL 12 = DSM 16493 5714514 YP_001542195.1 CDS Dshi_3986 NC_009957.1 44763 46667 R KEGG: rru:Rru_A0809 hypothetical protein; hypothetical protein complement(44763..46667) Dinoroseobacter shibae DFL 12 = DSM 16493 5714515 YP_001542196.1 CDS Dshi_3987 NC_009957.1 47163 48227 R KEGG: ter:Tery_4988 hypothetical protein; hypothetical protein complement(47163..48227) Dinoroseobacter shibae DFL 12 = DSM 16493 5714516 YP_001542197.1 CDS Dshi_3988 NC_009957.1 48594 50606 R PFAM: TRAG family protein; KEGG: sit:TM1040_3794 TraG protein; TRAG family protein complement(48594..50606) Dinoroseobacter shibae DFL 12 = DSM 16493 5714517 YP_001542198.1 CDS Dshi_3989 NC_009957.1 50603 52936 R PFAM: Relaxase/mobilization nuclease family protein; KEGG: sit:TM1040_3793 relaxase/mobilization nuclease domain; relaxase/mobilization nuclease family protein complement(50603..52936) Dinoroseobacter shibae DFL 12 = DSM 16493 5714518 YP_001542199.1 CDS Dshi_3990 NC_009957.1 52923 53516 R KEGG: sit:TM1040_3792 hypothetical protein; hypothetical protein complement(52923..53516) Dinoroseobacter shibae DFL 12 = DSM 16493 5714519 YP_001542200.1 CDS Dshi_3991 NC_009957.1 54078 54284 R KEGG: sit:TM1040_3791 hypothetical protein; hypothetical protein complement(54078..54284) Dinoroseobacter shibae DFL 12 = DSM 16493 5714520 YP_001542201.1 CDS Dshi_3993 NC_009957.1 54824 55849 R KEGG: sit:TM1040_3771 hypothetical protein; hypothetical protein complement(54824..55849) Dinoroseobacter shibae DFL 12 = DSM 16493 5714522 YP_001542202.1 CDS Dshi_3994 NC_009957.1 55973 56902 R KEGG: mes:Meso_4225 hypothetical protein; hypothetical protein complement(55973..56902) Dinoroseobacter shibae DFL 12 = DSM 16493 5714523 YP_001542203.1 CDS Dshi_3995 NC_009957.1 57594 58274 D PFAM: protein of unknown function DUF159; KEGG: bbt:BBta_3432 hypothetical protein; hypothetical protein 57594..58274 Dinoroseobacter shibae DFL 12 = DSM 16493 5714524 YP_001542204.1 CDS Dshi_3996 NC_009957.1 58264 58851 D KEGG: sil:SPO0672 hypothetical protein; hypothetical protein 58264..58851 Dinoroseobacter shibae DFL 12 = DSM 16493 5714525 YP_001542205.1 CDS Dshi_3997 NC_009957.1 58778 60277 D KEGG: sil:SPO0671 hypothetical protein; hypothetical protein 58778..60277 Dinoroseobacter shibae DFL 12 = DSM 16493 5714526 YP_001542206.1 CDS Dshi_3998 NC_009957.1 60274 63624 D KEGG: sit:TM1040_0175 DNA polymerase III, alpha subunit; TIGRFAM: DNA polymerase III, alpha subunit; PFAM: nucleic acid binding OB-fold tRNA/helicase-type; DNA polymerase III alpha subunit; SMART: phosphoesterase PHP domain protein; DNA polymerase III subunit alpha 60274..63624 Dinoroseobacter shibae DFL 12 = DSM 16493 5714527 YP_001542207.1 CDS Dshi_3999 NC_009957.1 63705 64433 R KEGG: jan:Jann_4220 ParB-like nuclease; ParB-like nuclease complement(63705..64433) Dinoroseobacter shibae DFL 12 = DSM 16493 5714528 YP_001542208.1 CDS Dshi_4000 NC_009957.1 64558 64860 R hypothetical protein complement(64558..64860) Dinoroseobacter shibae DFL 12 = DSM 16493 5714529 YP_001542209.1 CDS Dshi_4001 NC_009957.1 64961 65422 R KEGG: bbt:BBta_7341 hypothetical protein; hypothetical protein complement(64961..65422) Dinoroseobacter shibae DFL 12 = DSM 16493 5714530 YP_001542210.1 CDS Dshi_4002 NC_009957.1 65424 65810 R KEGG: sal:Sala_2657 hypothetical protein; hypothetical protein complement(65424..65810) Dinoroseobacter shibae DFL 12 = DSM 16493 5714531 YP_001542211.1 CDS Dshi_4003 NC_009957.1 65932 67803 R KEGG: ana:alr7089 hypothetical protein; hypothetical protein complement(65932..67803) Dinoroseobacter shibae DFL 12 = DSM 16493 5714532 YP_001542212.1 CDS Dshi_4004 NC_009957.1 67841 69367 D PFAM: integrase family protein; integrase domain protein SAM domain protein; KEGG: sal:Sala_0438 phage integrase; integrase family protein 67841..69367 Dinoroseobacter shibae DFL 12 = DSM 16493 5714533 YP_001542213.1 CDS Dshi_4005 NC_009957.1 69364 70275 D PFAM: integrase family protein; KEGG: sal:Sala_0439 phage integrase; integrase family protein 69364..70275 Dinoroseobacter shibae DFL 12 = DSM 16493 5714534 YP_001542214.1 CDS Dshi_4006 NC_009957.1 70272 71276 D PFAM: integrase family protein; integrase domain protein SAM domain protein; KEGG: sal:Sala_0440 phage integrase; integrase family protein 70272..71276 Dinoroseobacter shibae DFL 12 = DSM 16493 5714535 YP_001542215.1 CDS Dshi_4007 NC_009957.1 71315 73756 R PFAM: DNA primase small subunit; type III restriction protein res subunit; DEAD/DEAH box helicase domain protein; SMART: DEAD-like helicases; KEGG: sfu:Sfum_3271 type III restriction enzyme, res subunit; type III restriction protein res subunit complement(71315..73756) Dinoroseobacter shibae DFL 12 = DSM 16493 5714536 YP_001542216.1 CDS Dshi_4008 NC_009957.1 74000 76510 R KEGG: nar:Saro_2208 putative methylase/helicase; putative methylase/helicase complement(74000..76510) Dinoroseobacter shibae DFL 12 = DSM 16493 5714537 YP_001542217.1 CDS Dshi_4009 NC_009957.1 77303 78163 R PFAM: regulatory protein LysR; LysR substrate-binding; KEGG: pol:Bpro_1615 transcriptional regulator, LysR family; LysR family transcriptional regulator complement(77303..78163) Dinoroseobacter shibae DFL 12 = DSM 16493 5714538 YP_001542218.1 CDS Dshi_4010 NC_009957.1 78320 79039 D KEGG: lpn:lpg1968 hypothetical protein; hypothetical protein 78320..79039 Dinoroseobacter shibae DFL 12 = DSM 16493 5714539 YP_001542219.1 CDS Dshi_4011 NC_009957.1 79361 79879 R KEGG: psa:PST_3459 hypothetical protein; hypothetical protein complement(79361..79879) Dinoroseobacter shibae DFL 12 = DSM 16493 5714540 YP_001542220.1 CDS Dshi_4012 NC_009957.1 79876 80202 R SohA; PrlF; involved in protein secretion; when overproduced or mutated, it induces growth defect and increased export of a reporter protein; a PrlF mutation induces the activity of the Lon protease, and a Lon-deficient strain suppresses the phenotype conferred by the PrlF mutation; putative regulator PrlF complement(79876..80202) Dinoroseobacter shibae DFL 12 = DSM 16493 5714541 YP_001542221.1 CDS Dshi_4013 NC_009957.1 80329 80982 R KEGG: rde:RD1_A0106 RC187; hypothetical protein complement(80329..80982) Dinoroseobacter shibae DFL 12 = DSM 16493 5714542 YP_001542222.1 CDS Dshi_4014 NC_009957.1 80982 81674 R hypothetical protein complement(80982..81674) Dinoroseobacter shibae DFL 12 = DSM 16493 5714543 YP_001542223.1 CDS Dshi_4015 NC_009957.1 81749 83731 R TIGRFAM: parB-like partition protein; PFAM: ParB domain protein nuclease; KEGG: rde:RD1_A0072 plasmid stabilization protein, putative; parB-like partition protein complement(81749..83731) Dinoroseobacter shibae DFL 12 = DSM 16493 5714544 YP_001542224.1 CDS Dshi_4016 NC_009957.1 83888 84277 R KEGG: jan:Jann_4219 hypothetical protein; hypothetical protein complement(83888..84277) Dinoroseobacter shibae DFL 12 = DSM 16493 5714545 YP_001542225.1 CDS Dshi_4017 NC_009957.1 84365 84574 R hypothetical protein complement(84365..84574) Dinoroseobacter shibae DFL 12 = DSM 16493 5714546 YP_001542226.1 CDS Dshi_4018 NC_009957.1 84598 85536 R PFAM: domain of unknown function DUF1738; KEGG: nha:Nham_4029 peptidase M, neutral zinc metallopeptidases, zinc-binding site; hypothetical protein complement(84598..85536) Dinoroseobacter shibae DFL 12 = DSM 16493 5714547 YP_001542227.1 CDS Dshi_4019 NC_009957.1 85577 86062 R hypothetical protein complement(85577..86062) Dinoroseobacter shibae DFL 12 = DSM 16493 5714548 YP_001542228.1 CDS Dshi_4020 NC_009957.1 86341 87543 D PFAM: filamentation induced by cAMP protein Fic; KEGG: rsq:Rsph17025_4217 hypothetical protein; filamentation induced by cAMP protein fic 86341..87543 Dinoroseobacter shibae DFL 12 = DSM 16493 5714549 YP_001542229.1 CDS Dshi_4021 NC_009957.1 87675 88910 R PFAM: replication protein C; KEGG: rsp:RSP_7387 replication initiator RepC; replication initiation protein RepC complement(87675..88910) Dinoroseobacter shibae DFL 12 = DSM 16493 5714550 YP_001542230.1 CDS Dshi_4022 NC_009957.1 89088 90104 R TIGRFAM: parB-like partition protein; PFAM: ParB domain protein nuclease; KEGG: rsp:RSP_4185 RepB partitioning protein/ParB-like protein; parB-like partition protein complement(89088..90104) Dinoroseobacter shibae DFL 12 = DSM 16493 5714551 YP_001542231.1 CDS Dshi_4023 NC_009957.1 90101 91288 R PFAM: regulatory protein MerR; Cobyrinic acid ac-diamide synthase; KEGG: rsp:RSP_4186 RepA partitioning protein/ATPase, ParA type; cobyrinic acid ac-diamide synthase complement(90101..91288) Dinoroseobacter shibae DFL 12 = DSM 16493 5714552 YP_001542232.1 CDS Dshi_4024 NC_009957.1 91602 91829 D PFAM: SpoVT/AbrB domain protein; KEGG: rsp:RSP_7280 SpoVT/AbrB-like cell growth regulatory protein; transcriptional regulator/antitoxin MazE 91602..91829 Dinoroseobacter shibae DFL 12 = DSM 16493 5714553 YP_001542233.1 CDS Dshi_4025 NC_009957.1 91819 92214 D KEGG: rsp:RSP_4188 hypothetical memebrane protein; hypothetical protein 91819..92214 Dinoroseobacter shibae DFL 12 = DSM 16493 5714554 YP_001542234.1 CDS Dshi_4026 NC_009957.1 92198 93094 R PFAM: Resolvase domain; KEGG: rsp:RSP_2482 TonB-dependent receptor protein; resolvase domain-containing protein complement(92198..93094) Dinoroseobacter shibae DFL 12 = DSM 16493 5714555 YP_001542235.1 CDS Dshi_4027 NC_009957.1 93153 94271 R PFAM: integrase family protein; KEGG: rsq:Rsph17025_4239 hypothetical protein; integrase family protein complement(93153..94271) Dinoroseobacter shibae DFL 12 = DSM 16493 5714556 YP_001542236.1 CDS Dshi_4028 NC_009957.1 94398 95282 D PFAM: protein of unknown function DUF1403; KEGG: sit:TM1040_3403 protein of unknown function DUF1403; hypothetical protein 94398..95282 Dinoroseobacter shibae DFL 12 = DSM 16493 5714557 YP_001542237.1 CDS Dshi_4029 NC_009957.1 95285 95902 D PFAM: chromosome segregation and condensation protein ScpB; KEGG: rsq:Rsph17025_4232 hypothetical protein; chromosome segregation and condensation protein ScpB 95285..95902 Dinoroseobacter shibae DFL 12 = DSM 16493 5714558 YP_001542238.1 CDS Dshi_4030 NC_009957.1 95952 96215 D PFAM: WGR domain protein; KEGG: mlo:msl9076 hypothetical protein; WGR domain-containing protein 95952..96215 Dinoroseobacter shibae DFL 12 = DSM 16493 5714559 YP_001542239.1 CDS Dshi_4031 NC_009957.1 96285 97403 D PFAM: filamentation induced by cAMP protein Fic; KEGG: atc:AGR_pAT_503 hypothetical protein; filamentation induced by cAMP protein fic 96285..97403 Dinoroseobacter shibae DFL 12 = DSM 16493 5714560 YP_001542240.1 CDS Dshi_4032 NC_009957.1 97400 98122 R hypothetical protein complement(97400..98122) Dinoroseobacter shibae DFL 12 = DSM 16493 5714561 YP_001542241.1 CDS Dshi_4033 NC_009957.1 98233 98580 D KEGG: pde:Pden_2059 transposase orfA IS5 family element; IS5 family transposase OrfA 98233..98580 Dinoroseobacter shibae DFL 12 = DSM 16493 5714562 YP_001542242.1 CDS Dshi_4034 NC_009957.1 98601 98990 D PFAM: transposase IS4 family protein; KEGG: pde:Pden_3333 transposase, IS4 family protein; transposase IS4 family protein 98601..98990 Dinoroseobacter shibae DFL 12 = DSM 16493 5714563 YP_001542243.1 CDS Dshi_4035 NC_009957.1 99093 100121 D PFAM: transposase IS116/IS110/IS902 family protein; KEGG: rru:Rru_A0676 transposase IS116/IS110/IS902; transposase IS116/IS110/IS902 family protein 99093..100121 Dinoroseobacter shibae DFL 12 = DSM 16493 5714564 YP_001542244.1 CDS Dshi_4036 NC_009957.1 100475 100657 R KEGG: rsq:Rsph17025_2803 ubiquinol-cytochrome c reductase, iron-sulfur subunit; hypothetical protein complement(100475..100657) Dinoroseobacter shibae DFL 12 = DSM 16493 5714565 YP_001542245.1 CDS Dshi_4037 NC_009957.1 100987 101349 D KEGG: nha:Nham_4014 ISSpo6, transposase orf A; ISSpo6, transposase orf A 100987..101349 Dinoroseobacter shibae DFL 12 = DSM 16493 5714566 YP_001542246.1 CDS Dshi_4038 NC_009957.1 101411 101941 D KEGG: nha:Nham_4013 ISSpo6, transposase OrfB; ISSpo6, transposase OrfB 101411..101941 Dinoroseobacter shibae DFL 12 = DSM 16493 5714567 YP_001542247.1 CDS Dshi_4039 NC_009957.1 101913 102341 R KEGG: sru:SRU_1982 hypothetical protein; hypothetical protein complement(101913..102341) Dinoroseobacter shibae DFL 12 = DSM 16493 5714568 YP_001542248.1 CDS Dshi_4040 NC_009957.1 102417 102983 D PFAM: cyclic nucleotide-binding; KEGG: reh:H16_A1838 transcriptional regulator, NNR like; cyclic nucleotide-binding protein 102417..102983 Dinoroseobacter shibae DFL 12 = DSM 16493 5714569 YP_001542249.1 CDS Dshi_4041 NC_009957.1 102989 103441 R PFAM: protein of unknown function DUF411; KEGG: rde:RD1_2307 hypothetical protein; hypothetical protein complement(102989..103441) Dinoroseobacter shibae DFL 12 = DSM 16493 5714570 YP_001542250.1 CDS Dshi_4042 NC_009957.1 103356 104348 R PFAM: fatty acid hydroxylase; KEGG: aeh:Mlg_0287 sterol desaturase-like protein; fatty acid hydroxylase complement(103356..104348) Dinoroseobacter shibae DFL 12 = DSM 16493 5714571 YP_001542251.1 CDS Dshi_4043 NC_009957.1 104355 105341 R TIGRFAM: cation diffusion facilitator family transporter; PFAM: cation efflux protein; KEGG: dge:Dgeo_0215 cation diffusion facilitator family transporter; cation diffusion facilitator family transporter complement(104355..105341) Dinoroseobacter shibae DFL 12 = DSM 16493 5714572 YP_001542252.1 CDS Dshi_4044 NC_009957.1 105343 106005 R PFAM: SNARE associated Golgi protein; KEGG: sil:SPOA0363 hypothetical protein; SNARE associated Golgi protein complement(105343..106005) Dinoroseobacter shibae DFL 12 = DSM 16493 5714573 YP_001542253.1 CDS Dshi_4045 NC_009957.1 106009 106458 R KEGG: ddi:DDBDRAFT_0184550 hypothetical protein; hypothetical protein complement(106009..106458) Dinoroseobacter shibae DFL 12 = DSM 16493 5714574 YP_001542254.1 CDS Dshi_4046 NC_009957.1 106620 107057 R KEGG: maq:Maqu_0306 ion transport 2 domain protein; ion transport 2 domain-containing protein complement(106620..107057) Dinoroseobacter shibae DFL 12 = DSM 16493 5714575 YP_001542255.1 CDS Dshi_4047 NC_009957.1 107146 107619 R KEGG: rde:RD1_1666 hypothetical protein; hypothetical protein complement(107146..107619) Dinoroseobacter shibae DFL 12 = DSM 16493 5714576 YP_001542256.1 CDS Dshi_4048 NC_009957.1 107808 108530 D PFAM: response regulator receiver; transcriptional regulator domain protein; KEGG: sil:SPOA0357 DNA-binding response regulator; two component transcriptional regulator 107808..108530 Dinoroseobacter shibae DFL 12 = DSM 16493 5714577 YP_001542257.1 CDS Dshi_4049 NC_009957.1 108530 109996 D PFAM: ATP-binding region ATPase domain protein; histidine kinase HAMP region domain protein; histidine kinase A domain protein; KEGG: sil:SPOA0358 sensor histidine kinase; integral membrane sensor signal transduction histidine kinase 108530..109996 Dinoroseobacter shibae DFL 12 = DSM 16493 5714578 YP_001542258.1 CDS Dshi_4050 NC_009957.1 110046 110237 D KEGG: aeh:Mlg_1384 hypothetical protein; hypothetical protein 110046..110237 Dinoroseobacter shibae DFL 12 = DSM 16493 5714579 YP_001542259.1 CDS Dshi_4051 NC_009957.1 110303 112303 D TIGRFAM: cytochrome c-type biogenesis protein CcmF; PFAM: cytochrome c assembly protein; KEGG: mag:amb4200 cytochrome c biogenesis factor; cytochrome c-type biogenesis protein CcmF 110303..112303 Dinoroseobacter shibae DFL 12 = DSM 16493 5714580 YP_001542260.1 CDS Dshi_4052 NC_009957.1 112312 112878 D TIGRFAM: periplasmic protein thiol--disulphide oxidoreductase DsbE; PFAM: alkyl hydroperoxide reductase/ Thiol specific antioxidant/ Mal allergen; Redoxin domain protein; KEGG: mlo:mll4330 cytochrome c biogenesis protein CycX; periplasmic protein thiol--disulphide oxidoreductase DsbE 112312..112878 Dinoroseobacter shibae DFL 12 = DSM 16493 5714581 YP_001542261.1 CDS Dshi_4053 NC_009957.1 112875 113348 D PFAM: cytochrome C biogenesis protein; KEGG: atc:AGR_C_1789 cytochrome C-type biogenesis protein; cytochrome C biogenesis protein 112875..113348 Dinoroseobacter shibae DFL 12 = DSM 16493 5714582 YP_001542262.1 CDS Dshi_4054 NC_009957.1 113345 114496 D PFAM: TPR repeat-containing protein; Tetratricopeptide TPR_2 repeat protein; SMART: Tetratricopeptide domain protein; KEGG: smd:Smed_0633 cytochrome c-type biogenesis transmembrane protein; hypothetical protein 113345..114496 Dinoroseobacter shibae DFL 12 = DSM 16493 5714583 YP_001542263.1 CDS Dshi_4055 NC_009957.1 114525 116654 R KEGG: mag:amb3382 thiol:disulfide interchange protein DsbD 1 precursor; thiol:disulfide interchange protein DsbD 1 precursor complement(114525..116654) Dinoroseobacter shibae DFL 12 = DSM 16493 5714584 YP_001542264.1 CDS Dshi_4056 NC_009957.1 116938 117240 R hypothetical protein complement(116938..117240) Dinoroseobacter shibae DFL 12 = DSM 16493 5714585 YP_001542265.1 CDS Dshi_4057 NC_009957.1 117396 117956 D PFAM: ErfK/YbiS/YcfS/YnhG family protein; KEGG: sil:SPO2205 ErfK/YbiS/YcfS/YnhG family protein; ErfK/YbiS/YcfS/YnhG family protein 117396..117956 Dinoroseobacter shibae DFL 12 = DSM 16493 5714586 YP_001542266.1 CDS Dshi_4058 NC_009957.1 117985 118443 D PFAM: cytochrome c class I; KEGG: sil:SPOA0359 cytochrome c family protein; cytochrome c class I 117985..118443 Dinoroseobacter shibae DFL 12 = DSM 16493 5714587 YP_001542267.1 CDS Dshi_4059 NC_009957.1 118813 119406 D KEGG: ret:RHE_CH02511 putative cytochrome c-like protein; putative cytochrome c-like protein 118813..119406 Dinoroseobacter shibae DFL 12 = DSM 16493 5714588 YP_001542268.1 CDS Dshi_4060 NC_009957.1 119409 120326 D KEGG: psa:PST_0453 cytochrome c family protein; gluconate 2-dehydrogenase (acceptor) 119409..120326 Dinoroseobacter shibae DFL 12 = DSM 16493 5714589 YP_001542269.1 CDS Dshi_4061 NC_009957.1 120370 121764 D PFAM: multicopper oxidase type 1; multicopper oxidase type 2; multicopper oxidase type 3; KEGG: sil:SPOA0360 multicopper oxidase, putative; multicopper oxidase type 3 120370..121764 Dinoroseobacter shibae DFL 12 = DSM 16493 5714590 YP_001542270.1 CDS Dshi_4062 NC_009957.1 121761 122243 D PFAM: cytochrome c class I; KEGG: sil:SPOA0361 cytochrome c family protein; cytochrome c class I 121761..122243 Dinoroseobacter shibae DFL 12 = DSM 16493 5714591 YP_001542271.1 CDS Dshi_4063 NC_009957.1 122245 122976 D PFAM: DSBA oxidoreductase; KEGG: sil:SPOA0362 27kDa outer membrane protein; DSBA oxidoreductase 122245..122976 Dinoroseobacter shibae DFL 12 = DSM 16493 5714592 YP_001542272.1 CDS Dshi_4064 NC_009957.1 123019 123219 R PFAM: Heavy metal transport/detoxification protein; KEGG: pen:PSEEN0671 copper-binding protein; heavy metal transport/detoxification protein complement(123019..123219) Dinoroseobacter shibae DFL 12 = DSM 16493 5714593 YP_001542273.1 CDS Dshi_4065 NC_009957.1 123373 125883 D 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 123373..125883 Dinoroseobacter shibae DFL 12 = DSM 16493 5714594 YP_001542274.1 CDS Dshi_4066 NC_009957.1 125896 126294 D TIGRFAM: Cu(I)-responsive transcriptional regulator; PFAM: regulatory protein MerR; Transcription regulator MerR DNA binding; KEGG: sit:TM1040_0537 transcriptional regulator, MerR family; MerR family transcriptional regulator 125896..126294 Dinoroseobacter shibae DFL 12 = DSM 16493 5714595 YP_001542275.1 CDS Dshi_4067 NC_009958.1 42 731 R hypothetical protein complement(42..731) Dinoroseobacter shibae DFL 12 = DSM 16493 5714613 YP_001542276.1 CDS Dshi_4071 NC_009958.1 3168 6497 D SMART: Parallel beta-helix repeat; KEGG: tcx:Tcr_0105 VCBS; parallel beta-helix repeat-containing protein 3168..6497 Dinoroseobacter shibae DFL 12 = DSM 16493 5714623 YP_001542277.1 CDS Dshi_4074 NC_009958.1 7492 7764 R PFAM: transposase IS3/IS911 family protein; KEGG: xac:XAC4322 ISxac3 transposase; transposase IS3/IS911 family protein complement(7492..7764) Dinoroseobacter shibae DFL 12 = DSM 16493 5714620 YP_001542278.1 CDS Dshi_4075 NC_009958.1 8880 9245 D hypothetical protein 8880..9245 Dinoroseobacter shibae DFL 12 = DSM 16493 5714618 YP_001542279.1 CDS Dshi_4076 NC_009958.1 9370 10845 D KEGG: rsp:RSP_3838 capsule polysaccharide export protein; capsule polysaccharide export protein 9370..10845 Dinoroseobacter shibae DFL 12 = DSM 16493 5714621 YP_001542280.1 CDS Dshi_4077 NC_009958.1 10862 11521 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: pde:Pden_5037 ABC transporter related; ABC transporter related 10862..11521 Dinoroseobacter shibae DFL 12 = DSM 16493 5714615 YP_001542281.1 CDS Dshi_4078 NC_009958.1 11557 11931 D hypothetical protein 11557..11931 Dinoroseobacter shibae DFL 12 = DSM 16493 5714606 YP_001542282.1 CDS Dshi_4079 NC_009958.1 12125 13507 D PFAM: transposase IS4 family protein; KEGG: rde:RD1_3444 transposase, putative; transposase IS4 family protein 12125..13507 Dinoroseobacter shibae DFL 12 = DSM 16493 5714602 YP_001542283.1 CDS Dshi_4080 NC_009958.1 13911 15719 R required for the synthesis of the hydromethylpyrimidine moiety of thiamine; thiamine biosynthesis protein ThiC complement(13911..15719) Dinoroseobacter shibae DFL 12 = DSM 16493 5714635 YP_001542284.1 CDS Dshi_4081 NC_009958.1 16240 16839 R PFAM: Resolvase domain; Resolvase helix-turn-helix domain protein; KEGG: gox:GOX2646 DNA integration/recombination/invertion protein; resolvase domain-containing protein complement(16240..16839) Dinoroseobacter shibae DFL 12 = DSM 16493 5714632 YP_001542285.1 CDS Dshi_4082 NC_009958.1 16978 18471 D PFAM: Integrase catalytic region; Transposase-like Mu; KEGG: art:Arth_4385 integrase, catalytic region; integrase catalytic region 16978..18471 Dinoroseobacter shibae DFL 12 = DSM 16493 5714658 YP_001542286.1 CDS Dshi_4083 NC_009958.1 18468 19292 D KEGG: art:Arth_4384 ATP-binding protein; ATP-binding protein 18468..19292 Dinoroseobacter shibae DFL 12 = DSM 16493 5714665 YP_001542287.1 CDS Dshi_4084 NC_009958.1 19415 19981 D PFAM: Resolvase domain; Resolvase helix-turn-helix domain protein; KEGG: swi:Swit_5093 resolvase, N-terminal domain; resolvase domain-containing protein 19415..19981 Dinoroseobacter shibae DFL 12 = DSM 16493 5714647 YP_001542288.1 CDS Dshi_4085 NC_009958.1 19968 20222 D PFAM: WGR domain protein; KEGG: rsq:Rsph17025_4211 hypothetical protein; WGR domain-containing protein 19968..20222 Dinoroseobacter shibae DFL 12 = DSM 16493 5714604 YP_001542289.1 CDS Dshi_4086 NC_009958.1 20366 20572 D KEGG: noc:Noc_2541 hypothetical protein; hypothetical protein 20366..20572 Dinoroseobacter shibae DFL 12 = DSM 16493 5714600 YP_001542290.1 CDS Dshi_4087 NC_009958.1 20559 20852 D PFAM: plasmid stabilization system; KEGG: pha:PSHAa2625 hypothetical protein; plasmid stabilization system protein 20559..20852 Dinoroseobacter shibae DFL 12 = DSM 16493 5714633 YP_001542291.1 CDS Dshi_4088 NC_009958.1 20858 21250 D hypothetical protein 20858..21250 Dinoroseobacter shibae DFL 12 = DSM 16493 5714643 YP_001542292.1 CDS Dshi_4089 NC_009958.1 21412 22221 R PFAM: Integrase catalytic region; KEGG: bbt:BBta_7691 integrase, catalytic domain; integrase catalytic region complement(21412..22221) Dinoroseobacter shibae DFL 12 = DSM 16493 5714659 YP_001542293.1 CDS Dshi_4090 NC_009958.1 22245 22511 R PFAM: transposase IS3/IS911 family protein; KEGG: mag:amb0646 insertion element ISR1 hypothetical 10 kDa protein A3; transposase IS3/IS911 family protein complement(22245..22511) Dinoroseobacter shibae DFL 12 = DSM 16493 5714634 YP_001542294.1 CDS Dshi_4091 NC_009958.1 22571 23200 R hypothetical protein complement(22571..23200) Dinoroseobacter shibae DFL 12 = DSM 16493 5714666 YP_001542295.1 CDS Dshi_4092 NC_009958.1 24188 25219 R PFAM: transposase IS111A/IS1328/IS1533; transposase IS116/IS110/IS902 family protein; KEGG: rru:Rru_A0676 transposase IS116/IS110/IS902; transposase IS116/IS110/IS902 family protein complement(24188..25219) Dinoroseobacter shibae DFL 12 = DSM 16493 5714644 YP_001542296.1 CDS Dshi_4093 NC_009958.1 25327 25716 R PFAM: transposase IS4 family protein; KEGG: pde:Pden_3333 transposase, IS4 family protein; transposase IS4 family protein complement(25327..25716) Dinoroseobacter shibae DFL 12 = DSM 16493 5714645 YP_001542297.1 CDS Dshi_4094 NC_009958.1 25737 26090 R KEGG: pde:Pden_2059 transposase orfA IS5 family element; IS5 family transposase OrfA complement(25737..26090) Dinoroseobacter shibae DFL 12 = DSM 16493 5714641 YP_001542298.1 CDS Dshi_4095 NC_009958.1 26734 27168 D KEGG: bra:BRADO4296 putative insertion element (IS) transposase; putative insertion element (IS) transposase 26734..27168 Dinoroseobacter shibae DFL 12 = DSM 16493 5714598 YP_001542300.1 CDS Dshi_4102 NC_009958.1 30488 31699 R PFAM: replication protein C; KEGG: rsp:RSP_7387 replication initiator RepC; replication initiation protein RepC complement(30488..31699) Dinoroseobacter shibae DFL 12 = DSM 16493 5714599 YP_001542301.1 CDS Dshi_4103 NC_009958.1 31914 32738 R TIGRFAM: parB-like partition protein; PFAM: ParB domain protein nuclease; KEGG: rsp:RSP_4185 RepB partitioning protein/ParB-like protein; parB-like partition protein complement(31914..32738) Dinoroseobacter shibae DFL 12 = DSM 16493 5714640 YP_001542302.1 CDS Dshi_4104 NC_009958.1 32827 34020 R PFAM: regulatory protein MerR; Cobyrinic acid ac-diamide synthase; KEGG: rsp:RSP_4186 RepA partitioning protein/ATPase, ParA type; cobyrinic acid ac-diamide synthase complement(32827..34020) Dinoroseobacter shibae DFL 12 = DSM 16493 5714653 YP_001542303.1 CDS Dshi_4105 NC_009958.1 34155 35036 R PFAM: Resolvase domain; KEGG: rsp:RSP_2482 TonB-dependent receptor protein; resolvase domain-containing protein complement(34155..35036) Dinoroseobacter shibae DFL 12 = DSM 16493 5714630 YP_001542304.1 CDS Dshi_4106 NC_009958.1 35263 36330 D KEGG: rsh:Rsph17029_2968 hypothetical protein; hypothetical protein 35263..36330 Dinoroseobacter shibae DFL 12 = DSM 16493 5714629 YP_001542305.1 CDS Dshi_4107 NC_009958.1 36463 37227 D KEGG: smd:Smed_5442 transcriptional regulator; hypothetical protein 36463..37227 Dinoroseobacter shibae DFL 12 = DSM 16493 5714614 YP_001542306.1 CDS Dshi_4108 NC_009958.1 37700 37960 D hypothetical protein 37700..37960 Dinoroseobacter shibae DFL 12 = DSM 16493 5714612 YP_001542307.1 CDS Dshi_4109 NC_009958.1 39318 39818 D hypothetical protein 39318..39818 Dinoroseobacter shibae DFL 12 = DSM 16493 5714626 YP_001542308.1 CDS Dshi_4110 NC_009958.1 39815 41992 D hypothetical protein 39815..41992 Dinoroseobacter shibae DFL 12 = DSM 16493 5714611 YP_001542309.1 CDS Dshi_4111 NC_009958.1 41989 44979 D PFAM: integrase family protein; KEGG: shn:Shewana3_2354 phage integrase family protein; integrase family protein 41989..44979 Dinoroseobacter shibae DFL 12 = DSM 16493 5714619 YP_001542310.1 CDS Dshi_4112 NC_009958.1 45616 45843 D TIGRFAM: prevent-host-death family protein; PFAM: protein of unknown function DUF172; KEGG: rpe:RPE_3949 prevent-host-death family protein; prevent-host-death family protein 45616..45843 Dinoroseobacter shibae DFL 12 = DSM 16493 5714617 YP_001542311.1 CDS Dshi_4113 NC_009958.1 45840 46232 D TIGRFAM: death-on-curing family protein; PFAM: Death-on-curing protein; KEGG: hne:HNE_0348 putative addiction module toxin; death-on-curing family protein 45840..46232 Dinoroseobacter shibae DFL 12 = DSM 16493 5714652 YP_001542312.1 CDS Dshi_4114 NC_009958.1 46419 46973 D KEGG: sit:TM1040_3863 dTDP-4-dehydrorhamnose 3,5-epimerase; TIGRFAM: dTDP-4-dehydrorhamnose 3,5-epimerase; PFAM: dTDP-4-dehydrorhamnose 35-epimerase related; dTDP-4-dehydrorhamnose 3,5-epimerase 46419..46973 Dinoroseobacter shibae DFL 12 = DSM 16493 5714622 YP_001542313.1 CDS Dshi_4115 NC_009958.1 46978 48018 D 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 domain; KEGG: rde:RD1_B0019 dTDP-glucose 4,6-dehydratase; dTDP-glucose 4,6-dehydratase 46978..48018 Dinoroseobacter shibae DFL 12 = DSM 16493 5714616 YP_001542314.1 CDS Dshi_4116 NC_009958.1 48022 48855 D hypothetical protein 48022..48855 Dinoroseobacter shibae DFL 12 = DSM 16493 5714597 YP_001542315.1 CDS Dshi_4117 NC_009958.1 48852 49709 D PFAM: NAD-dependent epimerase/dehydratase; dTDP-4-dehydrorhamnose reductase; Male sterility domain; KEGG: rsp:RSP_3845 dTDP-4-dehydrorhamnose reductase; dTDP-4-dehydrorhamnose reductase 48852..49709 Dinoroseobacter shibae DFL 12 = DSM 16493 5714607 YP_001542316.1 CDS Dshi_4118 NC_009958.1 49744 50616 D TIGRFAM: glucose-1-phosphate thymidylyltransferase; PFAM: Nucleotidyl transferase; KEGG: sit:TM1040_3859 glucose-1-phosphate thymidylyltransferase; glucose-1-phosphate thymidylyltransferase 49744..50616 Dinoroseobacter shibae DFL 12 = DSM 16493 5714605 YP_001542317.1 CDS Dshi_4119 NC_009958.1 50748 51629 D PFAM: NAD-dependent epimerase/dehydratase; dTDP-4-dehydrorhamnose reductase; KEGG: rsq:Rsph17025_2629 NAD-dependent epimerase/dehydratase; NAD-dependent epimerase/dehydratase 50748..51629 Dinoroseobacter shibae DFL 12 = DSM 16493 5714663 YP_001542318.1 CDS Dshi_4120 NC_009958.1 51626 52234 D PFAM: sugar transferase; KEGG: rsh:Rsph17029_2851 sugar transferase; sugar transferase 51626..52234 Dinoroseobacter shibae DFL 12 = DSM 16493 5714657 YP_001542319.1 CDS Dshi_4121 NC_009958.1 52382 54934 D PFAM: glycosyl transferase family 2; KEGG: aav:Aave_4142 glycosyl transferase, family 2; glycosyl transferase family protein 52382..54934 Dinoroseobacter shibae DFL 12 = DSM 16493 5714667 YP_001542320.1 CDS Dshi_4122 NC_009958.1 54931 55707 D hypothetical protein 54931..55707 Dinoroseobacter shibae DFL 12 = DSM 16493 5714662 YP_001542321.1 CDS Dshi_4125 NC_009958.1 57015 59051 D hypothetical protein 57015..59051 Dinoroseobacter shibae DFL 12 = DSM 16493 5714603 YP_001542322.1 CDS Dshi_4128 NC_009958.1 60093 60374 D KEGG: acr:Acry_3373 IstB domain protein ATP-binding protein; hypothetical protein 60093..60374 Dinoroseobacter shibae DFL 12 = DSM 16493 5714636 YP_001542323.1 CDS Dshi_4129 NC_009958.1 60514 61947 R PFAM: polysaccharide biosynthesis protein; KEGG: bvi:Bcep1808_6521 polysaccharide biosynthesis protein; polysaccharide biosynthesis protein complement(60514..61947) Dinoroseobacter shibae DFL 12 = DSM 16493 5714668 YP_001542324.1 CDS Dshi_4130 NC_009958.1 62343 64739 D SMART: Parallel beta-helix repeat; parallel beta-helix repeat-containing protein 62343..64739 Dinoroseobacter shibae DFL 12 = DSM 16493 5714664 YP_001542325.1 CDS Dshi_4133 NC_009958.1 65809 66255 D PFAM: Oligosaccharide biosynthesis protein Alg14 like; KEGG: mjl:Mjls_0958 oligosaccharide biosynthesis protein Alg14 like; oligosaccharide biosynthesis protein Alg14-like protein 65809..66255 Dinoroseobacter shibae DFL 12 = DSM 16493 5714637 YP_001542326.1 CDS Dshi_4134 NC_009958.1 66252 66728 D PFAM: Glycosyltransferase 28 domain; KEGG: rle:RL3655 putative glycosyltransferase; glycosyltransferase family 28 protein 66252..66728 Dinoroseobacter shibae DFL 12 = DSM 16493 5714648 YP_001542327.1 CDS Dshi_4135 NC_009958.1 66718 68040 D KEGG: psa:PST_2497 hypothetical protein; hypothetical protein 66718..68040 Dinoroseobacter shibae DFL 12 = DSM 16493 5714650 YP_001542328.1 CDS Dshi_4136 NC_009958.1 68033 69217 D PFAM: polysaccharide pyruvyl transferase; KEGG: mfa:Mfla_2020 polysaccharide pyruvyl transferase; polysaccharide pyruvyl transferase 68033..69217 Dinoroseobacter shibae DFL 12 = DSM 16493 5714646 YP_001542329.1 CDS Dshi_4137 NC_009958.1 69126 70604 R KEGG: smd:Smed_4799 hypothetical protein; hypothetical protein complement(69126..70604) Dinoroseobacter shibae DFL 12 = DSM 16493 5714639 YP_001542330.1 CDS Dshi_4138 NC_009958.1 70715 71707 R hypothetical protein complement(70715..71707) Dinoroseobacter shibae DFL 12 = DSM 16493 5714649 YP_001542331.1 CDS Dshi_4139 NC_009958.1 71700 72764 R TIGRFAM: GDP-mannose 4,6-dehydratase; PFAM: NAD-dependent epimerase/dehydratase; KEGG: rle:pRL90133 putative GDP-mannose 4,6-dehydratase; GDP-mannose 4,6-dehydratase complement(71700..72764) Dinoroseobacter shibae DFL 12 = DSM 16493 5714601 YP_001542332.1 CDS Dshi_4140 NC_009958.1 72811 73542 R PFAM: sulfotransferase; KEGG: bta:282485 sulfotransferase family, cytosolic, 1A, phenol-preferring, member 1; sulfotransferase complement(72811..73542) Dinoroseobacter shibae DFL 12 = DSM 16493 5714656 YP_001542333.1 CDS Dshi_4141 NC_009958.1 73755 74459 R KEGG: ava:Ava_1042 methyltransferase FkbM; hypothetical protein complement(73755..74459) Dinoroseobacter shibae DFL 12 = DSM 16493 5714660 YP_001542334.1 CDS Dshi_4142 NC_009958.1 74668 75609 D PFAM: NAD-dependent epimerase/dehydratase; dTDP-4-dehydrorhamnose reductase; KEGG: ath:AT1G73250 ATFX/GER1 (GDP-4-KETO-6-DEOXYMANNOSE-3,5-EPIMERASE-4-REDUCTASE 1); GDP-L-fucose synthase; NAD-dependent epimerase/dehydratase 74668..75609 Dinoroseobacter shibae DFL 12 = DSM 16493 5714627 YP_001542335.1 CDS Dshi_4143 NC_009958.1 75619 76494 D PFAM: glycosyl transferase family 2; KEGG: nha:Nham_3045 glycosyl transferase, family 2; glycosyl transferase family protein 75619..76494 Dinoroseobacter shibae DFL 12 = DSM 16493 5714628 YP_001542336.1 CDS Dshi_4144 NC_009958.1 76612 77184 R PFAM: transferase hexapeptide repeat containing protein; KEGG: dde:Dde_3680 acetyltransferase (isoleucine patch superfamily)-like; hexapaptide repeat-containing transferase complement(76612..77184) Dinoroseobacter shibae DFL 12 = DSM 16493 5714610 YP_001542337.1 CDS Dshi_4145 NC_009958.1 77191 78195 R PFAM: glycosyl transferase family 2; KEGG: nar:Saro_3226 glycosyl transferase, family 2; glycosyl transferase family protein complement(77191..78195) Dinoroseobacter shibae DFL 12 = DSM 16493 5714625 YP_001542338.1 CDS Dshi_4146 NC_009958.1 78217 79641 R 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/mannose-6-phosphate isomerase complement(78217..79641) Dinoroseobacter shibae DFL 12 = DSM 16493 5714671 YP_001542339.1 CDS Dshi_4147 NC_009958.1 79830 80822 R PFAM: glycosyl transferase family 2; KEGG: rsh:Rsph17029_4080 glycosyl transferase, family 2; glycosyl transferase family protein complement(79830..80822) Dinoroseobacter shibae DFL 12 = DSM 16493 5714672 YP_001542340.1 CDS Dshi_4148 NC_009958.1 80815 81660 R PFAM: ABC-2 type transporter; KEGG: rsh:Rsph17029_4086 ABC-2 type transporter; ABC-2 type transporter complement(80815..81660) Dinoroseobacter shibae DFL 12 = DSM 16493 5714673 YP_001542341.1 CDS Dshi_4149 NC_009958.1 81926 82657 D PFAM: transferase hexapeptide repeat containing protein; KEGG: mag:amb0878 acetyltransferase; hexapaptide repeat-containing transferase 81926..82657 Dinoroseobacter shibae DFL 12 = DSM 16493 5714674 YP_001542342.1 CDS Dshi_4150 NC_009958.1 82654 83457 D hypothetical protein 82654..83457 Dinoroseobacter shibae DFL 12 = DSM 16493 5714675 YP_001542344.1 CDS Dshi_4152 NC_009958.1 84463 85098 R PFAM: autoinducer synthesis protein; KEGG: rde:RD1_1639 autoinducer synthesis protein TraL, putative; autoinducer synthesis protein complement(84463..85098) Dinoroseobacter shibae DFL 12 = DSM 16493 5714677 YP_001542345.1 CDS Dshi_4154 NC_009959.1 24 977 R PFAM: beta-lactamase domain protein; KEGG: sil:SPO1523 metallo-beta-lactamase family protein; beta-lactamase domain-containing protein complement(24..977) Dinoroseobacter shibae DFL 12 = DSM 16493 5714694 YP_001542346.1 CDS Dshi_4155 NC_009959.1 977 1759 R KEGG: sil:SPO1524 hypothetical protein; hypothetical protein complement(977..1759) Dinoroseobacter shibae DFL 12 = DSM 16493 5714725 YP_001542347.1 CDS Dshi_4156 NC_009959.1 1936 3684 D PFAM: sigma-54 factor interaction domain-containing protein; helix-turn-helix Fis-type; GAF domain protein; KEGG: acr:Acry_2975 GAF modulated sigma54 specific transcriptional regulator, fis family; Fis family GAF modulated sigma54 specific transcriptional regulator 1936..3684 Dinoroseobacter shibae DFL 12 = DSM 16493 5714726 YP_001542348.1 CDS Dshi_4157 NC_009959.1 3833 5632 D KEGG: rde:RD1_3706 monooxygenase; monooxygenase 3833..5632 Dinoroseobacter shibae DFL 12 = DSM 16493 5714727 YP_001542349.2 CDS Dshi_4158 NC_009959.1 5711 6484 D TIGRFAM: acetoin reductase; PFAM: short-chain dehydrogenase/reductase SDR; KR domain protein; KEGG: rha:RHA1_ro05279 acetoin dehydrogenase; acetoin reductase 5711..6484 Dinoroseobacter shibae DFL 12 = DSM 16493 5714728 YP_001542350.1 CDS Dshi_4159 NC_009959.1 6606 7658 D PFAM: Alcohol dehydrogenase zinc-binding domain protein; Alcohol dehydrogenase GroES domain protein; KEGG: bha:BH3949 L-iditol 2-dehydrogenase; alcohol dehydrogenase 6606..7658 Dinoroseobacter shibae DFL 12 = DSM 16493 5714729 YP_001542351.1 CDS Dshi_4160 NC_009959.1 7713 8699 R Converts chlorophyllide a into protochlorophyllide; light dependent; protochlorophyllide oxidoreductase complement(7713..8699) Dinoroseobacter shibae DFL 12 = DSM 16493 5714730 YP_001542352.1 CDS Dshi_4161 NC_009959.1 8902 9714 D PFAM: MltA-interacting MipA family protein; KEGG: reu:Reut_A3319 MltA-interacting MipA; MltA-interacting MipA family protein 8902..9714 Dinoroseobacter shibae DFL 12 = DSM 16493 5714731 YP_001542353.1 CDS Dshi_4162 NC_009959.1 9725 10768 R PFAM: glycosyl transferase group 1; KEGG: pde:Pden_4362 glycosyl transferase, group 1; glycosyl transferase group 1 complement(9725..10768) Dinoroseobacter shibae DFL 12 = DSM 16493 5714732 YP_001542354.1 CDS Dshi_4163 NC_009959.1 10765 12342 R 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 complement(10765..12342) Dinoroseobacter shibae DFL 12 = DSM 16493 5714733 YP_001542355.1 CDS Dshi_4164 NC_009959.1 12339 13145 R PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: jan:Jann_0307 ABC transporter related; ABC transporter related complement(12339..13145) Dinoroseobacter shibae DFL 12 = DSM 16493 5714679 YP_001542356.1 CDS Dshi_4165 NC_009959.1 13135 14130 R PFAM: NMT1/THI5 like domain protein; KEGG: jan:Jann_0306 twin-arginine translocation pathway signal; NMT1/THI5-like domain-containing protein complement(13135..14130) Dinoroseobacter shibae DFL 12 = DSM 16493 5714680 YP_001542357.1 CDS Dshi_4166 NC_009959.1 14227 15177 R KEGG: jan:Jann_0305 hypothetical protein; hypothetical protein complement(14227..15177) Dinoroseobacter shibae DFL 12 = DSM 16493 5714681 YP_001542358.1 CDS Dshi_4167 NC_009959.1 15174 16799 R PFAM: sulfatase; KEGG: jan:Jann_0304 hypothetical protein; sulfatase complement(15174..16799) Dinoroseobacter shibae DFL 12 = DSM 16493 5714682 YP_001542359.1 CDS Dshi_4168 NC_009959.1 16796 17545 R PFAM: CDP-alcohol phosphatidyltransferase; KEGG: pde:Pden_4357 CDP-alcohol phosphatidyltransferase; CDP-alcohol phosphatidyltransferase complement(16796..17545) Dinoroseobacter shibae DFL 12 = DSM 16493 5714683 YP_001542360.1 CDS Dshi_4169 NC_009959.1 17646 18203 D PFAM: cytochrome B561; KEGG: jan:Jann_0302 cytochrome b561; cytochrome B561 17646..18203 Dinoroseobacter shibae DFL 12 = DSM 16493 5714684 YP_001542361.1 CDS Dshi_4170 NC_009959.1 18287 19852 D necessary for biosynthesis of osmoregulated periplasmic glucans possibly involved in the transfer to the periplasmic space; glucosyltransferase MdoH 18287..19852 Dinoroseobacter shibae DFL 12 = DSM 16493 5714685 YP_001542362.1 CDS mdoD NC_009959.1 19852 21336 D involved in the control of the structural glucose backbone of osmoregulated periplasmic glucans; glucan biosynthesis protein D 19852..21336 Dinoroseobacter shibae DFL 12 = DSM 16493 5714686 YP_001542363.1 CDS Dshi_4172 NC_009959.1 21403 22290 D PFAM: helix-turn-helix- domain containing protein AraC type; KEGG: rde:RD1_0248 transcriptional regulator, AraC family; AraC family transcriptional regulator 21403..22290 Dinoroseobacter shibae DFL 12 = DSM 16493 5714687 YP_001542364.1 CDS Dshi_4173 NC_009959.1 22428 23387 D KEGG: jan:Jann_1319 hypothetical protein; hypothetical protein 22428..23387 Dinoroseobacter shibae DFL 12 = DSM 16493 5714688 YP_001542365.1 CDS Dshi_4174 NC_009959.1 23458 24015 D KEGG: jan:Jann_1320 hypothetical protein; hypothetical protein 23458..24015 Dinoroseobacter shibae DFL 12 = DSM 16493 5714689 YP_001542366.2 CDS Dshi_4175 NC_009959.1 24079 25098 R PFAM: protein of unknown function UPF0118; KEGG: rde:RD1_2476 hypothetical protein; hypothetical protein complement(24079..25098) Dinoroseobacter shibae DFL 12 = DSM 16493 5714690 YP_001542367.1 CDS Dshi_4176 NC_009959.1 25262 25924 D PFAM: oxidoreductase FAD/NAD(P)-binding domain protein; KEGG: eli:ELI_11485 oxidoreductase; oxidoreductase FAD/NAD(P)-binding subunit 25262..25924 Dinoroseobacter shibae DFL 12 = DSM 16493 5714691 YP_001542368.1 CDS Dshi_4177 NC_009959.1 26016 27332 R PFAM: Acetamidase/Formamidase; KEGG: rsh:Rsph17029_3153 acetamidase/formamidase; acetamidase/formamidase complement(26016..27332) Dinoroseobacter shibae DFL 12 = DSM 16493 5714692 YP_001542369.1 CDS Dshi_4178 NC_009959.1 27466 28224 R KEGG: rde:RD1_2481 hypothetical protein; hypothetical protein complement(27466..28224) Dinoroseobacter shibae DFL 12 = DSM 16493 5714693 YP_001542370.1 CDS Dshi_4179 NC_009959.1 28217 28627 R PFAM: protein of unknown function DUF1469; KEGG: rde:RD1_2479 hypothetical protein; hypothetical protein complement(28217..28627) Dinoroseobacter shibae DFL 12 = DSM 16493 5714710 YP_001542371.1 CDS Dshi_4180 NC_009959.1 28620 29135 R KEGG: rde:RD1_2478 hypothetical protein; hypothetical protein complement(28620..29135) Dinoroseobacter shibae DFL 12 = DSM 16493 5714711 YP_001542372.1 CDS Dshi_4181 NC_009959.1 29307 29495 R KEGG: jan:Jann_3633 hypothetical protein; hypothetical protein complement(29307..29495) Dinoroseobacter shibae DFL 12 = DSM 16493 5714712 YP_001542373.1 CDS Dshi_4182 NC_009959.1 29547 30521 D PFAM: MscS Mechanosensitive ion channel; KEGG: rde:RD1_2453 hypothetical protein; MscS mechanosensitive ion channel 29547..30521 Dinoroseobacter shibae DFL 12 = DSM 16493 5714713 YP_001542374.1 CDS Dshi_4183 NC_009959.1 30634 30933 R hypothetical protein complement(30634..30933) Dinoroseobacter shibae DFL 12 = DSM 16493 5714714 YP_001542375.1 CDS Dshi_4184 NC_009959.1 31088 31285 R PFAM: CsbD family protein; KEGG: jan:Jann_3572 CsbD-like; CsbD family protein complement(31088..31285) Dinoroseobacter shibae DFL 12 = DSM 16493 5714715 YP_001542376.1 CDS Dshi_4185 NC_009959.1 31537 32229 D PFAM: regulatory protein GntR HTH; GntR domain protein; KEGG: ent:Ent638_0750 GntR domain protein; GntR family transcriptional regulator 31537..32229 Dinoroseobacter shibae DFL 12 = DSM 16493 5714716 YP_001542377.1 CDS Dshi_4186 NC_009959.1 32317 33138 D PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sme:SMc02346 ATP-binding ABC transporter protein; ABC transporter related 32317..33138 Dinoroseobacter shibae DFL 12 = DSM 16493 5714717 YP_001542378.1 CDS Dshi_4187 NC_009959.1 33135 33890 D PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: mes:Meso_2078 binding-protein-dependent transport systems inner membrane component; binding-protein-dependent transport systems inner membrane component 33135..33890 Dinoroseobacter shibae DFL 12 = DSM 16493 5714718 YP_001542379.1 CDS Dshi_4188 NC_009959.1 33904 34665 D PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: mes:Meso_2078 binding-protein-dependent transport systems inner membrane component; binding-protein-dependent transport systems inner membrane component 33904..34665 Dinoroseobacter shibae DFL 12 = DSM 16493 5714719 YP_001542380.1 CDS Dshi_4189 NC_009959.1 34761 35777 D KEGG: mes:Meso_2921 ABC-type nitrate/sulfonate/bicarbonate transport systems periplasmic components-like; ABC-type nitrate/sulfonate/bicarbonate transport systems periplasmic components-like protein 34761..35777 Dinoroseobacter shibae DFL 12 = DSM 16493 5714720 YP_001542381.1 CDS Dshi_4190 NC_009959.1 35941 37218 D KEGG: mac:MA1904 hypothetical protein; hypothetical protein 35941..37218 Dinoroseobacter shibae DFL 12 = DSM 16493 5714721 YP_001542382.1 CDS Dshi_4191 NC_009959.1 37297 38292 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 37297..38292 Dinoroseobacter shibae DFL 12 = DSM 16493 5714722 YP_001542383.1 CDS Dshi_4192 NC_009959.1 38385 38972 D PFAM: Tripartite ATP-independent periplasmic transporter DctQ component; KEGG: bra:BRADO4761 TRAP-type C4-dicarboxylate transport system, fusion of small and large permeases (DctQ/DctM domains); tripartite ATP-independent periplasmic transporter DctQ 38385..38972 Dinoroseobacter shibae DFL 12 = DSM 16493 5714723 YP_001542384.1 CDS Dshi_4193 NC_009959.1 38969 40258 D TIGRFAM: TRAP dicarboxylate transporter, DctM subunit; PFAM: Citrate transporter; TRAP C4-dicarboxylate transport system permease DctM subunit; KEGG: bcl:ABC3355 C4-dicarboxylate transport system permease large protein; TRAP dicarboxylate transporter, DctM subunit 38969..40258 Dinoroseobacter shibae DFL 12 = DSM 16493 5714724 YP_001542385.1 CDS Dshi_4194 NC_009959.1 40279 41874 R PFAM: gamma-glutamyltranspeptidase; KEGG: rde:RD1_2179 gamma-glutamyltranspeptidase; gamma-glutamyltransferase complement(40279..41874) Dinoroseobacter shibae DFL 12 = DSM 16493 5714695 YP_001542386.1 CDS Dshi_4195 NC_009959.1 41874 43385 R PFAM: protein of unknown function DUF112 transmembrane; KEGG: oih:OB3268 hypothetical protein; hypothetical protein complement(41874..43385) Dinoroseobacter shibae DFL 12 = DSM 16493 5714696 YP_001542387.1 CDS Dshi_4196 NC_009959.1 43389 43895 R KEGG: oih:OB3269 hypothetical protein; hypothetical protein complement(43389..43895) Dinoroseobacter shibae DFL 12 = DSM 16493 5714697 YP_001542388.1 CDS Dshi_4197 NC_009959.1 43895 44845 R PFAM: conserved hypothetical protein; KEGG: oih:OB3270 hypothetical protein; hypothetical protein complement(43895..44845) Dinoroseobacter shibae DFL 12 = DSM 16493 5714698 YP_001542389.1 CDS Dshi_4198 NC_009959.1 44976 45887 D PFAM: regulatory protein LysR; LysR substrate-binding; KEGG: pde:Pden_3415 transcriptional regulator, LysR family; LysR family transcriptional regulator 44976..45887 Dinoroseobacter shibae DFL 12 = DSM 16493 5714699 YP_001542390.1 CDS Dshi_4199 NC_009959.1 45953 46597 R PFAM: regulatory protein TetR; KEGG: rle:pRL80035 TetR family transcriptional regulator; TetR family transcriptional regulator complement(45953..46597) Dinoroseobacter shibae DFL 12 = DSM 16493 5714700 YP_001542391.1 CDS Dshi_4200 NC_009959.1 46743 47576 D PFAM: molybdopterin dehydrogenase FAD-binding; CO dehydrogenase flavoprotein domain protein; KEGG: bja:bll6239 probable carbon monoxide dehydrogenase medium chain; carbon-monoxide dehydrogenase (acceptor) 46743..47576 Dinoroseobacter shibae DFL 12 = DSM 16493 5714701 YP_001542392.1 CDS Dshi_4201 NC_009959.1 47573 48073 D PFAM: ferredoxin; [2Fe-2S]-binding domain protein; KEGG: acr:Acry_2175 (2Fe-2S)-binding domain protein; 2Fe-2S iron-sulfur cluster binding domain-containing protein 47573..48073 Dinoroseobacter shibae DFL 12 = DSM 16493 5714702 YP_001542393.1 CDS Dshi_4202 NC_009959.1 48070 50451 D PFAM: aldehyde oxidase and xanthine dehydrogenase a/b hammerhead; aldehyde oxidase and xanthine dehydrogenase molybdopterin binding; KEGG: jan:Jann_2947 xanthine dehydrogenase; carbon-monoxide dehydrogenase (acceptor) 48070..50451 Dinoroseobacter shibae DFL 12 = DSM 16493 5714703 YP_001542394.1 CDS Dshi_4203 NC_009959.1 50499 51551 D PFAM: TRAP dicarboxylate transporter- DctP subunit; KEGG: jan:Jann_0870 TRAP dicarboxylate transporter-DctP subunit; TRAP dicarboxylate transporter- DctP subunit 50499..51551 Dinoroseobacter shibae DFL 12 = DSM 16493 5714704 YP_001542395.1 CDS Dshi_4204 NC_009959.1 51618 52199 D KEGG: jan:Jann_2036 hypothetical protein; hypothetical protein 51618..52199 Dinoroseobacter shibae DFL 12 = DSM 16493 5714705 YP_001542396.1 CDS Dshi_4205 NC_009959.1 52196 53524 D TIGRFAM: TRAP dicarboxylate transporter, DctM subunit; PFAM: TRAP C4-dicarboxylate transport system permease DctM subunit; KEGG: jan:Jann_0872 TRAP dicarboxylate transporter-DctM subunit; TRAP dicarboxylate transporter, DctM subunit 52196..53524 Dinoroseobacter shibae DFL 12 = DSM 16493 5714706 YP_001542397.1 CDS Dshi_4206 NC_009959.1 53586 54509 D PFAM: aminotransferase class IV; KEGG: jan:Jann_2852 aminotransferase, class IV; aminotransferase class IV 53586..54509 Dinoroseobacter shibae DFL 12 = DSM 16493 5714707 YP_001542398.1 CDS Dshi_4207 NC_009959.1 54580 55551 D PFAM: protein of unknown function DUF900 hydrolase family protein; KEGG: rde:RD1_3768 hypothetical protein; hypothetical protein 54580..55551 Dinoroseobacter shibae DFL 12 = DSM 16493 5714708 YP_001542399.1 CDS Dshi_4208 NC_009959.1 55567 56109 R KEGG: sil:SPO0302 hypothetical protein; hypothetical protein complement(55567..56109) Dinoroseobacter shibae DFL 12 = DSM 16493 5714709 YP_001542400.1 CDS Dshi_4209 NC_009959.1 56106 57956 R PFAM: glycerophosphoryl diester phosphodiesterase; KEGG: rde:RD1_0308 glycerophosphoryl diester phosphodiesterase family protein; glycerophosphoryl diester phosphodiesterase complement(56106..57956) Dinoroseobacter shibae DFL 12 = DSM 16493 5714738 YP_001542401.1 CDS Dshi_4210 NC_009959.1 58042 58482 R PFAM: PilT protein domain protein; KEGG: gvi:glr1678 plasmid stabilization protein StbB homolog; twitching motility protein PilT complement(58042..58482) Dinoroseobacter shibae DFL 12 = DSM 16493 5714739 YP_001542402.1 CDS Dshi_4211 NC_009959.1 58479 58724 R KEGG: gvi:gsr1677 hypothetical protein; hypothetical protein complement(58479..58724) Dinoroseobacter shibae DFL 12 = DSM 16493 5714740 YP_001542403.1 CDS Dshi_4212 NC_009959.1 58898 60001 R PFAM: ParB domain protein nuclease; KEGG: rsq:Rsph17025_3691 hypothetical protein; nuclease complement(58898..60001) Dinoroseobacter shibae DFL 12 = DSM 16493 5714741 YP_001542404.1 CDS Dshi_4213 NC_009959.1 59994 61394 R PFAM: Cobyrinic acid ac-diamide synthase; KEGG: sit:TM1040_3406 cobyrinic acid a,c-diamide synthase; cobyrinic acid ac-diamide synthase complement(59994..61394) Dinoroseobacter shibae DFL 12 = DSM 16493 5714742 YP_001542405.1 CDS Dshi_4214 NC_009959.1 61901 63073 D PFAM: initiator RepB protein; KEGG: rsq:Rsph17025_3693 hypothetical protein; initiator RepB protein 61901..63073 Dinoroseobacter shibae DFL 12 = DSM 16493 5714743 YP_001542406.1 CDS Dshi_4215 NC_009959.1 63125 63772 D KEGG: sru:SRU_1591 hypothetical protein; hypothetical protein 63125..63772 Dinoroseobacter shibae DFL 12 = DSM 16493 5714744 YP_001542407.1 CDS Dshi_4216 NC_009959.1 63812 65134 D PFAM: ABC-1 domain protein; KEGG: rpb:RPB_4322 ABC-1; hypothetical protein 63812..65134 Dinoroseobacter shibae DFL 12 = DSM 16493 5714745 YP_001542408.1 CDS Dshi_4217 NC_009959.1 65138 66145 R PFAM: regulatory protein LacI; periplasmic binding protein/LacI transcriptional regulator; KEGG: acr:Acry_2432 alanine racemase; LacI family transcription regulator complement(65138..66145) Dinoroseobacter shibae DFL 12 = DSM 16493 5714746 YP_001542409.1 CDS Dshi_4218 NC_009959.1 66272 67225 D PFAM: conserved hypothetical protein; KEGG: bbr:BB4749 hypothetical protein; hypothetical protein 66272..67225 Dinoroseobacter shibae DFL 12 = DSM 16493 5714747 YP_001542410.1 CDS Dshi_4219 NC_009959.1 67292 67747 D hypothetical protein 67292..67747 Dinoroseobacter shibae DFL 12 = DSM 16493 5714748 YP_001542411.1 CDS Dshi_4220 NC_009959.1 67749 69233 D PFAM: protein of unknown function DUF112 transmembrane; KEGG: jan:Jann_1159 protein of unknown function DUF112, transmembrane; hypothetical protein 67749..69233 Dinoroseobacter shibae DFL 12 = DSM 16493 5714749 YP_001542412.1 CDS Dshi_4221 NC_009959.1 69235 70116 D PFAM: 6-phosphogluconate dehydrogenase NAD-binding; KEGG: rde:RD1_3786 3-hydroxyisobutyrate dehydrogenase; 2-hydroxy-3-oxopropionate reductase 69235..70116 Dinoroseobacter shibae DFL 12 = DSM 16493 5714750 YP_001542413.1 CDS Dshi_4222 NC_009959.1 70201 70617 D KEGG: rde:RD1_0908 hypothetical protein; hypothetical protein 70201..70617 Dinoroseobacter shibae DFL 12 = DSM 16493 5714751 YP_001542414.1 CDS Dshi_4223 NC_009959.1 70690 71160 D PFAM: Ferritin Dps family protein; KEGG: rde:RD1_0909 hypothetical protein; Ferritin Dps family protein 70690..71160 Dinoroseobacter shibae DFL 12 = DSM 16493 5714734 YP_001542415.1 CDS Dshi_4224 NC_009959.1 71161 71427 R KEGG: rde:RD1_0910 hypothetical protein; hypothetical protein complement(71161..71427) Dinoroseobacter shibae DFL 12 = DSM 16493 5714735 YP_001542416.1 CDS Dshi_4225 NC_009959.1 71437 71592 R hypothetical protein complement(71437..71592) Dinoroseobacter shibae DFL 12 = DSM 16493 5714736 YP_001542417.2 CDS Dshi_4226 NC_009959.1 71714 72295 D KEGG: sil:SPO1522 hypothetical protein; hypothetical protein 71714..72295 Dinoroseobacter shibae DFL 12 = DSM 16493 5714737 Dshi_6001 tRNA Dshi_6001 NC_009952.1 77867 77943 R tRNA-Pro complement(77867..77943) Dinoroseobacter shibae DFL 12 = DSM 16493 5711701 Dshi_6002 tRNA Dshi_6002 NC_009952.1 223158 223233 D tRNA-Trp 223158..223233 Dinoroseobacter shibae DFL 12 = DSM 16493 5712150 Dshi_6003 tRNA Dshi_6003 NC_009952.1 319728 319803 D tRNA-Thr 319728..319803 Dinoroseobacter shibae DFL 12 = DSM 16493 5711581 Dshi_6004 tRNA Dshi_6004 NC_009952.1 320770 320846 R tRNA-Arg complement(320770..320846) Dinoroseobacter shibae DFL 12 = DSM 16493 5711585 Dshi_6005 tRNA Dshi_6005 NC_009952.1 369290 369364 D tRNA-Val 369290..369364 Dinoroseobacter shibae DFL 12 = DSM 16493 5711296 Dshi_6007 tRNA Dshi_6007 NC_009952.1 375220 375296 D tRNA-Ile 375220..375296 Dinoroseobacter shibae DFL 12 = DSM 16493 5711302 Dshi_6008 tRNA Dshi_6008 NC_009952.1 375472 375547 D tRNA-Ala 375472..375547 Dinoroseobacter shibae DFL 12 = DSM 16493 5711303 Dshi_6011 tRNA Dshi_6011 NC_009952.1 379296 379372 D tRNA-Met 379296..379372 Dinoroseobacter shibae DFL 12 = DSM 16493 5711306 Dshi_6012 tRNA Dshi_6012 NC_009952.1 573863 573937 R tRNA-Gln complement(573863..573937) Dinoroseobacter shibae DFL 12 = DSM 16493 5712036 Dshi_6014 tRNA Dshi_6014 NC_009952.1 618985 619061 D tRNA-Ile 618985..619061 Dinoroseobacter shibae DFL 12 = DSM 16493 5712080 Dshi_6015 tRNA Dshi_6015 NC_009952.1 619237 619312 D tRNA-Ala 619237..619312 Dinoroseobacter shibae DFL 12 = DSM 16493 5712081 Dshi_6018 tRNA Dshi_6018 NC_009952.1 785598 785674 D tRNA-His 785598..785674 Dinoroseobacter shibae DFL 12 = DSM 16493 5711215 Dshi_6019 tRNA Dshi_6019 NC_009952.1 862900 862973 D tRNA-Gly 862900..862973 Dinoroseobacter shibae DFL 12 = DSM 16493 5710541 Dshi_6020 tRNA Dshi_6020 NC_009952.1 949041 949130 D tRNA-Ser 949041..949130 Dinoroseobacter shibae DFL 12 = DSM 16493 5710615 Dshi_6021 tRNA Dshi_6021 NC_009952.1 998366 998440 R tRNA-Thr complement(998366..998440) Dinoroseobacter shibae DFL 12 = DSM 16493 5710490 Dshi_6022 tRNA Dshi_6022 NC_009952.1 1005076 1005150 D tRNA-Phe 1005076..1005150 Dinoroseobacter shibae DFL 12 = DSM 16493 5710499 Dshi_6023 tRNA Dshi_6023 NC_009952.1 1021732 1021821 R tRNA-Ser complement(1021732..1021821) Dinoroseobacter shibae DFL 12 = DSM 16493 5710508 Dshi_6024 tRNA Dshi_6024 NC_009952.1 1242383 1242468 D tRNA-Leu 1242383..1242468 Dinoroseobacter shibae DFL 12 = DSM 16493 5711970 Dshi_6025 tRNA Dshi_6025 NC_009952.1 1473081 1473156 D tRNA-Thr 1473081..1473156 Dinoroseobacter shibae DFL 12 = DSM 16493 5712597 Dshi_6026 tRNA Dshi_6026 NC_009952.1 1516436 1516524 R tRNA-Ser complement(1516436..1516524) Dinoroseobacter shibae DFL 12 = DSM 16493 5712636 Dshi_6027 tRNA Dshi_6027 NC_009952.1 1538245 1538331 D tRNA-Leu 1538245..1538331 Dinoroseobacter shibae DFL 12 = DSM 16493 5712661 Dshi_6028 tRNA Dshi_6028 NC_009952.1 1688687 1688763 R tRNA-Arg complement(1688687..1688763) Dinoroseobacter shibae DFL 12 = DSM 16493 5712767 Dshi_6029 tRNA Dshi_6029 NC_009952.1 1750240 1750313 D tRNA-Gly 1750240..1750313 Dinoroseobacter shibae DFL 12 = DSM 16493 5713246 Dshi_6030 tRNA Dshi_6030 NC_009952.1 1789492 1789568 D tRNA-Pro 1789492..1789568 Dinoroseobacter shibae DFL 12 = DSM 16493 5713289 Dshi_6031 tRNA Dshi_6031 NC_009952.1 1843959 1844033 R tRNA-Val complement(1843959..1844033) Dinoroseobacter shibae DFL 12 = DSM 16493 5713343 Dshi_6032 tRNA Dshi_6032 NC_009952.1 1859262 1859338 R tRNA-Pro complement(1859262..1859338) Dinoroseobacter shibae DFL 12 = DSM 16493 5713355 Dshi_6033 tRNA Dshi_6033 NC_009952.1 1891102 1891178 R tRNA-Asp complement(1891102..1891178) Dinoroseobacter shibae DFL 12 = DSM 16493 5712802 Dshi_6034 tRNA Dshi_6034 NC_009952.1 1891285 1891361 R tRNA-Asp complement(1891285..1891361) Dinoroseobacter shibae DFL 12 = DSM 16493 5712803 Dshi_6035 tRNA Dshi_6035 NC_009952.1 1897975 1898050 R tRNA-Val complement(1897975..1898050) Dinoroseobacter shibae DFL 12 = DSM 16493 5712810 Dshi_6036 tRNA Dshi_6036 NC_009952.1 1916616 1916700 R tRNA-Leu complement(1916616..1916700) Dinoroseobacter shibae DFL 12 = DSM 16493 5712827 Dshi_6037 tRNA Dshi_6037 NC_009952.1 1967401 1967477 D tRNA-Met 1967401..1967477 Dinoroseobacter shibae DFL 12 = DSM 16493 5712882 Dshi_6038 tRNA Dshi_6038 NC_009952.1 2004932 2005006 R tRNA-Asn complement(2004932..2005006) Dinoroseobacter shibae DFL 12 = DSM 16493 5712913 Dshi_6039 tRNA Dshi_6039 NC_009952.1 2104580 2104656 D tRNA-Arg 2104580..2104656 Dinoroseobacter shibae DFL 12 = DSM 16493 5712984 Dshi_6040 tRNA Dshi_6040 NC_009952.1 2223733 2223806 D tRNA-Cys 2223733..2223806 Dinoroseobacter shibae DFL 12 = DSM 16493 5713095 Dshi_6041 tRNA Dshi_6041 NC_009952.1 2399989 2400063 D tRNA-Glu 2399989..2400063 Dinoroseobacter shibae DFL 12 = DSM 16493 5713929 Dshi_6042 tRNA Dshi_6042 NC_009952.1 2444564 2444653 R tRNA-Ser complement(2444564..2444653) Dinoroseobacter shibae DFL 12 = DSM 16493 5713967 Dshi_6043 tRNA Dshi_6043 NC_009952.1 2515206 2515292 R tRNA-Leu complement(2515206..2515292) Dinoroseobacter shibae DFL 12 = DSM 16493 5714036 Dshi_6044 tRNA Dshi_6044 NC_009952.1 2643515 2643589 D tRNA-Gly 2643515..2643589 Dinoroseobacter shibae DFL 12 = DSM 16493 5713384 Dshi_6045 tRNA Dshi_6045 NC_009952.1 2738539 2738622 R tRNA-Tyr complement(2738539..2738622) Dinoroseobacter shibae DFL 12 = DSM 16493 5713468 Dshi_6046 tRNA Dshi_6046 NC_009952.1 2854072 2854148 R tRNA-Met complement(2854072..2854148) Dinoroseobacter shibae DFL 12 = DSM 16493 5713593 Dshi_6047 tRNA Dshi_6047 NC_009952.1 3153418 3153493 D tRNA-Ala 3153418..3153493 Dinoroseobacter shibae DFL 12 = DSM 16493 5710839 Dshi_6048 tRNA Dshi_6048 NC_009952.1 3396915 3396990 R tRNA-Lys complement(3396915..3396990) Dinoroseobacter shibae DFL 12 = DSM 16493 5712284 Dshi_6049 tRNA Dshi_6049 NC_009952.1 3495494 3495570 D tRNA-Arg 3495494..3495570 Dinoroseobacter shibae DFL 12 = DSM 16493 5712388 Dshi_6050 tRNA Dshi_6050 NC_009952.1 3779657 3779743 R tRNA-Leu complement(3779657..3779743) Dinoroseobacter shibae DFL 12 = DSM 16493 5713821 Dshi_6006 rRNA Dshi_6006 NC_009952.1 373482 374943 D 16S ribosomal RNA 373482..374943 Dinoroseobacter shibae DFL 12 = DSM 16493 5711301 Dshi_6009 rRNA Dshi_6009 NC_009952.1 376011 378902 D 23S ribosomal RNA join(376011..376174,376255..378902) Dinoroseobacter shibae DFL 12 = DSM 16493 5711304 Dshi_6010 rRNA Dshi_6010 NC_009952.1 379112 379229 D 5S ribosomal RNA 379112..379229 Dinoroseobacter shibae DFL 12 = DSM 16493 5711305 Dshi_6013 rRNA Dshi_6013 NC_009952.1 617247 618708 D 16S ribosomal RNA 617247..618708 Dinoroseobacter shibae DFL 12 = DSM 16493 5712079 Dshi_6016 rRNA Dshi_6016 NC_009952.1 619776 622667 D 23S ribosomal RNA join(619776..619939,620020..622667) Dinoroseobacter shibae DFL 12 = DSM 16493 5712082 Dshi_6017 rRNA Dshi_6017 NC_009952.1 622877 622994 D 5S ribosomal RNA 622877..622994 Dinoroseobacter shibae DFL 12 = DSM 16493 5712083