-- dump date 20140619_065658 -- class Genbank::CDS -- table cds -- table main -- field 1 id -- field 2 GI -- field 3 GeneID -- field 4 chrom_position -- field 5 chromosome -- field 6 codon_start -- field 7 contig -- field 8 description -- field 9 end_pos -- field 10 gene -- field 11 gene_id -- field 12 name -- field 13 organism -- field 14 product -- field 15 protein_id -- field 16 start_pos -- field 17 strand -- field 18 taxid -- field 19 type -- header -- id GI GeneID chrom_position chromosome codon_start contig description end_pos gene gene_id name organism product protein_id start_pos strand taxid type YP_001531351.1 159042557 5713708 128..1567 1 NC_009952.1 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 1567 gltD 5713708 gltD Dinoroseobacter shibae DFL 12 = DSM 16493 putative oxidoreductase YP_001531351.1 128 D 398580 CDS YP_001531352.1 159042558 5711754 1782..6320 1 NC_009952.1 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 6320 gltB 5711754 gltB Dinoroseobacter shibae DFL 12 = DSM 16493 glutamate synthase YP_001531352.1 1782 D 398580 CDS YP_001531354.1 159042560 5711756 complement(7257..8114) 1 NC_009952.1 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 8114 5711756 Dshi_0004 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531354.1 7257 R 398580 CDS YP_001531355.1 159042561 5711757 8220..8924 1 NC_009952.1 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 8924 5711757 Dshi_0005 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531355.1 8220 D 398580 CDS YP_001531356.1 159042562 5711758 9028..9855 1 NC_009952.1 catalyzes the formation of N-succinyl-2-amino-6-ketopimelate from succinyl-CoA and tetrahydrodipicolinate in the lysine biosynthetic pathway; 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase 9855 dapD 5711758 dapD Dinoroseobacter shibae DFL 12 = DSM 16493 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase YP_001531356.1 9028 D 398580 CDS YP_001531358.1 159042564 5711760 10683..11255 1 NC_009952.1 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 11255 5711760 Dshi_0008 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531358.1 10683 D 398580 CDS YP_001531359.1 159042565 5711761 complement(11747..11953) 1 NC_009952.1 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 11953 csp2 5711761 csp2 Dinoroseobacter shibae DFL 12 = DSM 16493 cold-shock DNA-binding domain-containing protein YP_001531359.1 11747 R 398580 CDS YP_001531360.1 159042566 5711588 complement(12121..12642) 1 NC_009952.1 PFAM: protein of unknown function DUF305 KEGG: psa:PST_3374 hypothetical protein, conserved in bacteria; hypothetical protein 12642 5711588 Dshi_0010 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531360.1 12121 R 398580 CDS YP_001531361.1 159042567 5711589 12777..13124 1 NC_009952.1 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 13124 5711589 Dshi_0011 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531361.1 12777 D 398580 CDS YP_001531362.1 159042568 5711590 13129..14268 1 NC_009952.1 dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase (DapE), catalyzes the hydrolysis of N-succinyl-L,Ldiaminopimelate L,L-SDAP to L,L-diaminopimelate and succinate. It is a metalloprotease containing dinuclear active sites. Its structure is similar to the carboxypeptidase G2 from Pseudomonas sp. strain RS-16 and the aminopeptidase from Aeromonas proteolytica.; succinyl-diaminopimelate desuccinylase 14268 dapE1 5711590 dapE1 Dinoroseobacter shibae DFL 12 = DSM 16493 succinyl-diaminopimelate desuccinylase YP_001531362.1 13129 D 398580 CDS YP_001531363.1 159042569 5711591 14265..14693 1 NC_009952.1 PFAM: GCN5-related N-acetyltransferase KEGG: rsh:Rsph17029_2788 GCN5-related N-acetyltransferase; N-acetyltransferase GCN5 14693 elaA 5711591 elaA Dinoroseobacter shibae DFL 12 = DSM 16493 N-acetyltransferase GCN5 YP_001531363.1 14265 D 398580 CDS YP_001531364.1 159042570 5711592 14693..15271 1 NC_009952.1 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 15271 5711592 Dshi_0014 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531364.1 14693 D 398580 CDS YP_001531365.1 159042571 5711593 15472..17727 1 NC_009952.1 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 17727 rnr 5711593 rnr Dinoroseobacter shibae DFL 12 = DSM 16493 ribonuclease R YP_001531365.1 15472 D 398580 CDS YP_001531366.1 159042572 5711594 18179..19426 1 NC_009952.1 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 19426 mltB2 5711594 mltB2 Dinoroseobacter shibae DFL 12 = DSM 16493 lytic murein transglycosylase YP_001531366.1 18179 D 398580 CDS YP_001531367.1 159042573 5711595 complement(19516..20166) 1 NC_009952.1 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 20166 5711595 Dshi_0017 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531367.1 19516 R 398580 CDS YP_001531368.1 159042574 5711596 complement(20326..22629) 1 NC_009952.1 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 22629 5711596 Dshi_0018 Dinoroseobacter shibae DFL 12 = DSM 16493 multicopper oxidase YP_001531368.1 20326 R 398580 CDS YP_001531369.1 159042575 5711597 22866..24683 1 NC_009952.1 TIGRFAM: small GTP-binding protein; GTP-binding protein TypA PFAM: elongation factor G domain protein; protein synthesis factor GTP-binding; elongation factor Tu domain 2 protein KEGG: 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 24683 5711597 Dshi_0019 Dinoroseobacter shibae DFL 12 = DSM 16493 GTP-binding protein TypA YP_001531369.1 22866 D 398580 CDS YP_001531370.1 159042576 5711598 complement(25297..26019) 1 NC_009952.1 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 26019 5711598 Dshi_0020 Dinoroseobacter shibae DFL 12 = DSM 16493 putative transcriptional regulator YP_001531370.1 25297 R 398580 CDS YP_001531371.1 159042577 5711643 complement(25973..26377) 1 NC_009952.1 KEGG: rsp:RSP_6002 hypothetical protein, one single transmembrane domain; hypothetical protein 26377 5711643 Dshi_0021 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531371.1 25973 R 398580 CDS YP_001531372.1 159042578 5711644 26400..26954 1 NC_009952.1 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 26954 5711644 Dshi_0022 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531372.1 26400 D 398580 CDS YP_001531373.1 159042579 5711645 26998..27618 1 NC_009952.1 RNH2; RNase HII; binds manganese; endonuclease which specifically degrades the RNA of RNA-DNA hybrids; ribonuclease HII 27618 rnhB 5711645 rnhB Dinoroseobacter shibae DFL 12 = DSM 16493 ribonuclease HII YP_001531373.1 26998 D 398580 CDS YP_001531374.1 159042580 5711646 27713..28819 1 NC_009952.1 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 28819 dam 5711646 dam Dinoroseobacter shibae DFL 12 = DSM 16493 adenine-specific methyltransferase YP_001531374.1 27713 D 398580 CDS YP_001531375.1 159042581 5711647 29143..29814 1 NC_009952.1 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 29814 chrR2 5711647 chrR2 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional activator anti-ECFsigma factor YP_001531375.1 29143 D 398580 CDS YP_001531376.1 159042582 5711648 29888..30529 1 NC_009952.1 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 30529 5711648 Dshi_0026 Dinoroseobacter shibae DFL 12 = DSM 16493 NAD-dependent epimerase/dehydratase YP_001531376.1 29888 D 398580 CDS YP_001531377.1 159042583 5711649 complement(30653..31807) 1 NC_009952.1 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 31807 alkB1 5711649 alkB1 Dinoroseobacter shibae DFL 12 = DSM 16493 alkane 1-monooxygenase YP_001531377.1 30653 R 398580 CDS YP_001531378.1 159042584 5711650 complement(31815..32909) 1 NC_009952.1 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 32909 mutY 5711650 mutY Dinoroseobacter shibae DFL 12 = DSM 16493 A/G-specific adenine glycosylase YP_001531378.1 31815 R 398580 CDS YP_001531379.1 159042585 5711651 32995..33507 1 NC_009952.1 PFAM: protein of unknown function DUF1159 KEGG: sit:TM1040_2644 protein of unknown function DUF1159; hypothetical protein 33507 5711651 Dshi_0029 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531379.1 32995 D 398580 CDS YP_001531380.1 159042586 5711652 33519..34190 1 NC_009952.1 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 34190 dsbA1 5711652 dsbA1 Dinoroseobacter shibae DFL 12 = DSM 16493 putative thiol-disulfide oxidoreductase D YP_001531380.1 33519 D 398580 CDS YP_001531381.1 159042587 5711653 complement(34226..35239) 1 NC_009952.1 transfers the gamma-phosphate of ATP to the 4' position of a tetraacyldisaccharide 1-phosphate intermediate to form tetraacyldisaccharide 1,4'-bis-phosphate; tetraacyldisaccharide 4'-kinase 35239 lpxK 5711653 lpxK Dinoroseobacter shibae DFL 12 = DSM 16493 tetraacyldisaccharide 4'-kinase YP_001531381.1 34226 R 398580 CDS YP_001531382.1 159042588 5711654 complement(35239..36555) 1 NC_009952.1 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 36555 kdtA 5711654 kdtA Dinoroseobacter shibae DFL 12 = DSM 16493 three-deoxy-D-manno-octulosonic-acid transferase domain-containing protein YP_001531382.1 35239 R 398580 CDS YP_001531383.1 159042589 5711655 complement(36716..36907) 1 NC_009952.1 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 36907 5711655 Dshi_0033 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531383.1 36716 R 398580 CDS YP_001531384.1 159042590 5711656 complement(36904..37551) 1 NC_009952.1 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 37551 5711656 Dshi_0034 Dinoroseobacter shibae DFL 12 = DSM 16493 ATP-dependent protease La YP_001531384.1 36904 R 398580 CDS YP_001531385.1 159042591 5711657 complement(37578..38489) 1 NC_009952.1 PFAM: Thioredoxin domain KEGG: rsp:RSP_1489 protein containing thioredoxin domain, swissprot hit to Thioredoxin (TRX) from Pasteurella multocida; thioredoxin domain-containing protein 38489 trxA2 5711657 trxA2 Dinoroseobacter shibae DFL 12 = DSM 16493 thioredoxin domain-containing protein YP_001531385.1 37578 R 398580 CDS YP_001531386.1 159042592 5711658 complement(38563..39351) 1 NC_009952.1 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 39351 xthA 5711658 xthA Dinoroseobacter shibae DFL 12 = DSM 16493 exodeoxyribonuclease III YP_001531386.1 38563 R 398580 CDS YP_001531387.1 159042593 5711659 39692..40216 1 NC_009952.1 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 40216 5711659 Dshi_0037 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531387.1 39692 D 398580 CDS YP_001531388.1 159042594 5711660 complement(40432..41118) 1 NC_009952.1 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 41118 5711660 Dshi_0038 Dinoroseobacter shibae DFL 12 = DSM 16493 two component transcriptional regulator YP_001531388.1 40432 R 398580 CDS YP_001531389.1 159042595 5711661 41277..42347 1 NC_009952.1 PFAM: GTP cyclohydrolase II KEGG: sil:SPO3427 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II; GTP cyclohydrolase II 42347 ribA 5711661 ribA Dinoroseobacter shibae DFL 12 = DSM 16493 GTP cyclohydrolase II YP_001531389.1 41277 D 398580 CDS YP_001531390.1 159042596 5711662 42375..42662 1 NC_009952.1 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 42662 5711662 Dshi_0040 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531390.1 42375 D 398580 CDS YP_001531391.1 159042597 5711663 42669..43163 1 NC_009952.1 KEGG: rde:RD1_0044 hypothetical protein, no significant swissprot hit, conserved domain found in several roseobacter function unknown; hypothetical protein 43163 5711663 Dshi_0041 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531391.1 42669 D 398580 CDS YP_001531392.1 159042598 5711664 complement(43160..43816) 1 NC_009952.1 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 43816 5711664 Dshi_0042 Dinoroseobacter shibae DFL 12 = DSM 16493 alanine racemase domain-containing protein YP_001531392.1 43160 R 398580 CDS YP_001531393.1 159042599 5711665 complement(43903..44862) 1 NC_009952.1 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 44862 5711665 Dshi_0043 Dinoroseobacter shibae DFL 12 = DSM 16493 porin YP_001531393.1 43903 R 398580 CDS YP_001531394.1 159042600 5711666 45163..45633 1 NC_009952.1 KEGG: rsq:Rsph17025_3134 hypothetical protein; hypothetical protein 45633 5711666 Dshi_0044 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531394.1 45163 D 398580 CDS YP_001531395.1 159042601 5711667 complement(45640..46014) 1 NC_009952.1 bad BLAST hits to hypothetical proteins, no significant swissprot hit, no domains detected by TIGRfam (no UspA domain); hypothetical protein 46014 5711667 Dshi_0045 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531395.1 45640 R 398580 CDS YP_001531396.1 159042602 5711668 46315..46704 1 NC_009952.1 no Interpro hits reported, unsure, bad GC frame plot, bad ref ZP hits to hypothetical protein ROS217_08770 from Roseovarius sp. 217; hypothetical protein 46704 5711668 Dshi_0046 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531396.1 46315 D 398580 CDS YP_001531397.1 159042603 5711669 complement(46984..47406) 1 NC_009952.1 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 47406 5711669 Dshi_0047 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531397.1 46984 R 398580 CDS YP_001531398.1 159042604 5711670 complement(47483..48445) 1 NC_009952.1 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 48445 5711670 Dshi_0048 Dinoroseobacter shibae DFL 12 = DSM 16493 putative transposase YP_001531398.1 47483 R 398580 CDS YP_001531399.1 159042605 5711671 48547..48753 1 NC_009952.1 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 48753 5711671 Dshi_0049 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531399.1 48547 D 398580 CDS YP_001531400.1 159042606 5711672 complement(48750..49232) 1 NC_009952.1 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 49232 5711672 Dshi_0050 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531400.1 48750 R 398580 CDS YP_001531401.1 159042607 5711673 complement(49229..49645) 1 NC_009952.1 no significant BLAST hits, short signal peptide and two transmembrane regions, bad GC frame plot; hypothetical protein 49645 5711673 Dshi_0051 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531401.1 49229 R 398580 CDS YP_001531402.1 159042608 5711674 complement(49656..49868) 1 NC_009952.1 no hits reported for InterPro Scan, BLAST hits similar to several hypothetical proteins in Roseobacter strains, bad GC frame plot; hypothetical protein 49868 5711674 Dshi_0052 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531402.1 49656 R 398580 CDS YP_001531403.1 159042609 5711675 49943..51163 1 NC_009952.1 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 51163 5711675 Dshi_0053 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531403.1 49943 D 398580 CDS YP_001531404.1 159042610 5711676 complement(51142..51732) 1 NC_009952.1 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 51732 gst2 5711676 gst2 Dinoroseobacter shibae DFL 12 = DSM 16493 glutathione S-transferase-like protein YP_001531404.1 51142 R 398580 CDS YP_001531405.1 159042611 5711677 complement(51747..52772) 1 NC_009952.1 KEGG: sit:TM1040_0043 DNA polymerase III, delta subunit; DNA polymerase III subunit delta 52772 holA 5711677 holA Dinoroseobacter shibae DFL 12 = DSM 16493 DNA polymerase III subunit delta YP_001531405.1 51747 R 398580 CDS YP_001531406.1 159042612 5711678 complement(52769..53263) 1 NC_009952.1 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 53263 5711678 Dshi_0056 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531406.1 52769 R 398580 CDS YP_001531407.1 159042613 5711679 complement(53250..55859) 1 NC_009952.1 leucine--tRNA ligase; LeuRS; class-I aminoacyl-tRNA synthetase; charges leucine by linking carboxyl group to alpha-phosphate of ATP and then transfers aminoacyl-adenylate to its tRNA; due to the large number of codons that tRNA(Leu) recognizes, the leucyl-tRNA synthetase does not recognize the anticodon loop of the tRNA, but instead recognition is dependent on a conserved discriminator base A37 and a long arm; an editing domain hydrolyzes misformed products; in Methanothermobacter thermautotrophicus this enzyme associates with prolyl-tRNA synthetase; leucyl-tRNA synthetase 55859 leuS 5711679 leuS Dinoroseobacter shibae DFL 12 = DSM 16493 leucyl-tRNA synthetase YP_001531407.1 53250 R 398580 CDS YP_001531408.1 159042614 5711680 complement(55941..56645) 1 NC_009952.1 PFAM: outer membrane lipoprotein carrier protein LolA KEGG: rsq:Rsph17025_2901 outer membrane lipoprotein carrier protein LolA; outer membrane lipoprotein carrier protein 56645 lolA 5711680 lolA Dinoroseobacter shibae DFL 12 = DSM 16493 outer membrane lipoprotein carrier protein YP_001531408.1 55941 R 398580 CDS YP_001531409.1 159042615 5711681 complement(56686..59673) 1 NC_009952.1 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 59673 ftsK 5711681 ftsK Dinoroseobacter shibae DFL 12 = DSM 16493 DNA translocase YP_001531409.1 56686 R 398580 CDS YP_001531410.1 159042616 5711682 complement(59687..60868) 1 NC_009952.1 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 60868 5711682 Dshi_0060 Dinoroseobacter shibae DFL 12 = DSM 16493 class I/II aminotransferase YP_001531410.1 59687 R 398580 CDS YP_001531411.1 159042617 5711683 complement(60992..62323) 1 NC_009952.1 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 62323 5711683 Dshi_0061 Dinoroseobacter shibae DFL 12 = DSM 16493 amidase YP_001531411.1 60992 R 398580 CDS YP_001531412.1 159042618 5711684 62385..63650 1 NC_009952.1 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 63650 ubiH 5711684 ubiH Dinoroseobacter shibae DFL 12 = DSM 16493 2-octaprenyl-6-methoxyphenol hydroxylase YP_001531412.1 62385 D 398580 CDS YP_001531413.1 159042619 5711685 complement(63773..64567) 1 NC_009952.1 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 64567 suhB2 5711685 suhB2 Dinoroseobacter shibae DFL 12 = DSM 16493 inositol-phosphate phosphatase YP_001531413.1 63773 R 398580 CDS YP_001531414.1 159042620 5711686 complement(64554..65900) 1 NC_009952.1 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 65900 pmbA 5711686 pmbA Dinoroseobacter shibae DFL 12 = DSM 16493 peptidase U62 modulator of DNA gyrase YP_001531414.1 64554 R 398580 CDS YP_001531415.1 159042621 5711687 complement(65978..67468) 1 NC_009952.1 KEGG: sil:SPO3441 hypothetical protein, no swissprot hit, ref hits to several hypothetical proteins in roseobacter strains; hypothetical protein 67468 5711687 Dshi_0065 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531415.1 65978 R 398580 CDS YP_001531416.1 159042622 5711688 67584..68342 1 NC_009952.1 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 68342 5711688 Dshi_0066 Dinoroseobacter shibae DFL 12 = DSM 16493 dehydrogenase/reductase YP_001531416.1 67584 D 398580 CDS YP_001531417.1 159042623 5711689 68339..69085 1 NC_009952.1 PFAM: Enoyl-CoA hydratase/isomerase KEGG: rsh:Rsph17029_2572 enoyl-CoA hydratase/isomerase; COG1024 Enoyl-CoA hydratase/carnithine racemase; enoyl-CoA hydratase/isomerase 69085 caiD 5711689 caiD Dinoroseobacter shibae DFL 12 = DSM 16493 enoyl-CoA hydratase/isomerase YP_001531417.1 68339 D 398580 CDS YP_001531418.1 159042624 5711690 complement(69090..69674) 1 NC_009952.1 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 69674 5711690 Dshi_0068 Dinoroseobacter shibae DFL 12 = DSM 16493 lipoprotein YP_001531418.1 69090 R 398580 CDS YP_001531419.1 159042625 5711691 complement(69751..70632) 1 NC_009952.1 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 70632 5711691 Dshi_0069 Dinoroseobacter shibae DFL 12 = DSM 16493 auxin efflux carrier YP_001531419.1 69751 R 398580 CDS YP_001531420.1 159042626 5711692 70719..71045 1 NC_009952.1 TIGRFAM: hemimethylated DNA binding protein PFAM: Hemimethylated DNA-binding region KEGG: sil:SPO3412 hypothetical protein, no swissprot; hemimethylated DNA-binding protein 71045 yccV 5711692 yccV Dinoroseobacter shibae DFL 12 = DSM 16493 hemimethylated DNA-binding protein YP_001531420.1 70719 D 398580 CDS YP_001531421.1 159042627 5711693 complement(71093..72676) 1 NC_009952.1 PFAM: gamma-glutamyltranspeptidase KEGG: sit:TM1040_0064 gamma-glutamyltransferase, good swissprot hit to Gamma-glutamyltranspeptidase precursor from Bacillus subtilis; gamma-glutamyltransferase 72676 ggt1 5711693 ggt1 Dinoroseobacter shibae DFL 12 = DSM 16493 gamma-glutamyltransferase YP_001531421.1 71093 R 398580 CDS YP_001531422.1 159042628 5711694 complement(72738..73247) 1 NC_009952.1 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 73247 rsbW 5711694 rsbW Dinoroseobacter shibae DFL 12 = DSM 16493 serine-protein kinase YP_001531422.1 72738 R 398580 CDS YP_001531423.1 159042629 5711695 complement(73262..73594) 1 NC_009952.1 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 73594 5711695 Dshi_0073 Dinoroseobacter shibae DFL 12 = DSM 16493 anti-sigma-factor antagonist YP_001531423.1 73262 R 398580 CDS YP_001531424.1 159042630 5711696 73694..74872 1 NC_009952.1 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 74872 thlA 5711696 thlA Dinoroseobacter shibae DFL 12 = DSM 16493 acetyl-CoA acetyltransferase YP_001531424.1 73694 D 398580 CDS YP_001531425.1 159042631 5711697 complement(75136..75378) 1 NC_009952.1 KEGG: rde:RD1_0777 hypothetical protein; bad BLAST hits, no swissprot: Calcium-binding EF-hand domain; hypothetical protein 75378 5711697 Dshi_0075 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531425.1 75136 R 398580 CDS YP_001531426.1 159042632 5711698 75771..76007 1 NC_009952.1 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 76007 5711698 Dshi_0076 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531426.1 75771 D 398580 CDS YP_001531427.1 159042633 5711699 76020..76910 1 NC_009952.1 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 76910 5711699 Dshi_0077 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531427.1 76020 D 398580 CDS YP_001531428.1 159042634 5711700 76953..77537 1 NC_009952.1 no significant BLAST hits, unsure GC frame plot, no InterPro Scan hits detected, but good RBS binding site AGGAT; hypothetical protein 77537 5711700 Dshi_0078 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531428.1 76953 D 398580 CDS YP_001531429.1 159042635 5711702 78091..78972 1 NC_009952.1 PFAM: lipid A biosynthesis acyltransferase KEGG: sil:SPO1058 acyltransferase, HtrB family; lipid A biosynthesis acyltransferase 78972 5711702 Dshi_0079 Dinoroseobacter shibae DFL 12 = DSM 16493 lipid A biosynthesis acyltransferase YP_001531429.1 78091 D 398580 CDS YP_001531430.1 159042636 5711703 complement(78969..79955) 1 NC_009952.1 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 79955 5711703 Dshi_0080 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531430.1 78969 R 398580 CDS YP_001531431.1 159042637 5711704 complement(80080..81186) 1 NC_009952.1 catalyzes the oxidation of 3-isopropylmalate to 3-carboxy-4-methyl-2-oxopentanoate in leucine biosynthesis; 3-isopropylmalate dehydrogenase 81186 imdh 5711704 imdh Dinoroseobacter shibae DFL 12 = DSM 16493 3-isopropylmalate dehydrogenase YP_001531431.1 80080 R 398580 CDS YP_001531432.1 159042638 5711705 complement(81262..82386) 1 NC_009952.1 KEGG: rde:RD1_0227 hypothetical protein, small signalpeptide; hypothetical protein 82386 5711705 Dshi_0082 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531432.1 81262 R 398580 CDS YP_001531433.1 159042639 5711706 complement(82492..83097) 1 NC_009952.1 catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate in leucine biosynthesis; forms a heterodimer of LeuC/D; isopropylmalate isomerase small subunit 83097 leuD 5711706 leuD Dinoroseobacter shibae DFL 12 = DSM 16493 isopropylmalate isomerase small subunit YP_001531433.1 82492 R 398580 CDS YP_001531434.1 159042640 5711707 complement(83135..83662) 1 NC_009952.1 KEGG: bja:blr2987 hypothetical protein, uncharacterized conserved protein function unknown, transmembrane regions, signalpeptide; hypothetical protein 83662 5711707 Dshi_0084 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531434.1 83135 R 398580 CDS YP_001531435.1 159042641 5711708 complement(83697..85100) 1 NC_009952.1 dehydratase component, catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; isopropylmalate isomerase large subunit 85100 ipmi1 5711708 ipmi1 Dinoroseobacter shibae DFL 12 = DSM 16493 isopropylmalate isomerase large subunit YP_001531435.1 83697 R 398580 CDS YP_001531436.1 159042642 5711709 85412..86014 1 NC_009952.1 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 86014 5711709 Dshi_0086 Dinoroseobacter shibae DFL 12 = DSM 16493 SOUL heme-binding protein YP_001531436.1 85412 D 398580 CDS YP_001531437.1 159042643 5711710 86213..86545 1 NC_009952.1 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 86545 5711710 Dshi_0087 Dinoroseobacter shibae DFL 12 = DSM 16493 iojap family protein YP_001531437.1 86213 D 398580 CDS YP_001531438.1 159042644 5711711 86564..87034 1 NC_009952.1 SPOUT methyltransferase family protein; crystal structure shows homodimer; in Escherichia coli this protein methylates pseudouridine at position 1915 of the 23S ribosomal RNA; rRNA large subunit methyltransferase 87034 5711711 Dshi_0088 Dinoroseobacter shibae DFL 12 = DSM 16493 rRNA large subunit methyltransferase YP_001531438.1 86564 D 398580 CDS YP_001531439.1 159042645 5711712 87158..88675 1 NC_009952.1 catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate; phosphoglyceromutase 88675 ipgm 5711712 ipgm Dinoroseobacter shibae DFL 12 = DSM 16493 phosphoglyceromutase YP_001531439.1 87158 D 398580 CDS YP_001531440.1 159042646 5711713 88672..89775 1 NC_009952.1 PFAM: peptidase M23B KEGG: rsh:Rsph17029_2592 peptidase M23B; peptidase M23B 89775 5711713 Dshi_0090 Dinoroseobacter shibae DFL 12 = DSM 16493 peptidase M23B YP_001531440.1 88672 D 398580 CDS YP_001531441.1 159042647 5711714 89783..91120 1 NC_009952.1 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 91120 prc 5711714 prc Dinoroseobacter shibae DFL 12 = DSM 16493 carboxyl-terminal protease YP_001531441.1 89783 D 398580 CDS YP_001531442.1 159042648 5711715 91122..91604 1 NC_009952.1 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 91604 5711715 Dshi_0092 Dinoroseobacter shibae DFL 12 = DSM 16493 NUDIX hydrolase YP_001531442.1 91122 D 398580 CDS YP_001531443.1 159042649 5711716 complement(91896..92264) 1 NC_009952.1 no significant BLAST hit, small signalpeptide, bad GC frame plot, Dshi_0100 putative transposase; hypothetical protein 92264 5711716 Dshi_0093 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531443.1 91896 R 398580 CDS YP_001531444.1 159042650 5711717 complement(92411..93343) 1 NC_009952.1 KEGG: rde:RD1_0345 hypothetical protein, domain of protease I prophage; no swissprot; hypothetical protein 93343 5711717 Dshi_0094 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531444.1 92411 R 398580 CDS YP_001531445.1 159042651 5711718 complement(93348..94247) 1 NC_009952.1 KEGG: rde:RD1_0344 hypothetical protein, no swissprot, no IPR Scan result, COG4397 Mu-like prophage major head subunit gpT; hypothetical protein 94247 5711718 Dshi_0095 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531445.1 93348 R 398580 CDS YP_001531446.1 159042652 5711719 complement(94244..94774) 1 NC_009952.1 unsure GC frame plot, no significant BLAST hits, no IPR Scan results; hypothetical protein 94774 5711719 Dshi_0096 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531446.1 94244 R 398580 CDS YP_001531447.1 159042653 5711720 complement(95154..95567) 1 NC_009952.1 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 95567 5711720 Dshi_0097 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531447.1 95154 R 398580 CDS YP_001531448.1 159042654 5711721 complement(95564..96019) 1 NC_009952.1 no significant BLAST hit, unsure GC frame plot, no IPR scan result; hypothetical protein 96019 5711721 Dshi_0098 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531448.1 95564 R 398580 CDS YP_001531449.1 159042655 5711722 complement(96161..96931) 1 NC_009952.1 KEGG: ecs:ECs4946 putative DNA transposition protein, bad BLAST hits, AAA ATPase domain (COG2842 Uncharacterized ATPase, putative transposase ); hypothetical protein 96931 5711722 Dshi_0099 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531449.1 96161 R 398580 CDS YP_001531450.1 159042656 5711723 complement(96999..98882) 1 NC_009952.1 KEGG: rde:RD1_0339 transposase, putative; swissprot hit to Transposase from Enterobacteria phage Mu; pfam02914 Mu_transposase; putative transposase 98882 5711723 Dshi_0100 Dinoroseobacter shibae DFL 12 = DSM 16493 putative transposase YP_001531450.1 96999 R 398580 CDS YP_001531451.1 159042657 5711724 99281..99538 1 NC_009952.1 unsure GC frame plot, no significant BLAST hits, no IPR Scan result; hypothetical protein 99538 5711724 Dshi_0101 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531451.1 99281 D 398580 CDS YP_001531452.1 159042658 5711725 99840..102824 1 NC_009952.1 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 102824 dnaE1 5711725 dnaE1 Dinoroseobacter shibae DFL 12 = DSM 16493 DNA polymerase III subunit alpha YP_001531452.1 99840 D 398580 CDS YP_001531453.1 159042659 5711726 102930..104042 1 NC_009952.1 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 104042 adhI 5711726 adhI Dinoroseobacter shibae DFL 12 = DSM 16493 alcohol dehydrogenase class III/S-(hydroxymethyl)glutathione dehydrogenase YP_001531453.1 102930 D 398580 CDS YP_001531454.1 159042660 5711727 104039..104527 1 NC_009952.1 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 104527 5711727 Dshi_0104 Dinoroseobacter shibae DFL 12 = DSM 16493 N-acetyltransferase GCN5 YP_001531454.1 104039 D 398580 CDS YP_001531455.1 159042661 5711728 104539..105249 1 NC_009952.1 PFAM: protein of unknown function DUF88 KEGG: jan:Jann_0048 protein of unknown function DUF88; no swissprot; hypothetical protein 105249 5711728 Dshi_0105 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531455.1 104539 D 398580 CDS YP_001531456.1 159042662 5711729 complement(105246..105869) 1 NC_009952.1 PFAM: regulatory protein TetR KEGG: rsh:Rsph17029_2507 transcriptional regulator, TetR family; TetR family; transcriptional regulator 105869 5711729 Dshi_0106 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001531456.1 105246 R 398580 CDS YP_001531457.1 159042663 5711730 105989..106960 1 NC_009952.1 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 106960 5711730 Dshi_0107 Dinoroseobacter shibae DFL 12 = DSM 16493 ferritin-like protein YP_001531457.1 105989 D 398580 CDS YP_001531458.1 159042664 5711731 complement(106968..107909) 1 NC_009952.1 KEGG: syw:SYNW1655 hypothetical protein, best ref ZP hit to Methyltransferase type 11 from Methylobacterium sp. 4-46, no IPR scan results; hypothetical protein 107909 5711731 Dshi_0108 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531458.1 106968 R 398580 CDS YP_001531459.1 159042665 5711732 108100..109035 1 NC_009952.1 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 109035 5711732 Dshi_0109 Dinoroseobacter shibae DFL 12 = DSM 16493 auxin efflux carrier YP_001531459.1 108100 D 398580 CDS YP_001531460.1 159042666 5711733 109035..109487 1 NC_009952.1 PFAM: protein of unknown function DUF188 KEGG: rde:RD1_0321 YaiI/YqxD family protein, putative; hypothetical protein 109487 5711733 Dshi_0110 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531460.1 109035 D 398580 CDS YP_001531461.1 159042667 5711734 complement(109578..110813) 1 NC_009952.1 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 110813 5711734 Dshi_0111 Dinoroseobacter shibae DFL 12 = DSM 16493 transmembrane transporter YP_001531461.1 109578 R 398580 CDS YP_001531462.1 159042668 5711735 110834..112003 1 NC_009952.1 PFAM: AFG1-family ATPase KEGG: rde:RD1_0326 ATPase, AFG1 family protein; AFG1 family ATPase 112003 5711735 Dshi_0112 Dinoroseobacter shibae DFL 12 = DSM 16493 AFG1 family ATPase YP_001531462.1 110834 D 398580 CDS YP_001531463.1 159042669 5711736 complement(112059..112541) 1 NC_009952.1 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 112541 ahpC 5711736 ahpC Dinoroseobacter shibae DFL 12 = DSM 16493 redoxin YP_001531463.1 112059 R 398580 CDS YP_001531464.1 159042670 5711737 112628..113833 1 NC_009952.1 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 113833 5711737 Dshi_0114 Dinoroseobacter shibae DFL 12 = DSM 16493 pyridine nucleotide-disulfide oxidoreductase family protein YP_001531464.1 112628 D 398580 CDS YP_001531465.1 159042671 5711738 113830..114387 1 NC_009952.1 TIGRFAM: putative methyltransferase PFAM: conserved hypothetical protein KEGG: sil:SPO3738 methyltransferase, putative; putative methyltransferase 114387 5711738 Dshi_0115 Dinoroseobacter shibae DFL 12 = DSM 16493 putative methyltransferase YP_001531465.1 113830 D 398580 CDS YP_001531466.1 159042672 5711739 complement(114678..115730) 1 NC_009952.1 PFAM: TRAP dicarboxylate transporter- DctP subunit KEGG: pol:Bpro_2121 TRAP dicarboxylate transporter-DctP subunit; TRAP dicarboxylate transporter subunit DctP 115730 5711739 Dshi_0116 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP dicarboxylate transporter subunit DctP YP_001531466.1 114678 R 398580 CDS YP_001531467.1 159042673 5711740 complement(116582..117397) 1 NC_009952.1 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 117397 map 5711740 map Dinoroseobacter shibae DFL 12 = DSM 16493 methionine aminopeptidase YP_001531467.1 116582 R 398580 CDS YP_001531468.1 159042674 5711741 complement(117444..118178) 1 NC_009952.1 Regulatory factor involved in maltose metabolism; sugar fermentation stimulation protein A 118178 sfsA 5711741 sfsA Dinoroseobacter shibae DFL 12 = DSM 16493 sugar fermentation stimulation protein A YP_001531468.1 117444 R 398580 CDS YP_001531469.1 159042675 5711742 118227..118955 1 NC_009952.1 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 118955 mogA 5711742 mogA Dinoroseobacter shibae DFL 12 = DSM 16493 molybdenum cofactor biosynthesis protein MogA YP_001531469.1 118227 D 398580 CDS YP_001531470.1 159042676 5711743 118952..119677 1 NC_009952.1 PFAM: GCN5-related N-acetyltransferase KEGG: rsq:Rsph17025_2991 GCN5-related N-acetyltransferase; N-acetyltransferase GCN5 119677 5711743 Dshi_0120 Dinoroseobacter shibae DFL 12 = DSM 16493 N-acetyltransferase GCN5 YP_001531470.1 118952 D 398580 CDS YP_001531471.1 159042677 5711744 119674..120249 1 NC_009952.1 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 120249 5711744 Dshi_0121 Dinoroseobacter shibae DFL 12 = DSM 16493 peroxidase-like protein YP_001531471.1 119674 D 398580 CDS YP_001531472.1 159042678 5711745 120246..121178 1 NC_009952.1 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 121178 5711745 Dshi_0122 Dinoroseobacter shibae DFL 12 = DSM 16493 OmpA/MotB domain-containing protein YP_001531472.1 120246 D 398580 CDS YP_001531473.1 159042679 5711746 complement(121186..122094) 1 NC_009952.1 PFAM: regulatory protein LysR; LysR substrate-binding KEGG: sit:TM1040_2460 transcriptional regulator, LysR family, good RBS site AGGAT; LysR family; transcriptional regulator 122094 5711746 Dshi_0123 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001531473.1 121186 R 398580 CDS YP_001531474.1 159042680 5711747 complement(122240..122824) 1 NC_009952.1 TIGRFAM: intracellular protease, PfpI family PFAM: ThiJ/PfpI domain protein KEGG: jan:Jann_1867 peptidase C56, PfpI; PfpI family; intracellular protease 122824 5711747 Dshi_0124 Dinoroseobacter shibae DFL 12 = DSM 16493 intracellular protease YP_001531474.1 122240 R 398580 CDS YP_001531475.1 159042681 5711748 complement(122863..124881) 1 NC_009952.1 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 124881 fadH 5711748 fadH Dinoroseobacter shibae DFL 12 = DSM 16493 NADPH:2,4-dienoyl-CoA reductase YP_001531475.1 122863 R 398580 CDS YP_001531476.1 159042682 5711749 complement(124985..125401) 1 NC_009952.1 KEGG: sit:TM1040_2681 hypothetical protein, bad BLAST hits, no IPR Scan results; hypothetical protein 125401 5711749 Dshi_0126 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531476.1 124985 R 398580 CDS YP_001531477.1 159042683 5711750 complement(125398..126168) 1 NC_009952.1 KEGG: sit:TM1040_2680 hypothetical protein; no swissprot, no IPR Scan results; hypothetical protein 126168 5711750 Dshi_0127 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531477.1 125398 R 398580 CDS YP_001531478.1 159042684 5711751 complement(126287..126946) 1 NC_009952.1 KEGG: jan:Jann_0063 hypothetical protein, no significant swissprot, middle Ref hit; hypothetical protein 126946 5711751 Dshi_0128 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531478.1 126287 R 398580 CDS YP_001531479.1 159042685 5711752 complement(126918..128651) 1 NC_009952.1 catalyzes the dehydration of 2,3-dihydroxy-3-methylbutanoate to 3-methyl-2-oxobutanoate in valine and isoleucine biosynthesis; dihydroxy-acid dehydratase 128651 ilvD1 5711752 ilvD1 Dinoroseobacter shibae DFL 12 = DSM 16493 dihydroxy-acid dehydratase YP_001531479.1 126918 R 398580 CDS YP_001531480.1 159042686 5711753 128795..129697 1 NC_009952.1 PFAM: Abortive infection protein KEGG: jan:Jann_0061 abortive infection protein, no significant swissprot; abortive infection protein 129697 abi 5711753 abi Dinoroseobacter shibae DFL 12 = DSM 16493 abortive infection protein YP_001531480.1 128795 D 398580 CDS YP_001531481.1 159042687 5711599 129763..130725 1 NC_009952.1 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 130725 accD 5711599 accD Dinoroseobacter shibae DFL 12 = DSM 16493 acetyl-CoA carboxylase YP_001531481.1 129763 D 398580 CDS YP_001531482.1 159042688 5711600 130730..131998 1 NC_009952.1 TIGRFAM: FolC bifunctional protein PFAM: cytoplasmic peptidoglycan synthetase domain protein; Mur ligase middle domain protein KEGG: sil:SPO3818 FolC bifunctional protein; folylpolyglutamate synthase 131998 folC 5711600 folC Dinoroseobacter shibae DFL 12 = DSM 16493 folylpolyglutamate synthase YP_001531482.1 130730 D 398580 CDS YP_001531483.1 159042689 5711601 132102..133061 1 NC_009952.1 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 133061 5711601 Dshi_0133 Dinoroseobacter shibae DFL 12 = DSM 16493 putative type I secretion target repeat protein YP_001531483.1 132102 D 398580 CDS YP_001531484.1 159042690 5711602 complement(133058..133351) 1 NC_009952.1 PFAM: transcriptional coactivator/pterin dehydratase KEGG: rde:RD1_0944 pterin-4-alpha-carbinolamine dehydratase; pterin-4-alpha-carbinolamine dehydratase 133351 pcd 5711602 pcd Dinoroseobacter shibae DFL 12 = DSM 16493 pterin-4-alpha-carbinolamine dehydratase YP_001531484.1 133058 R 398580 CDS YP_001531485.1 159042691 5711603 complement(133351..134571) 1 NC_009952.1 PFAM: protein of unknown function DUF482 KEGG: sil:SPO3732 hypothetical protein, no swissprot; hypothetical protein 134571 5711603 Dshi_0135 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531485.1 133351 R 398580 CDS YP_001531486.1 159042692 5711604 complement(134622..135395) 1 NC_009952.1 PFAM: glycerophosphoryl diester phosphodiesterase KEGG: jan:Jann_0436 glycerophosphoryl diester phosphodiesterase PRK: ugpQ; cytosolic glycerophosphoryl diester phosphodiesterase 135395 ugpQ 5711604 ugpQ Dinoroseobacter shibae DFL 12 = DSM 16493 cytosolic glycerophosphoryl diester phosphodiesterase YP_001531486.1 134622 R 398580 CDS YP_001531487.1 159042693 5711605 complement(135392..135859) 1 NC_009952.1 PFAM: Endoribonuclease L-PSP COG0251-Putative translation initiation inhibitor, yjgF family; endoribonuclease L-PSP 135859 5711605 Dshi_0137 Dinoroseobacter shibae DFL 12 = DSM 16493 endoribonuclease L-PSP YP_001531487.1 135392 R 398580 CDS YP_001531488.1 159042694 5711606 complement(135882..137189) 1 NC_009952.1 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 137189 hlyD 5711606 hlyD Dinoroseobacter shibae DFL 12 = DSM 16493 type I secretion membrane fusion protein YP_001531488.1 135882 R 398580 CDS YP_001531489.1 159042695 5711607 complement(137186..138925) 1 NC_009952.1 TIGRFAM: type I secretion system ATPase PFAM: ABC transporter related contains:pfam00005 pfam00664; type I secretion system ATPase 138925 5711607 Dshi_0139 Dinoroseobacter shibae DFL 12 = DSM 16493 type I secretion system ATPase YP_001531489.1 137186 R 398580 CDS YP_001531490.1 159042696 5711608 139098..139919 1 NC_009952.1 PFAM: VacJ family lipoprotein KEGG: rsp:RSP_0891 putative lipoprotein, middle swissprot to Lipoprotein vacJ precursor from Shigella flexneri; VacJ family lipoprotein 139919 5711608 Dshi_0140 Dinoroseobacter shibae DFL 12 = DSM 16493 VacJ family lipoprotein YP_001531490.1 139098 D 398580 CDS YP_001531491.1 159042697 5711609 139909..140529 1 NC_009952.1 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 140529 ttg2D 5711609 ttg2D Dinoroseobacter shibae DFL 12 = DSM 16493 toluene tolerance family protein YP_001531491.1 139909 D 398580 CDS YP_001531492.1 159042698 5711610 complement(140693..142882) 1 NC_009952.1 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 142882 mrcB 5711610 mrcB Dinoroseobacter shibae DFL 12 = DSM 16493 penicillin-binding protein YP_001531492.1 140693 R 398580 CDS YP_001531493.1 159042699 5711611 143197..143535 1 NC_009952.1 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 143535 glnK 5711611 glnK Dinoroseobacter shibae DFL 12 = DSM 16493 nitrogen regulatory protein P-II YP_001531493.1 143197 D 398580 CDS YP_001531494.1 159042700 5711612 143570..144883 1 NC_009952.1 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 144883 amtB 5711612 amtB Dinoroseobacter shibae DFL 12 = DSM 16493 ammonium transporter YP_001531494.1 143570 D 398580 CDS YP_001531495.1 159042701 5711613 complement(145044..146222) 1 NC_009952.1 catalyzes the formation of L-glutamate and an aromatic oxo acid from an aromatic amino acid and 2-oxoglutarate; aromatic amino acid aminotransferase 146222 5711613 Dshi_0145 Dinoroseobacter shibae DFL 12 = DSM 16493 aromatic amino acid aminotransferase YP_001531495.1 145044 R 398580 CDS YP_001531496.1 159042702 5711614 complement(146231..147106) 1 NC_009952.1 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 147106 sseA 5711614 sseA Dinoroseobacter shibae DFL 12 = DSM 16493 3-mercaptopyruvate sulfurtransferase YP_001531496.1 146231 R 398580 CDS YP_001531497.1 159042703 5711615 complement(147392..147874) 1 NC_009952.1 binds to ssrA RNA (tmRNA) and is required for its successful binding to ribosomes; also appears to function in the trans-translation step by promoting accommodation of tmRNA into the ribosomal A site; SmpB protects the tmRNA from RNase R degradation in Caulobacter crescentus; both the tmRNA and SmpB are regulated in cell cycle-dependent manner; functions in release of stalled ribosomes from damaged mRNAs and targeting proteins for degradation; SsrA-binding protein 147874 smpB 5711615 smpB Dinoroseobacter shibae DFL 12 = DSM 16493 SsrA-binding protein YP_001531497.1 147392 R 398580 CDS YP_001531498.1 159042704 5711616 complement(147905..148354) 1 NC_009952.1 PFAM: GCN5-related N-acetyltransferase KEGG: bur:Bcep18194_B2857 GCN5-related N-acetyltransferase, bad BLAST hits; N-acetyltransferase GCN5 148354 5711616 Dshi_0148 Dinoroseobacter shibae DFL 12 = DSM 16493 N-acetyltransferase GCN5 YP_001531498.1 147905 R 398580 CDS YP_001531499.1 159042705 5711617 complement(148351..149226) 1 NC_009952.1 catalyzes the formation of dihydrodipicolinate from L-aspartate 4-semialdehyde and pyruvate in lysine and diaminopimelate biosynthesis; dihydrodipicolinate synthase 149226 dapA 5711617 dapA Dinoroseobacter shibae DFL 12 = DSM 16493 dihydrodipicolinate synthase YP_001531499.1 148351 R 398580 CDS YP_001531500.1 159042706 5711618 149400..151349 1 NC_009952.1 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 151349 5711618 Dshi_0150 Dinoroseobacter shibae DFL 12 = DSM 16493 putative lytic transglycosylase catalytic subunit YP_001531500.1 149400 D 398580 CDS YP_001531501.1 159042707 5711619 complement(151387..152265) 1 NC_009952.1 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 152265 5711619 Dshi_0151 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531501.1 151387 R 398580 CDS YP_001531502.1 159042708 5711620 complement(152262..152954) 1 NC_009952.1 PFAM: protein of unknown function DUF752 KEGG: sil:SPO3553 hypothetical protein; hypothetical protein 152954 5711620 Dshi_0152 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531502.1 152262 R 398580 CDS YP_001531503.1 159042709 5711621 153035..154093 1 NC_009952.1 PFAM: FAD dependent oxidoreductase KEGG: sil:SPO3552 oxidoreductase, FAD-binding; FAD dependent oxidoreductase 154093 dao 5711621 dao Dinoroseobacter shibae DFL 12 = DSM 16493 FAD dependent oxidoreductase YP_001531503.1 153035 D 398580 CDS YP_001531504.1 159042710 5711622 complement(154275..154820) 1 NC_009952.1 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 154820 5711622 Dshi_0154 Dinoroseobacter shibae DFL 12 = DSM 16493 NADPH-dependent FMN reductase YP_001531504.1 154275 R 398580 CDS YP_001531505.1 159042711 5711623 155531..155887 1 NC_009952.1 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 155887 lrgA 5711623 lrgA Dinoroseobacter shibae DFL 12 = DSM 16493 putative LrgA family protein YP_001531505.1 155531 D 398580 CDS YP_001531506.1 159042712 5711624 155880..156596 1 NC_009952.1 PFAM: LrgB family protein KEGG: pde:Pden_2740 LrgB family protein; gene arrangement wtih Dshi_0155 putative LrgA protein; LrgB family protein 156596 lrgB 5711624 lrgB Dinoroseobacter shibae DFL 12 = DSM 16493 LrgB family protein YP_001531506.1 155880 D 398580 CDS YP_001531507.1 159042713 5711625 156608..157222 1 NC_009952.1 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 157222 cobA2 5711625 cobA2 Dinoroseobacter shibae DFL 12 = DSM 16493 cob(I)alamin adenosyltransferase YP_001531507.1 156608 D 398580 CDS YP_001531508.1 159042714 5711626 complement(157466..161173) 1 NC_009952.1 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 161173 cobN 5711626 cobN Dinoroseobacter shibae DFL 12 = DSM 16493 cobaltochelatase YP_001531508.1 157466 R 398580 CDS YP_001531509.1 159042715 5711627 complement(161242..161751) 1 NC_009952.1 no significant BLAST hits, no IPR Scan result; unsure GC frame plot; hypothetical protein 161751 5711627 Dshi_0159 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531509.1 161242 R 398580 CDS YP_001531510.1 159042716 5711628 complement(162047..163126) 1 NC_009952.1 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 163126 cobW 5711628 cobW Dinoroseobacter shibae DFL 12 = DSM 16493 cobalamin biosynthesis protein CobW YP_001531510.1 162047 R 398580 CDS YP_001531511.1 159042717 5711629 complement(163128..163817) 1 NC_009952.1 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 163817 cbtA 5711629 cbtA Dinoroseobacter shibae DFL 12 = DSM 16493 putative cobalt transporter subunit CbtA YP_001531511.1 163128 R 398580 CDS YP_001531512.1 159042718 5711630 complement(163833..164030) 1 NC_009952.1 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 164030 cbtB 5711630 cbtB Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531512.1 163833 R 398580 CDS YP_001531513.1 159042719 5711631 164463..167915 1 NC_009952.1 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 167915 smc 5711631 smc Dinoroseobacter shibae DFL 12 = DSM 16493 chromosome segregation protein SMC YP_001531513.1 164463 D 398580 CDS YP_001531514.1 159042720 5711632 complement(168135..169304) 1 NC_009952.1 TIGRFAM: lytic murein transglycosylase PFAM: Peptidoglycan-binding domain 1 protein KEGG: sil:SPO3226 hypothetical protein; lytic murein transglycosylase 169304 mltB1 5711632 mltB1 Dinoroseobacter shibae DFL 12 = DSM 16493 lytic murein transglycosylase YP_001531514.1 168135 R 398580 CDS YP_001531515.1 159042721 5711633 complement(169365..170276) 1 NC_009952.1 CobD; CbiD in Salmonella; converts cobyric acid to cobinamide by the addition of aminopropanol on the F carboxylic group; cobalamin biosynthesis protein 170276 cobD 5711633 cobD Dinoroseobacter shibae DFL 12 = DSM 16493 cobalamin biosynthesis protein YP_001531515.1 169365 R 398580 CDS YP_001531516.1 159042722 5711634 complement(170273..171229) 1 NC_009952.1 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 171229 cobC 5711634 cobC Dinoroseobacter shibae DFL 12 = DSM 16493 threonine-phosphate decarboxylase YP_001531516.1 170273 R 398580 CDS YP_001531517.1 159042723 5711635 complement(171226..171609) 1 NC_009952.1 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 171609 5711635 Dshi_0167 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531517.1 171226 R 398580 CDS YP_001531518.1 159042724 5711636 171888..172247 1 NC_009952.1 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 172247 5711636 Dshi_0168 Dinoroseobacter shibae DFL 12 = DSM 16493 response regulator receiver protein YP_001531518.1 171888 D 398580 CDS YP_001531519.1 159042725 5711637 complement(172349..173338) 1 NC_009952.1 KEGG: jan:Jann_0368 putative glutathione S-transferase; putative glutathione S-transferase 173338 5711637 Dshi_0169 Dinoroseobacter shibae DFL 12 = DSM 16493 putative glutathione S-transferase YP_001531519.1 172349 R 398580 CDS YP_001531520.1 159042726 5711638 173674..173919 1 NC_009952.1 no significant BLAST hits, bad GC frame plot, no conserved domains detected; hypothetical protein 173919 5711638 Dshi_0170 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531520.1 173674 D 398580 CDS YP_001531521.1 159042727 5711639 173916..175166 1 NC_009952.1 PFAM: cobalamin (vitamin B12) biosynthesis CbiX protein KEGG: sye:Syncc9902_0843 hypothetical protein; swissprot to Sirohydrochlorin cobaltochelatase (CbiXL) from Bacillus megaterium; sirohydrochlorin cobaltochelatase 175166 cbiX2 5711639 cbiX2 Dinoroseobacter shibae DFL 12 = DSM 16493 sirohydrochlorin cobaltochelatase YP_001531521.1 173916 D 398580 CDS YP_001531522.1 159042728 5711640 175166..176704 1 NC_009952.1 PFAM: Precorrin-8X methylmutase CbiC/CobH KEGG: bvi:Bcep1808_1609 precorrin-8X methylmutase; alternative gene name: cbiC; precorrin-8X methylmutase 176704 cobH 5711640 cobH Dinoroseobacter shibae DFL 12 = DSM 16493 precorrin-8X methylmutase YP_001531522.1 175166 D 398580 CDS YP_001531523.1 159042729 5711641 176787..177989 1 NC_009952.1 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 177989 cobL 5711641 cobL Dinoroseobacter shibae DFL 12 = DSM 16493 decarboxylating precorrin-6Y C(5,15)-methyltransferase YP_001531523.1 176787 D 398580 CDS YP_001531524.1 159042730 5711642 177986..178687 1 NC_009952.1 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 178687 cobI 5711642 cobI Dinoroseobacter shibae DFL 12 = DSM 16493 precorrin-2 C(20)-methyltransferase YP_001531524.1 177986 D 398580 CDS YP_001531525.1 159042731 5712100 178678..180483 1 NC_009952.1 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 180483 cbiG 5712100 cbiG Dinoroseobacter shibae DFL 12 = DSM 16493 precorrin-3B C(17)-methyltransferase YP_001531525.1 178678 D 398580 CDS YP_001531526.1 159042732 5712101 180607..181383 1 NC_009952.1 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 181383 cobM 5712101 cobM Dinoroseobacter shibae DFL 12 = DSM 16493 precorrin-4 C(11)-methyltransferase YP_001531526.1 180607 D 398580 CDS YP_001531527.1 159042733 5712102 181444..181797 1 NC_009952.1 KEGG: jan:Jann_0367 hypothetical protein, no significant swissprot, no IPR Scan results; hypothetical protein 181797 5712102 Dshi_0177 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531527.1 181444 D 398580 CDS YP_001531528.1 159042734 5712103 complement(181801..182973) 1 NC_009952.1 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 182973 5712103 Dshi_0178 Dinoroseobacter shibae DFL 12 = DSM 16493 class I/II aminotransferase YP_001531528.1 181801 R 398580 CDS YP_001531529.1 159042735 5712104 183047..183610 1 NC_009952.1 KEGG: rsh:Rsph17029_2532 peptide deformylase TIGRFAM: peptide deformylase PFAM: formylmethionine deformylase; peptide deformylase 183610 def1 5712104 def1 Dinoroseobacter shibae DFL 12 = DSM 16493 peptide deformylase YP_001531529.1 183047 D 398580 CDS YP_001531530.1 159042736 5712105 183683..184189 1 NC_009952.1 TIGRFAM: peptide deformylase PFAM: formylmethionine deformylase KEGG: sit:TM1040_2578 formylmethionine deformylase, worse BLAST hits than Dshi_0179, but same product result; peptide deformylase 184189 def2 5712105 def2 Dinoroseobacter shibae DFL 12 = DSM 16493 peptide deformylase YP_001531530.1 183683 D 398580 CDS YP_001531531.1 159042737 5712106 184186..185085 1 NC_009952.1 TIGRFAM: methionyl-tRNA formyltransferase PFAM: formyl transferase domain protein KEGG: sil:SPO3216 methionyl-tRNA formyltransferase; high swissprot; methionyl-tRNA formyltransferase 185085 fmt 5712106 fmt Dinoroseobacter shibae DFL 12 = DSM 16493 methionyl-tRNA formyltransferase YP_001531531.1 184186 D 398580 CDS YP_001531532.1 159042738 5712107 complement(185190..185663) 1 NC_009952.1 An endonuclease that specifically degrades the RNA strand of RNA-DNA hybrids; ribonuclease H 185663 rnhA 5712107 rnhA Dinoroseobacter shibae DFL 12 = DSM 16493 ribonuclease H YP_001531532.1 185190 R 398580 CDS YP_001531533.1 159042739 5712108 complement(185656..186255) 1 NC_009952.1 PFAM: Methyltransferase type 11; Methyltransferase type 12 KEGG: sil:SPO3211 hypothetical protein; type 11 methyltransferase 186255 5712108 Dshi_0183 Dinoroseobacter shibae DFL 12 = DSM 16493 type 11 methyltransferase YP_001531533.1 185656 R 398580 CDS YP_001531534.1 159042740 5712109 complement(186252..186704) 1 NC_009952.1 KEGG: rde:RD1_1353 hypothetical protein; hypothetical protein 186704 5712109 Dshi_0184 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531534.1 186252 R 398580 CDS YP_001531535.1 159042741 5712110 complement(186744..187694) 1 NC_009952.1 PFAM: phosphatidate cytidylyltransferase KEGG: reu:Reut_B4016 phosphatidate cytidylyltransferase; phosphatidate cytidylyltransferase 187694 cdsA2 5712110 cdsA2 Dinoroseobacter shibae DFL 12 = DSM 16493 phosphatidate cytidylyltransferase YP_001531535.1 186744 R 398580 CDS YP_001531536.1 159042742 5712111 complement(187691..188344) 1 NC_009952.1 PFAM: phospholipid/glycerol acyltransferase KEGG: reh:H16_A2089 1-acyl-sn-glycerol-3-phosphate acyltransferase; phospholipid/glycerol acyltransferase 188344 plsC 5712111 plsC Dinoroseobacter shibae DFL 12 = DSM 16493 phospholipid/glycerol acyltransferase YP_001531536.1 187691 R 398580 CDS YP_001531537.1 159042743 5712112 complement(188367..188981) 1 NC_009952.1 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 188981 5712112 Dshi_0187 Dinoroseobacter shibae DFL 12 = DSM 16493 amino-acid exporter protein YP_001531537.1 188367 R 398580 CDS YP_001531538.1 159042744 5712113 complement(189644..190600) 1 NC_009952.1 catalyzes the conversion of 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate into isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP); functions in the nonmevalonate isoprenoid biosynthesis pathway; 4-hydroxy-3-methylbut-2-enyl diphosphate reductase 190600 ispH 5712113 ispH Dinoroseobacter shibae DFL 12 = DSM 16493 4-hydroxy-3-methylbut-2-enyl diphosphate reductase YP_001531538.1 189644 R 398580 CDS YP_001531539.1 159042745 5712114 190754..191188 1 NC_009952.1 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 191188 5712114 Dshi_0189 Dinoroseobacter shibae DFL 12 = DSM 16493 putative cytochrome c class I YP_001531539.1 190754 D 398580 CDS YP_001531540.1 159042746 5712115 complement(191192..191707) 1 NC_009952.1 KEGG: pmy:Pmen_0684 membrane protein-like protein, middle Ref hits; hypothetical protein 191707 5712115 Dshi_0190 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531540.1 191192 R 398580 CDS YP_001531541.1 159042747 5712116 complement(191718..192290) 1 NC_009952.1 PFAM: protein of unknown function DUF88 KEGG: rsq:Rsph17025_2579 protein of unknown function DUF88; hypothetical protein 192290 5712116 Dshi_0191 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531541.1 191718 R 398580 CDS YP_001531542.1 159042748 5712117 192409..192978 1 NC_009952.1 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 192978 hppk 5712117 hppk Dinoroseobacter shibae DFL 12 = DSM 16493 2-amino-4-hydroxy-6- hydroxymethyldihydropteridine pyrophosphokinase YP_001531542.1 192409 D 398580 CDS YP_001531543.1 159042749 5712118 193056..193412 1 NC_009952.1 Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits; DNA-directed RNA polymerase subunit omega 193412 rpoZ 5712118 rpoZ Dinoroseobacter shibae DFL 12 = DSM 16493 DNA-directed RNA polymerase subunit omega YP_001531543.1 193056 D 398580 CDS YP_001531544.1 159042750 5712119 193417..195561 1 NC_009952.1 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 195561 relA 5712119 relA Dinoroseobacter shibae DFL 12 = DSM 16493 GTP pyrophosphokinase YP_001531544.1 193417 D 398580 CDS YP_001531545.1 159042751 5712120 195599..196255 1 NC_009952.1 KEGG: sil:SPO3202 hypothetical protein; hypothetical protein 196255 5712120 Dshi_0195 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531545.1 195599 D 398580 CDS YP_001531546.1 159042752 5712121 196281..197045 1 NC_009952.1 involved in the de novo synthesis of pyridoxine (Vitamin B6); pyridoxine 5'-phosphate synthase 197045 pdxJ 5712121 pdxJ Dinoroseobacter shibae DFL 12 = DSM 16493 pyridoxine 5'-phosphate synthase YP_001531546.1 196281 D 398580 CDS YP_001531547.1 159042753 5712122 197042..197704 1 NC_009952.1 KEGG: sit:TM1040_1321 hypothetical protein, no swissprot, no conserved domains; hypothetical protein 197704 5712122 Dshi_0197 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531547.1 197042 D 398580 CDS YP_001531548.1 159042754 5712123 197844..198263 1 NC_009952.1 Catalyzes the formation of holo-ACP, which mediates the essential transfer of acyl fatty acid intermediates during the biosynthesis of fatty acids and lipids; 4'-phosphopantetheinyl transferase 198263 acpS 5712123 acpS Dinoroseobacter shibae DFL 12 = DSM 16493 4'-phosphopantetheinyl transferase YP_001531548.1 197844 D 398580 CDS YP_001531549.1 159042755 5712124 198319..199104 1 NC_009952.1 KEGG: rsq:Rsph17025_2572 signal peptidase I TIGRFAM: signal peptidase I PFAM: peptidase S24 and S26 domain protein; signal peptidase I 199104 lepB 5712124 lepB Dinoroseobacter shibae DFL 12 = DSM 16493 signal peptidase I YP_001531549.1 198319 D 398580 CDS YP_001531550.1 159042756 5712125 199101..199790 1 NC_009952.1 PFAM: ribonuclease III; double-stranded RNA binding domain protein KEGG: rde:RD1_1366 ribonuclease III; ribonuclease III 199790 rnc 5712125 rnc Dinoroseobacter shibae DFL 12 = DSM 16493 ribonuclease III YP_001531550.1 199101 D 398580 CDS YP_001531551.1 159042757 5712126 199783..200709 1 NC_009952.1 Era; Escherichia coli Ras-like protein; Bex; Bacillus Era-complementing segment; essential protein in Escherichia coli that is involved in many cellular processes; GTPase; binds the cell membrane through apparent C-terminal domain; mutants are arrested during the cell cycle; Streptococcus pneumoniae Era binds to RNA and Escherichia coli Era binds 16S rRNA and 30S ribosome; GTP-binding protein Era 200709 era 5712126 era Dinoroseobacter shibae DFL 12 = DSM 16493 GTP-binding protein Era YP_001531551.1 199783 D 398580 CDS YP_001531552.1 159042758 5712127 200713..201045 1 NC_009952.1 PFAM: protein of unknown function DUF1491 KEGG: sil:SPO0690 hypothetical protein; hypothetical protein 201045 5712127 Dshi_0202 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531552.1 200713 D 398580 CDS YP_001531553.1 159042759 5712128 201114..201839 1 NC_009952.1 involved in DNA repair and RecFOR pathway recombination; RecFOR proteins displace ssDNA-binding protein and facilitate the production of RecA-coated ssDNA; DNA repair protein RecO 201839 recO 5712128 recO Dinoroseobacter shibae DFL 12 = DSM 16493 DNA repair protein RecO YP_001531553.1 201114 D 398580 CDS YP_001531554.1 159042760 5712129 complement(201901..203595) 1 NC_009952.1 PFAM: acyl-CoA dehydrogenase domain protein; Acyl-CoA dehydrogenase type 2 domain KEGG: rde:RD1_1372 isobutyryl-CoA dehydrogenase; acyl-CoA dehydrogenase 203595 mmgC 5712129 mmgC Dinoroseobacter shibae DFL 12 = DSM 16493 acyl-CoA dehydrogenase YP_001531554.1 201901 R 398580 CDS YP_001531555.1 159042761 5712130 203871..204635 1 NC_009952.1 PFAM: protein of unknown function DUF81 KEGG: sit:TM1040_2445 protein of unknown function DUF81; no significant swissprot; hypothetical protein 204635 5712130 Dshi_0205 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531555.1 203871 D 398580 CDS YP_001531556.1 159042762 5712131 complement(204628..205515) 1 NC_009952.1 KEGG: rde:RD1_1384 hypothetical protein, no significant swissprot, but conserved domains and good RBS site AGGAT; hypothetical protein 205515 5712131 Dshi_0206 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531556.1 204628 R 398580 CDS YP_001531557.1 159042763 5712132 complement(205596..205865) 1 NC_009952.1 TIGRFAM: phosphocarrier, HPr family PFAM: phosphocarrier HPr protein KEGG: sit:TM1040_2436 phosphotransferase system, HPr; phosphocarrier protein HPr; phosphotransferase system 205865 ptsH 5712132 ptsH Dinoroseobacter shibae DFL 12 = DSM 16493 phosphotransferase system YP_001531557.1 205596 R 398580 CDS YP_001531558.1 159042764 5712133 complement(205876..206265) 1 NC_009952.1 PFAM: PTS system fructose subfamily IIA component KEGG: sil:SPO0714 PTS system IIA component, Man family; Man family protein; PTS system transporter subunit IIA 206265 ptsL 5712133 ptsL Dinoroseobacter shibae DFL 12 = DSM 16493 PTS system transporter subunit IIA YP_001531558.1 205876 R 398580 CDS YP_001531559.1 159042765 5712134 complement(206303..207205) 1 NC_009952.1 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 207205 5712134 Dshi_0209 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531559.1 206303 R 398580 CDS YP_001531560.1 159042766 5712135 complement(207218..207655) 1 NC_009952.1 KEGG: sil:SPO0712 HPr serine kinase/phosphatase domain protein; HPr kinase/phosphorylase 207655 hprK 5712135 hprK Dinoroseobacter shibae DFL 12 = DSM 16493 HPr kinase/phosphorylase YP_001531560.1 207218 R 398580 CDS YP_001531561.1 159042767 5712136 complement(207658..209376) 1 NC_009952.1 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 209376 5712136 Dshi_0211 Dinoroseobacter shibae DFL 12 = DSM 16493 integral membrane sensor signal transduction histidine kinase YP_001531561.1 207658 R 398580 CDS YP_001531562.1 159042768 5712137 complement(209373..210074) 1 NC_009952.1 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 210074 5712137 Dshi_0212 Dinoroseobacter shibae DFL 12 = DSM 16493 two component transcriptional regulator YP_001531562.1 209373 R 398580 CDS YP_001531563.1 159042769 5712138 210410..212008 1 NC_009952.1 PEP carboxykinase; PEP carboxylase; PEPCK; catalyzes the phosphorylation and decarboxylation of oxaloacetate to form phosphoenolpyruvate using ATP; phosphoenolpyruvate carboxykinase 212008 pckA 5712138 pckA Dinoroseobacter shibae DFL 12 = DSM 16493 phosphoenolpyruvate carboxykinase YP_001531563.1 210410 D 398580 CDS YP_001531564.1 159042770 5712139 complement(212131..213006) 1 NC_009952.1 converts (S)-3-hydroxybutanoyl-CoA to 3-acetoacetyl-CoA; 3-hydroxybutyryl-CoA dehydrogenase 213006 hbdA 5712139 hbdA Dinoroseobacter shibae DFL 12 = DSM 16493 3-hydroxybutyryl-CoA dehydrogenase YP_001531564.1 212131 R 398580 CDS YP_001531565.1 159042771 5712140 213167..214024 1 NC_009952.1 KEGG: rde:RD1_1386 hypothetical protein; no significant swissprot; no IPR Scan results; hypothetical protein 214024 5712140 Dshi_0215 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531565.1 213167 D 398580 CDS YP_001531566.1 159042772 5712141 complement(214091..215017) 1 NC_009952.1 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 215017 eftA 5712141 eftA Dinoroseobacter shibae DFL 12 = DSM 16493 electron transfer flavoprotein subunit alpha YP_001531566.1 214091 R 398580 CDS YP_001531567.1 159042773 5712142 complement(215017..215775) 1 NC_009952.1 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 215775 eftB 5712142 eftB Dinoroseobacter shibae DFL 12 = DSM 16493 electron transfer flavoprotein subunit beta YP_001531567.1 215017 R 398580 CDS YP_001531568.1 159042774 5712143 complement(216003..216575) 1 NC_009952.1 TIGRFAM: ATP--cobalamin adenosyltransferase PFAM: cobalamin adenosyltransferase KEGG: rde:RD1_1389 cob(I)alamin adenosyltransferase, putative; putative ATP--cobalamin adenosyltransferase 216575 5712143 Dshi_0218 Dinoroseobacter shibae DFL 12 = DSM 16493 putative ATP--cobalamin adenosyltransferase YP_001531568.1 216003 R 398580 CDS YP_001531569.1 159042775 5712144 complement(216579..216794) 1 NC_009952.1 KEGG: rsq:Rsph17025_2554 hypothetical protein; no significant swissprot; no conserved domains; hypothetical protein 216794 5712144 Dshi_0219 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531569.1 216579 R 398580 CDS YP_001531570.1 159042776 5712145 complement(216879..217712) 1 NC_009952.1 PFAM: short-chain dehydrogenase/reductase SDR KEGG: rde:RD1_1391 oxidoreductase, putative; putative oxidoreductase NAD-/NADP-dependent 217712 5712145 Dshi_0220 Dinoroseobacter shibae DFL 12 = DSM 16493 putative oxidoreductase NAD-/NADP-dependent YP_001531570.1 216879 R 398580 CDS YP_001531571.1 159042777 5712146 217806..220139 1 NC_009952.1 decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling; DNA topoisomerase IV subunit A 220139 parC 5712146 parC Dinoroseobacter shibae DFL 12 = DSM 16493 DNA topoisomerase IV subunit A YP_001531571.1 217806 D 398580 CDS YP_001531572.1 159042778 5712147 220158..220832 1 NC_009952.1 KEGG: rsh:Rsph17029_0330 hypothetical protein, no significant swissprot; hypothetical protein 220832 5712147 Dshi_0222 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531572.1 220158 D 398580 CDS YP_001531573.1 159042779 5712148 220923..222098 1 NC_009952.1 EF-Tu; promotes GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis; when the tRNA anticodon matches the mRNA codon, GTP hydrolysis results; the inactive EF-Tu-GDP leaves the ribosome and release of GDP is promoted by elongation factor Ts; many prokaryotes have two copies of the gene encoding EF-Tu; elongation factor Tu 222098 tufA2 5712148 tufA2 Dinoroseobacter shibae DFL 12 = DSM 16493 elongation factor Tu YP_001531573.1 220923 D 398580 CDS YP_001531574.1 159042780 5712149 complement(222170..223045) 1 NC_009952.1 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 223045 5712149 Dshi_0224 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531574.1 222170 R 398580 CDS YP_001531575.1 159042781 5712151 223884..224186 1 NC_009952.1 KEGG: pde:Pden_3026 hypothetical protein, no swissprot, bad Ref hits, no conserved domains detected; hypothetical protein 224186 5712151 Dshi_0225 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531575.1 223884 D 398580 CDS YP_001531576.1 159042782 5712152 complement(224310..224642) 1 NC_009952.1 PFAM: protein of unknown function DUF1244 KEGG: sil:SPO3602 hypothetical protein; no significant swissprot hit; hypothetical protein 224642 5712152 Dshi_0226 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531576.1 224310 R 398580 CDS YP_001531577.1 159042783 5712153 complement(224639..225388) 1 NC_009952.1 PFAM: N-formylglutamate amidohydrolase KEGG: jan:Jann_0446 N-formylglutamate amidohydrolase; high Ref hit, but no significant swissprot hit; N-formylglutamate amidohydrolase 225388 5712153 Dshi_0227 Dinoroseobacter shibae DFL 12 = DSM 16493 N-formylglutamate amidohydrolase YP_001531577.1 224639 R 398580 CDS YP_001531578.1 159042784 5712154 225543..226991 1 NC_009952.1 KEGG: rsp:RSP_1766 pyruvate kinase TIGRFAM: pyruvate kinase PFAM: Pyruvate kinase barrel; Pyruvate kinase alpha/beta; high swissprot; pyruvate kinase 226991 pykA 5712154 pykA Dinoroseobacter shibae DFL 12 = DSM 16493 pyruvate kinase YP_001531578.1 225543 D 398580 CDS YP_001531579.1 159042785 5712155 226996..227220 1 NC_009952.1 bad BLAST hits, best swissprot to Prolyl-tRNA synthetase from Haemophilus ducreyi, but very unsure; no conserved domains detected; hypothetical protein 227220 5712155 Dshi_0229 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531579.1 226996 D 398580 CDS YP_001531580.1 159042786 5712156 227567..227767 1 NC_009952.1 PFAM: ribosomal protein L35 KEGG: sil:SPO3599 ribosomal protein L35; high swissprot; 50S ribosomal protein L35 227767 rpmI 5712156 rpmI Dinoroseobacter shibae DFL 12 = DSM 16493 50S ribosomal protein L35 YP_001531580.1 227567 D 398580 CDS YP_001531581.1 159042787 5712157 227780..228145 1 NC_009952.1 binds directly to 23S ribosomal RNA prior to in vitro assembly of the 50S ribosomal subunit; 50S ribosomal protein L20 228145 rplT 5712157 rplT Dinoroseobacter shibae DFL 12 = DSM 16493 50S ribosomal protein L20 YP_001531581.1 227780 D 398580 CDS YP_001531582.1 159042788 5712158 228403..229473 1 NC_009952.1 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 229473 5712158 Dshi_0232 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531582.1 228403 D 398580 CDS YP_001531583.1 159042789 5712159 229629..231512 1 NC_009952.1 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 231512 5712159 Dshi_0233 Dinoroseobacter shibae DFL 12 = DSM 16493 putative citrate transporter YP_001531583.1 229629 D 398580 CDS YP_001531584.1 159042790 5712160 231585..232649 1 NC_009952.1 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 232649 5712160 Dshi_0234 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531584.1 231585 D 398580 CDS YP_001531585.1 159042791 5712161 232709..233782 1 NC_009952.1 catalyzes a two-step reaction, first charging a phenylalanine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; forms a heterotetramer of alpha(2)beta(2); binds two magnesium ions per tetramer; type 1 subfamily; phenylalanyl-tRNA synthetase subunit alpha 233782 pheS 5712161 pheS Dinoroseobacter shibae DFL 12 = DSM 16493 phenylalanyl-tRNA synthetase subunit alpha YP_001531585.1 232709 D 398580 CDS YP_001531586.1 159042792 5712162 233956..234210 1 NC_009952.1 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 234210 5712162 Dshi_0236 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531586.1 233956 D 398580 CDS YP_001531587.1 159042793 5712163 234571..236967 1 NC_009952.1 catalyzes a two-step reaction, first charging a phenylalanine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; forms a tetramer of alpha(2)beta(2); binds two magnesium ions per tetramer; type 2 subfamily; phenylalanyl-tRNA synthetase subunit beta 236967 pheT 5712163 pheT Dinoroseobacter shibae DFL 12 = DSM 16493 phenylalanyl-tRNA synthetase subunit beta YP_001531587.1 234571 D 398580 CDS YP_001531588.1 159042794 5712164 237254..237724 1 NC_009952.1 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 237724 5712164 Dshi_0238 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531588.1 237254 D 398580 CDS YP_001531589.1 159042795 5712165 complement(237729..238490) 1 NC_009952.1 PFAM: aspartate dehydrogenase; homoserine dehydrogenase NAD-binding KEGG: mes:Meso_0824 aspartate dehydrogenase; aspartate dehydrogenase 238490 nadX 5712165 nadX Dinoroseobacter shibae DFL 12 = DSM 16493 aspartate dehydrogenase YP_001531589.1 237729 R 398580 CDS YP_001531590.1 159042796 5712166 complement(238487..239185) 1 NC_009952.1 PFAM: Glutathione S-transferase domain KEGG: sil:SPO3494 glutathione S-transferase family protein; glutathione S-transferase domain-containing protein 239185 gst3 5712166 gst3 Dinoroseobacter shibae DFL 12 = DSM 16493 glutathione S-transferase domain-containing protein YP_001531590.1 238487 R 398580 CDS YP_001531591.1 159042797 5712167 239334..239729 1 NC_009952.1 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 239729 mscL 5712167 mscL Dinoroseobacter shibae DFL 12 = DSM 16493 large conductance mechanosensitive channel protein YP_001531591.1 239334 D 398580 CDS YP_001531592.1 159042798 5712168 239815..240792 1 NC_009952.1 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 240792 5712168 Dshi_0242 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531592.1 239815 D 398580 CDS YP_001531593.1 159042799 5712169 240789..241940 1 NC_009952.1 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 241940 5712169 Dshi_0243 Dinoroseobacter shibae DFL 12 = DSM 16493 acyltransferase family protein YP_001531593.1 240789 D 398580 CDS YP_001531594.1 159042800 5712170 complement(241950..243065) 1 NC_009952.1 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 243065 adh 5712170 adh Dinoroseobacter shibae DFL 12 = DSM 16493 alanine dehydrogenase YP_001531594.1 241950 R 398580 CDS YP_001531595.1 159042801 5712171 243155..243664 1 NC_009952.1 PFAM: regulatory protein AsnC/Lrp family KEGG: jan:Jann_0459 transcriptional regulator, AsnC family; AsnC family; transcriptional regulator 243664 asnC 5712171 asnC Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001531595.1 243155 D 398580 CDS YP_001531596.1 159042802 5712172 complement(243756..243962) 1 NC_009952.1 a small basic protein that is one of the last in the subunit assembly; omission does not prevent assembly but the subunit is inactive; binds central domain of 16S rRNA; 30S ribosomal protein S21 243962 rpsU 5712172 rpsU Dinoroseobacter shibae DFL 12 = DSM 16493 30S ribosomal protein S21 YP_001531596.1 243756 R 398580 CDS YP_001531597.1 159042803 5712173 244084..244782 1 NC_009952.1 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 244782 5712173 Dshi_0247 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531597.1 244084 D 398580 CDS YP_001531598.1 159042804 5712174 244793..245779 1 NC_009952.1 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 245779 5712174 Dshi_0248 Dinoroseobacter shibae DFL 12 = DSM 16493 quinone oxidoreductase putative PIG3 YP_001531598.1 244793 D 398580 CDS YP_001531599.1 159042805 5712175 complement(246115..246699) 1 NC_009952.1 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 246699 5712175 Dshi_0249 Dinoroseobacter shibae DFL 12 = DSM 16493 efflux transporter YP_001531599.1 246115 R 398580 CDS YP_001531600.1 159042806 5712176 complement(246745..249237) 1 NC_009952.1 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 249237 5712176 Dshi_0250 Dinoroseobacter shibae DFL 12 = DSM 16493 efflux transporter YP_001531600.1 246745 R 398580 CDS YP_001531601.1 159042807 5712177 complement(249241..250392) 1 NC_009952.1 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 250392 5712177 Dshi_0251 Dinoroseobacter shibae DFL 12 = DSM 16493 efflux transporter YP_001531601.1 249241 R 398580 CDS YP_001531602.1 159042808 5712178 250470..251144 1 NC_009952.1 PFAM: regulatory protein TetR KEGG: jan:Jann_1309 transcriptional regulator, TetR family; TetR family; transcriptional regulator 251144 5712178 Dshi_0252 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001531602.1 250470 D 398580 CDS YP_001531603.1 159042809 5712179 251200..252759 1 NC_009952.1 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 252759 5712179 Dshi_0253 Dinoroseobacter shibae DFL 12 = DSM 16493 acyl-CoA synthetase/AMP-acid ligase II YP_001531603.1 251200 D 398580 CDS YP_001531604.1 159042810 5712180 complement(252790..253431) 1 NC_009952.1 PFAM: ribonuclease T2 KEGG: jan:Jann_3879 ribonuclease T2, unsure GC frame plot; ribonuclease T2 253431 5712180 Dshi_0254 Dinoroseobacter shibae DFL 12 = DSM 16493 ribonuclease T2 YP_001531604.1 252790 R 398580 CDS YP_001531605.1 159042811 5712181 253588..254340 1 NC_009952.1 PFAM: protein of unknown function DUF1013 KEGG: rde:RD1_1043 hypothetical protein; hypothetical protein 254340 5712181 Dshi_0255 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531605.1 253588 D 398580 CDS YP_001531606.1 159042812 5712182 complement(254419..254667) 1 NC_009952.1 no significant BLAST hits, no conserved domains; hypothetical protein 254667 5712182 Dshi_0256 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531606.1 254419 R 398580 CDS YP_001531607.1 159042813 5712183 complement(254727..256076) 1 NC_009952.1 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 256076 5712183 Dshi_0257 Dinoroseobacter shibae DFL 12 = DSM 16493 peptidase S8/S53 subtilisin kexin sedolisin YP_001531607.1 254727 R 398580 CDS YP_001531608.1 159042814 5712184 256271..256471 1 NC_009952.1 part of the sec system translocase; preprotein translocase subunit SecE 256471 secE 5712184 secE Dinoroseobacter shibae DFL 12 = DSM 16493 preprotein translocase subunit SecE YP_001531608.1 256271 D 398580 CDS YP_001531609.1 159042815 5712185 256673..257206 1 NC_009952.1 TIGRFAM: transcription termination/antitermination factor NusG PFAM: KOW domain protein; NGN domain protein KEGG: rsq:Rsph17025_2547 NusG antitermination factor; NusG antitermination factor 257206 nusG 5712185 nusG Dinoroseobacter shibae DFL 12 = DSM 16493 NusG antitermination factor YP_001531609.1 256673 D 398580 CDS YP_001531610.1 159042816 5712186 257310..257735 1 NC_009952.1 binds directly to 23S ribosomal RNA; 50S ribosomal protein L11 257735 rplK 5712186 rplK Dinoroseobacter shibae DFL 12 = DSM 16493 50S ribosomal protein L11 YP_001531610.1 257310 D 398580 CDS YP_001531611.1 159042817 5712187 257737..258435 1 NC_009952.1 in Escherichia coli and Methanococcus, this protein autoregulates expression; the binding site in the mRNA mimics the binding site in the 23S rRNA; 50S ribosomal protein L1 258435 rplA 5712187 rplA Dinoroseobacter shibae DFL 12 = DSM 16493 50S ribosomal protein L1 YP_001531611.1 257737 D 398580 CDS YP_001531612.1 159042818 5712188 258788..259516 1 NC_009952.1 KEGG: jan:Jann_2686 hypothetical protein; PEP-CTERM putative exosortase interaction domain; no significant swissprot, bad Ref hits; hypothetical protein 259516 5712188 Dshi_0262 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531612.1 258788 D 398580 CDS YP_001531613.1 159042819 5712189 259644..260429 1 NC_009952.1 TIGRFAM: methyltransferase FkbM family KEGG: jan:Jann_0310 methyltransferase FkbM; no significant swissprot; FkbM family methyltransferase 260429 fkbM 5712189 fkbM Dinoroseobacter shibae DFL 12 = DSM 16493 FkbM family methyltransferase YP_001531613.1 259644 D 398580 CDS YP_001531614.1 159042820 5712190 260484..261542 1 NC_009952.1 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 261542 5712190 Dshi_0264 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531614.1 260484 D 398580 CDS YP_001531615.1 159042821 5712191 261837..262355 1 NC_009952.1 binds the two ribosomal protein L7/L12 dimers and anchors them to the large ribosomal subunit; 50S ribosomal protein L10 262355 rplJ 5712191 rplJ Dinoroseobacter shibae DFL 12 = DSM 16493 50S ribosomal protein L10 YP_001531615.1 261837 D 398580 CDS YP_001531616.1 159042822 5712192 262428..262808 1 NC_009952.1 present in two forms; L12 is normal, while L7 is aminoacylated at the N-terminal serine; the only multicopy ribosomal protein; 4:1 ratio of L7/L12 per ribosome; two L12 dimers bind L10; critically important for translation efficiency and fidelity; stimulates GTPase activity of translation factors; 50S ribosomal protein L7/L12 262808 rplL 5712192 rplL Dinoroseobacter shibae DFL 12 = DSM 16493 50S ribosomal protein L7/L12 YP_001531616.1 262428 D 398580 CDS YP_001531617.1 159042823 5712193 262945..264294 1 NC_009952.1 KEGG: pde:Pden_2598 PpiC-type peptidyl-prolyl cis-trans isomerase; bad BLAST hits, unsure GC frame plot, RBS site AGGAT; hypothetical protein 264294 5712193 Dshi_0267 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531617.1 262945 D 398580 CDS YP_001531618.1 159042824 5712194 264787..268923 1 NC_009952.1 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates; beta subunit is part of the catalytic core which binds with a sigma factor to produce the holoenzyme; DNA-directed RNA polymerase subunit beta 268923 rpoB 5712194 rpoB Dinoroseobacter shibae DFL 12 = DSM 16493 DNA-directed RNA polymerase subunit beta YP_001531618.1 264787 D 398580 CDS YP_001531619.1 159042825 5711519 269021..273268 1 NC_009952.1 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Subunit beta' binds to sigma factor allowing it to bind to the -10 region of the promoter; DNA-directed RNA polymerase subunit beta' 273268 rpoC 5711519 rpoC Dinoroseobacter shibae DFL 12 = DSM 16493 DNA-directed RNA polymerase subunit beta' YP_001531619.1 269021 D 398580 CDS YP_001531620.1 159042826 5711520 273419..274324 1 NC_009952.1 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 274324 5711520 Dshi_0270 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531620.1 273419 D 398580 CDS YP_001531621.1 159042827 5711521 274606..274977 1 NC_009952.1 interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone; located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side; mutations in the S12 gene confer streptomycin resistance; 30S ribosomal protein S12 274977 rpsL 5711521 rpsL Dinoroseobacter shibae DFL 12 = DSM 16493 30S ribosomal protein S12 YP_001531621.1 274606 D 398580 CDS YP_001531622.1 159042828 5711522 274990..275460 1 NC_009952.1 binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit; 30S ribosomal protein S7 275460 rpsG 5711522 rpsG Dinoroseobacter shibae DFL 12 = DSM 16493 30S ribosomal protein S7 YP_001531622.1 274990 D 398580 CDS YP_001531623.1 159042829 5711523 275486..277603 1 NC_009952.1 EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene; elongation factor G 277603 fusA 5711523 fusA Dinoroseobacter shibae DFL 12 = DSM 16493 elongation factor G YP_001531623.1 275486 D 398580 CDS YP_001531624.1 159042830 5711524 277686..278861 1 NC_009952.1 EF-Tu; promotes GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis; when the tRNA anticodon matches the mRNA codon, GTP hydrolysis results; the inactive EF-Tu-GDP leaves the ribosome and release of GDP is promoted by elongation factor Ts; many prokaryotes have two copies of the gene encoding EF-Tu; elongation factor Tu 278861 tufA1 5711524 tufA1 Dinoroseobacter shibae DFL 12 = DSM 16493 elongation factor Tu YP_001531624.1 277686 D 398580 CDS YP_001531625.1 159042831 5711525 278960..279280 1 NC_009952.1 NusE; involved in assembly of the 30S subunit; in the ribosome, this protein is involved in the binding of tRNA; in Escherichia coli this protein was also found to be involved in transcription antitermination; NusB/S10 heterodimers bind boxA sequences in the leader RNA of rrn operons which is required for antitermination; binding of NusB/S10 to boxA nucleates assembly of the antitermination complex; 30S ribosomal protein S10 279280 rpsJ 5711525 rpsJ Dinoroseobacter shibae DFL 12 = DSM 16493 30S ribosomal protein S10 YP_001531625.1 278960 D 398580 CDS YP_001531626.1 159042832 5711526 279295..280134 1 NC_009952.1 binds directly near the 3' end of the 23S rRNA, where it nucleates assembly of the 50S subunit; essential for peptidyltransferase activity; mutations in this gene confer resistance to tiamulin; 50S ribosomal protein L3 280134 rplC 5711526 rplC Dinoroseobacter shibae DFL 12 = DSM 16493 50S ribosomal protein L3 YP_001531626.1 279295 D 398580 CDS YP_001531627.1 159042833 5711527 280131..280748 1 NC_009952.1 L4 is important during the early stages of 50S assembly; it initially binds near the 5' end of the 23S rRNA; 50S ribosomal protein L4 280748 rplD 5711527 rplD Dinoroseobacter shibae DFL 12 = DSM 16493 50S ribosomal protein L4 YP_001531627.1 280131 D 398580 CDS YP_001531628.1 159042834 5711528 280745..281041 1 NC_009952.1 binds third domain of 23S rRNA and protein L29; part of exit tunnel; 50S ribosomal protein L23 281041 rplW 5711528 rplW Dinoroseobacter shibae DFL 12 = DSM 16493 50S ribosomal protein L23 YP_001531628.1 280745 D 398580 CDS YP_001531629.1 159042835 5711529 complement(281137..281487) 1 NC_009952.1 no significant BLAST hits, no conserved domains, unsure GC frame plot; hypothetical protein 281487 5711529 Dshi_0279 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531629.1 281137 R 398580 CDS YP_001531630.1 159042836 5711530 complement(281779..282159) 1 NC_009952.1 KEGG: rde:RD1_1404 hypothetical protein, no significant swissprot hit, unsure GC frame plot; hypothetical protein 282159 5711530 Dshi_0280 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531630.1 281779 R 398580 CDS YP_001531631.1 159042837 5711531 complement(282323..282814) 1 NC_009952.1 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 282814 5711531 Dshi_0281 Dinoroseobacter shibae DFL 12 = DSM 16493 YHS domain-containing protein YP_001531631.1 282323 R 398580 CDS YP_001531632.1 159042838 5711532 283471..283737 1 NC_009952.1 no swissprot, bad Ref hits, no conserved domains, unsure GC frame plot; hypothetical protein 283737 5711532 Dshi_0282 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531632.1 283471 D 398580 CDS YP_001531633.1 159042839 5711533 283818..284120 1 NC_009952.1 no swissprot, bad Ref hits, no conserved domains, unsure GC frame plot; hypothetical protein 284120 5711533 Dshi_0283 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531633.1 283818 D 398580 CDS YP_001531634.1 159042840 5711534 284463..285113 1 NC_009952.1 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 285113 5711534 Dshi_0284 Dinoroseobacter shibae DFL 12 = DSM 16493 putative outer membrane protein YP_001531634.1 284463 D 398580 CDS YP_001531635.1 159042841 5711535 285409..286251 1 NC_009952.1 one of the primary rRNA-binding proteins; required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation; 50S ribosomal protein L2 286251 rplB 5711535 rplB Dinoroseobacter shibae DFL 12 = DSM 16493 50S ribosomal protein L2 YP_001531635.1 285409 D 398580 CDS YP_001531636.1 159042842 5711536 286255..286533 1 NC_009952.1 protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA; 30S ribosomal protein S19 286533 rpsS 5711536 rpsS Dinoroseobacter shibae DFL 12 = DSM 16493 30S ribosomal protein S19 YP_001531636.1 286255 D 398580 CDS YP_001531637.1 159042843 5711537 286537..286917 1 NC_009952.1 binds specifically to 23S rRNA during the early stages of 50S assembly; makes contact with all 6 domains of the 23S rRNA in the assembled 50S subunit and ribosome; mutations in this gene result in erythromycin resistance; located near peptidyl-transferase center; 50S ribosomal protein L22 286917 rplV 5711537 rplV Dinoroseobacter shibae DFL 12 = DSM 16493 50S ribosomal protein L22 YP_001531637.1 286537 D 398580 CDS YP_001531638.1 159042844 5711538 286917..287639 1 NC_009952.1 forms a complex with S10 and S14; binds the lower part of the 30S subunit head and the mRNA in the complete ribosome to position it for translation; 30S ribosomal protein S3 287639 rpsC 5711538 rpsC Dinoroseobacter shibae DFL 12 = DSM 16493 30S ribosomal protein S3 YP_001531638.1 286917 D 398580 CDS YP_001531639.1 159042845 5711539 287653..288066 1 NC_009952.1 located in the peptidyl transferase center and may be involved in peptidyl transferase activity; similar to archaeal L10e; 50S ribosomal protein L16 288066 rplP 5711539 rplP Dinoroseobacter shibae DFL 12 = DSM 16493 50S ribosomal protein L16 YP_001531639.1 287653 D 398580 CDS YP_001531640.1 159042846 5711540 288217..288447 1 NC_009952.1 KEGG: sit:TM1040_3827 hypothetical protein; short signalpeptide and three transmembrane region; no swissprot, bad Ref hits to hypothetical proteins; hypothetical protein 288447 5711540 Dshi_0290 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531640.1 288217 D 398580 CDS YP_001531641.1 159042847 5711541 complement(289020..289409) 1 NC_009952.1 KEGG: rde:RD1_0735 hypothetical protein; bad Ref hits to hypothetical proteins; short signalpeptide and four transmembrane regions; no significant swissprot; hypothetical protein 289409 5711541 Dshi_0291 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531641.1 289020 R 398580 CDS YP_001531642.1 159042848 5711542 complement(289461..290186) 1 NC_009952.1 KEGG: sil:SPO0491 hypothetical protein; no swissprot; TIGR02466 conserved hypothetical protein; hypothetical protein 290186 5711542 Dshi_0292 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531642.1 289461 R 398580 CDS YP_001531643.1 159042849 5711543 290274..290480 1 NC_009952.1 one of the stabilizing components for the large ribosomal subunit; 50S ribosomal protein L29 290480 rpmC 5711543 rpmC Dinoroseobacter shibae DFL 12 = DSM 16493 50S ribosomal protein L29 YP_001531643.1 290274 D 398580 CDS YP_001531644.1 159042850 5711544 290493..290723 1 NC_009952.1 PFAM: ribosomal protein S17 KEGG: sit:TM1040_0263 ribosomal protein S17; 30S ribosomal protein S17 290723 rpsQ 5711544 rpsQ Dinoroseobacter shibae DFL 12 = DSM 16493 30S ribosomal protein S17 YP_001531644.1 290493 D 398580 CDS YP_001531645.1 159042851 5711545 290797..291165 1 NC_009952.1 binds to the 23S rRNA between the centers for peptidyl transferase and GTPase; 50S ribosomal protein L14 291165 rplN 5711545 rplN Dinoroseobacter shibae DFL 12 = DSM 16493 50S ribosomal protein L14 YP_001531645.1 290797 D 398580 CDS YP_001531646.1 159042852 5711546 291165..291470 1 NC_009952.1 assembly initiator protein; binds to 5' end of 23S rRNA and nucleates assembly of the 50S; surrounds polypeptide exit tunnel; 50S ribosomal protein L24 291470 rplX 5711546 rplX Dinoroseobacter shibae DFL 12 = DSM 16493 50S ribosomal protein L24 YP_001531646.1 291165 D 398580 CDS YP_001531647.1 159042853 5711547 291470..292033 1 NC_009952.1 part of 50S and 5S/L5/L18/L25 subcomplex; contacts 5S rRNA and P site tRNA; forms a bridge to the 30S subunit in the ribosome by binding to S13; 50S ribosomal protein L5 292033 rplE 5711547 rplE Dinoroseobacter shibae DFL 12 = DSM 16493 50S ribosomal protein L5 YP_001531647.1 291470 D 398580 CDS YP_001531648.1 159042854 5711548 292052..292357 1 NC_009952.1 located in the peptidyl transferase center and involved in assembly of 30S ribosome subunit; similar to what is observed with proteins L31 and L33, some proteins in this family contain CXXC motifs that are involved in zinc binding; if two copies are present in a genome, then the duplicated copy appears to have lost the zinc-binding motif and is instead regulated by zinc; the proteins in this group do not appear to have the zinc-binding motif; 30S ribosomal protein S14 292357 rpsN 5711548 rpsN Dinoroseobacter shibae DFL 12 = DSM 16493 30S ribosomal protein S14 YP_001531648.1 292052 D 398580 CDS YP_001531649.1 159042855 5711549 292371..292763 1 NC_009952.1 binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit; 30S ribosomal protein S8 292763 rpsH 5711549 rpsH Dinoroseobacter shibae DFL 12 = DSM 16493 30S ribosomal protein S8 YP_001531649.1 292371 D 398580 CDS YP_001531650.1 159042856 5711550 292776..293309 1 NC_009952.1 ribosomal protein L6 appears to have arisen as a result of an ancient gene duplication as based on structural comparison of the Bacillus stearothermophilus protein; RNA-binding appears to be in the C-terminal domain; mutations in the L6 gene confer resistance to aminoglycoside antibiotics such as gentamicin and these occur in truncations of the C-terminal domain; it has been localized to a region between the base of the L7/L12 stalk and the central protuberance; 50S ribosomal protein L6 293309 rplF 5711550 rplF Dinoroseobacter shibae DFL 12 = DSM 16493 50S ribosomal protein L6 YP_001531650.1 292776 D 398580 CDS YP_001531651.1 159042857 5711551 293321..293680 1 NC_009952.1 binds 5S rRNA along with protein L5 and L25; 50S ribosomal protein L18 293680 rplR 5711551 rplR Dinoroseobacter shibae DFL 12 = DSM 16493 50S ribosomal protein L18 YP_001531651.1 293321 D 398580 CDS YP_001531652.1 159042858 5711552 293839..294414 1 NC_009952.1 located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body; contacts S4 and S8; with S4 and S12 plays a role in translational accuracy; mutations in this gene result in spectinomycin resistance; 30S ribosomal protein S5 294414 rpsE 5711552 rpsE Dinoroseobacter shibae DFL 12 = DSM 16493 30S ribosomal protein S5 YP_001531652.1 293839 D 398580 CDS YP_001531653.1 159042859 5711553 294427..294615 1 NC_009952.1 L30 binds domain II of the 23S rRNA and the 5S rRNA; similar to eukaryotic protein L7; 50S ribosomal protein L30 294615 rpmD 5711553 rpmD Dinoroseobacter shibae DFL 12 = DSM 16493 50S ribosomal protein L30 YP_001531653.1 294427 D 398580 CDS YP_001531654.1 159042860 5711554 294758..295231 1 NC_009952.1 late assembly protein; 50S ribosomal protein L15 295231 rplO 5711554 rplO Dinoroseobacter shibae DFL 12 = DSM 16493 50S ribosomal protein L15 YP_001531654.1 294758 D 398580 CDS YP_001531655.1 159042861 5711555 295343..296704 1 NC_009952.1 forms heterotrimeric complex in the membrane; in bacteria the complex consists of SecY which forms the channel pore and SecE and SecG; the SecG subunit is not essential; in bacteria translocation is driven via the SecA ATPase; preprotein translocase subunit SecY 296704 secY 5711555 secY Dinoroseobacter shibae DFL 12 = DSM 16493 preprotein translocase subunit SecY YP_001531655.1 295343 D 398580 CDS YP_001531656.1 159042862 5711556 296701..297342 1 NC_009952.1 essential enzyme that recycles AMP in active cells; converts ATP and AMP to two molecules of ADP; adenylate kinase 297342 adk 5711556 adk Dinoroseobacter shibae DFL 12 = DSM 16493 adenylate kinase YP_001531656.1 296701 D 398580 CDS YP_001531657.1 159042863 5711557 297504..297947 1 NC_009952.1 PFAM: ribosomal protein S13 KEGG: sil:SPO0509 ribosomal protein S13; 30S ribosomal protein S13 297947 rpsM 5711557 rpsM Dinoroseobacter shibae DFL 12 = DSM 16493 30S ribosomal protein S13 YP_001531657.1 297504 D 398580 CDS YP_001531658.1 159042864 5711558 297963..298352 1 NC_009952.1 located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA; forms part of the Shine-Dalgarno cleft in the 70S ribosome; interacts with S7 and S18 and IF-3; 30S ribosomal protein S11 298352 rpsK 5711558 rpsK Dinoroseobacter shibae DFL 12 = DSM 16493 30S ribosomal protein S11 YP_001531658.1 297963 D 398580 CDS YP_001531659.1 159042865 5711559 298455..299486 1 NC_009952.1 catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Dimerization of the alpha subunit is the first step in the sequential assembly of subunits to form the holoenzyme; DNA-directed RNA polymerase subunit alpha 299486 rpoA 5711559 rpoA Dinoroseobacter shibae DFL 12 = DSM 16493 DNA-directed RNA polymerase subunit alpha YP_001531659.1 298455 D 398580 CDS YP_001531660.1 159042866 5711560 299605..300021 1 NC_009952.1 is a component of the macrolide binding site in the peptidyl transferase center; 50S ribosomal protein L17 300021 rplQ 5711560 rplQ Dinoroseobacter shibae DFL 12 = DSM 16493 50S ribosomal protein L17 YP_001531660.1 299605 D 398580 CDS YP_001531661.1 159042867 5711561 300364..300975 1 NC_009952.1 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 300975 luxR1 5711561 luxR1 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001531661.1 300364 D 398580 CDS YP_001531662.1 159042868 5711562 301032..301619 1 NC_009952.1 KEGG: pde:Pden_0787 N-acyl-L-homoserine lactone synthetase-like; N-acyl-L-homoserine lactone synthetase-like protein 301619 luxI 5711562 luxI Dinoroseobacter shibae DFL 12 = DSM 16493 N-acyl-L-homoserine lactone synthetase-like protein YP_001531662.1 301032 D 398580 CDS YP_001531663.1 159042869 5711563 301799..303109 1 NC_009952.1 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 303109 5711563 Dshi_0313 Dinoroseobacter shibae DFL 12 = DSM 16493 recombination factor protein RarA YP_001531663.1 301799 D 398580 CDS YP_001531664.1 159042870 5711564 303192..303521 1 NC_009952.1 PFAM: Camphor resistance CrcB protein KEGG: rde:RD1_1440 CrcB-like protein; COG0239 Integral membrane protein possibly involved in chromosome condensation; integral membrane protein 303521 5711564 Dshi_0314 Dinoroseobacter shibae DFL 12 = DSM 16493 integral membrane protein YP_001531664.1 303192 D 398580 CDS YP_001531665.1 159042871 5711565 303518..304564 1 NC_009952.1 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 304564 rluC 5711565 rluC Dinoroseobacter shibae DFL 12 = DSM 16493 ribosomal large subunit pseudouridine synthase C YP_001531665.1 303518 D 398580 CDS YP_001531666.1 159042872 5711566 304561..305241 1 NC_009952.1 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 305241 gph 5711566 gph Dinoroseobacter shibae DFL 12 = DSM 16493 phosphoglycolate phosphatase YP_001531666.1 304561 D 398580 CDS YP_001531667.1 159042873 5711567 305238..305942 1 NC_009952.1 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 305942 5711567 Dshi_0317 Dinoroseobacter shibae DFL 12 = DSM 16493 ATP12 chaperone protein YP_001531667.1 305238 D 398580 CDS YP_001531668.1 159042874 5711568 306292..307308 1 NC_009952.1 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 307308 bztA 5711568 bztA Dinoroseobacter shibae DFL 12 = DSM 16493 glutamate/glutamine/aspartate/asparagine ABC transporter YP_001531668.1 306292 D 398580 CDS YP_001531669.1 159042875 5711569 307429..308664 1 NC_009952.1 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 308664 bztB 5711569 bztB Dinoroseobacter shibae DFL 12 = DSM 16493 glutamate/glutamine/aspartate/asparagine ABC transport system permease YP_001531669.1 307429 D 398580 CDS YP_001531670.1 159042876 5711570 308666..309964 1 NC_009952.1 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 309964 bztC 5711570 bztC Dinoroseobacter shibae DFL 12 = DSM 16493 glutamate/glutamine/aspartate/asparagine ABC transport system permease YP_001531670.1 308666 D 398580 CDS YP_001531671.1 159042877 5711571 309980..310756 1 NC_009952.1 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 310756 bztD 5711571 bztD Dinoroseobacter shibae DFL 12 = DSM 16493 glutamate/glutamine/aspartate/asparagine ABC transport ATP-binding YP_001531671.1 309980 D 398580 CDS YP_001531672.1 159042878 5711572 complement(310800..311300) 1 NC_009952.1 PFAM: Phosphoglycerate mutase KEGG: sil:SPO0523 phosphoglycerate mutase family protein; COG2062 Phosphohistidine phosphatase SixA; best Ref hits to hypothetical proteins; putative phosphatase 311300 5711572 Dshi_0322 Dinoroseobacter shibae DFL 12 = DSM 16493 putative phosphatase YP_001531672.1 310800 R 398580 CDS YP_001531673.1 159042879 5711573 complement(311297..311920) 1 NC_009952.1 KEGG: rde:RD1_1449 hypothetical protein, no significant swissprot; no conserved domains detected; hypothetical protein 311920 5711573 Dshi_0323 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531673.1 311297 R 398580 CDS YP_001531674.1 159042880 5711574 complement(311973..312836) 1 NC_009952.1 catalyzes the phosphorylation of N-acetyl-L-glutamate to form N-acetyl-L-glutamate 5-phosphate; acetylglutamate kinase 312836 argB 5711574 argB Dinoroseobacter shibae DFL 12 = DSM 16493 acetylglutamate kinase YP_001531674.1 311973 R 398580 CDS YP_001531675.1 159042881 5711575 312924..313655 1 NC_009952.1 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 313655 fabG3 5711575 fabG3 Dinoroseobacter shibae DFL 12 = DSM 16493 3-ketoacyl-ACP reductase YP_001531675.1 312924 D 398580 CDS YP_001531676.1 159042882 5711576 complement(313718..314371) 1 NC_009952.1 binds guanine nucleotides; in Escherichia coli depletion results in defective cell division and filamentation; in Bacillus subtilis this gene is essential; ribosome biogenesis GTP-binding protein YsxC 314371 engB 5711576 engB Dinoroseobacter shibae DFL 12 = DSM 16493 ribosome biogenesis GTP-binding protein YsxC YP_001531676.1 313718 R 398580 CDS YP_001531677.1 159042883 5711577 complement(314368..315117) 1 NC_009952.1 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 315117 mosc 5711577 mosc Dinoroseobacter shibae DFL 12 = DSM 16493 MOSC domain-containing protein YP_001531677.1 314368 R 398580 CDS YP_001531678.1 159042884 5711578 complement(315114..316934) 1 NC_009952.1 functions to insert inner membrane proteins into the IM in Escherichia coli; interacts with transmembrane segments; functions in both Sec-dependent and -independent membrane insertion; similar to Oxa1p in mitochondria; putative inner membrane protein translocase component YidC 316934 yidC 5711578 yidC Dinoroseobacter shibae DFL 12 = DSM 16493 putative inner membrane protein translocase component YidC YP_001531678.1 315114 R 398580 CDS YP_001531679.1 159042885 5711579 complement(317056..318645) 1 NC_009952.1 TIGRFAM: diguanylate cyclase PFAM: GGDEF domain containing protein; EAL domain protein KEGG: sil:SPO0533 diguanylate cyclase, putative; diguanylate cyclase/phosphodiesterase 318645 ydaM 5711579 ydaM Dinoroseobacter shibae DFL 12 = DSM 16493 diguanylate cyclase/phosphodiesterase YP_001531679.1 317056 R 398580 CDS YP_001531680.1 159042886 5711580 complement(318693..319556) 1 NC_009952.1 TtcA; YdaO; catalyzes the thiolation of cytosine 32 in specific tRNAs; C32 tRNA thiolase 319556 ydaO 5711580 ydaO Dinoroseobacter shibae DFL 12 = DSM 16493 C32 tRNA thiolase YP_001531680.1 318693 R 398580 CDS YP_001531681.1 159042887 5711582 complement(319810..320031) 1 NC_009952.1 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 320031 5711582 Dshi_0331 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531681.1 319810 R 398580 CDS YP_001531682.1 159042888 5711583 complement(320028..320417) 1 NC_009952.1 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 320417 rnpA 5711583 rnpA Dinoroseobacter shibae DFL 12 = DSM 16493 ribonuclease P protein component YP_001531682.1 320028 R 398580 CDS YP_001531683.1 159042889 5711584 complement(320480..320614) 1 NC_009952.1 in Escherichia coli transcription of this gene is enhanced by polyamines; 50S ribosomal protein L34 320614 rpmH 5711584 rpmH Dinoroseobacter shibae DFL 12 = DSM 16493 50S ribosomal protein L34 YP_001531683.1 320480 R 398580 CDS YP_001531684.1 159042890 5711586 complement(320898..322301) 1 NC_009952.1 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 322301 5711586 Dshi_0334 Dinoroseobacter shibae DFL 12 = DSM 16493 integral membrane sensor signal transduction histidine kinase YP_001531684.1 320898 R 398580 CDS YP_001531685.1 159042891 5711587 complement(322338..323750) 1 NC_009952.1 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 323750 merA 5711587 merA Dinoroseobacter shibae DFL 12 = DSM 16493 putative mercuric reductase MerA YP_001531685.1 322338 R 398580 CDS YP_001531686.1 159042892 5711245 complement(323755..324486) 1 NC_009952.1 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 324486 5711245 Dshi_0336 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531686.1 323755 R 398580 CDS YP_001531687.1 159042893 5711246 complement(325428..326237) 1 NC_009952.1 PFAM: ATPase MipZ KEGG: jan:Jann_0738 ATPases involved in chromosome partitioning-like;alternative gene name: mipZ; chromosome partitioning ATPase 326237 parA2 5711246 parA2 Dinoroseobacter shibae DFL 12 = DSM 16493 chromosome partitioning ATPase YP_001531687.1 325428 R 398580 CDS YP_001531688.1 159042894 5711247 326619..327452 1 NC_009952.1 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 327452 5711247 Dshi_0338 Dinoroseobacter shibae DFL 12 = DSM 16493 metallo-beta-lactamase family protein YP_001531688.1 326619 D 398580 CDS YP_001531689.1 159042895 5711248 complement(327660..328538) 1 NC_009952.1 PFAM: protein of unknown function DUF849 KEGG: bur:Bcep18194_B0612 protein of unknown function DUF849, no significant swissprot; hypothetical protein 328538 5711248 Dshi_0339 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531689.1 327660 R 398580 CDS YP_001531690.1 159042896 5711249 complement(328656..328877) 1 NC_009952.1 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 328877 rpmE 5711249 rpmE Dinoroseobacter shibae DFL 12 = DSM 16493 50S ribosomal protein L31 YP_001531690.1 328656 R 398580 CDS YP_001531691.1 159042897 5711250 complement(328889..329263) 1 NC_009952.1 this protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site; 50S ribosomal protein L19 329263 rplS 5711250 rplS Dinoroseobacter shibae DFL 12 = DSM 16493 50S ribosomal protein L19 YP_001531691.1 328889 R 398580 CDS YP_001531692.1 159042898 5711251 complement(329524..330321) 1 NC_009952.1 KEGG: rsq:Rsph17025_0184 tRNA (guanine-N1)-methyltransferase TIGRFAM: tRNA (guanine-N1)-methyltransferase PFAM: tRNA (guanine-N1-)-methyltransferase; tRNA (guanine-N1)-methyltransferase 330321 trmD 5711251 trmD Dinoroseobacter shibae DFL 12 = DSM 16493 tRNA (guanine-N1)-methyltransferase YP_001531692.1 329524 R 398580 CDS YP_001531693.1 159042899 5711252 330412..331401 1 NC_009952.1 PFAM: aminoglycoside phosphotransferase KEGG: sit:TM1040_2610 hypothetical protein; no significant swissprot hit; aminoglycoside phosphotransferase 331401 aph 5711252 aph Dinoroseobacter shibae DFL 12 = DSM 16493 aminoglycoside phosphotransferase YP_001531693.1 330412 D 398580 CDS YP_001531694.1 159042900 5711253 complement(331421..331921) 1 NC_009952.1 Essential for efficient processing of 16S rRNA; 16S rRNA-processing protein RimM 331921 rimM 5711253 rimM Dinoroseobacter shibae DFL 12 = DSM 16493 16S rRNA-processing protein RimM YP_001531694.1 331421 R 398580 CDS YP_001531695.1 159042901 5711254 complement(331918..332064) 1 NC_009952.1 no significant BLAST hits, unsure prosite hit to ribosomal protein S2; hypothetical protein 332064 5711254 Dshi_0345 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531695.1 331918 R 398580 CDS YP_001531696.1 159042902 5711255 complement(332071..332535) 1 NC_009952.1 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 332535 5711255 Dshi_0346 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531696.1 332071 R 398580 CDS YP_001531697.1 159042903 5711256 complement(332537..333166) 1 NC_009952.1 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 333166 bluB 5711256 bluB Dinoroseobacter shibae DFL 12 = DSM 16493 cob(II)yrinic acid a,c-diamide reductase YP_001531697.1 332537 R 398580 CDS YP_001531698.1 159042904 5711257 complement(333195..333587) 1 NC_009952.1 binds to lower part of 30S body where it stabilizes two domains; required for efficient assembly of 30S; in Escherichia coli this protein has nuclease activity; 30S ribosomal protein S16 333587 rpsP 5711257 rpsP Dinoroseobacter shibae DFL 12 = DSM 16493 30S ribosomal protein S16 YP_001531698.1 333195 R 398580 CDS YP_001531699.1 159042905 5711258 complement(333629..333925) 1 NC_009952.1 catalyzes the interconversion of chorismate to prephenate; chorismate mutase 333925 pheA1 5711258 pheA1 Dinoroseobacter shibae DFL 12 = DSM 16493 chorismate mutase YP_001531699.1 333629 R 398580 CDS YP_001531700.1 159042906 5711259 complement(334046..334651) 1 NC_009952.1 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 334651 5711259 Dshi_0350 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531700.1 334046 R 398580 CDS YP_001531701.1 159042907 5711260 complement(334651..335166) 1 NC_009952.1 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 335166 5711260 Dshi_0351 Dinoroseobacter shibae DFL 12 = DSM 16493 N-acetyltransferase GCN5 YP_001531701.1 334651 R 398580 CDS YP_001531702.1 159042908 5711261 complement(335163..335696) 1 NC_009952.1 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 335696 5711261 Dshi_0352 Dinoroseobacter shibae DFL 12 = DSM 16493 acetyltransferase YP_001531702.1 335163 R 398580 CDS YP_001531703.1 159042909 5711262 complement(335696..337210) 1 NC_009952.1 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 337210 ffh 5711262 ffh Dinoroseobacter shibae DFL 12 = DSM 16493 signal recognition particle protein YP_001531703.1 335696 R 398580 CDS YP_001531704.1 159042910 5711263 complement(337582..338226) 1 NC_009952.1 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 338226 azoR1 5711263 azoR1 Dinoroseobacter shibae DFL 12 = DSM 16493 FMN-dependent NADH-azoreductase 1 YP_001531704.1 337582 R 398580 CDS YP_001531705.1 159042911 5711264 338282..339163 1 NC_009952.1 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 339163 lysR 5711264 lysR Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001531705.1 338282 D 398580 CDS YP_001531706.1 159042912 5711265 339214..340104 1 NC_009952.1 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 340104 5711265 Dshi_0356 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531706.1 339214 D 398580 CDS YP_001531707.1 159042913 5711266 complement(340107..340445) 1 NC_009952.1 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 340445 arsR 5711266 arsR Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001531707.1 340107 R 398580 CDS YP_001531708.1 159042914 5711267 340610..342199 1 NC_009952.1 involved in de novo purine biosynthesis; bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase 342199 purH 5711267 purH Dinoroseobacter shibae DFL 12 = DSM 16493 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase YP_001531708.1 340610 D 398580 CDS YP_001531709.1 159042915 5711268 342204..342680 1 NC_009952.1 lipoprotein signal peptidase; integral membrane protein that removes signal peptides from prolipoproteins during lipoprotein biosynthesis; lipoprotein signal peptidase 342680 lspA 5711268 lspA Dinoroseobacter shibae DFL 12 = DSM 16493 lipoprotein signal peptidase YP_001531709.1 342204 D 398580 CDS YP_001531710.1 159042916 5711269 342734..343279 1 NC_009952.1 KEGG: rsq:Rsph17025_2930 hypothetical protein; no significant swissprot, no conserved domains; hypothetical protein 343279 5711269 Dshi_0360 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531710.1 342734 D 398580 CDS YP_001531711.1 159042917 5711270 343363..344724 1 NC_009952.1 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 344724 pqqL2 5711270 pqqL2 Dinoroseobacter shibae DFL 12 = DSM 16493 peptidase M16 protein YP_001531711.1 343363 D 398580 CDS YP_001531712.1 159042918 5711271 344721..346034 1 NC_009952.1 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 346034 pqqL1 5711271 pqqL1 Dinoroseobacter shibae DFL 12 = DSM 16493 peptidase M16 protein YP_001531712.1 344721 D 398580 CDS YP_001531713.1 159042919 5711272 346074..347939 1 NC_009952.1 This protein is involved in the repair of mismatches in DNA. It is required for dam-dependent methyl-directed DNA mismatch repair. Promotes the formation of a stable complex between two or more DNA-binding proteins in an ATP-dependent manner without itself being part of a final effector complex; DNA mismatch repair protein 347939 mutL 5711272 mutL Dinoroseobacter shibae DFL 12 = DSM 16493 DNA mismatch repair protein YP_001531713.1 346074 D 398580 CDS YP_001531714.1 159042920 5711273 347936..349168 1 NC_009952.1 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 349168 rmuC 5711273 rmuC Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531714.1 347936 D 398580 CDS YP_001531715.1 159042921 5711274 complement(349194..349865) 1 NC_009952.1 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 349865 chrR1 5711274 chrR1 Dinoroseobacter shibae DFL 12 = DSM 16493 anti-ECFsigma factor YP_001531715.1 349194 R 398580 CDS YP_001531716.1 159042922 5711275 complement(349872..350441) 1 NC_009952.1 Member of the extracytoplasmic function sigma factors which are active under specific conditions; binds with the catalytic core of RNA polymerase to produce the holoenzyme and directs bacterial core RNA polymerase to specific promoter elements to initiate transcription; this sigma factor is involved in heat shock and oxidative stress response; RNA polymerase sigma factor RpoE 350441 rpoE2 5711275 rpoE2 Dinoroseobacter shibae DFL 12 = DSM 16493 RNA polymerase sigma factor RpoE YP_001531716.1 349872 R 398580 CDS YP_001531717.1 159042923 5711276 350649..351953 1 NC_009952.1 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 351953 5711276 Dshi_0367 Dinoroseobacter shibae DFL 12 = DSM 16493 amine oxidase YP_001531717.1 350649 D 398580 CDS YP_001531718.1 159042924 5711277 351950..352708 1 NC_009952.1 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 352708 5711277 Dshi_0368 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531718.1 351950 D 398580 CDS YP_001531719.1 159042925 5711278 352726..353964 1 NC_009952.1 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 353964 5711278 Dshi_0369 Dinoroseobacter shibae DFL 12 = DSM 16493 putative sodium:galactoside symporter family protein YP_001531719.1 352726 D 398580 CDS YP_001531720.1 159042926 5711279 353964..354554 1 NC_009952.1 no significant swissprot, good Ref ZP hit to hypothetical protein RCCS2_10850 from Roseobacter sp. CCS2; no NCBI conserved domains; hypothetical protein 354554 5711279 Dshi_0370 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531720.1 353964 D 398580 CDS YP_001531721.1 159042927 5711280 354573..355304 1 NC_009952.1 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 355304 5711280 Dshi_0371 Dinoroseobacter shibae DFL 12 = DSM 16493 short-chain dehydrogenase/reductase SDR YP_001531721.1 354573 D 398580 CDS YP_001531722.1 159042928 5711281 355405..355728 1 NC_009952.1 no conserved domains detected, no significant swissprot, middle Ref ZP hit to hypothetical protein SKA53_12618 from Loktanella vestfoldensis SKA53; hypothetical protein 355728 5711281 Dshi_0372 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531722.1 355405 D 398580 CDS YP_001531723.1 159042929 5711282 355873..357843 1 NC_009952.1 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 357843 fadD3 5711282 fadD3 Dinoroseobacter shibae DFL 12 = DSM 16493 acyl-CoA synthetase YP_001531723.1 355873 D 398580 CDS YP_001531724.1 159042930 5711283 357902..358156 1 NC_009952.1 no significant BLAST hits, no conserved domains detected; normal GC frame plot; hypothetical protein 358156 5711283 Dshi_0374 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531724.1 357902 D 398580 CDS YP_001531725.1 159042931 5711284 358153..358974 1 NC_009952.1 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 358974 livG 5711284 livG Dinoroseobacter shibae DFL 12 = DSM 16493 high-affinity branched-chain amino acid transport ATP-binding protein livG YP_001531725.1 358153 D 398580 CDS YP_001531726.1 159042932 5711285 359118..360107 1 NC_009952.1 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 360107 livH 5711285 livH Dinoroseobacter shibae DFL 12 = DSM 16493 high-affinity branched-chain amino acid transport system permease livH YP_001531726.1 359118 D 398580 CDS YP_001531727.1 159042933 5711286 complement(360124..360432) 1 NC_009952.1 no significant BLAST hits, unsure GC frame plot, no conserved domains detected, lies in the middle of ABC transporter; hypothetical protein 360432 5711286 Dshi_0377 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531727.1 360124 R 398580 CDS YP_001531728.1 159042934 5711287 360675..360929 1 NC_009952.1 no significant BLAST hits, unsure GC frame plot, no conserved domains detected, lies in the middle of ABC transporter; hypothetical protein 360929 5711287 Dshi_0378 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531728.1 360675 D 398580 CDS YP_001531729.1 159042935 5711288 361062..362138 1 NC_009952.1 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 362138 livM 5711288 livM Dinoroseobacter shibae DFL 12 = DSM 16493 high-affinity branched-chain amino acid transport system permease livM YP_001531729.1 361062 D 398580 CDS YP_001531730.1 159042936 5711289 362188..363468 1 NC_009952.1 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 363468 livK 5711289 livK Dinoroseobacter shibae DFL 12 = DSM 16493 high-affinity branched-chain amino acid transport system periplasmic-binding protein livK YP_001531730.1 362188 D 398580 CDS YP_001531731.1 159042937 5711290 363531..364355 1 NC_009952.1 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 364355 livF1 5711290 livF1 Dinoroseobacter shibae DFL 12 = DSM 16493 high-affinity branched-chain amino acid transport ATP-binding protein livF YP_001531731.1 363531 D 398580 CDS YP_001531732.1 159042938 5711291 364512..365732 1 NC_009952.1 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 365732 paaK 5711291 paaK Dinoroseobacter shibae DFL 12 = DSM 16493 phenylacetate-CoA ligase YP_001531732.1 364512 D 398580 CDS YP_001531733.1 159042939 5711292 365857..366321 1 NC_009952.1 no significant BLAST hits, unsure GC frame plot, no conserved domains; hypothetical protein 366321 5711292 Dshi_0383 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531733.1 365857 D 398580 CDS YP_001531734.1 159042940 5711293 complement(366443..366901) 1 NC_009952.1 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 366901 5711293 Dshi_0384 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531734.1 366443 R 398580 CDS YP_001531735.1 159042941 5711294 366959..368212 1 NC_009952.1 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 368212 dinB 5711294 dinB Dinoroseobacter shibae DFL 12 = DSM 16493 DNA polymerase IV YP_001531735.1 366959 D 398580 CDS YP_001531736.1 159042942 5711295 complement(368291..369154) 1 NC_009952.1 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 369154 hutG 5711295 hutG Dinoroseobacter shibae DFL 12 = DSM 16493 N-formylglutamate amidohydrolase YP_001531736.1 368291 R 398580 CDS YP_001531737.1 159042943 5711297 369431..369556 1 NC_009952.1 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 369556 rpmJ 5711297 rpmJ Dinoroseobacter shibae DFL 12 = DSM 16493 50S ribosomal protein L36 YP_001531737.1 369431 D 398580 CDS YP_001531738.1 159042944 5711298 complement(369763..370548) 1 NC_009952.1 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 370548 rbsA5 5711298 rbsA5 Dinoroseobacter shibae DFL 12 = DSM 16493 ribose import ATP-binding protein rbsA YP_001531738.1 369763 R 398580 CDS YP_001531739.1 159042945 5711299 complement(370545..371618) 1 NC_009952.1 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 371618 rbsC2 5711299 rbsC2 Dinoroseobacter shibae DFL 12 = DSM 16493 ribose transport system permease rbsC YP_001531739.1 370545 R 398580 CDS YP_001531740.1 159042946 5711300 complement(371715..372728) 1 NC_009952.1 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 372728 rbsB3 5711300 rbsB3 Dinoroseobacter shibae DFL 12 = DSM 16493 D-ribose-binding periplasmic protein YP_001531740.1 371715 R 398580 CDS YP_001531741.1 159042947 5711307 379683..382190 1 NC_009952.1 no significant swissprot, high Ref ZP hit to hypothetical protein MELB17_00320 from Marinobacter sp. ELB17; pfam02810 SEC-C motif; hypothetical protein 382190 5711307 Dshi_0391 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531741.1 379683 D 398580 CDS YP_001531742.1 159042948 5711308 complement(382289..383437) 1 NC_009952.1 no significant swissprot, high Ref hit to hypothetical protein TM1040_3581 from Silicibacter sp. TM1040; no conserved domains, unsure GC frame plot; hypothetical protein 383437 5711308 Dshi_0392 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531742.1 382289 R 398580 CDS YP_001531743.1 159042949 5711309 complement(383697..383918) 1 NC_009952.1 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 383918 5711309 Dshi_0393 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531743.1 383697 R 398580 CDS YP_001531744.1 159042950 5711310 complement(383978..384751) 1 NC_009952.1 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 384751 5711310 Dshi_0394 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531744.1 383978 R 398580 CDS YP_001531745.1 159042951 5711311 complement(384765..385958) 1 NC_009952.1 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 385958 5711311 Dshi_0395 Dinoroseobacter shibae DFL 12 = DSM 16493 phage integrase family protein YP_001531745.1 384765 R 398580 CDS YP_001531746.1 159042952 5711312 complement(386137..387813) 1 NC_009952.1 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 387813 5711312 Dshi_0396 Dinoroseobacter shibae DFL 12 = DSM 16493 recombinase YP_001531746.1 386137 R 398580 CDS YP_001531747.1 159042953 5711313 complement(387910..388986) 1 NC_009952.1 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 388986 xerDC2 5711313 xerDC2 Dinoroseobacter shibae DFL 12 = DSM 16493 integrase family protein YP_001531747.1 387910 R 398580 CDS YP_001531748.1 159042954 5711314 complement(388979..390658) 1 NC_009952.1 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 390658 xerDC1 5711314 xerDC1 Dinoroseobacter shibae DFL 12 = DSM 16493 integrase family protein YP_001531748.1 388979 R 398580 CDS YP_001531749.1 159042955 5711315 complement(390817..391029) 1 NC_009952.1 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 391029 5711315 Dshi_0399 Dinoroseobacter shibae DFL 12 = DSM 16493 DNA-binding domain-containing protein YP_001531749.1 390817 R 398580 CDS YP_001531750.1 159042956 5711316 391798..395037 1 NC_009952.1 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 395037 5711316 Dshi_0400 Dinoroseobacter shibae DFL 12 = DSM 16493 CRISPR-associated protein YP_001531750.1 391798 D 398580 CDS YP_001531751.1 159042957 5711317 395098..396009 1 NC_009952.1 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 396009 5711317 Dshi_0401 Dinoroseobacter shibae DFL 12 = DSM 16493 CRISPR-associated protein Cas1 YP_001531751.1 395098 D 398580 CDS YP_001531752.1 159042958 5711318 396006..396350 1 NC_009952.1 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 396350 5711318 Dshi_0402 Dinoroseobacter shibae DFL 12 = DSM 16493 CRISPR-associated protein Cas2 YP_001531752.1 396006 D 398580 CDS YP_001531753.1 159042959 5711319 397989..398255 1 NC_009952.1 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 398255 5711319 Dshi_0403 Dinoroseobacter shibae DFL 12 = DSM 16493 insertion element ISR1 10 kDa protein A3 YP_001531753.1 397989 D 398580 CDS YP_001531754.1 159042960 5711320 398279..399088 1 NC_009952.1 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 399088 5711320 Dshi_0404 Dinoroseobacter shibae DFL 12 = DSM 16493 integrase catalytic subunit YP_001531754.1 398279 D 398580 CDS YP_001531755.1 159042961 5711321 complement(399227..400612) 1 NC_009952.1 no significant BLAST hits, no conserved domains, unsure GC frame plot, downstream of CRISPR region; hypothetical protein 400612 5711321 Dshi_0405 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531755.1 399227 R 398580 CDS YP_001531756.1 159042962 5711322 complement(400543..401841) 1 NC_009952.1 no significant BLAST hits, no conserved domains, unsure GC frame plot; hypothetical protein 401841 5711322 Dshi_0406 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531756.1 400543 R 398580 CDS YP_001531757.1 159042963 5711323 402104..402430 1 NC_009952.1 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 402430 5711323 Dshi_0407 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001531757.1 402104 D 398580 CDS YP_001531758.1 159042964 5711324 402441..403163 1 NC_009952.1 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 403163 5711324 Dshi_0408 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531758.1 402441 D 398580 CDS YP_001531759.1 159042965 5711325 403268..403912 1 NC_009952.1 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 403912 5711325 Dshi_0409 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531759.1 403268 D 398580 CDS YP_001531760.1 159042966 5711326 complement(404246..405190) 1 NC_009952.1 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 405190 5711326 Dshi_0410 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531760.1 404246 R 398580 CDS YP_001531761.1 159042967 5711327 complement(405174..406022) 1 NC_009952.1 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 406022 5711327 Dshi_0411 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531761.1 405174 R 398580 CDS YP_001531762.1 159042968 5711328 406254..407786 1 NC_009952.1 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 407786 fas 5711328 fas Dinoroseobacter shibae DFL 12 = DSM 16493 beta-Ig-H3/fasciclin YP_001531762.1 406254 D 398580 CDS YP_001531763.1 159042969 5711329 407836..408195 1 NC_009952.1 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 408195 5711329 Dshi_0413 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531763.1 407836 D 398580 CDS YP_001531764.1 159042970 5711330 complement(408427..408873) 1 NC_009952.1 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 408873 5711330 Dshi_0414 Dinoroseobacter shibae DFL 12 = DSM 16493 GreA/GreB family elongation factor YP_001531764.1 408427 R 398580 CDS YP_001531765.1 159042971 5711331 409020..409262 1 NC_009952.1 no significant BLAST hits, no conserved domains; unsure GC frame plot; hypothetical protein 409262 5711331 Dshi_0415 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531765.1 409020 D 398580 CDS YP_001531766.1 159042972 5711332 409608..409919 1 NC_009952.1 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 409919 5711332 Dshi_0416 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531766.1 409608 D 398580 CDS YP_001531767.1 159042973 5711333 410003..410209 1 NC_009952.1 no significant BLAST hits, no conserved domains, unsure GC frame plot; hypothetical protein 410209 5711333 Dshi_0417 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531767.1 410003 D 398580 CDS YP_001531768.1 159042974 5711334 410284..411177 1 NC_009952.1 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 411177 uspA2 5711334 uspA2 Dinoroseobacter shibae DFL 12 = DSM 16493 universal stress protein uspA YP_001531768.1 410284 D 398580 CDS YP_001531769.1 159042975 5711335 411331..412584 1 NC_009952.1 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 412584 5711335 Dshi_0419 Dinoroseobacter shibae DFL 12 = DSM 16493 major facilitator superfamily protein YP_001531769.1 411331 D 398580 CDS YP_001531770.1 159042976 5711336 412724..413434 1 NC_009952.1 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 413434 5711336 Dshi_0420 Dinoroseobacter shibae DFL 12 = DSM 16493 endonuclease/exonuclease/phosphatase YP_001531770.1 412724 D 398580 CDS YP_001531771.1 159042977 5711337 413435..414979 1 NC_009952.1 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 414979 5711337 Dshi_0421 Dinoroseobacter shibae DFL 12 = DSM 16493 phospholipase D/transphosphatidylase YP_001531771.1 413435 D 398580 CDS YP_001531772.1 159042978 5711338 415164..415685 1 NC_009952.1 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 415685 5711338 Dshi_0422 Dinoroseobacter shibae DFL 12 = DSM 16493 propeptide PepSY amd peptidase M4 YP_001531772.1 415164 D 398580 CDS YP_001531773.1 159042979 5711339 complement(415763..416488) 1 NC_009952.1 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 416488 pap 5711339 pap Dinoroseobacter shibae DFL 12 = DSM 16493 PA-phosphatase-like phosphoesterase YP_001531773.1 415763 R 398580 CDS YP_001531774.1 159042980 5711340 417105..417566 1 NC_009952.1 peptidase M41 417566 5711340 Dshi_0424 Dinoroseobacter shibae DFL 12 = DSM 16493 peptidase M41 YP_001531774.1 417105 D 398580 CDS YP_001531775.1 159042981 5711342 418488..418850 1 NC_009952.1 no significant swissprot; PD068243 REGULATORY BACTERIAL FAMILY MERR CYTOPLASMIC; middle Ref ZP hit to hypothetical protein ROS217_15345 from Roseovarius sp. 217; hypothetical protein 418850 5711342 Dshi_0426 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531775.1 418488 D 398580 CDS YP_001531776.1 159042982 5711343 418998..419249 1 NC_009952.1 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 419249 5711343 Dshi_0427 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531776.1 418998 D 398580 CDS YP_001531777.1 159042983 5711344 419269..421152 1 NC_009952.1 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 421152 phaC 5711344 phaC Dinoroseobacter shibae DFL 12 = DSM 16493 poly(3-hydroxyalkanoate) polymerase YP_001531777.1 419269 D 398580 CDS YP_001531778.1 159042984 5711345 complement(421265..421552) 1 NC_009952.1 no significant swissprot, no conserved domains, low Ref Yp hit to uncharacterized conserved coiled coil protein from Marinomonas sp. MWYL1; hypothetical protein 421552 5711345 Dshi_0429 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531778.1 421265 R 398580 CDS YP_001531779.1 159042985 5711346 complement(421575..422009) 1 NC_009952.1 no significant swissprot, no conserved domains, low Ref YP hit to hypothetical protein SPO0412 from Silicibacter pomeroyi DSS-3; hypothetical protein 422009 5711346 Dshi_0430 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531779.1 421575 R 398580 CDS YP_001531780.1 159042986 5711347 422213..423661 1 NC_009952.1 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 423661 dcuC 5711347 dcuC Dinoroseobacter shibae DFL 12 = DSM 16493 C4-dicarboxylate anaerobic carrier YP_001531780.1 422213 D 398580 CDS YP_001531781.1 159042987 5711348 423677..424906 1 NC_009952.1 catalyzes the degradation of arginine to citruline and ammonia; arginine deiminase 424906 arcA 5711348 arcA Dinoroseobacter shibae DFL 12 = DSM 16493 arginine deiminase YP_001531781.1 423677 D 398580 CDS YP_001531782.1 159042988 5711349 424920..425921 1 NC_009952.1 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 425921 arcB 5711349 arcB Dinoroseobacter shibae DFL 12 = DSM 16493 ornithine carbamoyltransferase YP_001531782.1 424920 D 398580 CDS YP_001531783.1 159042989 5711350 425925..426863 1 NC_009952.1 reversible synthesis of carbamate and ATP from carbamoyl phosphate and ADP; carbamate kinase 426863 arcC 5711350 arcC Dinoroseobacter shibae DFL 12 = DSM 16493 carbamate kinase YP_001531783.1 425925 D 398580 CDS YP_001531784.1 159042990 5711351 427117..428505 1 NC_009952.1 produces ATP from ADP in the presence of a proton gradient across the membrane; the beta chain is a regulatory subunit; F0F1 ATP synthase subunit beta 428505 atpD1 5711351 atpD1 Dinoroseobacter shibae DFL 12 = DSM 16493 F0F1 ATP synthase subunit beta YP_001531784.1 427117 D 398580 CDS YP_001531785.1 159042991 5711352 428502..428912 1 NC_009952.1 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 428912 atpC2 5711352 atpC2 Dinoroseobacter shibae DFL 12 = DSM 16493 ATP synthase F1 subunit epsilon YP_001531785.1 428502 D 398580 CDS YP_001531786.1 159042992 5711353 428909..429196 1 NC_009952.1 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 429196 5711353 Dshi_0437 Dinoroseobacter shibae DFL 12 = DSM 16493 ATP synthase F0F1 subunit YP_001531786.1 428909 D 398580 CDS YP_001531787.1 159042993 5711354 429193..429498 1 NC_009952.1 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 429498 5711354 Dshi_0438 Dinoroseobacter shibae DFL 12 = DSM 16493 ATP synthase F0F1 subunit YP_001531787.1 429193 D 398580 CDS YP_001531788.1 159042994 5711355 429489..430178 1 NC_009952.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit A is part of the membrane proton channel F0; F0F1 ATP synthase subunit A 430178 atpB2 5711355 atpB2 Dinoroseobacter shibae DFL 12 = DSM 16493 F0F1 ATP synthase subunit A YP_001531788.1 429489 D 398580 CDS YP_001531789.1 159042995 5711356 430175..430465 1 NC_009952.1 produces ATP from ADP in the presence of a proton gradient across the membrane; subunit C is part of the membrane proton channel F0; F0F1 ATP synthase subunit C 430465 atpE1 5711356 atpE1 Dinoroseobacter shibae DFL 12 = DSM 16493 F0F1 ATP synthase subunit C YP_001531789.1 430175 D 398580 CDS YP_001531790.1 159042996 5711357 430470..431237 1 NC_009952.1 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 431237 atpF1 5711357 atpF1 Dinoroseobacter shibae DFL 12 = DSM 16493 ATP synthase F0 subunit B YP_001531790.1 430470 D 398580 CDS YP_001531791.1 159042997 5711358 431227..432756 1 NC_009952.1 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 432756 atpA2 5711358 atpA2 Dinoroseobacter shibae DFL 12 = DSM 16493 ATP synthase F1 subunit alpha YP_001531791.1 431227 D 398580 CDS YP_001531792.1 159042998 5711359 432740..433687 1 NC_009952.1 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 433687 atpG1 5711359 atpG1 Dinoroseobacter shibae DFL 12 = DSM 16493 ATP synthase F1 subunit gamma YP_001531792.1 432740 D 398580 CDS YP_001531793.1 159042999 5711360 433725..434012 1 NC_009952.1 no significant swissprot, no conserved domains, low Ref YP hit to hypothetical protein Nham_4077 from Nitrobacter hamburgensis X14; hypothetical protein 434012 5711360 Dshi_0444 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531793.1 433725 D 398580 CDS YP_001531794.1 159043000 5711361 434046..434438 1 NC_009952.1 no significant swissprot, no conserved domains, low Ref ZP hit to hypothetical protein NB311A_09431 from Nitrobacter sp. Nb-311A; hypothetical protein 434438 5711361 Dshi_0445 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531794.1 434046 D 398580 CDS YP_001531795.1 159043001 5711362 434569..434979 1 NC_009952.1 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 434979 5711362 Dshi_0446 Dinoroseobacter shibae DFL 12 = DSM 16493 putative signal transduction protein YP_001531795.1 434569 D 398580 CDS YP_001531796.1 159043002 5711363 complement(434981..435769) 1 NC_009952.1 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 435769 5711363 Dshi_0447 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001531796.1 434981 R 398580 CDS YP_001531797.1 159043003 5711364 436086..437696 1 NC_009952.1 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 437696 5711364 Dshi_0448 Dinoroseobacter shibae DFL 12 = DSM 16493 integral membrane sensor signal transduction histidine kinase YP_001531797.1 436086 D 398580 CDS YP_001531798.1 159043004 5711365 437751..438434 1 NC_009952.1 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 438434 5711365 Dshi_0449 Dinoroseobacter shibae DFL 12 = DSM 16493 two component transcriptional regulator YP_001531798.1 437751 D 398580 CDS YP_001531799.1 159043005 5711366 438538..438636 1 NC_009952.1 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 438636 pqqA 5711366 pqqA Dinoroseobacter shibae DFL 12 = DSM 16493 coenzyme PQQ synthesis protein PqqA YP_001531799.1 438538 D 398580 CDS YP_001531800.1 159043006 5711367 438663..439556 1 NC_009952.1 possibly involved in transport of pyrroloquinoline quinone transport; pyrroloquinoline quinone biosynthesis protein PqqB 439556 pqqB 5711367 pqqB Dinoroseobacter shibae DFL 12 = DSM 16493 pyrroloquinoline quinone biosynthesis protein PqqB YP_001531800.1 438663 D 398580 CDS YP_001531801.1 159043007 5711368 439556..440308 1 NC_009952.1 Required in the synthesis of PPQ, but its exact function is unknown; pyrroloquinoline quinone biosynthesis protein PqqC 440308 pqqC 5711368 pqqC Dinoroseobacter shibae DFL 12 = DSM 16493 pyrroloquinoline quinone biosynthesis protein PqqC YP_001531801.1 439556 D 398580 CDS YP_001531802.1 159043008 5711369 440305..440583 1 NC_009952.1 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 440583 pqqD 5711369 pqqD Dinoroseobacter shibae DFL 12 = DSM 16493 coenzyme PQQ biosynthesis protein PqqD YP_001531802.1 440305 D 398580 CDS YP_001531803.1 159043009 5711370 440580..441686 1 NC_009952.1 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 441686 pqqE 5711370 pqqE Dinoroseobacter shibae DFL 12 = DSM 16493 pyrroloquinoline quinone biosynthesis protein PqqE YP_001531803.1 440580 D 398580 CDS YP_001531804.1 159043010 5711371 442029..442946 1 NC_009952.1 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 442946 5711371 Dshi_0455 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531804.1 442029 D 398580 CDS YP_001531805.1 159043011 5711372 443039..443995 1 NC_009952.1 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 443995 moxR 5711372 moxR Dinoroseobacter shibae DFL 12 = DSM 16493 MoxR-like ATPase YP_001531805.1 443039 D 398580 CDS YP_001531806.1 159043012 5711373 443992..444900 1 NC_009952.1 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 444900 5711373 Dshi_0457 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531806.1 443992 D 398580 CDS YP_001531807.1 159043013 5711374 444897..445268 1 NC_009952.1 no significant swissprot, no conserved domains; middle Ref YP hit to hypothetical protein RD1_0874 from Roseobacter denitrificans OCh 114; hypothetical protein 445268 5711374 Dshi_0458 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531807.1 444897 D 398580 CDS YP_001531808.1 159043014 5711375 445261..446223 1 NC_009952.1 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 446223 5711375 Dshi_0459 Dinoroseobacter shibae DFL 12 = DSM 16493 von Willebrand factor type A YP_001531808.1 445261 D 398580 CDS YP_001531809.1 159043015 5711376 446220..447119 1 NC_009952.1 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 447119 5711376 Dshi_0460 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531809.1 446220 D 398580 CDS YP_001531810.1 159043016 5711377 447116..447790 1 NC_009952.1 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 447790 5711377 Dshi_0461 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531810.1 447116 D 398580 CDS YP_001531811.1 159043017 5711378 447787..448983 1 NC_009952.1 no significant swissprot, unsure GC frame plot; high Ref YP hit to hypothetical protein RD1_0878 from Roseobacter denitrificans OCh 114; hypothetical protein 448983 5711378 Dshi_0462 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531811.1 447787 D 398580 CDS YP_001531812.1 159043018 5711379 449156..449422 1 NC_009952.1 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 449422 5711379 Dshi_0463 Dinoroseobacter shibae DFL 12 = DSM 16493 transposase IS3/IS911 family protein YP_001531812.1 449156 D 398580 CDS YP_001531813.1 159043019 5711380 449446..450267 1 NC_009952.1 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 450267 5711380 Dshi_0464 Dinoroseobacter shibae DFL 12 = DSM 16493 integrase catalytic subunit YP_001531813.1 449446 D 398580 CDS YP_001531814.1 159043020 5711381 450313..451032 1 NC_009952.1 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 451032 luxR2 5711381 luxR2 Dinoroseobacter shibae DFL 12 = DSM 16493 two component transcriptional regulator YP_001531814.1 450313 D 398580 CDS YP_001531815.1 159043021 5711382 451045..452202 1 NC_009952.1 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 452202 5711382 Dshi_0466 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531815.1 451045 D 398580 CDS YP_001531816.1 159043022 5711383 452199..454475 1 NC_009952.1 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 454475 5711383 Dshi_0467 Dinoroseobacter shibae DFL 12 = DSM 16493 sensor histidine kinase YP_001531816.1 452199 D 398580 CDS YP_001531817.1 159043023 5711384 454509..455171 1 NC_009952.1 no significant swissprot; high Ref YP hit to hypothetical protein RD1_0882 from Roseobacter denitrificans OCh 114; hypothetical protein 455171 5711384 Dshi_0468 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531817.1 454509 D 398580 CDS YP_001531818.1 159043024 5711385 455168..455518 1 NC_009952.1 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 455518 5711385 Dshi_0469 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531818.1 455168 D 398580 CDS YP_001531819.1 159043025 5711386 complement(455582..456454) 1 NC_009952.1 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 456454 soxZ 5711386 soxZ Dinoroseobacter shibae DFL 12 = DSM 16493 sulfur oxidation protein SoxZ YP_001531819.1 455582 R 398580 CDS YP_001531820.1 159043026 5711387 456517..457557 1 NC_009952.1 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 457557 5711387 Dshi_0471 Dinoroseobacter shibae DFL 12 = DSM 16493 beta-lactamase domain-containing protein YP_001531820.1 456517 D 398580 CDS YP_001531821.1 159043027 5711388 complement(457583..458197) 1 NC_009952.1 no significant swissprot, no conserved domains, high REf YP hit to hypothetical protein RD1_0886 from Roseobacter denitrificans OCh 114; hypothetical protein 458197 5711388 Dshi_0472 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531821.1 457583 R 398580 CDS YP_001531822.1 159043028 5711389 458365..459477 1 NC_009952.1 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 459477 5711389 Dshi_0473 Dinoroseobacter shibae DFL 12 = DSM 16493 alcohol dehydrogenase class III/S-(hydroxymethyl)glutathione dehydrogenase YP_001531822.1 458365 D 398580 CDS YP_001531823.1 159043029 5711390 459481..460308 1 NC_009952.1 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 460308 5711390 Dshi_0474 Dinoroseobacter shibae DFL 12 = DSM 16493 S-formylglutathione hydrolase YP_001531823.1 459481 D 398580 CDS YP_001531824.1 159043030 5711391 460328..460729 1 NC_009952.1 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 460729 cytC 5711391 cytC Dinoroseobacter shibae DFL 12 = DSM 16493 cytochrome c class I YP_001531824.1 460328 D 398580 CDS YP_001531825.1 159043031 5711392 460857..462659 1 NC_009952.1 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 462659 gcd 5711392 gcd Dinoroseobacter shibae DFL 12 = DSM 16493 quinoprotein glucose dehydrogenase YP_001531825.1 460857 D 398580 CDS YP_001531826.1 159043032 5711393 462744..463289 1 NC_009952.1 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 463289 cccA 5711393 cccA Dinoroseobacter shibae DFL 12 = DSM 16493 cytochrome c protein YP_001531826.1 462744 D 398580 CDS YP_001531827.1 159043033 5711394 463273..464121 1 NC_009952.1 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 464121 5711394 Dshi_0478 Dinoroseobacter shibae DFL 12 = DSM 16493 family 3 extracellular solute-binding protein YP_001531827.1 463273 D 398580 CDS YP_001531828.1 159043034 5711395 464118..464666 1 NC_009952.1 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 464666 5711395 Dshi_0479 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531828.1 464118 D 398580 CDS YP_001531829.1 159043035 5711396 464801..465967 1 NC_009952.1 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 465967 5711396 Dshi_0480 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531829.1 464801 D 398580 CDS YP_001531830.1 159043036 5711397 complement(466019..466831) 1 NC_009952.1 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 466831 5711397 Dshi_0481 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531830.1 466019 R 398580 CDS YP_001531831.1 159043037 5711398 complement(467299..467784) 1 NC_009952.1 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 467784 5711398 Dshi_0482 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531831.1 467299 R 398580 CDS YP_001531832.1 159043038 5711399 467943..469130 1 NC_009952.1 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 469130 5711399 Dshi_0483 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531832.1 467943 D 398580 CDS YP_001531833.1 159043039 5711400 469158..470129 1 NC_009952.1 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 470129 5711400 Dshi_0484 Dinoroseobacter shibae DFL 12 = DSM 16493 40-residue YVTN family beta-propeller repeat-containing protein YP_001531833.1 469158 D 398580 CDS YP_001531834.1 159043040 5711401 470179..470616 1 NC_009952.1 no significant swissprot, no conserved domains, high Ref YP hit to hypothetical protein RD1_0900 [Roseobacter denitrificans OCh 114]; hypothetical protein 470616 5711401 Dshi_0485 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531834.1 470179 D 398580 CDS YP_001531835.1 159043041 5711402 470635..470883 1 NC_009952.1 no significant swissprot, no conserved domains, middle gb hit to hypothetical protein RLO149_07809 [Roseobacter litoralis Och 149].; hypothetical protein 470883 5711402 Dshi_0486 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531835.1 470635 D 398580 CDS YP_001531836.1 159043042 5711403 complement(471449..472675) 1 NC_009952.1 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 472675 5711403 Dshi_0487 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531836.1 471449 R 398580 CDS YP_001531837.1 159043043 5711404 complement(472665..473018) 1 NC_009952.1 no significant BLAST hits, no conserved domains (except for two transmembr. regions); good RBS site : AGGAT; hypothetical protein 473018 5711404 Dshi_0488 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531837.1 472665 R 398580 CDS YP_001531838.1 159043044 5711405 complement(473039..474289) 1 NC_009952.1 no significant BLAST hits, unsure GC frame plot; NCBI conserved domains: mncomplete BisC domain, Anaerobic dehydrogenases, typically selenocysteine-containing; hypothetical protein 474289 5711405 Dshi_0489 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531838.1 473039 R 398580 CDS YP_001531839.1 159043045 5711406 475571..475996 1 NC_009952.1 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 475996 5711406 Dshi_0490 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531839.1 475571 D 398580 CDS YP_001531840.1 159043046 5711407 476139..477122 1 NC_009952.1 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 477122 ssuA1 5711407 ssuA1 Dinoroseobacter shibae DFL 12 = DSM 16493 putative sulfonate/nitrate transport system substrate-binding protein YP_001531840.1 476139 D 398580 CDS YP_001531841.1 159043047 5711408 477181..478005 1 NC_009952.1 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 478005 ssuC1 5711408 ssuC1 Dinoroseobacter shibae DFL 12 = DSM 16493 sulfonate/nitrate/taurine transport system permease YP_001531841.1 477181 D 398580 CDS YP_001531842.1 159043048 5711409 478002..478751 1 NC_009952.1 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 478751 ssuB1 5711409 ssuB1 Dinoroseobacter shibae DFL 12 = DSM 16493 sulfonate/nitrate/taurine transport system ATP-binding YP_001531842.1 478002 D 398580 CDS YP_001531843.1 159043049 5711410 478748..480028 1 NC_009952.1 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 480028 nnrS 5711410 nnrS Dinoroseobacter shibae DFL 12 = DSM 16493 NnrS family protein YP_001531843.1 478748 D 398580 CDS YP_001531844.1 159043050 5711411 480087..480497 1 NC_009952.1 no significant swissprot; low Ref NP hit to ferrienterobactin-like protein [Agrobacterium tumefaciens str. C58]; Pfam07715 TonB-dependent Receptor Plug Domain; hypothetical protein 480497 5711411 Dshi_0495 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531844.1 480087 D 398580 CDS YP_001531845.1 159043051 5711412 complement(480704..482722) 1 NC_009952.1 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 482722 5711412 Dshi_0496 Dinoroseobacter shibae DFL 12 = DSM 16493 4Fe-4S ferredoxin YP_001531845.1 480704 R 398580 CDS YP_001531846.1 159043052 5711413 482822..483556 1 NC_009952.1 no significant swissprot, unsure GC frame plot, no conserved domains; good Ref ZP hit to hypothetical protein SKA53_09144 [Loktanella vestfoldensis SKA53]; hypothetical protein 483556 5711413 Dshi_0497 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531846.1 482822 D 398580 CDS YP_001531847.1 159043053 5711414 483553..484110 1 NC_009952.1 no significant swissprot; unsure GC frame plot; no conserved domains; good Ref ZP hit to hypothetical protein SKA53_09139 [Loktanella vestfoldensis SKA53]; hypothetical protein 484110 5711414 Dshi_0498 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531847.1 483553 D 398580 CDS YP_001531848.1 159043054 5711415 484107..485120 1 NC_009952.1 no significant swissprot, unsure GC frame plot; no conserved domains; high Ref ZP hit to hypothetical protein SKA53_09134 [Loktanella vestfoldensis SKA53]; hypothetical protein 485120 5711415 Dshi_0499 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531848.1 484107 D 398580 CDS YP_001531849.1 159043055 5711416 485120..485656 1 NC_009952.1 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 485656 5711416 Dshi_0500 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531849.1 485120 D 398580 CDS YP_001531850.1 159043056 5711417 485653..486264 1 NC_009952.1 no significant swissprot, no conserved domains; low Ref ZP hit to hypothetical protein SKA53_09124 [Loktanella vestfoldensis SKA53].; hypothetical protein 486264 5711417 Dshi_0501 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531850.1 485653 D 398580 CDS YP_001531851.1 159043057 5711418 486380..487042 1 NC_009952.1 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 487042 torD 5711418 torD Dinoroseobacter shibae DFL 12 = DSM 16493 cytoplasmic chaperone TorD family protein YP_001531851.1 486380 D 398580 CDS YP_001531852.1 159043058 5711419 487101..487310 1 NC_009952.1 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 487310 5711419 Dshi_0503 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531852.1 487101 D 398580 CDS YP_001531853.1 159043059 5711420 487314..490274 1 NC_009952.1 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 490274 fdnG 5711420 fdnG Dinoroseobacter shibae DFL 12 = DSM 16493 formate dehydrogenase subunit alpha YP_001531853.1 487314 D 398580 CDS YP_001531854.1 159043060 5711421 490289..490885 1 NC_009952.1 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 490885 fdnH 5711421 fdnH Dinoroseobacter shibae DFL 12 = DSM 16493 formate dehydrogenase iron-sulfur subunit YP_001531854.1 490289 D 398580 CDS YP_001531855.1 159043061 5711422 490899..491927 1 NC_009952.1 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 491927 fdnI 5711422 fdnI Dinoroseobacter shibae DFL 12 = DSM 16493 formate dehydrogenase subunit gamma YP_001531855.1 490899 D 398580 CDS YP_001531856.1 159043062 5711423 492087..493133 1 NC_009952.1 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 493133 5711423 Dshi_0507 Dinoroseobacter shibae DFL 12 = DSM 16493 MRP-like protein YP_001531856.1 492087 D 398580 CDS YP_001531857.1 159043063 5711424 493317..494531 1 NC_009952.1 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 494531 5711424 Dshi_0508 Dinoroseobacter shibae DFL 12 = DSM 16493 cytochrome c class I YP_001531857.1 493317 D 398580 CDS YP_001531858.1 159043064 5711425 complement(494625..495407) 1 NC_009952.1 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 495407 5711425 Dshi_0509 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531858.1 494625 R 398580 CDS YP_003422323.1 284928590 5711426 complement(495589..496662) 1 NC_009952.1 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 496662 5711426 Dshi_0510 Dinoroseobacter shibae DFL 12 = DSM 16493 beta-lactamase YP_003422323.1 495589 R 398580 CDS YP_003422324.1 284928591 8130634 complement(496690..496893) 1 NC_009952.1 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 496893 8130634 Dshi_0511 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_003422324.1 496690 R 398580 CDS YP_001531859.1 159043065 5711427 complement(496905..497582) 1 NC_009952.1 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 497582 5711427 Dshi_0512 Dinoroseobacter shibae DFL 12 = DSM 16493 beta-lactamase domain-containing protein YP_001531859.1 496905 R 398580 CDS YP_001531860.1 159043066 5711428 complement(498319..498786) 1 NC_009952.1 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 498786 5711428 Dshi_0513 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001531860.1 498319 R 398580 CDS YP_001531861.1 159043067 5711429 complement(498765..498947) 1 NC_009952.1 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 498947 5711429 Dshi_0514 Dinoroseobacter shibae DFL 12 = DSM 16493 response regulator receiver protein YP_001531861.1 498765 R 398580 CDS YP_001531862.1 159043068 5711430 complement(498944..499843) 1 NC_009952.1 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 499843 5711430 Dshi_0515 Dinoroseobacter shibae DFL 12 = DSM 16493 histidine kinase YP_001531862.1 498944 R 398580 CDS YP_001531863.1 159043069 5711431 complement(499850..500836) 1 NC_009952.1 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 500836 5711431 Dshi_0516 Dinoroseobacter shibae DFL 12 = DSM 16493 putative two-component sensor kinase YP_001531863.1 499850 R 398580 CDS YP_001531864.1 159043070 5711432 complement(501109..502149) 1 NC_009952.1 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 502149 araF2 5711432 araF2 Dinoroseobacter shibae DFL 12 = DSM 16493 ribose/xylose/arabinose/galactoside ABC-type transport system protein YP_001531864.1 501109 R 398580 CDS YP_001531865.1 159043071 5711433 complement(502175..503185) 1 NC_009952.1 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 503185 araH1 5711433 araH1 Dinoroseobacter shibae DFL 12 = DSM 16493 ribose/xylose/arabinose/galactoside ABC-type transport system protein YP_001531865.1 502175 R 398580 CDS YP_001531866.1 159043072 5711434 complement(503182..504678) 1 NC_009952.1 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 504678 araG1 5711434 araG1 Dinoroseobacter shibae DFL 12 = DSM 16493 ribose/xylose/arabinose/galactoside ABC-type transport system protein YP_001531866.1 503182 R 398580 CDS YP_001531867.1 159043073 5711973 504830..506089 1 NC_009952.1 phosphorylates methylthioribose to form methylthioribose-1-phosphate; involved in methionine salvage pathway; methylthioribose kinase 506089 mtnK 5711973 mtnK Dinoroseobacter shibae DFL 12 = DSM 16493 methylthioribose kinase YP_001531867.1 504830 D 398580 CDS YP_001531868.1 159043074 5711974 506086..507189 1 NC_009952.1 isomerizes methylthioribose-1-phosphate into methylthioribulose-1-phosphate; involved in methionine salvage pathway; methylthioribose-1-phosphate isomerase 507189 mtnA 5711974 mtnA Dinoroseobacter shibae DFL 12 = DSM 16493 methylthioribose-1-phosphate isomerase YP_001531868.1 506086 D 398580 CDS YP_001531869.1 159043075 5711975 507247..508206 1 NC_009952.1 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 508206 deoR3 5711975 deoR3 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001531869.1 507247 D 398580 CDS YP_001531870.1 159043076 5711976 508203..508898 1 NC_009952.1 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 508898 fucA 5711976 fucA Dinoroseobacter shibae DFL 12 = DSM 16493 L-fuculose phosphate aldolase YP_001531870.1 508203 D 398580 CDS YP_001531871.1 159043077 5711977 508895..509974 1 NC_009952.1 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 509974 5711977 Dshi_0524 Dinoroseobacter shibae DFL 12 = DSM 16493 aldo/keto reductase YP_001531871.1 508895 D 398580 CDS YP_001531872.1 159043078 5711978 510058..510609 1 NC_009952.1 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 510609 5711978 Dshi_0525 Dinoroseobacter shibae DFL 12 = DSM 16493 ATPase-like protein YP_001531872.1 510058 D 398580 CDS YP_001531873.1 159043079 5711979 complement(510637..511236) 1 NC_009952.1 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 511236 dahL 5711979 dahL Dinoroseobacter shibae DFL 12 = DSM 16493 PTS-dependent dihydroxyacetone kinase YP_001531873.1 510637 R 398580 CDS YP_001531874.1 159043080 5711980 complement(511233..512234) 1 NC_009952.1 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 512234 dahK 5711980 dahK Dinoroseobacter shibae DFL 12 = DSM 16493 PTS-dependent dihydroxyacetone kinase YP_001531874.1 511233 R 398580 CDS YP_001531875.1 159043081 5711981 complement(512265..513269) 1 NC_009952.1 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 513269 araH2 5711981 araH2 Dinoroseobacter shibae DFL 12 = DSM 16493 ribose/xylose/arabinose/galactoside ABC-type transport system protein YP_001531875.1 512265 R 398580 CDS YP_001531876.1 159043082 5711982 complement(513283..514284) 1 NC_009952.1 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 514284 araH3 5711982 araH3 Dinoroseobacter shibae DFL 12 = DSM 16493 ribose/xylose/arabinose/galactoside ABC-type transport system protein YP_001531876.1 513283 R 398580 CDS YP_001531877.1 159043083 5711983 complement(514281..515777) 1 NC_009952.1 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 515777 araG2 5711983 araG2 Dinoroseobacter shibae DFL 12 = DSM 16493 ribose/xylose/arabinose/galactoside ABC-type transport system protein YP_001531877.1 514281 R 398580 CDS YP_001531878.1 159043084 5711984 complement(515852..516841) 1 NC_009952.1 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 516841 araF1 5711984 araF1 Dinoroseobacter shibae DFL 12 = DSM 16493 ribose/xylose/arabinose/galactoside ABC-type transport system protein YP_001531878.1 515852 R 398580 CDS YP_001531879.1 159043085 5711985 517065..518039 1 NC_009952.1 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 518039 deoR2 5711985 deoR2 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001531879.1 517065 D 398580 CDS YP_001531880.1 159043086 5711986 518039..518887 1 NC_009952.1 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 518887 5711986 Dshi_0533 Dinoroseobacter shibae DFL 12 = DSM 16493 xylose isomerase domain-containing protein YP_001531880.1 518039 D 398580 CDS YP_001531881.1 159043087 5711987 518910..519929 1 NC_009952.1 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 519929 pdhA2 5711987 pdhA2 Dinoroseobacter shibae DFL 12 = DSM 16493 pyruvate dehydrogenase E1 component subunit alpha YP_001531881.1 518910 D 398580 CDS YP_001531882.1 159043088 5711988 519929..520912 1 NC_009952.1 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 520912 pdhB1 5711988 pdhB1 Dinoroseobacter shibae DFL 12 = DSM 16493 pyruvate dehydrogenase E1 component subunit beta YP_001531882.1 519929 D 398580 CDS YP_001531883.1 159043089 5711989 520939..522135 1 NC_009952.1 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 522135 pdhC2 5711989 pdhC2 Dinoroseobacter shibae DFL 12 = DSM 16493 branched-chain alpha-keto acid dehydrogenase subunit E2 YP_001531883.1 520939 D 398580 CDS YP_001531884.1 159043090 5711990 522165..523658 1 NC_009952.1 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 523658 5711990 Dshi_0537 Dinoroseobacter shibae DFL 12 = DSM 16493 carbohydrate kinase FGGY YP_001531884.1 522165 D 398580 CDS YP_001531885.1 159043091 5711991 523844..524515 1 NC_009952.1 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 524515 5711991 Dshi_0538 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531885.1 523844 D 398580 CDS YP_001531886.1 159043092 5711992 complement(524529..525467) 1 NC_009952.1 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 525467 5711992 Dshi_0539 Dinoroseobacter shibae DFL 12 = DSM 16493 oxidoreductase YP_001531886.1 524529 R 398580 CDS YP_001531887.1 159043093 5711993 525545..526321 1 NC_009952.1 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 526321 5711993 Dshi_0540 Dinoroseobacter shibae DFL 12 = DSM 16493 NnrU family protein YP_001531887.1 525545 D 398580 CDS YP_001531888.1 159043094 5711994 526456..527820 1 NC_009952.1 catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III; coproporphyrinogen III oxidase 527820 hemN1 5711994 hemN1 Dinoroseobacter shibae DFL 12 = DSM 16493 coproporphyrinogen III oxidase YP_001531888.1 526456 D 398580 CDS YP_001531889.1 159043095 5711995 complement(528241..529869) 1 NC_009952.1 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 529869 5711995 Dshi_0542 Dinoroseobacter shibae DFL 12 = DSM 16493 phosphate transporter YP_001531889.1 528241 R 398580 CDS YP_001531890.1 159043096 5711996 529946..531796 1 NC_009952.1 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 531796 5711996 Dshi_0543 Dinoroseobacter shibae DFL 12 = DSM 16493 Na+/Pi-cotransporter YP_001531890.1 529946 D 398580 CDS YP_001531891.1 159043097 5711997 531843..532091 1 NC_009952.1 no significant BLAST hits, no conserved domains detected; hypothetical protein 532091 5711997 Dshi_0544 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531891.1 531843 D 398580 CDS YP_001531892.1 159043098 5711998 complement(532144..532884) 1 NC_009952.1 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 532884 5711998 Dshi_0545 Dinoroseobacter shibae DFL 12 = DSM 16493 HAD-superfamily hydrolase YP_001531892.1 532144 R 398580 CDS YP_001531893.1 159043099 5711999 complement(532894..533910) 1 NC_009952.1 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 533910 ugpC2 5711999 ugpC2 Dinoroseobacter shibae DFL 12 = DSM 16493 sugar/sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC YP_001531893.1 532894 R 398580 CDS YP_001531894.1 159043100 5712000 534071..535414 1 NC_009952.1 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 535414 ugpB4 5712000 ugpB4 Dinoroseobacter shibae DFL 12 = DSM 16493 sugar/sn-glycerol 3-phosphate ABC transporter protein YP_001531894.1 534071 D 398580 CDS YP_001531895.1 159043101 5712001 535489..536355 1 NC_009952.1 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 536355 ugpA1 5712001 ugpA1 Dinoroseobacter shibae DFL 12 = DSM 16493 sugar/sn-glycerol-3-phosphate ABC transporter permease UgpA YP_001531895.1 535489 D 398580 CDS YP_001531896.1 159043102 5712002 536359..537177 1 NC_009952.1 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 537177 ugpE4 5712002 ugpE4 Dinoroseobacter shibae DFL 12 = DSM 16493 sugar/sn-glycerol-3-phosphate ABC transporter permease UgpE YP_001531896.1 536359 D 398580 CDS YP_001531897.1 159043103 5712003 537246..538217 1 NC_009952.1 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 538217 deoR1 5712003 deoR1 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001531897.1 537246 D 398580 CDS YP_001531898.1 159043104 5712004 538237..539280 1 NC_009952.1 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 539280 xylD 5712004 xylD Dinoroseobacter shibae DFL 12 = DSM 16493 D-xylulose reductase YP_001531898.1 538237 D 398580 CDS YP_001531899.1 159043105 5712005 539277..539843 1 NC_009952.1 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 539843 5712005 Dshi_0552 Dinoroseobacter shibae DFL 12 = DSM 16493 sugar isomerase YP_001531899.1 539277 D 398580 CDS YP_001531900.1 159043106 5712006 539847..540614 1 NC_009952.1 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 540614 5712006 Dshi_0553 Dinoroseobacter shibae DFL 12 = DSM 16493 short-chain dehydrogenase/reductase SDR YP_001531900.1 539847 D 398580 CDS YP_001531901.1 159043107 5712007 541133..541858 1 NC_009952.1 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 541858 rbtD 5712007 rbtD Dinoroseobacter shibae DFL 12 = DSM 16493 ribitol 2-dehydrogenase YP_001531901.1 541133 D 398580 CDS YP_001531902.1 159043108 5712008 541855..543489 1 NC_009952.1 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 543489 araB 5712008 araB Dinoroseobacter shibae DFL 12 = DSM 16493 ribulokinase YP_001531902.1 541855 D 398580 CDS YP_001531903.1 159043109 5712009 544002..544445 1 NC_009952.1 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 544445 5712009 Dshi_0556 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531903.1 544002 D 398580 CDS YP_001531904.1 159043110 5712010 544496..544927 1 NC_009952.1 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 544927 greA2 5712010 greA2 Dinoroseobacter shibae DFL 12 = DSM 16493 GreA/GreB family elongation factor YP_001531904.1 544496 D 398580 CDS YP_001531905.1 159043111 5712011 545054..546313 1 NC_009952.1 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 546313 dadA 5712011 dadA Dinoroseobacter shibae DFL 12 = DSM 16493 D-amino-acid dehydrogenase YP_001531905.1 545054 D 398580 CDS YP_001531906.1 159043112 5712012 546760..547167 1 NC_009952.1 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 547167 5712012 Dshi_0559 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531906.1 546760 D 398580 CDS YP_001531907.1 159043113 5712013 547164..547937 1 NC_009952.1 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 547937 fhuC 5712013 fhuC Dinoroseobacter shibae DFL 12 = DSM 16493 cobalamin/Fe3+-siderophores ABC transporter protein YP_001531907.1 547164 D 398580 CDS YP_001531908.1 159043114 5712014 547953..548888 1 NC_009952.1 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 548888 fhuD 5712014 fhuD Dinoroseobacter shibae DFL 12 = DSM 16493 cobalamin/Fe3+-siderophores ABC transporter protein YP_001531908.1 547953 D 398580 CDS YP_001531909.1 159043115 5712015 548885..549931 1 NC_009952.1 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 549931 fhuB 5712015 fhuB Dinoroseobacter shibae DFL 12 = DSM 16493 cobalamin/Fe3+-siderophores ABC transporter protein YP_001531909.1 548885 D 398580 CDS YP_001531910.1 159043116 5712016 550566..551828 1 NC_009952.1 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 551828 irpA 5712016 irpA Dinoroseobacter shibae DFL 12 = DSM 16493 iron-regulated protein YP_001531910.1 550566 D 398580 CDS YP_001531911.1 159043117 5712017 551932..553464 1 NC_009952.1 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 553464 5712017 Dshi_0564 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531911.1 551932 D 398580 CDS YP_001531912.1 159043118 5712018 553461..554477 1 NC_009952.1 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 554477 5712018 Dshi_0565 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531912.1 553461 D 398580 CDS YP_001531913.1 159043119 5712019 554479..555561 1 NC_009952.1 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 555561 5712019 Dshi_0566 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531913.1 554479 D 398580 CDS YP_001531914.1 159043120 5712020 complement(555614..556162) 1 NC_009952.1 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 556162 5712020 Dshi_0567 Dinoroseobacter shibae DFL 12 = DSM 16493 TonB family protein YP_001531914.1 555614 R 398580 CDS YP_001531915.1 159043121 5712021 complement(556657..557049) 1 NC_009952.1 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 557049 exbD 5712021 exbD Dinoroseobacter shibae DFL 12 = DSM 16493 biopolymer transport protein ExbD/TolR YP_001531915.1 556657 R 398580 CDS YP_001531916.1 159043122 5712022 complement(557437..558129) 1 NC_009952.1 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 558129 exbB 5712022 exbB Dinoroseobacter shibae DFL 12 = DSM 16493 MotA/TolQ/ExbB proton channel YP_001531916.1 557437 R 398580 CDS YP_001531917.1 159043123 5712023 558999..561026 1 NC_009952.1 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 561026 fhuA 5712023 fhuA Dinoroseobacter shibae DFL 12 = DSM 16493 cobalamin/Fe3+-siderophores ABC transporter protein YP_001531917.1 558999 D 398580 CDS YP_001531918.1 159043124 5712024 complement(561072..561854) 1 NC_009952.1 with HmuTU is involved in the transport of hemin; hemin importer ATP-binding subunit 561854 hmuV 5712024 hmuV Dinoroseobacter shibae DFL 12 = DSM 16493 hemin importer ATP-binding subunit YP_001531918.1 561072 R 398580 CDS YP_001531919.1 159043125 5712025 complement(561851..562933) 1 NC_009952.1 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 562933 hmuU 5712025 hmuU Dinoroseobacter shibae DFL 12 = DSM 16493 hemin transport system permease hmuU YP_001531919.1 561851 R 398580 CDS YP_001531920.1 159043126 5712026 complement(562923..563759) 1 NC_009952.1 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 563759 hmuT 5712026 hmuT Dinoroseobacter shibae DFL 12 = DSM 16493 hemin-binding periplasmic protein HmuT YP_001531920.1 562923 R 398580 CDS YP_001531921.1 159043127 5712027 complement(563756..564787) 1 NC_009952.1 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 564787 hmuS 5712027 hmuS Dinoroseobacter shibae DFL 12 = DSM 16493 hemin transport protein hmuS YP_001531921.1 563756 R 398580 CDS YP_001531922.1 159043128 5712028 complement(564854..565354) 1 NC_009952.1 no significant swissprot, no conserved domains; low Ref ZP hit to hypothetical protein SSE37_21645 [Sagittula stellata E-37].; hypothetical protein 565354 5712028 Dshi_0575 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531922.1 564854 R 398580 CDS YP_001531923.1 159043129 5712029 complement(565766..566635) 1 NC_009952.1 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 566635 5712029 Dshi_0576 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001531923.1 565766 R 398580 CDS YP_001531924.1 159043130 5712030 566726..568177 1 NC_009952.1 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 568177 aldH2 5712030 aldH2 Dinoroseobacter shibae DFL 12 = DSM 16493 aldehyde dehydrogenase YP_001531924.1 566726 D 398580 CDS YP_001531925.1 159043131 5712031 568174..569184 1 NC_009952.1 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 569184 rDP 5712031 rDP Dinoroseobacter shibae DFL 12 = DSM 16493 peptidase M19 YP_001531925.1 568174 D 398580 CDS YP_001531926.1 159043132 5712032 569219..570778 1 NC_009952.1 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 570778 betT 5712032 betT Dinoroseobacter shibae DFL 12 = DSM 16493 choline-glycine betaine transporter YP_001531926.1 569219 D 398580 CDS YP_001531927.1 159043133 5712033 570846..572522 1 NC_009952.1 unsure GC frame plot, no significant swissprot, no conserved domains; high Ref ZP hit to hypothetical protein ROS217_07275 [Roseovarius sp. 217]; hypothetical protein 572522 5712033 Dshi_0580 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531927.1 570846 D 398580 CDS YP_001531928.1 159043134 5712034 572519..573250 1 NC_009952.1 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 573250 5712034 Dshi_0581 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531928.1 572519 D 398580 CDS YP_001531929.1 159043135 5712035 573264..573629 1 NC_009952.1 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 573629 5712035 Dshi_0582 Dinoroseobacter shibae DFL 12 = DSM 16493 putative Endoribonuclease L-PSP YP_001531929.1 573264 D 398580 CDS YP_001531930.1 159043136 5712037 complement(574071..574904) 1 NC_009952.1 catalyzes the formation of 2-dehydro-3-deoxy-D-octonate 8-phosphate from phosphoenolpyruvate and D-arabinose 5-phosphate in LPS biosynthesis; 2-dehydro-3-deoxyphosphooctonate aldolase 574904 kdsA 5712037 kdsA Dinoroseobacter shibae DFL 12 = DSM 16493 2-dehydro-3-deoxyphosphooctonate aldolase YP_001531930.1 574071 R 398580 CDS YP_001531931.1 159043137 5712038 complement(574921..576630) 1 NC_009952.1 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 576630 kpsE 5712038 kpsE Dinoroseobacter shibae DFL 12 = DSM 16493 capsule polysaccharide export YP_001531931.1 574921 R 398580 CDS YP_001531932.1 159043138 5712039 complement(576608..577267) 1 NC_009952.1 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 577267 kpsT 5712039 kpsT Dinoroseobacter shibae DFL 12 = DSM 16493 capsule polysaccharide export YP_001531932.1 576608 R 398580 CDS YP_001531933.1 159043139 5712040 complement(577452..578498) 1 NC_009952.1 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 578498 kpsM 5712040 kpsM Dinoroseobacter shibae DFL 12 = DSM 16493 capsule polysaccharide transport YP_001531933.1 577452 R 398580 CDS YP_001531934.1 159043140 5712041 complement(578470..578814) 1 NC_009952.1 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 578814 5712041 Dshi_0587 Dinoroseobacter shibae DFL 12 = DSM 16493 putative transcriptional regulator YP_001531934.1 578470 R 398580 CDS YP_001531935.1 159043141 5712042 578892..579500 1 NC_009952.1 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 579500 5712042 Dshi_0588 Dinoroseobacter shibae DFL 12 = DSM 16493 uracil-DNA glycosylase superfamily YP_001531935.1 578892 D 398580 CDS YP_001531936.1 159043142 5712043 579497..580282 1 NC_009952.1 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 580282 5712043 Dshi_0589 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531936.1 579497 D 398580 CDS YP_001531937.1 159043143 5712044 complement(580316..581251) 1 NC_009952.1 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 581251 5712044 Dshi_0590 Dinoroseobacter shibae DFL 12 = DSM 16493 D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding subunit YP_001531937.1 580316 R 398580 CDS YP_001531938.1 159043144 5712045 complement(581261..582400) 1 NC_009952.1 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 582400 mreD1 5712045 mreD1 Dinoroseobacter shibae DFL 12 = DSM 16493 rod shape-determining protein MreD YP_001531938.1 581261 R 398580 CDS YP_001531939.1 159043145 5712046 complement(582397..584340) 1 NC_009952.1 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 584340 ftsI1 5712046 ftsI1 Dinoroseobacter shibae DFL 12 = DSM 16493 division-specific transpeptidase YP_001531939.1 582397 R 398580 CDS YP_001531940.1 159043146 5712047 complement(584337..584876) 1 NC_009952.1 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 584876 mreD2 5712047 mreD2 Dinoroseobacter shibae DFL 12 = DSM 16493 putative rod shape-determining protein MreD YP_001531940.1 584337 R 398580 CDS YP_001531941.1 159043147 5712048 complement(584869..585768) 1 NC_009952.1 in some organisms this protein is a transmembrane protein while in others it is periplasmic; involved in some organisms with other components of the MreBCD complex and with penicillin binding proteins in the periplasm or cell wall; rod shape-determining protein MreC 585768 mreC 5712048 mreC Dinoroseobacter shibae DFL 12 = DSM 16493 rod shape-determining protein MreC YP_001531941.1 584869 R 398580 CDS YP_001531942.1 159043148 5712049 complement(585804..586841) 1 NC_009952.1 functions in MreBCD complex in some organisms; rod shape-determining protein MreB 586841 mreB 5712049 mreB Dinoroseobacter shibae DFL 12 = DSM 16493 rod shape-determining protein MreB YP_001531942.1 585804 R 398580 CDS YP_001531943.1 159043149 5712050 complement(587090..588667) 1 NC_009952.1 catalyzes the formation of 2-isopropylmalate from acetyl-CoA and 2-oxoisovalerate in leucine biosynthesis; 2-isopropylmalate synthase 588667 leuA 5712050 leuA Dinoroseobacter shibae DFL 12 = DSM 16493 2-isopropylmalate synthase YP_001531943.1 587090 R 398580 CDS YP_001531944.1 159043150 5712051 complement(588851..589648) 1 NC_009952.1 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 589648 5712051 Dshi_0597 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531944.1 588851 R 398580 CDS YP_001531945.1 159043151 5712052 589775..590440 1 NC_009952.1 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 590440 5712052 Dshi_0598 Dinoroseobacter shibae DFL 12 = DSM 16493 short-chain dehydrogenase/reductase SDR YP_001531945.1 589775 D 398580 CDS YP_001531946.1 159043152 5712053 590437..591963 1 NC_009952.1 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 591963 5712053 Dshi_0599 Dinoroseobacter shibae DFL 12 = DSM 16493 deoxyribodipyrimidine photolyase-like protein YP_001531946.1 590437 D 398580 CDS YP_001531947.1 159043153 5712054 complement(592010..593416) 1 NC_009952.1 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 593416 5712054 Dshi_0600 Dinoroseobacter shibae DFL 12 = DSM 16493 MORN repeat-containing protein YP_001531947.1 592010 R 398580 CDS YP_001531948.1 159043154 5712055 593670..595343 1 NC_009952.1 NH(3)-dependent; catalyzes the formation of nicotinamide adenine dinucleotide (NAD) from nicotinic acid adenine dinucleotide (NAAD) using either ammonia or glutamine as the amide donor and ATP; ammonia-utilizing enzymes include the ones from Bacillus and Escherichia coli while glutamine-utilizing enzymes include the Mycobacterial one; forms homodimers; NAD synthetase 595343 nadE 5712055 nadE Dinoroseobacter shibae DFL 12 = DSM 16493 NAD synthetase YP_001531948.1 593670 D 398580 CDS YP_001531949.1 159043155 5712056 complement(595527..595928) 1 NC_009952.1 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 595928 5712056 Dshi_0602 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531949.1 595527 R 398580 CDS YP_001531950.1 159043156 5712057 complement(596472..596903) 1 NC_009952.1 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 596903 5712057 Dshi_0603 Dinoroseobacter shibae DFL 12 = DSM 16493 thioesterase superfamily protein YP_001531950.1 596472 R 398580 CDS YP_001531951.1 159043157 5712058 complement(596939..597799) 1 NC_009952.1 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 597799 5712058 Dshi_0604 Dinoroseobacter shibae DFL 12 = DSM 16493 amidohydrolase family protein YP_001531951.1 596939 R 398580 CDS YP_001531952.1 159043158 5712059 complement(597820..599106) 1 NC_009952.1 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 599106 dctM5 5712059 dctM5 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP dicarboxylate transporter YP_001531952.1 597820 R 398580 CDS YP_001531953.1 159043159 5712060 complement(599132..599698) 1 NC_009952.1 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 599698 5712060 Dshi_0606 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531953.1 599132 R 398580 CDS YP_001531954.1 159043160 5712061 complement(599763..600845) 1 NC_009952.1 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 600845 dctP5 5712061 dctP5 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP dicarboxylate transporter subunit DctP YP_001531954.1 599763 R 398580 CDS YP_001531955.1 159043161 5712062 complement(600943..601713) 1 NC_009952.1 unsure GC frame plot; no significant swissprot; no conserved domains; low Ref YP hit to hypothetical protein TM1040_3278 [Silicibacter sp. TM1040].; hypothetical protein 601713 5712062 Dshi_0608 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531955.1 600943 R 398580 CDS YP_001531956.1 159043162 5712063 601843..603387 1 NC_009952.1 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 603387 5712063 Dshi_0609 Dinoroseobacter shibae DFL 12 = DSM 16493 GntR family transcriptional regulator YP_001531956.1 601843 D 398580 CDS YP_001531957.1 159043163 5712064 complement(603311..604093) 1 NC_009952.1 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 604093 5712064 Dshi_0610 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531957.1 603311 R 398580 CDS YP_001531958.1 159043164 5712065 complement(604086..604418) 1 NC_009952.1 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 604418 5712065 Dshi_0611 Dinoroseobacter shibae DFL 12 = DSM 16493 NIPSNAP family containing protein YP_001531958.1 604086 R 398580 CDS YP_001531959.1 159043165 5712066 complement(605184..606101) 1 NC_009952.1 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 606101 5712066 Dshi_0612 Dinoroseobacter shibae DFL 12 = DSM 16493 beta-lactamase domain-containing protein YP_001531959.1 605184 R 398580 CDS YP_001531960.1 159043166 5712067 606284..607171 1 NC_009952.1 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 607171 5712067 Dshi_0613 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531960.1 606284 D 398580 CDS YP_001531961.1 159043167 5712068 607171..607452 1 NC_009952.1 PFAM01957 Nodulation efficiency, NfeD; no significant swissprot; low Ref YP hit to hypothetical protein Rsph17025_2810 [Rhodobacter sphaeroides ATCC 17025].; hypothetical protein 607452 5712068 Dshi_0614 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531961.1 607171 D 398580 CDS YP_001531962.1 159043168 5712069 complement(607474..608172) 1 NC_009952.1 type 1 subfamily; involved in last step of pyrimidine biosynthesis; converts orotidine 5'-phosphate to UMP and carbon dioxide; OMP decarboxylase; OMPDCase; OMPdecase; orotidine 5'-phosphate decarboxylase 608172 pyrF 5712069 pyrF Dinoroseobacter shibae DFL 12 = DSM 16493 orotidine 5'-phosphate decarboxylase YP_001531962.1 607474 R 398580 CDS YP_001531963.1 159043169 5712070 608284..608697 1 NC_009952.1 unsure GC frame plot, no significant BLAST hits; no conserved domains; hypothetical protein 608697 5712070 Dshi_0616 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531963.1 608284 D 398580 CDS YP_001531964.1 159043170 5712071 609070..611685 1 NC_009952.1 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 611685 clpB 5712071 clpB Dinoroseobacter shibae DFL 12 = DSM 16493 chaperone protein clpB YP_001531964.1 609070 D 398580 CDS YP_001531965.1 159043171 5712072 611730..612320 1 NC_009952.1 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 612320 5712072 Dshi_0618 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531965.1 611730 D 398580 CDS YP_001531966.1 159043172 5712073 612549..612863 1 NC_009952.1 no significant swissprot, no conserved domains detected; bad Ref ZP hit to SNase-like nuclease [Roseobacter sp. AzwK-3b].; hypothetical protein 612863 5712073 Dshi_0619 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531966.1 612549 D 398580 CDS YP_001531967.1 159043173 5712074 complement(612860..613612) 1 NC_009952.1 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 613612 fabG2 5712074 fabG2 Dinoroseobacter shibae DFL 12 = DSM 16493 3-oxoacyl-ACP reductase YP_001531967.1 612860 R 398580 CDS YP_001531968.1 159043174 5712075 complement(613772..614260) 1 NC_009952.1 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 614260 5712075 Dshi_0621 Dinoroseobacter shibae DFL 12 = DSM 16493 fasciclin domain-containing protein YP_001531968.1 613772 R 398580 CDS YP_001531969.1 159043175 5712076 complement(614334..614825) 1 NC_009952.1 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 614825 5712076 Dshi_0622 Dinoroseobacter shibae DFL 12 = DSM 16493 fasciclin domain-containing protein YP_001531969.1 614334 R 398580 CDS YP_001531970.1 159043176 5712077 615171..616088 1 NC_009952.1 in Escherichia coli this periplasmic enzyme was found to encode the periplasmic catalytic subunit of an oxidoreductase; sulfite oxidase activity not demonstrated; requires inner membrane anchor protein YedZ; putative sulfite oxidase subunit YedY 616088 yedY 5712077 yedY Dinoroseobacter shibae DFL 12 = DSM 16493 putative sulfite oxidase subunit YedY YP_001531970.1 615171 D 398580 CDS YP_001531971.1 159043177 5712078 616088..616696 1 NC_009952.1 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 616696 yedZ 5712078 yedZ Dinoroseobacter shibae DFL 12 = DSM 16493 putative sulfite oxidase subunit YedZ YP_001531971.1 616088 D 398580 CDS YP_001531972.1 159043178 5712084 623104..623826 1 NC_009952.1 unsure GC frame plot, no significant BLAST hits; hypothetical protein 623826 5712084 Dshi_0625 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531972.1 623104 D 398580 CDS YP_001531973.1 159043179 5712085 624057..624743 1 NC_009952.1 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 624743 5712085 Dshi_0626 Dinoroseobacter shibae DFL 12 = DSM 16493 basic organic compound ABC-transporter YP_001531973.1 624057 D 398580 CDS YP_001531974.1 159043180 5712086 624736..625491 1 NC_009952.1 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 625491 5712086 Dshi_0627 Dinoroseobacter shibae DFL 12 = DSM 16493 basic organic compound ABC-transporter YP_001531974.1 624736 D 398580 CDS YP_001531975.1 159043181 5712087 625528..626358 1 NC_009952.1 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 626358 5712087 Dshi_0628 Dinoroseobacter shibae DFL 12 = DSM 16493 basic organic compound ABC-transporter YP_001531975.1 625528 D 398580 CDS YP_001531976.1 159043182 5712088 complement(626365..627237) 1 NC_009952.1 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 627237 5712088 Dshi_0629 Dinoroseobacter shibae DFL 12 = DSM 16493 periplasmic substrate-binding protein YP_001531976.1 626365 R 398580 CDS YP_001531977.1 159043183 5712089 complement(627302..628897) 1 NC_009952.1 in Escherichia coli this homodimeric enzyme is expressed under aerobic conditions; anaerobic expression is repressed by the arcAB system; converts sn-glycerol-3-phosphate and ubiquinone-8 to dihydroxy acetone phosphate and ubiquinol-8; associates with the cytoplasmic membrane; glycerol-3-phosphate dehydrogenase 628897 glpD 5712089 glpD Dinoroseobacter shibae DFL 12 = DSM 16493 glycerol-3-phosphate dehydrogenase YP_001531977.1 627302 R 398580 CDS YP_001531978.1 159043184 5712090 629081..629854 1 NC_009952.1 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 629854 glpR 5712090 glpR Dinoroseobacter shibae DFL 12 = DSM 16493 glycerol-3-phosphate regulon repressor YP_001531978.1 629081 D 398580 CDS YP_001531979.1 159043185 5712091 complement(629832..630980) 1 NC_009952.1 TIGRFAM: acetate kinase PFAM: acetate and butyrate kinase KEGG: rde:RD1_3831 acetate kinase; Acetokinase; acetate kinase 630980 ackA 5712091 ackA Dinoroseobacter shibae DFL 12 = DSM 16493 acetate kinase YP_001531979.1 629832 R 398580 CDS YP_001531980.1 159043186 5712092 complement(630977..632392) 1 NC_009952.1 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 632392 pta2 5712092 pta2 Dinoroseobacter shibae DFL 12 = DSM 16493 bifunctional enoyl-CoA hydratase/phosphate acetyltransferase YP_001531980.1 630977 R 398580 CDS YP_001531981.1 159043187 5712093 632597..633406 1 NC_009952.1 no significant swissprot, no conserved domains; high gb hit to glycosyltransferase, putative [Roseobacter litoralis Och 149].; hypothetical protein 633406 5712093 Dshi_0634 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531981.1 632597 D 398580 CDS YP_001531982.1 159043188 5712094 complement(633409..635610) 1 NC_009952.1 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 635610 5712094 Dshi_0635 Dinoroseobacter shibae DFL 12 = DSM 16493 putative sulfate permease with cyclic nucleotide-binding domain YP_001531982.1 633409 R 398580 CDS YP_001531983.1 159043189 5712095 complement(635809..636474) 1 NC_009952.1 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 636474 5712095 Dshi_0636 Dinoroseobacter shibae DFL 12 = DSM 16493 phospholipase/carboxylesterase YP_001531983.1 635809 R 398580 CDS YP_001531984.1 159043190 5712096 complement(636471..637394) 1 NC_009952.1 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 637394 5712096 Dshi_0637 Dinoroseobacter shibae DFL 12 = DSM 16493 glyoxalase/bleomycin resistance protein/dioxygenase YP_001531984.1 636471 R 398580 CDS YP_001531985.1 159043191 5712097 637586..638542 1 NC_009952.1 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 638542 5712097 Dshi_0638 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC-A-subfamily transporter YP_001531985.1 637586 D 398580 CDS YP_001531986.1 159043192 5712098 638539..639300 1 NC_009952.1 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 639300 5712098 Dshi_0639 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC transporter YP_001531986.1 638539 D 398580 CDS YP_001531987.1 159043193 5712099 639402..640199 1 NC_009952.1 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 640199 5712099 Dshi_0640 Dinoroseobacter shibae DFL 12 = DSM 16493 peptidase S49 YP_001531987.1 639402 D 398580 CDS YP_001531988.1 159043194 5711476 640204..640374 1 NC_009952.1 no swissprot, no conserved domains, bad Ref ZP hit to hypothetical protein ISM_10031 [Roseovarius nubinhibens ISM].; hypothetical protein 640374 5711476 Dshi_0641 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531988.1 640204 D 398580 CDS YP_001531989.1 159043195 5711477 640377..641315 1 NC_009952.1 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 641315 5711477 Dshi_0642 Dinoroseobacter shibae DFL 12 = DSM 16493 Na+/Ca+ antiporter YP_001531989.1 640377 D 398580 CDS YP_001531990.1 159043196 5711478 641326..642117 1 NC_009952.1 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 642117 5711478 Dshi_0643 Dinoroseobacter shibae DFL 12 = DSM 16493 short chain dehydrogenase YP_001531990.1 641326 D 398580 CDS YP_001531991.1 159043197 5711479 642411..644306 1 NC_009952.1 The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrC both incises the 5' and 3' sides of the lesion. The N-terminal half is responsible for the 3' incision and the C-terminal half is responsible for the 5' incision; excinuclease ABC subunit C 644306 uvrC 5711479 uvrC Dinoroseobacter shibae DFL 12 = DSM 16493 excinuclease ABC subunit C YP_001531991.1 642411 D 398580 CDS YP_001531992.1 159043198 5711480 644406..645413 1 NC_009952.1 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 645413 5711480 Dshi_0645 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP-type transport system YP_001531992.1 644406 D 398580 CDS YP_001531993.1 159043199 5711481 645472..647574 1 NC_009952.1 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 647574 5711481 Dshi_0646 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP-type transport system permease YP_001531993.1 645472 D 398580 CDS YP_001531994.1 159043200 5711482 647766..650513 1 NC_009952.1 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 650513 5711482 Dshi_0647 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531994.1 647766 D 398580 CDS YP_001531995.1 159043201 5711483 complement(650663..651262) 1 NC_009952.1 involved in a recombinational process of DNA repair, independent of the recBC complex; recombination protein RecR 651262 recR 5711483 recR Dinoroseobacter shibae DFL 12 = DSM 16493 recombination protein RecR YP_001531995.1 650663 R 398580 CDS YP_001531996.1 159043202 5711484 complement(651279..651623) 1 NC_009952.1 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 651623 5711484 Dshi_0649 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531996.1 651279 R 398580 CDS YP_001531997.1 159043203 5711485 complement(651643..653406) 1 NC_009952.1 catalyzes the DNA-template-directed extension of the 3'-end of a DNA strand; the tau chain serves as a scaffold to help in the dimerizaton of the alpha,epsilon and theta core complex; the gamma chain seems to interact with the delta and delta' subunits to transfer the beta subunit on the DNA; DNA polymerase III subunits gamma and tau 653406 dnaX 5711485 dnaX Dinoroseobacter shibae DFL 12 = DSM 16493 DNA polymerase III subunits gamma and tau YP_001531997.1 651643 R 398580 CDS YP_001531998.1 159043204 5711487 653737..654693 1 NC_009952.1 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 654693 5711487 Dshi_0651 Dinoroseobacter shibae DFL 12 = DSM 16493 NUDIX hydrolase YP_001531998.1 653737 D 398580 CDS YP_001531999.1 159043205 5711488 654714..655202 1 NC_009952.1 no significant swissprot; no conserved domains; low Ref ZP hit to hypothetical protein NAS141_10191 [Sulfitobacter sp. NAS-14.1].; hypothetical protein 655202 5711488 Dshi_0652 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001531999.1 654714 D 398580 CDS YP_001532000.1 159043206 5711489 complement(655248..656090) 1 NC_009952.1 catalyzes the formation of phenylpyruvate from prephenate in phenylalanine biosynthesis; prephenate dehydratase 656090 pheA2 5711489 pheA2 Dinoroseobacter shibae DFL 12 = DSM 16493 prephenate dehydratase YP_001532000.1 655248 R 398580 CDS YP_001532001.1 159043207 5711490 656214..656738 1 NC_009952.1 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 656738 cycM 5711490 cycM Dinoroseobacter shibae DFL 12 = DSM 16493 cytochrome c552 YP_001532001.1 656214 D 398580 CDS YP_001532002.1 159043208 5711491 656989..658890 1 NC_009952.1 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 658890 oppA 5711491 oppA Dinoroseobacter shibae DFL 12 = DSM 16493 ABC peptide transporter YP_001532002.1 656989 D 398580 CDS YP_001532003.1 159043209 5711492 658895..659992 1 NC_009952.1 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 659992 oppBC1 5711492 oppBC1 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC peptide transporter YP_001532003.1 658895 D 398580 CDS YP_001532004.1 159043210 5711493 659994..661172 1 NC_009952.1 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 661172 oppBC2 5711493 oppBC2 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC peptide transporter YP_001532004.1 659994 D 398580 CDS YP_001532005.1 159043211 5711494 661169..662770 1 NC_009952.1 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 662770 oppDF 5711494 oppDF Dinoroseobacter shibae DFL 12 = DSM 16493 ABC peptide transporter YP_001532005.1 661169 D 398580 CDS YP_001532006.1 159043212 5711495 complement(662948..664309) 1 NC_009952.1 catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III; coproporphyrinogen III oxidase 664309 hemN2 5711495 hemN2 Dinoroseobacter shibae DFL 12 = DSM 16493 coproporphyrinogen III oxidase YP_001532006.1 662948 R 398580 CDS YP_001532007.1 159043213 5711496 664362..665111 1 NC_009952.1 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 665111 fixK 5711496 fixK Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001532007.1 664362 D 398580 CDS YP_001532008.1 159043214 5711497 665449..667050 1 NC_009952.1 CcoN; FixN; cbb3-type cytochrome c oxidase subunit I 667050 fixN 5711497 fixN Dinoroseobacter shibae DFL 12 = DSM 16493 cbb3-type cytochrome c oxidase subunit I YP_001532008.1 665449 D 398580 CDS YP_001532009.1 159043215 5711498 667065..667790 1 NC_009952.1 CcoO; FixO; cbb3-type cytochrome c oxidase subunit II 667790 fixO 5711498 fixO Dinoroseobacter shibae DFL 12 = DSM 16493 cbb3-type cytochrome c oxidase subunit II YP_001532009.1 667065 D 398580 CDS YP_001532010.1 159043216 5711499 667803..668036 1 NC_009952.1 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 668036 fixQ 5711499 fixQ Dinoroseobacter shibae DFL 12 = DSM 16493 cytochrome c oxidase YP_001532010.1 667803 D 398580 CDS YP_001532011.1 159043217 5711500 668033..668896 1 NC_009952.1 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 668896 fixP 5711500 fixP Dinoroseobacter shibae DFL 12 = DSM 16493 cytochrome c oxidase YP_001532011.1 668033 D 398580 CDS YP_001532012.1 159043218 5711501 669212..670654 1 NC_009952.1 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 670654 fixG 5711501 fixG Dinoroseobacter shibae DFL 12 = DSM 16493 nitrogen fixation protein fixG YP_001532012.1 669212 D 398580 CDS YP_001532013.1 159043219 5711502 670651..671118 1 NC_009952.1 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 671118 fixH 5711502 fixH Dinoroseobacter shibae DFL 12 = DSM 16493 nitrogen fixation protein fixH YP_001532013.1 670651 D 398580 CDS YP_001532014.1 159043220 5711503 671120..673309 1 NC_009952.1 TIGRFAM: ATPase, P-type (transporting), HAD superfamily, subfamily IC; copper-translocating P-type ATPase; heavy metal translocating P-type ATPase PFAM: Haloacid dehalogenase domain protein hydrolase; Heavy metal transport/detoxification protein; E1-E2 ATPase-associated domain protein; 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 673309 fixI 5711503 fixI Dinoroseobacter shibae DFL 12 = DSM 16493 nitrogen fixation protein fixI YP_001532014.1 671120 D 398580 CDS YP_001532015.1 159043221 5711504 673314..673472 1 NC_009952.1 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 673472 fixS 5711504 fixS Dinoroseobacter shibae DFL 12 = DSM 16493 nitrogen fixation protein fixS YP_001532015.1 673314 D 398580 CDS YP_001532016.1 159043222 5711505 complement(673560..675041) 1 NC_009952.1 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 675041 dacC2 5711505 dacC2 Dinoroseobacter shibae DFL 12 = DSM 16493 D-alanyl-D-alanine carboxypeptidase YP_001532016.1 673560 R 398580 CDS YP_001532017.1 159043223 5711506 complement(675215..675919) 1 NC_009952.1 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 675919 5711506 Dshi_0670 Dinoroseobacter shibae DFL 12 = DSM 16493 haloacid dehalogenase domain-containing protein hydrolase YP_001532017.1 675215 R 398580 CDS YP_001532018.1 159043224 5711507 676410..677411 1 NC_009952.1 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 677411 rsmC 5711507 rsmC Dinoroseobacter shibae DFL 12 = DSM 16493 ribosomal RNA small subunit methyltransferase C YP_001532018.1 676410 D 398580 CDS YP_001532019.1 159043225 5711508 677442..678248 1 NC_009952.1 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 678248 5711508 Dshi_0672 Dinoroseobacter shibae DFL 12 = DSM 16493 short-chain dehydrogenase/reductase SDR YP_001532019.1 677442 D 398580 CDS YP_001532020.1 159043226 5711509 complement(678229..678606) 1 NC_009952.1 no significant swissprot, no conserved domains; bad Ref ZP hit to hypothetical protein RTM1035_19081 [Roseovarius sp. TM1035].; hypothetical protein 678606 5711509 Dshi_0673 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532020.1 678229 R 398580 CDS YP_001532021.1 159043227 5711510 678666..679559 1 NC_009952.1 catalyzes the conversion of the propionic acid groups of rings I and III to vinyl groups during heme synthesis; coproporphyrinogen III oxidase 679559 hemF 5711510 hemF Dinoroseobacter shibae DFL 12 = DSM 16493 coproporphyrinogen III oxidase YP_001532021.1 678666 D 398580 CDS YP_001532022.1 159043228 5711511 679714..681504 1 NC_009952.1 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 681504 ggt2 5711511 ggt2 Dinoroseobacter shibae DFL 12 = DSM 16493 gamma-glutamyltransferase YP_001532022.1 679714 D 398580 CDS YP_001532023.1 159043229 5711512 681643..683742 1 NC_009952.1 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 683742 5711512 Dshi_0676 Dinoroseobacter shibae DFL 12 = DSM 16493 beta-lactamase YP_001532023.1 681643 D 398580 CDS YP_001532024.1 159043230 5711513 complement(683755..684570) 1 NC_009952.1 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 684570 5711513 Dshi_0677 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532024.1 683755 R 398580 CDS YP_001532025.1 159043231 5711514 684684..686261 1 NC_009952.1 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 686261 5711514 Dshi_0678 Dinoroseobacter shibae DFL 12 = DSM 16493 glycosyl transferase family protein YP_001532025.1 684684 D 398580 CDS YP_001532026.1 159043232 5711515 686270..686641 1 NC_009952.1 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 686641 5711515 Dshi_0679 Dinoroseobacter shibae DFL 12 = DSM 16493 histidine triad (HIT) protein YP_001532026.1 686270 D 398580 CDS YP_001532027.1 159043233 5711516 complement(686761..687834) 1 NC_009952.1 With PurE catalyzes the conversion of aminoimidazole ribonucleotide to carboxyaminoimidazole ribonucleotide in the de novo purine nucleotide biosynthetic pathway; phosphoribosylaminoimidazole carboxylase ATPase subunit 687834 purK 5711516 purK Dinoroseobacter shibae DFL 12 = DSM 16493 phosphoribosylaminoimidazole carboxylase ATPase subunit YP_001532027.1 686761 R 398580 CDS YP_001532028.1 159043234 5711517 complement(687827..688312) 1 NC_009952.1 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 688312 purE 5711517 purE Dinoroseobacter shibae DFL 12 = DSM 16493 phosphoribosylaminoimidazole carboxylase YP_001532028.1 687827 R 398580 CDS YP_001532029.1 159043235 5711518 complement(688389..688613) 1 NC_009952.1 PFAM: protein of unknown function DUF465; no significant swissprot; low Ref ZP hit to Protein of unknown function DUF465 [Paracoccus denitrificans PD1222].; hypothetical protein 688613 5711518 Dshi_0682 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532029.1 688389 R 398580 CDS YP_001532030.1 159043236 5711118 688790..689233 1 NC_009952.1 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 689233 ibpAB 5711118 ibpAB Dinoroseobacter shibae DFL 12 = DSM 16493 heat shock protein YP_001532030.1 688790 D 398580 CDS YP_001532031.1 159043237 5711119 689230..689457 1 NC_009952.1 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 689457 5711119 Dshi_0684 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532031.1 689230 D 398580 CDS YP_001532032.1 159043238 5711120 complement(689465..690361) 1 NC_009952.1 PFAM: ApbE family lipoprotein KEGG: pde:Pden_2485 ApbE family lipoprotein; ApbE family lipoprotein 690361 apbE2 5711120 apbE2 Dinoroseobacter shibae DFL 12 = DSM 16493 ApbE family lipoprotein YP_001532032.1 689465 R 398580 CDS YP_001532033.1 159043239 5711121 complement(690358..692448) 1 NC_009952.1 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 692448 nosR1 5711121 nosR1 Dinoroseobacter shibae DFL 12 = DSM 16493 regulator of nitric oxide reductase transcription YP_001532033.1 690358 R 398580 CDS YP_001532034.1 159043240 5711122 692556..693332 1 NC_009952.1 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 693332 5711122 Dshi_0687 Dinoroseobacter shibae DFL 12 = DSM 16493 two-component system, permease YP_001532034.1 692556 D 398580 CDS YP_001532035.1 159043241 5711123 complement(693474..694838) 1 NC_009952.1 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 694838 5711123 Dshi_0688 Dinoroseobacter shibae DFL 12 = DSM 16493 fumarate reductase/succinate dehydrogenase flavoprotein domain-containing protein YP_001532035.1 693474 R 398580 CDS YP_001532036.1 159043242 5711124 complement(694835..695713) 1 NC_009952.1 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 695713 prpB 5711124 prpB Dinoroseobacter shibae DFL 12 = DSM 16493 methylisocitrate lyase YP_001532036.1 694835 R 398580 CDS YP_001532037.1 159043243 5711125 complement(695710..696312) 1 NC_009952.1 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 696312 entB 5711125 entB Dinoroseobacter shibae DFL 12 = DSM 16493 isochorismatase YP_001532037.1 695710 R 398580 CDS YP_001532038.1 159043244 5711126 complement(696309..698378) 1 NC_009952.1 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 698378 hyuA 5711126 hyuA Dinoroseobacter shibae DFL 12 = DSM 16493 hydantoin utilization protein A YP_001532038.1 696309 R 398580 CDS YP_001532039.1 159043245 5711127 complement(698375..700072) 1 NC_009952.1 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 700072 hyuB 5711127 hyuB Dinoroseobacter shibae DFL 12 = DSM 16493 hydantoin utilization protein B YP_001532039.1 698375 R 398580 CDS YP_001532040.1 159043246 5711128 complement(700069..700644) 1 NC_009952.1 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 700644 pptA 5711128 pptA Dinoroseobacter shibae DFL 12 = DSM 16493 4-oxalocrotonate tautomerase YP_001532040.1 700069 R 398580 CDS YP_001532041.1 159043247 5711129 700802..701602 1 NC_009952.1 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 701602 5711129 Dshi_0694 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001532041.1 700802 D 398580 CDS YP_001532042.1 159043248 5711130 701599..702993 1 NC_009952.1 dehydratase component, catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; isopropylmalate isomerase large subunit 702993 leuC 5711130 leuC Dinoroseobacter shibae DFL 12 = DSM 16493 isopropylmalate isomerase large subunit YP_001532042.1 701599 D 398580 CDS YP_001532043.1 159043249 5711131 702990..703649 1 NC_009952.1 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 703649 leuD 5711131 leuD Dinoroseobacter shibae DFL 12 = DSM 16493 3-isopropylmalate dehydratase small subunit YP_001532043.1 702990 D 398580 CDS YP_001532044.1 159043250 5711132 703665..704675 1 NC_009952.1 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 704675 dctP1 5711132 dctP1 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP dicarboxylate transporter subunit DctP YP_001532044.1 703665 D 398580 CDS YP_001532045.1 159043251 5711133 704719..705225 1 NC_009952.1 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 705225 dctQ3 5711133 dctQ3 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP dicarboxylate transporter subunit DctQ YP_001532045.1 704719 D 398580 CDS YP_001532046.1 159043252 5711134 705226..706539 1 NC_009952.1 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 706539 dctM1 5711134 dctM1 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP dicarboxylate transporter subunit DctM YP_001532046.1 705226 D 398580 CDS YP_001532047.1 159043253 5711135 706599..708116 1 NC_009952.1 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 708116 5711135 Dshi_0700 Dinoroseobacter shibae DFL 12 = DSM 16493 AMP-dependent synthetase and ligase YP_001532047.1 706599 D 398580 CDS YP_001532048.1 159043254 5711136 complement(708169..708822) 1 NC_009952.1 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 708822 5711136 Dshi_0701 Dinoroseobacter shibae DFL 12 = DSM 16493 methyltransferase domain-containing protein YP_001532048.1 708169 R 398580 CDS YP_001532049.1 159043255 5711137 complement(708819..709466) 1 NC_009952.1 InterPro Scan and NCBI conserved domains: pfam08889, WbqC; no significant swissprot; low gb hit to WbnG [Shigella dysenteriae].; WbqC-like family protein 709466 5711137 Dshi_0702 Dinoroseobacter shibae DFL 12 = DSM 16493 WbqC-like family protein YP_001532049.1 708819 R 398580 CDS YP_001532050.1 159043256 5711138 complement(709466..710386) 1 NC_009952.1 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 710386 5711138 Dshi_0703 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532050.1 709466 R 398580 CDS YP_001532051.1 159043257 5711139 710642..711829 1 NC_009952.1 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 711829 5711139 Dshi_0704 Dinoroseobacter shibae DFL 12 = DSM 16493 pyridoxal-phosphate-dependent aminotransferase YP_001532051.1 710642 D 398580 CDS YP_001532052.1 159043258 5711140 711826..713256 1 NC_009952.1 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 713256 5711140 Dshi_0705 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532052.1 711826 D 398580 CDS YP_001532053.1 159043259 5711142 714601..715269 1 NC_009952.1 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 715269 5711142 Dshi_0707 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532053.1 714601 D 398580 CDS YP_001532054.1 159043260 5711143 715275..716246 1 NC_009952.1 unsure GC frame Plot, no conserved domains; no significant swissprot; middle Ref YP hit to hypothetical protein BTH_I3215 [Burkholderia thailandensis E264].; hypothetical protein 716246 5711143 Dshi_0708 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532054.1 715275 D 398580 CDS YP_001532055.1 159043261 5711144 716718..718664 1 NC_009952.1 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 718664 atoDA 5711144 atoDA Dinoroseobacter shibae DFL 12 = DSM 16493 acyl CoA:acetate/3-ketoacid CoA transferase, alpha and subunit beta YP_001532055.1 716718 D 398580 CDS YP_001532056.1 159043262 5711145 718730..719377 1 NC_009952.1 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 719377 5711145 Dshi_0710 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532056.1 718730 D 398580 CDS YP_001532057.1 159043263 5711146 complement(719323..720249) 1 NC_009952.1 specific inhibitor of chromosomal initiation of replication in vitro; binds the three 13-mers in the origin (oriC) to block initiation of replication; also controls genes involved in arginine transport; chromosome replication initiation inhibitor protein 720249 5711146 Dshi_0711 Dinoroseobacter shibae DFL 12 = DSM 16493 chromosome replication initiation inhibitor protein YP_001532057.1 719323 R 398580 CDS YP_001532058.1 159043264 5711147 720340..720966 1 NC_009952.1 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 720966 lysE 5711147 lysE Dinoroseobacter shibae DFL 12 = DSM 16493 lysine exporter protein YP_001532058.1 720340 D 398580 CDS YP_001532059.1 159043265 5711148 721072..721935 1 NC_009952.1 NCBI conserved domains: COG3509, LpqC; no significant swissprot; low REf YP hit to polyhydroxybutyrate depolymerase [Frankia sp. EAN1pec].; poly(3-hydroxybutyrate) depolymerase-like protein 721935 5711148 Dshi_0713 Dinoroseobacter shibae DFL 12 = DSM 16493 poly(3-hydroxybutyrate) depolymerase-like protein YP_001532059.1 721072 D 398580 CDS YP_001532060.1 159043266 5711149 721916..722884 1 NC_009952.1 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 722884 5711149 Dshi_0714 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532060.1 721916 D 398580 CDS YP_001532061.1 159043267 5711150 722969..723211 1 NC_009952.1 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 723211 5711150 Dshi_0715 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532061.1 722969 D 398580 CDS YP_001532062.1 159043268 5711151 complement(723225..724619) 1 NC_009952.1 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 724619 5711151 Dshi_0716 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001532062.1 723225 R 398580 CDS YP_001532063.1 159043269 5711152 complement(724680..725906) 1 NC_009952.1 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 725906 5711152 Dshi_0717 Dinoroseobacter shibae DFL 12 = DSM 16493 multidrug resistance protein YP_001532063.1 724680 R 398580 CDS YP_001532064.1 159043270 5711153 726256..727788 1 NC_009952.1 Probably a dodecamer composed of six biotin-containing alpha subunits and six beta subunits.; carboxyl transferase 727788 pccB 5711153 pccB Dinoroseobacter shibae DFL 12 = DSM 16493 carboxyl transferase YP_001532064.1 726256 D 398580 CDS YP_001532065.1 159043271 5711154 727888..728286 1 NC_009952.1 hypothetical protein 728286 5711154 Dshi_0719 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532065.1 727888 D 398580 CDS YP_001532066.1 159043272 5711155 728279..728668 1 NC_009952.1 Active on single-stranded mRNA. Inhibits protein synthesis by cleavage of mRNA.; endoribonuclease L-PSP 728668 5711155 Dshi_0720 Dinoroseobacter shibae DFL 12 = DSM 16493 endoribonuclease L-PSP YP_001532066.1 728279 D 398580 CDS YP_001532067.1 159043273 5711156 728665..729036 1 NC_009952.1 weak similarity to genes in Rhodobacteraceae; hypothetical protein 729036 5711156 Dshi_0721 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532067.1 728665 D 398580 CDS YP_001532068.1 159043274 5711157 729051..729410 1 NC_009952.1 conserved in Rhodobacteraceae and Bradyrhizobiaceae; hypothetical protein 729410 5711157 Dshi_0722 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532068.1 729051 D 398580 CDS YP_001532069.1 159043275 5711158 729769..731814 1 NC_009952.1 biotin-dependent enzyme, Probably a dodecamer composed of six biotin-containing alpha subunits and six beta subunits.; carbamoyl-phosphate synthase L chain ATP-binding 731814 pccA 5711158 pccA Dinoroseobacter shibae DFL 12 = DSM 16493 carbamoyl-phosphate synthase L chain ATP-binding YP_001532069.1 729769 D 398580 CDS YP_001532070.1 159043276 5711159 complement(731879..732328) 1 NC_009952.1 hypothetical protein 732328 5711159 Dshi_0724 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532070.1 731879 R 398580 CDS YP_001532071.1 159043277 5711160 732437..733432 1 NC_009952.1 hypothetical protein 733432 5711160 Dshi_0725 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532071.1 732437 D 398580 CDS YP_001532072.1 159043278 5711161 733404..735542 1 NC_009952.1 MDM; functions in conversion of succinate to propionate; methylmalonyl-CoA mutase 735542 bhbA 5711161 bhbA Dinoroseobacter shibae DFL 12 = DSM 16493 methylmalonyl-CoA mutase YP_001532072.1 733404 D 398580 CDS YP_001532073.1 159043279 5711162 complement(735721..736650) 1 NC_009952.1 HTH and substrate binding domain; LysR family; transcriptional regulator 736650 5711162 Dshi_0727 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001532073.1 735721 R 398580 CDS YP_001532074.1 159043280 5711163 737004..739244 1 NC_009952.1 quinone dependent NADH dehydrogenase 739244 mnhA 5711163 mnhA Dinoroseobacter shibae DFL 12 = DSM 16493 quinone dependent NADH dehydrogenase YP_001532074.1 737004 D 398580 CDS YP_001532075.1 159043281 5711164 739241..739693 1 NC_009952.1 Na+/H+ antiporter MnhB subunit-like protein 739693 mnhB 5711164 mnhB Dinoroseobacter shibae DFL 12 = DSM 16493 Na+/H+ antiporter MnhB subunit-like protein YP_001532075.1 739241 D 398580 CDS YP_001532076.1 159043282 5711165 739693..740112 1 NC_009952.1 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 740112 mnhC 5711165 mnhC Dinoroseobacter shibae DFL 12 = DSM 16493 putative monovalent cation/H+ antiporter subunit C YP_001532076.1 739693 D 398580 CDS YP_001532077.1 159043283 5711166 740109..741644 1 NC_009952.1 quinone dependent NADH dehydrogenase 741644 mnhD 5711166 mnhD Dinoroseobacter shibae DFL 12 = DSM 16493 quinone dependent NADH dehydrogenase YP_001532077.1 740109 D 398580 CDS YP_001532078.1 159043284 5711167 741641..741994 1 NC_009952.1 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 741994 mnhE 5711167 mnhE Dinoroseobacter shibae DFL 12 = DSM 16493 cation antiporter YP_001532078.1 741641 D 398580 CDS YP_001532079.1 159043285 5711168 741987..742343 1 NC_009952.1 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 742343 mnhF 5711168 mnhF Dinoroseobacter shibae DFL 12 = DSM 16493 multiple resistance and pH regulation protein F YP_001532079.1 741987 D 398580 CDS YP_001532080.1 159043286 5711169 742340..742687 1 NC_009952.1 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 742687 mnhG 5711169 mnhG Dinoroseobacter shibae DFL 12 = DSM 16493 monovalent cation/proton antiporter YP_001532080.1 742340 D 398580 CDS YP_001532081.1 159043287 5711170 742674..743288 1 NC_009952.1 hypothetical protein 743288 5711170 Dshi_0735 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532081.1 742674 D 398580 CDS YP_001532082.1 159043288 5711171 743285..743770 1 NC_009952.1 protein N-Acetyl-transferase; N-acetyltransferase GCN5 743770 5711171 Dshi_0736 Dinoroseobacter shibae DFL 12 = DSM 16493 N-acetyltransferase GCN5 YP_001532082.1 743285 D 398580 CDS YP_001532083.1 159043289 5711172 743834..744517 1 NC_009952.1 heat shock protein DnaJ domain-containing protein 744517 5711172 Dshi_0737 Dinoroseobacter shibae DFL 12 = DSM 16493 heat shock protein DnaJ domain-containing protein YP_001532083.1 743834 D 398580 CDS YP_001532084.1 159043290 5711173 744578..744895 1 NC_009952.1 hypothetical protein 744895 5711173 Dshi_0738 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532084.1 744578 D 398580 CDS YP_001532085.1 159043291 5711174 complement(744912..746432) 1 NC_009952.1 This family consists of the N-terminal region of exopolyphosphatase (Ppx) and guanosine pentaphosphate phospho-hydrolase (GppA).; Ppx/GppA phosphatase 746432 ppx 5711174 ppx Dinoroseobacter shibae DFL 12 = DSM 16493 Ppx/GppA phosphatase YP_001532085.1 744912 R 398580 CDS YP_001532086.1 159043292 5711175 complement(746526..748700) 1 NC_009952.1 catalyzes the reversible transfer of the terminal phosphate of ATP to form a long chain polyphosphate; polyphosphate kinase 748700 ppk1 5711175 ppk1 Dinoroseobacter shibae DFL 12 = DSM 16493 polyphosphate kinase YP_001532086.1 746526 R 398580 CDS YP_001532087.1 159043293 5711176 complement(748740..749429) 1 NC_009952.1 weak evidence for predicted function; DnaA; chromosomal replication initiator 749429 5711176 Dshi_0741 Dinoroseobacter shibae DFL 12 = DSM 16493 chromosomal replication initiator YP_001532087.1 748740 R 398580 CDS YP_001532088.1 159043294 5711177 complement(749426..750511) 1 NC_009952.1 predicted transmembrane protein (10TMH); hypothetical protein 750511 5711177 Dshi_0742 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532088.1 749426 R 398580 CDS YP_001532089.1 159043295 5711178 750674..752056 1 NC_009952.1 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 752056 mcsS 5711178 mcsS Dinoroseobacter shibae DFL 12 = DSM 16493 mechanosensitive ion channel protein MscS YP_001532089.1 750674 D 398580 CDS YP_001532090.1 159043296 5711179 752138..753475 1 NC_009952.1 catalyzes the formation of prolyl-tRNA(Pro) from proline and tRNA(Pro); prolyl-tRNA synthetase 753475 proS 5711179 proS Dinoroseobacter shibae DFL 12 = DSM 16493 prolyl-tRNA synthetase YP_001532090.1 752138 D 398580 CDS YP_001532091.1 159043297 5711180 753664..754239 1 NC_009952.1 This family of redoxins includes peroxiredoxin, thioredoxin and glutaredoxin proteins.; redoxin domain-containing protein 754239 5711180 Dshi_0745 Dinoroseobacter shibae DFL 12 = DSM 16493 redoxin domain-containing protein YP_001532091.1 753664 D 398580 CDS YP_001532092.1 159043298 5711181 754337..755023 1 NC_009952.1 Transport of water across the membrane.; MIP family channel protein 755023 aqpZ 5711181 aqpZ Dinoroseobacter shibae DFL 12 = DSM 16493 MIP family channel protein YP_001532092.1 754337 D 398580 CDS YP_001532093.1 159043299 5711182 755116..756402 1 NC_009952.1 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 756402 lolC 5711182 lolC Dinoroseobacter shibae DFL 12 = DSM 16493 lipoprotein releasing system YP_001532093.1 755116 D 398580 CDS YP_001532094.1 159043300 5711183 756395..757078 1 NC_009952.1 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 757078 lolD 5711183 lolD Dinoroseobacter shibae DFL 12 = DSM 16493 ABC transporter-like protein YP_001532094.1 756395 D 398580 CDS YP_001532095.1 159043301 5711184 complement(758372..760336) 1 NC_009952.1 decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling; DNA topoisomerase IV subunit B 760336 5711184 Dshi_0749 Dinoroseobacter shibae DFL 12 = DSM 16493 DNA topoisomerase IV subunit B YP_001532095.1 758372 R 398580 CDS YP_001532096.1 159043302 5711185 760995..761789 1 NC_009952.1 hypothetical protein 761789 5711185 Dshi_0750 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532096.1 760995 D 398580 CDS YP_001532097.1 159043303 5711186 761970..762914 1 NC_009952.1 Protein with ppk2 Domain, cytoplasmatic; hypothetical protein 762914 ppk2 5711186 ppk2 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532097.1 761970 D 398580 CDS YP_001532098.1 159043304 5711187 762957..763637 1 NC_009952.1 contains DUF1007 domain; hypothetical protein 763637 5711187 Dshi_0752 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532098.1 762957 D 398580 CDS YP_001532099.1 159043305 5711188 763625..764581 1 NC_009952.1 incorporation of nickel into H2-uptake hydrogenase and urease, signal peptide cleveage after AA 22, inner membrane; high-affinity nickel-transporter 764581 nicO 5711188 nicO Dinoroseobacter shibae DFL 12 = DSM 16493 high-affinity nickel-transporter YP_001532099.1 763625 D 398580 CDS YP_001532100.1 159043306 5711189 764591..765187 1 NC_009952.1 SAM-dependent methyltransferase, Substrate not known KEGG: rsp:RSP_0765 SAM-dependent methyltransferase; type 11 methyltransferase 765187 5711189 Dshi_0754 Dinoroseobacter shibae DFL 12 = DSM 16493 type 11 methyltransferase YP_001532100.1 764591 D 398580 CDS YP_001532101.1 159043307 5711190 765229..766599 1 NC_009952.1 MATE efflux family protein 766599 5711190 Dshi_0755 Dinoroseobacter shibae DFL 12 = DSM 16493 MATE efflux family protein YP_001532101.1 765229 D 398580 CDS YP_001532102.1 159043308 5711191 complement(766585..767244) 1 NC_009952.1 hypothetical protein 767244 5711191 Dshi_0756 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532102.1 766585 R 398580 CDS YP_001532103.1 159043309 5711192 complement(767248..768648) 1 NC_009952.1 selenium-binding protein 768648 5711192 Dshi_0757 Dinoroseobacter shibae DFL 12 = DSM 16493 selenium-binding protein YP_001532103.1 767248 R 398580 CDS YP_001532104.1 159043310 5711193 complement(768813..769301) 1 NC_009952.1 MarR family; transcriptional regulator 769301 5711193 Dshi_0758 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001532104.1 768813 R 398580 CDS YP_001532105.1 159043311 5711194 769384..769752 1 NC_009952.1 hypothetical protein 769752 5711194 Dshi_0759 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532105.1 769384 D 398580 CDS YP_001532106.1 159043312 5711195 complement(770254..770736) 1 NC_009952.1 hypothetical protein 770736 5711195 Dshi_0760 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532106.1 770254 R 398580 CDS YP_001532107.1 159043313 5711196 complement(770763..771179) 1 NC_009952.1 conserved in Rhodobacteraceae; hypothetical protein 771179 5711196 Dshi_0761 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532107.1 770763 R 398580 CDS YP_001532108.1 159043314 5711197 complement(771187..772389) 1 NC_009952.1 catalyzes the formation of oxalozcetate and L-glutamate from L-aspartate and 2-oxoglutarate; aspartate aminotransferase 772389 aspC 5711197 aspC Dinoroseobacter shibae DFL 12 = DSM 16493 aspartate aminotransferase YP_001532108.1 771187 R 398580 CDS YP_001532109.1 159043315 5711198 772480..772872 1 NC_009952.1 Helix-Turn-Helix motif; XRE family; transcriptional regulator 772872 5711198 Dshi_0763 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001532109.1 772480 D 398580 CDS YP_001532110.1 159043316 5711199 772869..773168 1 NC_009952.1 hypothetical protein 773168 5711199 Dshi_0764 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532110.1 772869 D 398580 CDS YP_001532111.1 159043317 5711200 773281..773778 1 NC_009952.1 HTH domain; MarR family; transcriptional regulator 773778 5711200 Dshi_0765 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001532111.1 773281 D 398580 CDS YP_001532112.1 159043318 5711201 complement(773856..774593) 1 NC_009952.1 putative lipoprotein; hypothetical protein 774593 5711201 Dshi_0766 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532112.1 773856 R 398580 CDS YP_001532113.1 159043319 5711202 complement(774595..775023) 1 NC_009952.1 Lactoylglutathione lyase; glyoxalase/bleomycin resistance protein/dioxygenase 775023 5711202 Dshi_0767 Dinoroseobacter shibae DFL 12 = DSM 16493 glyoxalase/bleomycin resistance protein/dioxygenase YP_001532113.1 774595 R 398580 CDS YP_001532114.1 159043320 5711203 775200..776117 1 NC_009952.1 flavin dependent thymidylate synthase; ThyX; thymidylate synthase complementing protein; catalyzes the formation of dTMP and tetrahydrofolate from dUMP and methylenetetrahydrofolate; the enzyme from Mycobacterium tuberculosis forms homotetramers; uses FAD as a cofactor; FAD-dependent thymidylate synthase 776117 thyX 5711203 thyX Dinoroseobacter shibae DFL 12 = DSM 16493 FAD-dependent thymidylate synthase YP_001532114.1 775200 D 398580 CDS YP_001532115.1 159043321 5711204 complement(776205..776414) 1 NC_009952.1 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 776414 csp1 5711204 csp1 Dinoroseobacter shibae DFL 12 = DSM 16493 cold-shock DNA-binding domain-containing protein YP_001532115.1 776205 R 398580 CDS YP_001532116.1 159043322 5711205 776635..776946 1 NC_009952.1 conserved arsC domain; arsenate reductase-like protein 776946 5711205 Dshi_0770 Dinoroseobacter shibae DFL 12 = DSM 16493 arsenate reductase-like protein YP_001532116.1 776635 D 398580 CDS YP_001532117.1 159043323 5711206 complement(776904..777470) 1 NC_009952.1 DoxX family protein 777470 5711206 Dshi_0771 Dinoroseobacter shibae DFL 12 = DSM 16493 DoxX family protein YP_001532117.1 776904 R 398580 CDS YP_001532118.1 159043324 5711207 complement(777464..778210) 1 NC_009952.1 hypothetical protein 778210 5711207 Dshi_0772 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532118.1 777464 R 398580 CDS YP_001532119.1 159043325 5711208 complement(778207..779157) 1 NC_009952.1 hypothetical protein 779157 5711208 Dshi_0773 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532119.1 778207 R 398580 CDS YP_001532120.1 159043326 5711209 complement(779200..779487) 1 NC_009952.1 predicted inner membrane protein, conserved in Rhodobacteraceae; hypothetical protein 779487 5711209 Dshi_0774 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532120.1 779200 R 398580 CDS YP_001532121.1 159043327 5711210 780036..781115 1 NC_009952.1 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 781115 ttuC 5711210 ttuC Dinoroseobacter shibae DFL 12 = DSM 16493 tartrate dehydrogenase YP_001532121.1 780036 D 398580 CDS YP_001532122.1 159043328 5711211 781394..782179 1 NC_009952.1 similar to ppaA in the photosynthetic gene cluster, cytosolic; cobalamin B12-binding domain-containing protein 782179 5711211 Dshi_0776 Dinoroseobacter shibae DFL 12 = DSM 16493 cobalamin B12-binding domain-containing protein YP_001532122.1 781394 D 398580 CDS YP_001532123.1 159043329 5711212 complement(782164..784128) 1 NC_009952.1 catalyzes a two-step reaction, first charging a threonine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; catalyzes the formation of threonyl-tRNA(Thr) from threonine and tRNA(Thr); threonyl-tRNA synthetase 784128 thrS 5711212 thrS Dinoroseobacter shibae DFL 12 = DSM 16493 threonyl-tRNA synthetase YP_001532123.1 782164 R 398580 CDS YP_001532124.1 159043330 5711213 complement(784257..784445) 1 NC_009952.1 hypothetical protein 784445 5711213 Dshi_0778 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532124.1 784257 R 398580 CDS YP_001532125.1 159043331 5711214 784566..785522 1 NC_009952.1 protein with 2 functional domains: MarR and acetyltransferase (GNAT); MarR family with acetyltransferase activity; transcriptional regulator 785522 5711214 Dshi_0779 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001532125.1 784566 D 398580 CDS YP_001532126.1 159043332 5711216 complement(785693..786637) 1 NC_009952.1 Hydrolase, alpha/beta fold motiv with catalytic triade; alpha/beta hydrolase fold protein 786637 5711216 Dshi_0780 Dinoroseobacter shibae DFL 12 = DSM 16493 alpha/beta hydrolase fold protein YP_001532126.1 785693 R 398580 CDS YP_001532127.1 159043333 5711217 complement(786642..786929) 1 NC_009952.1 contains SCP-2 sterol transfer family domain; sterol-binding domain-containing protein 786929 5711217 Dshi_0781 Dinoroseobacter shibae DFL 12 = DSM 16493 sterol-binding domain-containing protein YP_001532127.1 786642 R 398580 CDS YP_001532128.1 159043334 5711218 787003..787569 1 NC_009952.1 putative Tetratricopeptide TPR_2 repeat protein; hypothetical protein 787569 5711218 Dshi_0782 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532128.1 787003 D 398580 CDS YP_001532129.1 159043335 5711219 787616..790579 1 NC_009952.1 contains Helicase domain; helicase domain-containing protein 790579 5711219 Dshi_0783 Dinoroseobacter shibae DFL 12 = DSM 16493 helicase domain-containing protein YP_001532129.1 787616 D 398580 CDS YP_001532130.1 159043336 5711220 790711..790959 1 NC_009952.1 RNA-binding protein S4 790959 5711220 Dshi_0784 Dinoroseobacter shibae DFL 12 = DSM 16493 RNA-binding protein S4 YP_001532130.1 790711 D 398580 CDS YP_001532131.1 159043337 5711221 791008..791346 1 NC_009952.1 contains [3Fe-4S] and [4Fe-4S] Cys cluster; 4Fe-4S ferredoxin 791346 fdxA 5711221 fdxA Dinoroseobacter shibae DFL 12 = DSM 16493 4Fe-4S ferredoxin YP_001532131.1 791008 D 398580 CDS YP_001532132.1 159043338 5711222 791654..792166 1 NC_009952.1 similar to N-terminus of M. xanthus carD protein; CarD family; transcriptional regulator 792166 5711222 Dshi_0786 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001532132.1 791654 D 398580 CDS YP_001532133.1 159043339 5711223 complement(792216..792992) 1 NC_009952.1 Cobalamin biosynthesis, Reaction: Cobamide coenzyme + GMP <=> Adenosine-GDP-cobinamide + alpha-Ribazole; cobalamin-5-phosphate synthase CobS 792992 cobS1 5711223 cobS1 Dinoroseobacter shibae DFL 12 = DSM 16493 cobalamin-5-phosphate synthase CobS YP_001532133.1 792216 R 398580 CDS YP_001532134.1 159043340 5711224 793089..794126 1 NC_009952.1 catalyzes the synthesis of alpha-ribazole-5'-phosphate from nicotinate mononucleotide and 5,6-dimethylbenzimidazole; nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase 794126 cobT 5711224 cobT Dinoroseobacter shibae DFL 12 = DSM 16493 nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase YP_001532134.1 793089 D 398580 CDS YP_001532135.1 159043341 5711225 complement(794130..796142) 1 NC_009952.1 glutathione regulated, K+/H+ antiporter, NAD-binding domain; potassium efflux system protein 796142 kefC 5711225 kefC Dinoroseobacter shibae DFL 12 = DSM 16493 potassium efflux system protein YP_001532135.1 794130 R 398580 CDS YP_001532136.1 159043342 5711226 complement(796285..798666) 1 NC_009952.1 conserved in Rhodobacteraceae; hypothetical protein 798666 5711226 Dshi_0790 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532136.1 796285 R 398580 CDS YP_001532137.1 159043343 5711227 798789..799526 1 NC_009952.1 protein of unknown function DUF541, bacterial membrane or periplasm protein; hypothetical protein 799526 5711227 Dshi_0791 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532137.1 798789 D 398580 CDS YP_001532138.1 159043344 5711228 complement(799585..799959) 1 NC_009952.1 hypothetical protein 799959 5711228 Dshi_0792 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532138.1 799585 R 398580 CDS YP_001532139.1 159043345 5711229 complement(800127..801422) 1 NC_009952.1 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 801422 metB2 5711229 metB2 Dinoroseobacter shibae DFL 12 = DSM 16493 O-acetylhomoserine/O-acetylserine sulfhydrylase YP_001532139.1 800127 R 398580 CDS YP_001532140.1 159043346 5711230 801568..802155 1 NC_009952.1 catalyzes the dehydration of D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate to 3-(imidazol-4-yl)-2-oxopropyl phosphate in histidine biosynthesis; imidazoleglycerol-phosphate dehydratase 802155 hisB 5711230 hisB Dinoroseobacter shibae DFL 12 = DSM 16493 imidazoleglycerol-phosphate dehydratase YP_001532140.1 801568 D 398580 CDS YP_001532141.1 159043347 5711231 802157..802795 1 NC_009952.1 with HisF IGPS catalyzes the conversion of phosphoribulosyl-formimino-5-aminoimidazole-4-carboxamide ribonucleotide phosphate and glutamine to imidazole-glycerol phosphate, 5-aminoimidazol-4-carboxamide ribonucleotide, and glutamate in histidine biosynthesis; the HisH subunit provides the glutamine amidotransferase activity that produces the ammonia necessary to HisF for the synthesis of imidazole-glycerol phosphate and 5-aminoimidazol-4-carboxamide ribonucleotide; imidazole glycerol phosphate synthase subunit HisH 802795 hisH 5711231 hisH Dinoroseobacter shibae DFL 12 = DSM 16493 imidazole glycerol phosphate synthase subunit HisH YP_001532141.1 802157 D 398580 CDS YP_001532142.1 159043348 5711232 complement(802986..803912) 1 NC_009952.1 catalyzes the formation of L-citrulline from carbamoyl phosphate and L-ornithine in arginine biosynthesis and degradation; ornithine carbamoyltransferase 803912 argF 5711232 argF Dinoroseobacter shibae DFL 12 = DSM 16493 ornithine carbamoyltransferase YP_001532142.1 802986 R 398580 CDS YP_001532143.1 159043349 5711233 complement(803909..804442) 1 NC_009952.1 weakly conserved GCN5-related N-acetyltransferase, possibly EC:3.5.1.16; N-acetyltransferase GCN5 804442 5711233 Dshi_0797 Dinoroseobacter shibae DFL 12 = DSM 16493 N-acetyltransferase GCN5 YP_001532143.1 803909 R 398580 CDS YP_001532144.1 159043350 5711234 complement(804432..805613) 1 NC_009952.1 DapATase; functions in arginine biosynthetic pathway; catalyzes the formation of N-acetyl-L-glutamate 5-semialdehyde from 2-oxoglutarate and N(2)-acetyl-L-ornithine; acetylornithine transaminase protein 805613 argD 5711234 argD Dinoroseobacter shibae DFL 12 = DSM 16493 acetylornithine transaminase protein YP_001532144.1 804432 R 398580 CDS YP_001532145.1 159043351 5711235 complement(805880..806218) 1 NC_009952.1 putative DNA-binding protein 806218 5711235 Dshi_0799 Dinoroseobacter shibae DFL 12 = DSM 16493 putative DNA-binding protein YP_001532145.1 805880 R 398580 CDS YP_001532146.1 159043352 5711236 complement(806381..807163) 1 NC_009952.1 Helix-Turn-Helix motiv, iclR subfamily; IclR family; transcriptional regulator 807163 5711236 Dshi_0800 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001532146.1 806381 R 398580 CDS YP_001532147.1 159043353 5711237 complement(807171..808529) 1 NC_009952.1 TRAP gene cluster - dctPQM; TRAP dicarboxylate transporter subunit DctM 808529 5711237 Dshi_0801 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP dicarboxylate transporter subunit DctM YP_001532147.1 807171 R 398580 CDS YP_001532148.1 159043354 5711238 complement(808526..809254) 1 NC_009952.1 TRAP gene cluster - dctPQM; tripartite ATP-independent periplasmic transporter subunit DctQ 809254 5711238 Dshi_0802 Dinoroseobacter shibae DFL 12 = DSM 16493 tripartite ATP-independent periplasmic transporter subunit DctQ YP_001532148.1 808526 R 398580 CDS YP_001532149.1 159043355 5711239 complement(809305..810537) 1 NC_009952.1 TRAP gene cluster - dctPQM; TRAP dicarboxylate transporter subunit DctP 810537 5711239 Dshi_0803 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP dicarboxylate transporter subunit DctP YP_001532149.1 809305 R 398580 CDS YP_001532150.1 159043356 5711240 810647..812269 1 NC_009952.1 contains N- and C-terminal GMC-oxidoreductase domain, FAD-binding; glucose-methanol-choline oxidoreductase 812269 5711240 Dshi_0804 Dinoroseobacter shibae DFL 12 = DSM 16493 glucose-methanol-choline oxidoreductase YP_001532150.1 810647 D 398580 CDS YP_001532151.1 159043357 5711241 812303..814081 1 NC_009952.1 catalyzes the formation of acetyl phosphate and sulfite from 2-sulfoacetaldehyde; is active when grown on taurine as a sole carbon source; sulfoacetaldehyde acetyltransferase 814081 5711241 Dshi_0805 Dinoroseobacter shibae DFL 12 = DSM 16493 sulfoacetaldehyde acetyltransferase YP_001532151.1 812303 D 398580 CDS YP_001532152.1 159043358 5711242 814089..815120 1 NC_009952.1 9 potential transmembrane domains; hypothetical protein 815120 tauZ 5711242 tauZ Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532152.1 814089 D 398580 CDS YP_001532153.1 159043359 5711243 complement(815127..816155) 1 NC_009952.1 hypothetical protein 816155 5711243 Dshi_0807 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532153.1 815127 R 398580 CDS YP_001532154.1 159043360 5711244 complement(816307..817050) 1 NC_009952.1 integrates membrane bound lytic transglycosylase and penicillin-binding protein into a complex; MltA-interacting MipA family protein 817050 mipA 5711244 mipA Dinoroseobacter shibae DFL 12 = DSM 16493 MltA-interacting MipA family protein YP_001532154.1 816307 R 398580 CDS YP_001532155.1 159043361 5711435 817541..819340 1 NC_009952.1 binds to the ribosome on the universally-conserved alpha-sarcin loop; GTP-binding protein LepA 819340 lepA 5711435 lepA Dinoroseobacter shibae DFL 12 = DSM 16493 GTP-binding protein LepA YP_001532155.1 817541 D 398580 CDS YP_001532156.1 159043362 5711436 820707..820949 1 NC_009952.1 hypothetical protein 820949 5711436 Dshi_0810 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532156.1 820707 D 398580 CDS YP_001532157.1 159043363 5711437 820930..821163 1 NC_009952.1 hypothetical protein 821163 5711437 Dshi_0811 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532157.1 820930 D 398580 CDS YP_001532158.1 159043364 5711438 821347..821664 1 NC_009952.1 TraR/DksA family; transcriptional regulator 821664 5711438 Dshi_0812 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001532158.1 821347 D 398580 CDS YP_001532159.1 159043365 5711439 821719..821967 1 NC_009952.1 2 predicted transmembrane domains; hypothetical protein 821967 5711439 Dshi_0813 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532159.1 821719 D 398580 CDS YP_001532160.1 159043366 5711440 822057..822242 1 NC_009952.1 conserved in Rhodobacteraceae and Bradyrhizobiaceae; hypothetical protein 822242 5711440 Dshi_0814 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532160.1 822057 D 398580 CDS YP_001532161.1 159043367 5711441 complement(822447..822863) 1 NC_009952.1 catalyzes the first step of the glyoxal pathway; glyoxalase/bleomycin resistance protein/dioxygenase 822863 5711441 Dshi_0815 Dinoroseobacter shibae DFL 12 = DSM 16493 glyoxalase/bleomycin resistance protein/dioxygenase YP_001532161.1 822447 R 398580 CDS YP_001532162.1 159043368 5711442 complement(822910..823185) 1 NC_009952.1 hypothetical protein 823185 5711442 Dshi_0816 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532162.1 822910 R 398580 CDS YP_001532163.1 159043369 5711443 823262..823522 1 NC_009952.1 hypothetical protein 823522 5711443 Dshi_0817 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532163.1 823262 D 398580 CDS YP_001532164.1 159043370 5711444 823519..823725 1 NC_009952.1 hypothetical protein 823725 5711444 Dshi_0818 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532164.1 823519 D 398580 CDS YP_001532165.1 159043371 5711445 823750..824046 1 NC_009952.1 hypothetical protein 824046 5711445 Dshi_0819 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532165.1 823750 D 398580 CDS YP_001532166.1 159043372 5711446 complement(824267..825034) 1 NC_009952.1 hydrolase, alpha/beta fold motif with catalytic triade; alpha/beta hydrolase fold protein 825034 5711446 Dshi_0820 Dinoroseobacter shibae DFL 12 = DSM 16493 alpha/beta hydrolase fold protein YP_001532166.1 824267 R 398580 CDS YP_003422325.1 284928592 8130631 825116..825505 1 NC_009952.1 hypothetical protein 825505 8130631 Dshi_5001 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_003422325.1 825116 D 398580 CDS YP_001532167.1 159043373 5711447 complement(825519..826814) 1 NC_009952.1 catalyzes the reaction of glycine with 5,10-methylenetetrahydrofolate to form L-serine and tetrahydrofolate; serine hydroxymethyltransferase 826814 glyA 5711447 glyA Dinoroseobacter shibae DFL 12 = DSM 16493 serine hydroxymethyltransferase YP_001532167.1 825519 R 398580 CDS YP_001532168.1 159043374 5711448 827012..827779 1 NC_009952.1 catalyzes the phosphorylation of NAD to NADP; inorganic polyphosphate/ATP-NAD kinase 827779 ppnK 5711448 ppnK Dinoroseobacter shibae DFL 12 = DSM 16493 inorganic polyphosphate/ATP-NAD kinase YP_001532168.1 827012 D 398580 CDS YP_001532169.1 159043375 5711449 complement(827784..829175) 1 NC_009952.1 Transcriptional regulater, ATP dependent Sigma54 interaction, part of two component system; Fis family; two component, sigma-54 specific, transcriptional regulator 829175 5711449 Dshi_0823 Dinoroseobacter shibae DFL 12 = DSM 16493 two component, sigma-54 specific, transcriptional regulator YP_001532169.1 827784 R 398580 CDS YP_001532170.1 159043376 5711450 complement(829172..830701) 1 NC_009952.1 C-Terminal domain of arcB (aerobic respiration control), no PAS domain (sensor); histidine kinase 830701 5711450 Dshi_0824 Dinoroseobacter shibae DFL 12 = DSM 16493 histidine kinase YP_001532170.1 829172 R 398580 CDS YP_001532171.1 159043377 5711451 complement(830837..832729) 1 NC_009952.1 AMP-binding domain, ligase similar to propionate-CoA and Acetyl-CoA ligase; AMP-dependent synthetase and ligase 832729 5711451 Dshi_0825 Dinoroseobacter shibae DFL 12 = DSM 16493 AMP-dependent synthetase and ligase YP_001532171.1 830837 R 398580 CDS YP_001532172.1 159043378 5711452 complement(832910..835189) 1 NC_009952.1 NAD-dependent; catalyzes the oxidative decarboxylation of malate to form pyruvate; does not decarboxylate oxaloacetate; malic enzyme 835189 5711452 Dshi_0826 Dinoroseobacter shibae DFL 12 = DSM 16493 malic enzyme YP_001532172.1 832910 R 398580 CDS YP_001532173.1 159043379 5711453 835363..835755 1 NC_009952.1 Reaction: Cytidine + H2O <=> Uridine + NH3; cytidine deaminase 835755 cdd 5711453 cdd Dinoroseobacter shibae DFL 12 = DSM 16493 cytidine deaminase YP_001532173.1 835363 D 398580 CDS YP_001532174.1 159043380 5711454 835752..837059 1 NC_009952.1 Catalyzes the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate; thymidine phosphorylase 837059 deoA 5711454 deoA Dinoroseobacter shibae DFL 12 = DSM 16493 thymidine phosphorylase YP_001532174.1 835752 D 398580 CDS YP_001532175.1 159043381 5711455 837056..838255 1 NC_009952.1 catalyzes the transfer of phosphate between the C1 and C5 carbons of pentose; phosphopentomutase 838255 deoB 5711455 deoB Dinoroseobacter shibae DFL 12 = DSM 16493 phosphopentomutase YP_001532175.1 837056 D 398580 CDS YP_001532176.1 159043382 5711456 838252..839247 1 NC_009952.1 catalyzes the formation of inosine from adenosine; adenosine deaminase 839247 add 5711456 add Dinoroseobacter shibae DFL 12 = DSM 16493 adenosine deaminase YP_001532176.1 838252 D 398580 CDS YP_001532177.1 159043383 5711457 839244..839876 1 NC_009952.1 Catalyzes the formation of uracil and 5-phospho-alpha-D-ribosy 1-diphosphate from UMP and diphosphate; uracil phosphoribosyltransferase 839876 upp 5711457 upp Dinoroseobacter shibae DFL 12 = DSM 16493 uracil phosphoribosyltransferase YP_001532177.1 839244 D 398580 CDS YP_001532178.1 159043384 5711458 complement(839877..840893) 1 NC_009952.1 conserved in Rhodobacteraceae; hypothetical protein 840893 5711458 Dshi_0832 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532178.1 839877 R 398580 CDS YP_001532179.1 159043385 5711459 complement(841358..842983) 1 NC_009952.1 putative Acyl-CoA-Ligase (inferred from Swiss-Prot); AMP-dependent synthetase and ligase 842983 5711459 Dshi_0833 Dinoroseobacter shibae DFL 12 = DSM 16493 AMP-dependent synthetase and ligase YP_001532179.1 841358 R 398580 CDS YP_001532180.1 159043386 5711460 843077..843994 1 NC_009952.1 contains 1 N-terminal DUF6-domain; hypothetical protein 843994 5711460 Dshi_0834 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532180.1 843077 D 398580 CDS YP_001532181.1 159043387 5711461 complement(844051..846264) 1 NC_009952.1 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 846264 fadJ 5711461 fadJ Dinoroseobacter shibae DFL 12 = DSM 16493 3-hydroxyacyl-CoA dehydrogenase YP_001532181.1 844051 R 398580 CDS YP_001532182.1 159043388 5711462 complement(846270..847481) 1 NC_009952.1 Catalyzes the synthesis of acetoacetyl coenzyme A from two molecules of acetyl coenzyme A. It can also act as a thiolase, catalyzing the reverse reaction and generating two-carbon units from the four-carbon product of fatty acid oxidation; acetyl-CoA acetyltransferase 847481 fadA 5711462 fadA Dinoroseobacter shibae DFL 12 = DSM 16493 acetyl-CoA acetyltransferase YP_001532182.1 846270 R 398580 CDS YP_001532183.1 159043389 5711463 complement(847493..848128) 1 NC_009952.1 not all GST-like proteins show catalytic activity; glutathione S-transferase domain-containing protein 848128 5711463 Dshi_0837 Dinoroseobacter shibae DFL 12 = DSM 16493 glutathione S-transferase domain-containing protein YP_001532183.1 847493 R 398580 CDS YP_001532184.1 159043390 5711464 complement(848409..849557) 1 NC_009952.1 contains all Acyl-CoA dehydrogenase domains; Reaction: Acyl-CoA + Acceptor <=> 2,3-Dehydroacyl-CoA + Reduced acceptor; acyl-CoA dehydrogenase domain-containing protein 849557 5711464 Dshi_0838 Dinoroseobacter shibae DFL 12 = DSM 16493 acyl-CoA dehydrogenase domain-containing protein YP_001532184.1 848409 R 398580 CDS YP_001532185.1 159043391 5711465 complement(849631..851409) 1 NC_009952.1 Oxidoreductase acting on the CH-CH group of donors with other acceptors; acyl-CoA dehydrogenase domain-containing protein 851409 5711465 Dshi_0839 Dinoroseobacter shibae DFL 12 = DSM 16493 acyl-CoA dehydrogenase domain-containing protein YP_001532185.1 849631 R 398580 CDS YP_001532186.1 159043392 5711466 complement(851439..851840) 1 NC_009952.1 contains winged helix DNA-binding motif; MerR family; transcriptional regulator 851840 5711466 Dshi_0840 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001532186.1 851439 R 398580 CDS YP_001532187.1 159043393 5711467 852286..853314 1 NC_009952.1 hypothetical protein 853314 5711467 Dshi_0841 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532187.1 852286 D 398580 CDS YP_001532188.1 159043394 5711468 complement(853357..853728) 1 NC_009952.1 contains winged helix DNA-binding motif; MerR family; transcriptional regulator 853728 5711468 Dshi_0842 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001532188.1 853357 R 398580 CDS YP_001532189.1 159043395 5711469 853842..854276 1 NC_009952.1 thioesterase superfamily protein 854276 5711469 Dshi_0843 Dinoroseobacter shibae DFL 12 = DSM 16493 thioesterase superfamily protein YP_001532189.1 853842 D 398580 CDS YP_001532190.1 159043396 5711470 854276..854797 1 NC_009952.1 thioesterase superfamily protein 854797 5711470 Dshi_0844 Dinoroseobacter shibae DFL 12 = DSM 16493 thioesterase superfamily protein YP_001532190.1 854276 D 398580 CDS YP_001532191.1 159043397 5711471 854790..856109 1 NC_009952.1 contains two multi antimicrobial extrusion (MATE) domains, drug/sodium antiporter; MATE efflux family protein 856109 5711471 Dshi_0845 Dinoroseobacter shibae DFL 12 = DSM 16493 MATE efflux family protein YP_001532191.1 854790 D 398580 CDS YP_001532192.1 159043398 5711472 complement(856144..856491) 1 NC_009952.1 related to glutaredoxins, Reaction: Arsenate ion + Glutaredoxin <=> Arsenite + Glutaredoxin disulfide; arsenate reductase 856491 arsC 5711472 arsC Dinoroseobacter shibae DFL 12 = DSM 16493 arsenate reductase YP_001532192.1 856144 R 398580 CDS YP_001532193.1 159043399 5711473 complement(856488..857546) 1 NC_009952.1 catalyzes the conversion of dihydroorotate to orotate in the pyrimidine biosynthesis pathway; uses a flavin nucleotide as an essential cofactor; class 2 enzymes are monomeric and compared to the class 1 class 2 possess an extended N terminus, which plays a role in the membrane association of the enzyme and provides the binding site for the respiratory quinones that serve as physiological electron acceptors; dihydroorotate dehydrogenase 2 857546 pyrD2 5711473 pyrD2 Dinoroseobacter shibae DFL 12 = DSM 16493 dihydroorotate dehydrogenase 2 YP_001532193.1 856488 R 398580 CDS YP_001532194.1 159043400 5711474 complement(857543..857878) 1 NC_009952.1 hypothetical bacterial and plant proteins of unknown function; hypothetical protein 857878 5711474 Dshi_0848 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532194.1 857543 R 398580 CDS YP_001532195.1 159043401 5711475 858004..859593 1 NC_009952.1 membrane bound, hydrolyzes extracellular nucleotides into membrane permeable nucleosides, Reaction: 5-Ribonucleotide + H2O <=> Ribonucleoside + Orthophosphate; 5'-nucleotidase 859593 5711475 Dshi_0849 Dinoroseobacter shibae DFL 12 = DSM 16493 5'-nucleotidase YP_001532195.1 858004 D 398580 CDS YP_001532196.1 159043402 5710539 complement(859653..861845) 1 NC_009952.1 he DEAD box helicases are involved in various aspects of RNA metabolism; DEAD/DEAH box helicase 861845 deaD 5710539 deaD Dinoroseobacter shibae DFL 12 = DSM 16493 DEAD/DEAH box helicase YP_001532196.1 859653 R 398580 CDS YP_001532197.1 159043403 5710540 862042..862707 1 NC_009952.1 contains DUF159 domain; hypothetical protein 862707 5710540 Dshi_0851 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532197.1 862042 D 398580 CDS YP_001532198.1 159043404 5710542 863045..864853 1 NC_009952.1 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 864853 msbA 5710542 msbA Dinoroseobacter shibae DFL 12 = DSM 16493 lipid A ABC exporter family YP_001532198.1 863045 D 398580 CDS YP_001532199.1 159043405 5710543 865066..866964 1 NC_009952.1 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 866964 fadD2 5710543 fadD2 Dinoroseobacter shibae DFL 12 = DSM 16493 AMP-binding domain-containing protein YP_001532199.1 865066 D 398580 CDS YP_001532200.1 159043406 5710544 867049..867252 1 NC_009952.1 hypothetical protein 867252 5710544 Dshi_0854 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532200.1 867049 D 398580 CDS YP_001532201.1 159043407 5710545 complement(867282..868169) 1 NC_009952.1 belongs to class of conserved hypothetical proteins with N-terminal transglutaminse domain, catalytic activity not proofed; transglutaminase domain-containing protein 868169 5710545 Dshi_0855 Dinoroseobacter shibae DFL 12 = DSM 16493 transglutaminase domain-containing protein YP_001532201.1 867282 R 398580 CDS YP_001532202.1 159043408 5710546 complement(868179..870593) 1 NC_009952.1 contains DUF404, 407, 403 domains; hypothetical protein 870593 5710546 Dshi_0856 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532202.1 868179 R 398580 CDS YP_001532203.1 159043409 5710547 complement(870602..873940) 1 NC_009952.1 belongs to clas of conserved hypothetical proteins with N-terminal transglutaminse domain, catalytic activity not proofed; transglutaminase domain-containing protein 873940 5710547 Dshi_0857 Dinoroseobacter shibae DFL 12 = DSM 16493 transglutaminase domain-containing protein YP_001532203.1 870602 R 398580 CDS YP_001532204.1 159043410 5710548 complement(874196..874888) 1 NC_009952.1 ABC transporter (importer) gene cluster: 2nd ATP binding cassette (ABC) domain; part of a heterotetramer; ABC transporter-like protein 874888 5710548 Dshi_0858 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC transporter-like protein YP_001532204.1 874196 R 398580 CDS YP_001532205.1 159043411 5710549 complement(874885..875637) 1 NC_009952.1 ABC transporter (importer) gene cluster: 1st ATP binding cassette (ABC) domain; part of a heterotetramer; ABC transporter-like protein 875637 5710549 Dshi_0859 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC transporter-like protein YP_001532205.1 874885 R 398580 CDS YP_001532206.1 159043412 5710550 complement(875634..876608) 1 NC_009952.1 ABC transporter (importer) gene cluster: 2nd membrane spanning domain (MSD); part of a heterotetramer; inner-membrane translocator 876608 5710550 Dshi_0860 Dinoroseobacter shibae DFL 12 = DSM 16493 inner-membrane translocator YP_001532206.1 875634 R 398580 CDS YP_001532207.1 159043413 5710551 complement(876610..877527) 1 NC_009952.1 ABC transporter (importer) gene cluster: 1st membrane spanning domain (MSD); part of a heterotetramer; inner-membrane translocator 877527 5710551 Dshi_0861 Dinoroseobacter shibae DFL 12 = DSM 16493 inner-membrane translocator YP_001532207.1 876610 R 398580 CDS YP_001532208.1 159043414 5710552 complement(877656..878795) 1 NC_009952.1 ABC transporter (importer) gene cluster: receptor; extracellular ligand-binding receptor 878795 5710552 Dshi_0862 Dinoroseobacter shibae DFL 12 = DSM 16493 extracellular ligand-binding receptor YP_001532208.1 877656 R 398580 CDS YP_001532209.1 159043415 5710553 complement(878828..879064) 1 NC_009952.1 helix-turn-helix DNA-binding motif; AsnC family; transcriptional regulator 879064 5710553 Dshi_0863 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001532209.1 878828 R 398580 CDS YP_001532210.1 159043416 5710554 879279..879737 1 NC_009952.1 putative oxidoreductase; (2Fe-2S)-binding domain-containing protein 879737 5710554 Dshi_0864 Dinoroseobacter shibae DFL 12 = DSM 16493 (2Fe-2S)-binding domain-containing protein YP_001532210.1 879279 D 398580 CDS YP_001532211.1 159043417 5710555 879739..881922 1 NC_009952.1 function not clear, similar to several Swiss-Prot curated proteins; aldehyde oxidase and xanthine dehydrogenase molybdopterin-binding 881922 5710555 Dshi_0865 Dinoroseobacter shibae DFL 12 = DSM 16493 aldehyde oxidase and xanthine dehydrogenase molybdopterin-binding YP_001532211.1 879739 D 398580 CDS YP_001532212.1 159043418 5710556 882060..882755 1 NC_009952.1 Hydrolase, alpha/beta fold motiv with catalytic triade, weak evidence; alpha/beta hydrolase fold protein 882755 5710556 Dshi_0866 Dinoroseobacter shibae DFL 12 = DSM 16493 alpha/beta hydrolase fold protein YP_001532212.1 882060 D 398580 CDS YP_001532213.1 159043419 5710557 882752..883624 1 NC_009952.1 contains amidohydrolase 2 domain; amidohydrolase 2 883624 5710557 Dshi_0867 Dinoroseobacter shibae DFL 12 = DSM 16493 amidohydrolase 2 YP_001532213.1 882752 D 398580 CDS YP_001532214.1 159043420 5710558 complement(883631..885007) 1 NC_009952.1 peptidase related (trEMBL); putative peptidase 885007 5710558 Dshi_0868 Dinoroseobacter shibae DFL 12 = DSM 16493 putative peptidase YP_001532214.1 883631 R 398580 CDS YP_001532215.1 159043421 5710559 complement(885019..885909) 1 NC_009952.1 phosphoesterase related (trEMBL); hypothetical protein 885909 5710559 Dshi_0869 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532215.1 885019 R 398580 CDS YP_001532216.1 159043422 5710560 complement(885921..887960) 1 NC_009952.1 weak similarity to transcriptional regulator, SARP family, TPR repeats; SARP family; transcriptional regulator 887960 5710560 Dshi_0870 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001532216.1 885921 R 398580 CDS YP_001532217.1 159043423 5710561 complement(888034..888300) 1 NC_009952.1 hypothetical protein 888300 5710561 Dshi_0871 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532217.1 888034 R 398580 CDS YP_001532218.1 159043424 5710562 888387..889970 1 NC_009952.1 ABC transporter (importer) gene cluster: receptor (cluster disrupted); family 5 extracellular solute-binding protein 889970 5710562 Dshi_0872 Dinoroseobacter shibae DFL 12 = DSM 16493 family 5 extracellular solute-binding protein YP_001532218.1 888387 D 398580 CDS YP_001532219.1 159043425 5710563 890141..890812 1 NC_009952.1 hypothetical protein 890812 5710563 Dshi_0873 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532219.1 890141 D 398580 CDS YP_001532220.1 159043426 5710564 890913..891137 1 NC_009952.1 part of extracellular ligand-binding receptor; family 5; extracellular solute-binding protein 891137 5710564 Dshi_0874 Dinoroseobacter shibae DFL 12 = DSM 16493 extracellular solute-binding protein YP_001532220.1 890913 D 398580 CDS YP_001532221.1 159043427 5710565 891165..891431 1 NC_009952.1 transposase IS3/IS911 family protein 891431 5710565 Dshi_0875 Dinoroseobacter shibae DFL 12 = DSM 16493 transposase IS3/IS911 family protein YP_001532221.1 891165 D 398580 CDS YP_001532222.1 159043428 5710566 891455..892276 1 NC_009952.1 integrase catalytic subunit 892276 5710566 Dshi_0876 Dinoroseobacter shibae DFL 12 = DSM 16493 integrase catalytic subunit YP_001532222.1 891455 D 398580 CDS YP_001532223.1 159043429 5710567 892303..893685 1 NC_009952.1 ABC transporter (importer) gene cluster: receptor, N-terminal truncated; 4-phytase 893685 5710567 Dshi_0877 Dinoroseobacter shibae DFL 12 = DSM 16493 4-phytase YP_001532223.1 892303 D 398580 CDS YP_001532224.1 159043430 5710568 complement(894073..894540) 1 NC_009952.1 hypothetical protein 894540 5710568 Dshi_0878 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532224.1 894073 R 398580 CDS YP_001532225.1 159043431 5710569 complement(895189..895593) 1 NC_009952.1 membrane protein 895593 5710569 Dshi_0879 Dinoroseobacter shibae DFL 12 = DSM 16493 membrane protein YP_001532225.1 895189 R 398580 CDS YP_001532226.1 159043432 5710570 complement(895664..896512) 1 NC_009952.1 involved in the bacterial meta-cleavage pathways for degradation of aromatic compounds; hydratase/decarboxylase 896512 5710570 Dshi_0880 Dinoroseobacter shibae DFL 12 = DSM 16493 hydratase/decarboxylase YP_001532226.1 895664 R 398580 CDS YP_001532227.1 159043433 5710571 896659..897645 1 NC_009952.1 ABC transporter (importer) gene cluster: 1st membrane spanning domain (MSD); part of a heterotetramer; binding-protein-dependent transport system inner membrane protein 897645 5710571 Dshi_0881 Dinoroseobacter shibae DFL 12 = DSM 16493 binding-protein-dependent transport system inner membrane protein YP_001532227.1 896659 D 398580 CDS YP_001532228.1 159043434 5710572 897647..898615 1 NC_009952.1 ABC transporter (importer) gene cluster: 2nd membrane spanning domain (MSD); part of a heterotetramer; binding-protein-dependent transport system inner membrane protein 898615 5710572 Dshi_0882 Dinoroseobacter shibae DFL 12 = DSM 16493 binding-protein-dependent transport system inner membrane protein YP_001532228.1 897647 D 398580 CDS YP_001532229.1 159043435 5710573 complement(898620..898811) 1 NC_009952.1 hypothetical protein 898811 5710573 Dshi_0883 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532229.1 898620 R 398580 CDS YP_001532230.1 159043436 5710574 899031..900113 1 NC_009952.1 ABC transporter (importer) gene cluster: 1st ATP binding cassette (ABC) domain; part of a heterotetramer; ATPase subunit; oligopeptide/dipeptide ABC transporter 900113 5710574 Dshi_0884 Dinoroseobacter shibae DFL 12 = DSM 16493 oligopeptide/dipeptide ABC transporter YP_001532230.1 899031 D 398580 CDS YP_001532231.1 159043437 5710575 900110..901078 1 NC_009952.1 ABC transporter (importer) gene cluster: 2nd ATP binding cassette (ABC) domain; part of a heterotetramer; ATPase subunit; oligopeptide/dipeptide ABC transporter 901078 5710575 Dshi_0885 Dinoroseobacter shibae DFL 12 = DSM 16493 oligopeptide/dipeptide ABC transporter YP_001532231.1 900110 D 398580 CDS YP_001532232.1 159043438 5710576 complement(901082..901924) 1 NC_009952.1 Helix-Turn-Helix motif, iclR subfamily; IclR family; transcriptional regulator 901924 5710576 Dshi_0886 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001532232.1 901082 R 398580 CDS YP_001532233.1 159043439 5710577 902124..903314 1 NC_009952.1 PLP-dependent enzyme, Reaction: L-serine + glyoxylate <=> 3-hydroxypyruvate + glycine; serine--glyoxylate transaminase 903314 sgaA2 5710577 sgaA2 Dinoroseobacter shibae DFL 12 = DSM 16493 serine--glyoxylate transaminase YP_001532233.1 902124 D 398580 CDS YP_001532234.1 159043440 5710578 903322..904296 1 NC_009952.1 PLP dependnet enzyme, catalytic activity not clear, Swiss-Prot hits to serine racemase, threonine dehydratase; pyridoxal-5'-phosphate-dependent protein subunit beta 904296 5710578 Dshi_0888 Dinoroseobacter shibae DFL 12 = DSM 16493 pyridoxal-5'-phosphate-dependent protein subunit beta YP_001532234.1 903322 D 398580 CDS YP_001532235.1 159043441 5710579 904311..905474 1 NC_009952.1 contains N-terminal domain of alanine racemase, C-terminal domain missing; alanine racemase domain-containing protein 905474 5710579 Dshi_0889 Dinoroseobacter shibae DFL 12 = DSM 16493 alanine racemase domain-containing protein YP_001532235.1 904311 D 398580 CDS YP_001532236.1 159043442 5710580 905581..906573 1 NC_009952.1 catalyses the deamination of ornithine to proline, Reaction: L-Ornithine <=> L-Proline + NH3; ornithine cyclodeaminase 906573 5710580 Dshi_0890 Dinoroseobacter shibae DFL 12 = DSM 16493 ornithine cyclodeaminase YP_001532236.1 905581 D 398580 CDS YP_001532237.1 159043443 5710581 complement(906667..907749) 1 NC_009952.1 PLP-dependent Enzyme, Reaction: O-Acetyl-L-serine + Hydrogen sulfide <=> L-Cysteine + Acetate; cysteine synthase A 907749 cysK 5710581 cysK Dinoroseobacter shibae DFL 12 = DSM 16493 cysteine synthase A YP_001532237.1 906667 R 398580 CDS YP_001532238.1 159043444 5710582 908084..909016 1 NC_009952.1 transposase IS4 family protein 909016 5710582 Dshi_0892 Dinoroseobacter shibae DFL 12 = DSM 16493 transposase IS4 family protein YP_001532238.1 908084 D 398580 CDS YP_001532239.1 159043445 5710583 909083..910375 1 NC_009952.1 inner membrane protein; peptidoglycan-binding domain 1 protein 910375 5710583 Dshi_0893 Dinoroseobacter shibae DFL 12 = DSM 16493 peptidoglycan-binding domain 1 protein YP_001532239.1 909083 D 398580 CDS YP_001532240.1 159043446 5710584 910592..911965 1 NC_009952.1 inner membrane protein; peptidoglycan-binding domain 1 protein 911965 5710584 Dshi_0894 Dinoroseobacter shibae DFL 12 = DSM 16493 peptidoglycan-binding domain 1 protein YP_001532240.1 910592 D 398580 CDS YP_001532241.1 159043447 5710585 912355..914220 1 NC_009952.1 peptidase S1 and S6 chymotrypsin/Hap 914220 5710585 Dshi_0895 Dinoroseobacter shibae DFL 12 = DSM 16493 peptidase S1 and S6 chymotrypsin/Hap YP_001532241.1 912355 D 398580 CDS YP_001532242.1 159043448 5710586 914230..915495 1 NC_009952.1 hypothetical protein 915495 5710586 Dshi_0896 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532242.1 914230 D 398580 CDS YP_001532243.1 159043449 5710587 915495..918620 1 NC_009952.1 Salmonella: activated by the global signal transduction/regulatory system SsrA/B, when in eukaryotic cells; virulence protein SrfB 918620 5710587 Dshi_0897 Dinoroseobacter shibae DFL 12 = DSM 16493 virulence protein SrfB YP_001532243.1 915495 D 398580 CDS YP_001532244.1 159043450 5710588 918640..921318 1 NC_009952.1 hypothetical protein 921318 5710588 Dshi_0898 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532244.1 918640 D 398580 CDS YP_001532245.1 159043451 5710589 921315..922355 1 NC_009952.1 hypothetical protein 922355 5710589 Dshi_0899 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532245.1 921315 D 398580 CDS YP_001532246.1 159043452 5710590 922370..924292 1 NC_009952.1 hypothetical protein 924292 5710590 Dshi_0900 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532246.1 922370 D 398580 CDS YP_001532247.1 159043453 5710591 924297..925022 1 NC_009952.1 ABC transporter (importer) gene cluster (disrupted): ATP binding cassette (ABC) domain; part of a heterotetramer; ABC transporter-like protein 925022 5710591 Dshi_0901 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC transporter-like protein YP_001532247.1 924297 D 398580 CDS YP_001532248.1 159043454 5710592 925019..926218 1 NC_009952.1 ABC transporter (importer) gene cluster (disrupted): membrane spanning domain (MSD); part of a heterotetramer; hypothetical protein 926218 5710592 Dshi_0902 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532248.1 925019 D 398580 CDS YP_001532249.1 159043455 5710593 926215..927828 1 NC_009952.1 hypothetical protein 927828 5710593 Dshi_0903 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532249.1 926215 D 398580 CDS YP_001532250.1 159043456 5710594 complement(927835..928704) 1 NC_009952.1 conserved only in R. denitrificans; hypothetical protein 928704 5710594 Dshi_0904 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532250.1 927835 R 398580 CDS YP_003422326.1 284928593 8130632 928897..929556 1 NC_009952.1 hypothetical protein 929556 8130632 Dshi_5007 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_003422326.1 928897 D 398580 CDS YP_001532251.1 159043457 5710595 929570..930199 1 NC_009952.1 membrane protein, contains a pair of UPF0126 domains; hypothetical protein 930199 5710595 Dshi_0905 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532251.1 929570 D 398580 CDS YP_001532252.1 159043458 5710596 complement(930196..930930) 1 NC_009952.1 ABC transporter (importer) gene cluster: membrane spanning domain (MSD); part of a heterotetramer; binding-protein-dependent transport system inner membrane protein 930930 5710596 Dshi_0906 Dinoroseobacter shibae DFL 12 = DSM 16493 binding-protein-dependent transport system inner membrane protein YP_001532252.1 930196 R 398580 CDS YP_001532253.1 159043459 5710597 complement(930927..931655) 1 NC_009952.1 ABC transporter (importer) gene cluster: 1st ATP binding cassette (ABC) domain; part of a heterotetramer; ABC transporter-like protein 931655 5710597 Dshi_0907 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC transporter-like protein YP_001532253.1 930927 R 398580 CDS YP_001532254.1 159043460 5710598 complement(931652..932350) 1 NC_009952.1 involved in thiamine biosynthesis; TenA family; transcriptional activator 932350 5710598 Dshi_0908 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional activator YP_001532254.1 931652 R 398580 CDS YP_001532255.1 159043461 5710599 complement(932347..933282) 1 NC_009952.1 ABC transporter (importer) gene cluster: receptor, NMT1/THI5 like domain, involved in Thiamine biosynthesis; NMT1/THI5 like domain-containing protein 933282 5710599 Dshi_0909 Dinoroseobacter shibae DFL 12 = DSM 16493 NMT1/THI5 like domain-containing protein YP_001532255.1 932347 R 398580 CDS YP_001532256.1 159043462 5710600 complement(933279..934244) 1 NC_009952.1 contains thiF and MoeZ/B-domain; UBA/THIF-type NAD/FAD-binding protein 934244 thiF 5710600 thiF Dinoroseobacter shibae DFL 12 = DSM 16493 UBA/THIF-type NAD/FAD-binding protein YP_001532256.1 933279 R 398580 CDS YP_001532257.1 159043463 5710601 complement(934241..934840) 1 NC_009952.1 Magnesium dependent, Reaction: 2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphate + 4-Methyl-5-(2-phosphoethyl)-thiazole <=> Pyrophosphate + Thiaminmonophosphate; thiamine-phosphate diphosphorylase 934840 thiE 5710601 thiE Dinoroseobacter shibae DFL 12 = DSM 16493 thiamine-phosphate diphosphorylase YP_001532257.1 934241 R 398580 CDS YP_001532258.1 159043464 5710602 complement(934837..935631) 1 NC_009952.1 Required for the synthesis of the thiazole moiety of thiamine; thiazole biosynthesis family protein 935631 thiG 5710602 thiG Dinoroseobacter shibae DFL 12 = DSM 16493 thiazole biosynthesis family protein YP_001532258.1 934837 R 398580 CDS YP_001532259.1 159043465 5710603 complement(935635..935829) 1 NC_009952.1 involved in sulphur transfer; thiamine biosynthesis protein ThiS 935829 5710603 Dshi_0913 Dinoroseobacter shibae DFL 12 = DSM 16493 thiamine biosynthesis protein ThiS YP_001532259.1 935635 R 398580 CDS YP_001532260.1 159043466 5710604 complement(935813..936790) 1 NC_009952.1 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 936790 thiO 5710604 thiO Dinoroseobacter shibae DFL 12 = DSM 16493 glycine oxidase ThiO YP_001532260.1 935813 R 398580 CDS YP_001532261.1 159043467 5710605 complement(936787..937584) 1 NC_009952.1 cofactor biosynthesis, Reaction: ATP + 4-amino-2-methyl-5-phosphomethylpyrimidine <=> ADP + 4-amino-2-methyl-5-diphosphomethylpyrimidine; phosphomethylpyrimidine kinase 937584 thiD 5710605 thiD Dinoroseobacter shibae DFL 12 = DSM 16493 phosphomethylpyrimidine kinase YP_001532261.1 936787 R 398580 CDS YP_001532262.1 159043468 5710606 937856..939046 1 NC_009952.1 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 939046 5710606 Dshi_0916 Dinoroseobacter shibae DFL 12 = DSM 16493 efflux transporter YP_001532262.1 937856 D 398580 CDS YP_001532263.1 159043469 5710607 939057..942221 1 NC_009952.1 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 942221 5710607 Dshi_0917 Dinoroseobacter shibae DFL 12 = DSM 16493 acriflavin resistance protein YP_001532263.1 939057 D 398580 CDS YP_001532264.1 159043470 5710608 complement(942472..943404) 1 NC_009952.1 belongs to a mostly uncharacterised family of membrane transport proteins found in eukaryotes, bacteria and archaea; auxin efflux carrier 943404 5710608 Dshi_0918 Dinoroseobacter shibae DFL 12 = DSM 16493 auxin efflux carrier YP_001532264.1 942472 R 398580 CDS YP_001532265.1 159043471 5710609 complement(943401..944207) 1 NC_009952.1 Metallo-beta-lactamase superfamily, apart from the beta-lactamases a number of other proteins contain this domain; beta-lactamase domain-containing protein 944207 5710609 Dshi_0919 Dinoroseobacter shibae DFL 12 = DSM 16493 beta-lactamase domain-containing protein YP_001532265.1 943401 R 398580 CDS YP_001532266.1 159043472 5710610 complement(944204..945013) 1 NC_009952.1 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 945013 5710610 Dshi_0920 Dinoroseobacter shibae DFL 12 = DSM 16493 hydrolase YP_001532266.1 944204 R 398580 CDS YP_001532267.1 159043473 5710611 complement(945036..946181) 1 NC_009952.1 catalyzes the DNA-template-directed extension of the 3'-end of a DNA strand; the delta' subunit seems to interact with the gamma subunit to transfer the beta subunit on the DNA; DNA polymerase III subunit delta' 946181 5710611 Dshi_0921 Dinoroseobacter shibae DFL 12 = DSM 16493 DNA polymerase III subunit delta' YP_001532267.1 945036 R 398580 CDS YP_001532268.1 159043474 5710612 complement(946178..946801) 1 NC_009952.1 Phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis, Reaction: ATP + dTMP <=> ADP + dTDP; dTMP kinase 946801 tmk 5710612 tmk Dinoroseobacter shibae DFL 12 = DSM 16493 dTMP kinase YP_001532268.1 946178 R 398580 CDS YP_001532269.1 159043475 5710613 complement(946801..947982) 1 NC_009952.1 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 947982 dacC1 5710613 dacC1 Dinoroseobacter shibae DFL 12 = DSM 16493 serine-type D-Ala-D-Ala carboxypeptidase YP_001532269.1 946801 R 398580 CDS YP_001532270.1 159043476 5710614 complement(947994..948800) 1 NC_009952.1 contains SPOR domain, involved in binding peptidoglycan; sporulation domain-containing protein 948800 5710614 Dshi_0924 Dinoroseobacter shibae DFL 12 = DSM 16493 sporulation domain-containing protein YP_001532270.1 947994 R 398580 CDS YP_001532271.1 159043477 5710616 949418..949618 1 NC_009952.1 weak conservation; hypothetical protein 949618 5710616 Dshi_0925 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532271.1 949418 D 398580 CDS YP_001532272.1 159043478 5710617 complement(949670..950479) 1 NC_009952.1 integrase catalytic subunit 950479 5710617 Dshi_0926 Dinoroseobacter shibae DFL 12 = DSM 16493 integrase catalytic subunit YP_001532272.1 949670 R 398580 CDS YP_001532273.1 159043479 5710618 complement(950503..950730) 1 NC_009952.1 transposase IS3/IS911 family protein 950730 5710618 Dshi_0927 Dinoroseobacter shibae DFL 12 = DSM 16493 transposase IS3/IS911 family protein YP_001532273.1 950503 R 398580 CDS YP_001532274.1 159043480 5710619 complement(950829..951632) 1 NC_009952.1 inner membrane protein; hypothetical protein 951632 5710619 Dshi_0928 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532274.1 950829 R 398580 CDS YP_001532275.1 159043481 5710620 complement(952573..953553) 1 NC_009952.1 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 953553 5710620 Dshi_0929 Dinoroseobacter shibae DFL 12 = DSM 16493 UspA domain-containing protein YP_001532275.1 952573 R 398580 CDS YP_001532276.1 159043482 5710621 complement(953550..955277) 1 NC_009952.1 Na/H antiporters are key transporters in maintaining the pH of actively metabolising cells; sodium/hydrogen exchanger 955277 5710621 Dshi_0930 Dinoroseobacter shibae DFL 12 = DSM 16493 sodium/hydrogen exchanger YP_001532276.1 953550 R 398580 CDS YP_001532277.1 159043483 5710622 complement(955308..956327) 1 NC_009952.1 zinc-containing alcohol dehydrogenase family, Reaction: An alcohol + NAD+ <=> an aldehyde or ketone + NADH; alcohol dehydrogenase GroES domain-containing protein 956327 adhA 5710622 adhA Dinoroseobacter shibae DFL 12 = DSM 16493 alcohol dehydrogenase GroES domain-containing protein YP_001532277.1 955308 R 398580 CDS YP_001532278.1 159043484 5710623 complement(956341..959109) 1 NC_009952.1 members of this ATPase-family are involved in Na+/K+, H+/K+, Ca++ and Mg++ transport; P-type (transporting), HAD superfamily, subfamily IC; ATPase 959109 5710623 Dshi_0932 Dinoroseobacter shibae DFL 12 = DSM 16493 ATPase YP_001532278.1 956341 R 398580 CDS YP_001532279.1 159043485 5710624 complement(959106..959327) 1 NC_009952.1 weak evidence for function as DNA binding domain, excisionase family; excisionase family; DNA-binding domain-containing protein 959327 5710624 Dshi_0933 Dinoroseobacter shibae DFL 12 = DSM 16493 DNA-binding domain-containing protein YP_001532279.1 959106 R 398580 CDS YP_001532280.1 159043486 5710625 959824..960150 1 NC_009952.1 transposase IS3/IS911 family protein 960150 5710625 Dshi_0934 Dinoroseobacter shibae DFL 12 = DSM 16493 transposase IS3/IS911 family protein YP_001532280.1 959824 D 398580 CDS YP_001532281.1 159043487 5710626 complement(960258..960719) 1 NC_009952.1 hypothetical protein 960719 5710626 Dshi_0935 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532281.1 960258 R 398580 CDS YP_001532282.1 159043488 5710627 complement(960784..963285) 1 NC_009952.1 exported or inner-membrane bound, catalyzes hydrolization of sulfate from organic compounds; sulfatase 963285 5710627 Dshi_0936 Dinoroseobacter shibae DFL 12 = DSM 16493 sulfatase YP_001532282.1 960784 R 398580 CDS YP_001532283.1 159043489 5710628 complement(963377..964288) 1 NC_009952.1 hypothetical protein 964288 5710628 Dshi_0937 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532283.1 963377 R 398580 CDS YP_001532284.1 159043490 5710629 964490..965500 1 NC_009952.1 helix-turn-helix DNA-binding motif; AraC family; transcriptional regulator 965500 5710629 Dshi_0938 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001532284.1 964490 D 398580 CDS YP_001532285.1 159043491 5710630 complement(965791..965877) 1 NC_009952.1 28aa of a transposase orfA IS5 family element (normally about 100-120aa); transposase orfA IS5 family element 965877 5710630 Dshi_0939 Dinoroseobacter shibae DFL 12 = DSM 16493 transposase orfA IS5 family element YP_001532285.1 965791 R 398580 CDS YP_001532286.1 159043492 5710631 965987..966301 1 NC_009952.1 hypothetical protein 966301 5710631 Dshi_0940 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532286.1 965987 D 398580 CDS YP_001532287.1 159043493 5710632 966631..967482 1 NC_009952.1 hypothetical protein 967482 5710632 Dshi_0941 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532287.1 966631 D 398580 CDS YP_001532288.1 159043494 5710633 967479..968444 1 NC_009952.1 Members of the M23 peptidase family are zinc-metallopeptidases, most are endopeptidases, inner membrane location: possible function as cell wall peptidase; peptidase M23B 968444 5710633 Dshi_0942 Dinoroseobacter shibae DFL 12 = DSM 16493 peptidase M23B YP_001532288.1 967479 D 398580 CDS YP_001532289.1 159043495 5710634 complement(968525..969388) 1 NC_009952.1 contains CAAX amino terminal protease domain; abortive infection protein 969388 5710634 Dshi_0943 Dinoroseobacter shibae DFL 12 = DSM 16493 abortive infection protein YP_001532289.1 968525 R 398580 CDS YP_001532290.1 159043496 5710635 complement(969742..970260) 1 NC_009952.1 putative transmembrane protein (PSORT); hypothetical protein 970260 5710635 Dshi_0944 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532290.1 969742 R 398580 CDS YP_001532291.1 159043497 5710636 complement(970257..971039) 1 NC_009952.1 contains C-terminal putative peptidoglycan-binding domain, found in metalloproteases, N-terminus not characterized; peptidoglycan-binding domain 1 protein 971039 5710636 Dshi_0945 Dinoroseobacter shibae DFL 12 = DSM 16493 peptidoglycan-binding domain 1 protein YP_001532291.1 970257 R 398580 CDS YP_001532292.1 159043498 5710637 complement(971323..971721) 1 NC_009952.1 conserved in bacteria; hypothetical protein 971721 5710637 Dshi_0946 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532292.1 971323 R 398580 CDS YP_001532293.1 159043499 5710638 complement(971779..972486) 1 NC_009952.1 Enables the recycling of peptidyl-tRNAs produced at termination of translation; peptidyl-tRNA hydrolase 972486 pthA 5710638 pthA Dinoroseobacter shibae DFL 12 = DSM 16493 peptidyl-tRNA hydrolase YP_001532293.1 971779 R 398580 CDS YP_001532294.1 159043500 5710639 972616..973788 1 NC_009952.1 FMN-dependent dehydrogenase, Reaction: (S)-lactate + 2 ferricytochrome c <=> pyruvate + 2 ferrocytochrome c + 2 H+; cytochrome; L-lactate dehydrogenase 973788 lldD2 5710639 lldD2 Dinoroseobacter shibae DFL 12 = DSM 16493 L-lactate dehydrogenase YP_001532294.1 972616 D 398580 CDS YP_001532295.1 159043501 5710640 973840..974457 1 NC_009952.1 hypothetical protein 974457 5710640 Dshi_0949 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532295.1 973840 D 398580 CDS YP_001532296.1 159043502 5710641 974567..975202 1 NC_009952.1 the Ctc family of proteins consists of two types, one that contains the N-terminal ribosomal protein L25 domain only which in Escherichia coli binds the 5S rRNA while a subset of proteins contain a C-terminal extension that is involved in the stress response; 50S ribosomal protein L25/general stress protein Ctc 975202 rplY 5710641 rplY Dinoroseobacter shibae DFL 12 = DSM 16493 50S ribosomal protein L25/general stress protein Ctc YP_001532296.1 974567 D 398580 CDS YP_001532297.1 159043503 5710642 complement(975412..975882) 1 NC_009952.1 hypothetical protein 975882 5710642 Dshi_0951 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532297.1 975412 R 398580 CDS YP_001532298.1 159043504 5710643 complement(976376..977194) 1 NC_009952.1 catalyzes the formation of indole and glyceraldehyde 3-phosphate from indoleglycerol phosphate in tryptophan biosynthesis; tryptophan synthase subunit alpha 977194 trpA 5710643 trpA Dinoroseobacter shibae DFL 12 = DSM 16493 tryptophan synthase subunit alpha YP_001532298.1 976376 R 398580 CDS YP_001532299.1 159043505 5710644 complement(977230..978582) 1 NC_009952.1 contains two multi antimicrobial extrusion (MATE) domains, drug/sodium antiporter; MATE efflux family protein 978582 5710644 Dshi_0953 Dinoroseobacter shibae DFL 12 = DSM 16493 MATE efflux family protein YP_001532299.1 977230 R 398580 CDS YP_001532300.1 159043506 5710645 978833..979930 1 NC_009952.1 translation-associated GTPase; the crystal structure of the Haemophilus influenzae YchF protein showed similarity to the yeast structure (PDB: 1NI3); fluorescence spectroscopy revealed nucleic acid binding; the yeast protein YBR025c interacts with the translation elongation factor eEF1; GTP-dependent nucleic acid-binding protein EngD 979930 engD 5710645 engD Dinoroseobacter shibae DFL 12 = DSM 16493 GTP-dependent nucleic acid-binding protein EngD YP_001532300.1 978833 D 398580 CDS YP_001532301.1 159043507 5710646 complement(979967..980662) 1 NC_009952.1 similar to predicted racemases; hydantoin racemase 980662 5710646 Dshi_0955 Dinoroseobacter shibae DFL 12 = DSM 16493 hydantoin racemase YP_001532301.1 979967 R 398580 CDS YP_001532302.1 159043508 5710647 complement(980662..981948) 1 NC_009952.1 TRAP gene cluster - dctPQM; DctM subunit; TRAP dicarboxylate transporter 981948 5710647 Dshi_0956 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP dicarboxylate transporter YP_001532302.1 980662 R 398580 CDS YP_001532303.1 159043509 5710648 complement(981948..982469) 1 NC_009952.1 TRAP gene cluster - dctPQM; tripartite ATP-independent periplasmic transporter subunit DctQ 982469 5710648 Dshi_0957 Dinoroseobacter shibae DFL 12 = DSM 16493 tripartite ATP-independent periplasmic transporter subunit DctQ YP_001532303.1 981948 R 398580 CDS YP_001532304.1 159043510 5710649 complement(982492..983472) 1 NC_009952.1 TRAP gene cluster - dctPQM; DctP subunit; TRAP dicarboxylate transporter 983472 5710649 Dshi_0958 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP dicarboxylate transporter YP_001532304.1 982492 R 398580 CDS YP_001532305.1 159043511 5710650 complement(983690..984535) 1 NC_009952.1 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 984535 5710650 Dshi_0959 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001532305.1 983690 R 398580 CDS YP_001532306.1 159043512 5710651 984738..985418 1 NC_009952.1 N-terminal HTH region, C-terminal FCD effector binding domain; GntR family; transcriptional regulator 985418 5710651 Dshi_0960 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001532306.1 984738 D 398580 CDS YP_001532307.1 159043513 5710652 complement(985534..986037) 1 NC_009952.1 C-terminal domain is missing, probable pseudogene; catechol dioxygenase domain-containing protein 986037 5710652 Dshi_0961 Dinoroseobacter shibae DFL 12 = DSM 16493 catechol dioxygenase domain-containing protein YP_001532307.1 985534 R 398580 CDS YP_001532308.1 159043514 5710655 complement(987364..987915) 1 NC_009952.1 hypothetical protein 987915 5710655 Dshi_0964 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532308.1 987364 R 398580 CDS YP_001532309.1 159043515 5710656 complement(988027..988380) 1 NC_009952.1 hypothetical protein 988380 5710656 Dshi_0965 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532309.1 988027 R 398580 CDS YP_001532310.1 159043516 5710658 complement(989049..989933) 1 NC_009952.1 FAA is the last enzyme in the tyrosine catabolic pathway; fumarylacetoacetate (FAA) hydrolase 989933 5710658 Dshi_0967 Dinoroseobacter shibae DFL 12 = DSM 16493 fumarylacetoacetate (FAA) hydrolase YP_001532310.1 989049 R 398580 CDS YP_001532311.1 159043517 5710481 990030..990485 1 NC_009952.1 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 990485 5710481 Dshi_0968 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532311.1 990030 D 398580 CDS YP_001532312.1 159043518 5710482 complement(990448..991947) 1 NC_009952.1 Reaction: D-mannitol + NAD+ <=> D-fructose + NADH; mannitol dehydrogenase domain-containing protein 991947 mtlK 5710482 mtlK Dinoroseobacter shibae DFL 12 = DSM 16493 mannitol dehydrogenase domain-containing protein YP_001532312.1 990448 R 398580 CDS YP_001532313.1 159043519 5710483 complement(991935..992426) 1 NC_009952.1 N-terminal truncated; short-chain dehydrogenase/reductase SDR 992426 5710483 Dshi_0970 Dinoroseobacter shibae DFL 12 = DSM 16493 short-chain dehydrogenase/reductase SDR YP_001532313.1 991935 R 398580 CDS YP_001532314.1 159043520 5710484 complement(992438..993442) 1 NC_009952.1 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 993442 5710484 Dshi_0971 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC transporter-like protein YP_001532314.1 992438 R 398580 CDS YP_001532315.1 159043521 5710485 complement(993455..994285) 1 NC_009952.1 ABC transporter (importer) gene cluster: 2nd membrane spanning domain (MSD); part of a heterotetramer; binding-protein-dependent transport system inner membrane protein 994285 5710485 Dshi_0972 Dinoroseobacter shibae DFL 12 = DSM 16493 binding-protein-dependent transport system inner membrane protein YP_001532315.1 993455 R 398580 CDS YP_001532316.1 159043522 5710486 complement(994296..995162) 1 NC_009952.1 ABC transporter (importer) gene cluster: 1st membrane spanning domain (MSD); part of a heterotetramer; binding-protein-dependent transport system inner membrane protein 995162 5710486 Dshi_0973 Dinoroseobacter shibae DFL 12 = DSM 16493 binding-protein-dependent transport system inner membrane protein YP_001532316.1 994296 R 398580 CDS YP_001532317.1 159043523 5710487 complement(995276..996583) 1 NC_009952.1 ABC transporter (importer) gene cluster: receptor; family 1 extracellular solute-binding protein 996583 5710487 Dshi_0974 Dinoroseobacter shibae DFL 12 = DSM 16493 family 1 extracellular solute-binding protein YP_001532317.1 995276 R 398580 CDS YP_001532318.1 159043524 5710488 complement(996698..997732) 1 NC_009952.1 LacI family; transcriptional regulator 997732 5710488 Dshi_0975 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001532318.1 996698 R 398580 CDS YP_001532319.1 159043525 5710489 997950..998168 1 NC_009952.1 resolvase-like protein 998168 5710489 Dshi_0976 Dinoroseobacter shibae DFL 12 = DSM 16493 resolvase-like protein YP_001532319.1 997950 D 398580 CDS YP_001532320.1 159043526 5710491 998735..1000003 1 NC_009952.1 adds enolpyruvyl to UDP-N-acetylglucosamine as a component of cell wall formation; gram-positive bacteria have 2 copies of MurA which are active; UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1000003 murA 5710491 murA Dinoroseobacter shibae DFL 12 = DSM 16493 UDP-N-acetylglucosamine 1-carboxyvinyltransferase YP_001532320.1 998735 D 398580 CDS YP_001532321.1 159043527 5710492 1000000..1000476 1 NC_009952.1 conserved in alphaproteobacteria; hypothetical protein 1000476 5710492 Dshi_0978 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532321.1 1000000 D 398580 CDS YP_001532322.1 159043528 5710493 1000537..1001853 1 NC_009952.1 catalyzes the oxidation of L-histidinol to L-histidinaldehyde and then to L-histidine in histidine biosynthesis; functions as a dimer; histidinol dehydrogenase 1001853 hisD 5710493 hisD Dinoroseobacter shibae DFL 12 = DSM 16493 histidinol dehydrogenase YP_001532322.1 1000537 D 398580 CDS YP_001532323.1 159043529 5710494 1001850..1002329 1 NC_009952.1 conserved uncharacterized protein; hypothetical protein 1002329 5710494 Dshi_0980 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532323.1 1001850 D 398580 CDS YP_001532324.1 159043530 5710495 1002333..1002788 1 NC_009952.1 function not clear, homology to protein tyrosine phosphatase and arsenate reductase; protein tyrosine phosphatase 1002788 5710495 Dshi_0981 Dinoroseobacter shibae DFL 12 = DSM 16493 protein tyrosine phosphatase YP_001532324.1 1002333 D 398580 CDS YP_001532325.1 159043531 5710496 1002938..1003156 1 NC_009952.1 stimulates the activities of the other two initiation factors, IF-2 and IF-3; translation initiation factor IF-1 1003156 infA 5710496 infA Dinoroseobacter shibae DFL 12 = DSM 16493 translation initiation factor IF-1 YP_001532325.1 1002938 D 398580 CDS YP_001532326.1 159043532 5710497 1003159..1003743 1 NC_009952.1 putative inhibitor of septum formation; maf protein 1003743 5710497 Dshi_0983 Dinoroseobacter shibae DFL 12 = DSM 16493 maf protein YP_001532326.1 1003159 D 398580 CDS YP_001532327.1 159043533 5710498 1003740..1004783 1 NC_009952.1 Ribonuclease G and E-like family; ribonuclease 1004783 5710498 Dshi_0984 Dinoroseobacter shibae DFL 12 = DSM 16493 ribonuclease YP_001532327.1 1003740 D 398580 CDS YP_001532328.1 159043534 5710500 complement(1005574..1005831) 1 NC_009952.1 hypothetical protein 1005831 5710500 Dshi_0985 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532328.1 1005574 R 398580 CDS YP_001532329.1 159043535 5710501 complement(1006009..1006383) 1 NC_009952.1 DNA-binding, putative transcriptional regulator; helix-turn-helix domain-containing protein 1006383 5710501 Dshi_0986 Dinoroseobacter shibae DFL 12 = DSM 16493 helix-turn-helix domain-containing protein YP_001532329.1 1006009 R 398580 CDS YP_001532330.1 159043536 5710502 complement(1006380..1006733) 1 NC_009952.1 conserved in bacteria; hypothetical protein 1006733 5710502 Dshi_0987 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532330.1 1006380 R 398580 CDS YP_001532331.1 159043537 5710503 complement(1007057..1008169) 1 NC_009952.1 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 1008169 5710503 Dshi_0988 Dinoroseobacter shibae DFL 12 = DSM 16493 integrase family protein YP_001532331.1 1007057 R 398580 CDS YP_001532332.1 159043538 5710504 complement(1008195..1008434) 1 NC_009952.1 hypothetical protein 1008434 5710504 Dshi_0989 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532332.1 1008195 R 398580 CDS YP_001532333.1 159043539 5710505 complement(1009203..1013882) 1 NC_009952.1 putative DNA helicase-like protein 1013882 5710505 Dshi_0990 Dinoroseobacter shibae DFL 12 = DSM 16493 putative DNA helicase-like protein YP_001532333.1 1009203 R 398580 CDS YP_001532334.1 159043540 5710506 complement(1014095..1017562) 1 NC_009952.1 hypothetical protein 1017562 5710506 Dshi_0991 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532334.1 1014095 R 398580 CDS YP_001532335.1 159043541 5710507 complement(1017620..1020436) 1 NC_009952.1 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 1020436 5710507 Dshi_0992 Dinoroseobacter shibae DFL 12 = DSM 16493 type III restriction protein res subunit YP_001532335.1 1017620 R 398580 CDS YP_001532336.1 159043542 5710509 1022112..1023083 1 NC_009952.1 TRAP gene cluster - dctPQM; TAXI family; TRAP transporter solute receptor 1023083 5710509 Dshi_0993 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP transporter solute receptor YP_001532336.1 1022112 D 398580 CDS YP_001532337.1 159043543 5710510 1023150..1025069 1 NC_009952.1 TRAP gene cluster - dctPQM; 4TM/12TM fusion protein; TRAP transporter 1025069 5710510 Dshi_0994 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP transporter YP_001532337.1 1023150 D 398580 CDS YP_001532338.1 159043544 5710511 complement(1025066..1025971) 1 NC_009952.1 contains substrate binding domain, putative homotetramer; LysR family; transcriptional regulator 1025971 5710511 Dshi_0995 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001532338.1 1025066 R 398580 CDS YP_001532339.1 159043545 5710512 1026072..1027577 1 NC_009952.1 subunit of NADH dehydrogenase, electron transport chain(ETC) complex I; NADH/Ubiquinone/plastoquinone 1027577 5710512 Dshi_0996 Dinoroseobacter shibae DFL 12 = DSM 16493 NADH/Ubiquinone/plastoquinone YP_001532339.1 1026072 D 398580 CDS YP_001532340.1 159043546 5710513 1027607..1029982 1 NC_009952.1 putative inner membrane protein; hypothetical protein 1029982 5710513 Dshi_0997 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532340.1 1027607 D 398580 CDS YP_001532341.1 159043547 5710514 complement(1030013..1031707) 1 NC_009952.1 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 1031707 ade 5710514 ade Dinoroseobacter shibae DFL 12 = DSM 16493 adenine deaminase YP_001532341.1 1030013 R 398580 CDS YP_001532342.1 159043548 5710515 complement(1031760..1032641) 1 NC_009952.1 found both in prokaryotes and eukaryotes; related to the human bile acid:sodium symporters; transmembrane proteins; bile acid:sodium symporter 1032641 5710515 Dshi_0999 Dinoroseobacter shibae DFL 12 = DSM 16493 bile acid:sodium symporter YP_001532342.1 1031760 R 398580 CDS YP_001532343.1 159043549 5710516 complement(1032645..1034366) 1 NC_009952.1 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 1034366 fadD4 5710516 fadD4 Dinoroseobacter shibae DFL 12 = DSM 16493 AMP-dependent synthetase and ligase YP_001532343.1 1032645 R 398580 CDS YP_001532344.1 159043550 5710517 complement(1034458..1035408) 1 NC_009952.1 NAD-binding, Reaction: 2-hydroxyglutarate + NAD+ <=> 2-oxoglutarate + NADH; D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding subunit 1035408 serA2 5710517 serA2 Dinoroseobacter shibae DFL 12 = DSM 16493 D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding subunit YP_001532344.1 1034458 R 398580 CDS YP_001532345.1 159043551 5710518 complement(1035541..1036683) 1 NC_009952.1 PLP-dependent enzyme, Methionine metabolism, Reaction: O4-succinyl-L-homoserine + L-cysteine <=> L-cystathionine + succinate; cystathionine gamma-synthase 1036683 metB1 5710518 metB1 Dinoroseobacter shibae DFL 12 = DSM 16493 cystathionine gamma-synthase YP_001532345.1 1035541 R 398580 CDS YP_001532346.1 159043552 5710519 complement(1036698..1037711) 1 NC_009952.1 This family consists of bacterial antibiotic resistance proteins, which confer resistance to various aminoglycosides; aminoglycoside phosphotransferase 1037711 5710519 Dshi_1003 Dinoroseobacter shibae DFL 12 = DSM 16493 aminoglycoside phosphotransferase YP_001532346.1 1036698 R 398580 CDS YP_001532347.1 159043553 5710520 complement(1037708..1038925) 1 NC_009952.1 contains middle and C-terminal domain, N-terminal domain not conserved; acyl-CoA dehydrogenase domain-containing protein 1038925 5710520 Dshi_1004 Dinoroseobacter shibae DFL 12 = DSM 16493 acyl-CoA dehydrogenase domain-containing protein YP_001532347.1 1037708 R 398580 CDS YP_001532348.1 159043554 5710521 1039022..1039978 1 NC_009952.1 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 1039978 5710521 Dshi_1005 Dinoroseobacter shibae DFL 12 = DSM 16493 putative ribonuclease BN YP_001532348.1 1039022 D 398580 CDS YP_001532349.1 159043555 5710522 complement(1039975..1041198) 1 NC_009952.1 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 1041198 5710522 Dshi_1006 Dinoroseobacter shibae DFL 12 = DSM 16493 major facilitator superfamily protein YP_001532349.1 1039975 R 398580 CDS YP_001532350.1 159043556 5710523 complement(1041475..1042281) 1 NC_009952.1 Reaction: 3-oxoadipate enol-lactone + H2O = 3-oxoadipate; 3-oxoadipate enol-lactonase 1042281 catD 5710523 catD Dinoroseobacter shibae DFL 12 = DSM 16493 3-oxoadipate enol-lactonase YP_001532350.1 1041475 R 398580 CDS YP_001532351.1 159043557 5710524 complement(1042293..1043081) 1 NC_009952.1 Substrate: acyl-carrier-protein (ACP), Reaction: Acyl-ACP + NAD+ = trans-2,3-dehydroacyl-ACP + NADH; enoyl-(acyl-carrier-protein) reductase 1043081 fabI1 5710524 fabI1 Dinoroseobacter shibae DFL 12 = DSM 16493 enoyl-(acyl-carrier-protein) reductase YP_001532351.1 1042293 R 398580 CDS YP_001532352.1 159043558 5710525 complement(1043106..1044335) 1 NC_009952.1 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 1044335 fabB 5710525 fabB Dinoroseobacter shibae DFL 12 = DSM 16493 beta-ketoacyl synthase YP_001532352.1 1043106 R 398580 CDS YP_001532353.1 159043559 5710526 complement(1044358..1044867) 1 NC_009952.1 catalyzes the dehydration of (3R)-3-hydroxydecanoyl-ACP to 2,3-decenoyl-ACP or 3,4-decenoyl-ACP; 3-hydroxydecanoyl-ACP dehydratase 1044867 fabA 5710526 fabA Dinoroseobacter shibae DFL 12 = DSM 16493 3-hydroxydecanoyl-ACP dehydratase YP_001532353.1 1044358 R 398580 CDS YP_001532354.1 159043560 5710527 1045050..1045466 1 NC_009952.1 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 1045466 5710527 Dshi_1011 Dinoroseobacter shibae DFL 12 = DSM 16493 ferric uptake regulator YP_001532354.1 1045050 D 398580 CDS YP_001532355.1 159043561 5710528 complement(1045725..1046909) 1 NC_009952.1 catalyzes the formation of S-adenosylmethionine from methionine and ATP; methionine adenosyltransferase; S-adenosylmethionine synthetase 1046909 metK 5710528 metK Dinoroseobacter shibae DFL 12 = DSM 16493 S-adenosylmethionine synthetase YP_001532355.1 1045725 R 398580 CDS YP_001532356.1 159043562 5710529 complement(1046997..1048490) 1 NC_009952.1 Transfers the fatty acyl group on membrane lipoproteins; apolipoprotein N-acyltransferase 1048490 5710529 Dshi_1013 Dinoroseobacter shibae DFL 12 = DSM 16493 apolipoprotein N-acyltransferase YP_001532356.1 1046997 R 398580 CDS YP_001532357.1 159043563 5710530 complement(1048493..1049401) 1 NC_009952.1 CBS domains have been shown to bind ligands with an adenosyl group such as AMP, ATP and S-AdoMet; hypothetical protein 1049401 5710530 Dshi_1014 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532357.1 1048493 R 398580 CDS YP_001532358.1 159043564 5710531 complement(1049443..1049988) 1 NC_009952.1 hypothetical protein 1049988 5710531 Dshi_1015 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532358.1 1049443 R 398580 CDS YP_001532359.1 159043565 5710532 complement(1049966..1050979) 1 NC_009952.1 PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation.; PhoH family protein 1050979 5710532 Dshi_1016 Dinoroseobacter shibae DFL 12 = DSM 16493 PhoH family protein YP_001532359.1 1049966 R 398580 CDS YP_001532360.1 159043566 5710533 1051254..1053368 1 NC_009952.1 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 1053368 hemB2 5710533 hemB2 Dinoroseobacter shibae DFL 12 = DSM 16493 TonB-dependent heme/hemoglobin receptor family protein YP_001532360.1 1051254 D 398580 CDS YP_001532361.1 159043567 5710534 1053428..1053700 1 NC_009952.1 putative inner membrane protein; hypothetical protein 1053700 5710534 Dshi_1018 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532361.1 1053428 D 398580 CDS YP_001532362.1 159043568 5710535 complement(1053712..1055025) 1 NC_009952.1 catalyzes the formation of 2-methylthio-N6-(dimethylallyl)adenosine (ms(2)i(6)A) at position 37 in tRNAs that read codons beginning with uridine from N6-(dimethylallyl)adenosine (i(6)A); (dimethylallyl)adenosine tRNA methylthiotransferase 1055025 5710535 Dshi_1019 Dinoroseobacter shibae DFL 12 = DSM 16493 (dimethylallyl)adenosine tRNA methylthiotransferase YP_001532362.1 1053712 R 398580 CDS YP_001532363.1 159043569 5710536 1055162..1056058 1 NC_009952.1 hypothetical protein 1056058 5710536 Dshi_1020 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532363.1 1055162 D 398580 CDS YP_001532364.1 159043570 5710537 1056510..1057241 1 NC_009952.1 tRNA (guanine-N(7)-)-methyltransferase; catalyzes the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA by transferring the methyl residue from S-adenosyl-L-methionine; tRNA (guanine-N(7)-)-methyltransferase 1057241 trmB 5710537 trmB Dinoroseobacter shibae DFL 12 = DSM 16493 tRNA (guanine-N(7)-)-methyltransferase YP_001532364.1 1056510 D 398580 CDS YP_001532365.1 159043571 5710538 1057354..1058706 1 NC_009952.1 catalyzes the formation of 5-O-(1-carboxyvinyl)-3-phosphoshikimate from phosphoenolpyruvate and 3-phosphoshikimate in tryptophan biosynthesis; 3-phosphoshikimate 1-carboxyvinyltransferase 1058706 aroA 5710538 aroA Dinoroseobacter shibae DFL 12 = DSM 16493 3-phosphoshikimate 1-carboxyvinyltransferase YP_001532365.1 1057354 D 398580 CDS YP_001532366.1 159043572 5710991 1058724..1059362 1 NC_009952.1 Catalyzes the formation of (d)CDP from ATP and (d)CMP; cytidylate kinase 1059362 cmk 5710991 cmk Dinoroseobacter shibae DFL 12 = DSM 16493 cytidylate kinase YP_001532366.1 1058724 D 398580 CDS YP_001532367.1 159043573 5710992 1059484..1059801 1 NC_009952.1 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 1059801 5710992 Dshi_1024 Dinoroseobacter shibae DFL 12 = DSM 16493 histone family protein nucleoid-structuring protein H-NS YP_001532367.1 1059484 D 398580 CDS YP_001532368.1 159043574 5710993 1060024..1061700 1 NC_009952.1 in Escherichia coli this protein is involved in binding to the leader sequence of mRNAs and is itself bound to the 30S subunit; autoregulates expression via a C-terminal domain; in most gram negative organisms this protein is composed of 6 repeats of the S1 domain while in gram positive there are 4 repeats; the S1 nucleic acid-binding domain is found associated with other proteins; 30S ribosomal protein S1 1061700 rpsA 5710993 rpsA Dinoroseobacter shibae DFL 12 = DSM 16493 30S ribosomal protein S1 YP_001532368.1 1060024 D 398580 CDS YP_001532369.1 159043575 5710994 complement(1061749..1062312) 1 NC_009952.1 involved in septum formation; intracellular septation protein A 1062312 5710994 Dshi_1026 Dinoroseobacter shibae DFL 12 = DSM 16493 intracellular septation protein A YP_001532369.1 1061749 R 398580 CDS YP_001532370.1 159043576 5710995 1062676..1062963 1 NC_009952.1 This protein is one of the two subunits of integration host factor, a specific DNA-binding protein that functions in genetic recombination as well as in transcriptional and translational control; integration host factor subunit beta 1062963 ihfB 5710995 ihfB Dinoroseobacter shibae DFL 12 = DSM 16493 integration host factor subunit beta YP_001532370.1 1062676 D 398580 CDS YP_001532371.1 159043577 5710996 1062968..1063333 1 NC_009952.1 conserved in Rhodobacteraceae; hypothetical protein 1063333 5710996 Dshi_1028 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532371.1 1062968 D 398580 CDS YP_001532372.1 159043578 5710997 1063346..1064032 1 NC_009952.1 tryptophan biosynthesis, Reaction: N-(5-phospho-beta-D-ribosyl)anthranilate <=> 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate; phosphoribosylanthranilate isomerase 1064032 trpF 5710997 trpF Dinoroseobacter shibae DFL 12 = DSM 16493 phosphoribosylanthranilate isomerase YP_001532372.1 1063346 D 398580 CDS YP_001532373.1 159043579 5710998 1064067..1064297 1 NC_009952.1 hypothetical protein 1064297 5710998 Dshi_1030 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532373.1 1064067 D 398580 CDS YP_001532374.1 159043580 5710999 1064459..1065691 1 NC_009952.1 catalyzes the formation of L-tryptophan from L-serine and 1-(indol-3-yl)glycerol 3-phosphate; tryptophan synthase subunit beta 1065691 trpB 5710999 trpB Dinoroseobacter shibae DFL 12 = DSM 16493 tryptophan synthase subunit beta YP_001532374.1 1064459 D 398580 CDS YP_001532375.1 159043581 5711000 1065916..1066362 1 NC_009952.1 structure: signal peptide, Poly-DDR-repeat domain; hypothetical protein 1066362 5711000 Dshi_1032 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532375.1 1065916 D 398580 CDS YP_001532376.1 159043582 5711001 1066444..1066914 1 NC_009952.1 structure: signal peptide, Poly-DDR-repeat domain; hypothetical protein 1066914 5711001 Dshi_1033 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532376.1 1066444 D 398580 CDS YP_001532377.1 159043583 5711002 1066907..1067449 1 NC_009952.1 C-terminal LuxR Helix-Turn-helix motif; LuxR family; transcriptional regulator 1067449 5711002 Dshi_1034 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001532377.1 1066907 D 398580 CDS YP_001532378.1 159043584 5711003 1067835..1068809 1 NC_009952.1 TRAP gene cluster - dctPQM; TRAP dicarboxylate transporter subunit DctP 1068809 5711003 Dshi_1035 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP dicarboxylate transporter subunit DctP YP_001532378.1 1067835 D 398580 CDS YP_001532379.1 159043585 5711004 1068862..1069407 1 NC_009952.1 TRAP gene cluster - dctPQM; tripartite ATP-independent periplasmic transporter subunit DctQ 1069407 5711004 Dshi_1036 Dinoroseobacter shibae DFL 12 = DSM 16493 tripartite ATP-independent periplasmic transporter subunit DctQ YP_001532379.1 1068862 D 398580 CDS YP_001532380.1 159043586 5711005 1069438..1070742 1 NC_009952.1 TRAP gene cluster - dctPQM; DctM subunit; TRAP dicarboxylate transporter 1070742 5711005 Dshi_1037 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP dicarboxylate transporter YP_001532380.1 1069438 D 398580 CDS YP_001532381.1 159043587 5711006 complement(1070739..1071509) 1 NC_009952.1 Glutamate racemase, which interconverts L-glutamate into D-glutamate, is required for the biosynthesis of peptidoglycan; Asp/Glu racemase 1071509 5711006 Dshi_1038 Dinoroseobacter shibae DFL 12 = DSM 16493 Asp/Glu racemase YP_001532381.1 1070739 R 398580 CDS YP_001532382.1 159043588 5711007 complement(1071506..1072714) 1 NC_009952.1 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 1072714 5711007 Dshi_1039 Dinoroseobacter shibae DFL 12 = DSM 16493 monooxygenase FAD-binding YP_001532382.1 1071506 R 398580 CDS YP_001532383.1 159043589 5711008 complement(1072711..1075002) 1 NC_009952.1 high similarity to predicted Carbon-monoxide dehydrogenase proteins; aldehyde oxidase and xanthine dehydrogenase molybdopterin-binding 1075002 5711008 Dshi_1040 Dinoroseobacter shibae DFL 12 = DSM 16493 aldehyde oxidase and xanthine dehydrogenase molybdopterin-binding YP_001532383.1 1072711 R 398580 CDS YP_001532384.1 159043590 5711009 complement(1075005..1076324) 1 NC_009952.1 TRAP gene cluster - dctPQM; DctM subunit; TRAP dicarboxylate transporter 1076324 5711009 Dshi_1041 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP dicarboxylate transporter YP_001532384.1 1075005 R 398580 CDS YP_001532385.1 159043591 5711010 complement(1076328..1076834) 1 NC_009952.1 TRAP gene cluster - dctPQM; tripartite ATP-independent periplasmic transporter subunit DctQ 1076834 5711010 Dshi_1042 Dinoroseobacter shibae DFL 12 = DSM 16493 tripartite ATP-independent periplasmic transporter subunit DctQ YP_001532385.1 1076328 R 398580 CDS YP_001532386.1 159043592 5711011 complement(1076851..1077846) 1 NC_009952.1 TRAP gene cluster - dctPQM; TRAP dicarboxylate transporter subunit DctP 1077846 5711011 Dshi_1043 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP dicarboxylate transporter subunit DctP YP_001532386.1 1076851 R 398580 CDS YP_001532387.1 159043593 5711012 1078350..1079054 1 NC_009952.1 N-terminal HTH region, C-terminal FCD effector binding domain; GntR family; transcriptional regulator 1079054 5711012 Dshi_1044 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001532387.1 1078350 D 398580 CDS YP_001532388.1 159043594 5711013 1079051..1079896 1 NC_009952.1 HpcH/HpaI aldolase 1079896 5711013 Dshi_1045 Dinoroseobacter shibae DFL 12 = DSM 16493 HpcH/HpaI aldolase YP_001532388.1 1079051 D 398580 CDS YP_001532389.1 159043595 5711014 1079893..1081023 1 NC_009952.1 contains Amidase signature (AS) motif, AS enzymes catalyse the hydrolysis of amide bonds (CO-NH2); amidase 1081023 5711014 Dshi_1046 Dinoroseobacter shibae DFL 12 = DSM 16493 amidase YP_001532389.1 1079893 D 398580 CDS YP_001532390.1 159043596 5711015 complement(1081020..1081880) 1 NC_009952.1 hypothetical protein 1081880 5711015 Dshi_1047 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532390.1 1081020 R 398580 CDS YP_001532391.1 159043597 5711016 complement(1081882..1082679) 1 NC_009952.1 Enoyl-CoA hydratase and 3-2trans-enoyl-CoA isomerase are two enzymes involved in fatty acid metabolism; enoyl-CoA hydratase/isomerase 1082679 5711016 Dshi_1048 Dinoroseobacter shibae DFL 12 = DSM 16493 enoyl-CoA hydratase/isomerase YP_001532391.1 1081882 R 398580 CDS YP_001532392.1 159043598 5711017 complement(1082676..1083461) 1 NC_009952.1 large family of oxidoreductases; short chain dehydrogenase 1083461 5711017 Dshi_1049 Dinoroseobacter shibae DFL 12 = DSM 16493 short chain dehydrogenase YP_001532392.1 1082676 R 398580 CDS YP_001532393.1 159043599 5711018 complement(1083469..1083843) 1 NC_009952.1 hypothetical protein 1083843 5711018 Dshi_1050 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532393.1 1083469 R 398580 CDS YP_001532394.1 159043600 5711019 complement(1083833..1085182) 1 NC_009952.1 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 1085182 5711019 Dshi_1051 Dinoroseobacter shibae DFL 12 = DSM 16493 MmgE/PrpD family protein YP_001532394.1 1083833 R 398580 CDS YP_001532395.1 159043601 5711020 1085608..1086777 1 NC_009952.1 ABC transporter (importer) gene cluster: receptor; spermidine/putrescine-binding periplasmic protein-like protein 1086777 5711020 Dshi_1052 Dinoroseobacter shibae DFL 12 = DSM 16493 spermidine/putrescine-binding periplasmic protein-like protein YP_001532395.1 1085608 D 398580 CDS YP_001532396.1 159043602 5711021 1086781..1087698 1 NC_009952.1 ABC transporter (importer) gene cluster: 1st membrane spanning domain (MSD); part of a heterotetramer; binding-protein-dependent transport system inner membrane protein 1087698 5711021 Dshi_1053 Dinoroseobacter shibae DFL 12 = DSM 16493 binding-protein-dependent transport system inner membrane protein YP_001532396.1 1086781 D 398580 CDS YP_001532397.1 159043603 5711022 1087709..1088599 1 NC_009952.1 ABC transporter (importer) gene cluster: 2nd membrane spanning domain (MSD); part of a heterotetramer; binding-protein-dependent transport system inner membrane protein 1088599 5711022 Dshi_1054 Dinoroseobacter shibae DFL 12 = DSM 16493 binding-protein-dependent transport system inner membrane protein YP_001532397.1 1087709 D 398580 CDS YP_001532398.1 159043604 5711023 1088608..1089708 1 NC_009952.1 ABC transporter (importer) gene cluster (disrupted): ATP binding cassette (ABC) domain; part of a heterotetramer; ABC transporter-like protein 1089708 5711023 Dshi_1055 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC transporter-like protein YP_001532398.1 1088608 D 398580 CDS YP_001532399.1 159043605 5711024 1089720..1090628 1 NC_009952.1 polysaccharide deacetylase 1090628 5711024 Dshi_1056 Dinoroseobacter shibae DFL 12 = DSM 16493 polysaccharide deacetylase YP_001532399.1 1089720 D 398580 CDS YP_001532400.1 159043606 5711025 1090625..1091812 1 NC_009952.1 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 1091812 5711025 Dshi_1057 Dinoroseobacter shibae DFL 12 = DSM 16493 L-carnitine dehydratase/bile acid-inducible protein F YP_001532400.1 1090625 D 398580 CDS YP_001532401.1 159043607 5711026 1091824..1093014 1 NC_009952.1 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 1093014 5711026 Dshi_1058 Dinoroseobacter shibae DFL 12 = DSM 16493 acyl-CoA dehydrogenase domain-containing protein YP_001532401.1 1091824 D 398580 CDS YP_001532402.1 159043608 5711027 complement(1093034..1094338) 1 NC_009952.1 hypothetical protein 1094338 5711027 Dshi_1059 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532402.1 1093034 R 398580 CDS YP_001532403.1 159043609 5711028 complement(1094355..1095233) 1 NC_009952.1 hypothetical protein 1095233 5711028 Dshi_1060 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532403.1 1094355 R 398580 CDS YP_001532404.1 159043610 5711029 complement(1095405..1096250) 1 NC_009952.1 hypothetical protein 1096250 5711029 Dshi_1061 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532404.1 1095405 R 398580 CDS YP_001532405.1 159043611 5711030 complement(1096310..1096927) 1 NC_009952.1 high similarity to cobalt-zinc-cadmium resistance protein czcN, but no other czc genes in genome, inner membrane protein; isoprenylcysteine carboxyl methyltransferase 1096927 5711030 Dshi_1062 Dinoroseobacter shibae DFL 12 = DSM 16493 isoprenylcysteine carboxyl methyltransferase YP_001532405.1 1096310 R 398580 CDS YP_001532406.1 159043612 5711031 complement(1097007..1097243) 1 NC_009952.1 hypothetical protein 1097243 5711031 Dshi_1063 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532406.1 1097007 R 398580 CDS YP_001532407.1 159043613 5711032 complement(1097236..1097727) 1 NC_009952.1 similar to RuvC resolvase with substantial differences; NMR structural information suggests this protein is monomeric; unknown cellular function; Holliday junction resolvase-like protein 1097727 rufX 5711032 rufX Dinoroseobacter shibae DFL 12 = DSM 16493 Holliday junction resolvase-like protein YP_001532407.1 1097236 R 398580 CDS YP_001532408.1 159043614 5711033 1098107..1098376 1 NC_009952.1 hypothetical protein 1098376 5711033 Dshi_1065 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532408.1 1098107 D 398580 CDS YP_001532409.1 159043615 5711034 1098458..1098886 1 NC_009952.1 hypothetical protein 1098886 5711034 Dshi_1066 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532409.1 1098458 D 398580 CDS YP_001532410.1 159043616 5711035 1099165..1099764 1 NC_009952.1 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 1099764 sod 5711035 sod Dinoroseobacter shibae DFL 12 = DSM 16493 superoxide dismutase YP_001532410.1 1099165 D 398580 CDS YP_001532411.1 159043617 5711036 complement(1099844..1100293) 1 NC_009952.1 conserved in Rhodobacteraceae; hypothetical protein 1100293 5711036 Dshi_1068 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532411.1 1099844 R 398580 CDS YP_001532412.1 159043618 5711037 1100355..1100849 1 NC_009952.1 This family consists of the SufE-related proteins. These have been implicated in Fe-S metabolism and export; Fe-S metabolism associated SufE 1100849 5711037 Dshi_1069 Dinoroseobacter shibae DFL 12 = DSM 16493 Fe-S metabolism associated SufE YP_001532412.1 1100355 D 398580 CDS YP_001532413.1 159043619 5711038 complement(1101037..1101669) 1 NC_009952.1 hypothetical protein 1101669 5711038 Dshi_1070 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532413.1 1101037 R 398580 CDS YP_001532414.1 159043620 5711039 complement(1101666..1102001) 1 NC_009952.1 hypothetical protein 1102001 5711039 Dshi_1071 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532414.1 1101666 R 398580 CDS YP_001532415.1 159043621 5711040 complement(1101982..1102200) 1 NC_009952.1 hypothetical protein 1102200 5711040 Dshi_1072 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532415.1 1101982 R 398580 CDS YP_001532416.1 159043622 5711041 complement(1102259..1103038) 1 NC_009952.1 contains B12-binding domain, enzymatic domain not present; methionine synthase 1103038 5711041 Dshi_1073 Dinoroseobacter shibae DFL 12 = DSM 16493 methionine synthase YP_001532416.1 1102259 R 398580 CDS YP_001532417.1 159043623 5711042 complement(1103070..1104095) 1 NC_009952.1 catalyzes the formation of methionine from L-homocysteine and S-adenosyl-L-methionine; methionine synthase I 1104095 5711042 Dshi_1074 Dinoroseobacter shibae DFL 12 = DSM 16493 methionine synthase I YP_001532417.1 1103070 R 398580 CDS YP_001532418.1 159043624 5711043 complement(1104398..1104712) 1 NC_009952.1 hypothetical protein 1104712 5711043 Dshi_1075 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532418.1 1104398 R 398580 CDS YP_001532419.1 159043625 5711044 1104888..1105649 1 NC_009952.1 catalyzes the formation of (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4- carboxamido)succinate from 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate and L-aspartate in purine biosynthesis; SAICAR synthase; phosphoribosylaminoimidazolesuccinocarboxamide synthase 1105649 purC 5711044 purC Dinoroseobacter shibae DFL 12 = DSM 16493 phosphoribosylaminoimidazolesuccinocarboxamide synthase YP_001532419.1 1104888 D 398580 CDS YP_001532420.1 159043626 5711045 1105786..1106016 1 NC_009952.1 part of heterotrimer with purL(2500131741) and purQ(2500131101), required for enzymatic activity of the complex; phosphoribosylformylglycinamidine synthase 1106016 purS 5711045 purS Dinoroseobacter shibae DFL 12 = DSM 16493 phosphoribosylformylglycinamidine synthase YP_001532420.1 1105786 D 398580 CDS YP_001532421.1 159043627 5711046 1106016..1107053 1 NC_009952.1 Reaction: An alcohol + NAD+ = an aldehyde or ketone + NADH; alcohol dehydrogenase zinc-binding domain-containing protein 1107053 5711046 Dshi_1078 Dinoroseobacter shibae DFL 12 = DSM 16493 alcohol dehydrogenase zinc-binding domain-containing protein YP_001532421.1 1106016 D 398580 CDS YP_001532422.1 159043628 5711047 1107066..1107737 1 NC_009952.1 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 1107737 purQ 5711047 purQ Dinoroseobacter shibae DFL 12 = DSM 16493 phosphoribosylformylglycinamidine synthase I YP_001532422.1 1107066 D 398580 CDS YP_001532423.1 159043629 5711048 1107811..1109568 1 NC_009952.1 integral membrane bound sensor histidine kinase, similar to C4-dicarboxylate transport sensor protein dctB; integral membrane sensor signal transduction histidine kinase 1109568 5711048 Dshi_1080 Dinoroseobacter shibae DFL 12 = DSM 16493 integral membrane sensor signal transduction histidine kinase YP_001532423.1 1107811 D 398580 CDS YP_001532424.1 159043630 5711049 1109596..1110921 1 NC_009952.1 sigma54 specific, similar to C4-dicarboxylate transport transcriptional regulatory protein dctD; sigma54 specific, transcriptional regulator, Fis family; two component 1110921 5711049 Dshi_1081 Dinoroseobacter shibae DFL 12 = DSM 16493 two component YP_001532424.1 1109596 D 398580 CDS YP_001532425.1 159043631 5711050 complement(1111025..1111882) 1 NC_009952.1 Conjugates Arg from its aminoacyl-tRNA to the N-termini of proteins containing an N-terminal aspartate or glutamate; arginyl-tRNA-protein transferase 1111882 ate 5711050 ate Dinoroseobacter shibae DFL 12 = DSM 16493 arginyl-tRNA-protein transferase YP_001532425.1 1111025 R 398580 CDS YP_001532426.1 159043632 5711051 complement(1111953..1112393) 1 NC_009952.1 two transmembrane domains, RDD domain; RDD domain-containing protein 1112393 5711051 Dshi_1083 Dinoroseobacter shibae DFL 12 = DSM 16493 RDD domain-containing protein YP_001532426.1 1111953 R 398580 CDS YP_001532427.1 159043633 5711052 complement(1112500..1112910) 1 NC_009952.1 hypothetical protein 1112910 5711052 Dshi_1084 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532427.1 1112500 R 398580 CDS YP_001532428.1 159043634 5711053 complement(1113043..1113513) 1 NC_009952.1 YbaK/prolyl-tRNA synthetase associated domain of unknown funktion; YbaK/prolyl-tRNA synthetase associated domain-containing protein 1113513 5711053 Dshi_1085 Dinoroseobacter shibae DFL 12 = DSM 16493 YbaK/prolyl-tRNA synthetase associated domain-containing protein YP_001532428.1 1113043 R 398580 CDS YP_001532429.1 159043635 5711054 1113620..1114048 1 NC_009952.1 hypothetical protein 1114048 5711054 Dshi_1086 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532429.1 1113620 D 398580 CDS YP_001532430.1 159043636 5711055 1114171..1115130 1 NC_009952.1 TRAP gene cluster - dctPQM; TAXI family; TRAP transporter solute receptor 1115130 5711055 Dshi_1087 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP transporter solute receptor YP_001532430.1 1114171 D 398580 CDS YP_001532431.1 159043637 5711056 1115143..1116930 1 NC_009952.1 TRAP gene cluster - dctPQM; 4TM/12TM fusion protein; TRAP transporter 1116930 5711056 Dshi_1088 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP transporter YP_001532431.1 1115143 D 398580 CDS YP_001532432.1 159043638 5711057 1117014..1118006 1 NC_009952.1 TRAP gene cluster - dctPQM; TRAP dicarboxylate transporter subunit DctP 1118006 5711057 Dshi_1089 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP dicarboxylate transporter subunit DctP YP_001532432.1 1117014 D 398580 CDS YP_001532433.1 159043639 5711058 1118068..1118565 1 NC_009952.1 TRAP gene cluster - dctPQM; tripartite ATP-independent periplasmic transporter subunit DctQ 1118565 5711058 Dshi_1090 Dinoroseobacter shibae DFL 12 = DSM 16493 tripartite ATP-independent periplasmic transporter subunit DctQ YP_001532433.1 1118068 D 398580 CDS YP_001532434.1 159043640 5711059 1118562..1119836 1 NC_009952.1 TRAP gene cluster - dctPQM; DctM subunit; TRAP dicarboxylate transporter 1119836 5711059 Dshi_1091 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP dicarboxylate transporter YP_001532434.1 1118562 D 398580 CDS YP_001532435.1 159043641 5711060 1119841..1120722 1 NC_009952.1 Reaction: 1-Carboxyvinyl carboxyphosphonate <=> 3-(Hydrohydroxyphosphoryl)pyruvate + CO2; carboxyvinyl-carboxyphosphonatephosphorylmutase 1120722 5711060 Dshi_1092 Dinoroseobacter shibae DFL 12 = DSM 16493 carboxyvinyl-carboxyphosphonatephosphorylmutase YP_001532435.1 1119841 D 398580 CDS YP_001532436.1 159043642 5711061 1120783..1121310 1 NC_009952.1 hypothetical protein 1121310 5711061 Dshi_1093 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532436.1 1120783 D 398580 CDS YP_001532437.1 159043643 5711062 1121391..1122380 1 NC_009952.1 Domains: GAF (present in phytochromes and cGMP-specific phosphodiesterases), FIS; Fis family; transcriptional regulator 1122380 5711062 Dshi_1094 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001532437.1 1121391 D 398580 CDS YP_001532438.1 159043644 5711063 1122494..1124014 1 NC_009952.1 Reaction: An aldehyde + NAD+ + H2O = an acid + NADH; aldehyde dehydrogenase 1124014 5711063 Dshi_1095 Dinoroseobacter shibae DFL 12 = DSM 16493 aldehyde dehydrogenase YP_001532438.1 1122494 D 398580 CDS YP_001532439.1 159043645 5711064 complement(1124071..1124751) 1 NC_009952.1 putative GDSL-like lipase; G-D-S-L; lipolytic protein 1124751 5711064 Dshi_1096 Dinoroseobacter shibae DFL 12 = DSM 16493 lipolytic protein YP_001532439.1 1124071 R 398580 CDS YP_001532440.1 159043646 5711065 complement(1124897..1125964) 1 NC_009952.1 two YeeE/YedE-domains; hypothetical protein 1125964 5711065 Dshi_1097 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532440.1 1124897 R 398580 CDS YP_001532441.1 159043647 5711066 1126077..1127306 1 NC_009952.1 inner membrane single-polypeptide secondary carrier; major facilitator superfamily protein 1127306 5711066 Dshi_1098 Dinoroseobacter shibae DFL 12 = DSM 16493 major facilitator superfamily protein YP_001532441.1 1126077 D 398580 CDS YP_001532442.1 159043648 5711067 1127361..1128023 1 NC_009952.1 repairs damaged proteins. Methionine sulfoxide in proteins is reduced to methionine.; peptide methionine sulfoxide reductase 1128023 msrA2 5711067 msrA2 Dinoroseobacter shibae DFL 12 = DSM 16493 peptide methionine sulfoxide reductase YP_001532442.1 1127361 D 398580 CDS YP_001532443.1 159043649 5711068 1128118..1128987 1 NC_009952.1 Methylates ribosomal protein L11; ribosomal L11 methyltransferase 1128987 prmA 5711068 prmA Dinoroseobacter shibae DFL 12 = DSM 16493 ribosomal L11 methyltransferase YP_001532443.1 1128118 D 398580 CDS YP_001532444.1 159043650 5711069 1129052..1129375 1 NC_009952.1 hypothetical protein 1129375 5711069 Dshi_1101 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532444.1 1129052 D 398580 CDS YP_001532445.1 159043651 5711070 complement(1129452..1129649) 1 NC_009952.1 hypothetical protein 1129649 5711070 Dshi_1102 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532445.1 1129452 R 398580 CDS YP_001532446.1 159043652 5711071 1129962..1130492 1 NC_009952.1 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 1130492 ruvC 5711071 ruvC Dinoroseobacter shibae DFL 12 = DSM 16493 Holliday junction resolvase YP_001532446.1 1129962 D 398580 CDS YP_001532447.1 159043653 5711072 1130489..1131163 1 NC_009952.1 plays an essential role in ATP-dependent branch migration of the Holliday junction; Holliday junction DNA helicase RuvA 1131163 ruvA 5711072 ruvA Dinoroseobacter shibae DFL 12 = DSM 16493 Holliday junction DNA helicase RuvA YP_001532447.1 1130489 D 398580 CDS YP_001532448.1 159043654 5711073 1131167..1132240 1 NC_009952.1 promotes strand exchange during homologous recombination; RuvAB complex promotes branch migration; RuvABC complex scans the DNA during branch migration and resolves Holliday junctions at consensus sequences; forms hexameric rings around opposite DNA arms; requires ATP for branch migration and orientation of RuvAB complex determines direction of migration; Holliday junction DNA helicase RuvB 1132240 ruvB 5711073 ruvB Dinoroseobacter shibae DFL 12 = DSM 16493 Holliday junction DNA helicase RuvB YP_001532448.1 1131167 D 398580 CDS YP_001532449.1 159043655 5711074 1132304..1132930 1 NC_009952.1 conserved in Rhodobacteraceae; hypothetical protein 1132930 5711074 Dshi_1106 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532449.1 1132304 D 398580 CDS YP_001532450.1 159043656 5711075 1132927..1133337 1 NC_009952.1 The significance of this thioesterase to the tol-pal system is unclear; Pol-Pal system-associated acyl-CoA thioesterase 1133337 5711075 Dshi_1107 Dinoroseobacter shibae DFL 12 = DSM 16493 Pol-Pal system-associated acyl-CoA thioesterase YP_001532450.1 1132927 D 398580 CDS YP_001532451.1 159043657 5711076 1133433..1134107 1 NC_009952.1 outer membrane integrity and transport system Tol-Pal: TolQRAB-Pal; Tol-Pal system protein TolQ 1134107 tolQ 5711076 tolQ Dinoroseobacter shibae DFL 12 = DSM 16493 Tol-Pal system protein TolQ YP_001532451.1 1133433 D 398580 CDS YP_001532452.1 159043658 5711077 1134195..1134599 1 NC_009952.1 outer membrane integrity and transport system Tol-Pal: TolQRAB-Pal; biopolymer transport TolR 1134599 tolR 5711077 tolR Dinoroseobacter shibae DFL 12 = DSM 16493 biopolymer transport TolR YP_001532452.1 1134195 D 398580 CDS YP_001532453.1 159043659 5711078 1134607..1135662 1 NC_009952.1 outer membrane integrity and transport system Tol-Pal: TolQRAB-Pal; hypothetical protein 1135662 tolA 5711078 tolA Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532453.1 1134607 D 398580 CDS YP_001532454.1 159043660 5711079 1135659..1136999 1 NC_009952.1 forms dimers; may be involved in cell envelope integrity; interacts with outer membrane proteins and with the C-terminal domain of inner membrane protein TolA; translocation protein TolB 1136999 tolB 5711079 tolB Dinoroseobacter shibae DFL 12 = DSM 16493 translocation protein TolB YP_001532454.1 1135659 D 398580 CDS YP_001532455.1 159043661 5711080 1137066..1137593 1 NC_009952.1 outer membrane integrity and transport system Tol-Pal: TolQRAB-Pal; peptidoglycan-associated lipoprotein 1137593 pal 5711080 pal Dinoroseobacter shibae DFL 12 = DSM 16493 peptidoglycan-associated lipoprotein YP_001532455.1 1137066 D 398580 CDS YP_001532456.1 159043662 5711081 1137614..1138432 1 NC_009952.1 contains 1 Tetratricopeptide repeat; Tol-Pal system protein YbgF 1138432 5711081 Dshi_1113 Dinoroseobacter shibae DFL 12 = DSM 16493 Tol-Pal system protein YbgF YP_001532456.1 1137614 D 398580 CDS YP_001532457.1 159043663 5711082 1138429..1139682 1 NC_009952.1 Ligates Lysine to a tRNA cytidine, thus changing the amino acid specificity of the tRNA from methionine to isoleucine; tRNA(Ile)-lysidine synthetase 1139682 tilS 5711082 tilS Dinoroseobacter shibae DFL 12 = DSM 16493 tRNA(Ile)-lysidine synthetase YP_001532457.1 1138429 D 398580 CDS YP_001532458.1 159043664 5711083 1139764..1141680 1 NC_009952.1 membrane-bound ATP-dependent protease universally conserved in prokaryotes; ATP-dependent metalloprotease FtsH 1141680 ftsH 5711083 ftsH Dinoroseobacter shibae DFL 12 = DSM 16493 ATP-dependent metalloprotease FtsH YP_001532458.1 1139764 D 398580 CDS YP_001532459.1 159043665 5711084 1141820..1142431 1 NC_009952.1 hypothetical protein 1142431 5711084 Dshi_1116 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532459.1 1141820 D 398580 CDS YP_001532460.1 159043666 5711085 complement(1142513..1142929) 1 NC_009952.1 thioesterase superfamily protein 1142929 5711085 Dshi_1117 Dinoroseobacter shibae DFL 12 = DSM 16493 thioesterase superfamily protein YP_001532460.1 1142513 R 398580 CDS YP_001532461.1 159043667 5711086 complement(1142926..1143639) 1 NC_009952.1 hypothetical protein 1143639 5711086 Dshi_1118 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532461.1 1142926 R 398580 CDS YP_001532462.1 159043668 5711087 complement(1143663..1146086) 1 NC_009952.1 contains DEAD/H associated domain; DEAD/DEAH box helicase 1146086 5711087 Dshi_1119 Dinoroseobacter shibae DFL 12 = DSM 16493 DEAD/DEAH box helicase YP_001532462.1 1143663 R 398580 CDS YP_001532463.1 159043669 5711088 complement(1146135..1147442) 1 NC_009952.1 hypothetical protein 1147442 5711088 Dshi_1120 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532463.1 1146135 R 398580 CDS YP_001532464.1 159043670 5711089 complement(1147479..1147988) 1 NC_009952.1 peptidase A24A prepilin type IV 1147988 5711089 Dshi_1121 Dinoroseobacter shibae DFL 12 = DSM 16493 peptidase A24A prepilin type IV YP_001532464.1 1147479 R 398580 CDS YP_001532465.1 159043671 5711090 complement(1147996..1148847) 1 NC_009952.1 hypothetical protein 1148847 5711090 Dshi_1122 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532465.1 1147996 R 398580 CDS YP_001532466.1 159043672 5711091 complement(1148895..1149425) 1 NC_009952.1 contains 2 TPR domains, involved in protein-protein interaction; hypothetical protein 1149425 5711091 Dshi_1123 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532466.1 1148895 R 398580 CDS YP_001532467.1 159043673 5711092 complement(1149478..1150473) 1 NC_009952.1 type II secretion system protein 1150473 5711092 Dshi_1124 Dinoroseobacter shibae DFL 12 = DSM 16493 type II secretion system protein YP_001532467.1 1149478 R 398580 CDS YP_001532468.1 159043674 5711093 complement(1150478..1151446) 1 NC_009952.1 type II secretion system protein 1151446 5711093 Dshi_1125 Dinoroseobacter shibae DFL 12 = DSM 16493 type II secretion system protein YP_001532468.1 1150478 R 398580 CDS YP_001532469.1 159043675 5711094 complement(1151449..1152903) 1 NC_009952.1 type II secretion system protein E 1152903 5711094 Dshi_1126 Dinoroseobacter shibae DFL 12 = DSM 16493 type II secretion system protein E YP_001532469.1 1151449 R 398580 CDS YP_001532470.1 159043676 5711095 complement(1152923..1154230) 1 NC_009952.1 response regulator receiver protein 1154230 5711095 Dshi_1127 Dinoroseobacter shibae DFL 12 = DSM 16493 response regulator receiver protein YP_001532470.1 1152923 R 398580 CDS YP_001532471.1 159043677 5711096 complement(1154427..1155065) 1 NC_009952.1 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 1155065 5711096 Dshi_1128 Dinoroseobacter shibae DFL 12 = DSM 16493 OmpA/MotB domain-containing protein YP_001532471.1 1154427 R 398580 CDS YP_001532472.1 159043678 5711097 complement(1155070..1156494) 1 NC_009952.1 Bacterial type II and III secretion system protein; type II and III secretion system protein 1156494 5711097 Dshi_1129 Dinoroseobacter shibae DFL 12 = DSM 16493 type II and III secretion system protein YP_001532472.1 1155070 R 398580 CDS YP_001532473.1 159043679 5711098 complement(1156688..1157530) 1 NC_009952.1 Domains: SAF; SAF domain-containing protein 1157530 5711098 Dshi_1130 Dinoroseobacter shibae DFL 12 = DSM 16493 SAF domain-containing protein YP_001532473.1 1156688 R 398580 CDS YP_001532474.1 159043680 5711099 complement(1157706..1157918) 1 NC_009952.1 conserved in Rhodobacteraceae; hypothetical protein 1157918 5711099 Dshi_1131 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532474.1 1157706 R 398580 CDS YP_001532475.1 159043681 5711100 complement(1158153..1158365) 1 NC_009952.1 conserved in Rhodobacteraceae; hypothetical protein 1158365 5711100 Dshi_1132 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532475.1 1158153 R 398580 CDS YP_001532476.1 159043682 5711101 1158693..1159541 1 NC_009952.1 found in phages, type II, type III and type IV secretion systems; lytic transglycosylase catalytic subunit 1159541 5711101 Dshi_1133 Dinoroseobacter shibae DFL 12 = DSM 16493 lytic transglycosylase catalytic subunit YP_001532476.1 1158693 D 398580 CDS YP_001532477.1 159043683 5711102 complement(1159632..1160258) 1 NC_009952.1 Reaction: Succinyl-CoA + a 3-oxo acid <=> succinate + a 3-oxoacyl-CoA; 3-oxoacid CoA-transferase subunit B 1160258 5711102 Dshi_1134 Dinoroseobacter shibae DFL 12 = DSM 16493 3-oxoacid CoA-transferase subunit B YP_001532477.1 1159632 R 398580 CDS YP_001532478.1 159043684 5711103 complement(1160285..1161301) 1 NC_009952.1 contains putative PAS photoreceptor domain; putative signal transduction histidine kinase 1161301 5711103 Dshi_1135 Dinoroseobacter shibae DFL 12 = DSM 16493 putative signal transduction histidine kinase YP_001532478.1 1160285 R 398580 CDS YP_001532479.1 159043685 5711104 complement(1161319..1162014) 1 NC_009952.1 Reaction: Succinyl-CoA + a 3-oxo acid <=> succinate + a 3-oxoacyl-CoA; 3-oxoacid CoA-transferase subunit A 1162014 5711104 Dshi_1136 Dinoroseobacter shibae DFL 12 = DSM 16493 3-oxoacid CoA-transferase subunit A YP_001532479.1 1161319 R 398580 CDS YP_001532480.1 159043686 5711105 complement(1162114..1164816) 1 NC_009952.1 catalyzes the ATP-dependent breakage of single-stranded DNA followed by passage and rejoining, maintains net negative superhelicity; DNA topoisomerase I 1164816 topA 5711105 topA Dinoroseobacter shibae DFL 12 = DSM 16493 DNA topoisomerase I YP_001532480.1 1162114 R 398580 CDS YP_001532481.1 159043687 5711106 complement(1165063..1166202) 1 NC_009952.1 required to protect incoming ssDNA from immediate degradation; DNA protecting protein DprA 1166202 5711106 Dshi_1138 Dinoroseobacter shibae DFL 12 = DSM 16493 DNA protecting protein DprA YP_001532481.1 1165063 R 398580 CDS YP_001532482.1 159043688 5711107 complement(1166474..1167895) 1 NC_009952.1 Suppresses the inhibitory activity of the carbon storage regulator; peptidase U62 modulator of DNA gyrase 1167895 tldD 5711107 tldD Dinoroseobacter shibae DFL 12 = DSM 16493 peptidase U62 modulator of DNA gyrase YP_001532482.1 1166474 R 398580 CDS YP_001532483.1 159043689 5711108 1168156..1168968 1 NC_009952.1 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 1168968 ctaC 5711108 ctaC Dinoroseobacter shibae DFL 12 = DSM 16493 cytochrome c oxidase subunit II YP_001532483.1 1168156 D 398580 CDS YP_001532484.1 159043690 5711109 1168989..1169975 1 NC_009952.1 converts protoheme IX and farnesyl diphosphate to heme O; protoheme IX farnesyltransferase 1169975 ctaB 5711109 ctaB Dinoroseobacter shibae DFL 12 = DSM 16493 protoheme IX farnesyltransferase YP_001532484.1 1168989 D 398580 CDS YP_001532485.1 159043691 5711110 1169979..1170164 1 NC_009952.1 hypothetical protein 1170164 5711110 Dshi_1142 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532485.1 1169979 D 398580 CDS YP_001532486.1 159043692 5711111 1170161..1170772 1 NC_009952.1 involved in the insertion of copper into subunit I of cytochrome C oxidase; cytochrome C oxidase assembly protein 1170772 ctaG 5711111 ctaG Dinoroseobacter shibae DFL 12 = DSM 16493 cytochrome C oxidase assembly protein YP_001532486.1 1170161 D 398580 CDS YP_001532487.1 159043693 5711112 1170794..1171600 1 NC_009952.1 part of oligomeric enzyme complex in the electron transport chain, subunit I and III form the catalytic active compound; cytochrome c oxidase subunit III 1171600 ctaE 5711112 ctaE Dinoroseobacter shibae DFL 12 = DSM 16493 cytochrome c oxidase subunit III YP_001532487.1 1170794 D 398580 CDS YP_001532488.1 159043694 5711113 1171698..1172399 1 NC_009952.1 similar to SURF1 protein, involved in cox complex assembly; hypothetical protein 1172399 5711113 Dshi_1145 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532488.1 1171698 D 398580 CDS YP_001532489.1 159043695 5711114 1172413..1173804 1 NC_009952.1 catalyzes the formation of L-threonine from O-phospho-L-homoserine; threonine synthase 1173804 thrC 5711114 thrC Dinoroseobacter shibae DFL 12 = DSM 16493 threonine synthase YP_001532489.1 1172413 D 398580 CDS YP_001532490.1 159043696 5711115 1173801..1175081 1 NC_009952.1 uncharacterized zinc protease M16 family; processing peptidase 1175081 5711115 Dshi_1147 Dinoroseobacter shibae DFL 12 = DSM 16493 processing peptidase YP_001532490.1 1173801 D 398580 CDS YP_001532491.1 159043697 5711116 1175081..1175665 1 NC_009952.1 protein N-Acetyl-transferase; N-acetyltransferase GCN5 1175665 5711116 Dshi_1148 Dinoroseobacter shibae DFL 12 = DSM 16493 N-acetyltransferase GCN5 YP_001532491.1 1175081 D 398580 CDS YP_001532492.1 159043698 5711117 complement(1175811..1176419) 1 NC_009952.1 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 1176419 infC 5711117 infC Dinoroseobacter shibae DFL 12 = DSM 16493 translation initiation factor IF-3 YP_001532492.1 1175811 R 398580 CDS YP_001532493.1 159043699 5711918 complement(1176572..1177432) 1 NC_009952.1 Reaction: 2 reduced ferredoxin + NADP+ <=> 2 oxidized ferredoxin + NADPH; ferredoxin--NADP(+) reductase 1177432 5711918 Dshi_1150 Dinoroseobacter shibae DFL 12 = DSM 16493 ferredoxin--NADP(+) reductase YP_001532493.1 1176572 R 398580 CDS YP_001532494.1 159043700 5711919 complement(1177500..1177916) 1 NC_009952.1 conserved in bacteria; hypothetical protein 1177916 5711919 Dshi_1151 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532494.1 1177500 R 398580 CDS YP_001532495.1 159043701 5711920 complement(1177913..1178668) 1 NC_009952.1 catalyzes the reduction of 3'-phosphoadenylyl sulfate into sulfite; phosphoadenosine phosphosulfate reductase 1178668 cysH 5711920 cysH Dinoroseobacter shibae DFL 12 = DSM 16493 phosphoadenosine phosphosulfate reductase YP_001532495.1 1177913 R 398580 CDS YP_001532496.1 159043702 5711921 complement(1178658..1180325) 1 NC_009952.1 catalyseses the six-electron reduction of sulphite to sulphide; nitrite/sulfite reductase hemoprotein beta-component ferrodoxin domain-containing protein 1180325 cysI 5711921 cysI Dinoroseobacter shibae DFL 12 = DSM 16493 nitrite/sulfite reductase hemoprotein beta-component ferrodoxin domain-containing protein YP_001532496.1 1178658 R 398580 CDS YP_001532497.1 159043703 5711922 complement(1180350..1180655) 1 NC_009952.1 conserved in Alphaproteobacteria; hypothetical protein 1180655 5711922 Dshi_1154 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532497.1 1180350 R 398580 CDS YP_001532498.1 159043704 5711923 complement(1180655..1182040) 1 NC_009952.1 For siroheme; for sulfite reductase.; uroporphyrin-III C-methyltransferase 1182040 5711923 Dshi_1155 Dinoroseobacter shibae DFL 12 = DSM 16493 uroporphyrin-III C-methyltransferase YP_001532498.1 1180655 R 398580 CDS YP_001532499.1 159043705 5711924 1182178..1182645 1 NC_009952.1 Helix-Turn-Helix motif, AsnC/Lrp subfamily; AsnC family; transcriptional regulator 1182645 5711924 Dshi_1156 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001532499.1 1182178 D 398580 CDS YP_001532500.1 159043706 5711925 complement(1182730..1184175) 1 NC_009952.1 hypothetical protein 1184175 5711925 Dshi_1157 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532500.1 1182730 R 398580 CDS YP_001532501.1 159043707 5711926 complement(1184225..1185181) 1 NC_009952.1 preference for inosine/uridine; inosine/uridine-preferring nucleoside hydrolase 1185181 rih 5711926 rih Dinoroseobacter shibae DFL 12 = DSM 16493 inosine/uridine-preferring nucleoside hydrolase YP_001532501.1 1184225 R 398580 CDS YP_001532502.1 159043708 5711927 1185626..1186144 1 NC_009952.1 hypothetical protein 1186144 5711927 Dshi_1159 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532502.1 1185626 D 398580 CDS YP_001532503.1 159043709 5711928 complement(1186149..1186988) 1 NC_009952.1 contains 2 MazG domains; MazG family protein 1186988 5711928 Dshi_1160 Dinoroseobacter shibae DFL 12 = DSM 16493 MazG family protein YP_001532503.1 1186149 R 398580 CDS YP_001532504.1 159043710 5711929 1187053..1188213 1 NC_009952.1 Degradation of proteins, peptides, and glycopeptides; amidohydrolase 1188213 5711929 Dshi_1161 Dinoroseobacter shibae DFL 12 = DSM 16493 amidohydrolase YP_001532504.1 1187053 D 398580 CDS YP_001532505.1 159043711 5711930 complement(1188220..1191789) 1 NC_009952.1 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 1191789 5711930 Dshi_1162 Dinoroseobacter shibae DFL 12 = DSM 16493 acriflavin resistance protein YP_001532505.1 1188220 R 398580 CDS YP_001532506.1 159043712 5711931 complement(1191786..1192937) 1 NC_009952.1 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 1192937 5711931 Dshi_1163 Dinoroseobacter shibae DFL 12 = DSM 16493 efflux transporter YP_001532506.1 1191786 R 398580 CDS YP_001532507.1 159043713 5711932 1193168..1193821 1 NC_009952.1 conserved in Rhodobacteraceae and Rhizobiales; hypothetical protein 1193821 5711932 Dshi_1164 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532507.1 1193168 D 398580 CDS YP_001532508.1 159043714 5711933 1193808..1195160 1 NC_009952.1 contains PQQ repeat domain involved in PQQ binding; pyrrolo-quinoline quinone 1195160 5711933 Dshi_1165 Dinoroseobacter shibae DFL 12 = DSM 16493 pyrrolo-quinoline quinone YP_001532508.1 1193808 D 398580 CDS YP_001532509.1 159043715 5711934 1195258..1196730 1 NC_009952.1 EngA; essential Neisserial GTPase; synchronizes cellular events by interacting with multiple targets with tandem G-domains; overexpression in Escherichia coli suppresses rrmJ mutation; structural analysis of the Thermotoga maritima ortholog shows different nucleotide binding affinities in the two binding domains; GTP-binding protein EngA 1196730 engA 5711934 engA Dinoroseobacter shibae DFL 12 = DSM 16493 GTP-binding protein EngA YP_001532509.1 1195258 D 398580 CDS YP_001532510.1 159043716 5711935 complement(1196727..1198073) 1 NC_009952.1 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 1198073 5711935 Dshi_1167 Dinoroseobacter shibae DFL 12 = DSM 16493 peptidase M48 Ste24p YP_001532510.1 1196727 R 398580 CDS YP_001532511.1 159043717 5711936 1198126..1199301 1 NC_009952.1 PLP-dependent enzyme; class I/II aminotransferase 1199301 5711936 Dshi_1168 Dinoroseobacter shibae DFL 12 = DSM 16493 class I/II aminotransferase YP_001532511.1 1198126 D 398580 CDS YP_001532512.1 159043718 5711937 1199349..1200617 1 NC_009952.1 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 1200617 amiC 5711937 amiC Dinoroseobacter shibae DFL 12 = DSM 16493 N-acetylmuramoyl-L-alanine amidase YP_001532512.1 1199349 D 398580 CDS YP_001532513.1 159043719 5711938 complement(1200611..1201234) 1 NC_009952.1 SAM dependent enzyme; type 11 methyltransferase 1201234 5711938 Dshi_1170 Dinoroseobacter shibae DFL 12 = DSM 16493 type 11 methyltransferase YP_001532513.1 1200611 R 398580 CDS YP_001532514.1 159043720 5711939 1201406..1203928 1 NC_009952.1 penicillin-binding proteins are bifunctional proteins consisting of transglycosylase and transpeptidase in the N- and C-terminus respectively; 1A family; penicillin-binding protein 1203928 5711939 Dshi_1171 Dinoroseobacter shibae DFL 12 = DSM 16493 penicillin-binding protein YP_001532514.1 1201406 D 398580 CDS YP_001532515.1 159043721 5711940 1204202..1205329 1 NC_009952.1 recognizes the termination signals UGA and UAA during protein translation a specificity which is dependent on amino acid residues residing in loops of the L-shaped tRNA-like molecule of RF2; in some organisms control of PrfB protein levels is maintained through a +1 ribosomal frameshifting mechanism; this protein is similar to release factor 1; peptide chain release factor 2 1205329 prfB 5711940 prfB Dinoroseobacter shibae DFL 12 = DSM 16493 peptide chain release factor 2 YP_001532515.1 1204202 D 398580 CDS YP_001532516.1 159043722 5711941 1205414..1206421 1 NC_009952.1 proposed to be required for the biosynthesis of the pyrimidine moiety of thiamine; NMT1/THI5 like domain-containing protein 1206421 5711941 Dshi_1173 Dinoroseobacter shibae DFL 12 = DSM 16493 NMT1/THI5 like domain-containing protein YP_001532516.1 1205414 D 398580 CDS YP_001532517.1 159043723 5711942 1206505..1207314 1 NC_009952.1 putative inner membrane protein; hypothetical protein 1207314 5711942 Dshi_1174 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532517.1 1206505 D 398580 CDS YP_001532518.1 159043724 5711943 complement(1207399..1207956) 1 NC_009952.1 hypothetical protein 1207956 5711943 Dshi_1175 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532518.1 1207399 R 398580 CDS YP_001532519.1 159043725 5711944 complement(1207946..1209274) 1 NC_009952.1 catalytic activity has not been demonstrated; peptidase M23B 1209274 5711944 Dshi_1176 Dinoroseobacter shibae DFL 12 = DSM 16493 peptidase M23B YP_001532519.1 1207946 R 398580 CDS YP_001532520.1 159043726 5711945 complement(1209449..1210306) 1 NC_009952.1 hypothetical protein 1210306 5711945 Dshi_1177 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532520.1 1209449 R 398580 CDS YP_001532521.1 159043727 5711946 complement(1210336..1210797) 1 NC_009952.1 related to alkyl hydroperoxide reductase/ Thiol specific antioxidant; alkyl hydroperoxide reductase 1210797 5711946 Dshi_1178 Dinoroseobacter shibae DFL 12 = DSM 16493 alkyl hydroperoxide reductase YP_001532521.1 1210336 R 398580 CDS YP_001532522.1 159043728 5711947 1210889..1214206 1 NC_009952.1 putative outer membrane protein; hypothetical protein 1214206 5711947 Dshi_1179 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532522.1 1210889 D 398580 CDS YP_001532523.1 159043729 5711948 1214235..1215296 1 NC_009952.1 Synthesizes oQ from preQ1 in a single S-adenosylmethionine-requiring step; S-adenosylmethionine--tRNA ribosyltransferase-isomerase 1215296 queA 5711948 queA Dinoroseobacter shibae DFL 12 = DSM 16493 S-adenosylmethionine--tRNA ribosyltransferase-isomerase YP_001532523.1 1214235 D 398580 CDS YP_001532524.1 159043730 5711949 complement(1215344..1216738) 1 NC_009952.1 Family M20 are Glutamate carboxypeptidases. Peptidase family M25 contains X-His dipeptidases; hypothetical protein 1216738 5711949 Dshi_1181 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532524.1 1215344 R 398580 CDS YP_001532525.1 159043731 5711950 1216936..1218159 1 NC_009952.1 catalyzes the formation of 5-aminolevulinate from succinyl-CoA and glycine; 5-aminolevulinate synthase 1218159 hemA2 5711950 hemA2 Dinoroseobacter shibae DFL 12 = DSM 16493 5-aminolevulinate synthase YP_001532525.1 1216936 D 398580 CDS YP_001532526.1 159043732 5711951 1218363..1219592 1 NC_009952.1 conserved in Rhodobacteraceae; hypothetical protein 1219592 5711951 Dshi_1183 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532526.1 1218363 D 398580 CDS YP_001532527.1 159043733 5711952 1219665..1220816 1 NC_009952.1 catalyzes the conversion of 2C-methyl-D-erythritol 2,4-cyclodiphosphate into 4-hydroxy-3-methyl-2-en-1-yl diphosphate; involved in isoprenoid synthesis; 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase 1220816 ispG 5711952 ispG Dinoroseobacter shibae DFL 12 = DSM 16493 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase YP_001532527.1 1219665 D 398580 CDS YP_001532528.1 159043734 5711953 complement(1220983..1221825) 1 NC_009952.1 catalyzes the transfer of a total of four methyl groups from S-adenosyl-l-methionine (S-AdoMet) to two adjacent adenosine bases A1518 and A1519 in 16S rRNA; mutations in ksgA causes resistance to the translation initiation inhibitor kasugamycin; dimethyladenosine transferase 1221825 ksgA 5711953 ksgA Dinoroseobacter shibae DFL 12 = DSM 16493 dimethyladenosine transferase YP_001532528.1 1220983 R 398580 CDS YP_001532529.1 159043735 5711954 complement(1221827..1222810) 1 NC_009952.1 catalyzes oxidation of 4-(phosphohydroxy)-L-threonine into 2-amino-3-oxo-4-(phosphohydroxy)butyric acid which decarboxylates to form 1-amino-3-(phosphohydroxy)propan-2-one (3-amino-2-oxopropyl phosphate); 4-hydroxythreonine-4-phosphate dehydrogenase 1222810 pdxA 5711954 pdxA Dinoroseobacter shibae DFL 12 = DSM 16493 4-hydroxythreonine-4-phosphate dehydrogenase YP_001532529.1 1221827 R 398580 CDS YP_001532530.1 159043736 5711955 complement(1222807..1224003) 1 NC_009952.1 contains SurA domain and Peptidyl-prolyl cis-trans isomerase domain, periplasmatic; SurA domain-containing protein 1224003 5711955 Dshi_1187 Dinoroseobacter shibae DFL 12 = DSM 16493 SurA domain-containing protein YP_001532530.1 1222807 R 398580 CDS YP_001532531.1 159043737 5711956 complement(1224020..1226170) 1 NC_009952.1 involved in outer membrane permeability; organic solvent tolerance protein 1226170 ostA 5711956 ostA Dinoroseobacter shibae DFL 12 = DSM 16493 organic solvent tolerance protein YP_001532531.1 1224020 R 398580 CDS YP_001532532.1 159043738 5711957 complement(1226167..1227264) 1 NC_009952.1 permease YjgP/YjgQ family of unknown function; YjgP/YjgQ family permease 1227264 5711957 Dshi_1189 Dinoroseobacter shibae DFL 12 = DSM 16493 YjgP/YjgQ family permease YP_001532532.1 1226167 R 398580 CDS YP_001532533.1 159043739 5711958 complement(1227261..1228403) 1 NC_009952.1 permease YjgP/YjgQ family of unknown function; YjgP/YjgQ family permease 1228403 5711958 Dshi_1190 Dinoroseobacter shibae DFL 12 = DSM 16493 YjgP/YjgQ family permease YP_001532533.1 1227261 R 398580 CDS YP_001532534.1 159043740 5711959 1228563..1230029 1 NC_009952.1 catalyzes the removal of N-terminal amino acids preferably leucine from various peptides; leucyl aminopeptidase 1230029 pepA1 5711959 pepA1 Dinoroseobacter shibae DFL 12 = DSM 16493 leucyl aminopeptidase YP_001532534.1 1228563 D 398580 CDS YP_001532535.1 159043741 5711960 1230035..1230490 1 NC_009952.1 binds to single-strand binding (SSB) protein and acts as a bridge between the DnaX clamp loader complex and the SSB; DNA polymerase III subunit chi 1230490 holC 5711960 holC Dinoroseobacter shibae DFL 12 = DSM 16493 DNA polymerase III subunit chi YP_001532535.1 1230035 D 398580 CDS YP_001532536.1 159043742 5711961 complement(1230737..1231909) 1 NC_009952.1 Cytochrome P450 enzymes are a superfamily of haem-containing mono-oxygenase; cytochrome P450 1231909 5711961 Dshi_1193 Dinoroseobacter shibae DFL 12 = DSM 16493 cytochrome P450 YP_001532536.1 1230737 R 398580 CDS YP_001532537.1 159043743 5711962 complement(1231911..1234142) 1 NC_009952.1 TRAP gene cluster - dctPQM; 4TM/12TM fusion protein; TRAP transporter 1234142 5711962 Dshi_1194 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP transporter YP_001532537.1 1231911 R 398580 CDS YP_001532538.1 159043744 5711963 complement(1234239..1235231) 1 NC_009952.1 TRAP gene cluster - dctPQM; TAXI family; TRAP transporter solute receptor 1235231 5711963 Dshi_1195 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP transporter solute receptor YP_001532538.1 1234239 R 398580 CDS YP_001532539.1 159043745 5711964 complement(1235704..1237050) 1 NC_009952.1 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 1237050 dctD 5711964 dctD Dinoroseobacter shibae DFL 12 = DSM 16493 two component, sigma-54 specific, transcriptional regulator YP_001532539.1 1235704 R 398580 CDS YP_001532540.1 159043746 5711965 complement(1237047..1238915) 1 NC_009952.1 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 1238915 dctB 5711965 dctB Dinoroseobacter shibae DFL 12 = DSM 16493 integral membrane sensor signal transduction histidine kinase YP_001532540.1 1237047 R 398580 CDS YP_001532541.1 159043747 5711966 complement(1238964..1239965) 1 NC_009952.1 beta-lactamase 1239965 5711966 Dshi_1198 Dinoroseobacter shibae DFL 12 = DSM 16493 beta-lactamase YP_001532541.1 1238964 R 398580 CDS YP_001532542.1 159043748 5711967 1240118..1240912 1 NC_009952.1 Mg-dependent, Reaction: Myo-inositol phosphate + H2O = myo-inositol + phosphate; inositol-phosphate phosphatase 1240912 suhB1 5711967 suhB1 Dinoroseobacter shibae DFL 12 = DSM 16493 inositol-phosphate phosphatase YP_001532542.1 1240118 D 398580 CDS YP_001532543.1 159043749 5711968 complement(1240915..1241691) 1 NC_009952.1 putative inner membrane serine protease; rhomboid family protein 1241691 5711968 Dshi_1200 Dinoroseobacter shibae DFL 12 = DSM 16493 rhomboid family protein YP_001532543.1 1240915 R 398580 CDS YP_001532544.1 159043750 5711969 1241780..1242331 1 NC_009952.1 2 TPR, TPR mediates protein-protein interactions and the assembly of multiprotein complexes; hypothetical protein 1242331 5711969 Dshi_1201 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532544.1 1241780 D 398580 CDS YP_001532545.1 159043751 5711971 complement(1242487..1243116) 1 NC_009952.1 contains DnaJ-Domain, wich mediats interaction with DnaK in heat shock proteins; heat shock protein DnaJ domain-containing protein 1243116 5711971 Dshi_1202 Dinoroseobacter shibae DFL 12 = DSM 16493 heat shock protein DnaJ domain-containing protein YP_001532545.1 1242487 R 398580 CDS YP_001532546.1 159043752 5711972 1243189..1243446 1 NC_009952.1 In E. coli overexpression of this protein causes round morphology; BolA family protein 1243446 5711972 Dshi_1203 Dinoroseobacter shibae DFL 12 = DSM 16493 BolA family protein YP_001532546.1 1243189 D 398580 CDS YP_001532547.1 159043753 5711762 complement(1243456..1243872) 1 NC_009952.1 conserved in Rhodobacteraceae; hypothetical protein 1243872 5711762 Dshi_1204 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532547.1 1243456 R 398580 CDS YP_001532548.1 159043754 5711763 1244215..1244763 1 NC_009952.1 hypothetical protein 1244763 5711763 Dshi_1205 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532548.1 1244215 D 398580 CDS YP_001532549.1 159043755 5711764 complement(1245054..1245302) 1 NC_009952.1 hypothetical protein 1245302 5711764 Dshi_1206 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532549.1 1245054 R 398580 CDS YP_001532550.1 159043756 5711765 complement(1245310..1246827) 1 NC_009952.1 allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases; reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA; aspartyl/glutamyl-tRNA amidotransferase subunit B 1246827 gatB 5711765 gatB Dinoroseobacter shibae DFL 12 = DSM 16493 aspartyl/glutamyl-tRNA amidotransferase subunit B YP_001532550.1 1245310 R 398580 CDS YP_001532551.1 159043757 5711766 1247009..1247605 1 NC_009952.1 hypothetical protein 1247605 5711766 Dshi_1208 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532551.1 1247009 D 398580 CDS YP_001532552.1 159043758 5711767 1247697..1248803 1 NC_009952.1 integral membrane sensor and DNA-binding protein; putative integral membrane sensor protein 1248803 coxC 5711767 coxC Dinoroseobacter shibae DFL 12 = DSM 16493 putative integral membrane sensor protein YP_001532552.1 1247697 D 398580 CDS YP_001532553.1 159043759 5711768 1249012..1249866 1 NC_009952.1 Aerobic-type carbon monoxide dehydrogenase, middle subunit, part of heterotrimer coxLMS; molybdopterin dehydrogenase FAD-binding 1249866 coxM 5711768 coxM Dinoroseobacter shibae DFL 12 = DSM 16493 molybdopterin dehydrogenase FAD-binding YP_001532553.1 1249012 D 398580 CDS YP_001532554.1 159043760 5711769 1249879..1250370 1 NC_009952.1 Aerobic-type carbon monoxide dehydrogenase, small subunit, part of heterotrimer coxLMS, (2Fe-2S)-binding; (2Fe-2S)-binding domain-containing protein 1250370 coxS 5711769 coxS Dinoroseobacter shibae DFL 12 = DSM 16493 (2Fe-2S)-binding domain-containing protein YP_001532554.1 1249879 D 398580 CDS YP_001532555.1 159043761 5711770 1250367..1252787 1 NC_009952.1 Aerobic-type carbon monoxide dehydrogenase, large subunit, part of heterotrimer coxLMS; carbon-monoxide dehydrogenase large subunit 1252787 coxL2 5711770 coxL2 Dinoroseobacter shibae DFL 12 = DSM 16493 carbon-monoxide dehydrogenase large subunit YP_001532555.1 1250367 D 398580 CDS YP_001532556.1 159043762 5711771 1252829..1253737 1 NC_009952.1 ATPase activity; ATPase 1253737 coxD 5711771 coxD Dinoroseobacter shibae DFL 12 = DSM 16493 ATPase YP_001532556.1 1252829 D 398580 CDS YP_001532557.1 159043763 5711772 1253734..1254912 1 NC_009952.1 Protein containing von Willebrand factor type A (vWA) domain; VWA containing CoxE family protein 1254912 coxE 5711772 coxE Dinoroseobacter shibae DFL 12 = DSM 16493 VWA containing CoxE family protein YP_001532557.1 1253734 D 398580 CDS YP_001532558.1 159043764 5711773 1254912..1255724 1 NC_009952.1 hypothetical protein 1255724 coxF 5711773 coxF Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532558.1 1254912 D 398580 CDS YP_001532559.1 159043765 5711774 complement(1255823..1256800) 1 NC_009952.1 ketopantoate reductase; catalyzes the NADPH reduction of ketopantoate to pantoate; functions in pantothenate (vitamin B5) biosynthesis; 2-dehydropantoate 2-reductase 1256800 panE 5711774 panE Dinoroseobacter shibae DFL 12 = DSM 16493 2-dehydropantoate 2-reductase YP_001532559.1 1255823 R 398580 CDS YP_001532560.1 159043766 5711775 complement(1256903..1258444) 1 NC_009952.1 putative acyl-coA synthetase; AMP-dependent synthetase and ligase 1258444 5711775 Dshi_1217 Dinoroseobacter shibae DFL 12 = DSM 16493 AMP-dependent synthetase and ligase YP_001532560.1 1256903 R 398580 CDS YP_001532561.1 159043767 5711776 complement(1258541..1260055) 1 NC_009952.1 hypothetical protein 1260055 5711776 Dshi_1218 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532561.1 1258541 R 398580 CDS YP_001532562.1 159043768 5711777 complement(1260068..1260553) 1 NC_009952.1 conserved in Rhodobacteraceae; hypothetical protein 1260553 5711777 Dshi_1219 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532562.1 1260068 R 398580 CDS YP_001532563.1 159043769 5711778 complement(1260637..1261623) 1 NC_009952.1 hypothetical protein 1261623 5711778 Dshi_1220 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532563.1 1260637 R 398580 CDS YP_001532564.1 159043770 5711779 1261791..1263197 1 NC_009952.1 Helix-Turn-Helix motif, XRE family, Domain of unknown funktion DUF955; XRE family; transcriptional regulator 1263197 5711779 Dshi_1221 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001532564.1 1261791 D 398580 CDS YP_001532565.1 159043771 5711780 complement(1263528..1264271) 1 NC_009952.1 most enzymes of this family are NAD/NADP-dependent oxidoreductases; short-chain dehydrogenase/reductase SDR 1264271 5711780 Dshi_1222 Dinoroseobacter shibae DFL 12 = DSM 16493 short-chain dehydrogenase/reductase SDR YP_001532565.1 1263528 R 398580 CDS YP_001532566.1 159043772 5711781 complement(1264297..1266852) 1 NC_009952.1 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 1266852 pepN 5711781 pepN Dinoroseobacter shibae DFL 12 = DSM 16493 aminopeptidase N YP_001532566.1 1264297 R 398580 CDS YP_001532567.1 159043773 5711782 1267060..1267575 1 NC_009952.1 hypothetical protein 1267575 5711782 Dshi_1224 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532567.1 1267060 D 398580 CDS YP_001532568.1 159043774 5711783 1267586..1269130 1 NC_009952.1 Photolyase/Cryptochrome family protein, catalytic activity not proved; deoxyribodipyrimidine photo-lyase 1269130 5711783 Dshi_1225 Dinoroseobacter shibae DFL 12 = DSM 16493 deoxyribodipyrimidine photo-lyase YP_001532568.1 1267586 D 398580 CDS YP_001532569.1 159043775 5711784 1269139..1269306 1 NC_009952.1 hypothetical protein 1269306 5711784 Dshi_1226 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532569.1 1269139 D 398580 CDS YP_001532570.1 159043776 5711785 1269474..1271648 1 NC_009952.1 catalyzes the formation of malate from glyoxylate and acetyl-CoA; malate synthase G 1271648 glcB 5711785 glcB Dinoroseobacter shibae DFL 12 = DSM 16493 malate synthase G YP_001532570.1 1269474 D 398580 CDS YP_001532571.1 159043777 5711786 1271732..1272154 1 NC_009952.1 hypothetical protein 1272154 5711786 Dshi_1228 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532571.1 1271732 D 398580 CDS YP_001532572.1 159043778 5711787 1272260..1273039 1 NC_009952.1 gamma-glutamyl hydrolase activity; peptidase C26 1273039 5711787 Dshi_1229 Dinoroseobacter shibae DFL 12 = DSM 16493 peptidase C26 YP_001532572.1 1272260 D 398580 CDS YP_001532573.1 159043779 5711788 complement(1273036..1274217) 1 NC_009952.1 Catalyzes the cleavage of L-kynurenine and L-3-hydroxykynurenine, PLP-dependent; kynureninase 1274217 5711788 Dshi_1230 Dinoroseobacter shibae DFL 12 = DSM 16493 kynureninase YP_001532573.1 1273036 R 398580 CDS YP_001532574.1 159043780 5711789 1274344..1275300 1 NC_009952.1 domain weakly conserved; beta-lactamase domain-containing protein 1275300 5711789 Dshi_1231 Dinoroseobacter shibae DFL 12 = DSM 16493 beta-lactamase domain-containing protein YP_001532574.1 1274344 D 398580 CDS YP_001532575.1 159043781 5711790 1275516..1275992 1 NC_009952.1 predicted domain weakly conserved; isoprenylcysteine carboxyl methyltransferase family protein 1275992 5711790 Dshi_1232 Dinoroseobacter shibae DFL 12 = DSM 16493 isoprenylcysteine carboxyl methyltransferase family protein YP_001532575.1 1275516 D 398580 CDS YP_001532576.1 159043782 5711791 1276126..1277742 1 NC_009952.1 forms a tetramer composed of 2 alpha subunits and 2 beta subunits in the inner membrane; involved in catalyzing transfer of hydride ion equivalents between NAD and NADP; stereospecific (AB-specific); functions as a proton pump by translocating protons from cytoplasm to periplasm; NAD(P) transhydrogenase subunit alpha 1277742 pntA 5711791 pntA Dinoroseobacter shibae DFL 12 = DSM 16493 NAD(P) transhydrogenase subunit alpha YP_001532576.1 1276126 D 398580 CDS YP_001532577.1 159043783 5711792 1277755..1279251 1 NC_009952.1 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 1279251 pntB 5711792 pntB Dinoroseobacter shibae DFL 12 = DSM 16493 NAD(P)(+) transhydrogenase YP_001532577.1 1277755 D 398580 CDS YP_001532578.1 159043784 5711793 1279366..1280808 1 NC_009952.1 Reaction: ATP + D-xylulose = ADP + D-xylulose 5-phosphate; xylulokinase 1280808 xylB1 5711793 xylB1 Dinoroseobacter shibae DFL 12 = DSM 16493 xylulokinase YP_001532578.1 1279366 D 398580 CDS YP_001532579.1 159043785 5711794 complement(1280772..1281659) 1 NC_009952.1 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 1281659 dmsC 5711794 dmsC Dinoroseobacter shibae DFL 12 = DSM 16493 DMSO reductase anchor subunit YP_001532579.1 1280772 R 398580 CDS YP_001532580.1 159043786 5711795 complement(1281663..1282409) 1 NC_009952.1 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 1282409 dmsB 5711795 dmsB Dinoroseobacter shibae DFL 12 = DSM 16493 4Fe-4S ferredoxin YP_001532580.1 1281663 R 398580 CDS YP_001532581.1 159043787 5711796 complement(1282492..1285278) 1 NC_009952.1 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 1285278 dmsA2 5711796 dmsA2 Dinoroseobacter shibae DFL 12 = DSM 16493 molybdopterin oxidoreductase Fe4S4 region YP_001532581.1 1282492 R 398580 CDS YP_001532582.1 159043788 5711797 complement(1285260..1287167) 1 NC_009952.1 Hydrolysis of terminal non-reducing beta-D-galactose residues in beta-D-galactosides, homotrimer; beta-galactosidase 1287167 lacZ 5711797 lacZ Dinoroseobacter shibae DFL 12 = DSM 16493 beta-galactosidase YP_001532582.1 1285260 R 398580 CDS YP_001532583.1 159043789 5711798 complement(1287164..1288024) 1 NC_009952.1 domain found in various proteins; SMP-30/gluconolaconase/LRE domain-containing protein 1288024 5711798 Dshi_1240 Dinoroseobacter shibae DFL 12 = DSM 16493 SMP-30/gluconolaconase/LRE domain-containing protein YP_001532583.1 1287164 R 398580 CDS YP_001532584.1 159043790 5711799 complement(1288021..1288626) 1 NC_009952.1 Keto-hydroxyglutarate-aldolase/keto-deoxy- phosphogluconate aldolase; KDPG and KHG aldolase 1288626 dgoA 5711799 dgoA Dinoroseobacter shibae DFL 12 = DSM 16493 KDPG and KHG aldolase YP_001532584.1 1288021 R 398580 CDS YP_001532585.1 159043791 5711800 complement(1288623..1289519) 1 NC_009952.1 catalyses the second step in D-galactonate degradation; 2-dehydro-3-deoxygalactonokinase 1289519 dgoK 5711800 dgoK Dinoroseobacter shibae DFL 12 = DSM 16493 2-dehydro-3-deoxygalactonokinase YP_001532585.1 1288623 R 398580 CDS YP_001532586.1 159043792 5711801 complement(1289516..1290292) 1 NC_009952.1 large family of oxidoreductases, NAD, NADP-dependent; short-chain dehydrogenase/reductase SDR 1290292 5711801 Dshi_1243 Dinoroseobacter shibae DFL 12 = DSM 16493 short-chain dehydrogenase/reductase SDR YP_001532586.1 1289516 R 398580 CDS YP_001532587.1 159043793 5711802 complement(1290292..1292001) 1 NC_009952.1 catalyzes the formation of 3-methyl-2-oxobutanoate from 2,3,-dihydroxy-3-methylbutanoate; dihydroxy-acid dehydratase 1292001 ilvD2 5711802 ilvD2 Dinoroseobacter shibae DFL 12 = DSM 16493 dihydroxy-acid dehydratase YP_001532587.1 1290292 R 398580 CDS YP_001532588.1 159043794 5711803 complement(1292045..1293385) 1 NC_009952.1 glycoside hydrolase family 4 protein, Hydrolysis of terminal, non-reducing alpha-D-galactose residues, NAD and Mn-dependent; glycoside hydrolase family protein 1293385 melA 5711803 melA Dinoroseobacter shibae DFL 12 = DSM 16493 glycoside hydrolase family protein YP_001532588.1 1292045 R 398580 CDS YP_001532589.1 159043795 5711804 complement(1293382..1294230) 1 NC_009952.1 ABC-type sugar transport system, permease component, no ATPase in cluster; binding-protein-dependent transport system inner membrane protein 1294230 5711804 Dshi_1246 Dinoroseobacter shibae DFL 12 = DSM 16493 binding-protein-dependent transport system inner membrane protein YP_001532589.1 1293382 R 398580 CDS YP_001532590.1 159043796 5711805 complement(1294232..1295158) 1 NC_009952.1 ABC-type sugar transport system, permease component, no ATPase in cluster; binding-protein-dependent transport system inner membrane protein 1295158 5711805 Dshi_1247 Dinoroseobacter shibae DFL 12 = DSM 16493 binding-protein-dependent transport system inner membrane protein YP_001532590.1 1294232 R 398580 CDS YP_001532591.1 159043797 5711806 complement(1295236..1296480) 1 NC_009952.1 ABC-type sugar transport system, ligand binding component, no ATPase in cluster; family 1 extracellular solute-binding protein 1296480 5711806 Dshi_1248 Dinoroseobacter shibae DFL 12 = DSM 16493 family 1 extracellular solute-binding protein YP_001532591.1 1295236 R 398580 CDS YP_001532592.1 159043798 5711807 1296622..1297437 1 NC_009952.1 Helix-Turn-Helix motif, iclR subfamily; IclR family; transcriptional regulator 1297437 5711807 Dshi_1249 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001532592.1 1296622 D 398580 CDS YP_001532593.1 159043799 5711808 1297453..1298508 1 NC_009952.1 ABC transporter (importer) gene cluster (disrupted): ATP binding cassette (ABC) domain; part of a heterotetramer; ABC transporter-like protein 1298508 5711808 Dshi_1250 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC transporter-like protein YP_001532593.1 1297453 D 398580 CDS YP_001532594.1 159043800 5711809 complement(1298515..1298802) 1 NC_009952.1 hypothetical protein 1298802 5711809 Dshi_1251 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532594.1 1298515 R 398580 CDS YP_001532595.1 159043801 5711810 complement(1299255..1299977) 1 NC_009952.1 hypothetical protein 1299977 5711810 Dshi_1252 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532595.1 1299255 R 398580 CDS YP_001532596.1 159043802 5711811 1300089..1300952 1 NC_009952.1 putative protein-phosphotyrosine-phosphatase activity, ArsR family regulators are sensitive to metal ions; ArsR family; transcriptional regulator 1300952 5711811 Dshi_1253 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001532596.1 1300089 D 398580 CDS YP_001532597.1 159043803 5711812 1300949..1301971 1 NC_009952.1 tetrameric NAD-binding enzyme involved in glycolysis and glyconeogenesis; type I; glyceraldehyde-3-phosphate dehydrogenase 1301971 5711812 Dshi_1254 Dinoroseobacter shibae DFL 12 = DSM 16493 glyceraldehyde-3-phosphate dehydrogenase YP_001532597.1 1300949 D 398580 CDS YP_001532598.1 159043804 5711813 1301968..1303236 1 NC_009952.1 The MFS transporters are single-polypeptide secondary carriers capable only of transporting small solutes in response to chemiosmotic ion gradients; major facilitator superfamily protein 1303236 5711813 Dshi_1255 Dinoroseobacter shibae DFL 12 = DSM 16493 major facilitator superfamily protein YP_001532598.1 1301968 D 398580 CDS YP_001532599.1 159043805 5711814 1303304..1303924 1 NC_009952.1 the exo genes are involved in exopolysaccharide biosynthesis, exoD of Rhizobium meliloti encodes a function needed for alfalfa nodule invasion; exopolysaccharide synthesis ExoD 1303924 5711814 Dshi_1256 Dinoroseobacter shibae DFL 12 = DSM 16493 exopolysaccharide synthesis ExoD YP_001532599.1 1303304 D 398580 CDS YP_001532600.1 159043806 5711815 complement(1303935..1304216) 1 NC_009952.1 hypothetical protein 1304216 5711815 Dshi_1257 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532600.1 1303935 R 398580 CDS YP_001532601.1 159043807 5711816 1304262..1305005 1 NC_009952.1 most enzymes of this family are NAD/NADP-dependent oxidoreductases; short-chain dehydrogenase/reductase SDR 1305005 5711816 Dshi_1258 Dinoroseobacter shibae DFL 12 = DSM 16493 short-chain dehydrogenase/reductase SDR YP_001532601.1 1304262 D 398580 CDS YP_001532602.1 159043808 5711817 1305092..1307596 1 NC_009952.1 heavy metal translocating P-type ATPase 1307596 5711817 Dshi_1259 Dinoroseobacter shibae DFL 12 = DSM 16493 heavy metal translocating P-type ATPase YP_001532602.1 1305092 D 398580 CDS YP_001532603.1 159043809 5711818 1307607..1308002 1 NC_009952.1 contains winged helix DNA-binding motif; MerR family; transcriptional regulator 1308002 5711818 Dshi_1260 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001532603.1 1307607 D 398580 CDS YP_001532604.1 159043810 5711819 1308092..1309300 1 NC_009952.1 sodium-dependent uptake of extracellular glutamate; sodium/glutamate symporter 1309300 gltS 5711819 gltS Dinoroseobacter shibae DFL 12 = DSM 16493 sodium/glutamate symporter YP_001532604.1 1308092 D 398580 CDS YP_001532605.1 159043811 5711820 complement(1309307..1312360) 1 NC_009952.1 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 1312360 5711820 Dshi_1262 Dinoroseobacter shibae DFL 12 = DSM 16493 acriflavin resistance protein YP_001532605.1 1309307 R 398580 CDS YP_001532606.1 159043812 5711821 complement(1312365..1313612) 1 NC_009952.1 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 1313612 5711821 Dshi_1263 Dinoroseobacter shibae DFL 12 = DSM 16493 efflux transporter YP_001532606.1 1312365 R 398580 CDS YP_001532607.1 159043813 5711822 1313689..1314135 1 NC_009952.1 two membrane helix type ion channel; ion transport 2 domain-containing protein 1314135 5711822 Dshi_1264 Dinoroseobacter shibae DFL 12 = DSM 16493 ion transport 2 domain-containing protein YP_001532607.1 1313689 D 398580 CDS YP_001532608.1 159043814 5711823 complement(1314155..1315138) 1 NC_009952.1 carbohydrate degradation; inositol 2-dehydrogenase 1315138 idhA 5711823 idhA Dinoroseobacter shibae DFL 12 = DSM 16493 inositol 2-dehydrogenase YP_001532608.1 1314155 R 398580 CDS YP_001532609.1 159043815 5711824 complement(1315135..1315977) 1 NC_009952.1 zinc-dependent, homodimeric enzyme; ketose-bisphosphate aldolase 1315977 fbaA 5711824 fbaA Dinoroseobacter shibae DFL 12 = DSM 16493 ketose-bisphosphate aldolase YP_001532609.1 1315135 R 398580 CDS YP_001532610.1 159043816 5711825 complement(1315974..1316834) 1 NC_009952.1 hypothetical protein 1316834 iolB 5711825 iolB Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532610.1 1315974 R 398580 CDS YP_001532611.1 159043817 5711826 complement(1316838..1317839) 1 NC_009952.1 putative enzyme involved in myo-inositol catabolism; PfkB domain-containing protein 1317839 iolC 5711826 iolC Dinoroseobacter shibae DFL 12 = DSM 16493 PfkB domain-containing protein YP_001532611.1 1316838 R 398580 CDS YP_001532612.1 159043818 5711827 complement(1317836..1319701) 1 NC_009952.1 putative enzyme involved in myo-inositol catabolism, Thiamine-dependent; thiamine pyrophosphate protein central region 1319701 iolD 5711827 iolD Dinoroseobacter shibae DFL 12 = DSM 16493 thiamine pyrophosphate protein central region YP_001532612.1 1317836 R 398580 CDS YP_001532613.1 159043819 5711828 1319800..1320918 1 NC_009952.1 NAD-dependent oxidoreductase; oxidoreductase domain-containing protein 1320918 5711828 Dshi_1270 Dinoroseobacter shibae DFL 12 = DSM 16493 oxidoreductase domain-containing protein YP_001532613.1 1319800 D 398580 CDS YP_001532614.1 159043820 5711829 1320915..1321811 1 NC_009952.1 putative enzyme involved in myo-inositol catabolism; xylose isomerase domain-containing protein 1321811 5711829 Dshi_1271 Dinoroseobacter shibae DFL 12 = DSM 16493 xylose isomerase domain-containing protein YP_001532614.1 1320915 D 398580 CDS YP_001532615.1 159043821 5711830 1321819..1322952 1 NC_009952.1 NAD-dependent oxidoreductase; oxidoreductase domain-containing protein 1322952 5711830 Dshi_1272 Dinoroseobacter shibae DFL 12 = DSM 16493 oxidoreductase domain-containing protein YP_001532615.1 1321819 D 398580 CDS YP_001532616.1 159043822 5711831 complement(1322983..1323981) 1 NC_009952.1 Helix-Turn-Helix motif, Sugar -binding domain; LacI family; transcriptional regulator 1323981 5711831 Dshi_1273 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001532616.1 1322983 R 398580 CDS YP_001532617.1 159043823 5711832 1324124..1325101 1 NC_009952.1 ATPase gene cluster: periplasmatic binding component, permease component, ATPase component; periplasmic-binding protein/LacI transcriptional regulator 1325101 5711832 Dshi_1274 Dinoroseobacter shibae DFL 12 = DSM 16493 periplasmic-binding protein/LacI transcriptional regulator YP_001532617.1 1324124 D 398580 CDS YP_001532618.1 159043824 5711833 1325167..1326291 1 NC_009952.1 ATPase gene cluster: periplasmatic binding component, permease component, ATPase component; monosaccharide-transporting ATPase 1326291 5711833 Dshi_1275 Dinoroseobacter shibae DFL 12 = DSM 16493 monosaccharide-transporting ATPase YP_001532618.1 1325167 D 398580 CDS YP_001532619.1 159043825 5711834 1326293..1327087 1 NC_009952.1 ATPase gene cluster: periplasmatic binding component, permease component, ATPase component; ABC transporter-like protein 1327087 5711834 Dshi_1276 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC transporter-like protein YP_001532619.1 1326293 D 398580 CDS YP_001532620.1 159043826 5711835 1327074..1327316 1 NC_009952.1 hypothetical protein 1327316 5711835 Dshi_1277 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532620.1 1327074 D 398580 CDS YP_001532621.1 159043827 5711836 1327313..1328482 1 NC_009952.1 phytanoyl-CoA dioxygenase 1328482 5711836 Dshi_1278 Dinoroseobacter shibae DFL 12 = DSM 16493 phytanoyl-CoA dioxygenase YP_001532621.1 1327313 D 398580 CDS YP_001532622.1 159043828 5711837 1328494..1329306 1 NC_009952.1 myo-inositol catabolism IolB domain-containing protein 1329306 iolB2 5711837 iolB2 Dinoroseobacter shibae DFL 12 = DSM 16493 myo-inositol catabolism IolB domain-containing protein YP_001532622.1 1328494 D 398580 CDS YP_001532623.1 159043829 5711838 complement(1329323..1330588) 1 NC_009952.1 domain is found in amino transferases, and other enzymes including cysteine desulphurase, PLP dependent enzyme; class V aminotransferase 1330588 5711838 Dshi_1280 Dinoroseobacter shibae DFL 12 = DSM 16493 class V aminotransferase YP_001532623.1 1329323 R 398580 CDS YP_001532624.1 159043830 5711839 1330881..1332578 1 NC_009952.1 high similarity to Respiratory-chain NADH dehydrogenase domain 24 kDa and 51 kDa subunits(PMID:2187144); respiratory-chain NADH dehydrogenase domain 51 kDa subunit 1332578 fdhB 5711839 fdhB Dinoroseobacter shibae DFL 12 = DSM 16493 respiratory-chain NADH dehydrogenase domain 51 kDa subunit YP_001532624.1 1330881 D 398580 CDS YP_001532625.1 159043831 5711840 1332581..1335382 1 NC_009952.1 complex with fdhB, Molybdopterin oxidoreductase, contains Fe-S clusters; formate dehydrogenase subunit alpha 1335382 fdhA 5711840 fdhA Dinoroseobacter shibae DFL 12 = DSM 16493 formate dehydrogenase subunit alpha YP_001532625.1 1332581 D 398580 CDS YP_001532626.1 159043832 5711841 1335512..1337179 1 NC_009952.1 catalyzes the formation of 10-formyltetrahydrofolate from formate and tetrahydrofolate; formate--tetrahydrofolate ligase 1337179 fhs 5711841 fhs Dinoroseobacter shibae DFL 12 = DSM 16493 formate--tetrahydrofolate ligase YP_001532626.1 1335512 D 398580 CDS YP_001532627.1 159043833 5711842 1337238..1337558 1 NC_009952.1 chorismate mutase related enzyme 1337558 5711842 Dshi_1284 Dinoroseobacter shibae DFL 12 = DSM 16493 chorismate mutase related enzyme YP_001532627.1 1337238 D 398580 CDS YP_001532628.1 159043834 5711843 1337555..1338454 1 NC_009952.1 catalyzes the formation of 5,10-methenyltetrahydrofolate from 5,10-methylenetetrahydrofolate and subsequent formation of 10-formyltetrahydrofolate from 5,10-methenyltetrahydrofolate; bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase 1338454 folD 5711843 folD Dinoroseobacter shibae DFL 12 = DSM 16493 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase YP_001532628.1 1337555 D 398580 CDS YP_001532629.1 159043835 5711844 1338659..1339942 1 NC_009952.1 hypothetical protein 1339942 5711844 Dshi_1286 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532629.1 1338659 D 398580 CDS YP_001532630.1 159043836 5711845 complement(1339875..1340969) 1 NC_009952.1 hypothetical protein 1340969 5711845 Dshi_1287 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532630.1 1339875 R 398580 CDS YP_001532631.1 159043837 5711846 1341315..1342481 1 NC_009952.1 amidohydrolase 1342481 5711846 Dshi_1288 Dinoroseobacter shibae DFL 12 = DSM 16493 amidohydrolase YP_001532631.1 1341315 D 398580 CDS YP_001532632.1 159043838 5711847 1342529..1343269 1 NC_009952.1 Catalyzes the transfer of the ammonia group from glutamine to a new carbon-nitrogen group; glutamine amidotransferase 1343269 5711847 Dshi_1289 Dinoroseobacter shibae DFL 12 = DSM 16493 glutamine amidotransferase YP_001532632.1 1342529 D 398580 CDS YP_001532633.1 159043839 5711848 complement(1343361..1344371) 1 NC_009952.1 together with moaC, is involved in the conversion of a guanosine derivative (GXP) into molybdopterin precursor Z; molybdenum cofactor biosynthesis protein A 1344371 moaA 5711848 moaA Dinoroseobacter shibae DFL 12 = DSM 16493 molybdenum cofactor biosynthesis protein A YP_001532633.1 1343361 R 398580 CDS YP_001532634.1 159043840 5711849 complement(1344604..1345305) 1 NC_009952.1 DNA alkylation repair protein 1345305 5711849 Dshi_1291 Dinoroseobacter shibae DFL 12 = DSM 16493 DNA alkylation repair protein YP_001532634.1 1344604 R 398580 CDS YP_001532635.1 159043841 5711850 complement(1345302..1345850) 1 NC_009952.1 pyridoxamine 5'-phosphate oxidase-like FMN-binding protein 1345850 5711850 Dshi_1292 Dinoroseobacter shibae DFL 12 = DSM 16493 pyridoxamine 5'-phosphate oxidase-like FMN-binding protein YP_001532635.1 1345302 R 398580 CDS YP_001532636.1 159043842 5711851 complement(1345854..1347674) 1 NC_009952.1 Catalyzes the first step in hexosamine metabolism, converting fructose-6P into glucosamine-6P using glutamine as a nitrogen source; glucosamine--fructose-6-phosphate aminotransferase 1347674 glmS 5711851 glmS Dinoroseobacter shibae DFL 12 = DSM 16493 glucosamine--fructose-6-phosphate aminotransferase YP_001532636.1 1345854 R 398580 CDS YP_001532637.1 159043843 5711852 complement(1347674..1349026) 1 NC_009952.1 forms a homotrimer; catalyzes the acetylation of glucosamine-1-phosphate and uridylation of N-acetylglucosamine-1-phosphate to produce UDP-GlcNAc; function in cell wall synthesis; bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase 1349026 glmU 5711852 glmU Dinoroseobacter shibae DFL 12 = DSM 16493 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase YP_001532637.1 1347674 R 398580 CDS YP_001532638.1 159043844 5711853 1349154..1349828 1 NC_009952.1 Specifically catalyzes the dephosphorylation of 2-phosphoglycolate; subfamily IA, variant 3; HAD-superfamily hydrolase 1349828 5711853 Dshi_1295 Dinoroseobacter shibae DFL 12 = DSM 16493 HAD-superfamily hydrolase YP_001532638.1 1349154 D 398580 CDS YP_001532639.1 159043845 5711854 1349879..1351090 1 NC_009952.1 DegT/DnrJ/EryC1/StrS aminotransferase 1351090 5711854 Dshi_1296 Dinoroseobacter shibae DFL 12 = DSM 16493 DegT/DnrJ/EryC1/StrS aminotransferase YP_001532639.1 1349879 D 398580 CDS YP_001532640.1 159043846 5711855 1351256..1352419 1 NC_009952.1 FAD-dependent, Reaction: 3-methylbutanoyl-CoA + acceptor = 3-methylbut-2-enoyl-CoA + reduced acceptor; acyl-CoA dehydrogenase domain-containing protein 1352419 ivd 5711855 ivd Dinoroseobacter shibae DFL 12 = DSM 16493 acyl-CoA dehydrogenase domain-containing protein YP_001532640.1 1351256 D 398580 CDS YP_001532641.1 159043847 5711856 1352444..1352782 1 NC_009952.1 hypothetical protein 1352782 5711856 Dshi_1298 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532641.1 1352444 D 398580 CDS YP_001532642.1 159043848 5711857 complement(1352857..1353465) 1 NC_009952.1 OmpW family protein 1353465 5711857 Dshi_1299 Dinoroseobacter shibae DFL 12 = DSM 16493 OmpW family protein YP_001532642.1 1352857 R 398580 CDS YP_001532643.1 159043849 5711858 1353609..1355213 1 NC_009952.1 involved in leucine catabolism; propionyl-CoA carboxylase 1355213 mccB 5711858 mccB Dinoroseobacter shibae DFL 12 = DSM 16493 propionyl-CoA carboxylase YP_001532643.1 1353609 D 398580 CDS YP_001532644.1 159043850 5711859 1355325..1357310 1 NC_009952.1 involved in leucine catabolism; carbamoyl-phosphate synthase L chain ATP-binding 1357310 mccA 5711859 mccA Dinoroseobacter shibae DFL 12 = DSM 16493 carbamoyl-phosphate synthase L chain ATP-binding YP_001532644.1 1355325 D 398580 CDS YP_001532645.1 159043851 5711860 1357307..1357975 1 NC_009952.1 glutathione S-transferase domain-containing protein 1357975 5711860 Dshi_1302 Dinoroseobacter shibae DFL 12 = DSM 16493 glutathione S-transferase domain-containing protein YP_001532645.1 1357307 D 398580 CDS YP_001532646.1 159043852 5711861 1357972..1358835 1 NC_009952.1 catalyzes the formation of acetoacetate and acetyl-CoA from 3-hydroxy-3-methylglutaryl-CoA; hydroxymethylglutaryl-CoA lyase 1358835 mvaB 5711861 mvaB Dinoroseobacter shibae DFL 12 = DSM 16493 hydroxymethylglutaryl-CoA lyase YP_001532646.1 1357972 D 398580 CDS YP_001532647.1 159043853 5711862 1358832..1359620 1 NC_009952.1 Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA; enoyl-CoA hydratase 1359620 mvaA 5711862 mvaA Dinoroseobacter shibae DFL 12 = DSM 16493 enoyl-CoA hydratase YP_001532647.1 1358832 D 398580 CDS YP_001532648.1 159043854 5711863 1359760..1359978 1 NC_009952.1 17 kDa surface antigen 1359978 5711863 Dshi_1305 Dinoroseobacter shibae DFL 12 = DSM 16493 17 kDa surface antigen YP_001532648.1 1359760 D 398580 CDS YP_001532649.1 159043855 5711864 complement(1359980..1360588) 1 NC_009952.1 hypothetical protein 1360588 5711864 Dshi_1306 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532649.1 1359980 R 398580 CDS YP_001532650.1 159043856 5711865 1360930..1361295 1 NC_009952.1 Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit A 1361295 nuoA 5711865 nuoA Dinoroseobacter shibae DFL 12 = DSM 16493 NADH dehydrogenase subunit A YP_001532650.1 1360930 D 398580 CDS YP_001532651.1 159043857 5711866 1361286..1361819 1 NC_009952.1 The point of entry for the majority of electrons that traverse the respiratory chain eventually resulting in the reduction of oxygen; NADH dehydrogenase subunit B 1361819 nuoB 5711866 nuoB Dinoroseobacter shibae DFL 12 = DSM 16493 NADH dehydrogenase subunit B YP_001532651.1 1361286 D 398580 CDS YP_001532652.1 159043858 5711867 1361883..1362530 1 NC_009952.1 Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit C 1362530 nuoC 5711867 nuoC Dinoroseobacter shibae DFL 12 = DSM 16493 NADH dehydrogenase subunit C YP_001532652.1 1361883 D 398580 CDS YP_001532653.1 159043859 5711868 1362535..1363413 1 NC_009952.1 hypothetical protein 1363413 5711868 Dshi_1310 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532653.1 1362535 D 398580 CDS YP_001532654.1 159043860 5711869 1363417..1364631 1 NC_009952.1 Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit D 1364631 nuoD 5711869 nuoD Dinoroseobacter shibae DFL 12 = DSM 16493 NADH dehydrogenase subunit D YP_001532654.1 1363417 D 398580 CDS YP_001532655.1 159043861 5711870 1364628..1364816 1 NC_009952.1 hypothetical protein 1364816 5711870 Dshi_1312 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532655.1 1364628 D 398580 CDS YP_001532656.1 159043862 5711871 1365222..1366430 1 NC_009952.1 catalyzes the transfer of electrons from NADH to ubiquinone; NADH dehydrogenase subunit E 1366430 nuoE 5711871 nuoE Dinoroseobacter shibae DFL 12 = DSM 16493 NADH dehydrogenase subunit E YP_001532656.1 1365222 D 398580 CDS YP_001532657.1 159043863 5711872 1366460..1367179 1 NC_009952.1 hypothetical protein 1367179 5711872 Dshi_1314 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532657.1 1366460 D 398580 CDS YP_001532658.1 159043864 5711873 1367176..1367412 1 NC_009952.1 conserved in Rhodobacteraceae; hypothetical protein 1367412 5711873 Dshi_1315 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532658.1 1367176 D 398580 CDS YP_001532659.1 159043865 5711874 1367416..1368717 1 NC_009952.1 part of NADH-ubiquinone oxidoreductase complex I; shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain; NuoF is part of the soluble NADH dehydrogenase fragment, which represents the electron input part of NADH dehydrogenase; NADH dehydrogenase subunit I F 1368717 nuoF 5711874 nuoF Dinoroseobacter shibae DFL 12 = DSM 16493 NADH dehydrogenase subunit I F YP_001532659.1 1367416 D 398580 CDS YP_001532660.1 159043866 5711875 1368714..1369106 1 NC_009952.1 hypothetical protein 1369106 5711875 Dshi_1317 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532660.1 1368714 D 398580 CDS YP_001532661.1 159043867 5711876 1369103..1369564 1 NC_009952.1 hypothetical protein 1369564 5711876 Dshi_1318 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532661.1 1369103 D 398580 CDS YP_001532662.1 159043868 5711877 1369561..1370079 1 NC_009952.1 hypothetical protein 1370079 5711877 Dshi_1319 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532662.1 1369561 D 398580 CDS YP_001532663.1 159043869 5711878 1370083..1372101 1 NC_009952.1 Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit G 1372101 nuoG 5711878 nuoG Dinoroseobacter shibae DFL 12 = DSM 16493 NADH dehydrogenase subunit G YP_001532663.1 1370083 D 398580 CDS YP_001532664.1 159043870 5711879 1372375..1373412 1 NC_009952.1 Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit H 1373412 nuoH 5711879 nuoH Dinoroseobacter shibae DFL 12 = DSM 16493 NADH dehydrogenase subunit H YP_001532664.1 1372375 D 398580 CDS YP_001532665.1 159043871 5711880 1373416..1373910 1 NC_009952.1 Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit I 1373910 nuoI 5711880 nuoI Dinoroseobacter shibae DFL 12 = DSM 16493 NADH dehydrogenase subunit I YP_001532665.1 1373416 D 398580 CDS YP_001532666.1 159043872 5711881 1373907..1374320 1 NC_009952.1 carboxymuconolactone decarboxylase 1374320 5711881 Dshi_1323 Dinoroseobacter shibae DFL 12 = DSM 16493 carboxymuconolactone decarboxylase YP_001532666.1 1373907 D 398580 CDS YP_001532667.1 159043873 5711882 1374343..1374957 1 NC_009952.1 Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit J 1374957 nuoJ 5711882 nuoJ Dinoroseobacter shibae DFL 12 = DSM 16493 NADH dehydrogenase subunit J YP_001532667.1 1374343 D 398580 CDS YP_001532668.1 159043874 5711883 1375139..1375633 1 NC_009952.1 hypothetical protein 1375633 5711883 Dshi_1325 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532668.1 1375139 D 398580 CDS YP_001532669.1 159043875 5711884 1375716..1376021 1 NC_009952.1 Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit K 1376021 nuoK 5711884 nuoK Dinoroseobacter shibae DFL 12 = DSM 16493 NADH dehydrogenase subunit K YP_001532669.1 1375716 D 398580 CDS YP_001532670.1 159043876 5711885 1376026..1378083 1 NC_009952.1 Catalyzes the transfer of electrons from NADH to ubiquinone; NADH dehydrogenase subunit L 1378083 nuoL 5711885 nuoL Dinoroseobacter shibae DFL 12 = DSM 16493 NADH dehydrogenase subunit L YP_001532670.1 1376026 D 398580 CDS YP_001532671.1 159043877 5711886 1378083..1379630 1 NC_009952.1 Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit M 1379630 nuoM 5711886 nuoM Dinoroseobacter shibae DFL 12 = DSM 16493 NADH dehydrogenase subunit M YP_001532671.1 1378083 D 398580 CDS YP_001532672.1 159043878 5711887 1379641..1381080 1 NC_009952.1 Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit N 1381080 nuoN 5711887 nuoN Dinoroseobacter shibae DFL 12 = DSM 16493 NADH dehydrogenase subunit N YP_001532672.1 1379641 D 398580 CDS YP_001532673.1 159043879 5711888 1381070..1381825 1 NC_009952.1 biotin--acetyl-CoA-carboxylase ligase 1381825 5711888 Dshi_1330 Dinoroseobacter shibae DFL 12 = DSM 16493 biotin--acetyl-CoA-carboxylase ligase YP_001532673.1 1381070 D 398580 CDS YP_001532674.1 159043880 5711889 1381846..1382616 1 NC_009952.1 type III; catalyzes the formation of (R)-4'-phosphopantothenate from (R)-pantothenate in coenzyme A biosynthesis; type III pantothenate kinases are not subject to feedback inhibition from coenzyme A and have a high Km for ATP; pantothenate kinase 1382616 5711889 Dshi_1331 Dinoroseobacter shibae DFL 12 = DSM 16493 pantothenate kinase YP_001532674.1 1381846 D 398580 CDS YP_001532675.1 159043881 5711890 1382616..1384286 1 NC_009952.1 beta-lactamase domain-containing protein 1384286 5711890 Dshi_1332 Dinoroseobacter shibae DFL 12 = DSM 16493 beta-lactamase domain-containing protein YP_001532675.1 1382616 D 398580 CDS YP_001532676.1 159043882 5711891 complement(1384375..1385856) 1 NC_009952.1 DEAD/DEAH box helicase 1385856 rhlE 5711891 rhlE Dinoroseobacter shibae DFL 12 = DSM 16493 DEAD/DEAH box helicase YP_001532676.1 1384375 R 398580 CDS YP_001532677.1 159043883 5711892 complement(1386187..1387725) 1 NC_009952.1 TPR containing proteins are involved in assambly of multiprotein complexes; hypothetical protein 1387725 5711892 Dshi_1334 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532677.1 1386187 R 398580 CDS YP_001532678.2 284928594 5711893 1388539..1389207 1 NC_009952.1 hypothetical protein 1389207 5711893 Dshi_1335 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532678.2 1388539 D 398580 CDS YP_001532679.1 159043885 5711894 complement(1389301..1390908) 1 NC_009952.1 Increases the formation of ribosomal termination complexes and stimulates activities of prfA and prfB, GTP binding; peptide chain release factor 3 1390908 prfC 5711894 prfC Dinoroseobacter shibae DFL 12 = DSM 16493 peptide chain release factor 3 YP_001532679.1 1389301 R 398580 CDS YP_001532680.1 159043886 5711895 1391022..1391393 1 NC_009952.1 hypothetical protein 1391393 5711895 Dshi_1337 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532680.1 1391022 D 398580 CDS YP_001532681.1 159043887 5711896 complement(1391461..1392303) 1 NC_009952.1 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 1392303 uspA1 5711896 uspA1 Dinoroseobacter shibae DFL 12 = DSM 16493 UspA domain-containing protein YP_001532681.1 1391461 R 398580 CDS YP_001532682.1 159043888 5711897 1392438..1393217 1 NC_009952.1 most enzymes of this family are NAD/NADP-dependent oxidoreductases; short-chain dehydrogenase/reductase SDR 1393217 5711897 Dshi_1339 Dinoroseobacter shibae DFL 12 = DSM 16493 short-chain dehydrogenase/reductase SDR YP_001532682.1 1392438 D 398580 CDS YP_001532683.1 159043889 5711898 1393332..1394720 1 NC_009952.1 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 1394720 5711898 Dshi_1340 Dinoroseobacter shibae DFL 12 = DSM 16493 Na+/solute symporter YP_001532683.1 1393332 D 398580 CDS YP_001532684.1 159043890 5711899 1394766..1395854 1 NC_009952.1 unknown specificity, high similarity to iron ABC transporters; ABC transporter-like protein 1395854 5711899 Dshi_1341 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC transporter-like protein YP_001532684.1 1394766 D 398580 CDS YP_001532685.1 159043891 5711900 complement(1395858..1396517) 1 NC_009952.1 Helix-turn-helix type 11 domain protein; helix-turn-helix domain-containing protein 1396517 5711900 Dshi_1342 Dinoroseobacter shibae DFL 12 = DSM 16493 helix-turn-helix domain-containing protein YP_001532685.1 1395858 R 398580 CDS YP_001532686.1 159043892 5711901 1396711..1396935 1 NC_009952.1 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 1396935 5711901 Dshi_1343 Dinoroseobacter shibae DFL 12 = DSM 16493 Sec-independent translocation protein mttA/Hcf106 YP_001532686.1 1396711 D 398580 CDS YP_001532687.1 159043893 5711902 1396954..1397421 1 NC_009952.1 Sec-independent protein secretion pathway components; TatB subunit; twin-arginine translocation protein 1397421 tatB 5711902 tatB Dinoroseobacter shibae DFL 12 = DSM 16493 twin-arginine translocation protein YP_001532687.1 1396954 D 398580 CDS YP_001532688.1 159043894 5711911 1397430..1398470 1 NC_009952.1 Sec-independent protein secretion pathway components; TatC subunit; sec-independent protein translocase 1398470 tatC 5711911 tatC Dinoroseobacter shibae DFL 12 = DSM 16493 sec-independent protein translocase YP_001532688.1 1397430 D 398580 CDS YP_001532689.1 159043895 5711912 1398467..1399318 1 NC_009952.1 hypothetical protein 1399318 5711912 Dshi_1346 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532689.1 1398467 D 398580 CDS YP_001532690.1 159043896 5711913 complement(1399416..1400000) 1 NC_009952.1 hypothetical protein 1400000 5711913 Dshi_1347 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532690.1 1399416 R 398580 CDS YP_001532691.1 159043897 5711914 complement(1400045..1400671) 1 NC_009952.1 Integral membrane protein family that includes the antibiotic resistance protein MarC. These proteins may be transporters.; multiple antibiotic resistance (MarC)-like protein 1400671 5711914 Dshi_1348 Dinoroseobacter shibae DFL 12 = DSM 16493 multiple antibiotic resistance (MarC)-like protein YP_001532691.1 1400045 R 398580 CDS YP_001532692.1 159043898 5711915 complement(1400718..1402574) 1 NC_009952.1 duplicated ATPase domain; ABC transporter-like protein 1402574 5711915 Dshi_1349 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC transporter-like protein YP_001532692.1 1400718 R 398580 CDS YP_001532693.1 159043899 5711916 1402713..1403135 1 NC_009952.1 catalyzes the formation of nucleoside triphosphate from ATP and nucleoside diphosphate; nucleoside diphosphate kinase 1403135 ndk 5711916 ndk Dinoroseobacter shibae DFL 12 = DSM 16493 nucleoside diphosphate kinase YP_001532693.1 1402713 D 398580 CDS YP_001532694.1 159043900 5711917 1403285..1403677 1 NC_009952.1 hypothetical protein 1403677 5711917 Dshi_1351 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532694.1 1403285 D 398580 CDS YP_001532695.1 159043901 5711903 complement(1403674..1404003) 1 NC_009952.1 no evidence for predicted domain; TfoX domain-containing protein 1404003 5711903 Dshi_1352 Dinoroseobacter shibae DFL 12 = DSM 16493 TfoX domain-containing protein YP_001532695.1 1403674 R 398580 CDS YP_001532696.1 159043902 5711904 1404655..1405959 1 NC_009952.1 ABC transporter (importer) gene cluster: receptor; family 1 extracellular solute-binding protein 1405959 5711904 Dshi_1353 Dinoroseobacter shibae DFL 12 = DSM 16493 family 1 extracellular solute-binding protein YP_001532696.1 1404655 D 398580 CDS YP_001532697.1 159043903 5711905 1406021..1407271 1 NC_009952.1 ABC transporter (importer) gene cluster: 1st membrane spanning domain (MSD); part of a heterotetramer; binding-protein-dependent transport system inner membrane protein 1407271 5711905 Dshi_1354 Dinoroseobacter shibae DFL 12 = DSM 16493 binding-protein-dependent transport system inner membrane protein YP_001532697.1 1406021 D 398580 CDS YP_001532698.1 159043904 5711906 1407459..1408673 1 NC_009952.1 ABC transporter (importer) gene cluster: 2nd membrane spanning domain (MSD); part of a heterotetramer; binding-protein-dependent transport system inner membrane protein 1408673 5711906 Dshi_1355 Dinoroseobacter shibae DFL 12 = DSM 16493 binding-protein-dependent transport system inner membrane protein YP_001532698.1 1407459 D 398580 CDS YP_001532699.1 159043905 5711907 1408670..1409944 1 NC_009952.1 hypothetical protein 1409944 5711907 Dshi_1356 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532699.1 1408670 D 398580 CDS YP_001532700.1 159043906 5711908 1409932..1410981 1 NC_009952.1 ABC transporter (importer) gene cluster: ATP binding cassette (ABC) domain; part of a heterotetramer; ABC transporter-like protein 1410981 5711908 Dshi_1357 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC transporter-like protein YP_001532700.1 1409932 D 398580 CDS YP_001532701.1 159043907 5711909 1410984..1411760 1 NC_009952.1 most enzymes of this family are NAD/NADP-dependent oxidoreductases; short-chain dehydrogenase/reductase SDR 1411760 5711909 Dshi_1358 Dinoroseobacter shibae DFL 12 = DSM 16493 short-chain dehydrogenase/reductase SDR YP_001532701.1 1410984 D 398580 CDS YP_001532702.1 159043908 5711910 1411909..1412286 1 NC_009952.1 hypothetical protein 1412286 5711910 Dshi_1359 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532702.1 1411909 D 398580 CDS YP_001532703.1 159043909 5712536 complement(1412275..1413312) 1 NC_009952.1 SnoaL-like polyketide cyclase family protein; hypothetical protein 1413312 5712536 Dshi_1360 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532703.1 1412275 R 398580 CDS YP_001532704.1 159043910 5712537 1413419..1414825 1 NC_009952.1 Catalyzes the stereospecific oxidation of D-lactate to pyruvate; cytochrome; D-lactate dehydrogenase 1414825 dld1 5712537 dld1 Dinoroseobacter shibae DFL 12 = DSM 16493 D-lactate dehydrogenase YP_001532704.1 1413419 D 398580 CDS YP_001532705.1 159043911 5712538 1414985..1416322 1 NC_009952.1 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 1416322 5712538 Dshi_1362 Dinoroseobacter shibae DFL 12 = DSM 16493 putative oxidoreductase YP_001532705.1 1414985 D 398580 CDS YP_001532706.1 159043912 5712539 1416350..1417648 1 NC_009952.1 catalyzes the first step in pyrimidine degradation: the NADPH-dependent reduction of uracil and thymine to the corresponding 5,6-dihydropyrimidines; dihydropyrimidine dehydrogenase 1417648 pyrD1 5712539 pyrD1 Dinoroseobacter shibae DFL 12 = DSM 16493 dihydropyrimidine dehydrogenase YP_001532706.1 1416350 D 398580 CDS YP_001532707.1 159043913 5712540 complement(1417662..1418054) 1 NC_009952.1 hypothetical protein 1418054 5712540 Dshi_1364 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532707.1 1417662 R 398580 CDS YP_001532708.1 159043914 5712541 complement(1418132..1418767) 1 NC_009952.1 Helix-Turn-Helix motif; TetR family; transcriptional regulator 1418767 5712541 Dshi_1365 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001532708.1 1418132 R 398580 CDS YP_001532709.1 159043915 5712542 1418987..1420312 1 NC_009952.1 catalyzes the formation of pyruvate and beta-alanine from L-alanine and 3-oxopropanoate; beta alanine--pyruvate transaminase 1420312 5712542 Dshi_1366 Dinoroseobacter shibae DFL 12 = DSM 16493 beta alanine--pyruvate transaminase YP_001532709.1 1418987 D 398580 CDS YP_001532710.1 159043916 5712543 1420347..1421621 1 NC_009952.1 allantoate amidohydrolase and N-carbamoyl-L-amino acid amidohydrolase are very similar; the allantoate amidohydrolase from Escherichia coli forms a dimer and binds zinc ions for catalytic activity and catalyzes the conversion of allantoate to (S)-ureidoglycolate and ammonia; carbamoyl amidohydrolase from Bacillus sp. converts N-carbamoyl amino acids to amino acids, ammonia, and carbon dioxide; allantoate amidohydrolase 1421621 amaB 5712543 amaB Dinoroseobacter shibae DFL 12 = DSM 16493 allantoate amidohydrolase YP_001532710.1 1420347 D 398580 CDS YP_001532711.1 159043917 5712544 1421652..1421951 1 NC_009952.1 hypothetical protein 1421951 5712544 Dshi_1368 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532711.1 1421652 D 398580 CDS YP_001532712.1 159043918 5712545 1421968..1422711 1 NC_009952.1 This family includes class II aldolases and adducins which have not been ascribed any enzymatic function.; class II aldolase/adducin family protein 1422711 5712545 Dshi_1369 Dinoroseobacter shibae DFL 12 = DSM 16493 class II aldolase/adducin family protein YP_001532712.1 1421968 D 398580 CDS YP_001532713.1 159043919 5712546 1422758..1424209 1 NC_009952.1 catalyzes the hydrolytic cleavage of hydantoin with aromatic side chains at the 5'position; phenylhydantoinase 1424209 dht 5712546 dht Dinoroseobacter shibae DFL 12 = DSM 16493 phenylhydantoinase YP_001532713.1 1422758 D 398580 CDS YP_001532714.1 159043920 5712547 1424219..1425220 1 NC_009952.1 ABC transporter (importer) gene cluster (disrupted): ATP binding cassette (ABC) domain; part of a heterotetramer; ABC transporter-like protein 1425220 5712547 Dshi_1371 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC transporter-like protein YP_001532714.1 1424219 D 398580 CDS YP_001532715.1 159043921 5712548 1425233..1426150 1 NC_009952.1 ABC transporter (importer) gene cluster: 1st membrane spanning domain (MSD); part of a heterotetramer; binding-protein-dependent transport system inner membrane protein 1426150 5712548 Dshi_1372 Dinoroseobacter shibae DFL 12 = DSM 16493 binding-protein-dependent transport system inner membrane protein YP_001532715.1 1425233 D 398580 CDS YP_001532716.1 159043922 5712549 1426147..1427058 1 NC_009952.1 ABC transporter (importer) gene cluster: 2nd membrane spanning domain (MSD); part of a heterotetramer; binding-protein-dependent transport system inner membrane protein 1427058 5712549 Dshi_1373 Dinoroseobacter shibae DFL 12 = DSM 16493 binding-protein-dependent transport system inner membrane protein YP_001532716.1 1426147 D 398580 CDS YP_001532717.1 159043923 5712550 1427332..1428321 1 NC_009952.1 ABC transporter (importer) gene cluster: receptor; NMT1/THI5 like domain-containing protein 1428321 5712550 Dshi_1374 Dinoroseobacter shibae DFL 12 = DSM 16493 NMT1/THI5 like domain-containing protein YP_001532717.1 1427332 D 398580 CDS YP_001532718.1 159043924 5712551 1428663..1429859 1 NC_009952.1 ornithine decarboxylase 1429859 5712551 Dshi_1375 Dinoroseobacter shibae DFL 12 = DSM 16493 ornithine decarboxylase YP_001532718.1 1428663 D 398580 CDS YP_001532719.1 159043925 5712552 complement(1429916..1430713) 1 NC_009952.1 catalyses the hydrolysis of creatinine to creatine; creatininase 1430713 5712552 Dshi_1376 Dinoroseobacter shibae DFL 12 = DSM 16493 creatininase YP_001532719.1 1429916 R 398580 CDS YP_001532720.1 159043926 5712553 complement(1430706..1431608) 1 NC_009952.1 This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily; 2OG-Fe(II) oxygenase 1431608 5712553 Dshi_1377 Dinoroseobacter shibae DFL 12 = DSM 16493 2OG-Fe(II) oxygenase YP_001532720.1 1430706 R 398580 CDS YP_001532721.1 159043927 5712554 complement(1431608..1432243) 1 NC_009952.1 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 1432243 5712554 Dshi_1378 Dinoroseobacter shibae DFL 12 = DSM 16493 quinone dependent NAD(P)H dehydrogenase YP_001532721.1 1431608 R 398580 CDS YP_001532722.1 159043928 5712555 complement(1432243..1432830) 1 NC_009952.1 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 1432830 5712555 Dshi_1379 Dinoroseobacter shibae DFL 12 = DSM 16493 quinone dependent NADH dehydrogenase YP_001532722.1 1432243 R 398580 CDS YP_001532723.1 159043929 5712556 complement(1432949..1434355) 1 NC_009952.1 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 1434355 5712556 Dshi_1380 Dinoroseobacter shibae DFL 12 = DSM 16493 FAD linked oxidase domain-containing protein YP_001532723.1 1432949 R 398580 CDS YP_001532724.1 159043930 5712557 complement(1434352..1435626) 1 NC_009952.1 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 1435626 5712557 Dshi_1381 Dinoroseobacter shibae DFL 12 = DSM 16493 cytosine deaminase YP_001532724.1 1434352 R 398580 CDS YP_001532725.1 159043931 5712558 complement(1435626..1436483) 1 NC_009952.1 ABC transporter (importer) gene cluster: 2nd membrane spanning domain (MSD); part of a heterotetramer; binding-protein-dependent transport system inner membrane protein 1436483 5712558 Dshi_1382 Dinoroseobacter shibae DFL 12 = DSM 16493 binding-protein-dependent transport system inner membrane protein YP_001532725.1 1435626 R 398580 CDS YP_001532726.1 159043932 5712559 complement(1436480..1437289) 1 NC_009952.1 ABC transporter (importer) gene cluster: ATP binding cassette (ABC) domain; part of a heterotetramer; ABC transporter-like protein 1437289 5712559 Dshi_1383 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC transporter-like protein YP_001532726.1 1436480 R 398580 CDS YP_001532727.1 159043933 5712560 complement(1437354..1438355) 1 NC_009952.1 ABC transporter (importer) gene cluster: 1st membrane spanning domain (MSD); part of a heterotetramer; ABC transporter permease 1438355 5712560 Dshi_1384 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC transporter permease YP_001532727.1 1437354 R 398580 CDS YP_001532728.1 159043934 5712561 1438594..1438992 1 NC_009952.1 Endoribonuclease active on single-stranded mRNA. Inhibits protein synthesis by cleavage of mRNA; endoribonuclease L-PSP 1438992 5712561 Dshi_1385 Dinoroseobacter shibae DFL 12 = DSM 16493 endoribonuclease L-PSP YP_001532728.1 1438594 D 398580 CDS YP_001532729.1 159043935 5712562 complement(1438996..1440408) 1 NC_009952.1 hypothetical protein 1440408 5712562 Dshi_1386 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532729.1 1438996 R 398580 CDS YP_001532730.1 159043936 5712563 complement(1440553..1441812) 1 NC_009952.1 binds and unfolds substrates as part of the ClpXP protease; ATP-dependent protease ATP-binding subunit ClpX 1441812 clpX 5712563 clpX Dinoroseobacter shibae DFL 12 = DSM 16493 ATP-dependent protease ATP-binding subunit ClpX YP_001532730.1 1440553 R 398580 CDS YP_001532731.1 159043937 5712564 complement(1442020..1442646) 1 NC_009952.1 hydrolyzes proteins to small peptides; with the ATPase subunits ClpA or ClpX, ClpP degrades specific substrates; ATP-dependent Clp protease proteolytic subunit 1442646 clpP 5712564 clpP Dinoroseobacter shibae DFL 12 = DSM 16493 ATP-dependent Clp protease proteolytic subunit YP_001532731.1 1442020 R 398580 CDS YP_001532732.1 159043938 5712565 1442883..1444100 1 NC_009952.1 putative deoxyribodipyrimidine photo-lyase 1444100 5712565 Dshi_1389 Dinoroseobacter shibae DFL 12 = DSM 16493 putative deoxyribodipyrimidine photo-lyase YP_001532732.1 1442883 D 398580 CDS YP_001532733.1 159043939 5712566 1444131..1444565 1 NC_009952.1 Provides the input to the respiratory chain from the NAD-linked dehydrogenases of the citric acid cycle. The complex couples the oxidation of NADH and the reduction of ubiquinone, to the generation of a proton gradient which is then used for ATP synthesis; NADH dehydrogenase 1444565 5712566 Dshi_1390 Dinoroseobacter shibae DFL 12 = DSM 16493 NADH dehydrogenase YP_001532733.1 1444131 D 398580 CDS YP_001532734.1 159043940 5712567 1444613..1445059 1 NC_009952.1 Mammalian cell entry related domain; hypothetical protein 1445059 5712567 Dshi_1391 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532734.1 1444613 D 398580 CDS YP_001532735.1 159043941 5712568 1445056..1445598 1 NC_009952.1 hypothetical protein 1445598 5712568 Dshi_1392 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532735.1 1445056 D 398580 CDS YP_001532736.1 159043942 5712569 complement(1445608..1446195) 1 NC_009952.1 hypothetical protein 1446195 5712569 Dshi_1393 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532736.1 1445608 R 398580 CDS YP_001532737.1 159043943 5712570 complement(1446363..1447034) 1 NC_009952.1 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 1447034 aat 5712570 aat Dinoroseobacter shibae DFL 12 = DSM 16493 leucyltransferase YP_001532737.1 1446363 R 398580 CDS YP_001532738.1 159043944 5712571 complement(1447094..1448440) 1 NC_009952.1 an AccC homodimer forms the biotin carboxylase subunit of the acetyl CoA carboxylase, an enzyme that catalyzes the formation of malonyl-CoA, which in turn controls the rate of fatty acid metabolism; acetyl-CoA carboxylase biotin carboxylase subunit 1448440 accC 5712571 accC Dinoroseobacter shibae DFL 12 = DSM 16493 acetyl-CoA carboxylase biotin carboxylase subunit YP_001532738.1 1447094 R 398580 CDS YP_001532739.1 159043945 5712572 complement(1448450..1448977) 1 NC_009952.1 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 1448977 accB 5712572 accB Dinoroseobacter shibae DFL 12 = DSM 16493 acetyl-CoA carboxylase YP_001532739.1 1448450 R 398580 CDS YP_001532740.1 159043946 5712573 1449132..1450748 1 NC_009952.1 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 1450748 5712573 Dshi_1397 Dinoroseobacter shibae DFL 12 = DSM 16493 phospholipase/lecithinase/hemolysin-like protein YP_001532740.1 1449132 D 398580 CDS YP_001532741.1 159043947 5712574 1450880..1451332 1 NC_009952.1 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 1451332 5712574 Dshi_1398 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532741.1 1450880 D 398580 CDS YP_001532742.1 159043948 5712575 complement(1451413..1453374) 1 NC_009952.1 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 1453374 acsA 5712575 acsA Dinoroseobacter shibae DFL 12 = DSM 16493 acetate--CoA ligase YP_001532742.1 1451413 R 398580 CDS YP_001532743.1 159043949 5712576 complement(1453619..1454374) 1 NC_009952.1 ABC transporter (importer) gene cluster: 2nd ATP binding cassette (ABC) domain; part of a heterotetramer; ABC transporter-like protein 1454374 5712576 Dshi_1400 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC transporter-like protein YP_001532743.1 1453619 R 398580 CDS YP_001532744.1 159043950 5712577 complement(1454386..1455144) 1 NC_009952.1 ABC transporter (importer) gene cluster: 1st ATP binding cassette (ABC) domain; part of a heterotetramer; ABC transporter-like protein 1455144 5712577 Dshi_1401 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC transporter-like protein YP_001532744.1 1454386 R 398580 CDS YP_001532745.1 159043951 5712578 complement(1455157..1456365) 1 NC_009952.1 ABC transporter (importer) gene cluster: 2nd membrane spanning domain (MSD); part of a heterotetramer; inner-membrane translocator 1456365 5712578 Dshi_1402 Dinoroseobacter shibae DFL 12 = DSM 16493 inner-membrane translocator YP_001532745.1 1455157 R 398580 CDS YP_001532746.1 159043952 5712579 complement(1456370..1457401) 1 NC_009952.1 ABC transporter (importer) gene cluster: 1st membrane spanning domain (MSD); part of a heterotetramer; inner-membrane translocator 1457401 5712579 Dshi_1403 Dinoroseobacter shibae DFL 12 = DSM 16493 inner-membrane translocator YP_001532746.1 1456370 R 398580 CDS YP_001532747.1 159043953 5712580 complement(1457511..1458866) 1 NC_009952.1 ABC transporter (importer) gene cluster: receptor; periplasmic binding protein, putative; branched-chain amino acid ABC transporter 1458866 5712580 Dshi_1404 Dinoroseobacter shibae DFL 12 = DSM 16493 branched-chain amino acid ABC transporter YP_001532747.1 1457511 R 398580 CDS YP_001532748.1 159043954 5712581 1459097..1460392 1 NC_009952.1 Helix-Turn-Helix motif; XRE family; transcriptional regulator 1460392 5712581 Dshi_1405 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001532748.1 1459097 D 398580 CDS YP_001532749.1 159043955 5712582 1460497..1460862 1 NC_009952.1 DNA-binding motif, normally found at the C-terminus, is missing; response regulator receiver protein 1460862 5712582 Dshi_1406 Dinoroseobacter shibae DFL 12 = DSM 16493 response regulator receiver protein YP_001532749.1 1460497 D 398580 CDS YP_001532750.1 159043956 5712583 1460864..1461184 1 NC_009952.1 hypothetical protein 1461184 5712583 Dshi_1407 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532750.1 1460864 D 398580 CDS YP_001532751.1 159043957 5712584 1461184..1463877 1 NC_009952.1 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 1463877 5712584 Dshi_1408 Dinoroseobacter shibae DFL 12 = DSM 16493 integral membrane sensor signal transduction histidine kinase YP_001532751.1 1461184 D 398580 CDS YP_001532752.1 159043958 5712585 1463926..1464975 1 NC_009952.1 hypothetical protein 1464975 5712585 Dshi_1409 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532752.1 1463926 D 398580 CDS YP_001532753.1 159043959 5712586 complement(1464988..1465500) 1 NC_009952.1 hypothetical protein 1465500 5712586 Dshi_1410 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532753.1 1464988 R 398580 CDS YP_001532754.1 159043960 5712587 1465574..1465852 1 NC_009952.1 TraR/DksA family; transcriptional regulator 1465852 5712587 Dshi_1411 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001532754.1 1465574 D 398580 CDS YP_001532755.1 159043961 5712588 1465891..1466133 1 NC_009952.1 hypothetical protein 1466133 5712588 Dshi_1412 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532755.1 1465891 D 398580 CDS YP_001532756.1 159043962 5712589 1466558..1467793 1 NC_009952.1 ABC transporter (importer) gene cluster: receptor; family 1 extracellular solute-binding protein 1467793 5712589 Dshi_1413 Dinoroseobacter shibae DFL 12 = DSM 16493 family 1 extracellular solute-binding protein YP_001532756.1 1466558 D 398580 CDS YP_001532757.1 159043963 5712590 1467854..1468885 1 NC_009952.1 ABC transporter (importer) gene cluster: 1st membrane spanning domain (MSD); part of a heterotetramer; binding-protein-dependent transport system inner membrane protein 1468885 5712590 Dshi_1414 Dinoroseobacter shibae DFL 12 = DSM 16493 binding-protein-dependent transport system inner membrane protein YP_001532757.1 1467854 D 398580 CDS YP_001532758.1 159043964 5712591 1468888..1469772 1 NC_009952.1 ABC transporter (importer) gene cluster: 2nd membrane spanning domain (MSD); part of a heterotetramer; binding-protein-dependent transport system inner membrane protein 1469772 5712591 Dshi_1415 Dinoroseobacter shibae DFL 12 = DSM 16493 binding-protein-dependent transport system inner membrane protein YP_001532758.1 1468888 D 398580 CDS YP_001532759.1 159043965 5712592 1469815..1470858 1 NC_009952.1 ABC transporter (importer) gene cluster: ATP binding cassette (ABC) domain; part of a heterotetramer; ABC transporter-like protein 1470858 5712592 Dshi_1416 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC transporter-like protein YP_001532759.1 1469815 D 398580 CDS YP_001532760.1 159043966 5712593 1470855..1471379 1 NC_009952.1 hypothetical protein 1471379 5712593 Dshi_1417 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532760.1 1470855 D 398580 CDS YP_001532761.1 159043967 5712594 complement(1471376..1471591) 1 NC_009952.1 conserved in Rhodobacteraceae; hypothetical protein 1471591 5712594 Dshi_1418 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532761.1 1471376 R 398580 CDS YP_001532762.1 159043968 5712595 1471738..1472016 1 NC_009952.1 hypothetical protein 1472016 5712595 Dshi_1419 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532762.1 1471738 D 398580 CDS YP_001532763.1 159043969 5712596 complement(1472033..1472908) 1 NC_009952.1 conserved in Rhodobacteraceae; hypothetical protein 1472908 5712596 Dshi_1420 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532763.1 1472033 R 398580 CDS YP_001532764.1 159043970 5712598 1473533..1474705 1 NC_009952.1 ABC transporter (importer) gene cluster: receptor; substrate-binding protein; ribose ABC transporter 1474705 5712598 Dshi_1421 Dinoroseobacter shibae DFL 12 = DSM 16493 ribose ABC transporter YP_001532764.1 1473533 D 398580 CDS YP_001532765.1 159043971 5712599 1474762..1476309 1 NC_009952.1 ABC transporter (importer) gene cluster: fused ATP binding cassette (ABC) domains; part of a heterotrimer; ABC transporter-like protein 1476309 rbsA3 5712599 rbsA3 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC transporter-like protein YP_001532765.1 1474762 D 398580 CDS YP_001532766.1 159043972 5712600 1476309..1477271 1 NC_009952.1 ABC transporter (importer) gene cluster: 1st membrane spanning domain (MSD); part of a heterotrimer; inner-membrane translocator 1477271 rbsB2 5712600 rbsB2 Dinoroseobacter shibae DFL 12 = DSM 16493 inner-membrane translocator YP_001532766.1 1476309 D 398580 CDS YP_001532767.1 159043973 5712601 1477271..1478302 1 NC_009952.1 ABC transporter (importer) gene cluster: 2nd membrane spanning domain (MSD); part of a heterotrimer; inner-membrane translocator 1478302 rbsC1 5712601 rbsC1 Dinoroseobacter shibae DFL 12 = DSM 16493 inner-membrane translocator YP_001532767.1 1477271 D 398580 CDS YP_001532768.1 159043974 5712602 1478321..1479775 1 NC_009952.1 This family of dehydrogenases act on aldehyde substrates. Members use NADP as a cofactor (PFAM, INTERPRO; COG: NAD-dependent enzyme).; aldehyde dehydrogenase 1479775 5712602 Dshi_1425 Dinoroseobacter shibae DFL 12 = DSM 16493 aldehyde dehydrogenase YP_001532768.1 1478321 D 398580 CDS YP_001532769.1 159043975 5712603 1479836..1481350 1 NC_009952.1 Fumarase, or fumarate hydratase, is a component of the citric acid cycle.; Fe-S type, tartrate/fumarate subfamily, alpha subunit; hydro-lyase 1481350 5712603 Dshi_1426 Dinoroseobacter shibae DFL 12 = DSM 16493 hydro-lyase YP_001532769.1 1479836 D 398580 CDS YP_001532770.1 159043976 5712604 1481361..1482908 1 NC_009952.1 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 1482908 citF 5712604 citF Dinoroseobacter shibae DFL 12 = DSM 16493 citrate CoA-transferase YP_001532770.1 1481361 D 398580 CDS YP_001532771.1 159043977 5712605 complement(1483002..1484636) 1 NC_009952.1 Can catalyze the oxidation of choline to betaine aldehyde and betaine aldehyde to glycine betaine; glucose-methanol-choline oxidoreductase 1484636 5712605 Dshi_1428 Dinoroseobacter shibae DFL 12 = DSM 16493 glucose-methanol-choline oxidoreductase YP_001532771.1 1483002 R 398580 CDS YP_001532772.1 159043978 5712606 complement(1484787..1485557) 1 NC_009952.1 Catalyzes the first of the two reduction steps in the elongation cycle of fatty acid synthesis; 3-ketoacyl-ACP reductase 1485557 fabG 5712606 fabG Dinoroseobacter shibae DFL 12 = DSM 16493 3-ketoacyl-ACP reductase YP_001532772.1 1484787 R 398580 CDS YP_001532773.1 159043979 5712607 complement(1485573..1487036) 1 NC_009952.1 This family of dehydrogenases act on aldehyde substrates. Members use NADP as a cofactor.; aldehyde dehydrogenase 1487036 5712607 Dshi_1430 Dinoroseobacter shibae DFL 12 = DSM 16493 aldehyde dehydrogenase YP_001532773.1 1485573 R 398580 CDS YP_001532774.1 159043980 5712608 complement(1487135..1488091) 1 NC_009952.1 contains substrate binding domain, putative homotetramer; LysR family; transcriptional regulator 1488091 5712608 Dshi_1431 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001532774.1 1487135 R 398580 CDS YP_001532775.1 159043981 5712609 1488222..1489370 1 NC_009952.1 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 1489370 5712609 Dshi_1432 Dinoroseobacter shibae DFL 12 = DSM 16493 L-carnitine dehydratase/bile acid-inducible protein F YP_001532775.1 1488222 D 398580 CDS YP_001532776.1 159043982 5712610 1489582..1490181 1 NC_009952.1 hypothetical protein 1490181 5712610 Dshi_1433 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532776.1 1489582 D 398580 CDS YP_001532777.1 159043983 5712611 1490184..1490399 1 NC_009952.1 remnant of Xaa-Pro dipeptidase; Xaa-Pro dipeptidase 1490399 5712611 Dshi_1434 Dinoroseobacter shibae DFL 12 = DSM 16493 Xaa-Pro dipeptidase YP_001532777.1 1490184 D 398580 CDS YP_001532778.1 159043984 5712612 complement(1490378..1491148) 1 NC_009952.1 domain is common to a number of hydrolytic enzymes of widely differing phylogenetic origin and catalytic function; alpha/beta hydrolase fold protein 1491148 5712612 Dshi_1435 Dinoroseobacter shibae DFL 12 = DSM 16493 alpha/beta hydrolase fold protein YP_001532778.1 1490378 R 398580 CDS YP_001532779.1 159043985 5712613 complement(1491145..1492686) 1 NC_009952.1 ABC transporter gene cluster, permease component; binding-protein-dependent transport system inner membrane protein 1492686 5712613 Dshi_1436 Dinoroseobacter shibae DFL 12 = DSM 16493 binding-protein-dependent transport system inner membrane protein YP_001532779.1 1491145 R 398580 CDS YP_001532780.1 159043986 5712614 complement(1492683..1493738) 1 NC_009952.1 ABC transporter gene cluster, ATPase component; ATPase subunit; glycine betaine/L-proline ABC transporter 1493738 5712614 Dshi_1437 Dinoroseobacter shibae DFL 12 = DSM 16493 glycine betaine/L-proline ABC transporter YP_001532780.1 1492683 R 398580 CDS YP_001532781.1 159043987 5712615 complement(1493812..1494777) 1 NC_009952.1 ABC transporter gene cluster, periplasmatic substrate binding component; glycine betaine ABC transporter substrate binding protein 1494777 5712615 Dshi_1438 Dinoroseobacter shibae DFL 12 = DSM 16493 glycine betaine ABC transporter substrate binding protein YP_001532781.1 1493812 R 398580 CDS YP_001532782.1 159043988 5712616 complement(1494829..1495872) 1 NC_009952.1 catalyzes the formation of pyruvate from D-cysteine; D-cysteine desulfhydrase 1495872 5712616 Dshi_1439 Dinoroseobacter shibae DFL 12 = DSM 16493 D-cysteine desulfhydrase YP_001532782.1 1494829 R 398580 CDS YP_001532783.1 159043989 5712617 1495960..1496892 1 NC_009952.1 contains substrate binding domain, putative homotetramer; LysR family; transcriptional regulator 1496892 5712617 Dshi_1440 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001532783.1 1495960 D 398580 CDS YP_001532784.1 159043990 5712618 1497052..1498287 1 NC_009952.1 C-Terminus conserved; hypothetical protein 1498287 5712618 Dshi_1441 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532784.1 1497052 D 398580 CDS YP_001532785.1 159043991 5712619 1498290..1499732 1 NC_009952.1 peroxidase 1499732 5712619 Dshi_1442 Dinoroseobacter shibae DFL 12 = DSM 16493 peroxidase YP_001532785.1 1498290 D 398580 CDS YP_001532786.1 159043992 5712620 1499876..1500844 1 NC_009952.1 TRAP gene cluster - dctPQM; TAXI family; TRAP transporter solute receptor 1500844 5712620 Dshi_1443 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP transporter solute receptor YP_001532786.1 1499876 D 398580 CDS YP_001532787.1 159043993 5712621 1500927..1503581 1 NC_009952.1 TRAP gene cluster - dctPQM; 4TM/12TM fusion protein; TRAP transporter 1503581 5712621 Dshi_1444 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP transporter YP_001532787.1 1500927 D 398580 CDS YP_001532788.1 159043994 5712622 1503594..1504028 1 NC_009952.1 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 1504028 uspG 5712622 uspG Dinoroseobacter shibae DFL 12 = DSM 16493 UspA domain-containing protein YP_001532788.1 1503594 D 398580 CDS YP_001532789.1 159043995 5712623 1504032..1505366 1 NC_009952.1 PLP-dependent enzyme; hypothetical protein 1505366 5712623 Dshi_1446 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532789.1 1504032 D 398580 CDS YP_001532790.1 159043996 5712624 complement(1505621..1505779) 1 NC_009952.1 transposase 1505779 5712624 Dshi_1447 Dinoroseobacter shibae DFL 12 = DSM 16493 transposase YP_001532790.1 1505621 R 398580 CDS YP_001532791.1 159043997 5712625 1506500..1506724 1 NC_009952.1 HTH-type transcriptional regulator ZntR 1506724 5712625 Dshi_1448 Dinoroseobacter shibae DFL 12 = DSM 16493 HTH-type transcriptional regulator ZntR YP_001532791.1 1506500 D 398580 CDS YP_001532792.1 159043998 5712626 complement(1506778..1509000) 1 NC_009952.1 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 1509000 5712626 Dshi_1449 Dinoroseobacter shibae DFL 12 = DSM 16493 TonB-dependent receptor YP_001532792.1 1506778 R 398580 CDS YP_001532793.1 159043999 5712627 complement(1509057..1510334) 1 NC_009952.1 NnrS is a putative heme-Cu protein (NnrS) and a member of the short-chain dehydrogenase family.; NnrS family protein 1510334 5712627 Dshi_1450 Dinoroseobacter shibae DFL 12 = DSM 16493 NnrS family protein YP_001532793.1 1509057 R 398580 CDS YP_001532794.1 159044000 5712628 complement(1510331..1511080) 1 NC_009952.1 Part of the ABC transporter complex ssuABC involved in aliphatic sulfonates import. Responsible for energy coupling to the transport system; ABC transporter-like protein 1511080 ssuB2 5712628 ssuB2 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC transporter-like protein YP_001532794.1 1510331 R 398580 CDS YP_001532795.1 159044001 5712629 complement(1511077..1511940) 1 NC_009952.1 Part of the ABC transporter complex ssuABC involved in aliphatic sulfonates import.; binding-protein-dependent transport system inner membrane protein 1511940 ssuC2 5712629 ssuC2 Dinoroseobacter shibae DFL 12 = DSM 16493 binding-protein-dependent transport system inner membrane protein YP_001532795.1 1511077 R 398580 CDS YP_001532796.1 159044002 5712630 complement(1511962..1512945) 1 NC_009952.1 Part of the ABC transporter complex ssuABC involved in aliphatic sulfonates import.; putative sulfonate/nitrate transport system substrate-binding protein 1512945 ssuA2 5712630 ssuA2 Dinoroseobacter shibae DFL 12 = DSM 16493 putative sulfonate/nitrate transport system substrate-binding protein YP_001532796.1 1511962 R 398580 CDS YP_001532797.1 159044003 5712631 complement(1513040..1513537) 1 NC_009952.1 hypothetical protein 1513537 5712631 Dshi_1454 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532797.1 1513040 R 398580 CDS YP_001532798.1 159044004 5712632 1513747..1513896 1 NC_009952.1 transposase 1513896 5712632 Dshi_1455 Dinoroseobacter shibae DFL 12 = DSM 16493 transposase YP_001532798.1 1513747 D 398580 CDS YP_001532799.1 159044005 5712633 1513896..1514609 1 NC_009952.1 Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains.; integrase catalytic subunit 1514609 5712633 Dshi_1456 Dinoroseobacter shibae DFL 12 = DSM 16493 integrase catalytic subunit YP_001532799.1 1513896 D 398580 CDS YP_001532800.1 159044006 5712634 1514658..1516022 1 NC_009952.1 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 1516022 5712634 Dshi_1457 Dinoroseobacter shibae DFL 12 = DSM 16493 type III restriction protein res subunit YP_001532800.1 1514658 D 398580 CDS YP_001532801.1 159044007 5712635 complement(1515973..1516368) 1 NC_009952.1 phage integrase family; site-specific recombinase 1516368 5712635 Dshi_1458 Dinoroseobacter shibae DFL 12 = DSM 16493 site-specific recombinase YP_001532801.1 1515973 R 398580 CDS YP_001532802.1 159044008 5712637 1516680..1517501 1 NC_009952.1 outer membrane protein; hypothetical protein 1517501 5712637 Dshi_1459 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532802.1 1516680 D 398580 CDS YP_001532803.1 159044009 5712638 1517692..1518357 1 NC_009952.1 fusion of ribosomal protein L21 and COG3743; 50S ribosomal protein L21 1518357 rplU 5712638 rplU Dinoroseobacter shibae DFL 12 = DSM 16493 50S ribosomal protein L21 YP_001532803.1 1517692 D 398580 CDS YP_001532804.1 159044010 5712639 1518373..1518642 1 NC_009952.1 involved in the peptidyltransferase reaction during translation; 50S ribosomal protein L27 1518642 rpmA 5712639 rpmA Dinoroseobacter shibae DFL 12 = DSM 16493 50S ribosomal protein L27 YP_001532804.1 1518373 D 398580 CDS YP_001532805.1 159044011 5712640 1518721..1519377 1 NC_009952.1 LysE family transport protein 1519377 5712640 Dshi_1462 Dinoroseobacter shibae DFL 12 = DSM 16493 LysE family transport protein YP_001532805.1 1518721 D 398580 CDS YP_001532806.1 159044012 5712641 1519374..1519913 1 NC_009952.1 N-acetyltransferase GCN5 1519913 5712641 Dshi_1463 Dinoroseobacter shibae DFL 12 = DSM 16493 N-acetyltransferase GCN5 YP_001532806.1 1519374 D 398580 CDS YP_001532807.1 159044013 5712642 1519918..1520427 1 NC_009952.1 N-acetyltransferase GCN5 1520427 5712642 Dshi_1464 Dinoroseobacter shibae DFL 12 = DSM 16493 N-acetyltransferase GCN5 YP_001532807.1 1519918 D 398580 CDS YP_001532808.1 159044014 5712643 1520424..1520951 1 NC_009952.1 N-acetyltransferase GCN5 1520951 5712643 Dshi_1465 Dinoroseobacter shibae DFL 12 = DSM 16493 N-acetyltransferase GCN5 YP_001532808.1 1520424 D 398580 CDS YP_001532809.1 159044015 5712644 1520948..1521985 1 NC_009952.1 essential GTPase; exhibits high exchange rate for GTP/GDP; associates with 50S ribosomal subunit; involved in regulation of chromosomal replication; GTPase ObgE 1521985 obgE 5712644 obgE Dinoroseobacter shibae DFL 12 = DSM 16493 GTPase ObgE YP_001532809.1 1520948 D 398580 CDS YP_001532810.1 159044016 5712645 1521973..1523079 1 NC_009952.1 catalyzes the formation of glutamate 5-phosphate from glutamate in proline biosynthesis; gamma-glutamyl kinase 1523079 proB 5712645 proB Dinoroseobacter shibae DFL 12 = DSM 16493 gamma-glutamyl kinase YP_001532810.1 1521973 D 398580 CDS YP_001532811.1 159044017 5712646 1523177..1523812 1 NC_009952.1 hypothetical protein 1523812 5712646 Dshi_1468 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532811.1 1523177 D 398580 CDS YP_001532812.1 159044018 5712647 1523915..1525180 1 NC_009952.1 Catalyzes the phosphorylation of L-glutamate during the proline biosynthesis pathway; gamma-glutamyl phosphate reductase 1525180 proA 5712647 proA Dinoroseobacter shibae DFL 12 = DSM 16493 gamma-glutamyl phosphate reductase YP_001532812.1 1523915 D 398580 CDS YP_001532813.1 159044019 5712648 complement(1525195..1525809) 1 NC_009952.1 hypothetical protein 1525809 5712648 Dshi_1470 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532813.1 1525195 R 398580 CDS YP_001532814.1 159044020 5712649 1525839..1526024 1 NC_009952.1 hypothetical protein 1526024 5712649 Dshi_1471 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532814.1 1525839 D 398580 CDS YP_001532815.1 159044021 5712650 1526145..1526921 1 NC_009952.1 similar to ornithine acyl[acyl carrier protein] N-acyltransferase in S. pomeroyi; phospholipid/glycerol acyltransferase 1526921 5712650 Dshi_1472 Dinoroseobacter shibae DFL 12 = DSM 16493 phospholipid/glycerol acyltransferase YP_001532815.1 1526145 D 398580 CDS YP_001532816.1 159044022 5712651 1526918..1527763 1 NC_009952.1 Glycerophospholipid metabolism; phospholipid/glycerol acyltransferase 1527763 5712651 Dshi_1473 Dinoroseobacter shibae DFL 12 = DSM 16493 phospholipid/glycerol acyltransferase YP_001532816.1 1526918 D 398580 CDS YP_001532817.1 159044023 5712652 complement(1527727..1528590) 1 NC_009952.1 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 1528590 5712652 Dshi_1474 Dinoroseobacter shibae DFL 12 = DSM 16493 glutamyl-tRNA synthetase YP_001532817.1 1527727 R 398580 CDS YP_001532818.1 159044024 5712653 complement(1528630..1529985) 1 NC_009952.1 TrmFO; Gid; glucose-inhibited division protein; similar to GidA; the gene from Bacillus subtilis encodes a tRNA-methyltransferase that utilizes folate as the carbon donor and bound flavin as reductant; modifies tRNA at position 54 (uridine) of the T-psi loop to form a C5-methyluridine; tRNA (uracil-5-)-methyltransferase Gid 1529985 gid 5712653 gid Dinoroseobacter shibae DFL 12 = DSM 16493 tRNA (uracil-5-)-methyltransferase Gid YP_001532818.1 1528630 R 398580 CDS YP_001532819.1 159044025 5712654 complement(1530153..1532894) 1 NC_009952.1 negatively supercoils closed circular double-stranded DNA; DNA gyrase subunit A 1532894 gyrA 5712654 gyrA Dinoroseobacter shibae DFL 12 = DSM 16493 DNA gyrase subunit A YP_001532819.1 1530153 R 398580 CDS YP_001532820.1 159044026 5712655 1533086..1533355 1 NC_009952.1 not in the trp operon, Usg is normally found in trpF, trpB, and trpA context; Usg family protein 1533355 5712655 Dshi_1477 Dinoroseobacter shibae DFL 12 = DSM 16493 Usg family protein YP_001532820.1 1533086 D 398580 CDS YP_001532821.1 159044027 5712656 complement(1533483..1533950) 1 NC_009952.1 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 1533950 5712656 Dshi_1478 Dinoroseobacter shibae DFL 12 = DSM 16493 disulfide bond formation protein DsbB YP_001532821.1 1533483 R 398580 CDS YP_001532822.1 159044028 5712657 complement(1534029..1534640) 1 NC_009952.1 the exo genes are involved in exopolysaccharide biosynthesis, exoD of Rhizobium meliloti encodes a function needed for alfalfa nodule invasion; exopolysaccharide synthesis ExoD 1534640 5712657 Dshi_1479 Dinoroseobacter shibae DFL 12 = DSM 16493 exopolysaccharide synthesis ExoD YP_001532822.1 1534029 R 398580 CDS YP_001532823.1 159044029 5712658 1535034..1536077 1 NC_009952.1 TRAP gene cluster - dctPQM; TRAP dicarboxylate transporter subunit DctP 1536077 5712658 Dshi_1480 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP dicarboxylate transporter subunit DctP YP_001532823.1 1535034 D 398580 CDS YP_001532824.1 159044030 5712659 1536263..1536844 1 NC_009952.1 TRAP gene cluster - dctPQM; hypothetical protein 1536844 5712659 Dshi_1481 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532824.1 1536263 D 398580 CDS YP_001532825.1 159044031 5712660 1536841..1538193 1 NC_009952.1 TRAP gene cluster - dctPQM; DctM subunit; TRAP dicarboxylate transporter 1538193 5712660 Dshi_1482 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP dicarboxylate transporter YP_001532825.1 1536841 D 398580 CDS YP_001532826.1 159044032 5712662 complement(1538375..1538743) 1 NC_009952.1 hypothetical protein 1538743 5712662 Dshi_1483 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532826.1 1538375 R 398580 CDS YP_001532827.1 159044033 5712663 complement(1538907..1539512) 1 NC_009952.1 hypothetical protein 1539512 5712663 Dshi_1484 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532827.1 1538907 R 398580 CDS YP_001532828.1 159044034 5712664 complement(1539700..1542114) 1 NC_009952.1 DOMAINS: FAD dependent oxidoreductase, Glycine cleavage T-protein, involved in amine and polyamine degradation; FAD dependent oxidoreductase 1542114 5712664 Dshi_1485 Dinoroseobacter shibae DFL 12 = DSM 16493 FAD dependent oxidoreductase YP_001532828.1 1539700 R 398580 CDS YP_001532829.1 159044035 5712665 complement(1542296..1544161) 1 NC_009952.1 Betaine / Carnitine / Choline Transporter, The BCCT proteins contain 12 transmembrane regions and are energized by proton symport; BCCT transporter 1544161 5712665 Dshi_1486 Dinoroseobacter shibae DFL 12 = DSM 16493 BCCT transporter YP_001532829.1 1542296 R 398580 CDS YP_001532830.1 159044036 5712666 complement(1544432..1546513) 1 NC_009952.1 ABC transporter (importer) gene cluster: 2 fused ATPase/ Oligopeptide/dipeptide transporter, C-terminal region domains; ATPase subunit; oligopeptide/dipeptide ABC transporter 1546513 5712666 Dshi_1487 Dinoroseobacter shibae DFL 12 = DSM 16493 oligopeptide/dipeptide ABC transporter YP_001532830.1 1544432 R 398580 CDS YP_001532831.1 159044037 5712667 complement(1546583..1547743) 1 NC_009952.1 ABC transporter (importer) gene cluster: 2nd membrane spanning domain (MSD); part of a heterotetramer; binding-protein-dependent transport system inner membrane protein 1547743 5712667 Dshi_1488 Dinoroseobacter shibae DFL 12 = DSM 16493 binding-protein-dependent transport system inner membrane protein YP_001532831.1 1546583 R 398580 CDS YP_001532832.1 159044038 5712668 complement(1547754..1548845) 1 NC_009952.1 ABC transporter (importer) gene cluster: 1st membrane spanning domain (MSD); part of a heterotetramer; binding-protein-dependent transport system inner membrane protein 1548845 5712668 Dshi_1489 Dinoroseobacter shibae DFL 12 = DSM 16493 binding-protein-dependent transport system inner membrane protein YP_001532832.1 1547754 R 398580 CDS YP_001532833.1 159044039 5712669 complement(1548941..1550608) 1 NC_009952.1 ABC transporter (importer) gene cluster: receptor; family 5 extracellular solute-binding protein 1550608 5712669 Dshi_1490 Dinoroseobacter shibae DFL 12 = DSM 16493 family 5 extracellular solute-binding protein YP_001532833.1 1548941 R 398580 CDS YP_001532834.1 159044040 5712670 complement(1550866..1551678) 1 NC_009952.1 only 1 DNA-binding domain, no substrate binding domain; AraC family; transcriptional regulator 1551678 5712670 Dshi_1491 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001532834.1 1550866 R 398580 CDS YP_001532835.1 159044041 5712671 complement(1551737..1552627) 1 NC_009952.1 IPP transferase; isopentenyltransferase; involved in tRNA modification; in Escherichia coli this enzyme catalyzes the addition of a delta2-isopentenyl group from dimethylallyl diphosphate to the N6-nitrogen of adenosine adjacent to the anticodon of tRNA species that read codons starting with uracil; further tRNA modifications may occur; mutations in miaA result in defects in translation efficiency and fidelity; tRNA delta(2)-isopentenylpyrophosphate transferase 1552627 miaA 5712671 miaA Dinoroseobacter shibae DFL 12 = DSM 16493 tRNA delta(2)-isopentenylpyrophosphate transferase YP_001532835.1 1551737 R 398580 CDS YP_001532836.1 159044042 5712672 1552737..1553468 1 NC_009952.1 Catalyzes the phosphorylation of UMP to UDP; uridylate kinase 1553468 pyrH 5712672 pyrH Dinoroseobacter shibae DFL 12 = DSM 16493 uridylate kinase YP_001532836.1 1552737 D 398580 CDS YP_001532837.1 159044043 5712673 1553599..1554165 1 NC_009952.1 Rrf; Frr; ribosome-recycling factor; release factor 4; RF4; recycles ribosomes upon translation termination along with release factor RF-3 and elongation factor EF-G; A GTPase-dependent process results in release of 50S from 70S; inhibited by release factor RF-1; essential for viability; structurally similar to tRNAs; ribosome recycling factor 1554165 frr 5712673 frr Dinoroseobacter shibae DFL 12 = DSM 16493 ribosome recycling factor YP_001532837.1 1553599 D 398580 CDS YP_001532838.1 159044044 5712674 1554231..1554962 1 NC_009952.1 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 1554962 uppS 5712674 uppS Dinoroseobacter shibae DFL 12 = DSM 16493 undecaprenyl diphosphate synthase YP_001532838.1 1554231 D 398580 CDS YP_001532839.1 159044045 5712675 1554983..1555774 1 NC_009952.1 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 1555774 cdsA1 5712675 cdsA1 Dinoroseobacter shibae DFL 12 = DSM 16493 phosphatidate cytidylyltransferase YP_001532839.1 1554983 D 398580 CDS YP_001532840.1 159044046 5712676 1555798..1556979 1 NC_009952.1 catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate; 1-deoxy-D-xylulose 5-phosphate reductoisomerase 1556979 dxr 5712676 dxr Dinoroseobacter shibae DFL 12 = DSM 16493 1-deoxy-D-xylulose 5-phosphate reductoisomerase YP_001532840.1 1555798 D 398580 CDS YP_001532841.1 159044047 5712677 1557041..1558378 1 NC_009952.1 Zinc-Metalloprotease; Degrades both heat shock sigma factors rpoE and rpoH.; putative membrane-associated zinc metalloprotease 1558378 ecfE 5712677 ecfE Dinoroseobacter shibae DFL 12 = DSM 16493 putative membrane-associated zinc metalloprotease YP_001532841.1 1557041 D 398580 CDS YP_001532842.1 159044048 5712678 1558817..1561063 1 NC_009952.1 involved in the assembly of proteins into the outer membrane of Gram-negative bacteria; hypothetical protein 1561063 yaeT 5712678 yaeT Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532842.1 1558817 D 398580 CDS YP_001532843.1 159044049 5712679 1561065..1561640 1 NC_009952.1 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 1561640 5712679 Dshi_1500 Dinoroseobacter shibae DFL 12 = DSM 16493 outer membrane chaperone Skp YP_001532843.1 1561065 D 398580 CDS YP_001532844.1 159044050 5712680 1561725..1562216 1 NC_009952.1 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 1562216 fabZ 5712680 fabZ Dinoroseobacter shibae DFL 12 = DSM 16493 (3R)-hydroxymyristoyl-ACP dehydratase YP_001532844.1 1561725 D 398580 CDS YP_001532845.1 159044051 5712681 1562213..1563013 1 NC_009952.1 catalyzes the addition of (R)-3-hydroxytetradecanoyl to the glucosamine disaccharide in lipid A biosynthesis; UDP-N-acetylglucosamine acyltransferase 1563013 lpxA 5712681 lpxA Dinoroseobacter shibae DFL 12 = DSM 16493 UDP-N-acetylglucosamine acyltransferase YP_001532845.1 1562213 D 398580 CDS YP_001532846.1 159044052 5712682 1563017..1563814 1 NC_009952.1 COG: COG3494 - Uncharacterized protein conserved in bacteria, PFAM: pfam06230 Protein of unknown function (DUF1009); hypothetical protein 1563814 5712682 Dshi_1503 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532846.1 1563017 D 398580 CDS YP_001532847.1 159044053 5712683 1563814..1564956 1 NC_009952.1 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 1564956 lpxB 5712683 lpxB Dinoroseobacter shibae DFL 12 = DSM 16493 lipid-A-disaccharide synthase YP_001532847.1 1563814 D 398580 CDS YP_001532848.1 159044054 5712684 complement(1564953..1566149) 1 NC_009952.1 SUPERFAMILY: SSF51294; hypothetical protein 1566149 5712684 Dshi_1505 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532848.1 1564953 R 398580 CDS YP_001532849.1 159044055 5712685 complement(1566319..1567473) 1 NC_009952.1 catalyzes a sulfuration reaction to synthesize 2-thiouridine at the U34 position of tRNAs; tRNA-specific 2-thiouridylase MnmA 1567473 mnmA 5712685 mnmA Dinoroseobacter shibae DFL 12 = DSM 16493 tRNA-specific 2-thiouridylase MnmA YP_001532849.1 1566319 R 398580 CDS YP_001532850.1 159044056 5712686 1567599..1567877 1 NC_009952.1 PFAM: PF06627; related to DUF1153; hypothetical protein 1567877 5712686 Dshi_1507 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532850.1 1567599 D 398580 CDS YP_001532851.1 159044057 5712687 1567977..1568690 1 NC_009952.1 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 1568690 ctrA 5712687 ctrA Dinoroseobacter shibae DFL 12 = DSM 16493 cell cycle transcriptional regulator ctrA YP_001532851.1 1567977 D 398580 CDS YP_001532852.1 159044058 5712688 1568730..1570955 1 NC_009952.1 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 1570955 ligA 5712688 ligA Dinoroseobacter shibae DFL 12 = DSM 16493 DNA ligase YP_001532852.1 1568730 D 398580 CDS YP_001532853.1 159044059 5712689 1570952..1573042 1 NC_009952.1 catalyzes branch migration in Holliday junction intermediates; ATP-dependent DNA helicase RecG 1573042 recG 5712689 recG Dinoroseobacter shibae DFL 12 = DSM 16493 ATP-dependent DNA helicase RecG YP_001532853.1 1570952 D 398580 CDS YP_001532854.1 159044060 5712690 complement(1573442..1574914) 1 NC_009952.1 SWISSPROT P42663: Thermostable carboxypeptidase 1; PFAM: pfam02074; COG: COG2317 - Zn-dependent carboxypeptidase; carboxypeptidase Taq 1574914 5712690 Dshi_1511 Dinoroseobacter shibae DFL 12 = DSM 16493 carboxypeptidase Taq YP_001532854.1 1573442 R 398580 CDS YP_001532855.1 159044061 5713169 complement(1574911..1576062) 1 NC_009952.1 PFAM: pfam02628; COG: COG1612 - Uncharacterized protein required for cytochrome oxidase assembly; putative cytochrome oxidase assembly protein 1576062 5713169 Dshi_1512 Dinoroseobacter shibae DFL 12 = DSM 16493 putative cytochrome oxidase assembly protein YP_001532855.1 1574911 R 398580 CDS YP_001532856.1 159044062 5713170 complement(1576115..1576882) 1 NC_009952.1 PFAM: pfam00588; COG: COG0565 - rRNA methylase; TIGRFAM: TIGR00050 rRNA methylase, putative, group 1; SpoU family; putative tRNA/rRNA methyltransferase 1576882 5713170 Dshi_1513 Dinoroseobacter shibae DFL 12 = DSM 16493 putative tRNA/rRNA methyltransferase YP_001532856.1 1576115 R 398580 CDS YP_001532857.1 159044063 5713171 1576962..1577585 1 NC_009952.1 PFAM: pfam02581; COG: COG0352 Thiamine monophosphate synthase; TIGRFAM: TIGR00693 thiamine-phosphate pyrophosphorylase; putative thiamine monophosphate synthase 1577585 5713171 Dshi_1514 Dinoroseobacter shibae DFL 12 = DSM 16493 putative thiamine monophosphate synthase YP_001532857.1 1576962 D 398580 CDS YP_001532858.1 159044064 5713172 complement(1577589..1577948) 1 NC_009952.1 SWISSPROT Q53158: Phosphoribosyl-AMP cyclohydrolase; PFAM: pfam01502, COG: COG0139 - Phosphoribosyl-AMP cyclohydrolase; phosphoribosyl-AMP cyclohydrolase 1577948 hisI 5713172 hisI Dinoroseobacter shibae DFL 12 = DSM 16493 phosphoribosyl-AMP cyclohydrolase YP_001532858.1 1577589 R 398580 CDS YP_001532859.1 159044065 5713173 1578009..1578458 1 NC_009952.1 PFAM: PF01592, COG: COG0822 - NifU homolog involved in Fe-S cluster formation.; related to NIFU; hypothetical protein 1578458 5713173 Dshi_1516 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532859.1 1578009 D 398580 CDS YP_001532860.1 159044066 5713174 complement(1578568..1579872) 1 NC_009952.1 PFAM: pfam02653, COG: COG4177- ABC-type branched-chain amino acid transport system / permease component; related to amino acid / sugar transport system; hypothetical protein 1579872 5713174 Dshi_1517 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532860.1 1578568 R 398580 CDS YP_001532861.1 159044067 5713175 complement(1579869..1580879) 1 NC_009952.1 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 1580879 5713175 Dshi_1518 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532861.1 1579869 R 398580 CDS YP_001532862.1 159044068 5713176 complement(1580879..1581238) 1 NC_009952.1 associated with ABC-transport system cluster; hypothetical protein 1581238 5713176 Dshi_1519 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532862.1 1580879 R 398580 CDS YP_001532863.1 159044069 5713177 complement(1581242..1582075) 1 NC_009952.1 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 1582075 livF2 5713177 livF2 Dinoroseobacter shibae DFL 12 = DSM 16493 high-affinity branched-chain amino acid transport ATP-binding protein YP_001532863.1 1581242 R 398580 CDS YP_001532864.1 159044070 5713178 complement(1582072..1582854) 1 NC_009952.1 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 1582854 5713178 Dshi_1521 Dinoroseobacter shibae DFL 12 = DSM 16493 putative high-affinity branched-chain amino acid transport ATP-binding protein YP_001532864.1 1582072 R 398580 CDS YP_001532865.1 159044071 5713179 complement(1582914..1584101) 1 NC_009952.1 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 1584101 5713179 Dshi_1522 Dinoroseobacter shibae DFL 12 = DSM 16493 putative periplasmic ligand-binding protein YP_001532865.1 1582914 R 398580 CDS YP_001532866.1 159044072 5713180 1584337..1585446 1 NC_009952.1 COG: COG2133, PFAM (GSDH): pfam07995, Gene3D: G3DSA:2.120.10.30, SUPERFAMILY: SSF50952, SWISSPROT P75804: Soluble aldose sugar dehydrogenase yliI [Precursor]; aldose sugar dehydrogenase 1585446 yliI 5713180 yliI Dinoroseobacter shibae DFL 12 = DSM 16493 aldose sugar dehydrogenase YP_001532866.1 1584337 D 398580 CDS YP_001532867.1 159044073 5713181 complement(1585464..1586033) 1 NC_009952.1 hypothetical protein 1586033 5713181 Dshi_1524 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532867.1 1585464 R 398580 CDS YP_001532868.1 159044074 5713182 complement(1586124..1587143) 1 NC_009952.1 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 1587143 5713182 Dshi_1525 Dinoroseobacter shibae DFL 12 = DSM 16493 HTH-type transcriptional regulator YP_001532868.1 1586124 R 398580 CDS YP_001532869.1 159044075 5713183 1587318..1588694 1 NC_009952.1 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 1588694 aroH 5713183 aroH Dinoroseobacter shibae DFL 12 = DSM 16493 phospho-2-dehydro-3-deoxyheptonate aldolase YP_001532869.1 1587318 D 398580 CDS YP_001532870.1 159044076 5713184 complement(1588773..1589510) 1 NC_009952.1 pfam07310, COG5388; hypothetical protein 1589510 5713184 Dshi_1527 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532870.1 1588773 R 398580 CDS YP_001532871.1 159044077 5713185 1589674..1590558 1 NC_009952.1 PFAM: pfam03755, pfam08340; COG: COG1561 Uncharacterized stress-induced protein; TIGRFAM: TIGR00255 conserved hypothetical protein; similar to YicC-like; hypothetical protein 1590558 5713185 Dshi_1528 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532871.1 1589674 D 398580 CDS YP_001532872.1 159044078 5713186 1590625..1591278 1 NC_009952.1 Essential for recycling GMP and indirectly, cGMP; guanylate kinase 1591278 gmk 5713186 gmk Dinoroseobacter shibae DFL 12 = DSM 16493 guanylate kinase YP_001532872.1 1590625 D 398580 CDS YP_001532873.1 159044079 5713187 1591275..1591799 1 NC_009952.1 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 1591799 5713187 Dshi_1530 Dinoroseobacter shibae DFL 12 = DSM 16493 gamma-class carbonic anhydrase family protein YP_001532873.1 1591275 D 398580 CDS YP_001532874.1 159044080 5713188 complement(1591903..1592376) 1 NC_009952.1 hypothetical protein 1592376 5713188 Dshi_1531 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532874.1 1591903 R 398580 CDS YP_001532875.1 159044081 5713189 1592488..1593549 1 NC_009952.1 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 1593549 phoR 5713189 phoR Dinoroseobacter shibae DFL 12 = DSM 16493 histidine kinase YP_001532875.1 1592488 D 398580 CDS YP_001532876.1 159044082 5713190 1593702..1594727 1 NC_009952.1 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 1594727 5713190 Dshi_1533 Dinoroseobacter shibae DFL 12 = DSM 16493 periplasmic-binding protein YP_001532876.1 1593702 D 398580 CDS YP_001532877.1 159044083 5713191 1594799..1596268 1 NC_009952.1 SWISSPROT: P0AGH8 Phosphate transport system permease protein pstC, TIGRFAM: TIGR02138, PFAM: PF00528, COG: COG0573, PROSITE: PS50928; phosphate ABC transporter permease 1596268 pstC 5713191 pstC Dinoroseobacter shibae DFL 12 = DSM 16493 phosphate ABC transporter permease YP_001532877.1 1594799 D 398580 CDS YP_001532878.1 159044084 5713192 1596265..1597617 1 NC_009952.1 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 1597617 pstA 5713192 pstA Dinoroseobacter shibae DFL 12 = DSM 16493 phosphate ABC transporter permease YP_001532878.1 1596265 D 398580 CDS YP_001532879.1 159044085 5713193 1597634..1598428 1 NC_009952.1 ATP-binding protein; PstABCS is an ATP dependent phosphate uptake system which is responsible for inorganic phosphate uptake during phosphate starvation; phosphate transporter ATP-binding protein 1598428 pstB 5713193 pstB Dinoroseobacter shibae DFL 12 = DSM 16493 phosphate transporter ATP-binding protein YP_001532879.1 1597634 D 398580 CDS YP_001532880.1 159044086 5713194 1598428..1599141 1 NC_009952.1 SWISSPROT: P0A9K7, TIGRFAM: TIGR02135, PFAM: pfam01895; phosphate transport system protein 1599141 phoU 5713194 phoU Dinoroseobacter shibae DFL 12 = DSM 16493 phosphate transport system protein YP_001532880.1 1598428 D 398580 CDS YP_001532881.1 159044087 5713195 1599146..1599832 1 NC_009952.1 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 1599832 phoB 5713195 phoB Dinoroseobacter shibae DFL 12 = DSM 16493 phosphate regulon transcriptional regulatory protein YP_001532881.1 1599146 D 398580 CDS YP_001532882.1 159044088 5713196 1599990..1600946 1 NC_009952.1 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 1600946 5713196 Dshi_1539 Dinoroseobacter shibae DFL 12 = DSM 16493 inner membrane protein YP_001532882.1 1599990 D 398580 CDS YP_001532883.1 159044089 5713197 1601019..1602053 1 NC_009952.1 COG: COG0265, SUPERFAMILY: SSF50494, PFAM: PF00595, PF00089; peptidase S1B family; precursor; protease 1602053 5713197 Dshi_1540 Dinoroseobacter shibae DFL 12 = DSM 16493 protease YP_001532883.1 1601019 D 398580 CDS YP_001532884.1 159044090 5713198 1602173..1604119 1 NC_009952.1 PFAM: PF07969, SUPERFAMILY: SSF51556; COG: COG1574 - Predicted metal-dependent hydrolase with the TIM-barrel fold; putative amidohydrolase 3 1604119 5713198 Dshi_1541 Dinoroseobacter shibae DFL 12 = DSM 16493 putative amidohydrolase 3 YP_001532884.1 1602173 D 398580 CDS YP_001532885.1 159044091 5713199 1604184..1604711 1 NC_009952.1 hypothetical protein 1604711 5713199 Dshi_1542 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532885.1 1604184 D 398580 CDS YP_001532886.1 159044092 5713200 complement(1604724..1605764) 1 NC_009952.1 PFAM: PF01734, SUPERFAMILY: SSF52151; COG: COG1752 Predicted esterase of the alpha-beta hydrolase superfamily; similar to Patatin-like phospholipase; hypothetical protein 1605764 5713200 Dshi_1543 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532886.1 1604724 R 398580 CDS YP_001532887.1 159044093 5713201 complement(1605788..1606561) 1 NC_009952.1 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 1606561 5713201 Dshi_1544 Dinoroseobacter shibae DFL 12 = DSM 16493 short-chain dehydrogenase/reductase family protein YP_001532887.1 1605788 R 398580 CDS YP_001532888.1 159044094 5713202 1606867..1608687 1 NC_009952.1 COG: COG4166 - ABC-type oligopeptide transport system, periplasmic component; PFAM: PF00496; putative extracellular solute-binding protein 1608687 5713202 Dshi_1545 Dinoroseobacter shibae DFL 12 = DSM 16493 putative extracellular solute-binding protein YP_001532888.1 1606867 D 398580 CDS YP_001532889.1 159044095 5713203 complement(1608891..1609703) 1 NC_009952.1 PFAM: PF04367; COG: COG2928 - Uncharacterized conserved protein; hypothetical protein 1609703 5713203 Dshi_1546 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532889.1 1608891 R 398580 CDS YP_001532890.1 159044096 5712691 complement(1609759..1610724) 1 NC_009952.1 SUPERFAMILY: SSF53613 Ribokinase-like; COG: COG0524, Sugar kinase, ribokinase family; PFAM: PF00294; ribokinase family; putative carbohydrate kinase 1610724 5712691 Dshi_1547 Dinoroseobacter shibae DFL 12 = DSM 16493 putative carbohydrate kinase YP_001532890.1 1609759 R 398580 CDS YP_001532891.1 159044097 5712692 1611039..1611818 1 NC_009952.1 one of the last subunits in the assembly of the 30S subunit; absence of S2 does not inhibit assembly but results in an inactive subunit; 30S ribosomal protein S2 1611818 rpsB 5712692 rpsB Dinoroseobacter shibae DFL 12 = DSM 16493 30S ribosomal protein S2 YP_001532891.1 1611039 D 398580 CDS YP_001532892.1 159044098 5712693 1611914..1612789 1 NC_009952.1 EF-Ts; functions during elongation stage of protein translation; forms a dimer; associates with EF-Tu-GDP complex and promotes exchange of GDP to GTP resulting in regeneration of the active form of EF-Tu; elongation factor Ts 1612789 tsf 5712693 tsf Dinoroseobacter shibae DFL 12 = DSM 16493 elongation factor Ts YP_001532892.1 1611914 D 398580 CDS YP_001532893.1 159044099 5712694 complement(1613091..1613873) 1 NC_009952.1 PFAM: PF00196, PF03472; PROSITE: PS50043; SUPERFAMILY: SSF75516, SSF46894; COG: COG2197; luxR family; putative regulatory protein 1613873 5712694 Dshi_1550 Dinoroseobacter shibae DFL 12 = DSM 16493 putative regulatory protein YP_001532893.1 1613091 R 398580 CDS YP_001532894.1 159044100 5712695 complement(1613870..1614322) 1 NC_009952.1 catalyzes the formation of 3-dehydroshikimate from 3-dehydroquinate in chorismate biosynthesis; 3-dehydroquinate dehydratase 1614322 5712695 Dshi_1551 Dinoroseobacter shibae DFL 12 = DSM 16493 3-dehydroquinate dehydratase YP_001532894.1 1613870 R 398580 CDS YP_001532895.1 159044101 5712696 1614497..1615753 1 NC_009952.1 SWISSPROT: P44093, PFAM: PF07005; similar to uncharacterized protein HI1011; hypothetical protein 1615753 5712696 Dshi_1552 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532895.1 1614497 D 398580 CDS YP_001532896.1 159044102 5712697 1615750..1616400 1 NC_009952.1 SUPERFAMILY: SSF53639; PFAM: PF00596; COG: COG0235, Ribulose-5-phosphate 4-epimerase and related epimerases and aldolases; putative aldolase 1616400 5712697 Dshi_1553 Dinoroseobacter shibae DFL 12 = DSM 16493 putative aldolase YP_001532896.1 1615750 D 398580 CDS YP_001532897.1 159044103 5712698 1616397..1617161 1 NC_009952.1 PFAM: PF01261, Gene3D: G3DSA:3.20.20.150, SUPERFAMILY: SSF51658, SWISSPROT: Q6NUD4, P30147; COG: COG3622; putative isomerase 1617161 5712698 Dshi_1554 Dinoroseobacter shibae DFL 12 = DSM 16493 putative isomerase YP_001532897.1 1616397 D 398580 CDS YP_001532898.1 159044104 5712699 complement(1617231..1617857) 1 NC_009952.1 PFAM: PF01381, PF07883; SUPERFAMILY: SSF51182; Gene3D: G3DSA:1.10.260.40; HTH type; putative transcriptional regulator 1617857 5712699 Dshi_1555 Dinoroseobacter shibae DFL 12 = DSM 16493 putative transcriptional regulator YP_001532898.1 1617231 R 398580 CDS YP_001532899.1 159044105 5712700 1617876..1619435 1 NC_009952.1 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 1619435 5712700 Dshi_1556 Dinoroseobacter shibae DFL 12 = DSM 16493 putative ATP-dependent AMP-binding enzyme YP_001532899.1 1617876 D 398580 CDS YP_001532900.1 159044106 5712701 1619422..1620090 1 NC_009952.1 PFAM: PF01323, SUPERFAMILY: SSF52833, COG: COG2761, Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis; putative DSBA oxidoreductase 1620090 5712701 Dshi_1557 Dinoroseobacter shibae DFL 12 = DSM 16493 putative DSBA oxidoreductase YP_001532900.1 1619422 D 398580 CDS YP_001532901.1 159044107 5712702 complement(1620057..1620377) 1 NC_009952.1 hypothetical protein 1620377 5712702 Dshi_1558 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532901.1 1620057 R 398580 CDS YP_001532902.1 159044108 5712703 1620493..1621701 1 NC_009952.1 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 1621701 5712703 Dshi_1559 Dinoroseobacter shibae DFL 12 = DSM 16493 major facilitator superfamily transporter YP_001532902.1 1620493 D 398580 CDS YP_001532903.1 159044109 5712704 1621839..1622270 1 NC_009952.1 hypothetical protein 1622270 5712704 Dshi_1560 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532903.1 1621839 D 398580 CDS YP_001532904.1 159044110 5712705 complement(1622403..1625885) 1 NC_009952.1 SWISSPROT P30958: Transcription-repair-coupling factor, TIGRFAM: TIGR00580 -Transcription-repair coupling factor; PFAM: PF03461, PF02559, PF00270, PF00271; transcription repair coupling factor 1625885 mfd 5712705 mfd Dinoroseobacter shibae DFL 12 = DSM 16493 transcription repair coupling factor YP_001532904.1 1622403 R 398580 CDS YP_001532905.1 159044111 5712706 complement(1626290..1626820) 1 NC_009952.1 hypothetical protein 1626820 5712706 Dshi_1562 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532905.1 1626290 R 398580 CDS YP_001532906.1 159044112 5712707 1626965..1627966 1 NC_009952.1 catalyzes the formation of porphobilinogen from 5-aminolevulinate; delta-aminolevulinic acid dehydratase 1627966 hemB1 5712707 hemB1 Dinoroseobacter shibae DFL 12 = DSM 16493 delta-aminolevulinic acid dehydratase YP_001532906.1 1626965 D 398580 CDS YP_001532907.1 159044113 5712708 1628155..1628724 1 NC_009952.1 PROSITE: PS51257, PFAM: pfam04366, COG: COG2930 - Uncharacterized conserved protein; hypothetical protein 1628724 5712708 Dshi_1564 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532907.1 1628155 D 398580 CDS YP_001532908.1 159044114 5712709 1628799..1631282 1 NC_009952.1 PFAM: PF01804, COG: COG2366 - Protein related to penicillin acylase; putative penicillin acylase; acylase 1631282 5712709 Dshi_1565 Dinoroseobacter shibae DFL 12 = DSM 16493 acylase YP_001532908.1 1628799 D 398580 CDS YP_001532909.1 159044115 5712710 complement(1631386..1632633) 1 NC_009952.1 SWISSPROT: P25519 - GTP-binding protein hflX, PANTHER: PTHR10229, PFAM: PF01926, SUPERFAMILY: SSF52540, Gene3D: G3DSA:3.40.50.300; GTP-binding protein 1632633 hflX 5712710 hflX Dinoroseobacter shibae DFL 12 = DSM 16493 GTP-binding protein YP_001532909.1 1631386 R 398580 CDS YP_001532910.1 159044116 5712711 complement(1632675..1632953) 1 NC_009952.1 Stimulates the elongation of poly(A) tails; RNA-binding protein Hfq 1632953 hfq 5712711 hfq Dinoroseobacter shibae DFL 12 = DSM 16493 RNA-binding protein Hfq YP_001532910.1 1632675 R 398580 CDS YP_001532911.1 159044117 5712712 complement(1633034..1634542) 1 NC_009952.1 SWISSPROT: Q9L6L2, P23849 - Trk system potassium uptake protein trkH; COG: COG0168 - Trk-type K+ transport systems, membrane components; PFAM: PF02386; potassium uptake protein 1634542 trkH 5712712 trkH Dinoroseobacter shibae DFL 12 = DSM 16493 potassium uptake protein YP_001532911.1 1633034 R 398580 CDS YP_001532912.1 159044118 5712713 complement(1634542..1635918) 1 NC_009952.1 involved in potassium uptake; found to be peripherally associated with the inner membrane in Escherichia coli; contains an NAD-binding domain; potassium transporter peripheral membrane protein 1635918 trkA 5712713 trkA Dinoroseobacter shibae DFL 12 = DSM 16493 potassium transporter peripheral membrane protein YP_001532912.1 1634542 R 398580 CDS YP_001532913.1 159044119 5712714 1636081..1636563 1 NC_009952.1 hypothetical protein 1636563 5712714 Dshi_1570 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532913.1 1636081 D 398580 CDS YP_001532914.1 159044120 5712715 1636586..1637023 1 NC_009952.1 hypothetical protein 1637023 5712715 Dshi_1571 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532914.1 1636586 D 398580 CDS YP_001532915.1 159044121 5712716 complement(1637185..1638600) 1 NC_009952.1 SWISSPROT: P03029 - Nitrogen assimilation regulatory protein ntrX; PFAM: PF00072, PF00158, PF02954; SUPERFAMILY: SSF52172, SSF52540; COG: COG2204; sigma factor 54; nitrogen assimilation regulator receiver protein 1638600 ntrX 5712716 ntrX Dinoroseobacter shibae DFL 12 = DSM 16493 nitrogen assimilation regulator receiver protein YP_001532915.1 1637185 R 398580 CDS YP_001532916.1 159044122 5712717 complement(1638597..1640900) 1 NC_009952.1 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 1640900 ntrY 5712717 ntrY Dinoroseobacter shibae DFL 12 = DSM 16493 histidine kinase YP_001532916.1 1638597 R 398580 CDS YP_001532917.1 159044123 5712718 complement(1640962..1642326) 1 NC_009952.1 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 1642326 ntrC 5712718 ntrC Dinoroseobacter shibae DFL 12 = DSM 16493 nitrogen assimilation regulator receiver protein YP_001532917.1 1640962 R 398580 CDS YP_001532918.1 159044124 5712719 complement(1642326..1643399) 1 NC_009952.1 SWISSPROT P09431, P0AFB5: Nitrogen regulation protein ntrB; COG: COG3852 - Signal transduction histidine kinase, nitrogen specific; PFAM: PF00512, PF02518; SMART: SM00091; nitrogen regulation protein 1643399 ntrB 5712719 ntrB Dinoroseobacter shibae DFL 12 = DSM 16493 nitrogen regulation protein YP_001532918.1 1642326 R 398580 CDS YP_001532919.1 159044125 5712720 complement(1643396..1644397) 1 NC_009952.1 TIGRFAM: Dihydrouridine synthase TIM-barrel, NifR3; COG: COG0042 - tRNA-dihydrouridine synthase, PFAM: pfam01207; alternative gene name: nifR; tRNA-dihydrouidine synthase 1644397 dus 5712720 dus Dinoroseobacter shibae DFL 12 = DSM 16493 tRNA-dihydrouidine synthase YP_001532919.1 1643396 R 398580 CDS YP_001532920.1 159044126 5712721 1644540..1645742 1 NC_009952.1 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 1645742 ispDF 5712721 ispDF Dinoroseobacter shibae DFL 12 = DSM 16493 bifunctional 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase/2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase YP_001532920.1 1644540 D 398580 CDS YP_001532921.1 159044127 5712722 1645739..1646227 1 NC_009952.1 SWISSPROT: P18200; COG: COG1267 - Phosphatidylglycerophosphatase A and related proteins; PFAM: PF04608; putative phosphatidylglycerophosphatase A 1646227 5712722 Dshi_1578 Dinoroseobacter shibae DFL 12 = DSM 16493 putative phosphatidylglycerophosphatase A YP_001532921.1 1645739 D 398580 CDS YP_001532922.1 159044128 5712723 1646224..1646706 1 NC_009952.1 TIGRFAM: TIGR00199 competence/damage-inducible protein CinA C-terminal domain; COG: COG1546 - Uncharacterized protein (competence- and mitomycin-induced); PFAM: pfam02464; CinA-like protein 1646706 5712723 Dshi_1579 Dinoroseobacter shibae DFL 12 = DSM 16493 CinA-like protein YP_001532922.1 1646224 D 398580 CDS YP_001532923.1 159044129 5712724 complement(1646685..1647200) 1 NC_009952.1 COG: COG2867-Oligoketide cyclase/lipid transport protein; PFAM: PF03364; putative polyketide cyclase / dehydrase 1647200 5712724 Dshi_1580 Dinoroseobacter shibae DFL 12 = DSM 16493 putative polyketide cyclase / dehydrase YP_001532923.1 1646685 R 398580 CDS YP_001532924.1 159044130 5712725 1647224..1647760 1 NC_009952.1 SWISSPROT P0A9M2: Hypoxanthine phosphoribosyltransferase, also high similarity to hypoxanthine-guanine phosphoribosyltransferase (SWISSPROT P37171); COG: COG0634 Hypoxanthine-guanine phosphoribosyltransferase; PFAM: PF00156; hypoxanthine phosphoribosyltransferase 1647760 hpt 5712725 hpt Dinoroseobacter shibae DFL 12 = DSM 16493 hypoxanthine phosphoribosyltransferase YP_001532924.1 1647224 D 398580 CDS YP_001532925.1 159044131 5712726 complement(1647958..1648476) 1 NC_009952.1 similar to transmembrane transport protein; hypothetical protein 1648476 5712726 Dshi_1582 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532925.1 1647958 R 398580 CDS YP_001532926.1 159044132 5712727 complement(1648653..1649603) 1 NC_009952.1 catalyzes the radical-mediated insertion of two sulfur atoms into an acyl carrier protein (ACP) bound to an octanoyl group to produce a lipoyl group; lipoyl synthase 1649603 lipA 5712727 lipA Dinoroseobacter shibae DFL 12 = DSM 16493 lipoyl synthase YP_001532926.1 1648653 R 398580 CDS YP_001532927.1 159044133 5712728 complement(1649803..1650927) 1 NC_009952.1 hypothetical protein 1650927 5712728 Dshi_1584 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532927.1 1649803 R 398580 CDS YP_001532928.1 159044134 5712729 1651121..1651423 1 NC_009952.1 hypothetical protein 1651423 5712729 Dshi_1585 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532928.1 1651121 D 398580 CDS YP_001532929.1 159044135 5712730 complement(1651441..1652988) 1 NC_009952.1 SWISSPROT O93658: Trimethylamine methyltransferase mttB; COG: COG5598 - Trimethylamine:corrinoid methyltransferase; PFAM: pfam06253; trimethylamine methyltransferase 1652988 mttb 5712730 mttb Dinoroseobacter shibae DFL 12 = DSM 16493 trimethylamine methyltransferase YP_001532929.1 1651441 R 398580 CDS YP_001532930.1 159044136 5712731 1653185..1654747 1 NC_009952.1 contains glutamine-hydrolyzing domain and glutamine amidotransferase; GMP-binding domain; functions to produce GMP from XMP in the IMP pathway; GMP synthase 1654747 guaA 5712731 guaA Dinoroseobacter shibae DFL 12 = DSM 16493 GMP synthase YP_001532930.1 1653185 D 398580 CDS YP_001532931.1 159044137 5712732 1654738..1655379 1 NC_009952.1 COG: COG1434-Uncharacterized conserved protein; PFAM: pfam02698- Uncharacterized ACR, COG1434; hypothetical protein 1655379 5712732 Dshi_1588 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532931.1 1654738 D 398580 CDS YP_001532932.1 159044138 5712733 1655376..1656263 1 NC_009952.1 SWISSPROT Q68XV0: S-adenosylmethionine uptake transporter; PFAM: pfam00892; similar to S-adenosylmethionine uptake transporter; hypothetical protein 1656263 5712733 Dshi_1589 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532932.1 1655376 D 398580 CDS YP_001532933.1 159044139 5712734 1656339..1657472 1 NC_009952.1 SUPERFAMILY; SST56935-Porins; PFAM: PF03349-Outer membrane protein transport protein (OMPP1/FadL/TodX); COG: COG2067-Long-chain fatty acid transport protein; porin 1657472 5712734 Dshi_1590 Dinoroseobacter shibae DFL 12 = DSM 16493 porin YP_001532933.1 1656339 D 398580 CDS YP_001532934.1 159044140 5712735 1657563..1658480 1 NC_009952.1 PFAM: PF00892, SUPERFAMILY: SSF103481; similar to Multidrug resistance efflux transporter EmrE; hypothetical protein 1658480 5712735 Dshi_1591 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532934.1 1657563 D 398580 CDS YP_001532935.1 159044141 5712736 1658518..1659390 1 NC_009952.1 SUPERFAMILY: SSF52540; hypothetical protein 1659390 5712736 Dshi_1592 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532935.1 1658518 D 398580 CDS YP_001532936.1 159044142 5712737 1659426..1660343 1 NC_009952.1 catalyzes the formation of O-succinyl-L-homoserine from succinyl-CoA and L-homoserine in methionine biosynthesis; homoserine O-succinyltransferase 1660343 metA 5712737 metA Dinoroseobacter shibae DFL 12 = DSM 16493 homoserine O-succinyltransferase YP_001532936.1 1659426 D 398580 CDS YP_001532937.1 159044143 5712738 1660318..1661280 1 NC_009952.1 COG: COG0596- Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily); PFAM: pfam00561; SPRINTS: PR00111; putative alpha/beta hydrolase 1661280 5712738 Dshi_1594 Dinoroseobacter shibae DFL 12 = DSM 16493 putative alpha/beta hydrolase YP_001532937.1 1660318 D 398580 CDS YP_001532938.1 159044144 5712739 1661362..1662231 1 NC_009952.1 PFAM: PF03976; putative polyphosphate kinase 2 1662231 5712739 Dshi_1595 Dinoroseobacter shibae DFL 12 = DSM 16493 putative polyphosphate kinase 2 YP_001532938.1 1661362 D 398580 CDS YP_001532939.1 159044145 5712740 1662224..1662841 1 NC_009952.1 PFAM: PF00440; COG: COG1309-Transcriptional regulator; similar to HTH-type transcriptional regulator (tetR family); hypothetical protein 1662841 5712740 Dshi_1596 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532939.1 1662224 D 398580 CDS YP_001532940.1 159044146 5712741 complement(1662856..1663923) 1 NC_009952.1 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 1663923 potA1 5712741 potA1 Dinoroseobacter shibae DFL 12 = DSM 16493 spermidine/putrescine import ATP-binding protein YP_001532940.1 1662856 R 398580 CDS YP_001532941.1 159044147 5712742 complement(1663920..1664726) 1 NC_009952.1 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 1664726 5712742 Dshi_1598 Dinoroseobacter shibae DFL 12 = DSM 16493 inner membrane ABC-transporter permease YP_001532941.1 1663920 R 398580 CDS YP_001532942.1 159044148 5712743 complement(1664723..1665604) 1 NC_009952.1 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 1665604 potB 5712743 potB Dinoroseobacter shibae DFL 12 = DSM 16493 spermidine/putrescine transport system permease YP_001532942.1 1664723 R 398580 CDS YP_001532943.1 159044149 5712744 complement(1665720..1666031) 1 NC_009952.1 COG: COG2329-Uncharacterized enzyme involved in biosynthesis of extracellular polysaccharides; PFAM: pfam03992; SUPERFAMILY: SSF54909; monooxygenase 1666031 5712744 Dshi_1600 Dinoroseobacter shibae DFL 12 = DSM 16493 monooxygenase YP_001532943.1 1665720 R 398580 CDS YP_001532944.1 159044150 5712745 complement(1666178..1666672) 1 NC_009952.1 forms a direct contact with the tRNA during translation; 30S ribosomal protein S9 1666672 rpsI 5712745 rpsI Dinoroseobacter shibae DFL 12 = DSM 16493 30S ribosomal protein S9 YP_001532944.1 1666178 R 398580 CDS YP_001532945.1 159044151 5712746 complement(1666677..1667135) 1 NC_009952.1 in Escherichia coli this protein is one of the earliest assembly proteins in the large subunit; 50S ribosomal protein L13 1667135 rplM 5712746 rplM Dinoroseobacter shibae DFL 12 = DSM 16493 50S ribosomal protein L13 YP_001532945.1 1666677 R 398580 CDS YP_001532946.1 159044152 5712747 complement(1667361..1667783) 1 NC_009952.1 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 1667783 5712747 Dshi_1603 Dinoroseobacter shibae DFL 12 = DSM 16493 putative thioesterase superfamily protein YP_001532946.1 1667361 R 398580 CDS YP_001532947.1 159044153 5712748 1667840..1668634 1 NC_009952.1 Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA; enoyl-CoA hydratase 1668634 5712748 Dshi_1604 Dinoroseobacter shibae DFL 12 = DSM 16493 enoyl-CoA hydratase YP_001532947.1 1667840 D 398580 CDS YP_001532948.1 159044154 5712749 complement(1668641..1669249) 1 NC_009952.1 COG: COG0741-Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains); PFAM: PF01464; lytic murein transglycosylase 1669249 5712749 Dshi_1605 Dinoroseobacter shibae DFL 12 = DSM 16493 lytic murein transglycosylase YP_001532948.1 1668641 R 398580 CDS YP_001532949.1 159044155 5712750 1669410..1669916 1 NC_009952.1 TIGRFAM: TIGR00621; COG: COG0629; PFAM: pfam00436; PANTHER: PTHR10302; PROSITE: PS50935; SWISSPROT P0AGE0; single stranded DNA-binding protein 1669916 ssb 5712750 ssb Dinoroseobacter shibae DFL 12 = DSM 16493 single stranded DNA-binding protein YP_001532949.1 1669410 D 398580 CDS YP_001532950.1 159044156 5712751 complement(1669966..1671222) 1 NC_009952.1 hypothetical protein 1671222 5712751 Dshi_1607 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532950.1 1669966 R 398580 CDS YP_001532951.1 159044157 5712752 complement(1671408..1672559) 1 NC_009952.1 catalyzes the formation of 3-dehydroquinate from 3-deoxy-arabino-heptulonate 7-phosphate; functions in aromatic amino acid biosynthesis; 3-dehydroquinate synthase 1672559 aroB 5712752 aroB Dinoroseobacter shibae DFL 12 = DSM 16493 3-dehydroquinate synthase YP_001532951.1 1671408 R 398580 CDS YP_001532952.1 159044158 5712753 complement(1672630..1673187) 1 NC_009952.1 catalyzes the formation of shikimate 3-phosphate from shikimate in aromatic amino acid biosynthesis; shikimate kinase 1673187 aroK 5712753 aroK Dinoroseobacter shibae DFL 12 = DSM 16493 shikimate kinase YP_001532952.1 1672630 R 398580 CDS YP_001532953.1 159044159 5712754 1673376..1674959 1 NC_009952.1 hypothetical protein 1674959 5712754 Dshi_1610 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532953.1 1673376 D 398580 CDS YP_001532954.1 159044160 5712755 1674956..1675882 1 NC_009952.1 SWISSPROT: P0A8P8 Tyrosine recombinase xerD; COG: COG4974 - Site-specific recombinase XerD; PFAM: pfam00589, pfam02899; SUPERFAMILY: SSF47823, SSF56349; tyrosine recombinase 1675882 xerD 5712755 xerD Dinoroseobacter shibae DFL 12 = DSM 16493 tyrosine recombinase YP_001532954.1 1674956 D 398580 CDS YP_001532955.1 159044161 5712756 complement(1675879..1676685) 1 NC_009952.1 COG: COG0622 - Predicted phosphoesterase; SUPERFAMILY: Metallo-dependent phosphatases; Gene3D: [PDB] Hydrolase; putative phosphatase 1676685 5712756 Dshi_1612 Dinoroseobacter shibae DFL 12 = DSM 16493 putative phosphatase YP_001532955.1 1675879 R 398580 CDS YP_001532956.1 159044162 5712757 1676755..1678056 1 NC_009952.1 SWISSPROT P37908: UPF0053 inner membrane protein yfjD; PFAM: pfam01595, pfam03471, pfam00571; PANTHER: PTHR22777; hypothetical protein 1678056 5712757 Dshi_1613 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532956.1 1676755 D 398580 CDS YP_001532957.1 159044163 5712758 complement(1678074..1679633) 1 NC_009952.1 SWISSPROT P39342: Uncharacterized protein yjgR; PFAM: pfam05872; SUPERFAMILY: SSF52540; Gene3D: G3DSA:3.40.50.300; similar to uncharacterized protein yjgR (E.coli); hypothetical protein 1679633 yjgR 5712758 yjgR Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532957.1 1678074 R 398580 CDS YP_001532958.1 159044164 5712759 1680082..1680672 1 NC_009952.1 COG: COG5342 - Invasion protein B, involved in pathogenesis, PFAM: pfam06776; similar to Invasion protein B; hypothetical protein 1680672 5712759 Dshi_1615 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532958.1 1680082 D 398580 CDS YP_001532959.1 159044165 5712760 complement(1680682..1681893) 1 NC_009952.1 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 1681893 5712760 Dshi_1616 Dinoroseobacter shibae DFL 12 = DSM 16493 beta ketoacyl synthase YP_001532959.1 1680682 R 398580 CDS YP_001532960.1 159044166 5712761 complement(1681897..1682166) 1 NC_009952.1 SWISSPROT P0A6A8: Acyl carrier protein; TIGRFAM: TIGR00517; PFAM: PF00550; PROSITE: PS50075, PS00012; phosphopantetheine attachment site; acyl carrier protein 1682166 5712761 Dshi_1617 Dinoroseobacter shibae DFL 12 = DSM 16493 acyl carrier protein YP_001532960.1 1681897 R 398580 CDS YP_001532961.1 159044167 5712762 complement(1682224..1683315) 1 NC_009952.1 COG: COG1044 - UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; TIGRFAM: TIGR01853; PFAM: pfam04613, PF00132; UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase 1683315 lpxD 5712762 lpxD Dinoroseobacter shibae DFL 12 = DSM 16493 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase YP_001532961.1 1682224 R 398580 CDS YP_001532962.1 159044168 5712763 complement(1683367..1684977) 1 NC_009952.1 COG: COG2989 - Uncharacterized protein conserved in bacteria; PFAM: pfam01471; SWISSPROT P22525:Uncharacterized protein ycbB; related to uncharacterized protein ycbB (E.coli); hypothetical protein 1684977 5712763 Dshi_1619 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532962.1 1683367 R 398580 CDS YP_001532963.1 159044169 5712764 1685275..1685844 1 NC_009952.1 COG: COG3108 - Uncharacterized protein conserved in bacteria; PFAM: pfam05951; SWISSPROT P0AB06: Uncharacterized protein ycbK; similar to uncharcaterized protein ycbK; hypothetical protein 1685844 5712764 Dshi_1620 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532963.1 1685275 D 398580 CDS YP_001532964.1 159044170 5712765 complement(1685849..1686799) 1 NC_009952.1 SWISSPROT: 6-phosphofructokinase isozyme 2 (Phosphofructokinase-2) [pfkB]; PROSITE: PS00583; PFAM: PF00294; SUPERFAMILY: SSF53613; putative 6-phosphofructokinase isozyme 2 1686799 5712765 Dshi_1621 Dinoroseobacter shibae DFL 12 = DSM 16493 putative 6-phosphofructokinase isozyme 2 YP_001532964.1 1685849 R 398580 CDS YP_001532965.1 159044171 5712766 complement(1686892..1688406) 1 NC_009952.1 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 1688406 5712766 Dshi_1622 Dinoroseobacter shibae DFL 12 = DSM 16493 putative hemolysin YP_001532965.1 1686892 R 398580 CDS YP_001532966.1 159044172 5712768 complement(1688923..1690143) 1 NC_009952.1 SWISSPROT P77444: Cysteine desulfurase. Synonym: Selenocysteine lyase; TIGRFAM: TIGR01979; COG: COG0520 - Selenocysteine lyase; PFAM: PF00266; PROSITE: PS00595; SUPERFAMILY: SSF53383; cysteine desulfurase 1690143 sufS 5712768 sufS Dinoroseobacter shibae DFL 12 = DSM 16493 cysteine desulfurase YP_001532966.1 1688923 R 398580 CDS YP_001532967.1 159044173 5712769 complement(1690144..1690743) 1 NC_009952.1 associated with suf system; hypothetical protein 1690743 5712769 Dshi_1624 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532967.1 1690144 R 398580 CDS YP_001532968.1 159044174 5712770 complement(1690773..1691270) 1 NC_009952.1 associated with suf sytem; hypothetical protein 1691270 5712770 Dshi_1625 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532968.1 1690773 R 398580 CDS YP_001532969.1 159044175 5712771 complement(1691270..1692553) 1 NC_009952.1 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 1692553 sufD 5712771 sufD Dinoroseobacter shibae DFL 12 = DSM 16493 sufD YP_001532969.1 1691270 R 398580 CDS YP_001532970.1 159044176 5712772 complement(1692553..1693308) 1 NC_009952.1 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 1693308 sufC 5712772 sufC Dinoroseobacter shibae DFL 12 = DSM 16493 ATP-dependent transporter YP_001532970.1 1692553 R 398580 CDS YP_001532971.1 159044177 5712773 complement(1693326..1693640) 1 NC_009952.1 PFAM: PF01906; COG: COG0393 - Uncharacterized conserved protein; hypothetical protein 1693640 5712773 Dshi_1628 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532971.1 1693326 R 398580 CDS YP_001532972.1 159044178 5712774 complement(1693637..1693837) 1 NC_009952.1 hypothetical protein 1693837 5712774 Dshi_1629 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532972.1 1693637 R 398580 CDS YP_001532973.1 159044179 5712775 complement(1694332..1694541) 1 NC_009952.1 hypothetical protein 1694541 5712775 Dshi_1630 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532973.1 1694332 R 398580 CDS YP_001532974.1 159044180 5712776 complement(1694568..1696079) 1 NC_009952.1 with SufCD activates cysteine desulfurase SufS; cysteine desulfurase activator complex subunit SufB 1696079 sufB 5712776 sufB Dinoroseobacter shibae DFL 12 = DSM 16493 cysteine desulfurase activator complex subunit SufB YP_001532974.1 1694568 R 398580 CDS YP_001532975.1 159044181 5712777 complement(1696137..1697183) 1 NC_009952.1 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 1697183 nifS 5712777 nifS Dinoroseobacter shibae DFL 12 = DSM 16493 cysteine desulfurase YP_001532975.1 1696137 R 398580 CDS YP_001532976.1 159044182 5712778 complement(1697195..1697683) 1 NC_009952.1 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 1697683 iscR 5712778 iscR Dinoroseobacter shibae DFL 12 = DSM 16493 HTH-type transcriptional regulator YP_001532976.1 1697195 R 398580 CDS YP_001532977.1 159044183 5712779 1697855..1698508 1 NC_009952.1 COG: COG2945 - Predicted hydrolase of the alpha/beta superfamily; PFAM: pfam00561; SUPERFAMILY: SSF53474; putative alpha/beta hydrolase 1698508 5712779 Dshi_1634 Dinoroseobacter shibae DFL 12 = DSM 16493 putative alpha/beta hydrolase YP_001532977.1 1697855 D 398580 CDS YP_001532978.1 159044184 5712780 1698511..1698726 1 NC_009952.1 hypothetical protein 1698726 5712780 Dshi_1635 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532978.1 1698511 D 398580 CDS YP_001532979.1 159044185 5712781 1698812..1699540 1 NC_009952.1 PFAM: pfam01988; COG: COG1814 - Uncharacterized membrane protein; hypothetical protein 1699540 5712781 Dshi_1636 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532979.1 1698812 D 398580 CDS YP_001532980.1 159044186 5712782 1699686..1700312 1 NC_009952.1 PFAM: PF02588; COG: COG1284 - Uncharacterized conserved protein; hypothetical protein 1700312 5712782 Dshi_1637 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532980.1 1699686 D 398580 CDS YP_001532981.1 159044187 5712783 1700339..1700668 1 NC_009952.1 SUPERFAMILY: Multidrug resistance efflux transporter EmrE; SWISSPROT P23895: Multidrug transporter emrE; PFAM: PF00893; SUPERFAMILY: SSF103481; efflux-multidrug resistance protein 1700668 emrE 5712783 emrE Dinoroseobacter shibae DFL 12 = DSM 16493 efflux-multidrug resistance protein YP_001532981.1 1700339 D 398580 CDS YP_001532982.1 159044188 5713204 1700730..1701272 1 NC_009952.1 hypothetical protein 1701272 5713204 Dshi_1639 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532982.1 1700730 D 398580 CDS YP_001532983.1 159044189 5713205 1701269..1701574 1 NC_009952.1 PROSITE: PS51257; hypothetical protein 1701574 5713205 Dshi_1640 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532983.1 1701269 D 398580 CDS YP_001532984.1 159044190 5713206 complement(1701587..1701880) 1 NC_009952.1 PFAM: PF07045; hypothetical protein 1701880 5713206 Dshi_1641 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001532984.1 1701587 R 398580 CDS YP_001532985.1 159044191 5713207 complement(1701885..1704548) 1 NC_009952.1 Catalyzes a two-step reaction, first charging an alanyl molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; alanyl-tRNA synthetase 1704548 alaS 5713207 alaS Dinoroseobacter shibae DFL 12 = DSM 16493 alanyl-tRNA synthetase YP_001532985.1 1701885 R 398580 CDS YP_001532986.1 159044192 5713208 complement(1704693..1705760) 1 NC_009952.1 catalyzes the hydrolysis of ATP in the presence of single-stranded DNA, the ATP-dependent uptake of single-stranded DNA by duplex DNA, and the ATP-dependent hybridization of homologous single-stranded DNAs; recombinase A 1705760 recA 5713208 recA Dinoroseobacter shibae DFL 12 = DSM 16493 recombinase A YP_001532986.1 1704693 R 398580 CDS YP_001532987.1 159044193 5713209 complement(1705935..1708274) 1 NC_009952.1 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 1708274 5713209 Dshi_1644 Dinoroseobacter shibae DFL 12 = DSM 16493 histidine kinase YP_001532987.1 1705935 R 398580 CDS YP_001532988.1 159044194 5713210 complement(1708348..1709526) 1 NC_009952.1 SWISSPROT P36929: Ribosomal RNA small subunit methyltransferas B / rRNA (cytosine-C(5)-)-methyltransferase; PFAM: PF01189; SUPERFAMILY: SSF53335; rRNA (cytosine-C(5)-)-methyltransferase 1709526 rsmB2 5713210 rsmB2 Dinoroseobacter shibae DFL 12 = DSM 16493 rRNA (cytosine-C(5)-)-methyltransferase YP_001532988.1 1708348 R 398580 CDS YP_001532989.1 159044195 5713211 complement(1709530..1710984) 1 NC_009952.1 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 1710984 guaB 5713211 guaB Dinoroseobacter shibae DFL 12 = DSM 16493 inosine-5'-monophosphate dehydrogenase YP_001532989.1 1709530 R 398580 CDS YP_001532990.1 159044196 5713212 complement(1711064..1711846) 1 NC_009952.1 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 1711846 hpcH 5713212 hpcH Dinoroseobacter shibae DFL 12 = DSM 16493 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase YP_001532990.1 1711064 R 398580 CDS YP_001532991.1 159044197 5713213 complement(1712121..1713242) 1 NC_009952.1 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 1713242 malK 5713213 malK Dinoroseobacter shibae DFL 12 = DSM 16493 maltose/maltodextrin import ATP-binding protein YP_001532991.1 1712121 R 398580 CDS YP_001532992.1 159044198 5713214 complement(1713282..1714940) 1 NC_009952.1 SWISSPROT Q9Z3R8: Probable alpha-glucosidase; COG: COG0366 - Glycosidases; PFAM: PF00128; SMART: SM00642; SUPERFAMILY: SSF51011, SSF51445; alpha-glucosidase 1714940 5713214 Dshi_1649 Dinoroseobacter shibae DFL 12 = DSM 16493 alpha-glucosidase YP_001532992.1 1713282 R 398580 CDS YP_001532993.1 159044199 5713215 complement(1714954..1716111) 1 NC_009952.1 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 1716111 5713215 Dshi_1650 Dinoroseobacter shibae DFL 12 = DSM 16493 inner membrane ABC transporter permease YP_001532993.1 1714954 R 398580 CDS YP_001532994.1 159044200 5713216 complement(1716129..1717133) 1 NC_009952.1 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 1717133 5713216 Dshi_1651 Dinoroseobacter shibae DFL 12 = DSM 16493 inner membrane ABC transporter permease YP_001532994.1 1716129 R 398580 CDS YP_001532995.1 159044201 5713217 complement(1717206..1718564) 1 NC_009952.1 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 1718564 5713217 Dshi_1652 Dinoroseobacter shibae DFL 12 = DSM 16493 putative solute-binding protein 1 family YP_001532995.1 1717206 R 398580 CDS YP_001532996.1 159044202 5713218 1718787..1719851 1 NC_009952.1 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 1719851 5713218 Dshi_1653 Dinoroseobacter shibae DFL 12 = DSM 16493 HTH-type transcriptional regulator YP_001532996.1 1718787 D 398580 CDS YP_001532997.1 159044203 5713219 1719861..1721168 1 NC_009952.1 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 1721168 bglA 5713219 bglA Dinoroseobacter shibae DFL 12 = DSM 16493 beta-glucosidase A YP_001532997.1 1719861 D 398580 CDS YP_001532998.1 159044204 5713220 1721208..1722179 1 NC_009952.1 SWISSPROT P64254: Glucokinase; TIGRFAM: TIGR00749 glucokinase, proteobacterial type; COG: COG0837; PFAM: PF02685; SUPERFAMILY: SSF53067; glucokinase 1722179 glk 5713220 glk Dinoroseobacter shibae DFL 12 = DSM 16493 glucokinase YP_001532998.1 1721208 D 398580 CDS YP_001532999.1 159044205 5713221 complement(1722176..1723027) 1 NC_009952.1 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 1723027 5713221 Dshi_1656 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC-3 metal transporter YP_001532999.1 1722176 R 398580 CDS YP_001533000.1 159044206 5713222 complement(1723024..1723923) 1 NC_009952.1 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 1723923 5713222 Dshi_1657 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC-3 metal transporter YP_001533000.1 1723024 R 398580 CDS YP_001533001.1 159044207 5713223 complement(1723920..1724816) 1 NC_009952.1 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 1724816 5713223 Dshi_1658 Dinoroseobacter shibae DFL 12 = DSM 16493 metal transport system ATP-binding protein YP_001533001.1 1723920 R 398580 CDS YP_001533002.1 159044208 5713224 complement(1724839..1725729) 1 NC_009952.1 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 1725729 5713224 Dshi_1659 Dinoroseobacter shibae DFL 12 = DSM 16493 metal ABC transporter substrate-binding lipoprotein YP_001533002.1 1724839 R 398580 CDS YP_001533003.1 159044209 5713225 complement(1725859..1726311) 1 NC_009952.1 TIGRFAM: TIGR00738; PFAM: PF02082; SUPERFAMILY: SSF46785; transcriptional regulator 1726311 5713225 Dshi_1660 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001533003.1 1725859 R 398580 CDS YP_001533004.1 159044210 5713226 1726594..1727178 1 NC_009952.1 COG: COG3707 - Response regulator with putative antiterminator output domain; PFAM: PF00072, PF03861; SUPERFAMILY: SSF52172; transcription antitermination regulatory protein 1727178 5713226 Dshi_1661 Dinoroseobacter shibae DFL 12 = DSM 16493 transcription antitermination regulatory protein YP_001533004.1 1726594 D 398580 CDS YP_001533005.1 159044211 5713227 1727175..1728353 1 NC_009952.1 COG: COG0715 - ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components; SUPERFAMILY: SSF53850; associated with nitrate transport system; periplasmic-binding protein-like II 1728353 5713227 Dshi_1662 Dinoroseobacter shibae DFL 12 = DSM 16493 periplasmic-binding protein-like II YP_001533005.1 1727175 D 398580 CDS YP_001533006.1 159044212 5713228 1728617..1729984 1 NC_009952.1 COG: COG0715 - ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components; SUPERFAMILY: SSF53850; associated with nitrate transport system; periplasmic-binding protein-like II 1729984 5713228 Dshi_1663 Dinoroseobacter shibae DFL 12 = DSM 16493 periplasmic-binding protein-like II YP_001533006.1 1728617 D 398580 CDS YP_001533007.1 159044213 5713229 1730124..1731206 1 NC_009952.1 COG: COG0600 - ABC-type nitrate/sulfonate/bicarbonate transport system, permease component; associated with nitrate transport system; putative ABC transporter permease 1731206 5713229 Dshi_1664 Dinoroseobacter shibae DFL 12 = DSM 16493 putative ABC transporter permease YP_001533007.1 1730124 D 398580 CDS YP_001533008.1 159044214 5713230 1731213..1732898 1 NC_009952.1 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 1732898 5713230 Dshi_1665 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC transporter YP_001533008.1 1731213 D 398580 CDS YP_001533009.1 159044215 5713231 1733027..1733473 1 NC_009952.1 COG: COG1017 - Hemoglobin-like flavoprotein; PFAM: PF00042-Globin; SUPERFAMILY: Globin-like SSF46458; Gene3D: G3DSA:1.10.490.10; SWISSPROT P04252: Bacterial hemoglobin; putative flavohemoglobin 1733473 5713231 Dshi_1666 Dinoroseobacter shibae DFL 12 = DSM 16493 putative flavohemoglobin YP_001533009.1 1733027 D 398580 CDS YP_001533010.1 159044216 5713232 1733528..1735960 1 NC_009952.1 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 1735960 nasD 5713232 nasD Dinoroseobacter shibae DFL 12 = DSM 16493 nitrite reductase [NAD(P)H] large subunit YP_001533010.1 1733528 D 398580 CDS YP_001533011.1 159044217 5713233 1735957..1736298 1 NC_009952.1 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 1736298 nasE 5713233 nasE Dinoroseobacter shibae DFL 12 = DSM 16493 assimilatory nitrite reductase [NAD(P)H] small subunit YP_001533011.1 1735957 D 398580 CDS YP_001533012.1 159044218 5713234 1736304..1738925 1 NC_009952.1 SWISSPROT Q06457: Nitrate reductase; COG: COG3383 - Uncharacterized anaerobic dehydrogenase; PFAM: pfam00384, pfam01568, pfam04324, pfam04879; nitrate reductase 1738925 nasA 5713234 nasA Dinoroseobacter shibae DFL 12 = DSM 16493 nitrate reductase YP_001533012.1 1736304 D 398580 CDS YP_001533013.1 159044219 5713235 1738922..1739893 1 NC_009952.1 SWISSPROT Q8R9M6: Anthranilate phosphoribosyltransferase; COG: COG0547 - Anthranilate phosphoribosyltransferase; PFAM: PF02885; Gene3D: G3DSA:3.40.1030.10; SUPERFAMILY: SSF47648, SSF52418; PANTHER: PTHR11922; hypothetical protein 1739893 5713235 Dshi_1670 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533013.1 1738922 D 398580 CDS YP_001533014.1 159044220 5713236 1739910..1741304 1 NC_009952.1 SWISSPROT P0AEA8: Siroheme synthase; TIGRFAM: TIGR01470, TIGR01469; PFAM: PF00590; Gene3D: G3DSA:3.40.1010.10, G3DSA:3.30.950.10; siroheme synthase 1741304 cysG 5713236 cysG Dinoroseobacter shibae DFL 12 = DSM 16493 siroheme synthase YP_001533014.1 1739910 D 398580 CDS YP_001533015.1 159044221 5713237 complement(1741348..1742121) 1 NC_009952.1 PANTHER: PTHR10920-Ribosomal RNA methyltransferase; PIR: PIRSF005461- 23S riosomal methyltransferase; PFAM: PF01728; ribosomal RNA methyltransferase 1742121 5713237 Dshi_1672 Dinoroseobacter shibae DFL 12 = DSM 16493 ribosomal RNA methyltransferase YP_001533015.1 1741348 R 398580 CDS YP_001533016.1 159044222 5713238 complement(1742093..1743274) 1 NC_009952.1 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 1743274 5713238 Dshi_1673 Dinoroseobacter shibae DFL 12 = DSM 16493 phosphatase YP_001533016.1 1742093 R 398580 CDS YP_001533017.1 159044223 5713239 1743527..1743829 1 NC_009952.1 hypothetical protein 1743829 5713239 Dshi_1674 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533017.1 1743527 D 398580 CDS YP_001533018.1 159044224 5713240 1743856..1744782 1 NC_009952.1 COG:COG0685, Gene3D: G3DSA:3.20.20.220; hypothetical protein 1744782 5713240 Dshi_1675 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533018.1 1743856 D 398580 CDS YP_001533019.1 159044225 5713241 1744794..1745453 1 NC_009952.1 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 1745453 5713241 Dshi_1676 Dinoroseobacter shibae DFL 12 = DSM 16493 HAD-like hydrolase YP_001533019.1 1744794 D 398580 CDS YP_001533020.1 159044226 5713242 1745450..1746439 1 NC_009952.1 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 1746439 5713242 Dshi_1677 Dinoroseobacter shibae DFL 12 = DSM 16493 methyltetrahydrofolate:corrinoid/iron-sulfur protein methyltransferase YP_001533020.1 1745450 D 398580 CDS YP_001533021.1 159044227 5713243 1746502..1747206 1 NC_009952.1 hypothetical protein 1747206 5713243 Dshi_1678 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533021.1 1746502 D 398580 CDS YP_001533022.1 159044228 5713244 1747369..1747983 1 NC_009952.1 hypothetical protein 1747983 5713244 Dshi_1679 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533022.1 1747369 D 398580 CDS YP_001533023.1 159044229 5713245 1748119..1750191 1 NC_009952.1 COG: COG3894 - Uncharacterized metal-binding protein; PFAM: PF00111; PROSITE: PS51085; similar to ferredoxin; hypothetical protein 1750191 5713245 Dshi_1680 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533023.1 1748119 D 398580 CDS YP_001533024.1 159044230 5713247 1750319..1750810 1 NC_009952.1 COG: COG0824 - Predicted thioesterase; TIGRFAM: TIGR00051-conserved hypothetical protein TIGR00051; PFAM: PF03061; SUPERFAMILY: SSF54637; putative Thioesterase/thiol ester dehydrase-isomerase 1750810 5713247 Dshi_1681 Dinoroseobacter shibae DFL 12 = DSM 16493 putative Thioesterase/thiol ester dehydrase-isomerase YP_001533024.1 1750319 D 398580 CDS YP_001533025.1 159044231 5713248 complement(1750801..1752405) 1 NC_009952.1 functions in sugar metabolism in glycolysis and the Embden-Meyerhof pathways (EMP) and in gluconeogenesis; catalyzes reversible isomerization of glucose-6-phosphate to fructose-6-phosphate; member of PGI family; glucose-6-phosphate isomerase 1752405 pgi 5713248 pgi Dinoroseobacter shibae DFL 12 = DSM 16493 glucose-6-phosphate isomerase YP_001533025.1 1750801 R 398580 CDS YP_001533026.1 159044232 5713249 complement(1752430..1753104) 1 NC_009952.1 TIGRFAM: TIGR01198 6-phosphogluconolactonase; COG: COG0363 - 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase; PANTHER: PTHR11054- 6-phosphogluconolactonase; putative 6-phosphogluconolactonase 1753104 5713249 Dshi_1683 Dinoroseobacter shibae DFL 12 = DSM 16493 putative 6-phosphogluconolactonase YP_001533026.1 1752430 R 398580 CDS YP_001533027.1 159044233 5713250 complement(1753116..1754570) 1 NC_009952.1 catalyzes the formation of D-glucono-1,5-lactone 6-phosphate from D-glucose 6-phosphate; glucose-6-phosphate 1-dehydrogenase 1754570 zwf 5713250 zwf Dinoroseobacter shibae DFL 12 = DSM 16493 glucose-6-phosphate 1-dehydrogenase YP_001533027.1 1753116 R 398580 CDS YP_001533028.1 159044234 5713251 1754813..1755757 1 NC_009952.1 COG: COG0535 - Predicted Fe-S oxidoreductases; PFAM: PF04055; hypothetical protein 1755757 5713251 Dshi_1685 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533028.1 1754813 D 398580 CDS YP_001533029.1 159044235 5713252 complement(1755768..1756544) 1 NC_009952.1 COG: COG1305 - Transglutaminase-like enzymes, putative cysteine proteases; PFAM: pfam01841; SMART: SM00460; SUPERFAMILY: SSF54001; transglutaminase-like; hypothetical protein 1756544 5713252 Dshi_1686 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533029.1 1755768 R 398580 CDS YP_001533030.1 159044236 5713253 complement(1756672..1757268) 1 NC_009952.1 COG: COG1403 - Restriction endonuclease; PFAM: PF01844-HNH endonuclease; SMART: SM00507-HNH nucleases; putative HNH endonuclease 1757268 5713253 Dshi_1687 Dinoroseobacter shibae DFL 12 = DSM 16493 putative HNH endonuclease YP_001533030.1 1756672 R 398580 CDS YP_001533031.1 159044237 5713254 complement(1757458..1758129) 1 NC_009952.1 COG: COG0400 - Predicted esterase; PFAM: PF02230; putative phospholipase / carboxylesterase 1758129 5713254 Dshi_1688 Dinoroseobacter shibae DFL 12 = DSM 16493 putative phospholipase / carboxylesterase YP_001533031.1 1757458 R 398580 CDS YP_001533032.1 159044238 5713255 complement(1758126..1758758) 1 NC_009952.1 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 1758758 5713255 Dshi_1689 Dinoroseobacter shibae DFL 12 = DSM 16493 DNA-glycosylase family protein YP_001533032.1 1758126 R 398580 CDS YP_001533033.1 159044239 5713256 complement(1758740..1759486) 1 NC_009952.1 SWISSPROT P21920: Precorrin-6A reductase; PFAM PF02571: Precorrin-6x reductase CbiJ/CobK; TIGRFAM: TIGR00715; COG: COG2099; precorrin-6A reductase 1759486 cobK 5713256 cobK Dinoroseobacter shibae DFL 12 = DSM 16493 precorrin-6A reductase YP_001533033.1 1758740 R 398580 CDS YP_001533034.1 159044240 5713257 complement(1759483..1760532) 1 NC_009952.1 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 1760532 cbiD 5713257 cbiD Dinoroseobacter shibae DFL 12 = DSM 16493 cobalamin (vitamin B12) biosynthesis CbiD protein YP_001533034.1 1759483 R 398580 CDS YP_001533035.1 159044241 5713258 1760630..1761475 1 NC_009952.1 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 1761475 cobA1 5713258 cobA1 Dinoroseobacter shibae DFL 12 = DSM 16493 uroporphyrinogen-III C-methyltransferase YP_001533035.1 1760630 D 398580 CDS YP_001533036.1 159044242 5713259 1761472..1762767 1 NC_009952.1 responsible for the amidation of carboxylic groups at position A and C of cobyrinic acid or hydrogenobrynic acid; cobyrinic acid a,c-diamide synthase 1762767 cobB 5713259 cobB Dinoroseobacter shibae DFL 12 = DSM 16493 cobyrinic acid a,c-diamide synthase YP_001533036.1 1761472 D 398580 CDS YP_001533037.1 159044243 5713260 1762829..1764055 1 NC_009952.1 PFAM: PF07690; PROSITE: PS50850; major facilitator superfamiy transporter 1764055 5713260 Dshi_1694 Dinoroseobacter shibae DFL 12 = DSM 16493 major facilitator superfamiy transporter YP_001533037.1 1762829 D 398580 CDS YP_001533038.1 159044244 5713261 complement(1764125..1764895) 1 NC_009952.1 COG: COG1562 - Phytoene/squalene synthetase; hypothetical protein 1764895 5713261 Dshi_1695 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533038.1 1764125 R 398580 CDS YP_001533039.1 159044245 5713262 complement(1764892..1766529) 1 NC_009952.1 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 1766529 5713262 Dshi_1696 Dinoroseobacter shibae DFL 12 = DSM 16493 putative alpha-isopropylmalate/homocitrate synthase family transferase YP_001533039.1 1764892 R 398580 CDS YP_001533040.1 159044246 5713263 complement(1766526..1766948) 1 NC_009952.1 hypothetical protein 1766948 5713263 Dshi_1697 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533040.1 1766526 R 398580 CDS YP_001533041.1 159044247 5713264 complement(1767125..1768501) 1 NC_009952.1 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 1768501 cysS 5713264 cysS Dinoroseobacter shibae DFL 12 = DSM 16493 cysteinyl-tRNA synthetase YP_001533041.1 1767125 R 398580 CDS YP_001533042.1 159044248 5713265 complement(1768734..1769330) 1 NC_009952.1 COG: COG3637 - Opacity protein and related surface antigens; hypothetical protein 1769330 5713265 Dshi_1699 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533042.1 1768734 R 398580 CDS YP_001533043.1 159044249 5713266 1769636..1770391 1 NC_009952.1 PFAM: PF00106-short chain dehydrogenase; PROSITE: PS00061-Short-chain dehydrogenases/reductases family signature; short-chain dehydrogenase/reductase family protein 1770391 5713266 Dshi_1700 Dinoroseobacter shibae DFL 12 = DSM 16493 short-chain dehydrogenase/reductase family protein YP_001533043.1 1769636 D 398580 CDS YP_001533044.1 159044250 5713267 complement(1770402..1771202) 1 NC_009952.1 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 1771202 5713267 Dshi_1701 Dinoroseobacter shibae DFL 12 = DSM 16493 putative high-affinity zinc uptake system membrane protein YP_001533044.1 1770402 R 398580 CDS YP_001533045.1 159044251 5713268 complement(1771199..1771942) 1 NC_009952.1 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 1771942 znuC 5713268 znuC Dinoroseobacter shibae DFL 12 = DSM 16493 zinc import ATP-binding protein YP_001533045.1 1771199 R 398580 CDS YP_001533046.1 159044252 5713269 complement(1771939..1772436) 1 NC_009952.1 SWISSPROT P0AC51: Zinc uptake regulation protein; PRODOM: PD002003; PFAM: pfam01475; zur; putative zinc uptake regulation protein 1772436 5713269 Dshi_1703 Dinoroseobacter shibae DFL 12 = DSM 16493 putative zinc uptake regulation protein YP_001533046.1 1771939 R 398580 CDS YP_001533047.1 159044253 5713270 1772514..1773584 1 NC_009952.1 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 1773584 5713270 Dshi_1704 Dinoroseobacter shibae DFL 12 = DSM 16493 putative high-affinity zinc uptake system protein YP_001533047.1 1772514 D 398580 CDS YP_001533048.1 159044254 5713271 1773613..1773951 1 NC_009952.1 hypothetical protein 1773951 5713271 Dshi_1705 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533048.1 1773613 D 398580 CDS YP_001533049.1 159044255 5713272 complement(1773917..1774366) 1 NC_009952.1 TIGRFAM: TIGR00357 methionine-R-sulfoxide reductase; COG: COG0229 - Conserved domain frequently associated with peptide methionine sulfoxide reductase; PFAM: pfam01641; peptide methionine sulfoxide reductase 1774366 msrB2 5713272 msrB2 Dinoroseobacter shibae DFL 12 = DSM 16493 peptide methionine sulfoxide reductase YP_001533049.1 1773917 R 398580 CDS YP_001533050.1 159044256 5713273 1774366..1775166 1 NC_009952.1 SUPERFAMILY: SSF55729; COG: COG3176 - Putative hemolysin; putative acyl-CoA N-acyltransferases (Nat) superfamily protein 1775166 5713273 Dshi_1707 Dinoroseobacter shibae DFL 12 = DSM 16493 putative acyl-CoA N-acyltransferases (Nat) superfamily protein YP_001533050.1 1774366 D 398580 CDS YP_001533051.1 159044257 5713274 1775173..1775952 1 NC_009952.1 PFAM: PF01396, PF08378; SUPERFAMILY: SSF57783; nuclease related; hypothetical protein 1775952 5713274 Dshi_1708 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533051.1 1775173 D 398580 CDS YP_001533052.1 159044258 5713275 complement(1776333..1777817) 1 NC_009952.1 SWISSPROT P0C0S1: Small-conductance mechanosensitive channel; COG: COG0668 - Small-conductance mechanosensitive channel; PFAM: PF00924; SUPERFAMILY: SSF50182, SSF82861, SSF82689; small conductance mechanosensitive channel 1777817 mscS 5713275 mscS Dinoroseobacter shibae DFL 12 = DSM 16493 small conductance mechanosensitive channel YP_001533052.1 1776333 R 398580 CDS YP_001533053.1 159044259 5713276 complement(1778048..1778410) 1 NC_009952.1 SWISSPROT P0AC69: Glutaredoxin-4; PFAM: Glutaredoxin; TIGRFAM: TIGR00365 glutaredoxin-related protein; COG: COG0278; putative monothiol glutaredoxin 1778410 5713276 Dshi_1710 Dinoroseobacter shibae DFL 12 = DSM 16493 putative monothiol glutaredoxin YP_001533053.1 1778048 R 398580 CDS YP_001533054.1 159044260 5713277 complement(1778403..1778669) 1 NC_009952.1 hypothetical protein 1778669 5713277 Dshi_1711 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533054.1 1778403 R 398580 CDS YP_001533055.1 159044261 5713278 complement(1778669..1778902) 1 NC_009952.1 PFAM: PF01722; PANTHER: PTHR12735; Gene3D: G3DSA:3.30.300.90; COG: COG0271 - Stress-induced morphogen (activity unknown); similar to bolA-like proteins; hypothetical protein 1778902 5713278 Dshi_1712 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533055.1 1778669 R 398580 CDS YP_001533056.1 159044262 5713279 complement(1779001..1781172) 1 NC_009952.1 catalyzes the formation of 2-(formamido)-N1-(5-phospho-D-ribosyl)acetamidine from N2-formyl-N1-(5-phospho-D-ribosyl)glycinamide and L-glutamine in purine biosynthesis; phosphoribosylformylglycinamidine synthase II 1781172 purL 5713279 purL Dinoroseobacter shibae DFL 12 = DSM 16493 phosphoribosylformylglycinamidine synthase II YP_001533056.1 1779001 R 398580 CDS YP_001533057.1 159044263 5713280 1781528..1783372 1 NC_009952.1 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 1783372 5713280 Dshi_1714 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC transporter ATP-binding protein YP_001533057.1 1781528 D 398580 CDS YP_001533058.1 159044264 5713281 1783558..1784403 1 NC_009952.1 SUPERFAMILY: SSF52540; Gene3D: G3DSA:3.40.50.300; PFAM: pfam00685; similar to sulfotransferase; hypothetical protein 1784403 5713281 Dshi_1715 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533058.1 1783558 D 398580 CDS YP_001533059.1 159044265 5713282 complement(1784400..1784858) 1 NC_009952.1 COG: COG2913 - Small protein A (tmRNA-binding); hypothetical protein 1784858 5713282 Dshi_1716 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533059.1 1784400 R 398580 CDS YP_001533060.1 159044266 5713283 1785059..1785622 1 NC_009952.1 COG: COG1399 - Predicted metal-binding, possibly nucleic acid-binding protein; PFAM: PF02620; hypothetical protein 1785622 5713283 Dshi_1717 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533060.1 1785059 D 398580 CDS YP_001533061.1 159044267 5713284 1785846..1786052 1 NC_009952.1 some L32 proteins have zinc finger motifs consisting of CXXC while others do not; 50S ribosomal protein L32 1786052 rpmF 5713284 rpmF Dinoroseobacter shibae DFL 12 = DSM 16493 50S ribosomal protein L32 YP_001533061.1 1785846 D 398580 CDS YP_001533062.1 159044268 5713285 1786088..1787245 1 NC_009952.1 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 1787245 plsX 5713285 plsX Dinoroseobacter shibae DFL 12 = DSM 16493 putative glycerol-3-phosphate acyltransferase PlsX YP_001533062.1 1786088 D 398580 CDS YP_001533063.1 159044269 5713286 1787238..1788212 1 NC_009952.1 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 1788212 fabH 5713286 fabH Dinoroseobacter shibae DFL 12 = DSM 16493 3-oxoacyl-ACP synthase YP_001533063.1 1787238 D 398580 CDS YP_001533064.1 159044270 5713287 1788324..1788629 1 NC_009952.1 This protein is one of the two subunits of integration host factor, a specific DNA-binding protein that functions in genetic recombination as well as in transcriptional and translational control; integration host factor subunit alpha 1788629 ihfA 5713287 ihfA Dinoroseobacter shibae DFL 12 = DSM 16493 integration host factor subunit alpha YP_001533064.1 1788324 D 398580 CDS YP_001533065.1 159044271 5713288 1788669..1789406 1 NC_009952.1 PFAM: PF00376; SMART: SM00422; COG: COG0789 - Predicted transcriptional regulators; similar to MerR family regulatory protein; hypothetical protein 1789406 5713288 Dshi_1722 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533065.1 1788669 D 398580 CDS YP_001533066.1 159044272 5713290 1789628..1790722 1 NC_009952.1 Catalyzes the deamination of dCTP to form dUTP; 2'-deoxycytidine 5'-triphosphate deaminase 1790722 5713290 Dshi_1723 Dinoroseobacter shibae DFL 12 = DSM 16493 2'-deoxycytidine 5'-triphosphate deaminase YP_001533066.1 1789628 D 398580 CDS YP_001533067.1 159044273 5713291 complement(1791066..1791755) 1 NC_009952.1 TIGRFAM: TIGR00281 segregation and condensation protein B; SWISSPROT Q65HX2: Segregation and condensation protein B; PFAM: PF04079; scpB; putative segregation and condensation protein B 1791755 5713291 Dshi_1724 Dinoroseobacter shibae DFL 12 = DSM 16493 putative segregation and condensation protein B YP_001533067.1 1791066 R 398580 CDS YP_001533068.1 159044274 5713292 complement(1791755..1792549) 1 NC_009952.1 SWISSPROT Q87BI4: Segregation and condensation protein A; PFAM: PF02616; scpA; putative Segregation and condensation protein A 1792549 5713292 Dshi_1725 Dinoroseobacter shibae DFL 12 = DSM 16493 putative Segregation and condensation protein A YP_001533068.1 1791755 R 398580 CDS YP_001533069.1 159044275 5713293 complement(1792572..1793558) 1 NC_009952.1 PFAM: PF00933; PROSITE: PS00775; SWISSPROT P75949: Beta-hexosaminidase; COG: COG1472 - Beta-glucosidase-related glycosidases; beta-hexosamidase 1793558 nagZ 5713293 nagZ Dinoroseobacter shibae DFL 12 = DSM 16493 beta-hexosamidase YP_001533069.1 1792572 R 398580 CDS YP_001533070.1 159044276 5713294 complement(1793568..1794512) 1 NC_009952.1 PFAM: PF05036; related to proteins involved in sporulation and cell division; hypothetical protein 1794512 5713294 Dshi_1727 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533070.1 1793568 R 398580 CDS YP_001533071.1 159044277 5713295 complement(1794601..1796346) 1 NC_009952.1 catalyzes a two-step reaction, first charging an arginine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; class-I aminoacyl-tRNA synthetase; arginyl-tRNA synthetase 1796346 argS 5713295 argS Dinoroseobacter shibae DFL 12 = DSM 16493 arginyl-tRNA synthetase YP_001533071.1 1794601 R 398580 CDS YP_001533072.1 159044278 5713296 complement(1796409..1797608) 1 NC_009952.1 TIGRFAM: TIGR01353 deoxyguanosinetriphosphate triphosphohydrolase, putative, TIGR00277; SWISSPROT P15723: Deoxyguanosinetriphosphate triphosphohydrolase, P63934: Deoxyguanosinetriphosphate triphosphohydrolase-like protein; COG: COG0232 - dGTP triphosphohydrolase; PFAM: pfam01966; putative deoxyguanosinetriphosphate triphosphohydrolase 1797608 5713296 Dshi_1729 Dinoroseobacter shibae DFL 12 = DSM 16493 putative deoxyguanosinetriphosphate triphosphohydrolase YP_001533072.1 1796409 R 398580 CDS YP_001533073.1 159044279 5713297 1797652..1797984 1 NC_009952.1 TIGRFAM: TIGR00049 Iron-sulfur cluster assembly accessory protein; PROSITE: PS01152; PFAM: PF01521; iron-sulfur cluster assembly accessory protein 1797984 5713297 Dshi_1730 Dinoroseobacter shibae DFL 12 = DSM 16493 iron-sulfur cluster assembly accessory protein YP_001533073.1 1797652 D 398580 CDS YP_001533074.1 159044280 5713298 complement(1798047..1798658) 1 NC_009952.1 hypothetical protein 1798658 5713298 Dshi_1731 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533074.1 1798047 R 398580 CDS YP_001533075.1 159044281 5713299 complement(1798913..1799737) 1 NC_009952.1 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 1799737 hemK 5713299 hemK Dinoroseobacter shibae DFL 12 = DSM 16493 putative protein methyltransferase YP_001533075.1 1798913 R 398580 CDS YP_001533076.1 159044282 5713300 complement(1799734..1800789) 1 NC_009952.1 recognizes the termination signals UAG and UAA during protein translation a specificity which is dependent on amino acid residues residing in loops of the L-shaped tRNA-like molecule of RF1; this protein is similar to release factor 2; peptide chain release factor 1 1800789 prfA 5713300 prfA Dinoroseobacter shibae DFL 12 = DSM 16493 peptide chain release factor 1 YP_001533076.1 1799734 R 398580 CDS YP_001533077.1 159044283 5713301 complement(1801041..1801505) 1 NC_009952.1 hypothetical protein 1801505 5713301 Dshi_1734 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533077.1 1801041 R 398580 CDS YP_001533078.1 159044284 5713302 complement(1801557..1802531) 1 NC_009952.1 catalyzes the formation of putrescine from agmatine; agmatinase 1802531 speB 5713302 speB Dinoroseobacter shibae DFL 12 = DSM 16493 agmatinase YP_001533078.1 1801557 R 398580 CDS YP_001533079.1 159044285 5713303 complement(1802535..1802939) 1 NC_009952.1 PFAM: PF05164- Cell division protein ZapA; putative cell division protein ZapA 1802939 5713303 Dshi_1736 Dinoroseobacter shibae DFL 12 = DSM 16493 putative cell division protein ZapA YP_001533079.1 1802535 R 398580 CDS YP_001533080.1 159044286 5713304 complement(1802941..1803369) 1 NC_009952.1 hypothetical protein 1803369 5713304 Dshi_1737 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533080.1 1802941 R 398580 CDS YP_001533081.1 159044287 5713305 1803674..1805647 1 NC_009952.1 catalyzes the formation of ribose 5-phosphate and xylulose 5-phosphate from sedoheptulose 7-phosphate and glyceraldehyde 3-phosphate; can transfer ketol groups between several groups; in Escherichia coli there are two tkt genes, tktA expressed during exponential growth and the tktB during stationary phase; transketolase 1805647 tktA 5713305 tktA Dinoroseobacter shibae DFL 12 = DSM 16493 transketolase YP_001533081.1 1803674 D 398580 CDS YP_001533082.1 159044288 5713306 complement(1805810..1806757) 1 NC_009952.1 PFAM: PF05661; COG: COG2354; hypothetical protein 1806757 5713306 Dshi_1739 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533082.1 1805810 R 398580 CDS YP_001533083.1 159044289 5713307 1807000..1808001 1 NC_009952.1 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 1808001 gap2 5713307 gap2 Dinoroseobacter shibae DFL 12 = DSM 16493 glyceraldehyde-3-phosphate dehydrogenase YP_001533083.1 1807000 D 398580 CDS YP_001533084.1 159044290 5713308 1808037..1808192 1 NC_009952.1 hypothetical protein 1808192 5713308 Dshi_1741 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533084.1 1808037 D 398580 CDS YP_001533085.1 159044291 5713309 1808288..1809310 1 NC_009952.1 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 1809310 gap1 5713309 gap1 Dinoroseobacter shibae DFL 12 = DSM 16493 glyceraldehyde-3-phosphate dehydrogenase YP_001533085.1 1808288 D 398580 CDS YP_001533086.1 159044292 5713310 complement(1809314..1809916) 1 NC_009952.1 PFAM: PF00583; PROSITE: PS51186; related to acetyltransferase, GNAT family; hypothetical protein 1809916 5713310 Dshi_1743 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533086.1 1809314 R 398580 CDS YP_001533087.1 159044293 5713311 complement(1810248..1810763) 1 NC_009952.1 Catalyzes the conversion of ATP and pantetheine 4'-phosphate to diphosphate and 3'-dephospho-coA; phosphopantetheine adenylyltransferase 1810763 coaD 5713311 coaD Dinoroseobacter shibae DFL 12 = DSM 16493 phosphopantetheine adenylyltransferase YP_001533087.1 1810248 R 398580 CDS YP_001533088.1 159044294 5713312 complement(1810852..1811286) 1 NC_009952.1 PFAM: PF00571; SMART: SM00116; COG: COG2905 - Predicted signal-transduction protein containing cAMP-binding and CBS domains; related to cystathionine beta synthase; hypothetical protein 1811286 5713312 Dshi_1745 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533088.1 1810852 R 398580 CDS YP_001533089.1 159044295 5713313 complement(1811339..1812232) 1 NC_009952.1 COG: COG0583 - Transcriptional regulator; PFAM: PF00126, PF03466; PROSITE: PS50931; SUPERFAMILY: SSF53850, SSF46785; HTH-type transcriptional regulator 1812232 5713313 Dshi_1746 Dinoroseobacter shibae DFL 12 = DSM 16493 HTH-type transcriptional regulator YP_001533089.1 1811339 R 398580 CDS YP_001533090.1 159044296 5713314 1812332..1813831 1 NC_009952.1 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 1813831 mmsA 5713314 mmsA Dinoroseobacter shibae DFL 12 = DSM 16493 acylating methylmalonate-semialdehyde dehydrogenase YP_001533090.1 1812332 D 398580 CDS YP_001533091.1 159044297 5713315 complement(1813903..1814532) 1 NC_009952.1 hypothetical protein 1814532 5713315 Dshi_1748 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533091.1 1813903 R 398580 CDS YP_001533092.1 159044298 5713316 1814843..1815970 1 NC_009952.1 ATP-dependent carboxylate-amine ligase; carboxylate-amine ligase 1815970 5713316 Dshi_1749 Dinoroseobacter shibae DFL 12 = DSM 16493 carboxylate-amine ligase YP_001533092.1 1814843 D 398580 CDS YP_001533093.1 159044299 5713317 1816051..1817196 1 NC_009952.1 PFAM: PF00441, PF02770, PF02771; PROSITE: PS00072, PS00073; COG: COG1960 - Acyl-CoA dehydrogenases; acyl-CoA dehydrogenase 1817196 5713317 Dshi_1750 Dinoroseobacter shibae DFL 12 = DSM 16493 acyl-CoA dehydrogenase YP_001533093.1 1816051 D 398580 CDS YP_001533094.1 159044300 5713318 1817193..1818239 1 NC_009952.1 COG: COG1024 - Enoyl-CoA hydratase/carnithine racemase; PFAM: PF00378; Gene3D: G3DSA:3.90.226.10; enoyl-CoA hydratase/isomerase family protein 1818239 5713318 Dshi_1751 Dinoroseobacter shibae DFL 12 = DSM 16493 enoyl-CoA hydratase/isomerase family protein YP_001533094.1 1817193 D 398580 CDS YP_001533095.1 159044301 5713319 1818236..1819111 1 NC_009952.1 TIGRFAM: TIGR01692 3-hydroxyisobutyrate dehydrogenase; PANTHER: PTHR22981; PROSITE: PS00895; PFAM: PF03446; Gene3D: G3DSA:1.10.1040.10; 3-hydroxyisobutyrate dehydrogenase 1819111 mmsB 5713319 mmsB Dinoroseobacter shibae DFL 12 = DSM 16493 3-hydroxyisobutyrate dehydrogenase YP_001533095.1 1818236 D 398580 CDS YP_001533096.1 159044302 5713320 complement(1819173..1819949) 1 NC_009952.1 COG: COG1024 - Enoyl-CoA hydratase/carnithine racemase; PFAM: PF00378; PROSITE: PS00166; enoyl-CoA hydratase 1819949 5713320 Dshi_1753 Dinoroseobacter shibae DFL 12 = DSM 16493 enoyl-CoA hydratase YP_001533096.1 1819173 R 398580 CDS YP_001533097.1 159044303 5713321 complement(1820040..1820456) 1 NC_009952.1 hypothetical protein 1820456 5713321 Dshi_1754 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533097.1 1820040 R 398580 CDS YP_001533098.1 159044304 5713322 complement(1820449..1820655) 1 NC_009952.1 SWISSPROT Q9WZW0: tRNA pseudouridine synthase B; PRODOM: PD012454; similar to tRNA pseudouridine synthase B; putative tRNA pseudouridine synthase B 1820655 5713322 Dshi_1755 Dinoroseobacter shibae DFL 12 = DSM 16493 putative tRNA pseudouridine synthase B YP_001533098.1 1820449 R 398580 CDS YP_001533099.1 159044305 5713323 complement(1820645..1821166) 1 NC_009952.1 SWISSPROT Q9K197: Carboxylesterase bioH, Q56841: 2-(S)-hydroxypropyl-CoM dehydrogenase; putative carboxylesterase 1821166 5713323 Dshi_1756 Dinoroseobacter shibae DFL 12 = DSM 16493 putative carboxylesterase YP_001533099.1 1820645 R 398580 CDS YP_001533100.1 159044306 5713324 complement(1821157..1821768) 1 NC_009952.1 COG: COG3926 - Putative secretion activating protein; PFAM: PF05838; hypothetical protein 1821768 5713324 Dshi_1757 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533100.1 1821157 R 398580 CDS YP_001533101.1 159044307 5713325 complement(1821878..1822360) 1 NC_009952.1 CycJ; periplasmic heme chaperone that binds heme transiently via a histidine residue and delivers it to newly synthesized and exported c-type cytochromes; requires the ATP hydrolysis activity of the CcmA protein in order to transfer the heme to the apocytochrome; part of the cytochrome c maturation system; periplasmic protein anchored to the inner membrane; cytochrome c-type biogenesis protein CcmE 1822360 ccmE 5713325 ccmE Dinoroseobacter shibae DFL 12 = DSM 16493 cytochrome c-type biogenesis protein CcmE YP_001533101.1 1821878 R 398580 CDS YP_001533102.1 159044308 5713326 complement(1822376..1823401) 1 NC_009952.1 catalyzes the reduction of N-acetyl-5-glutamyl phosphate to N-acetyl-L-glutamate 5-semialdehyde in arginine biosynthesis and the reduction of N-acetyl-gamma-aminoadipyl-phosphate to N-acetyl-L-aminoadipate-semialdehyde in lysine biosynthesis; involved in both the arginine and lysine biosynthetic pathways; lysine is produced via the AAA pathway, lysine from alpha-aminoadipate; N-acetyl-gamma-glutamyl-phosphate reductase 1823401 argC 5713326 argC Dinoroseobacter shibae DFL 12 = DSM 16493 N-acetyl-gamma-glutamyl-phosphate reductase YP_001533102.1 1822376 R 398580 CDS YP_001533103.1 159044309 5713327 complement(1823438..1824259) 1 NC_009952.1 TIGRFAM: TIGR00067 glutamate racemase; PFAM PF01177: Asp/Glu/Hydantoin racemase; PROSITE: PS00923; COG: COG0796 - Glutamate racemase; glutamate racemase 1824259 murI 5713327 murI Dinoroseobacter shibae DFL 12 = DSM 16493 glutamate racemase YP_001533103.1 1823438 R 398580 CDS YP_001533104.1 159044310 5713328 complement(1824259..1825137) 1 NC_009952.1 COG: COG3176-Putative hemolysin; PFAM: PF01553; SMART: SM00563; SUPERFAMILY: SSF69593; putative acyltransferase 1825137 5713328 Dshi_1761 Dinoroseobacter shibae DFL 12 = DSM 16493 putative acyltransferase YP_001533104.1 1824259 R 398580 CDS YP_001533105.1 159044311 5713329 complement(1825196..1828603) 1 NC_009952.1 Catalyzes the ferredoxin-dependent oxidative decarboxylation of arylpyruvates; indolepyruvate ferredoxin oxidoreductase 1828603 5713329 Dshi_1762 Dinoroseobacter shibae DFL 12 = DSM 16493 indolepyruvate ferredoxin oxidoreductase YP_001533105.1 1825196 R 398580 CDS YP_001533106.1 159044312 5713330 1828760..1829662 1 NC_009952.1 SWISSPROT P30846: Uncharacterized HTH-type transcriptional regulator yafC; COG: COG0583 - Transcriptional regulator; PFAM: PF00126, PF03466; PROSITE: PS50931; SUPERFAMILY: SSF53850, SSF46785; HTH-type transcriptional regulator 1829662 5713330 Dshi_1763 Dinoroseobacter shibae DFL 12 = DSM 16493 HTH-type transcriptional regulator YP_001533106.1 1828760 D 398580 CDS YP_001533107.1 159044313 5713331 1829905..1830690 1 NC_009952.1 SUPERFAMILY: SSF53474; PANTHER: PTHR11731; Gene3D: G3DSA:3.40.50.1820; COG: COG0657 - Esterase/lipase; putative hydrolase 1830690 5713331 Dshi_1764 Dinoroseobacter shibae DFL 12 = DSM 16493 putative hydrolase YP_001533107.1 1829905 D 398580 CDS YP_001533108.1 159044314 5713332 complement(1830691..1832526) 1 NC_009952.1 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 1832526 5713332 Dshi_1765 Dinoroseobacter shibae DFL 12 = DSM 16493 putative multidrug export ATP-binding/permease YP_001533108.1 1830691 R 398580 CDS YP_001533109.1 159044315 5713333 complement(1832580..1834175) 1 NC_009952.1 PFAM: PF01476; hypothetical protein 1834175 5713333 Dshi_1766 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533109.1 1832580 R 398580 CDS YP_001533110.1 159044316 5713334 1834326..1834865 1 NC_009952.1 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 1834865 5713334 Dshi_1767 Dinoroseobacter shibae DFL 12 = DSM 16493 putative lysine carboxylase YP_001533110.1 1834326 D 398580 CDS YP_001533111.1 159044317 5713335 complement(1835047..1835688) 1 NC_009952.1 SWISSPROT P0A955: KHG/KDPG aldolase; PFAM: PF01081; TIGRFAM: TIGR01182; COG: COG0800 - 2-keto-3-deoxy-6-phosphogluconate aldolase; KHG/KDPG aldolase 1835688 eda 5713335 eda Dinoroseobacter shibae DFL 12 = DSM 16493 KHG/KDPG aldolase YP_001533111.1 1835047 R 398580 CDS YP_001533112.1 159044318 5713336 complement(1835700..1837505) 1 NC_009952.1 catalyzes the formation of 2-dehydro-3-deoxy-6-phospho-D-gluconate from 6-phospho-D-gluconate; phosphogluconate dehydratase 1837505 edd 5713336 edd Dinoroseobacter shibae DFL 12 = DSM 16493 phosphogluconate dehydratase YP_001533112.1 1835700 R 398580 CDS YP_001533113.1 159044319 5713337 1837632..1837898 1 NC_009952.1 hypothetical protein 1837898 5713337 Dshi_1770 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533113.1 1837632 D 398580 CDS YP_001533114.1 159044320 5713338 1838034..1839236 1 NC_009952.1 COG: COG1092 - Predicted SAM-dependent methyltransferases; PFAM: PF03602; SUPERFAMILY: SSF53335; SWISSPROT P75876: UPF0064 protein yccW; similar to methyltransferase; hypothetical protein 1839236 5713338 Dshi_1771 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533114.1 1838034 D 398580 CDS YP_001533115.1 159044321 5713339 1839233..1839772 1 NC_009952.1 hypothetical protein 1839772 5713339 Dshi_1772 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533115.1 1839233 D 398580 CDS YP_001533116.1 159044322 5713340 complement(1839968..1840660) 1 NC_009952.1 SWISSPROT P25894: Uncharacterized metalloprotease yggG; PANTHER: OMA1 HOMOLOG, ZINC METALLOPEPTIDASE (PTHR22726); PFAM: PF01435; putative metalloprotease 1840660 5713340 Dshi_1773 Dinoroseobacter shibae DFL 12 = DSM 16493 putative metalloprotease YP_001533116.1 1839968 R 398580 CDS YP_001533117.1 159044323 5713341 complement(1840700..1840987) 1 NC_009952.1 hypothetical protein 1840987 5713341 Dshi_1774 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533117.1 1840700 R 398580 CDS YP_001533118.1 159044324 5713342 complement(1841055..1843865) 1 NC_009952.1 PFAM: PF03710; COG: COG1391 - Glutamine synthetase adenylyltransferase; putative glutamate--ammonia ligase adenyltransferase 1843865 5713342 Dshi_1775 Dinoroseobacter shibae DFL 12 = DSM 16493 putative glutamate--ammonia ligase adenyltransferase YP_001533118.1 1841055 R 398580 CDS YP_001533119.1 159044325 5713344 1844200..1844541 1 NC_009952.1 SWISSPROT P0ADU5: Protein ygiW [Precursor]; Gene3D: G3DSA:2.40.50.200; SUPERFAMILY: SSF101756; similar to hypothetical protein ygiW; hypothetical protein 1844541 5713344 Dshi_1776 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533119.1 1844200 D 398580 CDS YP_001533120.1 159044326 5713345 complement(1844619..1847027) 1 NC_009952.1 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 1847027 lon 5713345 lon Dinoroseobacter shibae DFL 12 = DSM 16493 ATP-dependent protease La YP_001533120.1 1844619 R 398580 CDS YP_001533121.1 159044327 5713346 1847401..1848006 1 NC_009952.1 hypothetical protein 1848006 5713346 Dshi_1778 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533121.1 1847401 D 398580 CDS YP_001533122.1 159044328 5713347 1848348..1850105 1 NC_009952.1 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 1850105 ilvI 5713347 ilvI Dinoroseobacter shibae DFL 12 = DSM 16493 acetolactate synthase 3 catalytic subunit YP_001533122.1 1848348 D 398580 CDS YP_001533123.1 159044329 5713348 1850105..1850416 1 NC_009952.1 PROSITE: PS51257; hypothetical protein 1850416 5713348 Dshi_1780 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533123.1 1850105 D 398580 CDS YP_001533124.1 159044330 5713349 1850474..1851046 1 NC_009952.1 with IlvI catalyzes the formation of 2-acetolactate from pyruvate, the small subunit is required for full activity and valine sensitivity; E.coli produces 3 isoenzymes of acetolactate synthase which differ in specificity to substrates, valine sensitivity and affinity for cofactors; also known as acetolactate synthase 3 small subunit; acetolactate synthase 3 regulatory subunit 1851046 ilvH 5713349 ilvH Dinoroseobacter shibae DFL 12 = DSM 16493 acetolactate synthase 3 regulatory subunit YP_001533124.1 1850474 D 398580 CDS YP_001533125.1 159044331 5713350 1851151..1852302 1 NC_009952.1 SWISSPROT P0ABR7: Putative dioxygenase subunit alpha yeaW; PFAM: PF00355; SPRINT: PR00090; putative ring-hydroxylating dioxygenase subunit alpha 1852302 5713350 Dshi_1782 Dinoroseobacter shibae DFL 12 = DSM 16493 putative ring-hydroxylating dioxygenase subunit alpha YP_001533125.1 1851151 D 398580 CDS YP_001533126.1 159044332 5713351 complement(1852555..1852800) 1 NC_009952.1 PROSITE: PS00018; hypothetical protein 1852800 5713351 Dshi_1783 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533126.1 1852555 R 398580 CDS YP_001533127.1 159044333 5713352 1853035..1853577 1 NC_009952.1 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 1853577 5713352 Dshi_1784 Dinoroseobacter shibae DFL 12 = DSM 16493 putative RNA polymerase sigma factor YP_001533127.1 1853035 D 398580 CDS YP_001533128.1 159044334 5713353 complement(1854290..1857964) 1 NC_009952.1 Catalyzes the rate-limiting step in dNTP synthesis; ribonucleotide-diphosphate reductase subunit alpha 1857964 nrdJ 5713353 nrdJ Dinoroseobacter shibae DFL 12 = DSM 16493 ribonucleotide-diphosphate reductase subunit alpha YP_001533128.1 1854290 R 398580 CDS YP_001533129.1 159044335 5713354 1858657..1859097 1 NC_009952.1 hypothetical protein 1859097 5713354 Dshi_1786 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533129.1 1858657 D 398580 CDS YP_001533130.1 159044336 5713356 complement(1859391..1859876) 1 NC_009952.1 COG: COG1430 - Uncharacterized conserved protein; PFAM: PF02643; hypothetical protein 1859876 5713356 Dshi_1787 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533130.1 1859391 R 398580 CDS YP_001533131.1 159044337 5713357 complement(1859873..1860394) 1 NC_009952.1 SWISSPROT P32081: Cold shock protein cspB; COG: COG1278 - Cold shock proteins; PFAM: PF00313; SMART: SM00357; SPRINT: PR00050; putative cold shock protein 1860394 5713357 Dshi_1788 Dinoroseobacter shibae DFL 12 = DSM 16493 putative cold shock protein YP_001533131.1 1859873 R 398580 CDS YP_001533132.1 159044338 5713358 complement(1860527..1861132) 1 NC_009952.1 TIGRFAM: TIGR00558 pyridoxamine-phosphate oxidase; COG: COG0259; PFAM: PF01243; PROSITE: PS01064; SUPERFAMILY: SSF50475; pyridoxamine 5'-phosphate oxidase 1861132 pdxH 5713358 pdxH Dinoroseobacter shibae DFL 12 = DSM 16493 pyridoxamine 5'-phosphate oxidase YP_001533132.1 1860527 R 398580 CDS YP_001533133.1 159044339 5713359 1861237..1862055 1 NC_009952.1 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 1862055 fabI2 5713359 fabI2 Dinoroseobacter shibae DFL 12 = DSM 16493 NADH dependent enoyl-[acyl-carrier-protein] reductase YP_001533133.1 1861237 D 398580 CDS YP_001533134.1 159044340 5713360 1862057..1862668 1 NC_009952.1 PFAM: PF01810-LysE type translocator; COG: COG1280 - Putative threonine efflux protein; SWISSPROT P0AG38: Threonine efflux protein (rhtC); putative LysE type translocator 1862668 5713360 Dshi_1791 Dinoroseobacter shibae DFL 12 = DSM 16493 putative LysE type translocator YP_001533134.1 1862057 D 398580 CDS YP_001533135.1 159044341 5713361 1862665..1863276 1 NC_009952.1 PFAM: PF01810-LysE type translocator; COG: COG1280 - Putative threonine efflux protein; SWISSPROT P0AG38: Threonine efflux protein (rhtC); putative LysE type translocator 1863276 5713361 Dshi_1792 Dinoroseobacter shibae DFL 12 = DSM 16493 putative LysE type translocator YP_001533135.1 1862665 D 398580 CDS YP_001533136.1 159044342 5713362 1863339..1863842 1 NC_009952.1 catalyzes the conversion of guanine, xanthine and, to a lesser extent, hypoxanthine to GMP, XMP and IMP, respectively; xanthine-guanine phosphoribosyltransferase 1863842 gpt 5713362 gpt Dinoroseobacter shibae DFL 12 = DSM 16493 xanthine-guanine phosphoribosyltransferase YP_001533136.1 1863339 D 398580 CDS YP_001533137.1 159044343 5713363 1863844..1865025 1 NC_009952.1 COG: COG0436 - Aspartate/tyrosine/aromatic aminotransferase; PFAM: PF00155; SPRINT: PR00753; Gene3D: G3DSA:3.40.640.10; SUPERFAMILY: SSF53383; hypothetical protein 1865025 5713363 Dshi_1794 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533137.1 1863844 D 398580 CDS YP_001533138.1 159044344 5713364 1865219..1867063 1 NC_009952.1 SWISSPROT P0ADY1: Peptidyl-prolyl cis-trans isomerase D; SUPERFAMILY: SSF54534, SSF81827; putative peptidyl-prolyl cis-trans isomerase 1867063 5713364 Dshi_1795 Dinoroseobacter shibae DFL 12 = DSM 16493 putative peptidyl-prolyl cis-trans isomerase YP_001533138.1 1865219 D 398580 CDS YP_001533139.1 159044345 5712784 1867111..1868640 1 NC_009952.1 with component II, the glutamine amidotransferase, catalyzes the formation of anthranilate from chorismate and glutamine; anthranilate synthase component I 1868640 trpE 5712784 trpE Dinoroseobacter shibae DFL 12 = DSM 16493 anthranilate synthase component I YP_001533139.1 1867111 D 398580 CDS YP_001533140.1 159044346 5712785 complement(1868767..1870593) 1 NC_009952.1 PFAM: PF04748; hypothetical protein 1870593 5712785 Dshi_1797 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533140.1 1868767 R 398580 CDS YP_001533141.1 159044347 5712786 1870777..1871382 1 NC_009952.1 TrpG; with TrpE catalyzes the formation of anthranilate and glutamate from chorismate and glutamine; TrpG provides the glutamine amidotransferase activity; anthranilate synthase component II 1871382 trpG 5712786 trpG Dinoroseobacter shibae DFL 12 = DSM 16493 anthranilate synthase component II YP_001533141.1 1870777 D 398580 CDS YP_001533142.1 159044348 5712787 1871379..1872398 1 NC_009952.1 Catalyzes the conversion of N-(5-phospho-D-ribosyl)-anthranilate and diphosphate to anthranilate and 5-phospho-alpha-D-ribose 1-diphosphate; anthranilate phosphoribosyltransferase 1872398 trpD 5712787 trpD Dinoroseobacter shibae DFL 12 = DSM 16493 anthranilate phosphoribosyltransferase YP_001533142.1 1871379 D 398580 CDS YP_001533143.1 159044349 5712788 1872395..1873210 1 NC_009952.1 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 1873210 trpC 5712788 trpC Dinoroseobacter shibae DFL 12 = DSM 16493 Indole-3-glycerol phosphate synthase YP_001533143.1 1872395 D 398580 CDS YP_001533144.1 159044350 5712789 1873207..1873683 1 NC_009952.1 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 1873683 moaC 5712789 moaC Dinoroseobacter shibae DFL 12 = DSM 16493 molybdenum cofactor biosynthesis protein MoaC YP_001533144.1 1873207 D 398580 CDS YP_001533145.1 159044351 5712790 1873680..1874888 1 NC_009952.1 SWISSPROT P12281: Molybdopterin biosynthesis protein moeA; TIGRFAM: TIGR00177; PFAM: pfam03453, pfam00994, pfam03454; COG: COG0303 - Molybdopterin biosynthesis enzyme; molybdopterin biosynthesis protein 1874888 moeA1 5712790 moeA1 Dinoroseobacter shibae DFL 12 = DSM 16493 molybdopterin biosynthesis protein YP_001533145.1 1873680 D 398580 CDS YP_001533146.1 159044352 5712791 1875043..1875738 1 NC_009952.1 Represses a number of genes involved in the response to DNA damage; LexA repressor 1875738 lexA 5712791 lexA Dinoroseobacter shibae DFL 12 = DSM 16493 LexA repressor YP_001533146.1 1875043 D 398580 CDS YP_001533147.1 159044353 5712792 complement(1875927..1878011) 1 NC_009952.1 PFAM: PF03772; TIGRFAM: TIGR00360; putative competence protein 1878011 5712792 Dshi_1804 Dinoroseobacter shibae DFL 12 = DSM 16493 putative competence protein YP_001533147.1 1875927 R 398580 CDS YP_001533148.1 159044354 5712793 1878120..1879535 1 NC_009952.1 Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation; glutamyl-tRNA synthetase 1879535 gltX 5712793 gltX Dinoroseobacter shibae DFL 12 = DSM 16493 glutamyl-tRNA synthetase YP_001533148.1 1878120 D 398580 CDS YP_001533149.1 159044355 5712794 1879651..1880943 1 NC_009952.1 SWISSPROT P0ABH7: Citrate synthase; TIGR01798 citrate synthase I (hexameric type); COG: COG0372; PFAM: PF00285; PROSITE: PS00480; PRINTS: PR00143; citrate synthase 1880943 gltA2 5712794 gltA2 Dinoroseobacter shibae DFL 12 = DSM 16493 citrate synthase YP_001533149.1 1879651 D 398580 CDS YP_001533150.1 159044356 5712795 1881214..1881651 1 NC_009952.1 PFAM: PF00582; PRINTS: PR01438; putative universal stress protein 1881651 5712795 Dshi_1807 Dinoroseobacter shibae DFL 12 = DSM 16493 putative universal stress protein YP_001533150.1 1881214 D 398580 CDS YP_001533151.1 159044357 5712796 1881663..1883201 1 NC_009952.1 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 1883201 5712796 Dshi_1808 Dinoroseobacter shibae DFL 12 = DSM 16493 putative sodium:alanine symporter family protein YP_001533151.1 1881663 D 398580 CDS YP_001533152.1 159044358 5712797 complement(1883361..1886222) 1 NC_009952.1 The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrA is an ATPase and a DNA-binding protein. A damage recognition complex composed of 2 uvrA and 2 uvrB subunits scans DNA for abnormalities. When the presence of a lesion has been verified by uvrB, the uvrA molecules dissociate; excinuclease ABC subunit A 1886222 uvrA 5712797 uvrA Dinoroseobacter shibae DFL 12 = DSM 16493 excinuclease ABC subunit A YP_001533152.1 1883361 R 398580 CDS YP_001533153.1 159044359 5712798 complement(1886324..1887496) 1 NC_009952.1 PFAM PF07690: Major facilitator superfamily; PROSITE: PS50850; putative major facilitator superfamily transport protein 1887496 5712798 Dshi_1810 Dinoroseobacter shibae DFL 12 = DSM 16493 putative major facilitator superfamily transport protein YP_001533153.1 1886324 R 398580 CDS YP_001533154.1 159044360 5712799 complement(1887561..1888958) 1 NC_009952.1 E3 component of pyruvate complex; catalyzes the oxidation of dihydrolipoamide to lipoamide; dihydrolipoamide dehydrogenase 1888958 lpdV 5712799 lpdV Dinoroseobacter shibae DFL 12 = DSM 16493 dihydrolipoamide dehydrogenase YP_001533154.1 1887561 R 398580 CDS YP_001533155.1 159044361 5712800 complement(1889023..1889616) 1 NC_009952.1 PFAM: PF06041; hypothetical protein 1889616 5712800 Dshi_1812 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533155.1 1889023 R 398580 CDS YP_001533156.1 159044362 5712801 complement(1889690..1890979) 1 NC_009952.1 PFAM PF07690: Major facilitator superfamily; PROSITE: PS50850; major facilitator superfamiy transporter 1890979 5712801 Dshi_1813 Dinoroseobacter shibae DFL 12 = DSM 16493 major facilitator superfamiy transporter YP_001533156.1 1889690 R 398580 CDS YP_001533157.1 159044363 5712804 1891703..1892863 1 NC_009952.1 PROSITE: PS00018; hypothetical protein 1892863 5712804 Dshi_1814 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533157.1 1891703 D 398580 CDS YP_001533158.1 159044364 5712805 complement(1893248..1894045) 1 NC_009952.1 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 1894045 5712805 Dshi_1815 Dinoroseobacter shibae DFL 12 = DSM 16493 putative transcriptional regulator YP_001533158.1 1893248 R 398580 CDS YP_001533159.1 159044365 5712806 complement(1894133..1895479) 1 NC_009952.1 COG3264 - Small-conductance mechanosensitive channel; PFAM: PF00924; SUPERFAMILY: SSF50182, SSF82861, SSF82689; mscS family protein 1895479 5712806 Dshi_1816 Dinoroseobacter shibae DFL 12 = DSM 16493 mscS family protein YP_001533159.1 1894133 R 398580 CDS YP_001533160.1 159044366 5712807 complement(1895702..1896640) 1 NC_009952.1 COG1741 - Pirin-related protein; PFAM: PF05726, PF02678; pirin-like protein 1896640 5712807 Dshi_1817 Dinoroseobacter shibae DFL 12 = DSM 16493 pirin-like protein YP_001533160.1 1895702 R 398580 CDS YP_001533161.1 159044367 5712808 complement(1896712..1896984) 1 NC_009952.1 hypothetical protein 1896984 5712808 Dshi_1818 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533161.1 1896712 R 398580 CDS YP_001533162.1 159044368 5712809 complement(1897085..1897816) 1 NC_009952.1 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 1897816 5712809 Dshi_1819 Dinoroseobacter shibae DFL 12 = DSM 16493 putative transcriptional regulator YP_001533162.1 1897085 R 398580 CDS YP_001533163.1 159044369 5712811 1898151..1898933 1 NC_009952.1 catalyzes the hydrolysis of mannosyl-3-phosphoglycerate to form the osmolyte mannosylglycerate; mannosyl-3-phosphoglycerate phosphatase 1898933 5712811 Dshi_1820 Dinoroseobacter shibae DFL 12 = DSM 16493 mannosyl-3-phosphoglycerate phosphatase YP_001533163.1 1898151 D 398580 CDS YP_001533164.1 159044370 5712812 1898926..1900176 1 NC_009952.1 hypothetical protein 1900176 5712812 Dshi_1821 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533164.1 1898926 D 398580 CDS YP_001533165.1 159044371 5712813 1900181..1901206 1 NC_009952.1 TIGRFAM: TIGR00832 arsenical-resistance protein; COG: COG0798 - Arsenite efflux pump ACR3 and related permeases; PFAM: PF01758; putative arsenic resistance protein 1901206 5712813 Dshi_1822 Dinoroseobacter shibae DFL 12 = DSM 16493 putative arsenic resistance protein YP_001533165.1 1900181 D 398580 CDS YP_001533166.1 159044372 5712814 complement(1901376..1902356) 1 NC_009952.1 hypothetical protein 1902356 5712814 Dshi_1823 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533166.1 1901376 R 398580 CDS YP_001533167.1 159044373 5712815 complement(1902502..1904265) 1 NC_009952.1 SWISSPROT P76041: Putative sucrose phosphorylase, P10249: Sucrose phosphorylase; COG: COG0366 - Glycosidases; PFAM: PF00128; putative sucrose phosphorylase 1904265 5712815 Dshi_1824 Dinoroseobacter shibae DFL 12 = DSM 16493 putative sucrose phosphorylase YP_001533167.1 1902502 R 398580 CDS YP_001533168.1 159044374 5712816 complement(1904769..1905794) 1 NC_009952.1 SWISSPROT P39646: Posphate acetyltransferase; TIGRFAM: TIGR00651; COG: COG0280; PFAM: PF01515-Phosphate acetyl/butaryl transferase; phosphate acetyl transferase 1905794 pta1 5712816 pta1 Dinoroseobacter shibae DFL 12 = DSM 16493 phosphate acetyl transferase YP_001533168.1 1904769 R 398580 CDS YP_001533169.1 159044375 5712817 complement(1905847..1906206) 1 NC_009952.1 PFAM: PF05899, SUPERFAMILY: SSF51182; hypothetical protein 1906206 5712817 Dshi_1826 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533169.1 1905847 R 398580 CDS YP_001533170.1 159044376 5712818 complement(1906223..1907263) 1 NC_009952.1 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 1907263 5712818 Dshi_1827 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533170.1 1906223 R 398580 CDS YP_001533171.1 159044377 5712819 complement(1907402..1909183) 1 NC_009952.1 catalyzes the formation of acetyl phosphate and sulfite from 2-sulfoacetaldehyde; is active when grown on taurine as a sole carbon source; sulfoacetaldehyde acetyltransferase 1909183 xcs 5712819 xcs Dinoroseobacter shibae DFL 12 = DSM 16493 sulfoacetaldehyde acetyltransferase YP_001533171.1 1907402 R 398580 CDS YP_001533172.1 159044378 5712820 complement(1909208..1910602) 1 NC_009952.1 PFAM: PF01266; COG: COG0665 - Glycine/D-amino acid oxidases (deaminating); putative FAD-dependent oxidoreductase 1910602 5712820 Dshi_1829 Dinoroseobacter shibae DFL 12 = DSM 16493 putative FAD-dependent oxidoreductase YP_001533172.1 1909208 R 398580 CDS YP_001533173.1 159044379 5712821 complement(1910630..1911016) 1 NC_009952.1 PFAM: PF07366; hypothetical protein 1911016 5712821 Dshi_1830 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533173.1 1910630 R 398580 CDS YP_001533174.1 159044380 5712822 complement(1911041..1911544) 1 NC_009952.1 PFAM: PF00582; PRINTS: PR01438; COG: COG0589 - Universal stress protein UspA and related nucleotide-binding proteins; putative universal stress protein 1911544 5712822 Dshi_1831 Dinoroseobacter shibae DFL 12 = DSM 16493 putative universal stress protein YP_001533174.1 1911041 R 398580 CDS YP_001533175.1 159044381 5712823 complement(1911569..1912909) 1 NC_009952.1 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 1912909 siaT 5712823 siaT Dinoroseobacter shibae DFL 12 = DSM 16493 sialic acid TRAP transporter permease YP_001533175.1 1911569 R 398580 CDS YP_001533176.1 159044382 5712824 complement(1912909..1913475) 1 NC_009952.1 PFAM: PF04290; DctQ component; putative TRAP transporter 1913475 5712824 Dshi_1833 Dinoroseobacter shibae DFL 12 = DSM 16493 putative TRAP transporter YP_001533176.1 1912909 R 398580 CDS YP_001533177.1 159044383 5712825 complement(1913539..1914555) 1 NC_009952.1 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 1914555 5712825 Dshi_1834 Dinoroseobacter shibae DFL 12 = DSM 16493 putative sialic acid-binding periplasmic protein YP_001533177.1 1913539 R 398580 CDS YP_001533178.1 159044384 5712826 1914712..1916187 1 NC_009952.1 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 1916187 5712826 Dshi_1835 Dinoroseobacter shibae DFL 12 = DSM 16493 putative transcriptional regulator YP_001533178.1 1914712 D 398580 CDS YP_001533179.1 159044385 5712828 1916867..1917976 1 NC_009952.1 PROSITE: PS50817; hypothetical protein 1917976 5712828 Dshi_1836 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533179.1 1916867 D 398580 CDS YP_001533180.1 159044386 5712829 complement(1917978..1919549) 1 NC_009952.1 SWISSPROT P31806: Uncharacterized protein yjeF; TIGRFAM: TIGR00197, TIGR00196; PFAM: PF03853, PF01256; COG: COG0063 - Predicted sugar kinase; yjeF-like protein 1919549 5712829 Dshi_1837 Dinoroseobacter shibae DFL 12 = DSM 16493 yjeF-like protein YP_001533180.1 1917978 R 398580 CDS YP_001533181.1 159044387 5712830 1919720..1920058 1 NC_009952.1 SWISSPROT P0A9Z1: Nitrogen regulation protein PII-1 (glnB); PROSITE: PS00496; PFAM: PF00543; putative nitrogen regulation protein PII 1920058 5712830 Dshi_1838 Dinoroseobacter shibae DFL 12 = DSM 16493 putative nitrogen regulation protein PII YP_001533181.1 1919720 D 398580 CDS YP_001533182.1 159044388 5712831 1920126..1921532 1 NC_009952.1 SWISSPROT P0A9C5: Glutamine synthetase; TIGRFAM: TIGR00653 glutamine synthetase, type I; COG: COG0174; glutamine synthetase 1921532 glnA 5712831 glnA Dinoroseobacter shibae DFL 12 = DSM 16493 glutamine synthetase YP_001533182.1 1920126 D 398580 CDS YP_001533183.1 159044389 5712832 1921699..1922916 1 NC_009952.1 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 1922916 5712832 Dshi_1840 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533183.1 1921699 D 398580 CDS YP_001533184.1 159044390 5712833 complement(1923108..1923518) 1 NC_009952.1 hypothetical protein 1923518 5712833 Dshi_1841 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533184.1 1923108 R 398580 CDS YP_001533185.1 159044391 5712834 1923555..1924907 1 NC_009952.1 Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide; adenylosuccinate lyase 1924907 purB 5712834 purB Dinoroseobacter shibae DFL 12 = DSM 16493 adenylosuccinate lyase YP_001533185.1 1923555 D 398580 CDS YP_001533186.1 159044392 5712835 1925007..1925174 1 NC_009952.1 hypothetical protein 1925174 5712835 Dshi_1843 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533186.1 1925007 D 398580 CDS YP_001533187.1 159044393 5712836 1925279..1925812 1 NC_009952.1 PFAM: pfam00515; PROSITE: PS50005, PS50293; related to tetratricopeptide-like; hypothetical protein 1925812 5712836 Dshi_1844 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533187.1 1925279 D 398580 CDS YP_001533188.1 159044394 5712837 1925869..1926918 1 NC_009952.1 SWISSPROT P0ABZ1: Flagellar motor switch protein fliG; COG: COG1536 - Flagellar motor switch protein; PFAM: PF01706; PRINTS: PR00954; putative flagellar motor switch protein fliG 1926918 5712837 Dshi_1845 Dinoroseobacter shibae DFL 12 = DSM 16493 putative flagellar motor switch protein fliG YP_001533188.1 1925869 D 398580 CDS YP_001533189.1 159044395 5712838 1927300..1927743 1 NC_009952.1 SUPERFAMILY: SSF75169; hypothetical protein 1927743 5712838 Dshi_1846 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533189.1 1927300 D 398580 CDS YP_001533190.1 159044396 5712839 1927842..1928210 1 NC_009952.1 PFAM: PF02211; SUPERFAMILY: SSF50090; similar to nitrile hydratase subunit beta; hypothetical protein 1928210 5712839 Dshi_1847 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533190.1 1927842 D 398580 CDS YP_001533191.1 159044397 5712840 1928185..1928493 1 NC_009952.1 PFAM: PF02211; SUPERFAMILY: SSF50090; similar to nitrile hydratase subunit beta; hypothetical protein 1928493 5712840 Dshi_1848 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533191.1 1928185 D 398580 CDS YP_001533192.1 159044398 5712841 1928483..1929094 1 NC_009952.1 SWISSPROT Q7SID2: Cobalt-containing nitrile hydratase subunit alpha, P97051: Nitrile hydratase subunit alpha; PFAM: PF02979; PIR: PIRSF001426; nitrile hydratse subunit alpha 1929094 nthA 5712841 nthA Dinoroseobacter shibae DFL 12 = DSM 16493 nitrile hydratse subunit alpha YP_001533192.1 1928483 D 398580 CDS YP_001533193.1 159044399 5712842 complement(1929104..1929808) 1 NC_009952.1 PFAM PF06764: Protein of unknown function DUF1223; hypothetical protein 1929808 5712842 Dshi_1850 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533193.1 1929104 R 398580 CDS YP_001533194.1 159044400 5712843 1930031..1932817 1 NC_009952.1 Catalyzes the conversion of citrate to isocitrate; aconitate hydratase 1932817 acnA 5712843 acnA Dinoroseobacter shibae DFL 12 = DSM 16493 aconitate hydratase YP_001533194.1 1930031 D 398580 CDS YP_001533195.1 159044401 5712844 complement(1932907..1933446) 1 NC_009952.1 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 1933446 5712844 Dshi_1852 Dinoroseobacter shibae DFL 12 = DSM 16493 putative thioredoxin YP_001533195.1 1932907 R 398580 CDS YP_001533196.1 159044402 5712845 complement(1933597..1934328) 1 NC_009952.1 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 1934328 ccmC 5712845 ccmC Dinoroseobacter shibae DFL 12 = DSM 16493 heme exporter protein C YP_001533196.1 1933597 R 398580 CDS YP_001533197.1 159044403 5712846 complement(1934384..1935040) 1 NC_009952.1 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 1935040 ccmB 5712846 ccmB Dinoroseobacter shibae DFL 12 = DSM 16493 heme exporter protein B YP_001533197.1 1934384 R 398580 CDS YP_001533198.1 159044404 5712847 complement(1935037..1935654) 1 NC_009952.1 ATP-binding protein; required for proper cytochrome c maturation; cytochrome c biogenesis protein CcmA 1935654 ccmA 5712847 ccmA Dinoroseobacter shibae DFL 12 = DSM 16493 cytochrome c biogenesis protein CcmA YP_001533198.1 1935037 R 398580 CDS YP_001533199.1 159044405 5712848 complement(1935699..1936058) 1 NC_009952.1 PFAM: Protein of unknown function (DUF498/DUF598); COG: COG3737; hypothetical protein 1936058 5712848 Dshi_1856 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533199.1 1935699 R 398580 CDS YP_001533200.1 159044406 5712849 complement(1936069..1936821) 1 NC_009952.1 PFAM: PF01925; PROSITE: PS00318; related to DUF81; hypothetical protein 1936821 5712849 Dshi_1857 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533200.1 1936069 R 398580 CDS YP_001533201.1 159044407 5712850 complement(1936814..1937776) 1 NC_009952.1 forms a complex with SecD and YajC; SecDFyajC stimulates the proton motive force-driven protein translocation; seems to modulate the cycling of SecA by stabilizing its membrane-inserted state and appears to be required for the release of mature proteins from the extracytoplasmic side of the membrane; in some organisms, such as Bacillus subtilis, SecD is fused to SecF; preprotein translocase subunit SecF 1937776 secF 5712850 secF Dinoroseobacter shibae DFL 12 = DSM 16493 preprotein translocase subunit SecF YP_001533201.1 1936814 R 398580 CDS YP_001533202.1 159044408 5712851 complement(1937778..1939442) 1 NC_009952.1 part of the preprotein secretory system; when complexed with proteins SecF and YajC, SecDFyajC stimulates the proton motive force-driven protein translocation, and appears to be required for the release of mature proteins from the extracytoplasmic side of the membrane; preprotein translocase subunit SecD 1939442 secD 5712851 secD Dinoroseobacter shibae DFL 12 = DSM 16493 preprotein translocase subunit SecD YP_001533202.1 1937778 R 398580 CDS YP_001533203.1 159044409 5712852 complement(1939449..1939766) 1 NC_009952.1 SV; Pfam: preprotein translocase subunit, ProDom: YajC preprotein translocase subunit, TIGRFAM: YajC; preprotein translocase subunit 1939766 yajC 5712852 yajC Dinoroseobacter shibae DFL 12 = DSM 16493 preprotein translocase subunit YP_001533203.1 1939449 R 398580 CDS YP_001533204.1 159044410 5712853 1940020..1940709 1 NC_009952.1 hypothetical protein 1940709 5712853 Dshi_1861 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533204.1 1940020 D 398580 CDS YP_001533205.1 159044411 5712854 1940803..1941114 1 NC_009952.1 PFAM: PF00805; COG: COG1357 - Uncharacterized low-complexity proteins; hypothetical protein 1941114 5712854 Dshi_1862 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533205.1 1940803 D 398580 CDS YP_001533206.1 159044412 5712855 1941457..1942752 1 NC_009952.1 catalyzes a two-step reaction, first charging a serine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; seryl-tRNA synthetase 1942752 serS 5712855 serS Dinoroseobacter shibae DFL 12 = DSM 16493 seryl-tRNA synthetase YP_001533206.1 1941457 D 398580 CDS YP_001533207.1 159044413 5712856 1942814..1943926 1 NC_009952.1 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 1943926 5712856 Dshi_1864 Dinoroseobacter shibae DFL 12 = DSM 16493 putative membrane-bound lytic murein transglycosylase YP_001533207.1 1942814 D 398580 CDS YP_001533208.1 159044414 5712857 complement(1944045..1944914) 1 NC_009952.1 hypothetical protein 1944914 5712857 Dshi_1865 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533208.1 1944045 R 398580 CDS YP_001533209.1 159044415 5712858 complement(1945208..1946029) 1 NC_009952.1 COG: COG5473 - Predicted integral membrane protein; hypothetical protein 1946029 5712858 Dshi_1866 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533209.1 1945208 R 398580 CDS YP_001533210.1 159044416 5712859 complement(1946164..1947480) 1 NC_009952.1 SWISSPROT P31592: Glutamine synthetase 3; COG: COG0174 - Glutamine synthetase; PFAM: PF00120; PROSITE: PS00181; SUPERFAMILY: SSF54368; glutamine synthetase 1947480 glnT 5712859 glnT Dinoroseobacter shibae DFL 12 = DSM 16493 glutamine synthetase YP_001533210.1 1946164 R 398580 CDS YP_001533211.1 159044417 5712860 complement(1947542..1948876) 1 NC_009952.1 SWISSPROT O87392: Glutamate synthase large subunit-like protein (glxD); PFAM: PF01645; COG: COG0069 - Glutamate synthase domain 2; putative glutamate synthase large subunit-like protein 1948876 5712860 Dshi_1868 Dinoroseobacter shibae DFL 12 = DSM 16493 putative glutamate synthase large subunit-like protein YP_001533211.1 1947542 R 398580 CDS YP_001533212.1 159044418 5712861 complement(1948897..1949574) 1 NC_009952.1 PFAM: PF01493; PIR: PIRSF006519; SWISSPROT O87391: Protein glxC; COG: COG0070 - Glutamate synthase domain 3; fwdC/fmdC family protein; putative glutamate synthase 1949574 5712861 Dshi_1869 Dinoroseobacter shibae DFL 12 = DSM 16493 putative glutamate synthase YP_001533212.1 1948897 R 398580 CDS YP_001533213.1 159044419 5712862 complement(1949574..1950500) 1 NC_009952.1 PFAM: PF00310; PROSITE: PS01039; SWISSPROT O87390: Glutamine amidotransferase-like protein glxB; COG: COG0067 - Glutamate synthase domain 1; class II; putative glutamine amidotransferase 1950500 5712862 Dshi_1870 Dinoroseobacter shibae DFL 12 = DSM 16493 putative glutamine amidotransferase YP_001533213.1 1949574 R 398580 CDS YP_001533214.1 159044420 5712863 complement(1950576..1951223) 1 NC_009952.1 PFAM: PF01381, PF07883; PROSITE: PS50943; SUPERFAMILY: SSF51182, SSF47413; COG: COG1396 - Predicted transcriptional regulators; putative HTH-type transcriptional regulator 1951223 5712863 Dshi_1871 Dinoroseobacter shibae DFL 12 = DSM 16493 putative HTH-type transcriptional regulator YP_001533214.1 1950576 R 398580 CDS YP_001533215.1 159044421 5712864 complement(1951375..1952643) 1 NC_009952.1 SUPERFAMILY: SSF50952; Gene3D: G3DSA:2.120.10.30; COG: COG2133 - Glucose/sorbosone dehydrogenases; putative soluble aldose sugar dehydrogenase 1952643 5712864 Dshi_1872 Dinoroseobacter shibae DFL 12 = DSM 16493 putative soluble aldose sugar dehydrogenase YP_001533215.1 1951375 R 398580 CDS YP_001533216.1 159044422 5712865 complement(1952797..1953105) 1 NC_009952.1 SWISSPROT P00105: Cytochrome c-554(548); PFAM: PF00034- cytochrome c; COG: COG2863 - Cytochrome c553; putative cytochrome c 1953105 5712865 Dshi_1873 Dinoroseobacter shibae DFL 12 = DSM 16493 putative cytochrome c YP_001533216.1 1952797 R 398580 CDS YP_001533217.1 159044423 5712866 complement(1953173..1953769) 1 NC_009952.1 PFAM: PF00440; PROSITE: PS50977; SUPERFAMILY: SSF46689, SSF48498; COG: COG1309 - Transcriptional regulator; tetR family; putative regulatory protein 1953769 5712866 Dshi_1874 Dinoroseobacter shibae DFL 12 = DSM 16493 putative regulatory protein YP_001533217.1 1953173 R 398580 CDS YP_001533218.1 159044424 5712867 1953908..1954423 1 NC_009952.1 PFAM: PF04224-Protein of unknown function, DUF417; COG: Predicted membrane protein; SWISSPROT P75685: Inner membrane protein ykgB; DUF417; putative inner membrane protein 1954423 5712867 Dshi_1875 Dinoroseobacter shibae DFL 12 = DSM 16493 putative inner membrane protein YP_001533218.1 1953908 D 398580 CDS YP_001533219.1 159044425 5712868 1954483..1954755 1 NC_009952.1 SWISSPROT P0AC62: Glutaredoxin-3; TIGRFAM: TIGR02181 Glutaredoxin, GrxC family; COG: COG0695 - Glutaredoxin and related proteins; PFAM: PF00462-Glutaredoxin; grxC; putative glutaredoxin 3 1954755 5712868 Dshi_1876 Dinoroseobacter shibae DFL 12 = DSM 16493 putative glutaredoxin 3 YP_001533219.1 1954483 D 398580 CDS YP_001533220.1 159044426 5712869 complement(1954772..1956046) 1 NC_009952.1 COG: COG4325 - Predicted membrane protein; hypothetical protein 1956046 5712869 Dshi_1877 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533220.1 1954772 R 398580 CDS YP_001533221.1 159044427 5712870 complement(1956140..1957117) 1 NC_009952.1 SUPERFAMILY: SSF56784; hypothetical protein 1957117 5712870 Dshi_1878 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533221.1 1956140 R 398580 CDS YP_001533222.1 159044428 5712871 complement(1957234..1958421) 1 NC_009952.1 COG: COG3825 - Uncharacterized protein conserved in bacteria; hypothetical protein 1958421 5712871 Dshi_1879 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533222.1 1957234 R 398580 CDS YP_001533223.1 159044429 5712872 complement(1958425..1958592) 1 NC_009952.1 hypothetical protein 1958592 5712872 Dshi_1880 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533223.1 1958425 R 398580 CDS YP_001533224.1 159044430 5712873 complement(1958592..1959968) 1 NC_009952.1 PROSITE: PS00214, PS51257; hypothetical protein 1959968 5712873 Dshi_1881 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533224.1 1958592 R 398580 CDS YP_001533225.1 159044431 5712874 complement(1959965..1960423) 1 NC_009952.1 PFAM: PF00583; PROSITE: PS51186; SUPERFAMILY: SSF55729; putative acetyltransferase 1960423 5712874 Dshi_1882 Dinoroseobacter shibae DFL 12 = DSM 16493 putative acetyltransferase YP_001533225.1 1959965 R 398580 CDS YP_001533226.1 159044432 5712875 complement(1960643..1961485) 1 NC_009952.1 COG: COG0714 - MoxR-like ATPases; PFAM: PF00004; SMART: SM00382 ; PRITNTS: PR00300; putative clpA/clpB family protein 1961485 5712875 Dshi_1883 Dinoroseobacter shibae DFL 12 = DSM 16493 putative clpA/clpB family protein YP_001533226.1 1960643 R 398580 CDS YP_001533227.1 159044433 5712876 1961615..1962088 1 NC_009952.1 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 1962088 5712876 Dshi_1884 Dinoroseobacter shibae DFL 12 = DSM 16493 putative DnaK suppressor protein YP_001533227.1 1961615 D 398580 CDS YP_001533228.1 159044434 5712877 1962221..1963390 1 NC_009952.1 COG: COG0654 - 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases; PFAM: PF01266; PRINTS: PR00420; putative salicylate hydroxylase 1963390 5712877 Dshi_1885 Dinoroseobacter shibae DFL 12 = DSM 16493 putative salicylate hydroxylase YP_001533228.1 1962221 D 398580 CDS YP_001533229.1 159044435 5712878 complement(1963398..1964177) 1 NC_009952.1 TIGRFAM: TIGR00195 exodeoxyribonuclease III, TIGR00633 exodeoxyribonuclease III (xth); COG: COG0708 - Exonuclease III; PFAM: PF03372-Endonuclease/Exonuclease/phosphatase family; PROSITE: PS00726; xthA; putative Exodeoxyribonuclease III 1964177 5712878 Dshi_1886 Dinoroseobacter shibae DFL 12 = DSM 16493 putative Exodeoxyribonuclease III YP_001533229.1 1963398 R 398580 CDS YP_001533230.1 159044436 5712879 complement(1964382..1965539) 1 NC_009952.1 TIGRFAM: TIGR01388; COG: COG0349; PFAM: PF01612; SMART: SM00474; PROSITE: PS50967; SUPERFAMILY: SSF53098; rnd; putative ribonuclease D 1965539 5712879 Dshi_1887 Dinoroseobacter shibae DFL 12 = DSM 16493 putative ribonuclease D YP_001533230.1 1964382 R 398580 CDS YP_001533231.1 159044437 5712880 complement(1965637..1966230) 1 NC_009952.1 TIGRFAM: TIGR00639 phosphoribosylglycinamide formyltransferase, formyltetrahydrofolate-dependent; COG: COG0299 - Folate-dependent phosphoribosylglycinamide formyltransferase PurN; PFAM PF00551: Formyl transferase; phosphoribosylglycinamide formyltransferase 1966230 purN 5712880 purN Dinoroseobacter shibae DFL 12 = DSM 16493 phosphoribosylglycinamide formyltransferase YP_001533231.1 1965637 R 398580 CDS YP_001533232.1 159044438 5712881 complement(1966227..1967288) 1 NC_009952.1 catalyzes the formation of 1-(5-phosphoribosyl)-5-aminoimidazole from 2-(formamido)-N1-(5-phosphoribosyl)acetamidine and ATP in purine biosynthesis; phosphoribosylaminoimidazole synthetase 1967288 purM 5712881 purM Dinoroseobacter shibae DFL 12 = DSM 16493 phosphoribosylaminoimidazole synthetase YP_001533232.1 1966227 R 398580 CDS YP_001533233.1 159044439 5712883 complement(1967456..1968577) 1 NC_009952.1 PFAM: PF08238; SMART: SM00671; SUPERFAMILY: SSF81901; hypothetical protein 1968577 5712883 Dshi_1890 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533233.1 1967456 R 398580 CDS YP_001533234.1 159044440 5712884 1968779..1969207 1 NC_009952.1 COG: COG1017 - Hemoglobin-like flavoprotein; PFAM: PF00042-Globin; SUPERFAMILY: Globin-like SSF46458; Gene3D: G3DSA:1.10.490.10; SWISSPROT P04252: Bacterial hemoglobin; putative flavohemoglobin 1969207 5712884 Dshi_1891 Dinoroseobacter shibae DFL 12 = DSM 16493 putative flavohemoglobin YP_001533234.1 1968779 D 398580 CDS YP_001533235.1 159044441 5712885 1969284..1970432 1 NC_009952.1 COG: COG3287 - Uncharacterized conserved protein; PFAM: PF08495; hypothetical protein 1970432 5712885 Dshi_1892 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533235.1 1969284 D 398580 CDS YP_001533236.1 159044442 5712886 1970454..1973216 1 NC_009952.1 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 1973216 5712886 Dshi_1893 Dinoroseobacter shibae DFL 12 = DSM 16493 LOV-regulator, Blue-light sensing YP_001533236.1 1970454 D 398580 CDS YP_001533237.1 159044443 5712887 1973228..1973842 1 NC_009952.1 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 1973842 5712887 Dshi_1894 Dinoroseobacter shibae DFL 12 = DSM 16493 putative response regulator receiver protein YP_001533237.1 1973228 D 398580 CDS YP_001533238.1 159044444 5712888 complement(1973861..1976413) 1 NC_009952.1 PFAM: PF00353; hypothetical protein 1976413 5712888 Dshi_1895 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533238.1 1973861 R 398580 CDS YP_001533239.1 159044445 5712889 complement(1976442..1977851) 1 NC_009952.1 SWISSPROT P11759: GDP-mannose 6-dehydrogenase; COG: COG1004 - Predicted UDP-glucose 6-dehydrogenase; PROSITE: PS00059; PFAM: PF03721, PF00984, PF03720; GDP-mannose 6-dehydrogenase 1977851 algD 5712889 algD Dinoroseobacter shibae DFL 12 = DSM 16493 GDP-mannose 6-dehydrogenase YP_001533239.1 1976442 R 398580 CDS YP_001533240.1 159044446 5712890 complement(1978068..1979498) 1 NC_009952.1 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 1979498 algA 5712890 algA Dinoroseobacter shibae DFL 12 = DSM 16493 alginate biosynthesis protein YP_001533240.1 1978068 R 398580 CDS YP_001533241.1 159044447 5712891 complement(1979617..1981209) 1 NC_009952.1 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 1981209 5712891 Dshi_1898 Dinoroseobacter shibae DFL 12 = DSM 16493 putative glycosyltransferase alg8 YP_001533241.1 1979617 R 398580 CDS YP_001533242.1 159044448 5712892 complement(1981196..1982602) 1 NC_009952.1 SWISSPROT P46682: p-hydroxybenzoic acid efflux pump subunit aaeA; related to efflux pump protein; hypothetical protein 1982602 5712892 Dshi_1899 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533242.1 1981196 R 398580 CDS YP_001533243.1 159044449 5712893 1982818..1984188 1 NC_009952.1 SWISSPROT P26276: Phosphomannomutase/phosphoglucomutase; COG: COG1109 - Phosphomannomutase; PFAM: PF02880, PF02879, PF02878, PF00408; PROSITE: PS00710; phosphomannomutase 1984188 algC 5712893 algC Dinoroseobacter shibae DFL 12 = DSM 16493 phosphomannomutase YP_001533243.1 1982818 D 398580 CDS YP_001533244.1 159044450 5712894 1984363..1984953 1 NC_009952.1 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 1984953 5712894 Dshi_1901 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533244.1 1984363 D 398580 CDS YP_001533245.1 159044451 5712895 1984955..1986331 1 NC_009952.1 COG: COG1696 - Predicted membrane protein involved in D-alanine export; PFAM: PF03062; putative poly(beta-D-mannuronate) O-acetylase 1986331 5712895 Dshi_1902 Dinoroseobacter shibae DFL 12 = DSM 16493 putative poly(beta-D-mannuronate) O-acetylase YP_001533245.1 1984955 D 398580 CDS YP_001533246.1 159044452 5712896 1986343..1987356 1 NC_009952.1 SWISSPROT Q51393; putative alginate biosynthesis protein algJ 1987356 5712896 Dshi_1903 Dinoroseobacter shibae DFL 12 = DSM 16493 putative alginate biosynthesis protein algJ YP_001533246.1 1986343 D 398580 CDS YP_001533247.1 159044453 5712897 1987353..1988663 1 NC_009952.1 SWISSPROT Q88NDO; similar to alginate biosynthesis protein algX; hypothetical protein 1988663 5712897 Dshi_1904 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533247.1 1987353 D 398580 CDS YP_001533248.1 159044454 5712898 1989272..1990372 1 NC_009952.1 PFAM: PF00589; Gene3D: G3DSA:1.10.443.10; similar to prophage integrase; hypothetical protein 1990372 5712898 Dshi_1905 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533248.1 1989272 D 398580 CDS YP_001533249.1 159044455 5712899 1990560..1990841 1 NC_009952.1 SUPERFAMILY: SSF46955; PFAM: PF00376; hypothetical protein 1990841 5712899 Dshi_1906 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533249.1 1990560 D 398580 CDS YP_001533250.1 159044456 5712900 1990957..1992414 1 NC_009952.1 PROSITE: PS00039; hypothetical protein 1992414 5712900 Dshi_1907 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533250.1 1990957 D 398580 CDS YP_001533251.1 159044457 5712901 1992667..1993284 1 NC_009952.1 hypothetical protein 1993284 5712901 Dshi_1908 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533251.1 1992667 D 398580 CDS YP_001533252.1 159044458 5712902 complement(1993959..1994612) 1 NC_009952.1 hypothetical protein 1994612 5712902 Dshi_1909 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533252.1 1993959 R 398580 CDS YP_001533253.1 159044459 5712903 1995268..1995951 1 NC_009952.1 hypothetical protein 1995951 5712903 Dshi_1910 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533253.1 1995268 D 398580 CDS YP_001533254.1 159044460 5712904 1995938..1996333 1 NC_009952.1 PS00527: Ribosomal protein S14 signature.; similar to ribosomal protein; hypothetical protein 1996333 5712904 Dshi_1911 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533254.1 1995938 D 398580 CDS YP_001533255.1 159044461 5712905 1996336..1996743 1 NC_009952.1 hypothetical protein 1996743 5712905 Dshi_1912 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533255.1 1996336 D 398580 CDS YP_001533256.1 159044462 5712906 complement(1996738..1997559) 1 NC_009952.1 PFAM: PF00665; PROSITE: PS50994; SUPERFAMILY: SSF53098; COG: COG2801 - Transposase and inactivated derivatives; putative insertion element 1997559 5712906 Dshi_1913 Dinoroseobacter shibae DFL 12 = DSM 16493 putative insertion element YP_001533256.1 1996738 R 398580 CDS YP_001533257.1 159044463 5712907 complement(1997583..1997849) 1 NC_009952.1 PFAM: PF01527-Transposase; putative insertion element / transposase 1997849 5712907 Dshi_1914 Dinoroseobacter shibae DFL 12 = DSM 16493 putative insertion element / transposase YP_001533257.1 1997583 R 398580 CDS YP_001533258.1 159044464 5712908 1998356..1999138 1 NC_009952.1 hypothetical protein 1999138 5712908 Dshi_1915 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533258.1 1998356 D 398580 CDS YP_001533259.1 159044465 5712909 1999123..1999854 1 NC_009952.1 hypothetical protein 1999854 5712909 Dshi_1916 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533259.1 1999123 D 398580 CDS YP_001533260.1 159044466 5712910 1999930..2001378 1 NC_009952.1 PROSITE: PS00093; PFAM: PF01555; putative modification methylase 2001378 5712910 Dshi_1917 Dinoroseobacter shibae DFL 12 = DSM 16493 putative modification methylase YP_001533260.1 1999930 D 398580 CDS YP_001533261.1 159044467 5712911 2001559..2002620 1 NC_009952.1 PROSITE: PS00093; PFAM: PF01555; putative modification methylase 2002620 5712911 Dshi_1918 Dinoroseobacter shibae DFL 12 = DSM 16493 putative modification methylase YP_001533261.1 2001559 D 398580 CDS YP_001533262.1 159044468 5712912 2002691..2004421 1 NC_009952.1 hypothetical protein 2004421 5712912 Dshi_1919 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533262.1 2002691 D 398580 CDS YP_001533263.1 159044469 5712914 complement(2005076..2005981) 1 NC_009952.1 PFAM: PF00753; hypothetical protein 2005981 5712914 Dshi_1920 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533263.1 2005076 R 398580 CDS YP_001533264.1 159044470 5712915 2006027..2007346 1 NC_009952.1 COG: COG0642 - Signal transduction histidine kinase; PFAM: PF02518, PF00672, PF00512; histidine kinase 2007346 5712915 Dshi_1921 Dinoroseobacter shibae DFL 12 = DSM 16493 histidine kinase YP_001533264.1 2006027 D 398580 CDS YP_001533265.1 159044471 5712916 complement(2007318..2007611) 1 NC_009952.1 hypothetical protein 2007611 5712916 Dshi_1922 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533265.1 2007318 R 398580 CDS YP_001533266.1 159044472 5712917 2007881..2009116 1 NC_009952.1 hypothetical protein 2009116 5712917 Dshi_1923 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533266.1 2007881 D 398580 CDS YP_001533267.1 159044473 5712918 2009151..2010203 1 NC_009952.1 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 2010203 5712918 Dshi_1924 Dinoroseobacter shibae DFL 12 = DSM 16493 putative TRAP transporter solute receptor YP_001533267.1 2009151 D 398580 CDS YP_001533268.1 159044474 5712919 complement(2010233..2012482) 1 NC_009952.1 COG: COG3267 - Type II secretory pathway, component ExeA (predicted ATPase); SMART: SM00382; SUPERFAMILY: SSF52540; putative ATPase 2012482 5712919 Dshi_1925 Dinoroseobacter shibae DFL 12 = DSM 16493 putative ATPase YP_001533268.1 2010233 R 398580 CDS YP_001533269.1 159044475 5712920 complement(2012570..2014753) 1 NC_009952.1 binding of PriA to forked DNA starts the assembly of the primosome, also possesses 3'-5' helicase activity; primosome assembly protein PriA 2014753 priA 5712920 priA Dinoroseobacter shibae DFL 12 = DSM 16493 primosome assembly protein PriA YP_001533269.1 2012570 R 398580 CDS YP_001533270.1 159044476 5712921 2014831..2015484 1 NC_009952.1 similar to novel fructose-6-phosphate aldolase from Escherichia coli; enzyme from Methanocaldococcus janaschii shows transaldolase activity; putative translaldolase 2015484 tal 5712921 tal Dinoroseobacter shibae DFL 12 = DSM 16493 putative translaldolase YP_001533270.1 2014831 D 398580 CDS YP_001533271.1 159044477 5712922 2015542..2016249 1 NC_009952.1 PFAM: PF04340 - Protein of unknown function, DUF484; hypothetical protein 2016249 5712922 Dshi_1928 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533271.1 2015542 D 398580 CDS YP_003422327.1 284928595 5712923 2016253..2017179 1 NC_009952.1 hypothetical protein 2017179 xerC 5712923 xerC Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_003422327.1 2016253 D 398580 CDS YP_001533272.1 159044478 5712924 complement(2017199..2018038) 1 NC_009952.1 PFAM: PF00892; SUPERFAMILY: SSF103481; hypothetical protein 2018038 5712924 Dshi_1930 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533272.1 2017199 R 398580 CDS YP_001533273.1 159044479 5712925 complement(2018101..2018352) 1 NC_009952.1 hypothetical protein 2018352 5712925 Dshi_1931 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533273.1 2018101 R 398580 CDS YP_001533274.1 159044480 5712926 complement(2018349..2019218) 1 NC_009952.1 COG: COG0625 - Glutathione S-transferase; PFAM: PF02798, PF00043; SUPERFAMILY: SSF47616, SSF52833; SWISSPROT Q46845: Uncharacterized GST-like protein yghU; putative glutathione S-transferase family protein 2019218 5712926 Dshi_1932 Dinoroseobacter shibae DFL 12 = DSM 16493 putative glutathione S-transferase family protein YP_001533274.1 2018349 R 398580 CDS YP_001533275.1 159044481 5712927 complement(2019318..2022293) 1 NC_009952.1 IleRS; catalyzes the formation of isoleucyl-tRNA(Ile) from isoleucine and tRNA(Ile); since isoleucine and other amino acids such as valine are similar, there are additional editing function in this enzyme; one is involved in hydrolysis of activated valine-AMP and the other is involved in deacylation of mischarged Val-tRNA(Ile); there are two active sites, one for aminoacylation and one for editing; class-I aminoacyl-tRNA synthetase family type 1 subfamily; some organisms carry two different copies of this enzyme; isoleucyl-tRNA synthetase 2022293 ileS 5712927 ileS Dinoroseobacter shibae DFL 12 = DSM 16493 isoleucyl-tRNA synthetase YP_001533275.1 2019318 R 398580 CDS YP_001533276.1 159044482 5712928 2022645..2023316 1 NC_009952.1 hypothetical protein 2023316 5712928 Dshi_1934 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533276.1 2022645 D 398580 CDS YP_001533277.1 159044483 5712929 complement(2023345..2024964) 1 NC_009952.1 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 2024964 5712929 Dshi_1935 Dinoroseobacter shibae DFL 12 = DSM 16493 putative thioredoxin reductase trxB with an additional cyclic nucleotide-monophosphate-binding domain YP_001533277.1 2023345 R 398580 CDS YP_001533278.1 159044484 5712930 complement(2024978..2025994) 1 NC_009952.1 TIGRFAM: TIGR01620 conserved hypothetical protein; COG: COG3768 - Predicted membrane protein; PFAM: pfam05128; family DUF697; hypothetical protein 2025994 5712930 Dshi_1936 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533278.1 2024978 R 398580 CDS YP_001533279.1 159044485 5712931 complement(2025991..2027403) 1 NC_009952.1 PFAM: PF04317-YcjX-like family, DUF463; SWISSPROT P76046: Uncharacterized protein ycjX; COG: COG3106 - Predicted ATPase; DUF463; YcjX-like family protein 2027403 5712931 Dshi_1937 Dinoroseobacter shibae DFL 12 = DSM 16493 YcjX-like family protein YP_001533279.1 2025991 R 398580 CDS YP_001533280.1 159044486 5712932 2027520..2028293 1 NC_009952.1 mediates pseudouridylation (positions 38, 39, 40) at the tRNA anticodon region which contributes to the structural stability; tRNA pseudouridine synthase A 2028293 truA 5712932 truA Dinoroseobacter shibae DFL 12 = DSM 16493 tRNA pseudouridine synthase A YP_001533280.1 2027520 D 398580 CDS YP_001533281.1 159044487 5712933 complement(2028410..2029231) 1 NC_009952.1 COG: COG0600 - ABC-type nitrate/sulfonate/bicarbonate transport system, permease component; PFAM: PF00528; PROSITE: PS50928; putative ABC transporter permease 2029231 5712933 Dshi_1939 Dinoroseobacter shibae DFL 12 = DSM 16493 putative ABC transporter permease YP_001533281.1 2028410 R 398580 CDS YP_001533282.1 159044488 5712934 complement(2029271..2030071) 1 NC_009952.1 COG: COG1116 - ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component; PFAM: PF00005; PROSITE: PS00211, PS50893; SMART: SM00382; ABC transporter ATP-binding protein 2030071 5712934 Dshi_1940 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC transporter ATP-binding protein YP_001533282.1 2029271 R 398580 CDS YP_001533283.1 159044489 5712935 complement(2030122..2031135) 1 NC_009952.1 PFAM: PF09084-NMT1/THI5 like; COG: COG0715 - ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components; NMT1/THI5 family protein 2031135 5712935 Dshi_1941 Dinoroseobacter shibae DFL 12 = DSM 16493 NMT1/THI5 family protein YP_001533283.1 2030122 R 398580 CDS YP_001533284.1 159044490 5712936 complement(2031291..2032652) 1 NC_009952.1 PFAM: PF08885; putative GSCFA family protein 2032652 5712936 Dshi_1942 Dinoroseobacter shibae DFL 12 = DSM 16493 putative GSCFA family protein YP_001533284.1 2031291 R 398580 CDS YP_001533285.1 159044491 5712937 complement(2032700..2033968) 1 NC_009952.1 Catalyzes the deamination of cytosine to uracil and ammonia; cytosine deaminase 2033968 codA 5712937 codA Dinoroseobacter shibae DFL 12 = DSM 16493 cytosine deaminase YP_001533285.1 2032700 R 398580 CDS YP_001533286.1 159044492 5712938 complement(2033976..2034707) 1 NC_009952.1 SUPERFAMILY: S-adenosyl-L-methionine-dependent methyltransferases; PFAM: PF05711 -Macrocin-O-methyltransferase (TylF); putative methyltransferase 2034707 5712938 Dshi_1944 Dinoroseobacter shibae DFL 12 = DSM 16493 putative methyltransferase YP_001533286.1 2033976 R 398580 CDS YP_001533287.1 159044493 5712939 complement(2034739..2035683) 1 NC_009952.1 COG: COG1079 - Uncharacterized ABC-type transport system, permease component; PFAM: PF02653; putative permease of branched-chain amino acid transport system 2035683 5712939 Dshi_1945 Dinoroseobacter shibae DFL 12 = DSM 16493 putative permease of branched-chain amino acid transport system YP_001533287.1 2034739 R 398580 CDS YP_001533288.1 159044494 5712940 complement(2035685..2036734) 1 NC_009952.1 COG4603 - ABC-type uncharacterized transport system, permease component; PFAM: PF02653; branched-chain amino acid ABCtransporter permease 2036734 5712940 Dshi_1946 Dinoroseobacter shibae DFL 12 = DSM 16493 branched-chain amino acid ABCtransporter permease YP_001533288.1 2035685 R 398580 CDS YP_001533289.1 159044495 5712941 complement(2036724..2038268) 1 NC_009952.1 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 2038268 rbsA4 5712941 rbsA4 Dinoroseobacter shibae DFL 12 = DSM 16493 ribose import ATP-binding protein YP_001533289.1 2036724 R 398580 CDS YP_001533290.1 159044496 5712942 complement(2038268..2039287) 1 NC_009952.1 COG: COG1744 - Uncharacterized ABC-type transport system, periplasmic component/surface lipoprotein; PFAM: PF02608; PROSITE: PS00024; putative basic membrane protein 2039287 5712942 Dshi_1948 Dinoroseobacter shibae DFL 12 = DSM 16493 putative basic membrane protein YP_001533290.1 2038268 R 398580 CDS YP_001533291.1 159044497 5712943 complement(2039513..2041096) 1 NC_009952.1 hypothetical protein 2041096 5712943 Dshi_1949 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533291.1 2039513 R 398580 CDS YP_001533292.1 159044498 5712944 2041261..2041860 1 NC_009952.1 SUPERFAMILY: SSF52540; similar to hydrolase; hypothetical protein 2041860 5712944 Dshi_1950 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533292.1 2041261 D 398580 CDS YP_001533293.1 159044499 5712945 complement(2041913..2045206) 1 NC_009952.1 PFAM: PF00529; COG: COG1566: Multidrug resistance efflux pump; related to HlyD family secretion proteins; hypothetical protein 2045206 5712945 Dshi_1951 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533293.1 2041913 R 398580 CDS YP_001533294.1 159044500 5712946 2045601..2046332 1 NC_009952.1 hypothetical protein 2046332 5712946 Dshi_1952 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533294.1 2045601 D 398580 CDS YP_001533295.1 159044501 5712947 2046386..2047312 1 NC_009952.1 COG: COG3509 - Poly(3-hydroxybutyrate) depolymerase; Gene3D: G3DSA:3.40.50.1820; SUPERFAMILY: SSF53474; putative hydrolase 2047312 5712947 Dshi_1953 Dinoroseobacter shibae DFL 12 = DSM 16493 putative hydrolase YP_001533295.1 2046386 D 398580 CDS YP_001533296.1 159044502 5712948 2047344..2048147 1 NC_009952.1 PFAM: PF00106-short chain dehydrogenase; PRINTS: PR00081; COG: COG0300 - Short-chain dehydrogenases of various substrate specificities; putative short-chain dehydrogenase 2048147 5712948 Dshi_1954 Dinoroseobacter shibae DFL 12 = DSM 16493 putative short-chain dehydrogenase YP_001533296.1 2047344 D 398580 CDS YP_001533297.1 159044503 5712949 complement(2048152..2049948) 1 NC_009952.1 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 2049948 5712949 Dshi_1955 Dinoroseobacter shibae DFL 12 = DSM 16493 putative short-chain dehydrogenase YP_001533297.1 2048152 R 398580 CDS YP_001533298.1 159044504 5712950 complement(2049974..2050936) 1 NC_009952.1 PFAM: PF01370; COG: COG0451 - Nucleoside-diphosphate-sugar epimerases; putative NAD-dependent epimerase/dehydratase 2050936 5712950 Dshi_1956 Dinoroseobacter shibae DFL 12 = DSM 16493 putative NAD-dependent epimerase/dehydratase YP_001533298.1 2049974 R 398580 CDS YP_001533299.1 159044505 5712951 complement(2051005..2052432) 1 NC_009952.1 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 2052432 5712951 Dshi_1957 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533299.1 2051005 R 398580 CDS YP_001533300.1 159044506 5712952 complement(2052491..2055133) 1 NC_009952.1 COG: COG0451 - Nucleoside-diphosphate-sugar epimerases; PFAM: PF01370; PROSITE: PS00178, PS00061; Gene3D: G3DSA:3.40.50.720; putative NAD-dependent epimerase/dehydratase 2055133 5712952 Dshi_1958 Dinoroseobacter shibae DFL 12 = DSM 16493 putative NAD-dependent epimerase/dehydratase YP_001533300.1 2052491 R 398580 CDS YP_003422328.1 284928596 5712953 complement(2055139..2056056) 1 NC_009952.1 hypothetical protein 2056056 5712953 Dshi_5003 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_003422328.1 2055139 R 398580 CDS YP_001533301.1 159044507 5712954 complement(2056060..2057664) 1 NC_009952.1 PFAM: PF01663-Type I phosphodiesterase / nucleotide pyrophosphatase; Gene3D: G3DSA:3.40.720.10-Alkaline Phosphatase, subunit A; SUPERFAMILY: Alkaline phosphatase-like; phosphodiesterase/nucleotide pyrophosphatase 2057664 5712954 Dshi_1960 Dinoroseobacter shibae DFL 12 = DSM 16493 phosphodiesterase/nucleotide pyrophosphatase YP_001533301.1 2056060 R 398580 CDS YP_001533302.1 159044508 5712955 complement(2057679..2057969) 1 NC_009952.1 PROSITE: PS50075; SUPERFAMILY: ACP-like; similar to acyl carrier protein; hypothetical protein 2057969 5712955 Dshi_1961 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533302.1 2057679 R 398580 CDS YP_001533303.1 159044509 5712956 complement(2057989..2062884) 1 NC_009952.1 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 2062884 5712956 Dshi_1962 Dinoroseobacter shibae DFL 12 = DSM 16493 putative modular PKS system YP_001533303.1 2057989 R 398580 CDS YP_001533304.1 159044510 5712957 complement(2062881..2070542) 1 NC_009952.1 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 2070542 5712957 Dshi_1963 Dinoroseobacter shibae DFL 12 = DSM 16493 putative modular PKS system YP_001533304.1 2062881 R 398580 CDS YP_001533305.1 159044511 5712958 complement(2071115..2072833) 1 NC_009952.1 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 2072833 5712958 Dshi_1964 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533305.1 2071115 R 398580 CDS YP_001533306.1 159044512 5712959 complement(2072939..2073871) 1 NC_009952.1 SUPERFAMILY: SSF52540; hypothetical protein 2073871 5712959 Dshi_1965 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533306.1 2072939 R 398580 CDS YP_001533307.1 159044513 5712960 complement(2074131..2075873) 1 NC_009952.1 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 2075873 lpdA 5712960 lpdA Dinoroseobacter shibae DFL 12 = DSM 16493 dihydrolipoyl dehydrogenase YP_001533307.1 2074131 R 398580 CDS YP_001533308.1 159044514 5712961 complement(2075886..2077187) 1 NC_009952.1 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 2077187 aceF 5712961 aceF Dinoroseobacter shibae DFL 12 = DSM 16493 dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex YP_001533308.1 2075886 R 398580 CDS YP_001533309.1 159044515 5712962 complement(2077242..2079899) 1 NC_009952.1 E1 component; part of pyruvate dehydrogenase; forms a complex with DlaT and LpdC; pyruvate dehydrogenase subunit E1 2079899 aceE 5712962 aceE Dinoroseobacter shibae DFL 12 = DSM 16493 pyruvate dehydrogenase subunit E1 YP_001533309.1 2077242 R 398580 CDS YP_003422329.1 284928597 5712963 complement(2080128..2081843) 1 NC_009952.1 D-lactate dehydrogenase 2081843 5712963 Dshi_5004 Dinoroseobacter shibae DFL 12 = DSM 16493 D-lactate dehydrogenase YP_003422329.1 2080128 R 398580 CDS YP_001533310.1 159044516 5712964 complement(2081843..2083909) 1 NC_009952.1 TIGRFAM: TIGR00786 TRAP transporter, DctM subunit; COG: COG4664 - TRAP-type mannitol/chloroaromatic compound transport system, large permease component; PFAM: PF04290, PF06808; TRAP dicarboxylate transporter 2083909 5712964 Dshi_1970 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP dicarboxylate transporter YP_001533310.1 2081843 R 398580 CDS YP_001533311.1 159044517 5712965 complement(2084030..2085007) 1 NC_009952.1 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 2085007 5712965 Dshi_1971 Dinoroseobacter shibae DFL 12 = DSM 16493 putative TRAP-transporter extracellular solute-binding protein YP_001533311.1 2084030 R 398580 CDS YP_001533312.1 159044518 5712966 2085434..2086216 1 NC_009952.1 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 2086216 5712966 Dshi_1972 Dinoroseobacter shibae DFL 12 = DSM 16493 putative pyruvate dehydrogenase complex repressor YP_001533312.1 2085434 D 398580 CDS YP_001533313.1 159044519 5712967 2086276..2087394 1 NC_009952.1 PFAM PF07726: ATPase family associated with various cellular activities (AAA); SMART: SM00382; COG: COG0714 - MoxR-like ATPases; related to ATPase (AAA); hypothetical protein 2087394 5712967 Dshi_1973 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533313.1 2086276 D 398580 CDS YP_001533314.1 159044520 5712968 2087391..2088665 1 NC_009952.1 COG: COG3864 - Uncharacterized protein conserved in bacteria; hypothetical protein 2088665 5712968 Dshi_1974 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533314.1 2087391 D 398580 CDS YP_001533315.1 159044521 5712969 complement(2088990..2089682) 1 NC_009952.1 hypothetical protein 2089682 5712969 Dshi_1975 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533315.1 2088990 R 398580 CDS YP_001533316.1 159044522 5712970 complement(2089743..2090660) 1 NC_009952.1 PFAM: PF00294; PRINTS: PR00990; putative ribokinase 2090660 5712970 Dshi_1976 Dinoroseobacter shibae DFL 12 = DSM 16493 putative ribokinase YP_001533316.1 2089743 R 398580 CDS YP_001533317.1 159044523 5712971 complement(2090945..2092207) 1 NC_009952.1 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 2092207 5712971 Dshi_1977 Dinoroseobacter shibae DFL 12 = DSM 16493 periplasmic-binding protein YP_001533317.1 2090945 R 398580 CDS YP_001533318.1 159044524 5712972 complement(2092224..2093177) 1 NC_009952.1 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 2093177 5712972 Dshi_1978 Dinoroseobacter shibae DFL 12 = DSM 16493 putative branched-chain amino acid transport system / permease YP_001533318.1 2092224 R 398580 CDS YP_001533319.1 159044525 5712973 complement(2093174..2094091) 1 NC_009952.1 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 2094091 5712973 Dshi_1979 Dinoroseobacter shibae DFL 12 = DSM 16493 putative branched-chain amino acid transport system / permease YP_001533319.1 2093174 R 398580 CDS YP_001533320.1 159044526 5712974 complement(2094088..2094810) 1 NC_009952.1 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 2094810 5712974 Dshi_1980 Dinoroseobacter shibae DFL 12 = DSM 16493 putative high-affinity branched-chain amino acid transport ATP-binding protein YP_001533320.1 2094088 R 398580 CDS YP_001533321.1 159044527 5712975 complement(2094803..2095576) 1 NC_009952.1 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 2095576 5712975 Dshi_1981 Dinoroseobacter shibae DFL 12 = DSM 16493 putative branched-chain amino acid transport ATP-binding protein YP_001533321.1 2094803 R 398580 CDS YP_001533322.1 159044528 5712976 complement(2095569..2096651) 1 NC_009952.1 PFAM: PF00248; aldo/keto reductase family protein 2096651 5712976 Dshi_1982 Dinoroseobacter shibae DFL 12 = DSM 16493 aldo/keto reductase family protein YP_001533322.1 2095569 R 398580 CDS YP_001533323.1 159044529 5712977 complement(2096648..2097025) 1 NC_009952.1 hypothetical protein 2097025 5712977 Dshi_1983 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533323.1 2096648 R 398580 CDS YP_001533324.1 159044530 5712978 2097130..2097777 1 NC_009952.1 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 2097777 5712978 Dshi_1984 Dinoroseobacter shibae DFL 12 = DSM 16493 putative HTH-type transcriptional regulator YP_001533324.1 2097130 D 398580 CDS YP_001533325.1 159044531 5712979 2097774..2099216 1 NC_009952.1 COG: COG0667 - Predicted oxidoreductases (related to aryl-alcohol dehydrogenases); PFAM: PF00248, PF01042; PRINTS: PR00069; SUPERFAMILY: SSF51430; aldo/keto reductase family protein 2099216 5712979 Dshi_1985 Dinoroseobacter shibae DFL 12 = DSM 16493 aldo/keto reductase family protein YP_001533325.1 2097774 D 398580 CDS YP_001533326.1 159044532 5712980 2099648..2101816 1 NC_009952.1 TIGRFAM: TIGR00178 isocitrate dehydrogenase, NADP-dependent, monomeric type; COG: COG2838 - Monomeric isocitrate dehydrogenase; PFAM PF03971: Monomeric isocitrate dehydrogenase; monomeric isocitrate dehydrogenase 2101816 icd 5712980 icd Dinoroseobacter shibae DFL 12 = DSM 16493 monomeric isocitrate dehydrogenase YP_001533326.1 2099648 D 398580 CDS YP_001533327.1 159044533 5712981 2102173..2102721 1 NC_009952.1 similar to molybdenum import ATP-binding protein modC2; hypothetical protein 2102721 5712981 Dshi_1987 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533327.1 2102173 D 398580 CDS YP_001533328.1 159044534 5712982 2102821..2103216 1 NC_009952.1 hypothetical protein 2103216 5712982 Dshi_1988 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533328.1 2102821 D 398580 CDS YP_001533329.1 159044535 5712983 2103220..2104452 1 NC_009952.1 PFAM: PF00529; COG: COG1566: Multidrug resistance efflux pump; related to HlyD family secretion proteins; hypothetical protein 2104452 5712983 Dshi_1989 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533329.1 2103220 D 398580 CDS YP_001533330.1 159044536 5712985 complement(2104752..2106995) 1 NC_009952.1 PFAM: PF01636; SUPERFAMILY: SSF56112; COG: COG0510 - Predicted choline kinase involved in LPS biosynthesis; protein kinase-like protein 2106995 5712985 Dshi_1990 Dinoroseobacter shibae DFL 12 = DSM 16493 protein kinase-like protein YP_001533330.1 2104752 R 398580 CDS YP_001533331.1 159044537 5712986 complement(2106982..2108817) 1 NC_009952.1 PROSITE: PS50893, PS50929; PFAM: PF00664, PF00005; SMART: SM00382; putative multidrug export ATP-binding/permease 2108817 5712986 Dshi_1991 Dinoroseobacter shibae DFL 12 = DSM 16493 putative multidrug export ATP-binding/permease YP_001533331.1 2106982 R 398580 CDS YP_001533332.1 159044538 5712987 complement(2108817..2109965) 1 NC_009952.1 PFAM: PF00534; related to glycosyl transferase group 1; hypothetical protein 2109965 5712987 Dshi_1992 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533332.1 2108817 R 398580 CDS YP_001533333.1 159044539 5712988 complement(2109965..2111209) 1 NC_009952.1 PFAM: PF00534; putative glycosyltransferase 2111209 5712988 Dshi_1993 Dinoroseobacter shibae DFL 12 = DSM 16493 putative glycosyltransferase YP_001533333.1 2109965 R 398580 CDS YP_001533334.1 159044540 5712989 complement(2111233..2112393) 1 NC_009952.1 COG: COG4671 - Predicted glycosyl transferase; SUPERFAMILY: SSF53756 UDP-Glycosyltransferase/glycogen phosphorylase; Gene3D: G3DSA:3.40.50.2000; putative glycosyltransferase 2112393 5712989 Dshi_1994 Dinoroseobacter shibae DFL 12 = DSM 16493 putative glycosyltransferase YP_001533334.1 2111233 R 398580 CDS YP_001533335.1 159044541 5712990 2113662..2114381 1 NC_009952.1 hypothetical protein 2114381 5712990 Dshi_1995 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533335.1 2113662 D 398580 CDS YP_001533336.1 159044542 5712991 complement(2114512..2115816) 1 NC_009952.1 catalyzes the interconversion of D-xylose to D-xylulose; xylose isomerase 2115816 xylA 5712991 xylA Dinoroseobacter shibae DFL 12 = DSM 16493 xylose isomerase YP_001533336.1 2114512 R 398580 CDS YP_001533337.1 159044543 5712992 complement(2115813..2117255) 1 NC_009952.1 SWISSPROT P09099: Xylose kinase; PFAM: PF00370, PF02782; TIGRFAM: TIGR01312 D-xylulose kinase; COG: COG1070 - Sugar (pentulose and hexulose) kinases; xylose kinase 2117255 xylB2 5712992 xylB2 Dinoroseobacter shibae DFL 12 = DSM 16493 xylose kinase YP_001533337.1 2115813 R 398580 CDS YP_001533338.1 159044544 5712993 complement(2117255..2118001) 1 NC_009952.1 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 2118001 5712993 Dshi_1998 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC transporter ATP-binding protein YP_001533338.1 2117255 R 398580 CDS YP_001533339.1 159044545 5712994 complement(2117998..2119305) 1 NC_009952.1 SWISSPROT P0AGI4: Xylose transport system permease protein xylH; COG: COG4214 - ABC-type xylose transport system, permease component; PFAM: PF02653; xylose transport system permease 2119305 xylH 5712994 xylH Dinoroseobacter shibae DFL 12 = DSM 16493 xylose transport system permease YP_001533339.1 2117998 R 398580 CDS YP_001533340.1 159044546 5712995 complement(2119423..2120445) 1 NC_009952.1 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 2120445 5712995 Dshi_2000 Dinoroseobacter shibae DFL 12 = DSM 16493 D-xylose-binding periplasmic protein xylF YP_001533340.1 2119423 R 398580 CDS YP_001533341.1 159044547 5712996 2120658..2121902 1 NC_009952.1 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 2121902 5712996 Dshi_2001 Dinoroseobacter shibae DFL 12 = DSM 16493 putative xylose repressor YP_001533341.1 2120658 D 398580 CDS YP_001533342.1 159044548 5712997 2121899..2123377 1 NC_009952.1 SUPERFAMILY: SSF69318; hypothetical protein 2123377 5712997 Dshi_2002 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533342.1 2121899 D 398580 CDS YP_001533343.1 159044549 5712998 2123844..2124359 1 NC_009952.1 TIGRFAM: TIGR01409; hypothetical protein 2124359 5712998 Dshi_2003 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533343.1 2123844 D 398580 CDS YP_001533344.1 159044550 5712999 2124331..2124954 1 NC_009952.1 PFAM: PF01794; hypothetical protein 2124954 5712999 Dshi_2004 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533344.1 2124331 D 398580 CDS YP_001533345.1 159044551 5713000 complement(2125127..2126482) 1 NC_009952.1 PFAM: PF03150; Gene3D: G3DSA:1.10.760.10; PROSITE: PS51007; putative cytochrome c peroxidase 2126482 5713000 Dshi_2005 Dinoroseobacter shibae DFL 12 = DSM 16493 putative cytochrome c peroxidase YP_001533345.1 2125127 R 398580 CDS YP_001533346.1 159044552 5713001 complement(2126545..2126964) 1 NC_009952.1 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 2126964 5713001 Dshi_2006 Dinoroseobacter shibae DFL 12 = DSM 16493 putative blue-light photoreceptor YP_001533346.1 2126545 R 398580 CDS YP_001533347.1 159044553 5713002 complement(2127207..2127674) 1 NC_009952.1 PFAM: PF00293; Gene3D: G3DSA:3.90.79.10; SUPERFAMILY: SSF55811; similar to NUDIX hydrolase; hypothetical protein 2127674 5713002 Dshi_2007 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533347.1 2127207 R 398580 CDS YP_001533348.1 159044554 5713003 2127799..2128614 1 NC_009952.1 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 2128614 5713003 Dshi_2008 Dinoroseobacter shibae DFL 12 = DSM 16493 putative glycerol-3-phosphate regulon repressor YP_001533348.1 2127799 D 398580 CDS YP_001533349.1 159044555 5713004 2128649..2129623 1 NC_009952.1 TIGRFAM: TIGR01098 phosphonates-binding periplasmic protein; COG: COG3221 - ABC-type phosphate/phosphonate transport system, periplasmic component; SUPERFAMILY: SSF53850; putative phosphonates-binding periplasmic protein 2129623 5713004 Dshi_2009 Dinoroseobacter shibae DFL 12 = DSM 16493 putative phosphonates-binding periplasmic protein YP_001533349.1 2128649 D 398580 CDS YP_001533350.1 159044556 5713005 2129686..2130483 1 NC_009952.1 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 2130483 phnC1 5713005 phnC1 Dinoroseobacter shibae DFL 12 = DSM 16493 phosphonates import ATP-binding protein YP_001533350.1 2129686 D 398580 CDS YP_001533351.1 159044557 5713006 2130480..2131292 1 NC_009952.1 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 5713006 Dshi_2011 Dinoroseobacter shibae DFL 12 = DSM 16493 putative ABC transporter inner membrane component YP_001533351.1 2130480 D 398580 CDS YP_001533352.1 159044558 5713007 2131292..2132107 1 NC_009952.1 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 2132107 5713007 Dshi_2012 Dinoroseobacter shibae DFL 12 = DSM 16493 putative ABC transporter inner membrane component YP_001533352.1 2131292 D 398580 CDS YP_001533353.1 159044559 5713008 2132104..2133009 1 NC_009952.1 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 2133009 5713008 Dshi_2013 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533353.1 2132104 D 398580 CDS YP_001533354.1 159044560 5713009 2133086..2134387 1 NC_009952.1 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 2134387 ugpB1 5713009 ugpB1 Dinoroseobacter shibae DFL 12 = DSM 16493 sn-glycerol-3-phosphate-binding periplasmic protein ugpB YP_001533354.1 2133086 D 398580 CDS YP_001533355.1 159044561 5713010 2134480..2135361 1 NC_009952.1 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 2135361 ugpA4 5713010 ugpA4 Dinoroseobacter shibae DFL 12 = DSM 16493 sn-glycerol-3-phosphate transport system permease YP_001533355.1 2134480 D 398580 CDS YP_001533356.1 159044562 5713011 2135361..2136215 1 NC_009952.1 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 2136215 ugpE3 5713011 ugpE3 Dinoroseobacter shibae DFL 12 = DSM 16493 sn-glycerol-3-phosphate transport system permease YP_001533356.1 2135361 D 398580 CDS YP_001533357.1 159044563 5713012 2136216..2137217 1 NC_009952.1 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 2137217 ugpC4 5713012 ugpC4 Dinoroseobacter shibae DFL 12 = DSM 16493 sn-glycerol-3-phosphate import ATP-binding protein YP_001533357.1 2136216 D 398580 CDS YP_001533358.1 159044564 5713013 2137369..2137632 1 NC_009952.1 hypothetical protein 2137632 5713013 Dshi_2018 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533358.1 2137369 D 398580 CDS YP_001533359.1 159044565 5713014 complement(2137715..2139322) 1 NC_009952.1 COG: COG0069 - Glutamate synthase domain 2; PFAM: PF01645; Gene3D: G3DSA:3.20.20.70; putative glutamate synthase [NADPH] large chain 2139322 5713014 Dshi_2019 Dinoroseobacter shibae DFL 12 = DSM 16493 putative glutamate synthase [NADPH] large chain YP_001533359.1 2137715 R 398580 CDS YP_001533360.1 159044566 5713015 complement(2139424..2141055) 1 NC_009952.1 catalyzes the interconversion of alpha-D-glucose 1-phosphate to alpha-D-glucose 6-phosphate; phosphoglucomutase 2141055 pgm 5713015 pgm Dinoroseobacter shibae DFL 12 = DSM 16493 phosphoglucomutase YP_001533360.1 2139424 R 398580 CDS YP_001533361.1 159044567 5713016 2141284..2142312 1 NC_009952.1 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 2142312 5713016 Dshi_2021 Dinoroseobacter shibae DFL 12 = DSM 16493 putative-binding protein component of ABC iron transporter YP_001533361.1 2141284 D 398580 CDS YP_001533362.1 159044568 5713017 2142399..2142815 1 NC_009952.1 no shine dalgarno sequence, no Swiss-Prot or InterPro Hits, no similar proteins in ncbi database. Probably pseudogene???; hypothetical protein 2142815 5713017 Dshi_2022 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533362.1 2142399 D 398580 CDS YP_001533363.1 159044569 5713018 complement(2142820..2144499) 1 NC_009952.1 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 2144499 5713018 Dshi_2023 Dinoroseobacter shibae DFL 12 = DSM 16493 putative ABC transporter permease YP_001533363.1 2142820 R 398580 CDS YP_001533364.1 159044570 5713019 complement(2144760..2145515) 1 NC_009952.1 PFAM: PF01925; hypothetical protein 2145515 5713019 Dshi_2024 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533364.1 2144760 R 398580 CDS YP_001533365.1 159044571 5713020 complement(2145522..2146214) 1 NC_009952.1 PFAM: PF07385-Protein of unknown function (DUF1498); COG: COG3822 - ABC-type sugar transport system, auxiliary component; hypothetical protein 2146214 5713020 Dshi_2025 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533365.1 2145522 R 398580 CDS YP_001533366.1 159044572 5713021 complement(2146276..2147046) 1 NC_009952.1 COG: COG1540 - Uncharacterized proteins, homologs of lactam utilization protein B; PFAM: PF03746; SWISPROT Q5LMA4: UPF0271 protein SPO3659; LamB/YcsF family protein 2147046 5713021 Dshi_2026 Dinoroseobacter shibae DFL 12 = DSM 16493 LamB/YcsF family protein YP_001533366.1 2146276 R 398580 CDS YP_001533367.1 159044573 5713022 complement(2147043..2148059) 1 NC_009952.1 PFAM: PF02626; SMART: SM00797; TIGRFAM: TIGR00724 biotin-dependent carboxylase uncharacterized domain; COG: COG1984 - Allophanate hydrolase subunit 2; putative allophanate hydrolase subunit 2 2148059 5713022 Dshi_2027 Dinoroseobacter shibae DFL 12 = DSM 16493 putative allophanate hydrolase subunit 2 YP_001533367.1 2147043 R 398580 CDS YP_001533368.1 159044574 5713023 complement(2148056..2148793) 1 NC_009952.1 TIGRFAM: TIGR00370 conserved hypothetical protein TIGR00370; COG: COG2049 - Allophanate hydrolase subunit 1; PFAM: PF02682; SMART: SM00796; putative allophanate hydrolase subunit 1 2148793 5713023 Dshi_2028 Dinoroseobacter shibae DFL 12 = DSM 16493 putative allophanate hydrolase subunit 1 YP_001533368.1 2148056 R 398580 CDS YP_001533369.1 159044575 5713024 complement(2149164..2150222) 1 NC_009952.1 SWISSPROT P0ACP7: HTH-type transcriptional repressor purR; PFAM: PF00356, PF00532; SMART: SM00354; PROSITE: PS50932; SUPERFAMILY: SSF47413; COG: COG1609 - Transcriptional regulators; HTH-type transcriptional repressor 2150222 5713024 Dshi_2029 Dinoroseobacter shibae DFL 12 = DSM 16493 HTH-type transcriptional repressor YP_001533369.1 2149164 R 398580 CDS YP_001533370.1 159044576 5713025 2150383..2150574 1 NC_009952.1 hypothetical protein 2150574 5713025 Dshi_2030 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533370.1 2150383 D 398580 CDS YP_001533371.1 159044577 5713026 2150586..2151734 1 NC_009952.1 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 2151734 5713026 Dshi_2031 Dinoroseobacter shibae DFL 12 = DSM 16493 putative TRAP-type C4-dicarboxylate transport sytem periplasmic protein YP_001533371.1 2150586 D 398580 CDS YP_001533372.1 159044578 5713027 2151852..2152367 1 NC_009952.1 COG: COG3090 - TRAP-type C4-dicarboxylate transport system, small permease component; PFAM: PF04290; PROSITE: PS00430; TRAP transporter permease 2152367 5713027 Dshi_2032 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP transporter permease YP_001533372.1 2151852 D 398580 CDS YP_001533373.1 159044579 5713028 2152380..2153708 1 NC_009952.1 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 2153708 5713028 Dshi_2033 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP dicarboxylate transporter subunit DctM YP_001533373.1 2152380 D 398580 CDS YP_001533374.1 159044580 5713029 2153718..2155025 1 NC_009952.1 catalyzes the oxidation of L-histidinol to L-histidinaldehyde and then to L-histidine in histidine biosynthesis; functions as a dimer; histidinol dehydrogenase 2155025 hisD2 5713029 hisD2 Dinoroseobacter shibae DFL 12 = DSM 16493 histidinol dehydrogenase YP_001533374.1 2153718 D 398580 CDS YP_001533375.1 159044581 5713030 2155018..2155782 1 NC_009952.1 COG: COG1028 - Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases); PFAM: PF00106; PROSITE: PS00061; PRINTS: PR00080, PR00081; putative gluconate 5-dehydrogenase 2155782 5713030 Dshi_2035 Dinoroseobacter shibae DFL 12 = DSM 16493 putative gluconate 5-dehydrogenase YP_001533375.1 2155018 D 398580 CDS YP_001533376.1 159044582 5713031 2155779..2156762 1 NC_009952.1 PFAM: PF00107, PF08240; SUPERFAMILY: SSF50129; PANTHER: PTHR11695: Alcohol dehydrogenase related; zinc-containing alcohol dehydrogenase 2156762 5713031 Dshi_2036 Dinoroseobacter shibae DFL 12 = DSM 16493 zinc-containing alcohol dehydrogenase YP_001533376.1 2155779 D 398580 CDS YP_001533377.1 159044583 5713032 2156778..2157068 1 NC_009952.1 SWISSPROT P42604: Altronate hydrolase; similar to altronate hydrolase; hypothetical protein 2157068 5713032 Dshi_2037 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533377.1 2156778 D 398580 CDS YP_001533378.1 159044584 5713033 2157081..2158262 1 NC_009952.1 COG: COG2721 - Altronate dehydratase; PFAM: PF04295; putative altronate hydrolase 2158262 5713033 Dshi_2038 Dinoroseobacter shibae DFL 12 = DSM 16493 putative altronate hydrolase YP_001533378.1 2157081 D 398580 CDS YP_001533379.1 159044585 5713034 2158316..2159335 1 NC_009952.1 COG: COG2055 - Malate/L-lactate dehydrogenases; PFAM: PF02615; SUPERFAMILY: SSF89733 L-sulfolactate dehydrogenase-like; malate/L-lactate dehydrogenase family protein 2159335 5713034 Dshi_2039 Dinoroseobacter shibae DFL 12 = DSM 16493 malate/L-lactate dehydrogenase family protein YP_001533379.1 2158316 D 398580 CDS YP_001533380.1 159044586 5713035 2159382..2159789 1 NC_009952.1 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 2159789 5713035 Dshi_2040 Dinoroseobacter shibae DFL 12 = DSM 16493 putative universal stress protein YP_001533380.1 2159382 D 398580 CDS YP_003422330.1 284928598 8130633 complement(2159773..2160468) 1 NC_009952.1 hypothetical protein 2160468 8130633 Dshi_5005 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_003422330.1 2159773 R 398580 CDS YP_001533381.1 159044587 5713037 complement(2160601..2161983) 1 NC_009952.1 SWISSPROT Q9APM5: Taurine--pyruvate aminotransferase; COG: COG0161 - Adenosylmethionine-8-amino-7-oxononanoate aminotransferase; PFAM: PF00202; PROSITE: PS00600; taurin--pyruvate aminotransferase 2161983 tpa 5713037 tpa Dinoroseobacter shibae DFL 12 = DSM 16493 taurin--pyruvate aminotransferase YP_001533381.1 2160601 R 398580 CDS YP_001533382.1 159044588 5713038 2162251..2162490 1 NC_009952.1 hypothetical protein 2162490 5713038 Dshi_2043 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533382.1 2162251 D 398580 CDS YP_001533383.1 159044589 5713039 2162631..2164097 1 NC_009952.1 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 2164097 5713039 Dshi_2044 Dinoroseobacter shibae DFL 12 = DSM 16493 HTH-type transcriptional regulator YP_001533383.1 2162631 D 398580 CDS YP_001533384.1 159044590 5713040 2164196..2165974 1 NC_009952.1 catalyzes the formation of acetyl phosphate and sulfite from 2-sulfoacetaldehyde; is active when grown on taurine as a sole carbon source; sulfoacetaldehyde acetyltransferase 2165974 xsc 5713040 xsc Dinoroseobacter shibae DFL 12 = DSM 16493 sulfoacetaldehyde acetyltransferase YP_001533384.1 2164196 D 398580 CDS YP_003422331.1 284928599 5713041 2165978..2167135 1 NC_009952.1 hypothetical protein 2167135 5713041 Dshi_5006 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_003422331.1 2165978 D 398580 CDS YP_001533385.1 159044591 5713042 complement(2167136..2167762) 1 NC_009952.1 PROSITE: PS51257; COG: COG3218 - ABC-type uncharacterized transport system, auxiliary component; related to membrane lipoprotein; hypothetical protein 2167762 5713042 Dshi_2047 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533385.1 2167136 R 398580 CDS YP_001533386.1 159044592 5713043 complement(2167769..2169508) 1 NC_009952.1 PFAM: PF02470; COG: COG1463 - ABC-type transport system involved in resistance to organic solvents, periplasmic component; hypothetical protein 2169508 5713043 Dshi_2048 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533386.1 2167769 R 398580 CDS YP_001533387.1 159044593 5713044 complement(2169530..2170309) 1 NC_009952.1 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 2170309 5713044 Dshi_2049 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC transporter ATP-binding protein YP_001533387.1 2169530 R 398580 CDS YP_001533388.1 159044594 5713045 complement(2170309..2171463) 1 NC_009952.1 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 2171463 5713045 Dshi_2050 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533388.1 2170309 R 398580 CDS YP_001533389.1 159044595 5713046 complement(2171569..2172045) 1 NC_009952.1 hypothetical protein 2172045 5713046 Dshi_2051 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533389.1 2171569 R 398580 CDS YP_001533390.1 159044596 5713047 complement(2172042..2172206) 1 NC_009952.1 COG: COG4256; similar to hemin uptake protein; hypothetical protein 2172206 5713047 Dshi_2052 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533390.1 2172042 R 398580 CDS YP_001533391.1 159044597 5713048 2172986..2173456 1 NC_009952.1 hypothetical protein 2173456 5713048 Dshi_2053 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533391.1 2172986 D 398580 CDS YP_001533392.1 159044598 5713049 complement(2173618..2174742) 1 NC_009952.1 COG: COG0123 - Deacetylases, including yeast histone deacetylase and acetoin utilization protein; PFAM: PF00850; PRINTS PR01270; histone deacetylase family protein 2174742 5713049 Dshi_2054 Dinoroseobacter shibae DFL 12 = DSM 16493 histone deacetylase family protein YP_001533392.1 2173618 R 398580 CDS YP_001533393.1 159044599 5713050 complement(2174739..2175272) 1 NC_009952.1 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 2175272 5713050 Dshi_2055 Dinoroseobacter shibae DFL 12 = DSM 16493 putative glutathione peroxidase YP_001533393.1 2174739 R 398580 CDS YP_001533394.1 159044600 5713051 2175483..2175962 1 NC_009952.1 PFAM: PF00293; PRINTS: PR00502; Gene3D: G3DSA:3.90.79.10; hypothetical protein 2175962 5713051 Dshi_2056 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533394.1 2175483 D 398580 CDS YP_001533395.1 159044601 5713052 2176088..2176564 1 NC_009952.1 COG: COG5319 - Uncharacterized protein conserved in bacteria; PFAM: PF06676-Protein of unknown function (DUF1178); hypothetical protein 2176564 5713052 Dshi_2057 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533395.1 2176088 D 398580 CDS YP_001533396.1 159044602 5713053 2176569..2177234 1 NC_009952.1 COG: COG1028 - Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases); short-chain dehydrogenase 2177234 5713053 Dshi_2058 Dinoroseobacter shibae DFL 12 = DSM 16493 short-chain dehydrogenase YP_001533396.1 2176569 D 398580 CDS YP_001533397.1 159044603 5713054 2177212..2177808 1 NC_009952.1 COG: COG0645 - Predicted kinase; similar to adenylyl sulfate kinase; hypothetical protein 2177808 5713054 Dshi_2059 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533397.1 2177212 D 398580 CDS YP_001533398.1 159044604 5713055 2178310..2181102 1 NC_009952.1 catalyzes the conversion of citrate to isocitrate and the conversion of 2-methylaconitate to 2-methylisocitrate; bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase 2181102 acnB 5713055 acnB Dinoroseobacter shibae DFL 12 = DSM 16493 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase YP_001533398.1 2178310 D 398580 CDS YP_001533399.1 159044605 5713056 2181413..2182651 1 NC_009952.1 SWISSPROT P26512: Aspartokinase; TIGRFAM: TIGR00656 aspartate kinase, monofunctional class, TIGR00657 aspartate kinase; COG: COG0527 - Aspartokinases; aspartokinase 2182651 lysC 5713056 lysC Dinoroseobacter shibae DFL 12 = DSM 16493 aspartokinase YP_001533399.1 2181413 D 398580 CDS YP_001533400.1 159044606 5713057 2182811..2185054 1 NC_009952.1 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 2185054 ptsI 5713057 ptsI Dinoroseobacter shibae DFL 12 = DSM 16493 phosphoenolpyruvate-protein phosphotransferase YP_001533400.1 2182811 D 398580 CDS YP_001533401.1 159044607 5713058 complement(2185051..2185806) 1 NC_009952.1 PFAM: PF00092; SMART: SM00327; PROSITE: PS50234; PRINTS: PR00453; related to von Willebrand factor type A; hypothetical protein 2185806 5713058 Dshi_2063 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533401.1 2185051 R 398580 CDS YP_001533402.1 159044608 5713059 complement(2185839..2186339) 1 NC_009952.1 COG: COG3153 - Predicted acetyltransferase; PFAM: PF00583; PROSITE: PS51186; related to acetyltransferase, GNAT family; hypothetical protein 2186339 5713059 Dshi_2064 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533402.1 2185839 R 398580 CDS YP_001533403.1 159044609 5713060 2186415..2187020 1 NC_009952.1 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 2187020 5713060 Dshi_2065 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533403.1 2186415 D 398580 CDS YP_001533404.1 159044610 5713061 complement(2187026..2187301) 1 NC_009952.1 hypothetical protein 2187301 5713061 Dshi_2066 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533404.1 2187026 R 398580 CDS YP_001533405.1 159044611 5713062 complement(2187413..2189017) 1 NC_009952.1 SWISSPROT P0AFR2: Putative sulfate transporter ychM; COG: COG0659 - Sulfate permease and related transporters (MFS superfamily); PFAM: PF01740, PF00916; PROSITE: PS50801; sulfate transporter 2189017 5713062 Dshi_2067 Dinoroseobacter shibae DFL 12 = DSM 16493 sulfate transporter YP_001533405.1 2187413 R 398580 CDS YP_001533406.1 159044612 5713063 2189203..2190072 1 NC_009952.1 Catalyzes the reversible phosphorolysis of 5'-deoxy-5'- methylthioadenosine (MTA) to adenine and 5-methylthio-D-ribose-1- phosphate; 5'-methylthioadenosine phosphorylase 2190072 5713063 Dshi_2068 Dinoroseobacter shibae DFL 12 = DSM 16493 5'-methylthioadenosine phosphorylase YP_001533406.1 2189203 D 398580 CDS YP_001533407.1 159044613 5713064 2190225..2190515 1 NC_009952.1 COG: COG4321 - Uncharacterized protein related to arylsulfate sulfotransferase involved in siderophore biosynthesis; hypothetical protein 2190515 5713064 Dshi_2069 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533407.1 2190225 D 398580 CDS YP_001533408.1 159044614 5713065 2190630..2191025 1 NC_009952.1 TIGRFAM: TIGR00068; COG: COG0346 - Lactoylglutathione lyase and related lyases; PFAM: PF00903-Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; similar to Lactoylglutathione lyase; hypothetical protein 2191025 5713065 Dshi_2070 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533408.1 2190630 D 398580 CDS YP_001533409.1 159044615 5713066 2191066..2191590 1 NC_009952.1 hypothetical protein 2191590 5713066 Dshi_2071 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533409.1 2191066 D 398580 CDS YP_001533410.1 159044616 5713067 2191605..2193176 1 NC_009952.1 COG: COG2303 - Choline dehydrogenase and related flavoproteins; PFAM: PF00732; putative gluconate 2-dehydrogenase flavoprotein 2193176 5713067 Dshi_2072 Dinoroseobacter shibae DFL 12 = DSM 16493 putative gluconate 2-dehydrogenase flavoprotein YP_001533410.1 2191605 D 398580 CDS YP_001533411.1 159044617 5713068 complement(2193621..2194550) 1 NC_009952.1 SUPERFAMILY: SSF51101; hypothetical protein 2194550 5713068 Dshi_2073 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533411.1 2193621 R 398580 CDS YP_001533412.1 159044618 5713069 2194887..2195426 1 NC_009952.1 catalyzes a salvage reaction resulting in the formation of AMP which is metabolically less costly than a de novo synthesis; adenine phosphoribosyltransferase 2195426 apt 5713069 apt Dinoroseobacter shibae DFL 12 = DSM 16493 adenine phosphoribosyltransferase YP_001533412.1 2194887 D 398580 CDS YP_001533413.1 159044619 5713070 2195526..2195978 1 NC_009952.1 COG: COG3439 - Uncharacterized conserved protein; PFAM: PF03625; SUPERFAMILY: TT1751-like; hypothetical protein 2195978 5713070 Dshi_2075 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533413.1 2195526 D 398580 CDS YP_001533414.1 159044620 5713071 complement(2196168..2197586) 1 NC_009952.1 COG: COG0277 - FAD/FMN-containing dehydrogenases; PFAM: PF02913, PF01565; FAD-linked oxidase 2197586 5713071 Dshi_2076 Dinoroseobacter shibae DFL 12 = DSM 16493 FAD-linked oxidase YP_001533414.1 2196168 R 398580 CDS YP_001533415.1 159044621 5713072 complement(2197642..2198481) 1 NC_009952.1 COG: COG2220 - Predicted Zn-dependent hydrolases of the beta-lactamase fold; related to metal-dependent hydrolase/oxidoreductase; hypothetical protein 2198481 5713072 Dshi_2077 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533415.1 2197642 R 398580 CDS YP_001533416.1 159044622 5713073 2198730..2199473 1 NC_009952.1 TIGRFAM: TIGR00419 triosephosphate isomerase; COG: COG0149; PFAM: PF00121; PROSITE: PS00171; triosephosphate isomerase 2199473 tpiA 5713073 tpiA Dinoroseobacter shibae DFL 12 = DSM 16493 triosephosphate isomerase YP_001533416.1 2198730 D 398580 CDS YP_001533417.1 159044623 5713074 complement(2199565..2200521) 1 NC_009952.1 COG: COG0583 - Transcriptional regulator; PFAM: PF00126, PF03466; PROSITE: PS50931; SUPERFAMILY: SSF53850, SSF46785; lysR family; HTH-type transcriptional regulator 2200521 5713074 Dshi_2079 Dinoroseobacter shibae DFL 12 = DSM 16493 HTH-type transcriptional regulator YP_001533417.1 2199565 R 398580 CDS YP_001533418.1 159044624 5713075 2200594..2201463 1 NC_009952.1 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 2201463 metF 5713075 metF Dinoroseobacter shibae DFL 12 = DSM 16493 5,10-methylenetetrahydrofolate reductase YP_001533418.1 2200594 D 398580 CDS YP_001533419.1 159044625 5713076 complement(2201530..2202114) 1 NC_009952.1 COG: COG2863 - Cytochrome c553; PROSITE: PS51007; Gene3D: G3DSA:1.10.760.10 ; SUPERFAMILY: SSF46626; putative cytochrome c 2202114 5713076 Dshi_2081 Dinoroseobacter shibae DFL 12 = DSM 16493 putative cytochrome c YP_001533419.1 2201530 R 398580 CDS YP_001533420.1 159044626 5713077 complement(2202111..2203370) 1 NC_009952.1 COG: COG2133 - Glucose/sorbosone dehydrogenases; SUPERFAMILY: Soluble quinoprotein glucose dehydrogenase; Gene3D: G3DSA:2.120.10.30; putative sorbosone/glucose dehydrogenase 2203370 5713077 Dshi_2082 Dinoroseobacter shibae DFL 12 = DSM 16493 putative sorbosone/glucose dehydrogenase YP_001533420.1 2202111 R 398580 CDS YP_001533421.1 159044627 5713078 2203522..2203989 1 NC_009952.1 COG: COG2050 - Uncharacterized protein, possibly involved in aromatic compounds catabolism; PFAM: PF03061; TIGRFAM: TIGR00369; related to thioesterase; hypothetical protein 2203989 5713078 Dshi_2083 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533421.1 2203522 D 398580 CDS YP_001533422.1 159044628 5713079 complement(2204080..2205153) 1 NC_009952.1 COG: COG3673 - Uncharacterized conserved protein; PROSITE: PS00120; hypothetical protein 2205153 5713079 Dshi_2084 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533422.1 2204080 R 398580 CDS YP_001533423.1 159044629 5713080 2205559..2206308 1 NC_009952.1 TIGRFAM: TIGR02595; hypothetical protein 2206308 5713080 Dshi_2085 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533423.1 2205559 D 398580 CDS YP_001533424.1 159044630 5713081 complement(2206881..2209178) 1 NC_009952.1 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 2209178 coxL3 5713081 coxL3 Dinoroseobacter shibae DFL 12 = DSM 16493 carbon monoxide dehydrogenase YP_001533424.1 2206881 R 398580 CDS YP_001533425.1 159044631 5713082 2209300..2212413 1 NC_009952.1 valine--tRNA ligase; ValRS; converts valine ATP and tRNA(Val) to AMP PPi and valyl-tRNA(Val); class-I aminoacyl-tRNA synthetase type 1 subfamily; has a posttransfer editing process to hydrolyze mischarged Thr-tRNA(Val) which is done by the editing domain; valyl-tRNA synthetase 2212413 valS 5713082 valS Dinoroseobacter shibae DFL 12 = DSM 16493 valyl-tRNA synthetase YP_001533425.1 2209300 D 398580 CDS YP_001533426.1 159044632 5713083 2212787..2213905 1 NC_009952.1 catalyzes the formation of histidinol phosphate and 2-oxoglutarate from glutamate and imidazole acetol-phosphate; histidinol-phosphate aminotransferase 2213905 5713083 Dshi_2088 Dinoroseobacter shibae DFL 12 = DSM 16493 histidinol-phosphate aminotransferase YP_001533426.1 2212787 D 398580 CDS YP_001533427.1 159044633 5713084 2213993..2214208 1 NC_009952.1 hypothetical protein 2214208 5713084 Dshi_2089 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533427.1 2213993 D 398580 CDS YP_001533428.1 159044634 5713085 complement(2214205..2215461) 1 NC_009952.1 COG: COG0075 - Serine-pyruvate aminotransferase/archaeal aspartate aminotransferase; PFAM: PF00266; putative serine--glyoxylate aminotransferase 2215461 5713085 Dshi_2090 Dinoroseobacter shibae DFL 12 = DSM 16493 putative serine--glyoxylate aminotransferase YP_001533428.1 2214205 R 398580 CDS YP_001533429.1 159044635 5713086 complement(2215514..2216209) 1 NC_009952.1 SUPERFAMILY: SSF53448-Nucleotide-diphospho-sugar transferases; PFAM: PF00535-Glycosyl transferase family 2; COG: COG0463 - Glycosyltransferases involved in cell wall biogenesis; putative glycosyltransferase 2216209 5713086 Dshi_2091 Dinoroseobacter shibae DFL 12 = DSM 16493 putative glycosyltransferase YP_001533429.1 2215514 R 398580 CDS YP_001533430.1 159044636 5713087 2216299..2217084 1 NC_009952.1 COG: COG0354 - Predicted aminomethyltransferase related to GcvT; PFAM: PF08669, PF01571; similar to aminomethyltransferase; hypothetical protein 2217084 5713087 Dshi_2092 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533430.1 2216299 D 398580 CDS YP_001533431.1 159044637 5713088 complement(2217100..2217546) 1 NC_009952.1 hypothetical protein 2217546 5713088 Dshi_2093 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533431.1 2217100 R 398580 CDS YP_001533432.1 159044638 5713089 complement(2217877..2218518) 1 NC_009952.1 Involved in peptide bond synthesis; alters the affinity of the ribosome for aminoacyl-tRNA; elongation factor P 2218518 efp 5713089 efp Dinoroseobacter shibae DFL 12 = DSM 16493 elongation factor P YP_001533432.1 2217877 R 398580 CDS YP_001533433.1 159044639 5713090 2218654..2218974 1 NC_009952.1 hypothetical protein 2218974 5713090 Dshi_2095 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533433.1 2218654 D 398580 CDS YP_001533434.1 159044640 5713091 2219140..2220600 1 NC_009952.1 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 2220600 cobQ 5713091 cobQ Dinoroseobacter shibae DFL 12 = DSM 16493 cobyric acid synthase YP_001533434.1 2219140 D 398580 CDS YP_001533435.1 159044641 5713092 complement(2220619..2221347) 1 NC_009952.1 hypothetical protein 2221347 5713092 Dshi_2097 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533435.1 2220619 R 398580 CDS YP_001533436.1 159044642 5713093 complement(2221467..2222837) 1 NC_009952.1 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 2222837 5713093 Dshi_2098 Dinoroseobacter shibae DFL 12 = DSM 16493 putative outer membrane protein tolC YP_001533436.1 2221467 R 398580 CDS YP_001533437.1 159044643 5713094 complement(2222900..2223553) 1 NC_009952.1 TIGRFAM: TIGR00080 protein-L-isoaspartate(D-aspartate) O-methyltransferase; COG: COG2518 - Protein-L-isoaspartate carboxylmethyltransferase; PFAM: PF01135; pcm; putative Protein-L-isoaspartate O-methyltransferase 2223553 5713094 Dshi_2099 Dinoroseobacter shibae DFL 12 = DSM 16493 putative Protein-L-isoaspartate O-methyltransferase YP_001533437.1 2222900 R 398580 CDS YP_001533438.1 159044644 5713096 2223872..2225461 1 NC_009952.1 PFAM: PF00589; SUPERFAMILY: SSF56349; Gene3D: G3DSA:1.10.443.10; COG: COG4974 - Site-specific recombinase XerD; putative integrase 2225461 5713096 Dshi_2100 Dinoroseobacter shibae DFL 12 = DSM 16493 putative integrase YP_001533438.1 2223872 D 398580 CDS YP_001533439.1 159044645 5713097 complement(2225466..2228060) 1 NC_009952.1 SUPERFAMILY: SSF52540; hypothetical protein 2228060 5713097 Dshi_2101 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533439.1 2225466 R 398580 CDS YP_001533440.1 159044646 5713098 complement(2228064..2229521) 1 NC_009952.1 PFAM: PF01555; related to DNA methylase N4/N6; hypothetical protein 2229521 5713098 Dshi_2102 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533440.1 2228064 R 398580 CDS YP_001533441.1 159044647 5713099 2229626..2229892 1 NC_009952.1 PFAM: PF01527-Transposase; putative transposase 2229892 5713099 Dshi_2103 Dinoroseobacter shibae DFL 12 = DSM 16493 putative transposase YP_001533441.1 2229626 D 398580 CDS YP_001533442.1 159044648 5713100 2229916..2230737 1 NC_009952.1 COG: COG2801 - Transposase and inactivated derivatives; PFAM: PF00665; PROSITE: PS50994; SUPERFAMILY: SSF53098; putative integrase 2230737 5713100 Dshi_2104 Dinoroseobacter shibae DFL 12 = DSM 16493 putative integrase YP_001533442.1 2229916 D 398580 CDS YP_001533443.1 159044649 5713101 complement(2230732..2231412) 1 NC_009952.1 PFAM: PF01555; PROSITE: PS00092; SUPERFAMILY: SSF53335; related to DNA methylase N6; hypothetical protein 2231412 5713101 Dshi_2105 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533443.1 2230732 R 398580 CDS YP_001533444.1 159044650 5713102 complement(2231752..2232006) 1 NC_009952.1 PFAM: PF01381; PROSITE: PS50943; SMART: SM00530; SUPERFAMILY: SSF47413; Gene3D: G3DSA:1.10.260.40; related to HTH-type lambda repressor; hypothetical protein 2232006 5713102 Dshi_2106 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533444.1 2231752 R 398580 CDS YP_001533445.1 159044651 5713103 2232133..2232831 1 NC_009952.1 hypothetical protein 2232831 5713103 Dshi_2107 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533445.1 2232133 D 398580 CDS YP_001533446.1 159044652 5713104 complement(2234212..2236719) 1 NC_009952.1 COG: COG0025 - NhaP-type Na+/H+ and K+/H+ antiporters; PFAM: PF00027, PF00999; SMART: SM00100; PROSITE: PS50042; related to sodium/hydrogen exchanger; hypothetical protein 2236719 5713104 Dshi_2108 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533446.1 2234212 R 398580 CDS YP_001533447.1 159044653 5713105 complement(2236892..2238043) 1 NC_009952.1 COG: COG3616 - Predicted amino acid aldolase or racemase; PFAM: PF01168; related to alanine racemase; hypothetical protein 2238043 5713105 Dshi_2109 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533447.1 2236892 R 398580 CDS YP_001533448.1 159044654 5713106 2238185..2239102 1 NC_009952.1 PFAM: PF04227- Indigoidine synthase A like protein; SUPERFAMILY SSF110581: Indigoidine synthase A-like; indigoidine synthase A-like protein 2239102 5713106 Dshi_2110 Dinoroseobacter shibae DFL 12 = DSM 16493 indigoidine synthase A-like protein YP_001533448.1 2238185 D 398580 CDS YP_001533449.1 159044655 5713107 complement(2239132..2240037) 1 NC_009952.1 SWISSPROT P37051: Formyltetrahydrofolate deformylase; TIGRFAM: TIGR00655; COG: COG0788; PFAM: PF00551, PF01842; PRINTS: PR01575; PIR: PIRSF036480- formyltetrahydrofolate deformylase; formyltetrahydrofolate deformylase 2240037 purU 5713107 purU Dinoroseobacter shibae DFL 12 = DSM 16493 formyltetrahydrofolate deformylase YP_001533449.1 2239132 R 398580 CDS YP_003422332.1 284928600 5713108 complement(2240003..2241415) 1 NC_009952.1 L-serine dehydratase 2241415 5713108 Dshi_5008 Dinoroseobacter shibae DFL 12 = DSM 16493 L-serine dehydratase YP_003422332.1 2240003 R 398580 CDS YP_001533450.1 159044656 5713109 complement(2241420..2242694) 1 NC_009952.1 catalyzes the reaction of glycine with 5,10-methylenetetrahydrofolate to form L-serine and tetrahydrofolate; serine hydroxymethyltransferase 2242694 glyA 5713109 glyA Dinoroseobacter shibae DFL 12 = DSM 16493 serine hydroxymethyltransferase YP_001533450.1 2241420 R 398580 CDS YP_001533451.1 159044657 5713110 complement(2242777..2243307) 1 NC_009952.1 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 2243307 5713110 Dshi_2114 Dinoroseobacter shibae DFL 12 = DSM 16493 putative sarcosine oxidase subunit gamma YP_001533451.1 2242777 R 398580 CDS YP_001533452.1 159044658 5713111 complement(2243321..2246323) 1 NC_009952.1 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 2246323 soxA2 5713111 soxA2 Dinoroseobacter shibae DFL 12 = DSM 16493 sarcosine oxidase subunit alpha YP_001533452.1 2243321 R 398580 CDS YP_001533453.1 159044659 5713112 complement(2246320..2246619) 1 NC_009952.1 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 2246619 5713112 Dshi_2116 Dinoroseobacter shibae DFL 12 = DSM 16493 putative sarcosine oxidase YP_001533453.1 2246320 R 398580 CDS YP_001533454.1 159044660 5713113 complement(2246632..2247885) 1 NC_009952.1 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 2247885 soxB 5713113 soxB Dinoroseobacter shibae DFL 12 = DSM 16493 sarcosine oxidase subunit beta YP_001533454.1 2246632 R 398580 CDS YP_001533455.1 159044661 5713114 2248012..2248998 1 NC_009952.1 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 2248998 5713114 Dshi_2118 Dinoroseobacter shibae DFL 12 = DSM 16493 HTH-type transcriptional regulator YP_001533455.1 2248012 D 398580 CDS YP_001533456.1 159044662 5713115 complement(2249037..2250611) 1 NC_009952.1 TIGRFAM: TIGR00842 - choline/carnitine/betaine transport; COG: COG1292 - Choline-glycine betaine transporter; PFAM: PF02028-BCCT family transporter; betaine/carnitine/choline transporter family protein 2250611 5713115 Dshi_2119 Dinoroseobacter shibae DFL 12 = DSM 16493 betaine/carnitine/choline transporter family protein YP_001533456.1 2249037 R 398580 CDS YP_001533457.1 159044663 5713116 complement(2250796..2251926) 1 NC_009952.1 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 2251926 potA2 5713116 potA2 Dinoroseobacter shibae DFL 12 = DSM 16493 spermidine/putrescine import ATP-binding protein YP_001533457.1 2250796 R 398580 CDS YP_001533458.1 159044664 5713117 complement(2251923..2252720) 1 NC_009952.1 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 2252720 5713117 Dshi_2121 Dinoroseobacter shibae DFL 12 = DSM 16493 putative spermidine/putrescine transport system permease YP_001533458.1 2251923 R 398580 CDS YP_001533459.1 159044665 5713118 complement(2252722..2253567) 1 NC_009952.1 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 2253567 5713118 Dshi_2122 Dinoroseobacter shibae DFL 12 = DSM 16493 putative spermidine/putrescine transport system permease YP_001533459.1 2252722 R 398580 CDS YP_001533460.1 159044666 5713119 complement(2253645..2254763) 1 NC_009952.1 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 2254763 5713119 Dshi_2123 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533460.1 2253645 R 398580 CDS YP_001533461.1 159044667 5713120 complement(2254814..2255617) 1 NC_009952.1 PFAM: PF02633; COG: COG1402 - Uncharacterized protein, putative amidase; related to creatininase; hypothetical protein 2255617 5713120 Dshi_2124 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533461.1 2254814 R 398580 CDS YP_001533462.1 159044668 5713121 2255710..2256606 1 NC_009952.1 COG: COG0583 - Transcriptional regulator; PFAM: PF00126, PF03466; PROSITE: PS50931; SUPERFAMILY: SSF53850, SSF46785; lysR family; HTH-type transcriptional regulator 2256606 5713121 Dshi_2125 Dinoroseobacter shibae DFL 12 = DSM 16493 HTH-type transcriptional regulator YP_001533462.1 2255710 D 398580 CDS YP_001533463.1 159044669 5713122 2256727..2257959 1 NC_009952.1 SWISSPROT P38488: Creatinase; COG: COG0006 - Xaa-Pro aminopeptidase; PFAM: PF00557, PF01321; creatinase 2257959 5713122 Dshi_2126 Dinoroseobacter shibae DFL 12 = DSM 16493 creatinase YP_001533463.1 2256727 D 398580 CDS YP_001533464.1 159044670 5713123 2258167..2258787 1 NC_009952.1 SUPERFAMILY: SSF51182; hypothetical protein 2258787 5713123 Dshi_2127 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533464.1 2258167 D 398580 CDS YP_001533465.1 159044671 5713124 2258972..2259460 1 NC_009952.1 PFAM PF04403: Paraquat-inducible protein A; similar to paraquat inducible protein A; hypothetical protein 2259460 5713124 Dshi_2128 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533465.1 2258972 D 398580 CDS YP_001533466.1 159044672 5713125 2259500..2260867 1 NC_009952.1 Sms; stabilizes the strand-invasion intermediate during the DNA repair; involved in recombination of donor DNA and plays an important role in DNA damage repair after exposure to mutagenic agents; DNA repair protein RadA 2260867 5713125 Dshi_2129 Dinoroseobacter shibae DFL 12 = DSM 16493 DNA repair protein RadA YP_001533466.1 2259500 D 398580 CDS YP_001533467.1 159044673 5713126 2260890..2261444 1 NC_009952.1 COG: COG1286 - Uncharacterized membrane protein, required for colicin V production; PFAM: PF02674-Colicin V production protein; putative colicin V production protein 2261444 5713126 Dshi_2130 Dinoroseobacter shibae DFL 12 = DSM 16493 putative colicin V production protein YP_001533467.1 2260890 D 398580 CDS YP_001533468.1 159044674 5713127 2261760..2262230 1 NC_009952.1 no database hits, no shine dalgarno. Pseudogene??; hypothetical protein 2262230 5713127 Dshi_2131 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533468.1 2261760 D 398580 CDS YP_001533469.1 159044675 5713128 2262378..2263904 1 NC_009952.1 Catalyzes first step of the de novo purine nucleotide biosynthetic pathway; amidophosphoribosyltransferase 2263904 purF 5713128 purF Dinoroseobacter shibae DFL 12 = DSM 16493 amidophosphoribosyltransferase YP_001533469.1 2262378 D 398580 CDS YP_001533470.1 159044676 5713129 2263901..2264419 1 NC_009952.1 COG: COG3543 - Uncharacterized conserved protein; PFAM: PF06935-Protein of unknown function; hypothetical protein 2264419 5713129 Dshi_2133 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533470.1 2263901 D 398580 CDS YP_001533471.1 159044677 5713130 complement(2264629..2265222) 1 NC_009952.1 COG: COG1268 - Uncharacterized conserved protein; PFAM: PF02632-BioY family; PIR: PIRSF016661- uncharacterized biotin biosynthesis protein, BioY type; putative BioY protein 2265222 5713130 Dshi_2134 Dinoroseobacter shibae DFL 12 = DSM 16493 putative BioY protein YP_001533471.1 2264629 R 398580 CDS YP_001533472.1 159044678 5713131 2265345..2266010 1 NC_009952.1 COG: COG4221 - Short-chain alcohol dehydrogenase of unknown specificity; PFAM: PF00106; PRINTS: PR00081; short-chain dehydrogenase 2266010 5713131 Dshi_2135 Dinoroseobacter shibae DFL 12 = DSM 16493 short-chain dehydrogenase YP_001533472.1 2265345 D 398580 CDS YP_001533473.1 159044679 5713132 2266110..2266895 1 NC_009952.1 catalyzes the conversion of a phosphate monoester to an alcohol and a phosphate; stationary phase survival protein SurE 2266895 surE 5713132 surE Dinoroseobacter shibae DFL 12 = DSM 16493 stationary phase survival protein SurE YP_001533473.1 2266110 D 398580 CDS YP_001533474.1 159044680 5713133 2266892..2267542 1 NC_009952.1 TIGRFAM: TIGR00080 protein-L-isoaspartate(D-aspartate) O-methyltransferase; COG: COG2518 - Protein-L-isoaspartate carboxylmethyltransferase; PFAM: PF01135; PROSITE: PS01279; protein-L-isoaspartate O-methyltransferase 2267542 pcm 5713133 pcm Dinoroseobacter shibae DFL 12 = DSM 16493 protein-L-isoaspartate O-methyltransferase YP_001533474.1 2266892 D 398580 CDS YP_001533475.1 159044681 5713134 2267574..2268803 1 NC_009952.1 COG: COG0739 - Membrane proteins related to metalloendopeptidases; PFAM: PF01476, PF01551; SMART: SM00257; SUPERFAMILY: SSF51261; related to metalloprotease; hypothetical protein 2268803 5713134 Dshi_2138 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533475.1 2267574 D 398580 CDS YP_001533476.1 159044682 5713135 complement(2268877..2269770) 1 NC_009952.1 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 2269770 5713135 Dshi_2139 Dinoroseobacter shibae DFL 12 = DSM 16493 integral membrane protein YP_001533476.1 2268877 R 398580 CDS YP_001533477.1 159044683 5713136 2269849..2271162 1 NC_009952.1 PFAM: PF00999; COG: COG0025 - NhaP-type Na+/H+ and K+/H+ antiporters; related to sodium/hydrogen exchanger; hypothetical protein 2271162 5713136 Dshi_2140 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533477.1 2269849 D 398580 CDS YP_001533478.1 159044684 5713137 2271249..2271968 1 NC_009952.1 PFAM: PF04391; hypothetical protein 2271968 5713137 Dshi_2141 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533478.1 2271249 D 398580 CDS YP_001533479.1 159044685 5713138 2272078..2272491 1 NC_009952.1 SWISSPROT P0A9A9: Ferric uptake regulation protein (fur); COG: COG0735 - Fe2+/Zn2+ uptake regulation proteins; PFAM: PF01475; SUPERFAMILY: SSF46785; putative ferric uptake regulation protein 2272491 5713138 Dshi_2142 Dinoroseobacter shibae DFL 12 = DSM 16493 putative ferric uptake regulation protein YP_001533479.1 2272078 D 398580 CDS YP_001533480.1 159044686 5713139 2272576..2273487 1 NC_009952.1 COG: COG1741 - Pirin-related protein; PFAM: PF02678, PF05726; SUPERFAMILY: SSF51182; pirin-like protein 2273487 5713139 Dshi_2143 Dinoroseobacter shibae DFL 12 = DSM 16493 pirin-like protein YP_001533480.1 2272576 D 398580 CDS YP_001533481.1 159044687 5713140 complement(2273605..2274639) 1 NC_009952.1 SWISSPROT P75823: Low specificity L-threonine aldolase; O07051: L-allo-threonine aldolase COG: COG2008 - Threonine aldolase; PFAM: PF01212; SUPERFAMILY: SSF53383; threonine aldolase 2274639 5713140 Dshi_2144 Dinoroseobacter shibae DFL 12 = DSM 16493 threonine aldolase YP_001533481.1 2273605 R 398580 CDS YP_001533482.1 159044688 5713141 2274839..2276113 1 NC_009952.1 enolase; catalyzes the formation of phosphoenolpyruvate from 2-phospho-D-glycerate in glycolysis; phosphopyruvate hydratase 2276113 eno 5713141 eno Dinoroseobacter shibae DFL 12 = DSM 16493 phosphopyruvate hydratase YP_001533482.1 2274839 D 398580 CDS YP_001533483.1 159044689 5713142 complement(2276189..2276938) 1 NC_009952.1 PFAM: PF05239; related to PRC-barrel; hypothetical protein 2276938 5713142 Dshi_2146 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533483.1 2276189 R 398580 CDS YP_001533484.1 159044690 5713143 complement(2277080..2277499) 1 NC_009952.1 hypothetical protein 2277499 5713143 Dshi_2147 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533484.1 2277080 R 398580 CDS YP_001533485.1 159044691 5713144 2277653..2278543 1 NC_009952.1 SWISSPROT Q68XV0: S-adenosylmethionine uptake transporter; PFAM: pfam00892; COG: COG5006 - Predicted permease, DMT superfamily; putative S-adenosylmethionine uptake transporter 2278543 5713144 Dshi_2148 Dinoroseobacter shibae DFL 12 = DSM 16493 putative S-adenosylmethionine uptake transporter YP_001533485.1 2277653 D 398580 CDS YP_001533486.1 159044692 5713145 2278551..2278991 1 NC_009952.1 COG: COG3542 - Uncharacterized conserved protein; PFAM: PF06172 Cupin superfamily (DUF985); putative cupin 2278991 5713145 Dshi_2149 Dinoroseobacter shibae DFL 12 = DSM 16493 putative cupin YP_001533486.1 2278551 D 398580 CDS YP_001533487.1 159044693 5713146 complement(2279010..2280089) 1 NC_009952.1 catalyzes hydrolysis of 1,6-anhydro bond of anyhydro-N-acetylmuramic acid (anhMurNAc) and phosphorylates anhMurNAc to produce N-acetyl-muramate-6-phosphate; involved in murein recycling; anhydro-N-acetylmuramic acid kinase 2280089 anmK 5713146 anmK Dinoroseobacter shibae DFL 12 = DSM 16493 anhydro-N-acetylmuramic acid kinase YP_001533487.1 2279010 R 398580 CDS YP_001533488.1 159044694 5713147 2280141..2281394 1 NC_009952.1 Swiss-Prot: P0AGJ9-Tyrosyl-tRNA synthetase TIGRFAM: tyrosyl-tRNA synthetase PFAM: aminoacyl-tRNA synthetase class Ib; tyrosyl-tRNA synthetase 2281394 tyrS 5713147 tyrS Dinoroseobacter shibae DFL 12 = DSM 16493 tyrosyl-tRNA synthetase YP_001533488.1 2280141 D 398580 CDS YP_001533489.1 159044695 5713148 complement(2281595..2282566) 1 NC_009952.1 -# KEGG: sil:SPO2232 hypothetical protein; hypothetical protein 2282566 5713148 Dshi_2152 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533489.1 2281595 R 398580 CDS YP_001533490.1 159044696 5713149 complement(2282789..2283337) 1 NC_009952.1 Swiss-Prot: P23869-Peptidyl-prolyl cis-trans isomerase B PFAM: peptidyl-prolyl cis-trans isomerase cyclophilin type; putative peptidyl-prolyl cis-trans isomerase 2283337 5713149 Dshi_2153 Dinoroseobacter shibae DFL 12 = DSM 16493 putative peptidyl-prolyl cis-trans isomerase YP_001533490.1 2282789 R 398580 CDS YP_001533491.1 159044697 5713150 complement(2283330..2283854) 1 NC_009952.1 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 2283854 5713150 Dshi_2154 Dinoroseobacter shibae DFL 12 = DSM 16493 putative peptidyl-prolyl cis-trans isomerase YP_001533491.1 2283330 R 398580 CDS YP_001533492.1 159044698 5713151 2284018..2285199 1 NC_009952.1 Converts 3-phospho-D-glycerate to 3-phospho-D-glyceroyl phosphate during the glycolysis pathway; phosphoglycerate kinase 2285199 pgk 5713151 pgk Dinoroseobacter shibae DFL 12 = DSM 16493 phosphoglycerate kinase YP_001533492.1 2284018 D 398580 CDS YP_001533493.1 159044699 5713152 2285294..2286178 1 NC_009952.1 catalyzes the formation of glycerone phosphate and D-glyceraldehyde 3-phosphate from D-fructose 1,6-bisphosphate in glycolysis; fructose-1,6-bisphosphate aldolase 2286178 fda 5713152 fda Dinoroseobacter shibae DFL 12 = DSM 16493 fructose-1,6-bisphosphate aldolase YP_001533493.1 2285294 D 398580 CDS YP_001533494.1 159044700 5713153 2286453..2286755 1 NC_009952.1 PFAM: Septum formation initiator KEGG: jan:Jann_1692 septum formation initiator; similar to septum formation initiator; hypothetical protein 2286755 5713153 Dshi_2157 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533494.1 2286453 D 398580 CDS YP_001533495.1 159044701 5713154 2286855..2287850 1 NC_009952.1 Swiss-Prot: Q820A6-Pyruvate dehydrogenase E1 component subunit alpha PFAM: dehydrogenase E1 component; pyruvate dehydrogenase E1 component subunit alpha 2287850 pdhA1 5713154 pdhA1 Dinoroseobacter shibae DFL 12 = DSM 16493 pyruvate dehydrogenase E1 component subunit alpha YP_001533495.1 2286855 D 398580 CDS YP_001533496.1 159044702 5713155 2287863..2289218 1 NC_009952.1 catalyzes the oxidative decarboxylation of pyruvate with concomitant acetylation of a lipoic acid-containing dihydrolipoamide acetyltransferase within the complex. The E1 component of the pyruvate dehydrogenase complex catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2). It contains multiple copies of three enzymatic components: pyruvate dehydrogenase (E1), dihydrolipoamide acetyltransferase(E2) and lipoamide dehydrogenase; pyruvate dehydrogenase subunit beta 2289218 pdhB2 5713155 pdhB2 Dinoroseobacter shibae DFL 12 = DSM 16493 pyruvate dehydrogenase subunit beta YP_001533496.1 2287863 D 398580 CDS YP_001533497.1 159044703 5713156 2289232..2290494 1 NC_009952.1 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 2290494 pdhC1 5713156 pdhC1 Dinoroseobacter shibae DFL 12 = DSM 16493 branched-chain alpha-keto acid dehydrogenase subunit E2 YP_001533497.1 2289232 D 398580 CDS YP_001533498.1 159044704 5713157 complement(2290509..2291318) 1 NC_009952.1 Swiss-Prot: P0A9D4-Serine acetyltransferase TIGRFAM: serine O-acetyltransferase PFAM: transferase hexapeptide repeat containing protein; serine acetyltransferase domain protein; serine O-acetyltransferase 2291318 cysE 5713157 cysE Dinoroseobacter shibae DFL 12 = DSM 16493 serine O-acetyltransferase YP_001533498.1 2290509 R 398580 CDS YP_001533499.1 159044705 5713158 complement(2291686..2292393) 1 NC_009952.1 hypothetical protein 2292393 5713158 Dshi_2162 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533499.1 2291686 R 398580 CDS YP_001533500.1 159044706 5713159 complement(2292386..2296303) 1 NC_009952.1 KEGG: sil:SPO2250 hypothetical protein; hypothetical protein 2296303 5713159 Dshi_2163 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533500.1 2292386 R 398580 CDS YP_001533501.1 159044707 5713160 complement(2296307..2296747) 1 NC_009952.1 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 2296747 5713160 Dshi_2164 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533501.1 2296307 R 398580 CDS YP_001533502.1 159044708 5713161 complement(2296744..2297634) 1 NC_009952.1 PFAM: conserved hypothetical protein KEGG: rsq:Rsph17025_1087 hypothetical protein; hypothetical protein 2297634 5713161 Dshi_2165 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533502.1 2296744 R 398580 CDS YP_001533503.1 159044709 5713162 complement(2297631..2298263) 1 NC_009952.1 Conserved hypothetical protein TIGR02217, PFAM: conserved hypothetical protein, KEGG: sil:SPO2253 hypothetical protein; hypothetical protein 2298263 5713162 Dshi_2166 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533503.1 2297631 R 398580 CDS YP_001533504.1 159044710 5713163 complement(2298277..2298945) 1 NC_009952.1 COG5281, Phage-related minor tail protein [Function unknown].; similar to Phage-related minor tail protein; hypothetical protein 2298945 5713163 Dshi_2167 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533504.1 2298277 R 398580 CDS YP_001533505.1 159044711 5713164 complement(2298929..2299144) 1 NC_009952.1 TIGR02216# phage conserved hypothetical protein; hypothetical protein 2299144 5713164 Dshi_2168 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533505.1 2298929 R 398580 CDS YP_001533506.1 159044712 5713165 complement(2299141..2299470) 1 NC_009952.1 KEGG: rsq:Rsph17025_1083 hypothetical protein; hypothetical protein 2299470 5713165 Dshi_2169 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533506.1 2299141 R 398580 CDS YP_001533507.1 159044713 5713166 complement(2299476..2299889) 1 NC_009952.1 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 2299889 5713166 Dshi_2170 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533507.1 2299476 R 398580 CDS YP_001533508.1 159044714 5713167 complement(2299911..2300321) 1 NC_009952.1 KEGG: sil:SPO2258 hypothetical protein; hypothetical protein 2300321 5713167 Dshi_2171 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533508.1 2299911 R 398580 CDS YP_001533509.1 159044715 5713168 complement(2300318..2300656) 1 NC_009952.1 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 2300656 5713168 Dshi_2172 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533509.1 2300318 R 398580 CDS YP_001533510.1 159044716 5713826 complement(2300653..2301243) 1 NC_009952.1 KEGG: rde:RD1_3027 hypothetical protein, TIGR02215 phage conserved hypothetical protein, phiE125 gp8 family; hypothetical protein 2301243 5713826 Dshi_2173 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533510.1 2300653 R 398580 CDS YP_001533511.1 159044717 5713827 complement(2301398..2302615) 1 NC_009952.1 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 2302615 5713827 Dshi_2174 Dinoroseobacter shibae DFL 12 = DSM 16493 putative phage major capsid protein YP_001533511.1 2301398 R 398580 CDS YP_001533512.1 159044718 5713828 complement(2302612..2303229) 1 NC_009952.1 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 2303229 5713828 Dshi_2175 Dinoroseobacter shibae DFL 12 = DSM 16493 putative phage prohead protease YP_001533512.1 2302612 R 398580 CDS YP_001533513.1 159044719 5713829 complement(2303242..2303508) 1 NC_009952.1 KEGG: jan:Jann_1633 hypothetical protein; hypothetical protein 2303508 5713829 Dshi_2176 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533513.1 2303242 R 398580 CDS YP_001533514.1 159044720 5713830 complement(2303499..2304689) 1 NC_009952.1 TIGRFAM: phage portal protein, HK97 family PFAM: portal protein KEGG: rde:RD1_3033 phage portal protein, putative; HK97 family; putative phage portal protein 2304689 5713830 Dshi_2177 Dinoroseobacter shibae DFL 12 = DSM 16493 putative phage portal protein YP_001533514.1 2303499 R 398580 CDS YP_001533515.1 159044721 5713831 complement(2304797..2306155) 1 NC_009952.1 PFAM: protein of unknown function DUF264 KEGG: rde:RD1_3034 hypothetical protein; hypothetical protein 2306155 5713831 Dshi_2178 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533515.1 2304797 R 398580 CDS YP_001533516.1 159044722 5713832 complement(2306608..2307762) 1 NC_009952.1 PFAM: aminodeoxychorismate lyase KEGG: jan:Jann_1630 aminodeoxychorismate lyase; related to aminodeoxychorismate lyase; hypothetical protein 2307762 5713832 Dshi_2179 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533516.1 2306608 R 398580 CDS YP_001533517.1 159044723 5713833 complement(2307762..2309024) 1 NC_009952.1 FabF; beta-ketoacyl-ACP synthase II, KASII; catalyzes a condensation reaction in fatty acid biosynthesis: addition of an acyl acceptor of two carbons from malonyl-ACP; required for the elongation of short-chain unsaturated acyl-ACP; 3-oxoacyl-(acyl carrier protein) synthase II 2309024 fabF 5713833 fabF Dinoroseobacter shibae DFL 12 = DSM 16493 3-oxoacyl-(acyl carrier protein) synthase II YP_001533517.1 2307762 R 398580 CDS YP_001533518.1 159044724 5713834 complement(2309189..2309422) 1 NC_009952.1 carries the fatty acid chain in fatty acid biosynthesis; acyl carrier protein 2309422 acpP 5713834 acpP Dinoroseobacter shibae DFL 12 = DSM 16493 acyl carrier protein YP_001533518.1 2309189 R 398580 CDS YP_001533519.1 159044725 5713835 complement(2309595..2310332) 1 NC_009952.1 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 2310332 5713835 Dshi_2182 Dinoroseobacter shibae DFL 12 = DSM 16493 putative 3-oxoacyl-[acyl-carrier-protein] reductase YP_001533519.1 2309595 R 398580 CDS YP_001533520.1 159044726 5713836 complement(2310332..2311279) 1 NC_009952.1 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 2311279 fabD 5713836 fabD Dinoroseobacter shibae DFL 12 = DSM 16493 malonyl CoA-acyl carrier protein transacylase YP_001533520.1 2310332 R 398580 CDS YP_001533521.1 159044727 5713837 2311440..2312642 1 NC_009952.1 PFAM: YceI family protein; cytochrome B561 KEGG: rde:RD1_3041 cytochrome b561, putative; putative cytochrome B561 2312642 5713837 Dshi_2184 Dinoroseobacter shibae DFL 12 = DSM 16493 putative cytochrome B561 YP_001533521.1 2311440 D 398580 CDS YP_001533522.1 159044728 5713838 complement(2312706..2313290) 1 NC_009952.1 COG2353 - Uncharacterized conserved protein PFAM: YceI family protein; related to YceI family protein; hypothetical protein 2313290 5713838 Dshi_2185 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533522.1 2312706 R 398580 CDS YP_001533523.1 159044729 5713839 2313554..2313907 1 NC_009952.1 binds cooperatively with S18 to the S15-16S complex, allowing platform assembly to continue with S11 and S21; 30S ribosomal protein S6 2313907 rpsF 5713839 rpsF Dinoroseobacter shibae DFL 12 = DSM 16493 30S ribosomal protein S6 YP_001533523.1 2313554 D 398580 CDS YP_001533524.1 159044730 5713840 2313936..2314163 1 NC_009952.1 binds as a heterodimer with protein S6 to the central domain of the 16S rRNA; helps stabilize the platform of the 30S subunit; 30S ribosomal protein S18 2314163 rpsR 5713840 rpsR Dinoroseobacter shibae DFL 12 = DSM 16493 30S ribosomal protein S18 YP_001533524.1 2313936 D 398580 CDS YP_001533525.1 159044731 5713841 2314176..2314805 1 NC_009952.1 in Escherichia coli this protein is wrapped around the base of the L1 stalk; 50S ribosomal protein L9 2314805 rplI 5713841 rplI Dinoroseobacter shibae DFL 12 = DSM 16493 50S ribosomal protein L9 YP_001533525.1 2314176 D 398580 CDS YP_001533526.1 159044732 5713842 2314997..2316958 1 NC_009952.1 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 2316958 cpdB 5713842 cpdB Dinoroseobacter shibae DFL 12 = DSM 16493 bifunctional 2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase periplasmic protein YP_001533526.1 2314997 D 398580 CDS YP_001533527.1 159044733 5713843 complement(2317027..2318355) 1 NC_009952.1 Tig; RopA; peptidyl-prolyl cis/trans isomerase; promotes folding of newly synthesized proteins; binds ribosomal 50S subunit; forms a homodimer; trigger factor 2318355 tig 5713843 tig Dinoroseobacter shibae DFL 12 = DSM 16493 trigger factor YP_001533527.1 2317027 R 398580 CDS YP_001533528.1 159044734 5713844 complement(2318521..2318832) 1 NC_009952.1 PFAM: ETC complex I subunit conserved region KEGG: sit:TM1040_0143 ETC complex I subunit conserved region; putative ETC complex subunit I conserved region 2318832 5713844 Dshi_2191 Dinoroseobacter shibae DFL 12 = DSM 16493 putative ETC complex subunit I conserved region YP_001533528.1 2318521 R 398580 CDS YP_001533529.1 159044735 5713845 2319332..2321509 1 NC_009952.1 The UvrABC repair system catalyzes the recognition and processing of DNA lesions. The beta-hairpin of the Uvr-B subunit is inserted between the strands, where it probes for the presence of a lesion; excinuclease ABC subunit B 2321509 uvrB 5713845 uvrB Dinoroseobacter shibae DFL 12 = DSM 16493 excinuclease ABC subunit B YP_001533529.1 2319332 D 398580 CDS YP_001533530.1 159044736 5713846 complement(2321538..2321693) 1 NC_009952.1 hypothetical protein 2321693 5713846 Dshi_2193 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533530.1 2321538 R 398580 CDS YP_001533531.1 159044737 5713847 2321854..2322237 1 NC_009952.1 hypothetical protein 2322237 5713847 Dshi_2194 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533531.1 2321854 D 398580 CDS YP_001533532.1 159044738 5713848 complement(2322507..2322644) 1 NC_009952.1 PFAM: Entericidin EcnAB; similar to Entericidin EcnAB; hypothetical protein 2322644 5713848 Dshi_2195 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533532.1 2322507 R 398580 CDS YP_001533533.1 159044739 5713849 complement(2323007..2324029) 1 NC_009952.1 hypothetical protein 2324029 5713849 Dshi_2196 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533533.1 2323007 R 398580 CDS YP_001533534.1 159044740 5713850 complement(2324302..2325957) 1 NC_009952.1 ChvD; in Agrobacterium tumefaciens, mutations in both Walker boxes were found to affect virulence; putative ABC transporter ATP-binding protein 2325957 5713850 Dshi_2197 Dinoroseobacter shibae DFL 12 = DSM 16493 putative ABC transporter ATP-binding protein YP_001533534.1 2324302 R 398580 CDS YP_001533535.1 159044741 5713851 2326037..2326516 1 NC_009952.1 PFAM: MOSC domain containing protein (pfam03473) KEGG: sil:SPO0448 MOSC domain protein; similar to MOCO sulphurase (MOSC domain); hypothetical protein 2326516 5713851 Dshi_2198 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533535.1 2326037 D 398580 CDS YP_001533536.1 159044742 5713852 2326735..2327424 1 NC_009952.1 TIGRFAM: aspartate racemase PFAM: Asp/Glu racemase KEGG: atc:AGR_L_3474 hypothetical protein; aspartate/glutamate racemase family protein 2327424 5713852 Dshi_2199 Dinoroseobacter shibae DFL 12 = DSM 16493 aspartate/glutamate racemase family protein YP_001533536.1 2326735 D 398580 CDS YP_001533537.1 159044743 5713853 complement(2327502..2328092) 1 NC_009952.1 PFAM: regulatory protein TetR KEGG: gvi:gll0188 TetR family transcriptional regulatory protein; putative regulatory protein TetR 2328092 5713853 Dshi_2200 Dinoroseobacter shibae DFL 12 = DSM 16493 putative regulatory protein TetR YP_001533537.1 2327502 R 398580 CDS YP_001533538.1 159044744 5713854 complement(2328093..2328536) 1 NC_009952.1 KEGG: tbd:Tbd_0484 hypothetical protein PFAM: Isoprenylcysteine carboxyl methyltransferase (ICMT) family (pfam04140) COG2020: Putative protein-S-isoprenylcysteine methyltransferase; hypothetical protein 2328536 5713854 Dshi_2201 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533538.1 2328093 R 398580 CDS YP_001533539.1 159044745 5713855 complement(2328739..2329656) 1 NC_009952.1 hypothetical protein 2329656 5713855 Dshi_2202 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533539.1 2328739 R 398580 CDS YP_001533540.1 159044746 5713856 2329752..2330339 1 NC_009952.1 transfers an adenyl group from ATP to NaMN to form nicotinic acid adenine dinucleotide (NaAD) which is then converted to the ubiquitous compound NAD by NAD synthetase; essential enzyme in bacteria; nicotinic acid mononucleotide adenylyltransferase 2330339 nadD 5713856 nadD Dinoroseobacter shibae DFL 12 = DSM 16493 nicotinic acid mononucleotide adenylyltransferase YP_001533540.1 2329752 D 398580 CDS YP_001533541.1 159044747 5713857 2330428..2330763 1 NC_009952.1 hypothetical protein 2330763 5713857 Dshi_2204 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533541.1 2330428 D 398580 CDS YP_001533542.1 159044748 5713858 complement(2330803..2331225) 1 NC_009952.1 hypothetical protein 2331225 5713858 Dshi_2205 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533542.1 2330803 R 398580 CDS YP_001533543.1 159044749 5713859 2331348..2333006 1 NC_009952.1 class I; LysRS1; catalyzes a two-step reaction, first charging a lysine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; in Methanosarcina barkeri this enzyme charges both tRNA molecules for lysine that exist in this organism (but the tRNALysUUU very poorly) and in the presence of LysRS2 can charge tRNAPyl with lysine; lysyl-tRNA synthetase 2333006 lysK 5713859 lysK Dinoroseobacter shibae DFL 12 = DSM 16493 lysyl-tRNA synthetase YP_001533543.1 2331348 D 398580 CDS YP_001533544.1 159044750 5713860 2333095..2333496 1 NC_009952.1 KEGG:sil:SPO0457 hypothetical protein; hypothetical protein 2333496 5713860 Dshi_2207 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533544.1 2333095 D 398580 CDS YP_001533545.1 159044751 5713861 complement(2333780..2335267) 1 NC_009952.1 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 2335267 5713861 Dshi_2208 Dinoroseobacter shibae DFL 12 = DSM 16493 putative D-alanyl-D-alanine carboxypeptidase/endopeptidase YP_001533545.1 2333780 R 398580 CDS YP_001533546.1 159044752 5713862 2335419..2336249 1 NC_009952.1 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 2336249 5713862 Dshi_2209 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533546.1 2335419 D 398580 CDS YP_001533547.1 159044753 5713863 2336408..2338699 1 NC_009952.1 KEGG: sil:SPO0459 hypothetical protein; hypothetical protein 2338699 5713863 Dshi_2210 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533547.1 2336408 D 398580 CDS YP_001533548.1 159044754 5713864 2338802..2339278 1 NC_009952.1 PFAM: protein of unknown function DUF427 KEGG: jan:Jann_3615 protein of unknown function DUF427; hypothetical protein 2339278 5713864 Dshi_2211 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533548.1 2338802 D 398580 CDS YP_001533549.1 159044755 5713865 complement(2339288..2339782) 1 NC_009952.1 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 2339782 5713865 Dshi_2212 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533549.1 2339288 R 398580 CDS YP_001533550.1 159044756 5713866 2339879..2340286 1 NC_009952.1 PFAM: UspA domain protein KEGG: rde:RD1_4076 universal stress family protein, putative; putative UspA domain-containing protein 2340286 5713866 Dshi_2213 Dinoroseobacter shibae DFL 12 = DSM 16493 putative UspA domain-containing protein YP_001533550.1 2339879 D 398580 CDS YP_001533551.1 159044757 5713867 2340335..2340664 1 NC_009952.1 PFAM: Antibiotic biosynthesis monooxygenase KEGG: sil:SPO0462 antibiotic biosynthesis monooxygenase domain protein; related to antibiotic biosynthesis monooxygenase; hypothetical protein 2340664 5713867 Dshi_2214 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533551.1 2340335 D 398580 CDS YP_001533552.1 159044758 5713868 complement(2340674..2341336) 1 NC_009952.1 KEGG: rsq:Rsph17025_2878 hypothetical protein; hypothetical protein 2341336 5713868 Dshi_2215 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533552.1 2340674 R 398580 CDS YP_001533553.1 159044759 5713869 2341451..2342086 1 NC_009952.1 PFAM: pfam00991 ParA family ATPase COG1192: ATPases involved in chromosome partitioning; associated with ATPases involved in chromosome partitioning; hypothetical protein 2342086 5713869 Dshi_2216 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533553.1 2341451 D 398580 CDS YP_001533554.1 159044760 5713870 2342145..2342387 1 NC_009952.1 COG3809: Uncharacterized protein conserved in bacteria KEGG: rde:RD1_1249 hypothetical protein; hypothetical protein 2342387 5713870 Dshi_2217 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533554.1 2342145 D 398580 CDS YP_001533555.1 159044761 5713871 complement(2343059..2343469) 1 NC_009952.1 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 2343469 5713871 Dshi_2218 Dinoroseobacter shibae DFL 12 = DSM 16493 putative Acyl-CoA thioester hydrolase YP_001533555.1 2343059 R 398580 CDS YP_001533556.1 159044762 5713872 2343691..2343897 1 NC_009952.1 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 2343897 5713872 Dshi_2219 Dinoroseobacter shibae DFL 12 = DSM 16493 putative cold-shock DNA-binding domain-containing protein YP_001533556.1 2343691 D 398580 CDS YP_001533557.1 159044763 5713873 2343977..2344417 1 NC_009952.1 PFAM: protein of unknown function DUF1332 KEGG: sil:SPO1309 hypothetical protein COG4103: Uncharacterized protein conserved in bacteria; hypothetical protein 2344417 5713873 Dshi_2220 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533557.1 2343977 D 398580 CDS YP_001533558.1 159044764 5713874 2344582..2345361 1 NC_009952.1 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 2345361 5713874 Dshi_2221 Dinoroseobacter shibae DFL 12 = DSM 16493 putative amino acid ABC transporter YP_001533558.1 2344582 D 398580 CDS YP_001533559.1 159044765 5713875 2345400..2346128 1 NC_009952.1 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 2346128 5713875 Dshi_2222 Dinoroseobacter shibae DFL 12 = DSM 16493 extracellular solute-binding protein YP_001533559.1 2345400 D 398580 CDS YP_001533560.1 159044766 5713876 2346203..2347090 1 NC_009952.1 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 2347090 5713876 Dshi_2223 Dinoroseobacter shibae DFL 12 = DSM 16493 putative amino-acid ABC transporter permease YP_001533560.1 2346203 D 398580 CDS YP_001533561.1 159044767 5713877 2347087..2347893 1 NC_009952.1 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 2347893 5713877 Dshi_2224 Dinoroseobacter shibae DFL 12 = DSM 16493 putative polar amino acid ABC transporter YP_001533561.1 2347087 D 398580 CDS YP_001533562.1 159044768 5713878 2347962..2348672 1 NC_009952.1 PFAM: glutamine amidotransferase class-I KEGG: pde:Pden_1396 glutamine amidotransferase class-I COG0518: GMP synthase - Glutamine amidotransferase domain; putative glutamine amidotransferase class-I 2348672 5713878 Dshi_2225 Dinoroseobacter shibae DFL 12 = DSM 16493 putative glutamine amidotransferase class-I YP_001533562.1 2347962 D 398580 CDS YP_001533563.1 159044769 5713879 2348653..2350023 1 NC_009952.1 Swiss-Prot: P78061-Gamma-glutamylputrescine synthetase / Q9HNI2-Glutamine synthetase PFAM: glutamine synthetase catalytic region KEGG: sil:SPO1300 glutamine synthetase family protein; glutamine synthetase 2350023 5713879 Dshi_2226 Dinoroseobacter shibae DFL 12 = DSM 16493 glutamine synthetase YP_001533563.1 2348653 D 398580 CDS YP_001533564.1 159044770 5713880 2350024..2351328 1 NC_009952.1 Swiss-Prot: P37906-Probable oxidoreductase PFAM: FAD dependent oxidoreductase KEGG: sit:TM1040_1839 FAD dependent oxidoreductase; putative FAD dependent oxidoreductase 2351328 5713880 Dshi_2227 Dinoroseobacter shibae DFL 12 = DSM 16493 putative FAD dependent oxidoreductase YP_001533564.1 2350024 D 398580 CDS YP_001533565.1 159044771 5713881 2351401..2352594 1 NC_009952.1 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 2352594 5713881 Dshi_2228 Dinoroseobacter shibae DFL 12 = DSM 16493 putative aminotransferase YP_001533565.1 2351401 D 398580 CDS YP_001533566.1 159044772 5713882 complement(2352591..2353535) 1 NC_009952.1 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 2353535 5713882 Dshi_2229 Dinoroseobacter shibae DFL 12 = DSM 16493 putative transcriptional regulator YP_001533566.1 2352591 R 398580 CDS YP_001533567.1 159044773 5713883 complement(2353581..2354141) 1 NC_009952.1 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 2354141 5713883 Dshi_2230 Dinoroseobacter shibae DFL 12 = DSM 16493 putative polyhydroxyalkonate synthesis repressor YP_001533567.1 2353581 R 398580 CDS YP_001533568.1 159044774 5713884 complement(2354276..2354704) 1 NC_009952.1 NCBI: YP_001043910 - hypothetical protein Rsph17029_2035; hypothetical protein 2354704 5713884 Dshi_2231 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533568.1 2354276 R 398580 CDS YP_001533569.1 159044775 5713885 complement(2354912..2355358) 1 NC_009952.1 NCBI: YP_682186 - hypothetical protein RD1_1889; hypothetical protein 2355358 5713885 Dshi_2232 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533569.1 2354912 R 398580 CDS YP_001533570.1 159044776 5713886 complement(2355488..2357302) 1 NC_009952.1 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 2357302 phbC 5713886 phbC Dinoroseobacter shibae DFL 12 = DSM 16493 poly-beta-hydroxybutyrate polymerase YP_001533570.1 2355488 R 398580 CDS YP_001533571.1 159044777 5713887 2357406..2358683 1 NC_009952.1 TIGRFAM: polyhydroxyalkanoate depolymerase, intracellular PFAM: PHB de-polymerase domain protein KEGG: sil:SPO1291 polyhydroxyalkanoate depolymerase, intracellular; intracellular; putative polyhydroxyalkanoate depolymerase 2358683 5713887 Dshi_2234 Dinoroseobacter shibae DFL 12 = DSM 16493 putative polyhydroxyalkanoate depolymerase YP_001533571.1 2357406 D 398580 CDS YP_001533572.1 159044778 5713888 complement(2358775..2359911) 1 NC_009952.1 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 2359911 5713888 Dshi_2235 Dinoroseobacter shibae DFL 12 = DSM 16493 putative methionine synthase vitamin-B12 independent YP_001533572.1 2358775 R 398580 CDS YP_001533573.1 159044779 5713889 complement(2359966..2360964) 1 NC_009952.1 hypothetical protein 2360964 5713889 Dshi_2236 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533573.1 2359966 R 398580 CDS YP_001533574.1 159044780 5713890 complement(2361020..2362003) 1 NC_009952.1 PFAM: protein of unknown function DUF1486 KEGG: rde:RD1_3943 hypothetical protein; hypothetical protein 2362003 5713890 Dshi_2237 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533574.1 2361020 R 398580 CDS YP_001533575.1 159044781 5713891 complement(2361990..2363024) 1 NC_009952.1 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 2363024 5713891 Dshi_2238 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001533575.1 2361990 R 398580 CDS YP_001533576.1 159044782 5713892 complement(2363027..2363779) 1 NC_009952.1 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 2363779 5713892 Dshi_2239 Dinoroseobacter shibae DFL 12 = DSM 16493 short-chain dehydrogenase/reductase SDR YP_001533576.1 2363027 R 398580 CDS YP_001533577.1 159044783 5713893 complement(2363849..2364484) 1 NC_009952.1 hypothetical protein 2364484 5713893 Dshi_2240 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533577.1 2363849 R 398580 CDS YP_001533578.1 159044784 5713894 complement(2364498..2365532) 1 NC_009952.1 PFAM: protein of unknown function DUF1486 KEGG: rde:RD1_3946 hypothetical protein; hypothetical protein 2365532 5713894 Dshi_2241 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533578.1 2364498 R 398580 CDS YP_001533579.1 159044785 5713895 complement(2365495..2366820) 1 NC_009952.1 catalyzes the oxidation of L-histidinol to L-histidinaldehyde and then to L-histidine in histidine biosynthesis; functions as a dimer; histidinol dehydrogenase 2366820 hisD3 5713895 hisD3 Dinoroseobacter shibae DFL 12 = DSM 16493 histidinol dehydrogenase YP_001533579.1 2365495 R 398580 CDS YP_001533580.1 159044786 5713896 complement(2366910..2367665) 1 NC_009952.1 PFAM: alpha/beta hydrolase fold KEGG: rsp:RSP_0384 hypothetical protein; hypothetical protein 2367665 5713896 Dshi_2243 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533580.1 2366910 R 398580 CDS YP_001533581.1 159044787 5713897 complement(2367721..2368161) 1 NC_009952.1 PFAM: protein of unknown function DUF1052 KEGG: jan:Jann_3406 protein of unknown function DUF1052; hypothetical protein 2368161 5713897 Dshi_2244 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533581.1 2367721 R 398580 CDS YP_001533582.1 159044788 5713898 complement(2368423..2368770) 1 NC_009952.1 KEGG: rsq:Rsph17025_0423 hypothetical protein; hypothetical protein 2368770 5713898 Dshi_2245 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533582.1 2368423 R 398580 CDS YP_001533583.1 159044789 5713899 complement(2369013..2369543) 1 NC_009952.1 COG3335: Transposase and inactivated derivatives PFAM: Integrase core domain; related to transposase and inactivated derivatives; hypothetical protein 2369543 5713899 Dshi_2246 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533583.1 2369013 R 398580 CDS YP_001533584.1 159044790 5713900 complement(2369605..2369967) 1 NC_009952.1 COG3415 Transposase and inactivated derivatives; related to transposase and inactivated derivatives; hypothetical protein 2369967 5713900 Dshi_2247 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533584.1 2369605 R 398580 CDS YP_001533585.1 159044791 5713901 2370080..2370526 1 NC_009952.1 hypothetical protein 2370526 5713901 Dshi_2248 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533585.1 2370080 D 398580 CDS YP_001533586.1 159044792 5713902 complement(2370535..2371014) 1 NC_009952.1 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 2371014 nusB 5713902 nusB Dinoroseobacter shibae DFL 12 = DSM 16493 N utilization substance protein B-like protein YP_001533586.1 2370535 R 398580 CDS YP_001533587.1 159044793 5713903 complement(2371011..2371562) 1 NC_009952.1 RibE; 6,7-diimethyl-8-ribityllumazine synthase; DMRL synthase; lumazine synthase; beta subunit of riboflavin synthase; condenses 5-amino-6-(1'-D)-ribityl-amino-2,4(1H,3H)-pyrimidinedione with L-3,4-dihydrohy-2-butanone-4-phosphate to generate 6,6-dimethyl-8-lumazine (DMRL); riboflavin synthase then uses 2 molecules of DMRL to produce riboflavin (vitamin B12); involved in the last steps of riboflavin biosynthesis; forms a 60mer (icosahedral shell) in both Bacillus subtilis and Escherichia coli; in Bacillus subtilis this 60mer is associated with the riboflavin synthase subunit (alpha) while in Escherichia coli it is not; 6,7-dimethyl-8-ribityllumazine synthase 2371562 ribH 5713903 ribH Dinoroseobacter shibae DFL 12 = DSM 16493 6,7-dimethyl-8-ribityllumazine synthase YP_001533587.1 2371011 R 398580 CDS YP_001533588.1 159044794 5713904 complement(2371565..2372680) 1 NC_009952.1 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 2372680 ribB 5713904 ribB Dinoroseobacter shibae DFL 12 = DSM 16493 3,4-dihydroxy-2-butanone 4-phosphate synthase YP_001533588.1 2371565 R 398580 CDS YP_001533589.1 159044795 5713905 complement(2372819..2373421) 1 NC_009952.1 catalyzes the formation of riboflavin from 6,7-dimethyl-8-(1-D-ribityl)lumazine; riboflavin synthase subunit alpha 2373421 ribC 5713905 ribC Dinoroseobacter shibae DFL 12 = DSM 16493 riboflavin synthase subunit alpha YP_001533589.1 2372819 R 398580 CDS YP_001533590.1 159044796 5713906 2373608..2374894 1 NC_009952.1 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 2374894 5713906 Dshi_2253 Dinoroseobacter shibae DFL 12 = DSM 16493 putative capsule polysaccharide export protein YP_001533590.1 2373608 D 398580 CDS YP_001533591.1 159044797 5713907 2375007..2376164 1 NC_009952.1 Swiss-Prot: P0A932 - Putative polysaccharide export protein yccZ [Precursor] PFAM: polysaccharide export protein KEGG: sil:SPO1756 polysaccharide biosynthesis/export protein; putative polysaccharide export protein 2376164 5713907 Dshi_2254 Dinoroseobacter shibae DFL 12 = DSM 16493 putative polysaccharide export protein YP_001533591.1 2375007 D 398580 CDS YP_001533592.1 159044798 5713908 2376242..2378218 1 NC_009952.1 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 2378218 5713908 Dshi_2255 Dinoroseobacter shibae DFL 12 = DSM 16493 putative capsule polysaccharide export protein YP_001533592.1 2376242 D 398580 CDS YP_001533593.1 159044799 5713909 complement(2378215..2379312) 1 NC_009952.1 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 2379312 ribD 5713909 ribD Dinoroseobacter shibae DFL 12 = DSM 16493 riboflavin biosynthesis protein YP_001533593.1 2378215 R 398580 CDS YP_001533594.1 159044800 5713910 complement(2379314..2379781) 1 NC_009952.1 Swiss-Prot: Q1GEP8 and P0A8D0 - Transcriptional repressor nrdR PFAM: ATP-cone domain protein KEGG: rsq:Rsph17025_0843 ATP-cone domain protein; transcriptional regulator NrdR 2379781 nrdR 5713910 nrdR Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator NrdR YP_001533594.1 2379314 R 398580 CDS YP_001533595.1 159044801 5713911 complement(2379941..2380360) 1 NC_009952.1 PFAM: protein of unknown function UPF0047 KEGG: sit:TM1040_2137 protein of unknown function UPF0047; hypothetical protein 2380360 5713911 Dshi_2258 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533595.1 2379941 R 398580 CDS YP_001533596.1 159044802 5713912 complement(2380410..2380916) 1 NC_009952.1 hypothetical protein 2380916 5713912 Dshi_2259 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533596.1 2380410 R 398580 CDS YP_001533597.1 159044803 5713913 complement(2381127..2381549) 1 NC_009952.1 hypothetical protein 2381549 5713913 Dshi_2260 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533597.1 2381127 R 398580 CDS YP_001533598.1 159044804 5713914 complement(2381601..2383595) 1 NC_009952.1 sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released; this is the primary sigma factor of bacteria; RNA polymerase sigma factor RpoD 2383595 rpoD 5713914 rpoD Dinoroseobacter shibae DFL 12 = DSM 16493 RNA polymerase sigma factor RpoD YP_001533598.1 2381601 R 398580 CDS YP_001533599.1 159044805 5713915 complement(2383717..2385669) 1 NC_009952.1 synthesizes RNA primers at the replication forks; DNA primase 2385669 dnaG 5713915 dnaG Dinoroseobacter shibae DFL 12 = DSM 16493 DNA primase YP_001533599.1 2383717 R 398580 CDS YP_001533600.1 159044806 5713916 complement(2385725..2386303) 1 NC_009952.1 Swiss-Prot: Q46338 - Sarcosine oxidase subunit gamma TIGR01375# sarcosine oxidase, gamma subunit family, heterotetrameric form; gamma subunit; putative sarcosine oxidase 2386303 5713916 Dshi_2263 Dinoroseobacter shibae DFL 12 = DSM 16493 putative sarcosine oxidase YP_001533600.1 2385725 R 398580 CDS YP_001533601.1 159044807 5713917 complement(2386296..2389238) 1 NC_009952.1 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 2389238 5713917 Dshi_2264 Dinoroseobacter shibae DFL 12 = DSM 16493 putative sarcosine oxidase YP_001533601.1 2386296 R 398580 CDS YP_001533602.1 159044808 5713918 complement(2389235..2389498) 1 NC_009952.1 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 2389498 5713918 Dshi_2265 Dinoroseobacter shibae DFL 12 = DSM 16493 putative sarcosine oxidase YP_001533602.1 2389235 R 398580 CDS YP_001533603.1 159044809 5713919 complement(2389926..2391176) 1 NC_009952.1 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 2391176 5713919 Dshi_2266 Dinoroseobacter shibae DFL 12 = DSM 16493 putative sarcosine oxidase subunit beta YP_001533603.1 2389926 R 398580 CDS YP_001533604.1 159044810 5713920 2391484..2393145 1 NC_009952.1 IPR002035: von Willebrand factor, type A; hypothetical protein 2393145 5713920 Dshi_2267 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533604.1 2391484 D 398580 CDS YP_001533605.1 159044811 5713921 2393142..2393666 1 NC_009952.1 PFAM: TadE family protein KEGG: rsh:Rsph17029_2053 hypothetical protein; associated with TadE-like protein family; hypothetical protein 2393666 5713921 Dshi_2268 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533605.1 2393142 D 398580 CDS YP_001533606.1 159044812 5713922 2393676..2394230 1 NC_009952.1 KEGG: rde:RD1_2616 hypothetical protein; hypothetical protein 2394230 5713922 Dshi_2269 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533606.1 2393676 D 398580 CDS YP_001533607.1 159044813 5713923 complement(2394227..2394736) 1 NC_009952.1 KEGG: sil:SPO1739 hypothetical protein; hypothetical protein 2394736 5713923 Dshi_2270 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533607.1 2394227 R 398580 CDS YP_001533608.1 159044814 5713924 complement(2394736..2395365) 1 NC_009952.1 PFAM: regulatory protein TetR KEGG: rsq:Rsph17025_0835 transcriptional regulator, TetR family; TetR-related; transcriptional regulator 2395365 5713924 Dshi_2271 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001533608.1 2394736 R 398580 CDS YP_001533609.1 159044815 5713925 2395380..2395685 1 NC_009952.1 hypothetical protein 2395685 5713925 Dshi_2272 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533609.1 2395380 D 398580 CDS YP_001533610.1 159044816 5713926 2395765..2397051 1 NC_009952.1 catalyzes the formation of L-aspartate 4-semialdehyde from L-homoserine; homoserine dehydrogenase 2397051 5713926 Dshi_2273 Dinoroseobacter shibae DFL 12 = DSM 16493 homoserine dehydrogenase YP_001533610.1 2395765 D 398580 CDS YP_001533611.1 159044817 5713927 2397177..2398148 1 NC_009952.1 type II fructose 1,6-bisphosphatae; in Escherichia coli this protein forms a dimer and binds manganese; fructose 1,6-bisphosphatase II 2398148 glpX 5713927 glpX Dinoroseobacter shibae DFL 12 = DSM 16493 fructose 1,6-bisphosphatase II YP_001533611.1 2397177 D 398580 CDS YP_001533612.1 159044818 5713928 2398150..2399907 1 NC_009952.1 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 2399907 recJ 5713928 recJ Dinoroseobacter shibae DFL 12 = DSM 16493 single-stranded-DNA-specific exonuclease YP_001533612.1 2398150 D 398580 CDS YP_001533613.1 159044819 5713930 complement(2400364..2400894) 1 NC_009952.1 hypothetical protein 2400894 5713930 Dshi_2276 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533613.1 2400364 R 398580 CDS YP_001533614.1 159044820 5713931 complement(2400891..2402162) 1 NC_009952.1 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 2402162 moeA2 5713931 moeA2 Dinoroseobacter shibae DFL 12 = DSM 16493 molybdopterin biosynthesis protein YP_001533614.1 2400891 R 398580 CDS YP_001533615.1 159044821 5713932 complement(2402247..2404919) 1 NC_009952.1 Swiss-Prot: Q57366 - Dimethyl sulfoxide reductase [Precursor] PFAM: molybdopterin oxidoreductase; molydopterin dinucleotide-binding region KEGG: rde:RD1_3664 dimethyl sulfoxide reductase; dimethyl sulfoxide reductase 2404919 dmsA1 5713932 dmsA1 Dinoroseobacter shibae DFL 12 = DSM 16493 dimethyl sulfoxide reductase YP_001533615.1 2402247 R 398580 CDS YP_001533616.1 159044822 5713933 2405034..2405738 1 NC_009952.1 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 2405738 5713933 Dshi_2279 Dinoroseobacter shibae DFL 12 = DSM 16493 two component transcriptional regulator YP_001533616.1 2405034 D 398580 CDS YP_001533617.1 159044823 5713934 complement(2405708..2408494) 1 NC_009952.1 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 2408494 5713934 Dshi_2280 Dinoroseobacter shibae DFL 12 = DSM 16493 signal transduction histidine kinase YP_001533617.1 2405708 R 398580 CDS YP_001533618.1 159044824 5713935 2408517..2409482 1 NC_009952.1 periplasmic sensory protein associated with the TorRS two-component regulatory system; TMAO reductase system periplasmic protein TorT 2409482 5713935 Dshi_2281 Dinoroseobacter shibae DFL 12 = DSM 16493 TMAO reductase system periplasmic protein TorT YP_001533618.1 2408517 D 398580 CDS YP_001533619.1 159044825 5713936 2409776..2410660 1 NC_009952.1 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 2410660 5713936 Dshi_2282 Dinoroseobacter shibae DFL 12 = DSM 16493 putative transcriptional regulator YP_001533619.1 2409776 D 398580 CDS YP_001533620.1 159044826 5713937 2410872..2412536 1 NC_009952.1 Swiss-Prot: Q47PU3-Phenylacetone monooxygenase pfam00743: Flavin-binding monooxygenase-like KEGG: rha:RHA1_ro08185 monooxygenase; phenylacetone monooxygenase 2412536 pamO 5713937 pamO Dinoroseobacter shibae DFL 12 = DSM 16493 phenylacetone monooxygenase YP_001533620.1 2410872 D 398580 CDS YP_001533621.1 159044827 5713938 2412606..2413793 1 NC_009952.1 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 2413793 5713938 Dshi_2284 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533621.1 2412606 D 398580 CDS YP_001533622.1 159044828 5713939 complement(2413857..2414513) 1 NC_009952.1 hypothetical protein 2414513 5713939 Dshi_2285 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533622.1 2413857 R 398580 CDS YP_001533623.1 159044829 5713940 2414815..2415318 1 NC_009952.1 COG1846: Transcriptional regulators PFAM: regulatory protein MarR KEGG: reu:Reut_B5322 regulatory protein, MarR; associated with transcriptional regulators, marR family; hypothetical protein 2415318 5713940 Dshi_2286 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533623.1 2414815 D 398580 CDS YP_001533624.1 159044830 5713941 2415315..2417234 1 NC_009952.1 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 2417234 5713941 Dshi_2287 Dinoroseobacter shibae DFL 12 = DSM 16493 putative TRAP transporter YP_001533624.1 2415315 D 398580 CDS YP_001533625.1 159044831 5713942 2417255..2418247 1 NC_009952.1 TIGRFAM: TRAP transporter solute receptor, TAXI family KEGG: rde:RD1_3647 TRAP-type transporter, periplasmic component , putative; TAXI family; putative TRAP transporter solute receptor 2418247 5713942 Dshi_2288 Dinoroseobacter shibae DFL 12 = DSM 16493 putative TRAP transporter solute receptor YP_001533625.1 2417255 D 398580 CDS YP_001533626.1 159044832 5713943 2418278..2419648 1 NC_009952.1 PFAM: amidohydrolase; Amidohydrolase 3 KEGG: slo:Shew_0983 amidohydrolase; amidohydrolase 2419648 5713943 Dshi_2289 Dinoroseobacter shibae DFL 12 = DSM 16493 amidohydrolase YP_001533626.1 2418278 D 398580 CDS YP_001533627.1 159044833 5713944 2419657..2420955 1 NC_009952.1 probably associated with sugar transport; PFAM: Carbohydrate-selective porin OprB KEGG: cps:CPS_0267 hypothetical protein; hypothetical protein 2420955 5713944 Dshi_2290 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533627.1 2419657 D 398580 CDS YP_001533628.1 159044834 5713945 2420989..2421627 1 NC_009952.1 PFAM: protein of unknown function DUF306 Meta and HslJ; hypothetical protein 2421627 5713945 Dshi_2291 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533628.1 2420989 D 398580 CDS YP_001533629.1 159044835 5713946 complement(2421771..2422820) 1 NC_009952.1 pfam05976: DUF893; hypothetical protein 2422820 5713946 Dshi_2292 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533629.1 2421771 R 398580 CDS YP_001533630.1 159044836 5713947 complement(2422831..2423928) 1 NC_009952.1 PFAM: secretion protein HlyD family protein KEGG: rde:RD1_3593 multidrug resistance efflux pump, putative; HlyD family; secretion protein 2423928 5713947 Dshi_2293 Dinoroseobacter shibae DFL 12 = DSM 16493 secretion protein YP_001533630.1 2422831 R 398580 CDS YP_001533631.1 159044837 5713948 complement(2423982..2426291) 1 NC_009952.1 PFAM: Pyrrolo-quinoline quinone KEGG: pfl:PFL_5668 quinate/shikimate dehydrogenase, putative COG4993: Glucose dehydrogenase; PQQ dehydrogenase family protein 2426291 5713948 Dshi_2294 Dinoroseobacter shibae DFL 12 = DSM 16493 PQQ dehydrogenase family protein YP_001533631.1 2423982 R 398580 CDS YP_001533632.1 159044838 5713949 complement(2426408..2427880) 1 NC_009952.1 PFAM: amidohydrolase; Amidohydrolase 3 COG1228: Imidazolonepropionase and related amidohydrolases KEGG: sus:Acid_5787 amidohydrolase; putative amidohydrolase 2427880 5713949 Dshi_2295 Dinoroseobacter shibae DFL 12 = DSM 16493 putative amidohydrolase YP_001533632.1 2426408 R 398580 CDS YP_001533633.1 159044839 5713950 complement(2427999..2428427) 1 NC_009952.1 PFAM: transposase IS4 family protein COG3293: Transposase and inactivated derivatives KEGG: pde:Pden_3333 transposase, IS4 family protein; transposase 2428427 5713950 Dshi_2296 Dinoroseobacter shibae DFL 12 = DSM 16493 transposase YP_001533633.1 2427999 R 398580 CDS YP_001533634.1 159044840 5713951 complement(2428514..2428810) 1 NC_009952.1 COG3293: Transposase and inactivated derivatives KEGG: sit:TM1040_0173 transposase orfA IS5 family element; associated with replication, recombination and repair; hypothetical protein 2428810 5713951 Dshi_2297 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533634.1 2428514 R 398580 CDS YP_001533635.1 159044841 5713952 complement(2429143..2430264) 1 NC_009952.1 COG3457: Predicted amino acid racemase PFAM: alanine racemase domain protein, N-terminal domain; no C-terminal domain; putative amino acid racemase 2430264 5713952 Dshi_2298 Dinoroseobacter shibae DFL 12 = DSM 16493 putative amino acid racemase YP_001533635.1 2429143 R 398580 CDS YP_001533636.1 159044842 5713953 complement(2430261..2431439) 1 NC_009952.1 IPR011669: protein of unknown function DUF1611; hypothetical protein 2431439 5713953 Dshi_2299 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533636.1 2430261 R 398580 CDS YP_001533637.1 159044843 5713954 complement(2431492..2432319) 1 NC_009952.1 hypothetical protein 2432319 5713954 Dshi_2300 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533637.1 2431492 R 398580 CDS YP_001533638.1 159044844 5713955 complement(2432309..2432662) 1 NC_009952.1 hypothetical protein 2432662 5713955 Dshi_2301 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533638.1 2432309 R 398580 CDS YP_001533639.1 159044845 5713956 complement(2433069..2433371) 1 NC_009952.1 hypothetical protein 2433371 5713956 Dshi_2302 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533639.1 2433069 R 398580 CDS YP_001533640.1 159044846 5713957 complement(2433393..2434691) 1 NC_009952.1 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 2434691 5713957 Dshi_2303 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533640.1 2433393 R 398580 CDS YP_001533641.1 159044847 5713958 complement(2434878..2435366) 1 NC_009952.1 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 2435366 5713958 Dshi_2304 Dinoroseobacter shibae DFL 12 = DSM 16493 putative regulator of cell morphogenesis and NO signaling YP_001533641.1 2434878 R 398580 CDS YP_001533642.1 159044848 5713959 complement(2435382..2435837) 1 NC_009952.1 PFAM: globin KEGG: hne:HNE_1540 protozoan/cyanobacterial globin family protein COG2346: truncated hemoglobins; similar to bacterial-like globin; hypothetical protein 2435837 5713959 Dshi_2305 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533642.1 2435382 R 398580 CDS YP_001533643.1 159044849 5713960 2435930..2436349 1 NC_009952.1 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 2436349 5713960 Dshi_2306 Dinoroseobacter shibae DFL 12 = DSM 16493 putative transcriptional regulator YP_001533643.1 2435930 D 398580 CDS YP_001533644.1 159044850 5713961 2436374..2436607 1 NC_009952.1 hypothetical protein 2436607 5713961 Dshi_2307 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533644.1 2436374 D 398580 CDS YP_001533645.1 159044851 5713962 2436607..2436873 1 NC_009952.1 hypothetical protein 2436873 5713962 Dshi_2308 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533645.1 2436607 D 398580 CDS YP_001533646.1 159044852 5713963 2437551..2438477 1 NC_009952.1 Swiss-Prot: P39138-Arginase TIGRFAM: arginase PFAM: Arginase/agmatinase/formiminoglutamase COG0010: Arginase/agmatinase/formimionoglutamate hydrolase, arginase family KEGG: rde:RD1_1416 arginase; arginase 2438477 5713963 Dshi_2309 Dinoroseobacter shibae DFL 12 = DSM 16493 arginase YP_001533646.1 2437551 D 398580 CDS YP_001533647.1 159044853 5713964 2438486..2439559 1 NC_009952.1 catalyzes the formation of L-proline from L-ornithine; ornithine cyclodeaminase 2439559 5713964 Dshi_2310 Dinoroseobacter shibae DFL 12 = DSM 16493 ornithine cyclodeaminase YP_001533647.1 2438486 D 398580 CDS YP_001533648.1 159044854 5713965 2439747..2443412 1 NC_009952.1 proline utilization protein A; multifunctional protein that functions in proline catabolism in the first two enzymatic steps resulting in the conversion of proline to glutamate; in Escherichia coli this protein self regulates transcription via a DNA-binding domain at the N-terminus but the protein from Pseudomonas does not have this domain; bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase 2443412 putA 5713965 putA Dinoroseobacter shibae DFL 12 = DSM 16493 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase YP_001533648.1 2439747 D 398580 CDS YP_001533649.1 159044855 5713966 2443877..2444392 1 NC_009952.1 hypothetical protein 2444392 5713966 Dshi_2312 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533649.1 2443877 D 398580 CDS YP_001533650.1 159044856 5713968 complement(2444714..2445433) 1 NC_009952.1 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 2445433 5713968 Dshi_2313 Dinoroseobacter shibae DFL 12 = DSM 16493 aminoacyl-tRNA synthetase YP_001533650.1 2444714 R 398580 CDS YP_001533651.1 159044857 5713969 complement(2445430..2446467) 1 NC_009952.1 Swiss-Prot: P0ABK5-Cysteine synthase A PFAM: Pyridoxal-5-phosphate-dependent protein beta subunit COG0031: Cysteine synthase IMG Term; putative cysteine synthase A 2446467 5713969 Dshi_2314 Dinoroseobacter shibae DFL 12 = DSM 16493 putative cysteine synthase A YP_001533651.1 2445430 R 398580 CDS YP_001533652.1 159044858 5713970 complement(2446520..2447656) 1 NC_009952.1 PFAM: NUDIX hydrolase; AIG2 family protein KEGG: jan:Jann_1992 nucleoside diphosphate pyrophosphatase; NUDIX hydrolase 2447656 5713970 Dshi_2315 Dinoroseobacter shibae DFL 12 = DSM 16493 NUDIX hydrolase YP_001533652.1 2446520 R 398580 CDS YP_001533653.1 159044859 5713971 complement(2447670..2448110) 1 NC_009952.1 hypothetical protein 2448110 5713971 Dshi_2316 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533653.1 2447670 R 398580 CDS YP_001533654.1 159044860 5713972 complement(2448130..2449374) 1 NC_009952.1 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 2449374 cfa 5713972 cfa Dinoroseobacter shibae DFL 12 = DSM 16493 cyclopropane-fatty-acyl-phospholipid synthase YP_001533654.1 2448130 R 398580 CDS YP_001533655.1 159044861 5713973 complement(2449473..2450903) 1 NC_009952.1 Swiss-Prot: P00914-deoxyribodipyrimidine photo-lyase phrB PFAM: DNA photolyase FAD-binding; DNA photolyase domain protein; deoxyribodipyrimidine photo-lyase 2450903 phrB 5713973 phrB Dinoroseobacter shibae DFL 12 = DSM 16493 deoxyribodipyrimidine photo-lyase YP_001533655.1 2449473 R 398580 CDS YP_001533656.1 159044862 5713974 complement(2451184..2452170) 1 NC_009952.1 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 2452170 5713974 Dshi_2319 Dinoroseobacter shibae DFL 12 = DSM 16493 putative quinone oxidoreductase YP_001533656.1 2451184 R 398580 CDS YP_001533657.1 159044863 5713975 complement(2452182..2453288) 1 NC_009952.1 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 2453288 dmdA 5713975 dmdA Dinoroseobacter shibae DFL 12 = DSM 16493 putative dimethyl sulfoniopropionate demethylase YP_001533657.1 2452182 R 398580 CDS YP_001533658.1 159044864 5713976 complement(2453285..2453764) 1 NC_009952.1 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 2453764 5713976 Dshi_2321 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533658.1 2453285 R 398580 CDS YP_001533659.1 159044865 5713977 complement(2453788..2454489) 1 NC_009952.1 PFAM: protein of unknown function DUF1326 KEGG: rde:RD1_2286 hypothetical protein; hypothetical protein 2454489 5713977 Dshi_2322 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533659.1 2453788 R 398580 CDS YP_001533660.1 159044866 5713978 complement(2454501..2455259) 1 NC_009952.1 hypothetical protein 2455259 5713978 Dshi_2323 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533660.1 2454501 R 398580 CDS YP_001533661.1 159044867 5713979 2455350..2456078 1 NC_009952.1 PFAM: regulatory protein GntR HTH; GntR domain protein KEGG: rde:RD1_2283 transcriptional regulator, GntR family, putative; GntR HTH; regulatory protein 2456078 5713979 Dshi_2324 Dinoroseobacter shibae DFL 12 = DSM 16493 regulatory protein YP_001533661.1 2455350 D 398580 CDS YP_001533662.1 159044868 5713980 2456174..2457220 1 NC_009952.1 Swiss-Prot: P31133-Putrescine-binding periplasmic protein [Precursor] SSF53850: Periplasmic binding protein-like II superfamily; putative periplasmic-binding protein 2457220 5713980 Dshi_2325 Dinoroseobacter shibae DFL 12 = DSM 16493 putative periplasmic-binding protein YP_001533662.1 2456174 D 398580 CDS YP_001533663.1 159044869 5713981 2457262..2457699 1 NC_009952.1 hypothetical protein 2457699 5713981 Dshi_2326 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533663.1 2457262 D 398580 CDS YP_001533664.1 159044870 5713982 2458342..2459106 1 NC_009952.1 hypothetical protein 2459106 5713982 Dshi_2327 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533664.1 2458342 D 398580 CDS YP_001533665.1 159044871 5713983 2459215..2459814 1 NC_009952.1 SSF88874: Receptor-binding domain of short tail fibre protein gp12 superfamily PFAM: Tail Collar domain protein; hypothetical protein 2459814 5713983 Dshi_2328 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533665.1 2459215 D 398580 CDS YP_001533666.1 159044872 5713984 2459914..2460507 1 NC_009952.1 PFAM: Tail Collar domain protein; hypothetical protein 2460507 5713984 Dshi_2329 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533666.1 2459914 D 398580 CDS YP_001533667.1 159044873 5713985 2460588..2461223 1 NC_009952.1 PFAM: protein of unknown function DUF1194 KEGG: rsq:Rsph17025_0723 protein of unknown function DUF1194; hypothetical protein 2461223 5713985 Dshi_2330 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533667.1 2460588 D 398580 CDS YP_001533668.1 159044874 5713986 2461236..2461580 1 NC_009952.1 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 2461580 5713986 Dshi_2331 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533668.1 2461236 D 398580 CDS YP_001533669.1 159044875 5713987 2461615..2462868 1 NC_009952.1 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 2462868 5713987 Dshi_2332 Dinoroseobacter shibae DFL 12 = DSM 16493 putative chromate transport protein YP_001533669.1 2461615 D 398580 CDS YP_001533670.1 159044876 5713988 2462966..2463493 1 NC_009952.1 COG3814: Uncharacterized protein conserved in bacteria PFAM: protein of unknown function DUF1321 KEGG: sit:TM1040_1450 protein of unknown function DUF1321; hypothetical protein 2463493 5713988 Dshi_2333 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533670.1 2462966 D 398580 CDS YP_001533671.1 159044877 5713989 2463610..2465007 1 NC_009952.1 class II family (does not require metal); tetrameric enzyme; fumarase C; reversibly converts (S)-malate to fumarate and water; functions in the TCA cycle; fumarate hydratase 2465007 fumC 5713989 fumC Dinoroseobacter shibae DFL 12 = DSM 16493 fumarate hydratase YP_001533671.1 2463610 D 398580 CDS YP_001533672.1 159044878 5713990 2465235..2465534 1 NC_009952.1 PFAM: Ribbon-helix-helix protein, copG family COG4321:Uncharacterized protein related to arylsulfate sulfotransferase involved in siderophore biosynthesis; hypothetical protein 2465534 5713990 Dshi_2335 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533672.1 2465235 D 398580 CDS YP_001533673.1 159044879 5713991 2465612..2465803 1 NC_009952.1 KEGG: jan:Jann_3588 hypothetical protein; hypothetical protein 2465803 5713991 Dshi_2336 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533673.1 2465612 D 398580 CDS YP_001533674.1 159044880 5713992 complement(2465843..2467219) 1 NC_009952.1 PFAM: cytochrome P450 KEGG: jan:Jann_2396 cytochrome P450; cytochrome P450 2467219 5713992 Dshi_2337 Dinoroseobacter shibae DFL 12 = DSM 16493 cytochrome P450 YP_001533674.1 2465843 R 398580 CDS YP_001533675.1 159044881 5713993 complement(2467216..2468406) 1 NC_009952.1 KEGG: sil:SPO1897 hypothetical protein; hypothetical protein 2468406 5713993 Dshi_2338 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533675.1 2467216 R 398580 CDS YP_001533676.1 159044882 5713994 2468530..2468757 1 NC_009952.1 PFAM: SirA family protein KEGG: sil:SPO1895 SirA family protein Swiss-Prot: Q2NWX1-Sulfurtransferase tusA; SirA family protein 2468757 5713994 Dshi_2339 Dinoroseobacter shibae DFL 12 = DSM 16493 SirA family protein YP_001533676.1 2468530 D 398580 CDS YP_001533677.1 159044883 5713995 complement(2468813..2471893) 1 NC_009952.1 Swiss-Prot: P21513-Ribonuclease E TIGRFAM: ribonuclease, Rne/Rng family KEGG: sit:TM1040_1459 ribonuclease, Rne/Rng family; Rne/Rng family; ribonuclease 2471893 5713995 Dshi_2340 Dinoroseobacter shibae DFL 12 = DSM 16493 ribonuclease YP_001533677.1 2468813 R 398580 CDS YP_001533678.1 159044884 5713996 complement(2472393..2474747) 1 NC_009952.1 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 2474747 5713996 Dshi_2341 Dinoroseobacter shibae DFL 12 = DSM 16493 putative TRAP C4-dicarboxylate transport system permease YP_001533678.1 2472393 R 398580 CDS YP_001533679.1 159044885 5713997 complement(2474765..2475718) 1 NC_009952.1 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 2475718 5713997 Dshi_2342 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533679.1 2474765 R 398580 CDS YP_001533680.1 159044886 5713998 complement(2475833..2476918) 1 NC_009952.1 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 2476918 5713998 Dshi_2343 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533680.1 2475833 R 398580 CDS YP_001533681.1 159044887 5713999 2477127..2478569 1 NC_009952.1 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 2478569 5713999 Dshi_2344 Dinoroseobacter shibae DFL 12 = DSM 16493 integral membrane sensor signal transduction histidine kinase YP_001533681.1 2477127 D 398580 CDS YP_001533682.1 159044888 5714000 2478566..2479228 1 NC_009952.1 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 2479228 5714000 Dshi_2345 Dinoroseobacter shibae DFL 12 = DSM 16493 two component transcriptional regulator YP_001533682.1 2478566 D 398580 CDS YP_001533683.1 159044889 5714001 complement(2479455..2480585) 1 NC_009952.1 Exchanges the guanine residue with 7-aminomethyl-7-deazaguanine in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr); queuine tRNA-ribosyltransferase 2480585 tgt 5714001 tgt Dinoroseobacter shibae DFL 12 = DSM 16493 queuine tRNA-ribosyltransferase YP_001533683.1 2479455 R 398580 CDS YP_001533684.1 159044890 5714002 2481051..2482004 1 NC_009952.1 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 2482004 5714002 Dshi_2347 Dinoroseobacter shibae DFL 12 = DSM 16493 LysR family transcriptional regulator YP_001533684.1 2481051 D 398580 CDS YP_001533685.1 159044891 5714003 2482067..2482429 1 NC_009952.1 PFAM: protein of unknown function DUF59; hypothetical protein 2482429 5714003 Dshi_2348 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533685.1 2482067 D 398580 CDS YP_001533686.1 159044892 5714004 2482501..2482866 1 NC_009952.1 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 2482866 5714004 Dshi_2349 Dinoroseobacter shibae DFL 12 = DSM 16493 putative iron-binding protein iscA YP_001533686.1 2482501 D 398580 CDS YP_001533687.1 159044893 5714005 complement(2482885..2483898) 1 NC_009952.1 Swiss-Prot: Q58296-Putative molybdopterin biosynthesis protein MJ0886 PFAM: molybdopterin binding domain COG0303: Molybdopterin biosynthesis enzyme; putative molybdopterin biosynthesis protein 2483898 5714005 Dshi_2350 Dinoroseobacter shibae DFL 12 = DSM 16493 putative molybdopterin biosynthesis protein YP_001533687.1 2482885 R 398580 CDS YP_001533688.1 159044894 5714006 complement(2483895..2484884) 1 NC_009952.1 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 2484884 5714006 Dshi_2351 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533688.1 2483895 R 398580 CDS YP_001533689.1 159044895 5714007 2485055..2486401 1 NC_009952.1 PFAM: Protein of unknown function DUF1800 COG5267: Uncharacterized protein conserved in bacteria; hypothetical protein 2486401 5714007 Dshi_2352 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533689.1 2485055 D 398580 CDS YP_001533690.1 159044896 5714008 2486413..2487582 1 NC_009952.1 PFAM: protein of unknown function DUF1501 COG4102: Uncharacterized protein conserved in bacteria; hypothetical protein 2487582 5714008 Dshi_2353 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533690.1 2486413 D 398580 CDS YP_001533691.1 159044897 5714009 2487671..2488822 1 NC_009952.1 PFAM: major facilitator superfamily MFS_1 KEGG: reu:Reut_A3422 major facilitator superfamily MFS_1 Swiss-Prot: P77389-Inner membrane transport protein; MFS transporter 2488822 5714009 Dshi_2354 Dinoroseobacter shibae DFL 12 = DSM 16493 MFS transporter YP_001533691.1 2487671 D 398580 CDS YP_001533692.1 159044898 5714010 complement(2488833..2490095) 1 NC_009952.1 PFAM: VWA containing CoxE family protein KEGG: jan:Jann_1760 VWA containing CoxE-like; hypothetical protein 2490095 5714010 Dshi_2355 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533692.1 2488833 R 398580 CDS YP_001533693.1 159044899 5714011 complement(2490196..2491107) 1 NC_009952.1 PFAM: ATPase associated with various cellular activities AAA_5 KEGG: sil:SPO2646 hypothetical protein Swiss-Prot: Q4L6B6-Uncharacterized protein SH1500; hypothetical protein 2491107 5714011 Dshi_2356 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533693.1 2490196 R 398580 CDS YP_001533694.1 159044900 5714012 2491250..2492470 1 NC_009952.1 COG1960: Acyl-CoA dehydrogenases PFAM: Acyl-CoA dehydrogenase; acyl-CoA dehydrogenase 2492470 5714012 Dshi_2357 Dinoroseobacter shibae DFL 12 = DSM 16493 acyl-CoA dehydrogenase YP_001533694.1 2491250 D 398580 CDS YP_001533695.1 159044901 5714013 2492678..2493325 1 NC_009952.1 PFAM: Lysine exporter protein (LYSE/YGGA) KEGG: jan:Jann_3206 lysine exporter protein (LysE/YggA); putative lysine exporter protein 2493325 5714013 Dshi_2358 Dinoroseobacter shibae DFL 12 = DSM 16493 putative lysine exporter protein YP_001533695.1 2492678 D 398580 CDS YP_001533696.1 159044902 5714014 2493841..2495091 1 NC_009952.1 hypothetical protein 2495091 5714014 Dshi_2359 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533696.1 2493841 D 398580 CDS YP_001533697.1 159044903 5714015 complement(2495217..2495825) 1 NC_009952.1 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 2495825 ureG 5714015 ureG Dinoroseobacter shibae DFL 12 = DSM 16493 urease accessory protein YP_001533697.1 2495217 R 398580 CDS YP_001533698.1 159044904 5714016 complement(2495818..2496201) 1 NC_009952.1 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 2496201 5714016 Dshi_2361 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533698.1 2495818 R 398580 CDS YP_001533699.1 159044905 5714017 complement(2496198..2496830) 1 NC_009952.1 Swiss-Prot: Q9HUS1-Urease accessory protein ureF PFAM: Urease accessory protein UreF COG0830: Urease accessory protein UreF; putative urease accessory protein 2496830 ureF 5714017 ureF Dinoroseobacter shibae DFL 12 = DSM 16493 putative urease accessory protein YP_001533699.1 2496198 R 398580 CDS YP_001533700.1 159044906 5714018 complement(2496832..2497314) 1 NC_009952.1 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 2497314 ureE 5714018 ureE Dinoroseobacter shibae DFL 12 = DSM 16493 urease accessory domain-containing protein YP_001533700.1 2496832 R 398580 CDS YP_001533701.1 159044907 5714019 complement(2497676..2497882) 1 NC_009952.1 hypothetical protein 2497882 5714019 Dshi_2364 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533701.1 2497676 R 398580 CDS YP_001533702.1 159044908 5714020 complement(2498640..2500349) 1 NC_009952.1 ureases catalyze the hydrolysis of urea into ammonia and carbon dioxide; in Helicobacter pylori the ammonia released plays a key role in bacterial survival by neutralizing acids when colonizing the gastric mucosa; the holoenzyme is composed of 3 ureC (alpha) and 3 ureAB (gamma/beta) subunits; urease subunit alpha 2500349 ureC 5714020 ureC Dinoroseobacter shibae DFL 12 = DSM 16493 urease subunit alpha YP_001533702.1 2498640 R 398580 CDS YP_001533703.1 159044909 5714021 complement(2500485..2500814) 1 NC_009952.1 hypothetical protein 2500814 5714021 Dshi_2366 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533703.1 2500485 R 398580 CDS YP_001533704.1 159044910 5714022 complement(2500927..2501649) 1 NC_009952.1 hypothetical protein 2501649 5714022 Dshi_2367 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533704.1 2500927 R 398580 CDS YP_001533705.1 159044911 5714023 complement(2501649..2501954) 1 NC_009952.1 Swiss-Prot: Q28RJ8-Urease subunit beta ureB TIGRFAM: urease, beta subunit PFAM: Urease beta subunit; urease subunit beta 2501954 ureB 5714023 ureB Dinoroseobacter shibae DFL 12 = DSM 16493 urease subunit beta YP_001533705.1 2501649 R 398580 CDS YP_001533706.1 159044912 5714024 complement(2502086..2502388) 1 NC_009952.1 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 2502388 ureA 5714024 ureA Dinoroseobacter shibae DFL 12 = DSM 16493 urease subunit gamma YP_001533706.1 2502086 R 398580 CDS YP_001533707.1 159044913 5714025 complement(2502483..2503328) 1 NC_009952.1 Swiss-Prot: P42888-Urease accessory protein ureD PFAM: Urease accessory protein UreD KEGG: rsh:Rsph17029_1955 urease accessory protein UreD; urease accessory protein 2503328 ureD 5714025 ureD Dinoroseobacter shibae DFL 12 = DSM 16493 urease accessory protein YP_001533707.1 2502483 R 398580 CDS YP_001533708.1 159044914 5714026 2503566..2504603 1 NC_009952.1 catalyzes the formation of N-carbamoyl-L-aspartate from (S)-dihydroorotate in pyrimidine biosynthesis; dihydroorotase 2504603 pyrC2 5714026 pyrC2 Dinoroseobacter shibae DFL 12 = DSM 16493 dihydroorotase YP_001533708.1 2503566 D 398580 CDS YP_001533709.1 159044915 5714027 2504743..2505423 1 NC_009952.1 involved in fifth step of pyrimidine biosynthesis; converts orotidine 5'-phosphate and diphosphate to orotate and 5-phospho-alpha-D-ribose 1-diphosphate; orotate phosphoribosyltransferase 2505423 pyrE 5714027 pyrE Dinoroseobacter shibae DFL 12 = DSM 16493 orotate phosphoribosyltransferase YP_001533709.1 2504743 D 398580 CDS YP_001533710.1 159044916 5714028 2505654..2507174 1 NC_009952.1 unwinds double stranded DNA; replicative DNA helicase 2507174 dnaB 5714028 dnaB Dinoroseobacter shibae DFL 12 = DSM 16493 replicative DNA helicase YP_001533710.1 2505654 D 398580 CDS YP_001533711.1 159044917 5714029 2507462..2508685 1 NC_009952.1 PFAM: histidine kinase HAMP region domain protein KEGG: rde:RD1_0232 HAMP domain protein, putative; hypothetical protein 2508685 5714029 Dshi_2374 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533711.1 2507462 D 398580 CDS YP_001533712.1 159044918 5714030 2508782..2509588 1 NC_009952.1 PFAM: protein of unknown function DUF1194 KEGG: mes:Meso_1299 protein of unknown function DUF1194; hypothetical protein 2509588 5714030 Dshi_2375 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533712.1 2508782 D 398580 CDS YP_001533713.1 159044919 5714031 complement(2509613..2510089) 1 NC_009952.1 hypothetical protein 2510089 5714031 Dshi_2376 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533713.1 2509613 R 398580 CDS YP_001533714.1 159044920 5714032 complement(2510218..2512242) 1 NC_009952.1 PFAM: protein of unknown function DUF839 KEGG: rde:RD1_0767 hypothetical protein COG3211: Predicted phosphatase; hypothetical protein 2512242 5714032 Dshi_2377 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533714.1 2510218 R 398580 CDS YP_001533715.1 159044921 5714033 2512525..2513574 1 NC_009952.1 Swiss-Prot: Q92R07-Alanine racemase alr TIGRFAM: alanine racemase PFAM: alanine racemase domain protein; alanine racemase 2513574 alr 5714033 alr Dinoroseobacter shibae DFL 12 = DSM 16493 alanine racemase YP_001533715.1 2512525 D 398580 CDS YP_001533716.1 159044922 5714034 2513571..2514347 1 NC_009952.1 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 2514347 5714034 Dshi_2379 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533716.1 2513571 D 398580 CDS YP_001533717.1 159044923 5714035 2514344..2515117 1 NC_009952.1 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 2515117 5714035 Dshi_2380 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC transporter YP_001533717.1 2514344 D 398580 CDS YP_001533718.1 159044924 5714037 2515483..2516145 1 NC_009952.1 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 2516145 lipB 5714037 lipB Dinoroseobacter shibae DFL 12 = DSM 16493 lipoate-protein ligase B YP_001533718.1 2515483 D 398580 CDS YP_001533719.1 159044925 5714038 2516182..2516721 1 NC_009952.1 hypothetical protein 2516721 5714038 Dshi_2382 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533719.1 2516182 D 398580 CDS YP_001533720.1 159044926 5714039 2517133..2518809 1 NC_009952.1 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 2518809 ctaD 5714039 ctaD Dinoroseobacter shibae DFL 12 = DSM 16493 cytochrome c oxidase subunit 1 YP_001533720.1 2517133 D 398580 CDS YP_001533721.1 159044927 5714040 2518819..2519340 1 NC_009952.1 hypothetical protein 2519340 5714040 Dshi_2384 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533721.1 2518819 D 398580 CDS YP_001533722.1 159044928 5714041 complement(2519748..2520101) 1 NC_009952.1 Swiss-Prot:P0ABS1-DnaK suppressor protein dksA COG1734: DnaK suppressor protein; related to DnaK suppressor protein; hypothetical protein 2520101 5714041 Dshi_2385 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533722.1 2519748 R 398580 CDS YP_001533723.1 159044929 5714042 complement(2520173..2520634) 1 NC_009952.1 COG1610: Uncharacterized conserved protein Swiss-Prot: P54464-Uncharacterized protein yqeY; hypothetical protein 2520634 5714042 Dshi_2386 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533723.1 2520173 R 398580 CDS YP_001533724.1 159044930 5714043 2520801..2521970 1 NC_009952.1 catalyzes production of carbamoyl phosphate from bicarbonate and glutamine in pyrimidine and arginine biosynthesis pathways; forms an octamer composed of four CarAB dimers; carbamoyl phosphate synthase small subunit 2521970 carA 5714043 carA Dinoroseobacter shibae DFL 12 = DSM 16493 carbamoyl phosphate synthase small subunit YP_001533724.1 2520801 D 398580 CDS YP_001533725.1 159044931 5714044 2522050..2523957 1 NC_009952.1 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 2523957 5714044 Dshi_2388 Dinoroseobacter shibae DFL 12 = DSM 16493 glycosyl transferase family protein YP_001533725.1 2522050 D 398580 CDS YP_001533726.1 159044932 5714045 complement(2523970..2524611) 1 NC_009952.1 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 2524611 5714045 Dshi_2389 Dinoroseobacter shibae DFL 12 = DSM 16493 putative transcriptional regulator YP_001533726.1 2523970 R 398580 CDS YP_001533727.1 159044933 5714046 2524704..2525351 1 NC_009952.1 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 2525351 5714046 Dshi_2390 Dinoroseobacter shibae DFL 12 = DSM 16493 putative pyrimidine 5'-nucleotidase YP_001533727.1 2524704 D 398580 CDS YP_001533728.1 159044934 5714047 2525481..2525726 1 NC_009952.1 hypothetical protein 2525726 5714047 Dshi_2391 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533728.1 2525481 D 398580 CDS YP_001533729.1 159044935 5714048 2525802..2527001 1 NC_009952.1 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 2527001 5714048 Dshi_2392 Dinoroseobacter shibae DFL 12 = DSM 16493 2-octaprenyl-6-methoxyphenyl hydroxylase YP_001533729.1 2525802 D 398580 CDS YP_001533730.1 159044936 5714049 complement(2527234..2528364) 1 NC_009952.1 PFAM: Aminotransferase class-V KEGG: rde:RD1_1957 aminotransferase family protein, putative COG0075: Serine-pyruvate aminotransferase/archaeal aspartate aminotransferase; class 5; aminotransferase 2528364 5714049 Dshi_2393 Dinoroseobacter shibae DFL 12 = DSM 16493 aminotransferase YP_001533730.1 2527234 R 398580 CDS YP_001533731.1 159044937 5714050 complement(2528605..2529063) 1 NC_009952.1 PFAM: regulatory protein AsnC/Lrp family; regulatory protein ArsR KEGG: sil:SPO1368 transcriptional regulator, AsnC family COG1522: Transcriptional regulators; AsnC family; transcriptional regulator 2529063 5714050 Dshi_2394 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001533731.1 2528605 R 398580 CDS YP_001533732.1 159044938 5714051 complement(2529060..2529518) 1 NC_009952.1 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 2529518 5714051 Dshi_2395 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001533732.1 2529060 R 398580 CDS YP_001533733.1 159044939 5714052 2529653..2530675 1 NC_009952.1 catalyzes the formation of (R)-2,3-dihydroxy-3-methylbutanoate from (S)-2-hydroxy-2-methyl-3-oxobutanoate in valine and isoleucine biosynthesis; ketol-acid reductoisomerase 2530675 ilvC 5714052 ilvC Dinoroseobacter shibae DFL 12 = DSM 16493 ketol-acid reductoisomerase YP_001533733.1 2529653 D 398580 CDS YP_001533734.1 159044940 5714053 complement(2531044..2532387) 1 NC_009952.1 catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate; phosphoglucosamine mutase 2532387 glmM 5714053 glmM Dinoroseobacter shibae DFL 12 = DSM 16493 phosphoglucosamine mutase YP_001533734.1 2531044 R 398580 CDS YP_001533735.1 159044941 5714054 complement(2532406..2533419) 1 NC_009952.1 Swiss-Prot: P0AC13-Dihydropteroate synthase folP TIGRFAM: dihydropteroate synthase PFAM: dihydropteroate synthase DHPS; dihydropteroate synthase 2533419 folP 5714054 folP Dinoroseobacter shibae DFL 12 = DSM 16493 dihydropteroate synthase YP_001533735.1 2532406 R 398580 CDS YP_001533736.1 159044942 5714055 complement(2533430..2534281) 1 NC_009952.1 Swiss-Prot: Q9X8I0-Dihydroneopterin aldolase folB PFAM: dihydroneopterin aldolase TIGR00525: dihydroneopterin aldolase TIGR00526: FolB domain; putative dihydroneopterin aldolase 2534281 5714055 Dshi_2399 Dinoroseobacter shibae DFL 12 = DSM 16493 putative dihydroneopterin aldolase YP_001533736.1 2533430 R 398580 CDS YP_001533737.1 159044943 5714056 complement(2534372..2535064) 1 NC_009952.1 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 2535064 5714056 Dshi_2400 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533737.1 2534372 R 398580 CDS YP_001533738.1 159044944 5714057 complement(2535240..2537828) 1 NC_009952.1 catalyzes the formation of phosphoenolpyruvate from pyruvate; pyruvate phosphate dikinase 2537828 5714057 Dshi_2401 Dinoroseobacter shibae DFL 12 = DSM 16493 pyruvate phosphate dikinase YP_001533738.1 2535240 R 398580 CDS YP_001533739.1 159044945 5714058 complement(2537985..2540147) 1 NC_009952.1 Swiss-Prot: Q986B5-Glycyl-tRNA synthetase beta chain glyS TIGRFAM: glycyl-tRNA synthetase, beta subunit; glycyl-tRNA synthetase subunit beta 2540147 glyS 5714058 glyS Dinoroseobacter shibae DFL 12 = DSM 16493 glycyl-tRNA synthetase subunit beta YP_001533739.1 2537985 R 398580 CDS YP_001533740.1 159044946 5714059 complement(2540151..2540627) 1 NC_009952.1 hypothetical protein 2540627 5714059 Dshi_2403 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533740.1 2540151 R 398580 CDS YP_001533741.1 159044947 5714060 complement(2540624..2541607) 1 NC_009952.1 glycine--tRNA ligase alpha chain; GlyRS; class II aminoacyl tRNA synthetase; tetramer of alpha(2)beta(2); catalyzes a two-step reaction; first charging a glycine molecule by linking its carboxyl group to the alpha-phosphate of ATP; second by transfer of the aminoacyl-adenylate to its tRNA; glycyl-tRNA synthetase subunit alpha 2541607 glyQ 5714060 glyQ Dinoroseobacter shibae DFL 12 = DSM 16493 glycyl-tRNA synthetase subunit alpha YP_001533741.1 2540624 R 398580 CDS YP_001533742.1 159044948 5714061 2541693..2543423 1 NC_009952.1 Swiss-Prot: P55377-Uncharacterized protein y4bJ; hypothetical protein 2543423 5714061 Dshi_2405 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533742.1 2541693 D 398580 CDS YP_001533743.1 159044949 5714062 complement(2543430..2544878) 1 NC_009952.1 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 2544878 trkG 5714062 trkG Dinoroseobacter shibae DFL 12 = DSM 16493 Trk system potassium uptake protein YP_001533743.1 2543430 R 398580 CDS YP_001533744.1 159044950 5714063 complement(2544924..2545631) 1 NC_009952.1 Swiss-Prot: P77526-Uncharacterized GST-like protein PFAM: Glutathione S-transferase domain KEGG: rde:RD1_1937 glutathione S-transferase, putative; putative glutathione S-transferase 2545631 5714063 Dshi_2407 Dinoroseobacter shibae DFL 12 = DSM 16493 putative glutathione S-transferase YP_001533744.1 2544924 R 398580 CDS YP_001533745.1 159044951 5714066 2546843..2548021 1 NC_009952.1 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 2548021 5714066 Dshi_2410 Dinoroseobacter shibae DFL 12 = DSM 16493 trans-sulfuration enzyme family protein YP_001533745.1 2546843 D 398580 CDS YP_001533746.1 159044952 5714067 2548194..2549297 1 NC_009952.1 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 2549297 5714067 Dshi_2411 Dinoroseobacter shibae DFL 12 = DSM 16493 putative GTP cyclohydrolase YP_001533746.1 2548194 D 398580 CDS YP_001533747.1 159044953 5714068 complement(2549412..2551100) 1 NC_009952.1 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 2551100 5714068 Dshi_2412 Dinoroseobacter shibae DFL 12 = DSM 16493 putative chloride channel protein YP_001533747.1 2549412 R 398580 CDS YP_001533748.1 159044954 5714069 complement(2551263..2552924) 1 NC_009952.1 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 2552924 recN 5714069 recN Dinoroseobacter shibae DFL 12 = DSM 16493 DNA repair protein YP_001533748.1 2551263 R 398580 CDS YP_001533749.1 159044955 5714070 complement(2553013..2553852) 1 NC_009952.1 Swiss-Prot: P0AC02-UPF0169 lipoprotein yfiO [Precursor]; hypothetical protein 2553852 5714070 Dshi_2414 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533749.1 2553013 R 398580 CDS YP_001533750.1 159044956 5714071 complement(2553954..2554874) 1 NC_009952.1 zinc-dependent; catalyzes the deacetylation of UDP-(3-O-acyl)-N-acetylglucosamine to UDP-3-O-(3-hydroxytetradecanoyl)-glucosamine in the second step of lipid A biosynthesis; UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase 2554874 lpxC 5714071 lpxC Dinoroseobacter shibae DFL 12 = DSM 16493 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase YP_001533750.1 2553954 R 398580 CDS YP_001533751.1 159044957 5714072 complement(2555094..2556689) 1 NC_009952.1 GTPase; similar structure to tubulin; forms ring-shaped polymers at the site of cell division; other proteins such as FtsA, ZipA, and ZapA, interact with and regulate FtsZ function; cell division protein FtsZ 2556689 ftsZ 5714072 ftsZ Dinoroseobacter shibae DFL 12 = DSM 16493 cell division protein FtsZ YP_001533751.1 2555094 R 398580 CDS YP_001533752.1 159044958 5714073 complement(2557114..2558451) 1 NC_009952.1 Swiss-Prot: P0ABH0-Cell division protein ftsA TIGR01174: cell division protein FtsA; colocated with ftsZ and ftsQ; cell division protein 2558451 ftsA 5714073 ftsA Dinoroseobacter shibae DFL 12 = DSM 16493 cell division protein YP_001533752.1 2557114 R 398580 CDS YP_001533753.1 159044959 5714074 complement(2558448..2559341) 1 NC_009952.1 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 2559341 5714074 Dshi_2418 Dinoroseobacter shibae DFL 12 = DSM 16493 putative cell division protein FtsQ YP_001533753.1 2558448 R 398580 CDS YP_001533754.1 159044960 5714075 complement(2559329..2560255) 1 NC_009952.1 D-alanine--D-alanine ligase; DdlA; DdlB; cytoplasmic; catalyzes the formation of D-alanyl-D-alanine from two D-alanines in peptidoglycan synthesis; there are two forms of this enzyme in Escherichia coli; D-alanine--D-alanine ligase 2560255 ddl 5714075 ddl Dinoroseobacter shibae DFL 12 = DSM 16493 D-alanine--D-alanine ligase YP_001533754.1 2559329 R 398580 CDS YP_001533755.1 159044961 5714076 complement(2560320..2561243) 1 NC_009952.1 catalyzes the reduction of UDP-N-acetylglucosamine enolpyruvate to form UDP-N-acetylmuramate in peptidoglycan biosynthesis; UDP-N-acetylenolpyruvoylglucosamine reductase 2561243 murB 5714076 murB Dinoroseobacter shibae DFL 12 = DSM 16493 UDP-N-acetylenolpyruvoylglucosamine reductase YP_001533755.1 2560320 R 398580 CDS YP_001533756.1 159044962 5714077 complement(2561240..2561506) 1 NC_009952.1 hypothetical protein 2561506 5714077 Dshi_2421 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533756.1 2561240 R 398580 CDS YP_001533757.1 159044963 5714078 complement(2561559..2562971) 1 NC_009952.1 Catalyzes the formation of UDP-N-acetylmuramoyl-L-alanine from UDP-N-acetylmuramate and L-alanine in peptidoglycan synthesis; UDP-N-acetylmuramate--L-alanine ligase 2562971 murC 5714078 murC Dinoroseobacter shibae DFL 12 = DSM 16493 UDP-N-acetylmuramate--L-alanine ligase YP_001533757.1 2561559 R 398580 CDS YP_001533758.1 159044964 5714079 complement(2562998..2564107) 1 NC_009952.1 UDP-N-acetylglucosamine--N-acetylmuramyl- (pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase; involved in cell wall formation; inner membrane-associated; last step of peptidoglycan synthesis; undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase 2564107 murG 5714079 murG Dinoroseobacter shibae DFL 12 = DSM 16493 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase YP_001533758.1 2562998 R 398580 CDS YP_001533759.1 159044965 5714080 complement(2564111..2565277) 1 NC_009952.1 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 2565277 5714080 Dshi_2424 Dinoroseobacter shibae DFL 12 = DSM 16493 putative cell division protein ftsW YP_001533759.1 2564111 R 398580 CDS YP_001533760.1 159044966 5714081 2565692..2567371 1 NC_009952.1 PFAM: Hemolysin-type calcium-binding region; hypothetical protein 2567371 5714081 Dshi_2425 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533760.1 2565692 D 398580 CDS YP_001533761.1 159044967 5714082 complement(2567452..2568609) 1 NC_009952.1 PFAM: peptidase S8 / subtilase family KEGG: rde:RD1_4002 subtilisin carlsberg precursor, putative PTHR10795: subtilisin-related serine protease; related to subtilase; hypothetical protein 2568609 5714082 Dshi_2426 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533761.1 2567452 R 398580 CDS YP_001533762.1 159044968 5714083 2568795..2569361 1 NC_009952.1 KEGG: rde:RD1_4000 hypothetical protein; hypothetical protein 2569361 5714083 Dshi_2427 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533762.1 2568795 D 398580 CDS YP_001533763.1 159044969 5714084 complement(2569367..2569903) 1 NC_009952.1 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 2569903 5714084 Dshi_2428 Dinoroseobacter shibae DFL 12 = DSM 16493 RNA polymerase YP_001533763.1 2569367 R 398580 CDS YP_001533764.1 159044970 5714085 complement(2570227..2571612) 1 NC_009952.1 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 2571612 5714085 Dshi_2429 Dinoroseobacter shibae DFL 12 = DSM 16493 carbohydrate kinase YP_001533764.1 2570227 R 398580 CDS YP_001533765.1 159044971 5714086 complement(2571609..2571947) 1 NC_009952.1 TIGRFAM: L-rhamnose 1-epimerase PFAM: protein of unknown function DUF718 KEGG: jan:Jann_2598 protein of unknown function DUF718; hypothetical protein 2571947 5714086 Dshi_2430 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533765.1 2571609 R 398580 CDS YP_001533766.1 159044972 5714087 complement(2571923..2572909) 1 NC_009952.1 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 2572909 5714087 Dshi_2431 Dinoroseobacter shibae DFL 12 = DSM 16493 (monosaccharide) transport system permease YP_001533766.1 2571923 R 398580 CDS YP_001533767.1 159044973 5714088 complement(2572906..2573889) 1 NC_009952.1 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 2573889 5714088 Dshi_2432 Dinoroseobacter shibae DFL 12 = DSM 16493 putative-binding-protein-dependent transport system permease YP_001533767.1 2572906 R 398580 CDS YP_001533768.1 159044974 5714089 complement(2573902..2575434) 1 NC_009952.1 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 2575434 rbsA1 5714089 rbsA1 Dinoroseobacter shibae DFL 12 = DSM 16493 ribose import ATP-binding protein YP_001533768.1 2573902 R 398580 CDS YP_001533769.1 159044975 5714090 complement(2575507..2576508) 1 NC_009952.1 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 2576508 5714090 Dshi_2434 Dinoroseobacter shibae DFL 12 = DSM 16493 putative periplasmic-binding abc transporter protein YP_001533769.1 2575507 R 398580 CDS YP_001533770.1 159044976 5714091 complement(2576547..2577401) 1 NC_009952.1 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 2577401 5714091 Dshi_2435 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001533770.1 2576547 R 398580 CDS YP_001533771.1 159044977 5714092 2577535..2579637 1 NC_009952.1 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 2579637 5714092 Dshi_2436 Dinoroseobacter shibae DFL 12 = DSM 16493 short chain dehydrogenase YP_001533771.1 2577535 D 398580 CDS YP_001533772.1 159044978 5714093 2579647..2580885 1 NC_009952.1 catalyzes the formation of L-rhamnulose from L-rhamnose; L-rhamnose isomerase 2580885 rhaA 5714093 rhaA Dinoroseobacter shibae DFL 12 = DSM 16493 L-rhamnose isomerase YP_001533772.1 2579647 D 398580 CDS YP_001533773.1 159044979 5714094 complement(2580993..2581871) 1 NC_009952.1 PFAM: amidohydrolase 2 KEGG: pau:PA14_36110 putative hydrolase COG3618: Predicted metal-dependent hydrolase of the TIM-barrel fold; putative amidohydrolase 2 2581871 5714094 Dshi_2438 Dinoroseobacter shibae DFL 12 = DSM 16493 putative amidohydrolase 2 YP_001533773.1 2580993 R 398580 CDS YP_001533774.1 159044980 5714095 complement(2581868..2583352) 1 NC_009952.1 PFAM: protein of unknown function DUF112 transmembrane COG3333: Uncharacterized protein conserved in bacteria; hypothetical protein 2583352 5714095 Dshi_2439 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533774.1 2581868 R 398580 CDS YP_001533775.1 159044981 5714096 complement(2583349..2583807) 1 NC_009952.1 hypothetical protein 2583807 5714096 Dshi_2440 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533775.1 2583349 R 398580 CDS YP_001533776.1 159044982 5714097 complement(2583868..2584830) 1 NC_009952.1 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 2584830 5714097 Dshi_2441 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533776.1 2583868 R 398580 CDS YP_001533777.1 159044983 5714098 complement(2584873..2586378) 1 NC_009952.1 Swiss-Prot: Q56694-NADP-dependent fatty aldehyde dehydrogenase aldH PFAM: aldehyde dehydrogenase KEGG: pde:Pden_4865 aldehyde dehydrogenase; NADP-dependent fatty aldehyde dehydrogenase 2586378 aldH1 5714098 aldH1 Dinoroseobacter shibae DFL 12 = DSM 16493 NADP-dependent fatty aldehyde dehydrogenase YP_001533777.1 2584873 R 398580 CDS YP_001533778.1 159044984 5714099 complement(2586430..2587299) 1 NC_009952.1 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 2587299 5714099 Dshi_2443 Dinoroseobacter shibae DFL 12 = DSM 16493 3-hydroxyisobutyrate dehydrogenase YP_001533778.1 2586430 R 398580 CDS YP_001533779.1 159044985 5714100 complement(2587296..2588300) 1 NC_009952.1 catalyzes oxidation of 4-(phosphohydroxy)-L-threonine into 2-amino-3-oxo-4-(phosphohydroxy)butyric acid which decarboxylates to form 1-amino-3-(phosphohydroxy)propan-2-one (3-amino-2-oxopropyl phosphate); 4-hydroxythreonine-4-phosphate dehydrogenase 2588300 pdxA 5714100 pdxA Dinoroseobacter shibae DFL 12 = DSM 16493 4-hydroxythreonine-4-phosphate dehydrogenase YP_001533779.1 2587296 R 398580 CDS YP_001533780.1 159044986 5714101 complement(2588300..2589013) 1 NC_009952.1 PFAM: regulatory protein GntR HTH; GntR domain protein KEGG: sil:SPO2434 transcriptional regulator, GntR family COG1802: Transcriptional regulators; GntR family; transcriptional regulator 2589013 5714101 Dshi_2445 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001533780.1 2588300 R 398580 CDS YP_001533781.1 159044987 5714102 complement(2589015..2589926) 1 NC_009952.1 PFAM: dihydrodipicolinate synthetase Swiss-Prot: O69782-Dihydrodipicolinate synthase KEGG: sil:SPOA0244 dihydrodipicolinate synthase family protein; dihydrodipicolinate synthase 2589926 5714102 Dshi_2446 Dinoroseobacter shibae DFL 12 = DSM 16493 dihydrodipicolinate synthase YP_001533781.1 2589015 R 398580 CDS YP_001533782.1 159044988 5714103 complement(2589923..2591098) 1 NC_009952.1 PFAM: Mandelate racemase/muconate lactonizing protein PTHR13794: enolase superfamily, mandelate racemase; putative mandelate racemase/muconate lactonizing protein 2591098 5714103 Dshi_2447 Dinoroseobacter shibae DFL 12 = DSM 16493 putative mandelate racemase/muconate lactonizing protein YP_001533782.1 2589923 R 398580 CDS YP_001533783.1 159044989 5714104 complement(2591102..2592598) 1 NC_009952.1 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 2592598 5714104 Dshi_2448 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533783.1 2591102 R 398580 CDS YP_001533784.1 159044990 5714105 complement(2592604..2593044) 1 NC_009952.1 hypothetical protein 2593044 5714105 Dshi_2449 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533784.1 2592604 R 398580 CDS YP_001533785.1 159044991 5714106 complement(2593114..2594058) 1 NC_009952.1 PFAM: conserved hypothetical protein KEGG: ecp:ECP_4043 hypothetical protein; similar to UPF0065 protein; hypothetical protein 2594058 5714106 Dshi_2450 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533785.1 2593114 R 398580 CDS YP_001533786.1 159044992 5714107 complement(2594434..2595828) 1 NC_009952.1 UDP-N-acetylmuramoylalanine--D-glutamate ligase; involved in peptidoglycan biosynthesis; cytoplasmic; catalyzes the addition of glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanine during cell wall formation; UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase 2595828 murD 5714107 murD Dinoroseobacter shibae DFL 12 = DSM 16493 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase YP_001533786.1 2594434 R 398580 CDS YP_001533787.1 159044993 5714108 complement(2596056..2596997) 1 NC_009952.1 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 2596997 5714108 Dshi_2452 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533787.1 2596056 R 398580 CDS YP_001533788.1 159044994 5714109 complement(2597049..2598080) 1 NC_009952.1 hypothetical protein 2598080 5714109 Dshi_2453 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533788.1 2597049 R 398580 CDS YP_001533789.1 159044995 5714110 complement(2598124..2598690) 1 NC_009952.1 hypothetical protein 2598690 5714110 Dshi_2454 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533789.1 2598124 R 398580 CDS YP_001533790.1 159044996 5714111 complement(2598687..2600012) 1 NC_009952.1 PFAM: AAA ATPase central domain protein SMART: AAA ATPase KEGG: ppd:Ppro_0362 AAA ATPase, central domain protein; AAA family; putative ATPase 2600012 5714111 Dshi_2455 Dinoroseobacter shibae DFL 12 = DSM 16493 putative ATPase YP_001533790.1 2598687 R 398580 CDS YP_001533791.1 159044997 5714112 complement(2600009..2604343) 1 NC_009952.1 hypothetical protein 2604343 5714112 Dshi_2456 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533791.1 2600009 R 398580 CDS YP_001533792.1 159044998 5714113 complement(2604619..2607219) 1 NC_009952.1 hypothetical protein 2607219 5714113 Dshi_2457 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533792.1 2604619 R 398580 CDS YP_001533793.1 159044999 5714114 complement(2607235..2608275) 1 NC_009952.1 hypothetical protein 2608275 5714114 Dshi_2458 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533793.1 2607235 R 398580 CDS YP_001533794.1 159045000 5714115 complement(2608289..2612149) 1 NC_009952.1 KEGG: ppd:Ppro_0366 hypothetical protein; hypothetical protein 2612149 5714115 Dshi_2459 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533794.1 2608289 R 398580 CDS YP_001533795.1 159045001 5714116 complement(2612167..2612616) 1 NC_009952.1 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 2612616 5714116 Dshi_2460 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533795.1 2612167 R 398580 CDS YP_001533796.1 159045002 5714117 complement(2612621..2612920) 1 NC_009952.1 PFAM: PAAR repeat-containing protein KEGG: sdn:Sden_3002 PaaR COG4104: Uncharacterized conserved protein; hypothetical protein 2612920 5714117 Dshi_2461 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533796.1 2612621 R 398580 CDS YP_001533797.1 159045003 5714118 complement(2612931..2614718) 1 NC_009952.1 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 2614718 5714118 Dshi_2462 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533797.1 2612931 R 398580 CDS YP_001533798.1 159045004 5714119 complement(2614711..2615373) 1 NC_009952.1 hypothetical protein 2615373 5714119 Dshi_2463 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533798.1 2614711 R 398580 CDS YP_001533799.1 159045005 5714120 complement(2615591..2616073) 1 NC_009952.1 TIGRFAM: conserved hypothetical phage tail protein (TIGR02241) PFAM: conserved hypothetical protein KEGG: rde:RD1_4219 hypothetical protein; phage tail region protein; hypothetical protein 2616073 5714120 Dshi_2464 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533799.1 2615591 R 398580 CDS YP_001533800.1 159045006 5714121 complement(2616086..2616544) 1 NC_009952.1 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 2616544 5714121 Dshi_2465 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533800.1 2616086 R 398580 CDS YP_001533801.1 159045007 5714122 complement(2616568..2618061) 1 NC_009952.1 PFAM:Phage tail sheath protein KEGG: sdn:Sden_3007 hypothetical protein; related to phage tail sheath protein; hypothetical protein 2618061 5714122 Dshi_2466 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533801.1 2616568 R 398580 CDS YP_001533802.1 159045008 5714123 complement(2618145..2619143) 1 NC_009952.1 hypothetical protein 2619143 5714123 Dshi_2467 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533802.1 2618145 R 398580 CDS YP_001533803.1 159045009 5714124 2619421..2620425 1 NC_009952.1 hypothetical protein 2620425 5714124 Dshi_2468 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533803.1 2619421 D 398580 CDS YP_001533804.1 159045010 5713365 complement(2620435..2621520) 1 NC_009952.1 First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan; phospho-N-acetylmuramoyl-pentapeptide- transferase 2621520 mraY 5713365 mraY Dinoroseobacter shibae DFL 12 = DSM 16493 phospho-N-acetylmuramoyl-pentapeptide- transferase YP_001533804.1 2620435 R 398580 CDS YP_001533805.1 159045011 5713366 complement(2621533..2622972) 1 NC_009952.1 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 2622972 murF 5713366 murF Dinoroseobacter shibae DFL 12 = DSM 16493 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D- alanine ligase YP_001533805.1 2621533 R 398580 CDS YP_001533806.1 159045012 5713367 complement(2622969..2624450) 1 NC_009952.1 involved in cell wall formation; peptidoglycan synthesis; cytoplasmic enzyme; catalyzes the addition of meso-diaminopimelic acid to the nucleotide precursor UDP-N-aceylmuramoyl-l-alanyl-d-glutamate; UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase 2624450 murE 5713367 murE Dinoroseobacter shibae DFL 12 = DSM 16493 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase YP_001533806.1 2622969 R 398580 CDS YP_001533807.1 159045013 5713368 complement(2624468..2626261) 1 NC_009952.1 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 2626261 ftsI2 5713368 ftsI2 Dinoroseobacter shibae DFL 12 = DSM 16493 peptidoglycan synthetase ftsI YP_001533807.1 2624468 R 398580 CDS YP_001533808.1 159045014 5713369 complement(2626258..2626614) 1 NC_009952.1 hypothetical protein 2626614 5713369 Dshi_2473 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533808.1 2626258 R 398580 CDS YP_001533809.1 159045015 5713370 complement(2626611..2627612) 1 NC_009952.1 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 2627612 mraW 5713370 mraW Dinoroseobacter shibae DFL 12 = DSM 16493 S-adenosyl-methyltransferase MraW YP_001533809.1 2626611 R 398580 CDS YP_001533810.1 159045016 5713371 complement(2627617..2628129) 1 NC_009952.1 MraZ; UPF0040; crystal structure shows similarity to AbrB; cell division protein MraZ 2628129 5713371 Dshi_2475 Dinoroseobacter shibae DFL 12 = DSM 16493 cell division protein MraZ YP_001533810.1 2627617 R 398580 CDS YP_001533811.1 159045017 5713372 complement(2628776..2629864) 1 NC_009952.1 Swiss-Prot: P0AF08-Protein mrp COG0489: ATPases involved in chromosome partitioning; related to protein mrp; hypothetical protein 2629864 5713372 Dshi_2476 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533811.1 2628776 R 398580 CDS YP_001533812.1 159045018 5713373 complement(2630248..2630712) 1 NC_009952.1 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 2630712 5713373 Dshi_2477 Dinoroseobacter shibae DFL 12 = DSM 16493 putative leucine-responsive regulatory protein YP_001533812.1 2630248 R 398580 CDS YP_001533813.1 159045019 5713374 2630776..2631372 1 NC_009952.1 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 2631372 5713374 Dshi_2478 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533813.1 2630776 D 398580 CDS YP_001533814.1 159045020 5713375 complement(2631379..2632347) 1 NC_009952.1 Swiss-Prot:P30864-Uncharacterized HTH-type transcriptional regulator yafC PFAM: regulatory protein LysR; LysR substrate-binding; LysR family; transcriptional regulator 2632347 5713375 Dshi_2479 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001533814.1 2631379 R 398580 CDS YP_001533815.1 159045021 5713376 2632408..2633268 1 NC_009952.1 PFAM: short-chain dehydrogenase/reductase SDR COG1028: Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases); short-chain dehydrogenase/reductase SDR 2633268 5713376 Dshi_2480 Dinoroseobacter shibae DFL 12 = DSM 16493 short-chain dehydrogenase/reductase SDR YP_001533815.1 2632408 D 398580 CDS YP_001533816.1 159045022 5713377 2633360..2633482 1 NC_009952.1 hypothetical protein 2633482 5713377 Dshi_2481 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533816.1 2633360 D 398580 CDS YP_001533817.1 159045023 5713378 2633707..2634015 1 NC_009952.1 TIGRFAM / PFAM: Ethyl tert-butyl ether degradation EthD; similar to EthD protein; hypothetical protein 2634015 5713378 Dshi_2482 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533817.1 2633707 D 398580 CDS YP_001533818.1 159045024 5713379 complement(2634052..2636475) 1 NC_009952.1 Swiss-Prot: P03018-DNA helicase II PFAM: UvrD/REP helicase KEGG: jan:Jann_2777 UvrD/REP helicase; DNA helicase II 2636475 uvrD 5713379 uvrD Dinoroseobacter shibae DFL 12 = DSM 16493 DNA helicase II YP_001533818.1 2634052 R 398580 CDS YP_001533819.1 159045025 5713380 2636566..2637735 1 NC_009952.1 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 2637735 lldD1 5713380 lldD1 Dinoroseobacter shibae DFL 12 = DSM 16493 cytochrome containing L-lactate dehydrogenase YP_001533819.1 2636566 D 398580 CDS YP_001533820.1 159045026 5713381 2637777..2641214 1 NC_009952.1 biotin-containing enzyme that catalyzes a two step carboxylation of pyruvate to oxaloacetate; pyruvate carboxylase 2641214 5713381 Dshi_2485 Dinoroseobacter shibae DFL 12 = DSM 16493 pyruvate carboxylase YP_001533820.1 2637777 D 398580 CDS YP_001533821.1 159045027 5713382 complement(2641492..2642133) 1 NC_009952.1 PFAM: Protein of unknown function DUF1826 KEGG: rde:RD1_1857 hypothetical protein; hypothetical protein 2642133 5713382 Dshi_2486 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533821.1 2641492 R 398580 CDS YP_001533822.1 159045028 5713383 complement(2642133..2643338) 1 NC_009952.1 Swiss-Prot: P31521- 47 kDa protein; PFAM: cobalamin synthesis protein P47K; cobalamin synthesis CobW domain protein; putative 47 kDa protein 2643338 5713383 Dshi_2487 Dinoroseobacter shibae DFL 12 = DSM 16493 putative 47 kDa protein YP_001533822.1 2642133 R 398580 CDS YP_001533823.1 159045029 5713385 complement(2643636..2645039) 1 NC_009952.1 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 2645039 5713385 Dshi_2488 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533823.1 2643636 R 398580 CDS YP_001533824.1 159045030 5713386 2645177..2646379 1 NC_009952.1 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 2646379 5713386 Dshi_2489 Dinoroseobacter shibae DFL 12 = DSM 16493 putative serine--glyoxylate aminotransferase YP_001533824.1 2645177 D 398580 CDS YP_001533825.1 159045031 5713387 2646434..2647366 1 NC_009952.1 Swiss-Prot: P0A9I1-Citrate lyase subunit beta PIRSF015582: citrate lyase, beta subunit [Validated]; subunit beta; citrate lyase 2647366 citE1 5713387 citE1 Dinoroseobacter shibae DFL 12 = DSM 16493 citrate lyase YP_001533825.1 2646434 D 398580 CDS YP_001533826.1 159045032 5713388 2647390..2648568 1 NC_009952.1 catalyzes the formation of malyl-CoA from malate and CoA; malate--CoA ligase subunit beta 2648568 sucC2 5713388 sucC2 Dinoroseobacter shibae DFL 12 = DSM 16493 malate--CoA ligase subunit beta YP_001533826.1 2647390 D 398580 CDS YP_001533827.1 159045033 5713389 2648581..2649480 1 NC_009952.1 Catalyzes the only substrate-level phosphorylation in the TCA cycle; succinyl-CoA synthetase subunit alpha 2649480 sucD2 5713389 sucD2 Dinoroseobacter shibae DFL 12 = DSM 16493 succinyl-CoA synthetase subunit alpha YP_001533827.1 2648581 D 398580 CDS YP_001533828.1 159045034 5713390 2649470..2650336 1 NC_009952.1 KEGG: pde:Pden_4111 hypothetical protein; hypothetical protein 2650336 5713390 Dshi_2493 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533828.1 2649470 D 398580 CDS YP_001533829.1 159045035 5713391 2650338..2651579 1 NC_009952.1 IPR003673: CoA-transferase family III KEGG: rrs:RoseRS_4174 acyl-CoA transferase/carnitine dehydratase-like protei; CoA-transferase 2651579 5713391 Dshi_2494 Dinoroseobacter shibae DFL 12 = DSM 16493 CoA-transferase YP_001533829.1 2650338 D 398580 CDS YP_001533830.1 159045036 5713392 complement(2651711..2652277) 1 NC_009952.1 Swiss-Prot: P75925-Cytochrome b561 homolog 2 PFAM: cytochrome B561; putative cytochrome B561 2652277 5713392 Dshi_2495 Dinoroseobacter shibae DFL 12 = DSM 16493 putative cytochrome B561 YP_001533830.1 2651711 R 398580 CDS YP_001533831.1 159045037 5713393 complement(2652382..2652942) 1 NC_009952.1 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 2652942 5713393 Dshi_2496 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533831.1 2652382 R 398580 CDS YP_001533832.1 159045038 5713394 2653184..2653903 1 NC_009952.1 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 2653903 5713394 Dshi_2497 Dinoroseobacter shibae DFL 12 = DSM 16493 two component transcriptional regulator YP_001533832.1 2653184 D 398580 CDS YP_001533833.1 159045039 5713395 2653900..2655261 1 NC_009952.1 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 2655261 5713395 Dshi_2498 Dinoroseobacter shibae DFL 12 = DSM 16493 integral membrane sensor signal transduction histidine kinase YP_001533833.1 2653900 D 398580 CDS YP_001533834.1 159045040 5713396 complement(2655477..2656199) 1 NC_009952.1 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 2656199 5713396 Dshi_2499 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533834.1 2655477 R 398580 CDS YP_001533835.1 159045041 5713398 2657746..2659947 1 NC_009952.1 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 2659947 5713398 Dshi_2501 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC transporter YP_001533835.1 2657746 D 398580 CDS YP_001533836.1 159045042 5713399 2659944..2661263 1 NC_009952.1 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 2661263 5713399 Dshi_2502 Dinoroseobacter shibae DFL 12 = DSM 16493 secretion protein YP_001533836.1 2659944 D 398580 CDS YP_001533837.1 159045043 5713400 complement(2661268..2668737) 1 NC_009952.1 hypothetical protein 2668737 5713400 Dshi_2503 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533837.1 2661268 R 398580 CDS YP_001533838.1 159045044 5713401 2668891..2670234 1 NC_009952.1 KEGG: jan:Jann_0233 hypothetical protein; hypothetical protein 2670234 5713401 Dshi_2504 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533838.1 2668891 D 398580 CDS YP_001533839.1 159045045 5713402 complement(2670313..2670798) 1 NC_009952.1 hypothetical protein 2670798 5713402 Dshi_2505 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533839.1 2670313 R 398580 CDS YP_001533840.1 159045046 5713403 complement(2670795..2671211) 1 NC_009952.1 hypothetical protein 2671211 5713403 Dshi_2506 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533840.1 2670795 R 398580 CDS YP_001533841.1 159045047 5713404 2672204..2672470 1 NC_009952.1 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 2672470 5713404 Dshi_2507 Dinoroseobacter shibae DFL 12 = DSM 16493 transposase YP_001533841.1 2672204 D 398580 CDS YP_001533842.1 159045048 5713405 2672494..2673315 1 NC_009952.1 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 2673315 5713405 Dshi_2508 Dinoroseobacter shibae DFL 12 = DSM 16493 integrase YP_001533842.1 2672494 D 398580 CDS YP_001533843.1 159045049 5713406 complement(2673339..2674034) 1 NC_009952.1 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 2674034 5713406 Dshi_2509 Dinoroseobacter shibae DFL 12 = DSM 16493 integrase YP_001533843.1 2673339 R 398580 CDS YP_001533844.1 159045050 5713407 complement(2674058..2674324) 1 NC_009952.1 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 2674324 5713407 Dshi_2510 Dinoroseobacter shibae DFL 12 = DSM 16493 transposase YP_001533844.1 2674058 R 398580 CDS YP_001533845.1 159045051 5713408 complement(2675127..2675798) 1 NC_009952.1 hypothetical protein 2675798 5713408 Dshi_2511 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533845.1 2675127 R 398580 CDS YP_001533846.1 159045052 5713409 2676018..2677034 1 NC_009952.1 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 2677034 dusA 5713409 dusA Dinoroseobacter shibae DFL 12 = DSM 16493 tRNA-dihydrouridine synthase A YP_001533846.1 2676018 D 398580 CDS YP_001533847.1 159045053 5713410 complement(2677050..2677463) 1 NC_009952.1 KEGG: sil:SPO1770 hypothetical protein; hypothetical protein 2677463 5713410 Dshi_2513 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533847.1 2677050 R 398580 CDS YP_001533848.1 159045054 5713411 2677548..2678540 1 NC_009952.1 KEGG: sil:SPO1769 hypothetical protein; hypothetical protein 2678540 5713411 Dshi_2514 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533848.1 2677548 D 398580 CDS YP_001533849.1 159045055 5713412 complement(2678672..2680408) 1 NC_009952.1 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 2680408 5713412 Dshi_2515 Dinoroseobacter shibae DFL 12 = DSM 16493 putative sulfate transporter YP_001533849.1 2678672 R 398580 CDS YP_001533850.1 159045056 5713413 2680474..2680680 1 NC_009952.1 hypothetical protein 2680680 5713413 Dshi_2516 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533850.1 2680474 D 398580 CDS YP_001533851.1 159045057 5713414 complement(2680792..2681676) 1 NC_009952.1 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 2681676 5713414 Dshi_2517 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533851.1 2680792 R 398580 CDS YP_001533852.1 159045058 5713415 complement(2681705..2682142) 1 NC_009952.1 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 2682142 5713415 Dshi_2518 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533852.1 2681705 R 398580 CDS YP_001533853.1 159045059 5713416 complement(2682147..2682581) 1 NC_009952.1 PFAM: protein of unknown function DUF395 YeeE/YedE KEGG: jan:Jann_2818 protein of unknown function DUF395, YeeE/YedE; hypothetical protein 2682581 5713416 Dshi_2519 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533853.1 2682147 R 398580 CDS YP_001533854.1 159045060 5713417 complement(2682578..2682790) 1 NC_009952.1 KEGG: rde:RD1_0788 hypothetical protein; hypothetical protein 2682790 5713417 Dshi_2520 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533854.1 2682578 R 398580 CDS YP_001533855.1 159045061 5713418 complement(2682892..2683569) 1 NC_009952.1 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 2683569 5713418 Dshi_2521 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001533855.1 2682892 R 398580 CDS YP_001533856.1 159045062 5713419 complement(2683654..2684346) 1 NC_009952.1 Swiss-Prot: Q8PYP6-Probable peroxiredoxin PFAM: alkyl hydroperoxide reductase/ Thiol specific antioxidant/ Mal allergen; Redoxin domain protein; putative peroxiredoxin 2684346 5713419 Dshi_2522 Dinoroseobacter shibae DFL 12 = DSM 16493 putative peroxiredoxin YP_001533856.1 2683654 R 398580 CDS YP_001533857.1 159045063 5713420 2684418..2685335 1 NC_009952.1 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 2685335 5713420 Dshi_2523 Dinoroseobacter shibae DFL 12 = DSM 16493 putative hydrogen peroxide-inducible genes activator YP_001533857.1 2684418 D 398580 CDS YP_001533858.1 159045064 5713421 complement(2685358..2686335) 1 NC_009952.1 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 2686335 5713421 Dshi_2524 Dinoroseobacter shibae DFL 12 = DSM 16493 putative C4-dicarboxylate transporter / malic acid transport protein YP_001533858.1 2685358 R 398580 CDS YP_001533859.1 159045065 5713422 complement(2686607..2686975) 1 NC_009952.1 KEGG: sil:SPO1613 hypothetical protein; hypothetical protein 2686975 5713422 Dshi_2525 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533859.1 2686607 R 398580 CDS YP_001533860.1 159045066 5713423 complement(2686988..2688289) 1 NC_009952.1 PTHR10632: Sulfide quinone-reductase PFAM: FAD-dependent pyridine nucleotide-disulphide oxidoreductase; putative sulfide quinone-rductase 2688289 5713423 Dshi_2526 Dinoroseobacter shibae DFL 12 = DSM 16493 putative sulfide quinone-rductase YP_001533860.1 2686988 R 398580 CDS YP_001533861.1 159045067 5713424 complement(2688731..2689123) 1 NC_009952.1 hypothetical protein 2689123 5713424 Dshi_2527 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533861.1 2688731 R 398580 CDS YP_001533862.1 159045068 5713425 complement(2689216..2689971) 1 NC_009952.1 PFAM: Bacterial regulatory proteins, crp family KEGG: rru:Rru_A1245 transcriptional regulator, Crp/Fnr family; Crp/Fnr family; putative transcriptional regulator 2689971 5713425 Dshi_2528 Dinoroseobacter shibae DFL 12 = DSM 16493 putative transcriptional regulator YP_001533862.1 2689216 R 398580 CDS YP_001533863.1 159045069 5713426 complement(2689949..2691163) 1 NC_009952.1 KEGG: sil:SPO1611 hypothetical protein; hypothetical protein 2691163 5713426 Dshi_2529 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533863.1 2689949 R 398580 CDS YP_001533864.1 159045070 5713427 complement(2691359..2691556) 1 NC_009952.1 hypothetical protein 2691556 5713427 Dshi_2530 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533864.1 2691359 R 398580 CDS YP_001533865.1 159045071 5713428 complement(2691653..2691925) 1 NC_009952.1 hypothetical protein 2691925 5713428 Dshi_2531 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533865.1 2691653 R 398580 CDS YP_001533866.1 159045072 5713429 complement(2692195..2692497) 1 NC_009952.1 hypothetical protein 2692497 5713429 Dshi_2532 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533866.1 2692195 R 398580 CDS YP_001533867.1 159045073 5713430 complement(2692835..2693023) 1 NC_009952.1 hypothetical protein 2693023 5713430 Dshi_2533 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533867.1 2692835 R 398580 CDS YP_001533868.1 159045074 5713431 complement(2693038..2693469) 1 NC_009952.1 PFAM: Integral membrane protein DUF112 COG3333: Uncharacterized protein conserved in bacteria; hypothetical protein 2693469 5713431 Dshi_2534 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533868.1 2693038 R 398580 CDS YP_001533869.1 159045075 5713432 complement(2693658..2693837) 1 NC_009952.1 hypothetical protein 2693837 5713432 Dshi_2535 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533869.1 2693658 R 398580 CDS YP_001533870.1 159045076 5713433 complement(2693913..2694260) 1 NC_009952.1 hypothetical protein 2694260 5713433 Dshi_2536 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533870.1 2693913 R 398580 CDS YP_001533871.1 159045077 5713434 complement(2694263..2695291) 1 NC_009952.1 Swiss-Prot: Q59727- 4,5-dihydroxyphthalate decarboxylase [predicted]; putative 4,5-dihydroxyphthalate decarboxylase 2695291 5713434 Dshi_2537 Dinoroseobacter shibae DFL 12 = DSM 16493 putative 4,5-dihydroxyphthalate decarboxylase YP_001533871.1 2694263 R 398580 CDS YP_001533872.1 159045078 5713435 complement(2695338..2696024) 1 NC_009952.1 Swiss-Prot: P76004-Uncharacterized protein ycgM PFAM: fumarylacetoacetate (FAA) hydrolase KEGG: rsh:Rsph17029_0213 fumarylacetoacetate (FAA) hydrolase; related to fumarylacetoacetate (FAA) hydrolase; hypothetical protein 2696024 5713435 Dshi_2538 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533872.1 2695338 R 398580 CDS YP_001533873.1 159045079 5713436 2696193..2696882 1 NC_009952.1 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 2696882 5713436 Dshi_2539 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001533873.1 2696193 D 398580 CDS YP_001533874.1 159045080 5713437 2696948..2697499 1 NC_009952.1 hypothetical protein 2697499 5713437 Dshi_2540 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533874.1 2696948 D 398580 CDS YP_001533875.1 159045081 5713438 complement(2697654..2698334) 1 NC_009952.1 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 2698334 5713438 Dshi_2541 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001533875.1 2697654 R 398580 CDS YP_001533876.1 159045082 5713439 2698518..2699444 1 NC_009952.1 Swiss-Prot: P76004-Uncharacterized protein ycgM PFAM: fumarylacetoacetate (FAA) hydrolase KEGG: bxe:Bxe_A3618 putative hydrolase; related to fumarylacetoacetate (FAA) hydrolase; hypothetical protein 2699444 5713439 Dshi_2542 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533876.1 2698518 D 398580 CDS YP_001533877.1 159045083 5713440 2699475..2700533 1 NC_009952.1 Swiss-Prot: P40400-Putative aliphatic sulfonates-binding protein [Precursor] PFAM: NMT1/THI5 like domain protein; putative-binding protein 2700533 5713440 Dshi_2543 Dinoroseobacter shibae DFL 12 = DSM 16493 putative-binding protein YP_001533877.1 2699475 D 398580 CDS YP_001533878.1 159045084 5713441 2700533..2701342 1 NC_009952.1 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 2701342 5713441 Dshi_2544 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC transporter YP_001533878.1 2700533 D 398580 CDS YP_001533879.1 159045085 5713442 2701339..2702202 1 NC_009952.1 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 2702202 5713442 Dshi_2545 Dinoroseobacter shibae DFL 12 = DSM 16493 binding-protein-dependent transport system protein YP_001533879.1 2701339 D 398580 CDS YP_001533880.1 159045086 5713443 2702195..2703250 1 NC_009952.1 Swiss-Prot: O34736-Uncharacterized oxidoreductase yjmC PFAM: Malate/L-lactate dehydrogenase KEGG: tth:TT_P0035 dehydrogenase; dehydrogenase 2703250 5713443 Dshi_2546 Dinoroseobacter shibae DFL 12 = DSM 16493 dehydrogenase YP_001533880.1 2702195 D 398580 CDS YP_001533881.1 159045087 5713444 complement(2703342..2703722) 1 NC_009952.1 hypothetical protein 2703722 5713444 Dshi_2547 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533881.1 2703342 R 398580 CDS YP_001533882.1 159045088 5713445 complement(2703739..2707950) 1 NC_009952.1 COG5412: Phage-related protein; hypothetical protein 2707950 5713445 Dshi_2548 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533882.1 2703739 R 398580 CDS YP_001533883.1 159045089 5713446 complement(2707954..2709441) 1 NC_009952.1 PFAM: cell surface receptor IPT/TIG domain protein KEGG: rrs:RoseRS_1653 hypothetical protein; hypothetical protein 2709441 5713446 Dshi_2549 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533883.1 2707954 R 398580 CDS YP_001533884.1 159045090 5713447 complement(2709454..2713869) 1 NC_009952.1 PFAM: impB/mucB/samB family SSF50969: quinoprotein amine dehydrogenase, beta chain-like KEGG: gme:Gmet_1144 hypothetical protein; hypothetical protein 2713869 5713447 Dshi_2550 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533884.1 2709454 R 398580 CDS YP_001533885.1 159045091 5713448 complement(2713924..2715474) 1 NC_009952.1 KEGG: gme:Gmet_1142 hypothetical protein; hypothetical protein 2715474 5713448 Dshi_2551 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533885.1 2713924 R 398580 CDS YP_001533886.1 159045092 5713449 complement(2715478..2718297) 1 NC_009952.1 TIGR02243: conserved hypothetical protein, phage tail-like region KEGG: aeh:Mlg_1745 hypothetical protein; hypothetical protein 2718297 5713449 Dshi_2552 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533886.1 2715478 R 398580 CDS YP_001533887.1 159045093 5713450 complement(2718294..2719487) 1 NC_009952.1 hypothetical protein 2719487 5713450 Dshi_2553 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533887.1 2718294 R 398580 CDS YP_001533888.1 159045094 5713451 complement(2719489..2719884) 1 NC_009952.1 PFAM: Gene 25-like lysozyme KEGG: aeh:Mlg_1747 hypothetical protein; related to gene 25-like lysozyme; hypothetical protein 2719884 5713451 Dshi_2554 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533888.1 2719489 R 398580 CDS YP_001533889.1 159045095 5713452 complement(2719895..2720716) 1 NC_009952.1 PFAM: Protein of unknown function, DUF586 COG3501: Uncharacterized protein conserved in bacteria; hypothetical protein 2720716 5713452 Dshi_2555 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533889.1 2719895 R 398580 CDS YP_001533890.1 159045096 5713453 complement(2720713..2721852) 1 NC_009952.1 PFAM: Phage late control gene D protein KEGG: gme:Gmet_1137 hypothetical protein COG3500: Phage protein D; hypothetical protein 2721852 5713453 Dshi_2556 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533890.1 2720713 R 398580 CDS YP_001533891.1 159045097 5713454 complement(2721857..2722219) 1 NC_009952.1 hypothetical protein 2722219 5713454 Dshi_2557 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533891.1 2721857 R 398580 CDS YP_001533892.1 159045098 5713455 complement(2722223..2722885) 1 NC_009952.1 hypothetical protein 2722885 5713455 Dshi_2558 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533892.1 2722223 R 398580 CDS YP_001533893.1 159045099 5713456 complement(2723112..2724446) 1 NC_009952.1 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 2724446 5713456 Dshi_2559 Dinoroseobacter shibae DFL 12 = DSM 16493 AAA ATPase YP_001533893.1 2723112 R 398580 CDS YP_001533894.1 159045100 5713457 complement(2724452..2725531) 1 NC_009952.1 ##; hypothetical protein 2725531 5713457 Dshi_2560 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533894.1 2724452 R 398580 CDS YP_001533895.1 159045101 5713458 complement(2725535..2726218) 1 NC_009952.1 hypothetical protein 2726218 5713458 Dshi_2561 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533895.1 2725535 R 398580 CDS YP_001533896.1 159045102 5713459 complement(2726402..2727220) 1 NC_009952.1 hypothetical protein 2727220 5713459 Dshi_2562 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533896.1 2726402 R 398580 CDS YP_001533897.1 159045103 5713460 complement(2727217..2727726) 1 NC_009952.1 TIGRFAM: conserved hypothetical phage tail protein PFAM: conserved hypothetical protein KEGG: aeh:Mlg_1757 conserved hypothetical phage tail protein; phage tail region; hypothetical protein 2727726 5713460 Dshi_2563 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533897.1 2727217 R 398580 CDS YP_001533898.1 159045104 5713461 complement(2727753..2730098) 1 NC_009952.1 PFAM: tail sheath protein KEGG: gme:Gmet_1128 phage tail sheath protein; related to phage tail sheath protein; hypothetical protein 2730098 5713461 Dshi_2564 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533898.1 2727753 R 398580 CDS YP_001533899.1 159045105 5713462 complement(2730319..2730960) 1 NC_009952.1 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 2730960 5713462 Dshi_2565 Dinoroseobacter shibae DFL 12 = DSM 16493 response regulator protein YP_001533899.1 2730319 R 398580 CDS YP_001533900.1 159045106 5713463 2731137..2733368 1 NC_009952.1 PFAM: dehydrogenase E1 component; Transketolase central region; Transketolase domain protein; transketolase / dehydrogenase; putative bifunctional enzyme 2733368 5713463 Dshi_2566 Dinoroseobacter shibae DFL 12 = DSM 16493 putative bifunctional enzyme YP_001533900.1 2731137 D 398580 CDS YP_001533901.1 159045107 5713464 2733766..2736072 1 NC_009952.1 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 2736072 5713464 Dshi_2567 Dinoroseobacter shibae DFL 12 = DSM 16493 multi-sensor signal transduction histidine kinase YP_001533901.1 2733766 D 398580 CDS YP_001533902.1 159045108 5713465 2736065..2736709 1 NC_009952.1 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 2736709 5713465 Dshi_2568 Dinoroseobacter shibae DFL 12 = DSM 16493 response regulator protein YP_001533902.1 2736065 D 398580 CDS YP_001533903.1 159045109 5713466 complement(2736718..2737746) 1 NC_009952.1 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 2737746 5713466 Dshi_2569 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533903.1 2736718 R 398580 CDS YP_001533904.1 159045110 5713467 complement(2737743..2738384) 1 NC_009952.1 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 2738384 5713467 Dshi_2570 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001533904.1 2737743 R 398580 CDS YP_001533905.1 159045111 5713469 2738741..2739532 1 NC_009952.1 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 2739532 5713469 Dshi_2571 Dinoroseobacter shibae DFL 12 = DSM 16493 RNA methyltransferase YP_001533905.1 2738741 D 398580 CDS YP_001533906.1 159045112 5713470 2739576..2739908 1 NC_009952.1 KEGG: jan:Jann_2800 hypothetical protein; hypothetical protein 2739908 5713470 Dshi_2572 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533906.1 2739576 D 398580 CDS YP_001533907.1 159045113 5713471 2740015..2740470 1 NC_009952.1 KEGG: rde:RD1_2147 hypothetical protein; hypothetical protein 2740470 5713471 Dshi_2573 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533907.1 2740015 D 398580 CDS YP_001533908.1 159045114 5713472 2740741..2741226 1 NC_009952.1 PFAM: CoA-binding domain protein KEGG: sil:SPO1153 CoA-binding domain protein; hypothetical protein 2741226 5713472 Dshi_2574 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533908.1 2740741 D 398580 CDS YP_001533909.1 159045115 5713473 complement(2741315..2741623) 1 NC_009952.1 catalyzes the formation of 1-(5-phosphoribosyl)-AMP from 1-(5-phosphoribolsyl)-ATP in histidine biosynthesis; phosphoribosyl-ATP pyrophosphatase 2741623 hisE 5713473 hisE Dinoroseobacter shibae DFL 12 = DSM 16493 phosphoribosyl-ATP pyrophosphatase YP_001533909.1 2741315 R 398580 CDS YP_001533910.1 159045116 5713474 complement(2741620..2742381) 1 NC_009952.1 catalyzes the conversion of 5-[(5-phospho-1-deoxyribulos-1-ylamino)methylideneamino]- 1-(5-phosphoribosyl)imidazole-4-carboxamideand glutamine to imidazole-glycerol phosphate, 5-aminoimidazol-4-carboxamideribonucleotide and glutamate; the HisF subunit acts as a cyclase; imidazole glycerol phosphate synthase subunit HisF 2742381 hisF 5713474 hisF Dinoroseobacter shibae DFL 12 = DSM 16493 imidazole glycerol phosphate synthase subunit HisF YP_001533910.1 2741620 R 398580 CDS YP_001533911.1 159045117 5713475 2742482..2743606 1 NC_009952.1 PFAM: putative RNA methylase KEGG: pde:Pden_2378 putative RNA methylase; putative RNA methylase 2743606 5713475 Dshi_2577 Dinoroseobacter shibae DFL 12 = DSM 16493 putative RNA methylase YP_001533911.1 2742482 D 398580 CDS YP_001533912.1 159045118 5713476 complement(2743867..2744589) 1 NC_009952.1 catalyzes the formation of 5-(5-phospho-1-deoxyribulos-1-ylamino)methylideneamino-l- (5-phosphoribosyl)imidazole-4-carboxamide from 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide; 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase 2744589 hisA 5713476 hisA Dinoroseobacter shibae DFL 12 = DSM 16493 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase YP_001533912.1 2743867 R 398580 CDS YP_001533913.1 159045119 5713477 2744733..2745137 1 NC_009952.1 COG4731: Uncharacterized protein conserved in bacteria; hypothetical protein 2745137 5713477 Dshi_2579 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533913.1 2744733 D 398580 CDS YP_001533914.1 159045120 5713478 complement(2745303..2747807) 1 NC_009952.1 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 2747807 hrpB 5713478 hrpB Dinoroseobacter shibae DFL 12 = DSM 16493 ATP-dependent RNA helicase YP_001533914.1 2745303 R 398580 CDS YP_001533915.1 159045121 5713479 complement(2747856..2748656) 1 NC_009952.1 hypothetical protein 2748656 5713479 Dshi_2581 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533915.1 2747856 R 398580 CDS YP_001533916.1 159045122 5713480 2748739..2749815 1 NC_009952.1 functions in transport of arginine/ornithine; inner membrane ATPase that cleaves ATP and phosphorylates two periplasmic proteins that function as two distinct transport systems, the AO (arginine and ornithine) and LAO (lysine, arginine, and ornithine) periplasmic binding proteins; arginine/ornithine transport system ATPase 2749815 5713480 Dshi_2582 Dinoroseobacter shibae DFL 12 = DSM 16493 arginine/ornithine transport system ATPase YP_001533916.1 2748739 D 398580 CDS YP_001533917.1 159045123 5713481 2749939..2750226 1 NC_009952.1 required for 70S ribosome assembly; 50S ribosomal protein L28 2750226 rpmB 5713481 rpmB Dinoroseobacter shibae DFL 12 = DSM 16493 50S ribosomal protein L28 YP_001533917.1 2749939 D 398580 CDS YP_001533918.1 159045124 5713482 2750551..2750907 1 NC_009952.1 KEGG: rsq:Rsph17025_3115 hypothetical protein; hypothetical protein 2750907 5713482 Dshi_2584 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533918.1 2750551 D 398580 CDS YP_001533919.1 159045125 5713483 2750951..2751463 1 NC_009952.1 PFAM: protein of unknown function DUF461 KEGG: rde:RD1_1682 hypothetical protein COG2847: Uncharacterized protein conserved in bacteria; hypothetical protein 2751463 5713483 Dshi_2585 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533919.1 2750951 D 398580 CDS YP_001533920.1 159045126 5713484 complement(2751482..2752237) 1 NC_009952.1 PFAM: HpcH/HpaI aldolase KEGG: jan:Jann_2691 HpcH/HpaI aldolase; HpcH/HpaI aldolase 2752237 5713484 Dshi_2586 Dinoroseobacter shibae DFL 12 = DSM 16493 HpcH/HpaI aldolase YP_001533920.1 2751482 R 398580 CDS YP_001533921.1 159045127 5713485 2752527..2753555 1 NC_009952.1 PFAM: Metallo-beta-lactamase superfamily COG1236: Predicted exonuclease of the beta-lactamase fold involved in RNA processing; related to beta-lactamases; hypothetical protein 2753555 5713485 Dshi_2587 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533921.1 2752527 D 398580 CDS YP_001533922.1 159045128 5713486 2753552..2754448 1 NC_009952.1 PFAM: Alpha/beta hydrolase fold-3 domain protein COG0657: Esterase/lipase; putative esterase/lipase 2754448 5713486 Dshi_2588 Dinoroseobacter shibae DFL 12 = DSM 16493 putative esterase/lipase YP_001533922.1 2753552 D 398580 CDS YP_001533923.1 159045129 5713487 2754445..2756049 1 NC_009952.1 catalyzes the ATP-dependent formation of a phosphodiester at the site of a single strand break in duplex DNA; ATP-dependent DNA ligase 2756049 5713487 Dshi_2589 Dinoroseobacter shibae DFL 12 = DSM 16493 ATP-dependent DNA ligase YP_001533923.1 2754445 D 398580 CDS YP_001533924.1 159045130 5713488 2756272..2756904 1 NC_009952.1 PFAM: integrase family protein KEGG: rsh:Rsph17029_2267 phage integrase family protein; related to phage integrase; hypothetical protein 2756904 5713488 Dshi_2590 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533924.1 2756272 D 398580 CDS YP_001533925.1 159045131 5713489 complement(2757021..2757491) 1 NC_009952.1 TIGRFAM: putative transcriptional regulator, Rrf2 family PFAM: protein of unknown function UPF0074 KEGG: rde:RD1_1855 transcriptional regulator, rrf2 family, putative; transcriptional regulator 2757491 5713489 Dshi_2591 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001533925.1 2757021 R 398580 CDS YP_001533926.1 159045132 5713490 2757530..2758741 1 NC_009952.1 Swiss-Prot: P31521- 47 kDa protein; PFAM: cobalamin synthesis protein P47K COG0523: Putative GTPases (G3E family); putative 47 kDa protein 2758741 5713490 Dshi_2592 Dinoroseobacter shibae DFL 12 = DSM 16493 putative 47 kDa protein YP_001533926.1 2757530 D 398580 CDS YP_001533927.1 159045133 5713491 2758738..2759373 1 NC_009952.1 PFAM: Protein of unknown function DUF1826 KEGG: rde:RD1_1857 hypothetical protein; hypothetical protein 2759373 5713491 Dshi_2593 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533927.1 2758738 D 398580 CDS YP_001533928.1 159045134 5713492 2759370..2759642 1 NC_009952.1 hypothetical protein 2759642 5713492 Dshi_2594 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533928.1 2759370 D 398580 CDS YP_001533929.1 159045135 5713493 2759653..2761176 1 NC_009952.1 PFAM: extracellular solute-binding protein family Swiss-Prot: P76128-Putative ABC transporter periplasmic-binding protein yddS [Precursor]; putative extracellular solute-binding protein 2761176 5713493 Dshi_2595 Dinoroseobacter shibae DFL 12 = DSM 16493 putative extracellular solute-binding protein YP_001533929.1 2759653 D 398580 CDS YP_001533930.1 159045136 5713494 2761173..2761856 1 NC_009952.1 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 2761856 5713494 Dshi_2596 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC transporter YP_001533930.1 2761173 D 398580 CDS YP_001533931.1 159045137 5713495 2761850..2762575 1 NC_009952.1 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 2762575 5713495 Dshi_2597 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC transporter YP_001533931.1 2761850 D 398580 CDS YP_001533932.1 159045138 5713496 2762572..2763510 1 NC_009952.1 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 2763510 5713496 Dshi_2598 Dinoroseobacter shibae DFL 12 = DSM 16493 binding-protein-dependent transport system permease YP_001533932.1 2762572 D 398580 CDS YP_001533933.1 159045139 5713497 2763494..2764297 1 NC_009952.1 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 2764297 5713497 Dshi_2599 Dinoroseobacter shibae DFL 12 = DSM 16493 binding-protein-dependent transport system permease YP_001533933.1 2763494 D 398580 CDS YP_001533934.1 159045140 5713498 2764294..2765190 1 NC_009952.1 PFAM: protein of unknown function DUF6 transmembrane KEGG: rde:RD1_1864 integral membrane protein, putative; hypothetical protein 2765190 5713498 Dshi_2600 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533934.1 2764294 D 398580 CDS YP_001533935.1 159045141 5713499 2765180..2766208 1 NC_009952.1 PFAM: helix-turn-helix- domain containing protein AraC type KEGG: rde:RD1_0249 transcriptional regulator, AraC family, putative; putative transcriptional regulator 2766208 5713499 Dshi_2601 Dinoroseobacter shibae DFL 12 = DSM 16493 putative transcriptional regulator YP_001533935.1 2765180 D 398580 CDS YP_001533936.1 159045142 5713500 2766389..2767594 1 NC_009952.1 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 2767594 5713500 Dshi_2602 Dinoroseobacter shibae DFL 12 = DSM 16493 acyl-CoA dehydrogenase YP_001533936.1 2766389 D 398580 CDS YP_001533937.1 159045143 5713501 2767996..2769831 1 NC_009952.1 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 2769831 5713501 Dshi_2603 Dinoroseobacter shibae DFL 12 = DSM 16493 oligoendopeptidase YP_001533937.1 2767996 D 398580 CDS YP_001533938.1 159045144 5713502 complement(2769916..2770317) 1 NC_009952.1 Swiss-Prot: P64590-Inner membrane protein yhaH PFAM: protein of unknown function DUF805; similar to inner membrane protein yhaH; hypothetical protein 2770317 5713502 Dshi_2604 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533938.1 2769916 R 398580 CDS YP_001533939.1 159045145 5713503 complement(2770330..2770554) 1 NC_009952.1 hypothetical protein 2770554 5713503 Dshi_2605 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533939.1 2770330 R 398580 CDS YP_001533940.1 159045146 5713504 complement(2770620..2770862) 1 NC_009952.1 SMART: zinc finger CDGSH-type domain protein KEGG: rde:RD1_1658 hypothetical protein; hypothetical protein 2770862 5713504 Dshi_2606 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533940.1 2770620 R 398580 CDS YP_001533941.1 159045147 5713505 complement(2770982..2771284) 1 NC_009952.1 KEGG: sil:SPO0456 hypothetical protein; hypothetical protein 2771284 5713505 Dshi_2607 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533941.1 2770982 R 398580 CDS YP_001533942.1 159045148 5713506 complement(2771502..2772488) 1 NC_009952.1 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 2772488 5713506 Dshi_2608 Dinoroseobacter shibae DFL 12 = DSM 16493 putative oxidoreductase YP_001533942.1 2771502 R 398580 CDS YP_001533943.1 159045149 5713507 complement(2772541..2773437) 1 NC_009952.1 binds with the catalytic core of RNA polymerase to produce the holoenzyme; this sigma factor is responsible for the expression of heat shock promoters; RNA polymerase factor sigma-32 2773437 rpoH2 5713507 rpoH2 Dinoroseobacter shibae DFL 12 = DSM 16493 RNA polymerase factor sigma-32 YP_001533943.1 2772541 R 398580 CDS YP_001533944.1 159045150 5713508 complement(2773631..2774674) 1 NC_009952.1 Swiss-Prot: P33643-Ribosomal large subunit pseudouridine synthase D TIGR00005: pseudouridine synthase, RluA family; ribosomal large subunit pseudouridine synthase D 2774674 rluD 5713508 rluD Dinoroseobacter shibae DFL 12 = DSM 16493 ribosomal large subunit pseudouridine synthase D YP_001533944.1 2773631 R 398580 CDS YP_001533945.1 159045151 5713509 2774718..2775005 1 NC_009952.1 hypothetical protein 2775005 5713509 Dshi_2611 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533945.1 2774718 D 398580 CDS YP_001533946.1 159045152 5713510 complement(2775209..2775895) 1 NC_009952.1 Modulates the activities of several enzymes which are inactive in their acetylated form; NAD-dependent deacetylase 2775895 npdA 5713510 npdA Dinoroseobacter shibae DFL 12 = DSM 16493 NAD-dependent deacetylase YP_001533946.1 2775209 R 398580 CDS YP_001533947.1 159045153 5713511 2775951..2776406 1 NC_009952.1 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 2776406 5713511 Dshi_2613 Dinoroseobacter shibae DFL 12 = DSM 16493 low molecular weight protein-tyrosine-phosphatase YP_001533947.1 2775951 D 398580 CDS YP_001533948.1 159045154 5713512 complement(2776403..2776708) 1 NC_009952.1 KEGG: sit:TM1040_0677 hypothetical protein; hypothetical protein 2776708 5713512 Dshi_2614 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533948.1 2776403 R 398580 CDS YP_001533949.1 159045155 5713513 complement(2776824..2777627) 1 NC_009952.1 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 2777627 5713513 Dshi_2615 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC transporter YP_001533949.1 2776824 R 398580 CDS YP_001533950.1 159045156 5713514 2777782..2778405 1 NC_009952.1 PFAM: GcrA cell cycle regulator KEGG: jan:Jann_1020 GcrA cell cycle regulator; putative gcrA cell cycle regulator 2778405 5713514 Dshi_2616 Dinoroseobacter shibae DFL 12 = DSM 16493 putative gcrA cell cycle regulator YP_001533950.1 2777782 D 398580 CDS YP_001533951.1 159045157 5713515 complement(2778606..2779247) 1 NC_009952.1 KEGG: sde:Sde_2877 hypothetical protein; hypothetical protein 2779247 5713515 Dshi_2617 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533951.1 2778606 R 398580 CDS YP_001533952.1 159045158 5713516 2779585..2780955 1 NC_009952.1 catalyzes the methylthiolation of an aspartic acid residue of the S12 protein of the 30S ribosomal subunit; 30S ribosomal protein S12 methylthiotransferase 2780955 rimO 5713516 rimO Dinoroseobacter shibae DFL 12 = DSM 16493 30S ribosomal protein S12 methylthiotransferase YP_001533952.1 2779585 D 398580 CDS YP_001533953.1 159045159 5713517 2781030..2781365 1 NC_009952.1 Swiss-Prot: P69488-Divalent-cation tolerance protein cutA PFAM: CutA1 divalent ion tolerance protein; putative divalent-cation tolerance protein 2781365 cutA 5713517 cutA Dinoroseobacter shibae DFL 12 = DSM 16493 putative divalent-cation tolerance protein YP_001533953.1 2781030 D 398580 CDS YP_001533954.1 159045160 5713518 complement(2781369..2781725) 1 NC_009952.1 KEGG: rde:RD1_3491 hypothetical protein; hypothetical protein 2781725 5713518 Dshi_2620 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533954.1 2781369 R 398580 CDS YP_001533955.1 159045161 5713519 complement(2781735..2782070) 1 NC_009952.1 KEGG: sil:SPO0942 hypothetical protein; hypothetical protein 2782070 5713519 Dshi_2621 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533955.1 2781735 R 398580 CDS YP_001533956.1 159045162 5713520 complement(2782124..2782372) 1 NC_009952.1 KEGG: sil:SPO0941 hypothetical protein; hypothetical protein 2782372 5713520 Dshi_2622 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533956.1 2782124 R 398580 CDS YP_001533957.1 159045163 5713521 complement(2782469..2783221) 1 NC_009952.1 PFAM: peptidase M48 Ste24p KEGG: rde:RD1_1656 peptidase, M48 family, putative; Ste24p; peptidase M48 2783221 5713521 Dshi_2623 Dinoroseobacter shibae DFL 12 = DSM 16493 peptidase M48 YP_001533957.1 2782469 R 398580 CDS YP_001533958.1 159045164 5713522 2783358..2783780 1 NC_009952.1 KEGG: rde:RD1_1657 hypothetical protein; hypothetical protein 2783780 5713522 Dshi_2624 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533958.1 2783358 D 398580 CDS YP_001533959.1 159045165 5713523 2783790..2784044 1 NC_009952.1 KEGG: sil:SPO0938 hypothetical protein; hypothetical protein 2784044 5713523 Dshi_2625 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533959.1 2783790 D 398580 CDS YP_001533960.1 159045166 5713524 2784148..2785326 1 NC_009952.1 Swiss-Prot: P55682-Uncharacterized transporter y4wD PFAM: major facilitator superfamily MFS_1; putative major facilitator superfamily transporter 2785326 5713524 Dshi_2626 Dinoroseobacter shibae DFL 12 = DSM 16493 putative major facilitator superfamily transporter YP_001533960.1 2784148 D 398580 CDS YP_001533961.1 159045167 5713525 2785328..2785978 1 NC_009952.1 Swiss-Prot: P0ACY1-Protein ydjA PFAM: nitroreductase KEGG: rsq:Rsph17025_0371 nitroreductase; related to nitroreductase; hypothetical protein 2785978 5713525 Dshi_2627 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533961.1 2785328 D 398580 CDS YP_001533962.1 159045168 5713526 2785975..2786685 1 NC_009952.1 PFAM: Protein of unknown function (DUF540); hypothetical protein 2786685 5713526 Dshi_2628 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533962.1 2785975 D 398580 CDS YP_001533963.1 159045169 5713527 complement(2786713..2787000) 1 NC_009952.1 PFAM: protein of unknown function DUF1467 KEGG: sil:SPO0933 hypothetical protein; hypothetical protein 2787000 5713527 Dshi_2629 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533963.1 2786713 R 398580 CDS YP_001533964.1 159045170 5713528 complement(2787004..2787408) 1 NC_009952.1 PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase Swiss-Prot: P54540-Uncharacterized protein yqjC; putative glyoxalase 2787408 5713528 Dshi_2630 Dinoroseobacter shibae DFL 12 = DSM 16493 putative glyoxalase YP_001533964.1 2787004 R 398580 CDS YP_001533965.1 159045171 5713529 2787540..2788244 1 NC_009952.1 PFAM: response regulator receiver KEGG: rde:RD1_1178 response regulator, putative; putative response regulator 2788244 5713529 Dshi_2631 Dinoroseobacter shibae DFL 12 = DSM 16493 putative response regulator YP_001533965.1 2787540 D 398580 CDS YP_001533966.1 159045172 5713530 2788411..2788605 1 NC_009952.1 hypothetical protein 2788605 5713530 Dshi_2632 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533966.1 2788411 D 398580 CDS YP_001533967.1 159045173 5713531 complement(2788656..2790428) 1 NC_009952.1 catalyzes a two-step reaction, first charging an aspartate molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; contains discriminating and non-discriminating subtypes; aspartyl-tRNA synthetase 2790428 aspS 5713531 aspS Dinoroseobacter shibae DFL 12 = DSM 16493 aspartyl-tRNA synthetase YP_001533967.1 2788656 R 398580 CDS YP_001533968.1 159045174 5713532 complement(2790528..2790977) 1 NC_009952.1 hypothetical protein 2790977 5713532 Dshi_2634 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533968.1 2790528 R 398580 CDS YP_001533969.1 159045175 5713533 2791005..2791742 1 NC_009952.1 PFAM: pentapeptide repeat protein; hypothetical protein 2791742 5713533 Dshi_2635 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533969.1 2791005 D 398580 CDS YP_001533970.1 159045176 5713534 complement(2791785..2792408) 1 NC_009952.1 Swiss-Prot: Q9Z5D7-Bacteriochlorophyll synthase 23 kDa chain (4-vinyl reductase) TIGRFAM: bacteriochlorophyll 4-vinyl reductase PFAM: 4-vinyl reductase 4VR; bacteriochlorophyll synthase 2792408 5713534 Dshi_2636 Dinoroseobacter shibae DFL 12 = DSM 16493 bacteriochlorophyll synthase YP_001533970.1 2791785 R 398580 CDS YP_001533971.1 159045177 5713535 complement(2792408..2794051) 1 NC_009952.1 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 2794051 5713535 Dshi_2637 Dinoroseobacter shibae DFL 12 = DSM 16493 putative anaerobic magnesium-protoporphyrin IX monomethyl ester [oxidative] cyclase YP_001533971.1 2792408 R 398580 CDS YP_001533972.1 159045178 5713536 complement(2794120..2794332) 1 NC_009952.1 hypothetical protein 2794332 5713536 Dshi_2638 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533972.1 2794120 R 398580 CDS YP_001533973.1 159045179 5713537 2794515..2797832 1 NC_009952.1 four CarB-CarA dimers form the carbamoyl phosphate synthetase holoenzyme that catalyzes the production of carbamoyl phosphate; CarB is responsible for the amidotransferase activity; carbamoyl phosphate synthase large subunit 2797832 carB 5713537 carB Dinoroseobacter shibae DFL 12 = DSM 16493 carbamoyl phosphate synthase large subunit YP_001533973.1 2794515 D 398580 CDS YP_001533974.1 159045180 5713538 complement(2797947..2798738) 1 NC_009952.1 hypothetical protein 2798738 5713538 Dshi_2640 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533974.1 2797947 R 398580 CDS YP_001533975.1 159045181 5713539 2798852..2799451 1 NC_009952.1 catalyzes the formation of thymidine 5'-phosphate from thymidine; thymidine kinase 2799451 tdk 5713539 tdk Dinoroseobacter shibae DFL 12 = DSM 16493 thymidine kinase YP_001533975.1 2798852 D 398580 CDS YP_001533976.1 159045182 5713540 complement(2799448..2800284) 1 NC_009952.1 hypothetical protein 2800284 5713540 Dshi_2642 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533976.1 2799448 R 398580 CDS YP_001533977.1 159045183 5713541 complement(2800367..2801317) 1 NC_009952.1 Swiss-Prot: P36234-Glycerate dehydrogenase; putative glycerate dehydrogenase 2801317 5713541 Dshi_2643 Dinoroseobacter shibae DFL 12 = DSM 16493 putative glycerate dehydrogenase YP_001533977.1 2800367 R 398580 CDS YP_001533978.1 159045184 5713542 complement(2801317..2801655) 1 NC_009952.1 Swiss-Prot: P37584-Protein csaA TIGRFAM: export-related chaperone CsaA PFAM: t-RNA-binding domain protein; putative export-like chaperone 2801655 5713542 Dshi_2644 Dinoroseobacter shibae DFL 12 = DSM 16493 putative export-like chaperone YP_001533978.1 2801317 R 398580 CDS YP_001533979.1 159045185 5713543 complement(2801659..2802480) 1 NC_009952.1 catalyzes the formation of L-proline from pyrroline-5-carboxylate; pyrroline-5-carboxylate reductase 2802480 proC 5713543 proC Dinoroseobacter shibae DFL 12 = DSM 16493 pyrroline-5-carboxylate reductase YP_001533979.1 2801659 R 398580 CDS YP_001533980.1 159045186 5713544 complement(2802512..2803042) 1 NC_009952.1 PFAM: Protein of unknown function DUF1790 COG5465: Uncharacterized conserved protein; hypothetical protein 2803042 5713544 Dshi_2646 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533980.1 2802512 R 398580 CDS YP_001533981.1 159045187 5713545 2803326..2804246 1 NC_009952.1 hypothetical protein 2804246 5713545 Dshi_2647 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533981.1 2803326 D 398580 CDS YP_001533982.1 159045188 5713546 complement(2804249..2804491) 1 NC_009952.1 PFAM: protein of unknown function DUF526 COG2960: Uncharacterized protein conserved in bacteria; hypothetical protein 2804491 5713546 Dshi_2648 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533982.1 2804249 R 398580 CDS YP_001533983.1 159045189 5713547 2804601..2805491 1 NC_009952.1 transfers the N-acyl diglyceride moiety to the prospective N-terminal cysteine in prolipoprotein; prolipoprotein diacylglyceryl transferase 2805491 lgt 5713547 lgt Dinoroseobacter shibae DFL 12 = DSM 16493 prolipoprotein diacylglyceryl transferase YP_001533983.1 2804601 D 398580 CDS YP_001533984.1 159045190 5713548 2805488..2806579 1 NC_009952.1 PFAM: protein of unknown function DUF185 COG1565: Uncharacterized conserved protein; hypothetical protein 2806579 5713548 Dshi_2650 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533984.1 2805488 D 398580 CDS YP_001533985.1 159045191 5713549 2806576..2807334 1 NC_009952.1 PFAM: protein of unknown function DUF152 TIGR00726: conserved hypothetical protein TIGR00726; hypothetical protein 2807334 5713549 Dshi_2651 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533985.1 2806576 D 398580 CDS YP_001533986.1 159045192 5713550 2807834..2808538 1 NC_009952.1 KEGG: sil:SPO0905 hypothetical protein; hypothetical protein 2808538 5713550 Dshi_2652 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533986.1 2807834 D 398580 CDS YP_001533987.1 159045193 5713551 complement(2808558..2809058) 1 NC_009952.1 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 2809058 5713551 Dshi_2653 Dinoroseobacter shibae DFL 12 = DSM 16493 putative leucine-responsive regulatory protein YP_001533987.1 2808558 R 398580 CDS YP_001533988.1 159045194 5713552 2809223..2810221 1 NC_009952.1 Swiss-Prot: P0A9P4-Thioredoxin reductase TIGRFAM: thioredoxin reductase PFAM: FAD-dependent pyridine nucleotide-disulphide oxidoreductase; glucose-inhibited division protein A; thioredoxin reductase 2810221 trxB 5713552 trxB Dinoroseobacter shibae DFL 12 = DSM 16493 thioredoxin reductase YP_001533988.1 2809223 D 398580 CDS YP_001533989.1 159045195 5713553 complement(2810268..2811320) 1 NC_009952.1 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 2811320 ccpA 5713553 ccpA Dinoroseobacter shibae DFL 12 = DSM 16493 cytochrome-c peroxidase YP_001533989.1 2810268 R 398580 CDS YP_001533990.1 159045196 5713554 2811577..2813652 1 NC_009952.1 in Rhizobium meliloti this protein is involved in the synthesis of nodulation factors that are active on the roots of alfalfa; catalyzes formation of activated sulfate intermediate; converts ATP and sulfate to diphosphate and adenylylsulfate and then ATP and adenylyl sulfate to ADP and 3'-phosphoadenylyl sulfate; the activated intermediate is transferred to the nodulation factors by NodH; may interact with NodP and NodQ; similar to the CysD and CysN proteins from Escherichia coli involved in cysteine biosynthesis; bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase 2813652 5713554 Dshi_2656 Dinoroseobacter shibae DFL 12 = DSM 16493 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase YP_001533990.1 2811577 D 398580 CDS YP_001533991.1 159045197 5713555 complement(2813746..2814336) 1 NC_009952.1 hypothetical protein 2814336 5713555 Dshi_2657 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533991.1 2813746 R 398580 CDS YP_001533992.1 159045198 5713556 complement(2814514..2815302) 1 NC_009952.1 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 2815302 5713556 Dshi_2658 Dinoroseobacter shibae DFL 12 = DSM 16493 putative carbon monoxide dehydrogenase YP_001533992.1 2814514 R 398580 CDS YP_001533993.1 159045199 5713557 complement(2815351..2817726) 1 NC_009952.1 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 2817726 coxL1 5713557 coxL1 Dinoroseobacter shibae DFL 12 = DSM 16493 carbon monoxide dehydrogenase YP_001533993.1 2815351 R 398580 CDS YP_001533994.1 159045200 5713558 complement(2817800..2818288) 1 NC_009952.1 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 2818288 5713558 Dshi_2660 Dinoroseobacter shibae DFL 12 = DSM 16493 putative carbon monoxide dehydrogenase YP_001533994.1 2817800 R 398580 CDS YP_001533995.1 159045201 5713559 complement(2818337..2818867) 1 NC_009952.1 PFAM: carbon monoxide dehydrogenase subunit G COG3427: Uncharacterized conserved protein; subunit G; putative carbon monoxide dehydrogenase 2818867 5713559 Dshi_2661 Dinoroseobacter shibae DFL 12 = DSM 16493 putative carbon monoxide dehydrogenase YP_001533995.1 2818337 R 398580 CDS YP_001533996.1 159045202 5713560 complement(2818944..2819846) 1 NC_009952.1 PFAM: Bacterial extracellular solute-binding proteins, family 3 SMART: extracellular solute-binding protein family; similar to extracellular solute-binding protein (family 3); hypothetical protein 2819846 5713560 Dshi_2662 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533996.1 2818944 R 398580 CDS YP_001533997.1 159045203 5713561 complement(2819920..2820594) 1 NC_009952.1 PS51007: CYTC SSF46626: Cytochrome_c KEGG: sil:SPO1515 cytochrome c550, putative; related to cytochrome c; hypothetical protein 2820594 5713561 Dshi_2663 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533997.1 2819920 R 398580 CDS YP_001533998.1 159045204 5713562 2820907..2822067 1 NC_009952.1 KEGG: sil:SPO1514 hypothetical protein; hypothetical protein 2822067 5713562 Dshi_2664 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533998.1 2820907 D 398580 CDS YP_001533999.1 159045205 5713563 2822130..2823107 1 NC_009952.1 TIGRFAM: 40-residue YVTN family beta-propeller repeat protein KEGG: sil:SPO1513 hypothetical protein; hypothetical protein 2823107 5713563 Dshi_2665 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001533999.1 2822130 D 398580 CDS YP_001534000.1 159045206 5713564 2823214..2823660 1 NC_009952.1 hypothetical protein 2823660 5713564 Dshi_2666 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534000.1 2823214 D 398580 CDS YP_001534001.1 159045207 5713565 2823667..2824386 1 NC_009952.1 Swiss-Prot: P0A9U1-Uncharacterized ABC transporter ATP-binding protein ybhF PFAM: ABC transporter related SMART: AAA ATPase; ATP-binding protein; ABC transporter 2824386 5713565 Dshi_2667 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC transporter YP_001534001.1 2823667 D 398580 CDS YP_001534002.1 159045208 5713566 2824868..2825659 1 NC_009952.1 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 2825659 5713566 Dshi_2668 Dinoroseobacter shibae DFL 12 = DSM 16493 putative ABC-2 type transporter YP_001534002.1 2824868 D 398580 CDS YP_001534003.1 159045209 5713567 2825706..2826251 1 NC_009952.1 hypothetical protein 2826251 5713567 Dshi_2669 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534003.1 2825706 D 398580 CDS YP_001534004.1 159045210 5713568 complement(2826191..2826901) 1 NC_009952.1 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 2826901 5713568 Dshi_2670 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC transporter YP_001534004.1 2826191 R 398580 CDS YP_001534005.1 159045211 5713569 complement(2826918..2827889) 1 NC_009952.1 SSF53850: Periplasmic binding protein-like II COG0715: ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components; similar to periplasmic binding protein; hypothetical protein 2827889 5713569 Dshi_2671 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534005.1 2826918 R 398580 CDS YP_001534006.1 159045212 5713570 2828064..2828483 1 NC_009952.1 PFAM: cytochrome c class I KEGG: sil:SPO1509 cytochrome c family protein; cytochrome c class I; hypothetical protein 2828483 5713570 Dshi_2672 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534006.1 2828064 D 398580 CDS YP_001534007.1 159045213 5713571 2828781..2830547 1 NC_009952.1 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 2830547 exaA 5713571 exaA Dinoroseobacter shibae DFL 12 = DSM 16493 quinoprotein ethanol dehydrogenase YP_001534007.1 2828781 D 398580 CDS YP_001534008.1 159045214 5713572 2830905..2831591 1 NC_009952.1 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 2831591 5713572 Dshi_2674 Dinoroseobacter shibae DFL 12 = DSM 16493 two component transcriptional regulator YP_001534008.1 2830905 D 398580 CDS YP_001534009.1 159045215 5713573 2831646..2832845 1 NC_009952.1 PFAM: domain of unknown function DUF1745 COG3287- Uncharacterized conserved protein; hypothetical protein 2832845 5713573 Dshi_2675 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534009.1 2831646 D 398580 CDS YP_001534010.1 159045216 5713574 2832817..2834847 1 NC_009952.1 PFAM: response regulator receiver; ATP-binding region ATPase domain protein; histidine kinase A domain protein; histidine kinase 2834847 5713574 Dshi_2676 Dinoroseobacter shibae DFL 12 = DSM 16493 histidine kinase YP_001534010.1 2832817 D 398580 CDS YP_001534011.1 159045217 5713575 complement(2834844..2835545) 1 NC_009952.1 PFAM: lipolytic protein G-D-S-L family; G-D-S-L family; lipolytic protein 2835545 5713575 Dshi_2677 Dinoroseobacter shibae DFL 12 = DSM 16493 lipolytic protein YP_001534011.1 2834844 R 398580 CDS YP_001534012.1 159045218 5713576 2835568..2836272 1 NC_009952.1 Swiss-Prot: P0A9T8-Uncharacterized ABC transporter ATP-binding protein ybbA PFAM: ABC transporter related SMART: AAA ATPase; ATP-binding protein; ABC transporter 2836272 5713576 Dshi_2678 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC transporter YP_001534012.1 2835568 D 398580 CDS YP_001534013.1 159045219 5713577 2836269..2838797 1 NC_009952.1 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 2838797 5713577 Dshi_2679 Dinoroseobacter shibae DFL 12 = DSM 16493 putative ABC transporter permease YP_001534013.1 2836269 D 398580 CDS YP_001534014.1 159045220 5713578 complement(2839208..2842072) 1 NC_009952.1 acts in conjunction with GvcH to form H-protein-S-aminomethyldihydrolipoyllysine from glycine; glycine dehydrogenase 2842072 gcvP 5713578 gcvP Dinoroseobacter shibae DFL 12 = DSM 16493 glycine dehydrogenase YP_001534014.1 2839208 R 398580 CDS YP_001534015.1 159045221 5713579 complement(2842164..2842532) 1 NC_009952.1 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 2842532 gcvH 5713579 gcvH Dinoroseobacter shibae DFL 12 = DSM 16493 glycine cleavage system protein H YP_001534015.1 2842164 R 398580 CDS YP_001534016.1 159045222 5713580 complement(2842546..2843631) 1 NC_009952.1 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 2843631 gcvT2 5713580 gcvT2 Dinoroseobacter shibae DFL 12 = DSM 16493 aminomethyltransferase, glycine cleavage system T protein YP_001534016.1 2842546 R 398580 CDS YP_001534017.1 159045223 5713581 2843824..2844828 1 NC_009952.1 Swiss-Prot: P05149-aldose 1-epimerase [Precursor] PFAM: Aldose 1-epimerase; aldose 1-epimerase 2844828 mro 5713581 mro Dinoroseobacter shibae DFL 12 = DSM 16493 aldose 1-epimerase YP_001534017.1 2843824 D 398580 CDS YP_001534018.1 159045224 5713582 complement(2844910..2845275) 1 NC_009952.1 Swiss-Prot: Q92UG5-Putative transthyretin-like protein RB1166 TIGRFAM: Hydroxyisourate hydrolase PFAM: Transthyretin; putative transthyretin-like protein 2845275 5713582 Dshi_2684 Dinoroseobacter shibae DFL 12 = DSM 16493 putative transthyretin-like protein YP_001534018.1 2844910 R 398580 CDS YP_001534019.1 159045225 5713583 complement(2845670..2846659) 1 NC_009952.1 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 2846659 gap3 5713583 gap3 Dinoroseobacter shibae DFL 12 = DSM 16493 glyceraldehyde-3-phosphate dehydrogenase YP_001534019.1 2845670 R 398580 CDS YP_001534020.1 159045226 5713584 2846962..2847378 1 NC_009952.1 Swiss-Prot: P37903-Universal stress protein F PFAM: UspA domain protein KEGG: sit:TM1040_2126 UspA; universal stress protein 2847378 5713584 Dshi_2686 Dinoroseobacter shibae DFL 12 = DSM 16493 universal stress protein YP_001534020.1 2846962 D 398580 CDS YP_001534021.1 159045227 5713585 2847605..2848090 1 NC_009952.1 Swiss-Prot: P19567-Pseudoazurin [Precursor] TIGR02375# pseudoazurin; putative pseudoazurin 2848090 5713585 Dshi_2687 Dinoroseobacter shibae DFL 12 = DSM 16493 putative pseudoazurin YP_001534021.1 2847605 D 398580 CDS YP_001534022.1 159045228 5713586 2848368..2849762 1 NC_009952.1 Swiss-Prot: P26459-Cytochrome bd-II oxidase subunit 1 PFAM: cytochrome bd ubiquinol oxidase subunit I; cytochrome bd-II oxidase subunit 1 2849762 appC 5713586 appC Dinoroseobacter shibae DFL 12 = DSM 16493 cytochrome bd-II oxidase subunit 1 YP_001534022.1 2848368 D 398580 CDS YP_001534023.1 159045229 5713587 2849767..2850780 1 NC_009952.1 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 2850780 cydB 5713587 cydB Dinoroseobacter shibae DFL 12 = DSM 16493 cytochrome bd-I oxidase subunit II YP_001534023.1 2849767 D 398580 CDS YP_001534024.1 159045230 5713588 complement(2850801..2851355) 1 NC_009952.1 KEGG: jan:Jann_3427 hypothetical protein; hypothetical protein 2851355 5713588 Dshi_2690 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534024.1 2850801 R 398580 CDS YP_001534025.1 159045231 5713589 2851499..2852269 1 NC_009952.1 Swiss-Prot: P0AC84-Probable hydroxyacylglutathione hydrolase ( Glyoxalase II) PFAM: beta-lactamase domain protein KEGG: mlo:mlr3546 putative glyoxalase II; putative hydroxyacylglutathione hydrolase 2852269 5713589 Dshi_2691 Dinoroseobacter shibae DFL 12 = DSM 16493 putative hydroxyacylglutathione hydrolase YP_001534025.1 2851499 D 398580 CDS YP_001534026.1 159045232 5713590 complement(2852282..2853010) 1 NC_009952.1 PFAM: protein of unknown function DUF1194; hypothetical protein 2853010 5713590 Dshi_2692 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534026.1 2852282 R 398580 CDS YP_001534027.1 159045233 5713591 complement(2853046..2853459) 1 NC_009952.1 PFAM: protein of unknown function DUF606 COG3238: Uncharacterized protein conserved in bacteria; hypothetical protein 2853459 5713591 Dshi_2693 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534027.1 2853046 R 398580 CDS YP_001534028.1 159045234 5713592 2853623..2854024 1 NC_009952.1 SSF46626: Cytochrome c superfamily PS51007: CYTC (Cytochrome c family profile); putative cytochrome c family protein 2854024 5713592 Dshi_2694 Dinoroseobacter shibae DFL 12 = DSM 16493 putative cytochrome c family protein YP_001534028.1 2853623 D 398580 CDS YP_001534029.1 159045235 5713594 2854595..2855953 1 NC_009952.1 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 2855953 5713594 Dshi_2695 Dinoroseobacter shibae DFL 12 = DSM 16493 putative aliphatic amidase expression-regulating protein YP_001534029.1 2854595 D 398580 CDS YP_001534030.1 159045236 5713595 2856015..2857679 1 NC_009952.1 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 2857679 5713595 Dshi_2696 Dinoroseobacter shibae DFL 12 = DSM 16493 inner-membrane translocator YP_001534030.1 2856015 D 398580 CDS YP_001534031.1 159045237 5713596 2857981..2859084 1 NC_009952.1 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 2859084 5713596 Dshi_2697 Dinoroseobacter shibae DFL 12 = DSM 16493 putative high-affinity branched-chain amino acid transport system YP_001534031.1 2857981 D 398580 CDS YP_001534032.1 159045238 5713597 2859081..2859818 1 NC_009952.1 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 2859818 5713597 Dshi_2698 Dinoroseobacter shibae DFL 12 = DSM 16493 putative high-affinity branched-chain amino acid transport ATP-binding protein YP_001534032.1 2859081 D 398580 CDS YP_001534033.1 159045239 5713598 2859820..2860515 1 NC_009952.1 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 2860515 5713598 Dshi_2699 Dinoroseobacter shibae DFL 12 = DSM 16493 putative high-affinity branched-chain amino acid transport ATP-binding protein YP_001534033.1 2859820 D 398580 CDS YP_001534034.1 159045240 5713599 2860992..2861681 1 NC_009952.1 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 2861681 dhlB 5713599 dhlB Dinoroseobacter shibae DFL 12 = DSM 16493 (S)-2-haloacid dehalogenase YP_001534034.1 2860992 D 398580 CDS YP_001534035.1 159045241 5713600 2861681..2862505 1 NC_009952.1 PFAM: alpha/beta hydrolase fold KEGG: rsh:Rsph17029_0927 alpha/beta hydrolase fold; alpha/beta hydrolase superfamily; putative hydrolase / acyltransferase 2862505 5713600 Dshi_2701 Dinoroseobacter shibae DFL 12 = DSM 16493 putative hydrolase / acyltransferase YP_001534035.1 2861681 D 398580 CDS YP_001534036.1 159045242 5713601 2862502..2863494 1 NC_009952.1 Swiss-Prot: P0AGF6-Threonine dehydratase catabolic tdcB PFAM: Pyridoxal-5-phosphate-dependent protein beta subunit; catabolic; putative threonine dehydratase 2863494 5713601 Dshi_2702 Dinoroseobacter shibae DFL 12 = DSM 16493 putative threonine dehydratase YP_001534036.1 2862502 D 398580 CDS YP_001534037.1 159045243 5713602 complement(2863568..2863975) 1 NC_009952.1 KEGG: rde:RD1_0908 hypothetical protein; hypothetical protein 2863975 5713602 Dshi_2703 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534037.1 2863568 R 398580 CDS YP_001534038.1 159045244 5713603 complement(2864136..2865179) 1 NC_009952.1 transformation of porphobilinogen to hydroxymethylbilane in porphyrin biosynthesis; porphobilinogen deaminase 2865179 hemC 5713603 hemC Dinoroseobacter shibae DFL 12 = DSM 16493 porphobilinogen deaminase YP_001534038.1 2864136 R 398580 CDS YP_001534039.1 159045245 5713604 2865197..2866231 1 NC_009952.1 catalyzes the formation of coproporphyrinogen from uroporphyrinogen III; uroporphyrinogen decarboxylase 2866231 hemE 5713604 hemE Dinoroseobacter shibae DFL 12 = DSM 16493 uroporphyrinogen decarboxylase YP_001534039.1 2865197 D 398580 CDS YP_001534040.1 159045246 5713605 2866405..2867619 1 NC_009952.1 Swiss-Prot: P21503-Uncharacterized MFS-type transporter ycaD PFAM: major facilitator superfamily MFS_1; putative major facilitator superfamily transporter 2867619 5713605 Dshi_2706 Dinoroseobacter shibae DFL 12 = DSM 16493 putative major facilitator superfamily transporter YP_001534040.1 2866405 D 398580 CDS YP_001534041.1 159045247 5713606 2867674..2869392 1 NC_009952.1 methionine--tRNA ligase; MetRS; adds methionine to tRNA(Met) with cleavage of ATP to AMP and diphosphate; some MetRS enzymes form dimers depending on a C-terminal domain that is also found in other proteins such as Trbp111 in Aquifex aeolicus and the cold-shock protein CsaA from Bacillus subtilis while others do not; four subfamilies exist based on sequence motifs and zinc content; methionyl-tRNA synthetase 2869392 metG 5713606 metG Dinoroseobacter shibae DFL 12 = DSM 16493 methionyl-tRNA synthetase YP_001534041.1 2867674 D 398580 CDS YP_001534042.1 159045248 5713607 2869501..2871093 1 NC_009952.1 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 2871093 5713607 Dshi_2708 Dinoroseobacter shibae DFL 12 = DSM 16493 sensor hybrid histidine kinase YP_001534042.1 2869501 D 398580 CDS YP_001534043.1 159045249 5713608 complement(2871102..2871578) 1 NC_009952.1 Swiss-Prot: Q92RA4-Peptide methionine sulfoxide reductase msrB 1 TIGRFAM: methionine-R-sulfoxide reductase PFAM: Methionine sulfoxide reductase B; peptide methionine sulfoxide reductase 2871578 msrB1 5713608 msrB1 Dinoroseobacter shibae DFL 12 = DSM 16493 peptide methionine sulfoxide reductase YP_001534043.1 2871102 R 398580 CDS YP_001534044.1 159045250 5713609 2871715..2872920 1 NC_009952.1 PFAM: HI0933 family protein; FAD dependent oxidoreductase TIGR00275: conserved hypothetical protein SSF51905: FAD/NAD(P)-binding domain superfamily; hypothetical protein 2872920 5713609 Dshi_2710 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534044.1 2871715 D 398580 CDS YP_001534045.1 159045251 5713610 2873040..2874023 1 NC_009952.1 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 2874023 cobS2 5713610 cobS2 Dinoroseobacter shibae DFL 12 = DSM 16493 aerobic cobaltochelatase subunit cobS YP_001534045.1 2873040 D 398580 CDS YP_001534046.1 159045252 5713611 complement(2874084..2874764) 1 NC_009952.1 Swiss-Prot: Q05197-Phosphatidylethanolamine N-methyltransferase [predicted] PFAM: UbiE/COQ5 methyltransferase; Methyltransferase type 11; Methyltransferase type 12; putative phosphatidylethanolamine N-methyltransferase 2874764 5713611 Dshi_2712 Dinoroseobacter shibae DFL 12 = DSM 16493 putative phosphatidylethanolamine N-methyltransferase YP_001534046.1 2874084 R 398580 CDS YP_001534047.1 159045253 5713612 complement(2874781..2875530) 1 NC_009952.1 Swiss-Prot: Q9ZBM2- CDP-diacylglycerol--serine O-phosphatidyltransferase TIGRFAM: CDP-diacylglycerol--serine O-phosphatidyltransferase PFAM: CDP-alcohol phosphatidyltransferase; putative CDP-diacylglycerol--serine O-phosphatidyltransferase 2875530 5713612 Dshi_2713 Dinoroseobacter shibae DFL 12 = DSM 16493 putative CDP-diacylglycerol--serine O-phosphatidyltransferase YP_001534047.1 2874781 R 398580 CDS YP_001534048.1 159045254 5713613 complement(2875527..2876204) 1 NC_009952.1 catalyzes the decarboxylaton of phospatidyl-L-sering to phosphatidylethanolamine; phosphatidylserine decarboxylase 2876204 psd 5713613 psd Dinoroseobacter shibae DFL 12 = DSM 16493 phosphatidylserine decarboxylase YP_001534048.1 2875527 R 398580 CDS YP_001534049.1 159045255 5713614 2876659..2877963 1 NC_009952.1 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 2877963 5713614 Dshi_2715 Dinoroseobacter shibae DFL 12 = DSM 16493 putative ATP-dependent RNA helicase YP_001534049.1 2876659 D 398580 CDS YP_001534050.1 159045256 5713615 complement(2878109..2878555) 1 NC_009952.1 hypothetical protein 2878555 5713615 Dshi_2716 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534050.1 2878109 R 398580 CDS YP_001534051.1 159045257 5713616 2878689..2879210 1 NC_009952.1 hypothetical protein 2879210 5713616 Dshi_2717 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534051.1 2878689 D 398580 CDS YP_001534052.1 159045258 5713617 2879224..2879460 1 NC_009952.1 SMART: Helix-turn-helix XRE-family like proteins; XRE family; putative transcriptional regulator 2879460 5713617 Dshi_2718 Dinoroseobacter shibae DFL 12 = DSM 16493 putative transcriptional regulator YP_001534052.1 2879224 D 398580 CDS YP_001534053.1 159045259 5713618 2879516..2881390 1 NC_009952.1 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 2881390 cobT1 5713618 cobT1 Dinoroseobacter shibae DFL 12 = DSM 16493 aerobic cobaltochelatase subunit cobT YP_001534053.1 2879516 D 398580 CDS YP_001534054.1 159045260 5713619 2881448..2882575 1 NC_009952.1 PFAM: Endonuclease/exonuclease/phosphatase; putative endonuclease/exonuclease/phosphatase 2882575 5713619 Dshi_2720 Dinoroseobacter shibae DFL 12 = DSM 16493 putative endonuclease/exonuclease/phosphatase YP_001534054.1 2881448 D 398580 CDS YP_001534055.1 159045261 5713620 2882651..2884507 1 NC_009952.1 PFAM: creatinase; peptidase M24; putative metallopeptidase 2884507 5713620 Dshi_2721 Dinoroseobacter shibae DFL 12 = DSM 16493 putative metallopeptidase YP_001534055.1 2882651 D 398580 CDS YP_001534056.1 159045262 5713621 2884592..2884933 1 NC_009952.1 PFAM: protein of unknown function DUF427 COG2343: Uncharacterized protein conserved in bacteria; hypothetical protein 2884933 5713621 Dshi_2722 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534056.1 2884592 D 398580 CDS YP_001534057.1 159045263 5713622 complement(2885147..2885776) 1 NC_009952.1 TIGR00997: intracellular septation protein A PFAM: Intracellular septation protein A; intracellular septation protein A 2885776 5713622 Dshi_2723 Dinoroseobacter shibae DFL 12 = DSM 16493 intracellular septation protein A YP_001534057.1 2885147 R 398580 CDS YP_001534058.1 159045264 5713623 complement(2885773..2886675) 1 NC_009952.1 PFAM: protein of unknown function DUF6 transmembrane; hypothetical protein 2886675 5713623 Dshi_2724 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534058.1 2885773 R 398580 CDS YP_001534059.1 159045265 5713624 complement(2886699..2888198) 1 NC_009952.1 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 2888198 5713624 Dshi_2725 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534059.1 2886699 R 398580 CDS YP_001534060.1 159045266 5713625 2888326..2888730 1 NC_009952.1 hypothetical protein 2888730 5713625 Dshi_2726 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534060.1 2888326 D 398580 CDS YP_001534061.1 159045267 5713626 complement(2888799..2890370) 1 NC_009952.1 Swiss-Prot: Q1GF88-Exodeoxyribonuclease 7 large subunit; exodeoxyribonuclease 7 large subunit 2890370 xseA 5713626 xseA Dinoroseobacter shibae DFL 12 = DSM 16493 exodeoxyribonuclease 7 large subunit YP_001534061.1 2888799 R 398580 CDS YP_001534062.1 159045268 5713627 2890448..2891710 1 NC_009952.1 catalyzes the formation of N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-D-ribosylamine and glycine in purine biosynthesis; phosphoribosylamine--glycine ligase 2891710 purD 5713627 purD Dinoroseobacter shibae DFL 12 = DSM 16493 phosphoribosylamine--glycine ligase YP_001534062.1 2890448 D 398580 CDS YP_001534063.1 159045269 5713628 2891789..2892655 1 NC_009952.1 PFAM: Ion transport 2 domain protein; putative ion transport protein 2892655 5713628 Dshi_2729 Dinoroseobacter shibae DFL 12 = DSM 16493 putative ion transport protein YP_001534063.1 2891789 D 398580 CDS YP_001534064.1 159045270 5713629 complement(2892698..2893456) 1 NC_009952.1 hypothetical protein 2893456 5713629 Dshi_2730 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534064.1 2892698 R 398580 CDS YP_001534065.1 159045271 5713630 complement(2893456..2893779) 1 NC_009952.1 Swiss-Prot: P80306-Ferredoxin-6 PFAM: ferredoxin; ferredoxin 2893779 5713630 Dshi_2731 Dinoroseobacter shibae DFL 12 = DSM 16493 ferredoxin YP_001534065.1 2893456 R 398580 CDS YP_001534066.1 159045272 5713631 2893851..2894264 1 NC_009952.1 PFAM: nucleic acid binding OB-fold tRNA/helicase-type COG0587: DNA polymerase III, alpha subunit; associated with nucleic acid binding; hypothetical protein 2894264 5713631 Dshi_2732 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534066.1 2893851 D 398580 CDS YP_001534067.1 159045273 5713632 complement(2894377..2895882) 1 NC_009952.1 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 2895882 degP 5713632 degP Dinoroseobacter shibae DFL 12 = DSM 16493 protease do YP_001534067.1 2894377 R 398580 CDS YP_001534068.1 159045274 5713633 complement(2896047..2896241) 1 NC_009952.1 hypothetical protein 2896241 5713633 Dshi_2734 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534068.1 2896047 R 398580 CDS YP_001534069.1 159045275 5713634 complement(2896241..2897134) 1 NC_009952.1 Swiss-Prot: P0ABC3-Protein hflC TIGRFAM: HflC protein PFAM: band 7 protein; colocated with hflK; protein hflC 2897134 hflC 5713634 hflC Dinoroseobacter shibae DFL 12 = DSM 16493 protein hflC YP_001534069.1 2896241 R 398580 CDS YP_001534070.1 159045276 5713635 complement(2897134..2898282) 1 NC_009952.1 Swiss-Prot: P0ABC7-Protein hflK TIGRFAM: HflK protein; colocated with hflC; Protein HflK 2898282 hflK 5713635 hflK Dinoroseobacter shibae DFL 12 = DSM 16493 Protein HflK YP_001534070.1 2897134 R 398580 CDS YP_001534071.1 159045277 5713636 complement(2898349..2899800) 1 NC_009952.1 Swiss-Prot: P06715-Glutathione reductase PFAM: FAD-dependent pyridine nucleotide-disulphide oxidoreductase; pyridine nucleotide-disulphide oxidoreductase dimerisation region; glutathione reductase 2899800 gor 5713636 gor Dinoroseobacter shibae DFL 12 = DSM 16493 glutathione reductase YP_001534071.1 2898349 R 398580 CDS YP_001534072.1 159045278 5713637 complement(2899846..2900628) 1 NC_009952.1 Catalyzes D-ribose 5-phosphate --> D-ribulose 5-phosphate in the nonoxidative branch of the pentose phosphate pathway; ribose-5-phosphate isomerase A 2900628 rpiA 5713637 rpiA Dinoroseobacter shibae DFL 12 = DSM 16493 ribose-5-phosphate isomerase A YP_001534072.1 2899846 R 398580 CDS YP_001534073.1 159045279 5713638 complement(2900734..2901423) 1 NC_009952.1 TIGRFAM: thiamine pyrophosphokinase PFAM: Thiamin pyrophosphokinase catalytic region; putative thiamine pyrophosphokinase 2901423 5713638 Dshi_2739 Dinoroseobacter shibae DFL 12 = DSM 16493 putative thiamine pyrophosphokinase YP_001534073.1 2900734 R 398580 CDS YP_001534074.1 159045280 5713639 2901566..2903512 1 NC_009952.1 PFAM: herpesvirus transcription activation factor; related to transactivator; hypothetical protein 2903512 5713639 Dshi_2740 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534074.1 2901566 D 398580 CDS YP_001534075.1 159045281 5713640 complement(2903555..2903791) 1 NC_009952.1 Swiss-Prot: P45566-Uncharacterized protein yhdT; hypothetical protein 2903791 5713640 Dshi_2741 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534075.1 2903555 R 398580 CDS YP_001534076.1 159045282 5713641 complement(2903816..2905111) 1 NC_009952.1 catalyzes the formation of N6-(1,2,-dicarboxyethyl)-AMP from L-aspartate, inosine monophosphate and GTP in AMP biosynthesis; adenylosuccinate synthetase 2905111 purA 5713641 purA Dinoroseobacter shibae DFL 12 = DSM 16493 adenylosuccinate synthetase YP_001534076.1 2903816 R 398580 CDS YP_001534077.1 159045283 5713642 2905312..2905680 1 NC_009952.1 TIGRFAM: preprotein translocase, SecG subunit PFAM: Preprotein translocase SecG subunit; SecG subunit; preprotein translocase subunit SecG 2905680 secG 5713642 secG Dinoroseobacter shibae DFL 12 = DSM 16493 preprotein translocase subunit SecG YP_001534077.1 2905312 D 398580 CDS YP_001534078.1 159045284 5713643 2905872..2907515 1 NC_009952.1 CTP synthase; cytidine triphosphate synthetase; catalyzes the ATP-dependent amination of UTP to CTP with either L-glutamine or ammonia as the source of nitrogen; in Escherichia coli this enzyme forms a homotetramer; CTP synthetase 2907515 pyrG 5713643 pyrG Dinoroseobacter shibae DFL 12 = DSM 16493 CTP synthetase YP_001534078.1 2905872 D 398580 CDS YP_001534079.1 159045285 5713644 2907576..2908436 1 NC_009952.1 Swiss-Prot: P37757-Uncharacterized isomerase yddE TIGRFAM: phenazine biosynthesis protein PhzF family PFAM: Phenazine biosynthesis PhzC/PhzF protein; isomerase 2908436 5713644 Dshi_2745 Dinoroseobacter shibae DFL 12 = DSM 16493 isomerase YP_001534079.1 2907576 D 398580 CDS YP_001534080.1 159045286 5713645 complement(2908468..2908728) 1 NC_009952.1 KEGG: rde:RD1_1231 hypothetical protein; hypothetical protein 2908728 5713645 Dshi_2746 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534080.1 2908468 R 398580 CDS YP_001534081.1 159045287 5713646 2908850..2909440 1 NC_009952.1 KEGG: sil:SPO0431 hypothetical protein; hypothetical protein 2909440 5713646 Dshi_2747 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534081.1 2908850 D 398580 CDS YP_001534082.1 159045288 5713647 complement(2909448..2910770) 1 NC_009952.1 Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation; glutamyl-tRNA synthetase 2910770 gltX 5713647 gltX Dinoroseobacter shibae DFL 12 = DSM 16493 glutamyl-tRNA synthetase YP_001534082.1 2909448 R 398580 CDS YP_001534083.1 159045289 5713648 complement(2910830..2912143) 1 NC_009952.1 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 2912143 5713648 Dshi_2749 Dinoroseobacter shibae DFL 12 = DSM 16493 putative cytochrome c peroxidase YP_001534083.1 2910830 R 398580 CDS YP_001534084.1 159045290 5713649 2912622..2913089 1 NC_009952.1 hypothetical protein 2913089 5713649 Dshi_2750 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534084.1 2912622 D 398580 CDS YP_001534085.1 159045291 5713650 complement(2913448..2913789) 1 NC_009952.1 hypothetical protein 2913789 5713650 Dshi_2751 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534085.1 2913448 R 398580 CDS YP_001534086.1 159045292 5713651 complement(2913824..2914882) 1 NC_009952.1 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 2914882 5713651 Dshi_2752 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP dicarboxylate transporter YP_001534086.1 2913824 R 398580 CDS YP_001534087.1 159045293 5713652 complement(2914929..2916218) 1 NC_009952.1 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 2916218 5713652 Dshi_2753 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP dicarboxylate transporter YP_001534087.1 2914929 R 398580 CDS YP_001534088.1 159045294 5713653 complement(2916220..2916810) 1 NC_009952.1 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 2916810 5713653 Dshi_2754 Dinoroseobacter shibae DFL 12 = DSM 16493 tripartite ATP-independent periplasmic transporter YP_001534088.1 2916220 R 398580 CDS YP_001534089.1 159045295 5713654 complement(2916877..2917410) 1 NC_009952.1 Swiss-Prot: P54990-Nitrilotriacetate monooxygenase component B PFAM: flavin reductase domain protein FMN-binding; FMN-binding; flavin reductase domain-containing protein 2917410 5713654 Dshi_2755 Dinoroseobacter shibae DFL 12 = DSM 16493 flavin reductase domain-containing protein YP_001534089.1 2916877 R 398580 CDS YP_001534090.1 159045296 5713655 complement(2917412..2918302) 1 NC_009952.1 Swiss-Prot: P42972-Uncharacterized oxidoreductase ycsN PFAM: aldo/keto reductase COG4989: Predicted oxidoreductase; aldo/keto reductase 2918302 5713655 Dshi_2756 Dinoroseobacter shibae DFL 12 = DSM 16493 aldo/keto reductase YP_001534090.1 2917412 R 398580 CDS YP_001534091.1 159045297 5713656 complement(2918302..2919456) 1 NC_009952.1 Swiss-Prot: P80645-Alkanesulfonate monooxygenase PFAM: luciferase family protein; alkanesulfonate monooxygenase 2919456 ssuD 5713656 ssuD Dinoroseobacter shibae DFL 12 = DSM 16493 alkanesulfonate monooxygenase YP_001534091.1 2918302 R 398580 CDS YP_001534092.1 159045298 5713657 2919558..2920268 1 NC_009952.1 PFAM: regulatory protein GntR HTH; UbiC transcription regulator-associated domain protein; GntR family; transcriptional regulator 2920268 5713657 Dshi_2758 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001534092.1 2919558 D 398580 CDS YP_001534093.1 159045299 5713658 2920265..2921386 1 NC_009952.1 Swiss-Prot: O05389-Putative oxidoreductase yrbE PFAM: oxidoreductase domain protein; Oxidoreductase domain COG0673: Predicted dehydrogenases and related proteins; putative oxidoreductase 2921386 5713658 Dshi_2759 Dinoroseobacter shibae DFL 12 = DSM 16493 putative oxidoreductase YP_001534093.1 2920265 D 398580 CDS YP_001534094.1 159045300 5713659 complement(2921376..2922041) 1 NC_009952.1 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 2922041 5713659 Dshi_2760 Dinoroseobacter shibae DFL 12 = DSM 16493 putative phosphoglycolate phosphatase YP_001534094.1 2921376 R 398580 CDS YP_001534095.1 159045301 5713660 complement(2922178..2923956) 1 NC_009952.1 Swiss-Prot: P0AFU2-Uncharacterized transporter yfbS PFAM: Citrate transporter; TrkA-C domain protein; transporter 2923956 5713660 Dshi_2761 Dinoroseobacter shibae DFL 12 = DSM 16493 transporter YP_001534095.1 2922178 R 398580 CDS YP_001534096.1 159045302 5713661 2924076..2924816 1 NC_009952.1 Swiss-Prot: P0A8A0-UPF0082 protein yebC TIGR01033 conserved hypothetical protein COG0217: Uncharacterized conserved protein; hypothetical protein 2924816 5713661 Dshi_2762 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534096.1 2924076 D 398580 CDS YP_001534097.1 159045303 5713662 complement(2924884..2926548) 1 NC_009952.1 Swiss-Prot: P09983-Hemolysin, chromosomal PFAM: Hemolysin-type calcium-binding region; related to hemolysin; hypothetical protein 2926548 5713662 Dshi_2763 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534097.1 2924884 R 398580 CDS YP_001534098.1 159045304 5713663 complement(2926666..2927010) 1 NC_009952.1 hypothetical protein 2927010 5713663 Dshi_2764 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534098.1 2926666 R 398580 CDS YP_001534099.1 159045305 5713664 complement(2927040..2927444) 1 NC_009952.1 hypothetical protein 2927444 5713664 Dshi_2765 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534099.1 2927040 R 398580 CDS YP_001534100.1 159045306 5713665 complement(2927535..2929334) 1 NC_009952.1 Swiss-Prot: P72958-Uncharacterized transporter sll0640 PFAM: Citrate transporter; TrkA-C domain protein; TRAP C4-dicarboxylate transport system permease DctM subunit; transporter 2929334 5713665 Dshi_2766 Dinoroseobacter shibae DFL 12 = DSM 16493 transporter YP_001534100.1 2927535 R 398580 CDS YP_001534101.1 159045307 5713666 complement(2929331..2930296) 1 NC_009952.1 PFAM: protein of unknown function DUF6 transmembrane; hypothetical protein 2930296 5713666 Dshi_2767 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534101.1 2929331 R 398580 CDS YP_001534102.1 159045308 5713667 complement(2930293..2931126) 1 NC_009952.1 Swiss-Prot: P75429-Uncharacterized protein MG246 homolog TIGR00282# conserved hypothetical protein COG1692: Uncharacterized protein conserved in bacteria; hypothetical protein 2931126 5713667 Dshi_2768 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534102.1 2930293 R 398580 CDS YP_001534103.1 159045309 5713668 complement(2931169..2931762) 1 NC_009952.1 Swiss-Prot: P0AC28-Uncharacterized protein ygfA PFAM: 5-formyltetrahydrofolate cyclo-ligase TIGR02727: 5,10-methenyltetrahydrofolate synthetase; related to 5-formyltetrahydrofolate cyclo-ligase; hypothetical protein 2931762 5713668 Dshi_2769 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534103.1 2931169 R 398580 CDS YP_001534104.1 159045310 5713669 complement(2931759..2933141) 1 NC_009952.1 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 2933141 5713669 Dshi_2770 Dinoroseobacter shibae DFL 12 = DSM 16493 putative magnesium transporter YP_001534104.1 2931759 R 398580 CDS YP_001534105.1 159045311 5713670 2933279..2934565 1 NC_009952.1 Catalyzes the deamination of guanine; guanine deaminase 2934565 guaD 5713670 guaD Dinoroseobacter shibae DFL 12 = DSM 16493 guanine deaminase YP_001534105.1 2933279 D 398580 CDS YP_001534106.1 159045312 5713671 complement(2934712..2935170) 1 NC_009952.1 Swiss-Prot: PFAM: SCP-like extracellular COG2340: Uncharacterized protein with SCP/PR1 domains; related to SCP-like extracellular protein; hypothetical protein 2935170 5713671 Dshi_2772 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534106.1 2934712 R 398580 CDS YP_001534107.1 159045313 5713672 complement(2935167..2936507) 1 NC_009952.1 catalyzes the transformation of hydroxyatrazine to N-isopropylammelide and ethylamine in the atrazine degradation pathway.; hydroxydechloroatrazine ethylaminohydrolase 2936507 5713672 Dshi_2773 Dinoroseobacter shibae DFL 12 = DSM 16493 hydroxydechloroatrazine ethylaminohydrolase YP_001534107.1 2935167 R 398580 CDS YP_001534108.1 159045314 5713673 complement(2936504..2937325) 1 NC_009952.1 Swiss-Prot: P0ADG4-Inositol-1-monophosphatase suhB TIGRFAM: histidinol-phosphate phosphatase, putative PFAM: inositol monophosphatase; putative inositol-1-monophosphatase 2937325 5713673 Dshi_2774 Dinoroseobacter shibae DFL 12 = DSM 16493 putative inositol-1-monophosphatase YP_001534108.1 2936504 R 398580 CDS YP_001534109.1 159045315 5713674 complement(2937384..2937755) 1 NC_009952.1 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 2937755 5713674 Dshi_2775 Dinoroseobacter shibae DFL 12 = DSM 16493 putative transcriptional regulator YP_001534109.1 2937384 R 398580 CDS YP_001534110.1 159045316 5713675 2938108..2939067 1 NC_009952.1 Swiss-Prot: P12311-Alcohol dehydrogenase PFAM: Alcohol dehydrogenase zinc-binding domain protein; Alcohol dehydrogenase GroES domain protein; putative alcohol dehydrogenase 2939067 5713675 Dshi_2776 Dinoroseobacter shibae DFL 12 = DSM 16493 putative alcohol dehydrogenase YP_001534110.1 2938108 D 398580 CDS YP_001534111.1 159045317 5713676 complement(2939244..2940098) 1 NC_009952.1 Swiss-Prot:P36771-Probable HTH-type transcriptional regulator lrhA PFAM: regulatory protein LysR; LysR substrate-binding; LysR family; putative transcriptional regulator 2940098 5713676 Dshi_2777 Dinoroseobacter shibae DFL 12 = DSM 16493 putative transcriptional regulator YP_001534111.1 2939244 R 398580 CDS YP_001534112.1 159045318 5713677 2940224..2940442 1 NC_009952.1 hypothetical protein 2940442 5713677 Dshi_2778 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534112.1 2940224 D 398580 CDS YP_001534113.1 159045319 5713678 2940622..2941344 1 NC_009952.1 Swiss-Prot: P0AAC4-Inner membrane protein ybhL PFAM: protein of unknown function UPF0005; hypothetical protein 2941344 5713678 Dshi_2779 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534113.1 2940622 D 398580 CDS YP_001534114.1 159045320 5713679 complement(2941414..2941887) 1 NC_009952.1 hypothetical protein 2941887 5713679 Dshi_2780 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534114.1 2941414 R 398580 CDS YP_001534115.1 159045321 5713680 complement(2942214..2942381) 1 NC_009952.1 in Escherichia coli BM108, a mutation that results in lack of L33 synthesis had no effect on ribosome synthesis or function; there are paralogous genes in several bacterial genomes, and a CXXC motif for zinc binding and an upstream regulation region of the paralog lacking this motif that are regulated by zinc similar to other ribosomal proteins like L31; the proteins in this group lack the CXXC motif; 50S ribosomal protein L33 2942381 rpmG 5713680 rpmG Dinoroseobacter shibae DFL 12 = DSM 16493 50S ribosomal protein L33 YP_001534115.1 2942214 R 398580 CDS YP_001534116.1 159045322 5713681 complement(2942514..2943002) 1 NC_009952.1 hypothetical protein 2943002 5713681 Dshi_2782 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534116.1 2942514 R 398580 CDS YP_001534117.1 159045323 5713683 complement(2943475..2944113) 1 NC_009952.1 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 2944113 5713683 Dshi_2783 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534117.1 2943475 R 398580 CDS YP_001534118.1 159045324 5713684 complement(2944167..2944769) 1 NC_009952.1 hypothetical protein 2944769 5713684 Dshi_2784 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534118.1 2944167 R 398580 CDS YP_001534119.1 159045325 5713685 complement(2944803..2946290) 1 NC_009952.1 allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases; reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA; aspartyl/glutamyl-tRNA amidotransferase subunit A 2946290 gatA 5713685 gatA Dinoroseobacter shibae DFL 12 = DSM 16493 aspartyl/glutamyl-tRNA amidotransferase subunit A YP_001534119.1 2944803 R 398580 CDS YP_001534120.1 159045326 5713686 complement(2946295..2946582) 1 NC_009952.1 allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases; reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA; some Mycoplasma proteins contain an N-terminal fusion to an unknown domain; aspartyl/glutamyl-tRNA amidotransferase subunit C 2946582 gatC 5713686 gatC Dinoroseobacter shibae DFL 12 = DSM 16493 aspartyl/glutamyl-tRNA amidotransferase subunit C YP_001534120.1 2946295 R 398580 CDS YP_001534121.1 159045327 5713687 complement(2946619..2947284) 1 NC_009952.1 hypothetical protein 2947284 5713687 Dshi_2787 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534121.1 2946619 R 398580 CDS YP_001534122.1 159045328 5713688 2947338..2948030 1 NC_009952.1 Swiss-Prot:Q98M91- UPF0173 metal-dependent hydrolase PFAM:beta-lactamase domain protein COG2220: Predicted Zn-dependent hydrolases of the beta-lactamase fold; hypothetical protein 2948030 5713688 Dshi_2788 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534122.1 2947338 D 398580 CDS YP_001534123.1 159045329 5713689 complement(2948196..2948651) 1 NC_009952.1 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 2948651 5713689 Dshi_2789 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534123.1 2948196 R 398580 CDS YP_001534124.1 159045330 5713690 2948736..2949704 1 NC_009952.1 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 2949704 5713690 Dshi_2790 Dinoroseobacter shibae DFL 12 = DSM 16493 RNA pseudouridine synthase YP_001534124.1 2948736 D 398580 CDS YP_001534125.1 159045331 5713691 2950066..2950944 1 NC_009952.1 KEGG: sil:SPO2985 hypothetical protein; hypothetical protein 2950944 5713691 Dshi_2791 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534125.1 2950066 D 398580 CDS YP_001534126.1 159045332 5713692 2950980..2952173 1 NC_009952.1 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 2952173 5713692 Dshi_2792 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534126.1 2950980 D 398580 CDS YP_001534127.1 159045333 5713693 2952170..2953117 1 NC_009952.1 hypothetical protein 2953117 5713693 Dshi_2793 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534127.1 2952170 D 398580 CDS YP_001534128.1 159045334 5713694 2953140..2954270 1 NC_009952.1 hypothetical protein 2954270 5713694 Dshi_2794 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534128.1 2953140 D 398580 CDS YP_001534129.1 159045335 5713695 2954277..2955392 1 NC_009952.1 hypothetical protein 2955392 5713695 Dshi_2795 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534129.1 2954277 D 398580 CDS YP_001534130.1 159045336 5713696 complement(2955399..2955857) 1 NC_009952.1 PFAM: heat shock protein Hsp20 SSF49764: HSP20-like chaperones superfamily; Hsp20; heat shock protein 2955857 5713696 Dshi_2796 Dinoroseobacter shibae DFL 12 = DSM 16493 heat shock protein YP_001534130.1 2955399 R 398580 CDS YP_001534131.1 159045337 5713697 2955983..2956909 1 NC_009952.1 PFAM: PfkB domain protein COG0524: Sugar kinases, ribokinase family PTHR10584: sugar kinase related; pfkB family; carbohydrate kinase 2956909 5713697 Dshi_2797 Dinoroseobacter shibae DFL 12 = DSM 16493 carbohydrate kinase YP_001534131.1 2955983 D 398580 CDS YP_001534132.1 159045338 5713698 2956906..2957343 1 NC_009952.1 hydrolyzes D-tyrosyl-tRNA(Tyr) into D-tyrosine and free tRNA(Tyr); possible defense mechanism against a harmful effect of D-tyrosine; D-tyrosyl-tRNA(Tyr) deacylase 2957343 dtd 5713698 dtd Dinoroseobacter shibae DFL 12 = DSM 16493 D-tyrosyl-tRNA(Tyr) deacylase YP_001534132.1 2956906 D 398580 CDS YP_001534133.1 159045339 5713699 complement(2957464..2958732) 1 NC_009952.1 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 2958732 fccB 5713699 fccB Dinoroseobacter shibae DFL 12 = DSM 16493 sulfide dehydrogenase [flavocytochrome c] flavoprotein chain YP_001534133.1 2957464 R 398580 CDS YP_001534134.1 159045340 5713700 complement(2958766..2959473) 1 NC_009952.1 Swiss-Prot: P00082-Cytochrome c2 PFAM: cytochrome c class I; cytochrome c 2959473 5713700 Dshi_2800 Dinoroseobacter shibae DFL 12 = DSM 16493 cytochrome c YP_001534134.1 2958766 R 398580 CDS YP_001534135.1 159045341 5713701 complement(2959478..2960506) 1 NC_009952.1 Swiss-Prot: P00081-Cytochrome c2 PFAM: cytochrome c class I; cytochrome c 2960506 5713701 Dshi_2801 Dinoroseobacter shibae DFL 12 = DSM 16493 cytochrome c YP_001534135.1 2959478 R 398580 CDS YP_001534136.1 159045342 5713702 complement(2960490..2961767) 1 NC_009952.1 Swiss-Prot: PFAM: oxidoreductase molybdopterin binding; Mo-co oxidoreductase dimerisation domain; molybdopterin binding; oxidoreductase 2961767 5713702 Dshi_2802 Dinoroseobacter shibae DFL 12 = DSM 16493 oxidoreductase YP_001534136.1 2960490 R 398580 CDS YP_001534137.1 159045343 5713703 complement(2961826..2963520) 1 NC_009952.1 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 2963520 5713703 Dshi_2803 Dinoroseobacter shibae DFL 12 = DSM 16493 putative 5'-nucleotidase YP_001534137.1 2961826 R 398580 CDS YP_001534138.1 159045344 5713704 complement(2963655..2964509) 1 NC_009952.1 Swiss-Prot: Q939U1-Diheme cytochrome c GENE3D / SSF46626: Cytochrome c, monohaem PS51008: Multihaem cytochrome; diheme cytochrome c 2964509 soxA1 5713704 soxA1 Dinoroseobacter shibae DFL 12 = DSM 16493 diheme cytochrome c YP_001534138.1 2963655 R 398580 CDS YP_001534139.1 159045345 5713705 complement(2964559..2964888) 1 NC_009952.1 PFAM: Sulphur oxidation protein SoxZ Swiss-Prot: Q939U2- SoxZ [predicted]; soxZ; putative sulfur oxidation protein 2964888 5713705 Dshi_2805 Dinoroseobacter shibae DFL 12 = DSM 16493 putative sulfur oxidation protein YP_001534139.1 2964559 R 398580 CDS YP_001534140.1 159045346 5713706 complement(2964907..2965323) 1 NC_009952.1 with SoxZ catalyzes the oxidation of sulfur compounds; sulfur oxidation protein SoxY 2965323 5713706 Dshi_2806 Dinoroseobacter shibae DFL 12 = DSM 16493 sulfur oxidation protein SoxY YP_001534140.1 2964907 R 398580 CDS YP_001534141.1 159045347 5713707 complement(2965359..2965841) 1 NC_009952.1 PFAM: cytochrome c SSF46626 / PS51007 / G3DSA:1.10.760.10: Cytochrome c, monohaem Swiss-Prot: A3W521- Monoheme cytochrome c SoxX [predicted]; monohaem; cytochrome c 2965841 5713707 Dshi_2807 Dinoroseobacter shibae DFL 12 = DSM 16493 cytochrome c YP_001534141.1 2965359 R 398580 CDS YP_001534142.1 159045348 5710659 complement(2965958..2966524) 1 NC_009952.1 SSF52833: Thioredoxin-like superfamily COG2143: Thioredoxin-related protein Swiss-Prot: Q16A50-Thioredoxin SoxW [predicted]; putative thioredoxin 2966524 5710659 Dshi_2808 Dinoroseobacter shibae DFL 12 = DSM 16493 putative thioredoxin YP_001534142.1 2965958 R 398580 CDS YP_001534143.1 159045349 5710660 complement(2966552..2967286) 1 NC_009952.1 PFAM: cytochrome c biogenesis protein transmembrane region COG0785: Cytochrome c biogenesis protein; transmembrane region; cytochrome c biogenesis protein 2967286 5710660 Dshi_2809 Dinoroseobacter shibae DFL 12 = DSM 16493 cytochrome c biogenesis protein YP_001534143.1 2966552 R 398580 CDS YP_001534144.1 159045350 5710661 2967368..2967775 1 NC_009952.1 hypothetical protein 2967775 5710661 Dshi_2810 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534144.1 2967368 D 398580 CDS YP_001534145.1 159045351 5710662 2967772..2968284 1 NC_009952.1 PFAM: protein of unknown function DUF336; hypothetical protein 2968284 5710662 Dshi_2811 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534145.1 2967772 D 398580 CDS YP_001534146.1 159045352 5710663 2968306..2968641 1 NC_009952.1 PFAM: regulatory protein ArsR; ArsR family; transcriptional regulator 2968641 5710663 Dshi_2812 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001534146.1 2968306 D 398580 CDS YP_001534147.1 159045353 5710664 2968662..2969750 1 NC_009952.1 PFAM: protein of unknown function DUF395 YeeE/YedE; hypothetical protein 2969750 5710664 Dshi_2813 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534147.1 2968662 D 398580 CDS YP_001534148.1 159045354 5710665 complement(2969763..2970803) 1 NC_009952.1 TIGRFAM: diguanylate cyclase (GGDEF) domain PFAM: GGDEF domain containing protein; hypothetical protein 2970803 5710665 Dshi_2814 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534148.1 2969763 R 398580 CDS YP_001534149.1 159045355 5710666 complement(2970800..2971384) 1 NC_009952.1 PFAM: Heme NO binding domain protein; hypothetical protein 2971384 5710666 Dshi_2815 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534149.1 2970800 R 398580 CDS YP_001534150.1 159045356 5710667 complement(2971486..2973201) 1 NC_009952.1 hypothetical protein 2973201 5710667 Dshi_2816 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534150.1 2971486 R 398580 CDS YP_001534151.1 159045357 5710668 complement(2973240..2974799) 1 NC_009952.1 Swiss-Prot: PFAM: trimethylamine methyltransferase PIRSF037567: trimethylamine methyltransferase, MttB type; trimethylamine methyltransferase 2974799 5710668 Dshi_2817 Dinoroseobacter shibae DFL 12 = DSM 16493 trimethylamine methyltransferase YP_001534151.1 2973240 R 398580 CDS YP_001534152.1 159045358 5710669 complement(2974910..2975632) 1 NC_009952.1 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 2975632 5710669 Dshi_2818 Dinoroseobacter shibae DFL 12 = DSM 16493 HAD-like hydrolase YP_001534152.1 2974910 R 398580 CDS YP_001534153.1 159045359 5710670 complement(2976015..2976293) 1 NC_009952.1 KEGG: sil:SPO2752 hypothetical protein; hypothetical protein 2976293 5710670 Dshi_2819 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534153.1 2976015 R 398580 CDS YP_001534154.1 159045360 5710671 2976378..2977766 1 NC_009952.1 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 2977766 5710671 Dshi_2820 Dinoroseobacter shibae DFL 12 = DSM 16493 response regulator YP_001534154.1 2976378 D 398580 CDS YP_001534155.1 159045361 5710672 2977988..2978386 1 NC_009952.1 PFAM: protein of unknown function DUF983 COG5349: Uncharacterized protein conserved in bacteria; hypothetical protein 2978386 5710672 Dshi_2821 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534155.1 2977988 D 398580 CDS YP_001534156.1 159045362 5710673 2978410..2979087 1 NC_009952.1 Swiss-Prot: PFAM: NUDIX hydrolase; NUDIX hydrolase 2979087 5710673 Dshi_2822 Dinoroseobacter shibae DFL 12 = DSM 16493 NUDIX hydrolase YP_001534156.1 2978410 D 398580 CDS YP_001534157.1 159045363 5710674 complement(2979098..2980144) 1 NC_009952.1 PFAM: aldo/keto reductase IPR001395: Aldo/keto reductase; aldo/keto reductase 2980144 5710674 Dshi_2823 Dinoroseobacter shibae DFL 12 = DSM 16493 aldo/keto reductase YP_001534157.1 2979098 R 398580 CDS YP_001534158.1 159045364 5710675 2980248..2981147 1 NC_009952.1 hypothetical protein 2981147 5710675 Dshi_2824 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534158.1 2980248 D 398580 CDS YP_001534159.1 159045365 5710676 2981199..2982374 1 NC_009952.1 PFAM: 3-hydroxyacyl-CoA dehydrogenase NAD-binding COG1250: 3-hydroxyacyl-CoA dehydrogenase; related to 3-hydroxyacyl-CoA dehydrogenase; hypothetical protein 2982374 5710676 Dshi_2825 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534159.1 2981199 D 398580 CDS YP_001534160.1 159045366 5710677 2982421..2983074 1 NC_009952.1 KEGG: rde:RD1_2519 hypothetical protein COG4544: Uncharacterized conserved protein; hypothetical protein 2983074 5710677 Dshi_2826 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534160.1 2982421 D 398580 CDS YP_001534161.1 159045367 5710678 2983112..2983675 1 NC_009952.1 Swiss-Prot: P0A8X2-Protein yceI [Precursor] PFAM: YceI family protein COG2353: Uncharacterized conserved protein; similar to protein yceI [Precursor]; hypothetical protein 2983675 5710678 Dshi_2827 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534161.1 2983112 D 398580 CDS YP_001534162.1 159045368 5710679 2983768..2985282 1 NC_009952.1 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 2985282 5710679 Dshi_2828 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534162.1 2983768 D 398580 CDS YP_001534163.1 159045369 5710680 complement(2985279..2986226) 1 NC_009952.1 catalyzes the second step in the glutathione biosynthesis pathway, where it synthesizes ATP + gamma-L-glutamyl-L-cysteine + glycine = ADP + phosphate + glutathione; glutathione synthetase 2986226 gshB 5710680 gshB Dinoroseobacter shibae DFL 12 = DSM 16493 glutathione synthetase YP_001534163.1 2985279 R 398580 CDS YP_001534164.1 159045370 5710681 complement(2986303..2986707) 1 NC_009952.1 TIGR00252 conserved hypothetical protein PFAM: protein of unknown function UPF0102; hypothetical protein 2986707 5710681 Dshi_2830 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534164.1 2986303 R 398580 CDS YP_001534165.1 159045371 5710682 complement(2986732..2987586) 1 NC_009952.1 Swiss-Prot: P67087-UPF0011 protein yraL TIGR00096: conserved hypothetical protein TIGR00096 PFAM: Uroporphyrin-III C/tetrapyrrole (Corrin/Porphyrin) methyltransferase; hypothetical protein 2987586 5710682 Dshi_2831 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534165.1 2986732 R 398580 CDS YP_001534166.1 159045372 5710683 2987697..2988881 1 NC_009952.1 SSF53822: Periplasmic binding protein-like I superfamily PS51257: Prokaryotic membrane lipoprotein lipid attachment site profile; hypothetical protein 2988881 5710683 Dshi_2832 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534166.1 2987697 D 398580 CDS YP_001534167.1 159045373 5710684 2988886..2991717 1 NC_009952.1 catalyzes the uridylylation or deuridylylation of the PII nitrogen regulatory protein; PII uridylyl-transferase 2991717 glnD 5710684 glnD Dinoroseobacter shibae DFL 12 = DSM 16493 PII uridylyl-transferase YP_001534167.1 2988886 D 398580 CDS YP_001534168.1 159045374 5710685 2991755..2993359 1 NC_009952.1 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 2993359 5710685 Dshi_2834 Dinoroseobacter shibae DFL 12 = DSM 16493 putative virulence factor YP_001534168.1 2991755 D 398580 CDS YP_001534169.1 159045375 5710686 complement(2993548..2994231) 1 NC_009952.1 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 2994231 5710686 Dshi_2835 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534169.1 2993548 R 398580 CDS YP_001534170.1 159045376 5710687 2994331..2995356 1 NC_009952.1 catalyzes a two-step reaction, first charging a tryptophan molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; tryptophanyl-tRNA synthetase 2995356 trpS 5710687 trpS Dinoroseobacter shibae DFL 12 = DSM 16493 tryptophanyl-tRNA synthetase YP_001534170.1 2994331 D 398580 CDS YP_001534171.1 159045377 5710688 2995862..2996722 1 NC_009952.1 Swiss-Prot: P0AB80-Branched-chain-amino-acid aminotransferase PFAM: aminotransferase class IV; class IV; aminotransferase 2996722 5710688 Dshi_2837 Dinoroseobacter shibae DFL 12 = DSM 16493 aminotransferase YP_001534171.1 2995862 D 398580 CDS YP_001534172.1 159045378 5710689 2996802..2997257 1 NC_009952.1 PFAM: UspA domain protein COG0589: Universal stress protein UspA and related nucleotide-binding proteins; related to universal stress protein; hypothetical protein 2997257 5710689 Dshi_2838 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534172.1 2996802 D 398580 CDS YP_001534173.1 159045379 5710690 2997347..2997910 1 NC_009952.1 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 2997910 5710690 Dshi_2839 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534173.1 2997347 D 398580 CDS YP_001534174.1 159045380 5710691 2997915..2998571 1 NC_009952.1 PFAM: peptidase M22 glycoprotease; glycoprotease; peptidase M22 2998571 5710691 Dshi_2840 Dinoroseobacter shibae DFL 12 = DSM 16493 peptidase M22 YP_001534174.1 2997915 D 398580 CDS YP_001534175.1 159045381 5710692 2998568..2998987 1 NC_009952.1 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 2998987 5710692 Dshi_2841 Dinoroseobacter shibae DFL 12 = DSM 16493 putative ribosomal-protein-alanine acetyltransferase YP_001534175.1 2998568 D 398580 CDS YP_001534176.1 159045382 5710693 2999169..3000158 1 NC_009952.1 PFAM: basic membrane lipoprotein SSF53822: Periplasmic binding protein-like I superfamily; putative lipoprotein 3000158 5710693 Dshi_2842 Dinoroseobacter shibae DFL 12 = DSM 16493 putative lipoprotein YP_001534176.1 2999169 D 398580 CDS YP_001534177.1 159045383 5710694 3000182..3001828 1 NC_009952.1 Swiss-Prot: P04983-Ribose import ATP-binding protein rbsA; ribose import ATP-binding protein 3001828 rbsA2 5710694 rbsA2 Dinoroseobacter shibae DFL 12 = DSM 16493 ribose import ATP-binding protein YP_001534177.1 3000182 D 398580 CDS YP_001534178.1 159045384 5710695 3001828..3002946 1 NC_009952.1 Swiss-Prot: P0AGI1-Ribose transport system permease protein rbsC PFAM: inner-membrane translocator; similar to ribose transport system permease protein; integral inner-membrane protein 3002946 5710695 Dshi_2844 Dinoroseobacter shibae DFL 12 = DSM 16493 integral inner-membrane protein YP_001534178.1 3001828 D 398580 CDS YP_001534179.1 159045385 5710696 3002943..3003572 1 NC_009952.1 PFAM: Lysine exporter protein (LYSE/YGGA) Swiss-Prot: P75693-Uncharacterized membrane protein yahN; related to LysE type translocator; hypothetical protein 3003572 5710696 Dshi_2845 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534179.1 3002943 D 398580 CDS YP_001534180.1 159045386 5710697 3003577..3004542 1 NC_009952.1 PFAM: inner-membrane translocator COG1079: Uncharacterized ABC-type transport system, permease component; inner-membrane translocator 3004542 5710697 Dshi_2846 Dinoroseobacter shibae DFL 12 = DSM 16493 inner-membrane translocator YP_001534180.1 3003577 D 398580 CDS YP_001534181.1 159045387 5710698 3004600..3005520 1 NC_009952.1 Swiss-Prot: PFAM: protein of unknown function DUF81 KEGG: sil:SPO0375 membrane protein; hypothetical protein 3005520 5710698 Dshi_2847 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534181.1 3004600 D 398580 CDS YP_001534182.1 159045388 5710699 3005517..3006275 1 NC_009952.1 TIGR02186# conserved hypothetical protein; hypothetical protein 3006275 5710699 Dshi_2848 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534182.1 3005517 D 398580 CDS YP_001534183.1 159045389 5710700 complement(3006406..3007137) 1 NC_009952.1 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 3007137 5710700 Dshi_2849 Dinoroseobacter shibae DFL 12 = DSM 16493 short-chain dehydrogenase/reductase YP_001534183.1 3006406 R 398580 CDS YP_001534184.1 159045390 5710701 complement(3007134..3008669) 1 NC_009952.1 SMART 00382: AAA - ATPases associated with a variety of cellular activities; AAA family; putative ATPase 3008669 5710701 Dshi_2850 Dinoroseobacter shibae DFL 12 = DSM 16493 putative ATPase YP_001534184.1 3007134 R 398580 CDS YP_001534185.1 159045391 5710702 complement(3008719..3009339) 1 NC_009952.1 Swiss-Prot: P33883-Autoinducer synthesis protein lasI PFAM: autoinducer synthesis protein; autoinducer synthetase 3009339 5710702 Dshi_2851 Dinoroseobacter shibae DFL 12 = DSM 16493 autoinducer synthetase YP_001534185.1 3008719 R 398580 CDS YP_001534186.1 159045392 5710703 complement(3009442..3010152) 1 NC_009952.1 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 3010152 5710703 Dshi_2852 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001534186.1 3009442 R 398580 CDS YP_001534187.1 159045393 5710704 complement(3010523..3011815) 1 NC_009952.1 TIGRFAM: crotonyl-CoA reductase PFAM: Alcohol dehydrogenase zinc-binding domain protein; Alcohol dehydrogenase GroES domain protein Swiss-Prot: P42328-Alcohol dehydrogenase; alcohol dehydrogenase 3011815 5710704 Dshi_2853 Dinoroseobacter shibae DFL 12 = DSM 16493 alcohol dehydrogenase YP_001534187.1 3010523 R 398580 CDS YP_001534188.1 159045394 5710705 complement(3011938..3013380) 1 NC_009952.1 Swiss-Prot: P0A7A7-Glycerol-3-phosphate acyltransferase PFAM: phospholipid/glycerol acyltransferase; putative glycerol-3-phosphate acyltransferase 3013380 5710705 Dshi_2854 Dinoroseobacter shibae DFL 12 = DSM 16493 putative glycerol-3-phosphate acyltransferase YP_001534188.1 3011938 R 398580 CDS YP_001534189.1 159045395 5710706 3013589..3015562 1 NC_009952.1 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 3015562 mutB 5710706 mutB Dinoroseobacter shibae DFL 12 = DSM 16493 methylmalonyl-CoA mutase YP_001534189.1 3013589 D 398580 CDS YP_001534190.1 159045396 5710707 complement(3015677..3016192) 1 NC_009952.1 hypothetical protein 3016192 5710707 Dshi_2856 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534190.1 3015677 R 398580 CDS YP_001534191.1 159045397 5710708 3016278..3016748 1 NC_009952.1 hypothetical protein 3016748 5710708 Dshi_2857 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534191.1 3016278 D 398580 CDS YP_001534192.1 159045398 5710709 3016895..3017599 1 NC_009952.1 catalyzes the reversible phosphorolysis of ribonucleosides and 2'- deoxyribonucleosides to the free base and (2'-deoxy)ribose-1- phosphate; purine nucleoside phosphorylase 3017599 deoD 5710709 deoD Dinoroseobacter shibae DFL 12 = DSM 16493 purine nucleoside phosphorylase YP_001534192.1 3016895 D 398580 CDS YP_001534193.1 159045399 5710710 3017596..3018039 1 NC_009952.1 hypothetical protein 3018039 5710710 Dshi_2859 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534193.1 3017596 D 398580 CDS YP_001534194.1 159045400 5710711 complement(3018036..3018221) 1 NC_009952.1 hypothetical protein 3018221 5710711 Dshi_2860 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534194.1 3018036 R 398580 CDS YP_001534195.1 159045401 5710712 complement(3018314..3019093) 1 NC_009952.1 part of four member succinate dehydrogenase enzyme complex that forms a trimeric complex (trimer of tetramers); SdhA/B are the catalytic subcomplex and can exhibit succinate dehydrogenase activity in the absence of SdhC/D which are the membrane components and form cytochrome b556; SdhC binds ubiquinone; oxidizes succinate to fumarate while reducing ubiquinone to ubiquinol; the catalytic subunits are similar to fumarate reductase; succinate dehydrogenase iron-sulfur subunit 3019093 sdhB 5710712 sdhB Dinoroseobacter shibae DFL 12 = DSM 16493 succinate dehydrogenase iron-sulfur subunit YP_001534195.1 3018314 R 398580 CDS YP_001534196.1 159045402 5710713 complement(3019123..3019902) 1 NC_009952.1 hypothetical protein 3019902 5710713 Dshi_2862 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534196.1 3019123 R 398580 CDS YP_001534197.1 159045403 5710714 complement(3019899..3020720) 1 NC_009952.1 hypothetical protein 3020720 5710714 Dshi_2863 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534197.1 3019899 R 398580 CDS YP_001534198.1 159045404 5710715 complement(3020723..3021550) 1 NC_009952.1 hypothetical protein 3021550 5710715 Dshi_2864 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534198.1 3020723 R 398580 CDS YP_001534199.1 159045405 5710716 complement(3021696..3023498) 1 NC_009952.1 part of four member succinate dehydrogenase enzyme complex that forms a trimeric complex (trimer of tetramers); SdhA/B are the catalytic subcomplex and can exhibit succinate dehydrogenase activity in the absence of SdhC/D which are the membrane components and form cytochrome b556; SdhC binds ubiquinone; oxidizes succinate to fumarate while reducing ubiquinone to ubiquinol; succinate dehydrogenase flavoprotein subunit 3023498 sdhA 5710716 sdhA Dinoroseobacter shibae DFL 12 = DSM 16493 succinate dehydrogenase flavoprotein subunit YP_001534199.1 3021696 R 398580 CDS YP_001534200.1 159045406 5710717 complement(3023515..3023886) 1 NC_009952.1 TIGRFAM: TIGR02968 succinate dehydrogenase, hydrophobic membrane anchor protein; COG: COG2142 - Succinate dehydrogenase, hydrophobic anchor subunit; similar to succinate dehydrogenase; hypothetical protein 3023886 5710717 Dshi_2866 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534200.1 3023515 R 398580 CDS YP_001534201.1 159045407 5710718 complement(3023898..3024281) 1 NC_009952.1 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 3024281 5710718 Dshi_2867 Dinoroseobacter shibae DFL 12 = DSM 16493 putative succinate dehydrogenase cytochrome subunit B YP_001534201.1 3023898 R 398580 CDS YP_001534202.1 159045408 5710719 3024581..3025060 1 NC_009952.1 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 3025060 5710719 Dshi_2868 Dinoroseobacter shibae DFL 12 = DSM 16493 cytochrome c YP_001534202.1 3024581 D 398580 CDS YP_001534203.1 159045409 5710720 3025070..3025948 1 NC_009952.1 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 3025948 5710720 Dshi_2869 Dinoroseobacter shibae DFL 12 = DSM 16493 putative alcohol dehydrogenase cytochrome subunit C YP_001534203.1 3025070 D 398580 CDS YP_001534204.1 159045410 5710721 3026023..3026229 1 NC_009952.1 hypothetical protein 3026229 5710721 Dshi_2870 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534204.1 3026023 D 398580 CDS YP_001534205.1 159045411 5710722 complement(3026266..3027297) 1 NC_009952.1 COG: COG2030 - Acyl dehydratase; PIR: PIRSF021494; SUPERFAMILY: SSF54637; putative thiol ester dehydrase/isomerase 3027297 5710722 Dshi_2871 Dinoroseobacter shibae DFL 12 = DSM 16493 putative thiol ester dehydrase/isomerase YP_001534205.1 3026266 R 398580 CDS YP_001534206.1 159045412 5710723 complement(3027297..3027500) 1 NC_009952.1 COG: COG5515 - Uncharacterized conserved small protein; hypothetical protein 3027500 5710723 Dshi_2872 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534206.1 3027297 R 398580 CDS YP_001534207.1 159045413 5710724 complement(3027513..3028076) 1 NC_009952.1 COG: COG4094 - Predicted membrane protein; PFAM: PF07298 - NnrU protein; putative NnrU protein 3028076 5710724 Dshi_2873 Dinoroseobacter shibae DFL 12 = DSM 16493 putative NnrU protein YP_001534207.1 3027513 R 398580 CDS YP_001534208.1 159045414 5710725 complement(3028080..3028967) 1 NC_009952.1 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 3028967 5710725 Dshi_2874 Dinoroseobacter shibae DFL 12 = DSM 16493 putative citrate lyase subunit beta YP_001534208.1 3028080 R 398580 CDS YP_001534209.1 159045415 5710726 3029274..3029597 1 NC_009952.1 hypothetical protein 3029597 5710726 Dshi_2875 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534209.1 3029274 D 398580 CDS YP_001534210.1 159045416 5710727 3029964..3030926 1 NC_009952.1 Catalyzes the reversible oxidation of malate to oxaloacetate; malate dehydrogenase 3030926 mdh 5710727 mdh Dinoroseobacter shibae DFL 12 = DSM 16493 malate dehydrogenase YP_001534210.1 3029964 D 398580 CDS YP_001534211.1 159045417 5710728 3031039..3032007 1 NC_009952.1 hypothetical protein 3032007 5710728 Dshi_2877 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534211.1 3031039 D 398580 CDS YP_001534212.1 159045418 5710729 3032211..3033404 1 NC_009952.1 catalyzes the interconversion of succinyl-CoA and succinate; succinyl-CoA synthetase subunit beta 3033404 sucC 5710729 sucC Dinoroseobacter shibae DFL 12 = DSM 16493 succinyl-CoA synthetase subunit beta YP_001534212.1 3032211 D 398580 CDS YP_001534213.1 159045419 5710730 3033534..3034235 1 NC_009952.1 hypothetical protein 3034235 5710730 Dshi_2879 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534213.1 3033534 D 398580 CDS YP_001534214.1 159045420 5710731 3034232..3034780 1 NC_009952.1 hypothetical protein 3034780 5710731 Dshi_2880 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534214.1 3034232 D 398580 CDS YP_001534215.1 159045421 5710732 3034840..3035316 1 NC_009952.1 hypothetical protein 3035316 5710732 Dshi_2881 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534215.1 3034840 D 398580 CDS YP_001534216.1 159045422 5710733 3035436..3036317 1 NC_009952.1 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 3036317 sucD1 5710733 sucD1 Dinoroseobacter shibae DFL 12 = DSM 16493 succinyl-CoA ligase [ADP-forming] subunit alpha YP_001534216.1 3035436 D 398580 CDS YP_001534217.1 159045423 5710734 3036507..3039470 1 NC_009952.1 SucA; E1 component of the oxoglutarate dehydrogenase complex which catalyzes the formation of succinyl-CoA from 2-oxoglutarate; SucA catalyzes the reaction of 2-oxoglutarate with dihydrolipoamide succinyltransferase-lipoate to form dihydrolipoamide succinyltransferase-succinyldihydrolipoate and carbon dioxide; 2-oxoglutarate dehydrogenase E1 component 3039470 sucA 5710734 sucA Dinoroseobacter shibae DFL 12 = DSM 16493 2-oxoglutarate dehydrogenase E1 component YP_001534217.1 3036507 D 398580 CDS YP_001534218.1 159045424 5710735 3039475..3040965 1 NC_009952.1 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 3040965 sucB 5710735 sucB Dinoroseobacter shibae DFL 12 = DSM 16493 dihydrolipoamide succinyltransferase YP_001534218.1 3039475 D 398580 CDS YP_001534219.1 159045425 5710736 3041239..3041628 1 NC_009952.1 COG: COG3686 - Predicted membrane protein; hypothetical protein 3041628 5710736 Dshi_2885 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534219.1 3041239 D 398580 CDS YP_001534220.1 159045426 5710737 3041719..3043113 1 NC_009952.1 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 3043113 lpd 5710737 lpd Dinoroseobacter shibae DFL 12 = DSM 16493 dihydrolipoyl dehydrogenase YP_001534220.1 3041719 D 398580 CDS YP_001534221.1 159045427 5710738 complement(3043208..3044686) 1 NC_009952.1 TIGRFAM: TIGR01780 succinic semialdehyde dehydrogenase; COG: COG1012 - NAD-dependent aldehyde dehydrogenases; PFAM: PF00171; PROSITE: PS00070, PS00687; NADP(+) dependentsuccinate-semialdehyde dehydrogenase 3044686 gabD 5710738 gabD Dinoroseobacter shibae DFL 12 = DSM 16493 NADP(+) dependentsuccinate-semialdehyde dehydrogenase YP_001534221.1 3043208 R 398580 CDS YP_001534222.1 159045428 5710739 3044761..3045534 1 NC_009952.1 SUPERFAMILY: SSF53474; Gene3D: G3DSA:3.40.50.1820; COG: COG0657 - Esterase/lipase; putative alpha/beta hydrolase 3045534 5710739 Dshi_2888 Dinoroseobacter shibae DFL 12 = DSM 16493 putative alpha/beta hydrolase YP_001534222.1 3044761 D 398580 CDS YP_001534223.1 159045429 5710740 complement(3045531..3046514) 1 NC_009952.1 COG: COG3191 - L-aminopeptidase/D-esterase; putative peptidase 3046514 5710740 Dshi_2889 Dinoroseobacter shibae DFL 12 = DSM 16493 putative peptidase YP_001534223.1 3045531 R 398580 CDS YP_001534224.1 159045430 5710741 complement(3046511..3046822) 1 NC_009952.1 hypothetical protein 3046822 5710741 Dshi_2890 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534224.1 3046511 R 398580 CDS YP_001534225.1 159045431 5710742 complement(3046819..3047547) 1 NC_009952.1 Catalyzes the first of the two reduction steps in the elongation cycle of fatty acid synthesis; 3-ketoacyl-ACP reductase 3047547 fabG 5710742 fabG Dinoroseobacter shibae DFL 12 = DSM 16493 3-ketoacyl-ACP reductase YP_001534225.1 3046819 R 398580 CDS YP_001534226.1 159045432 5710743 complement(3047660..3048118) 1 NC_009952.1 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 3048118 5710743 Dshi_2892 Dinoroseobacter shibae DFL 12 = DSM 16493 putative small heat shock (HSP20) protein YP_001534226.1 3047660 R 398580 CDS YP_001534227.1 159045433 5710744 complement(3048258..3049076) 1 NC_009952.1 COG: COG3591 - V8-like Glu-specific endopeptidase; PFAM: PF00089; SMART: SM00020; PROSITE: PS00134, PS50240; PRINTS: PR00722; similar to serine protease; hypothetical protein 3049076 5710744 Dshi_2893 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534227.1 3048258 R 398580 CDS YP_001534228.1 159045434 5710745 complement(3049140..3050444) 1 NC_009952.1 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 3050444 5710745 Dshi_2894 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534228.1 3049140 R 398580 CDS YP_001534229.1 159045435 5710746 complement(3050467..3051603) 1 NC_009952.1 COG: COG0277 - FAD/FMN-containing dehydrogenases; PFAM: PF01565; similar to glycolate oxidase subunit glcE; hypothetical protein 3051603 5710746 Dshi_2895 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534229.1 3050467 R 398580 CDS YP_001534230.1 159045436 5710747 complement(3051689..3053131) 1 NC_009952.1 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 3053131 5710747 Dshi_2896 Dinoroseobacter shibae DFL 12 = DSM 16493 FAD-binding oxidoreductase/transferase YP_001534230.1 3051689 R 398580 CDS YP_001534231.1 159045437 5710748 complement(3053287..3053973) 1 NC_009952.1 SWISSPROT P23461: Protein pucD; associated with puc operon, related to protein pucD; hypothetical protein 3053973 5710748 Dshi_2897 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534231.1 3053287 R 398580 CDS YP_001534232.1 159045438 5710749 complement(3054022..3055425) 1 NC_009952.1 SWISSPROT P23462: Protein pucC; PFAM: PF03209; PucC protein 3055425 pucC1 5710749 pucC1 Dinoroseobacter shibae DFL 12 = DSM 16493 PucC protein YP_001534232.1 3054022 R 398580 CDS YP_001534233.1 159045439 5710750 complement(3055496..3055837) 1 NC_009952.1 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 3055837 5710750 Dshi_2899 Dinoroseobacter shibae DFL 12 = DSM 16493 putative light-harvesting protein B-800/850 subunit alpha YP_001534233.1 3055496 R 398580 CDS YP_001534234.1 159045440 5710751 complement(3055850..3056005) 1 NC_009952.1 SWISSPROT P07368: Light-harvesting protein B-800/850 beta chain; PFAM: PF00556; PRINTS: PR00674; PROSITE: PS00969; light-harvesting protein B-800/850 subunit beta 3056005 pucB 5710751 pucB Dinoroseobacter shibae DFL 12 = DSM 16493 light-harvesting protein B-800/850 subunit beta YP_001534234.1 3055850 R 398580 CDS YP_001534235.1 159045441 5710752 complement(3056406..3058565) 1 NC_009952.1 hypothetical protein 3058565 5710752 Dshi_2901 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534235.1 3056406 R 398580 CDS YP_001534236.1 159045442 5710753 3058709..3059089 1 NC_009952.1 hypothetical protein 3059089 5710753 Dshi_2902 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534236.1 3058709 D 398580 CDS YP_001534237.1 159045443 5710754 complement(3059093..3061177) 1 NC_009952.1 hypothetical protein 3061177 5710754 Dshi_2903 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534237.1 3059093 R 398580 CDS YP_001534238.1 159045444 5710755 complement(3061174..3063948) 1 NC_009952.1 TIGRFAM: TIGR02226; hypothetical protein 3063948 5710755 Dshi_2904 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534238.1 3061174 R 398580 CDS YP_001534239.1 159045445 5710756 complement(3063948..3064850) 1 NC_009952.1 PFAM: PF01882; COG: COG1721 - Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain); related to DUF58; hypothetical protein 3064850 5710756 Dshi_2905 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534239.1 3063948 R 398580 CDS YP_001534240.1 159045446 5710757 complement(3064847..3065854) 1 NC_009952.1 COG: COG0714 - MoxR-like ATPases; PFAM: PF07726; SMART: SM00382; related to AAA ATPase; hypothetical protein 3065854 5710757 Dshi_2906 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534240.1 3064847 R 398580 CDS YP_001534241.1 159045447 5710758 3065916..3066521 1 NC_009952.1 COG: COG3816 - Uncharacterized protein conserved in bacteria; PFAM: PF06938 - Protein of unknown function (DUF1285); hypothetical protein 3066521 5710758 Dshi_2907 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534241.1 3065916 D 398580 CDS YP_001534242.1 159045448 5710759 complement(3066582..3067118) 1 NC_009952.1 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 3067118 rluE 5710759 rluE Dinoroseobacter shibae DFL 12 = DSM 16493 ribosomal large subunit pseudouridine synthase E YP_001534242.1 3066582 R 398580 CDS YP_001534243.1 159045449 5710760 complement(3067301..3070099) 1 NC_009952.1 has 3'-5' exonuclease, 5'-3' exonuclease and 5'-3'polymerase activities, primarily functions to fill gaps during DNA replication and repair; DNA polymerase I 3070099 polA 5710760 polA Dinoroseobacter shibae DFL 12 = DSM 16493 DNA polymerase I YP_001534243.1 3067301 R 398580 CDS YP_001534244.1 159045450 5710761 complement(3070163..3070828) 1 NC_009952.1 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 3070828 5710761 Dshi_2910 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534244.1 3070163 R 398580 CDS YP_001534245.1 159045451 5710762 complement(3070889..3071575) 1 NC_009952.1 TIGRFAM: TIGR02117 conserved hypothetical protein; hypothetical protein 3071575 5710762 Dshi_2911 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534245.1 3070889 R 398580 CDS YP_001534246.1 159045452 5710763 complement(3071600..3071788) 1 NC_009952.1 COG: COG4391 - Uncharacterized protein conserved in bacteria; hypothetical protein 3071788 5710763 Dshi_2912 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534246.1 3071600 R 398580 CDS YP_001534247.1 159045453 5710764 3071922..3072887 1 NC_009952.1 SWISSPROT P36879: Uncharacterized ABC transporter ATP-binding protein yadG; PFAM: PF00005; PROSITE: PS00211, PS50893; ABC transporter ATP-binding protein 3072887 5710764 Dshi_2913 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC transporter ATP-binding protein YP_001534247.1 3071922 D 398580 CDS YP_001534248.1 159045454 5710765 complement(3072942..3073709) 1 NC_009952.1 COG: COG1075 - Predicted acetyltransferases and hydrolases with the alpha/beta hydrolase fold; PROSITE: PS51257; SUPERFAMILY: SSF53474; putative alpha/beta hydrolase 3073709 5710765 Dshi_2914 Dinoroseobacter shibae DFL 12 = DSM 16493 putative alpha/beta hydrolase YP_001534248.1 3072942 R 398580 CDS YP_001534249.1 159045455 5710766 3073785..3074231 1 NC_009952.1 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 3074231 5710766 Dshi_2915 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534249.1 3073785 D 398580 CDS YP_001534250.1 159045456 5710767 complement(3074228..3075076) 1 NC_009952.1 PFAM: PF00892 - integral membrane protein DUF6; COG: COG5006 - Predicted permease, DMT superfamily; similar to integral membrane protein DUF6; hypothetical protein 3075076 5710767 Dshi_2916 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534250.1 3074228 R 398580 CDS YP_001534251.1 159045457 5710768 complement(3075327..3076484) 1 NC_009952.1 TIGRFAM: TIGR02318 phosphonate metabolism protein PhnM; COG: COG3454 - Metal-dependent hydrolase involved in phosphonate metabolism; PFAM: PF01979 - Amidohydrolase family; similar to amidohydrolase; hypothetical protein 3076484 5710768 Dshi_2917 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534251.1 3075327 R 398580 CDS YP_001534252.1 159045458 5710769 complement(3076513..3077004) 1 NC_009952.1 PFAM: Acetyltransferase (GNAT) family; PROSITE: PS51186; COG: COG3153 - Predicted acetyltransferase; similar to acetyltransferase (GNAT); hypothetical protein 3077004 5710769 Dshi_2918 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534252.1 3076513 R 398580 CDS YP_001534253.1 159045459 5710770 complement(3077174..3078817) 1 NC_009952.1 60 kDa chaperone family; promotes refolding of misfolded polypeptides especially under stressful conditions; forms two stacked rings of heptamers to form a barrel-shaped 14mer; ends can be capped by GroES; misfolded proteins enter the barrel where they are refolded when GroES binds; many bacteria have multiple copies of the groEL gene which are active under different environmental conditions; the B.japonicum protein in this cluster is expressed constitutively; in Rhodobacter, Corynebacterium and Rhizobium this protein is not essential for growth; chaperonin GroEL 3078817 groEL 5710770 groEL Dinoroseobacter shibae DFL 12 = DSM 16493 chaperonin GroEL YP_001534253.1 3077174 R 398580 CDS YP_001534254.1 159045460 5710771 complement(3078861..3079172) 1 NC_009952.1 COG: COG0234 - Co-chaperonin GroES (HSP10); PFAM: PF00166; PROSITE: PS00681; PRINTS: PR00297; chaperonin 10 Kd subunit 3079172 5710771 Dshi_2920 Dinoroseobacter shibae DFL 12 = DSM 16493 chaperonin 10 Kd subunit YP_001534254.1 3078861 R 398580 CDS YP_001534255.1 159045461 5710772 3079549..3080532 1 NC_009952.1 hypothetical protein 3080532 5710772 Dshi_2921 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534255.1 3079549 D 398580 CDS YP_001534256.1 159045462 5710773 complement(3080559..3081224) 1 NC_009952.1 COG: COG5482 - Uncharacterized conserved protein; hypothetical protein 3081224 5710773 Dshi_2922 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534256.1 3080559 R 398580 CDS YP_001534257.1 159045463 5710774 3081428..3082663 1 NC_009952.1 PFAM: PF07694; related to 5TMR of 5TMR-LYT; hypothetical protein 3082663 5710774 Dshi_2923 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534257.1 3081428 D 398580 CDS YP_001534258.1 159045464 5710775 3082742..3083743 1 NC_009952.1 catalyzes the hydrolysis of pyrophosphate to phosphate; putative manganese-dependent inorganic pyrophosphatase 3083743 ppaC 5710775 ppaC Dinoroseobacter shibae DFL 12 = DSM 16493 putative manganese-dependent inorganic pyrophosphatase YP_001534258.1 3082742 D 398580 CDS YP_001534259.1 159045465 5710776 3084036..3084908 1 NC_009952.1 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 3084908 5710776 Dshi_2925 Dinoroseobacter shibae DFL 12 = DSM 16493 putative Haloacid dehalogenase-like hydrolase YP_001534259.1 3084036 D 398580 CDS YP_001534260.1 159045466 5710777 3085029..3085472 1 NC_009952.1 SWISSPROT P77455: Protein maoC; PFAM: PF01575; COG: COG2030 - Acyl dehydratase; putative MaoC-like dehydratase 3085472 5710777 Dshi_2926 Dinoroseobacter shibae DFL 12 = DSM 16493 putative MaoC-like dehydratase YP_001534260.1 3085029 D 398580 CDS YP_001534261.1 159045467 5710778 3085522..3086475 1 NC_009952.1 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 3086475 ribF 5710778 ribF Dinoroseobacter shibae DFL 12 = DSM 16493 riboflavin biosynthesis protein YP_001534261.1 3085522 D 398580 CDS YP_001534262.1 159045468 5710779 3086472..3086963 1 NC_009952.1 COG: COG2983 - Uncharacterized conserved protein; PFAM: PF03692 - Uncharacterized protein family (UPF0153); hypothetical protein 3086963 5710779 Dshi_2928 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534262.1 3086472 D 398580 CDS YP_001534263.1 159045469 5710780 complement(3086930..3087763) 1 NC_009952.1 COG: COG0596 - Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily); PFAM: PF00561; PRINTS: PR00412, PR00111; PROSITE: PS00120; putative alpha/beta hydrolase 3087763 5710780 Dshi_2929 Dinoroseobacter shibae DFL 12 = DSM 16493 putative alpha/beta hydrolase YP_001534263.1 3086930 R 398580 CDS YP_001534264.1 159045470 5710781 complement(3087763..3088362) 1 NC_009952.1 COG: COG3917 - 2-hydroxychromene-2-carboxylate isomerase; SWISSPROT Q51948: 2-hydroxychromene-2-carboxylate isomerase nahD; putative 2-hydroxychromene-2-carboxylate isomerase 3088362 5710781 Dshi_2930 Dinoroseobacter shibae DFL 12 = DSM 16493 putative 2-hydroxychromene-2-carboxylate isomerase YP_001534264.1 3087763 R 398580 CDS YP_001534265.1 159045471 5710782 3088497..3089519 1 NC_009952.1 SWISSPROT P0A717: ribose-phosphate pyrophosphokinase; TIGRFAM: TIGR01251 ribose-phosphate pyrophosphokinase; COG: COG0462 - Phosphoribosylpyrophosphate synthetase; PFAM: PF00156; PROSITE: PS00114; ribose-phosphate pyrophosphokinase 3089519 prs 5710782 prs Dinoroseobacter shibae DFL 12 = DSM 16493 ribose-phosphate pyrophosphokinase YP_001534265.1 3088497 D 398580 CDS YP_001534266.1 159045472 5710783 complement(3089529..3089879) 1 NC_009952.1 associated with ATP synthase gene cluster; hypothetical protein 3089879 5710783 Dshi_2932 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534266.1 3089529 R 398580 CDS YP_001534267.1 159045473 5710784 complement(3089986..3090381) 1 NC_009952.1 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 3090381 atpC1 5710784 atpC1 Dinoroseobacter shibae DFL 12 = DSM 16493 ATP synhtase epsilon chain YP_001534267.1 3089986 R 398580 CDS YP_001534268.1 159045474 5710785 complement(3090391..3091815) 1 NC_009952.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. The beta chain is a regulatory subunit; F0F1 ATP synthase subunit beta 3091815 atpD2 5710785 atpD2 Dinoroseobacter shibae DFL 12 = DSM 16493 F0F1 ATP synthase subunit beta YP_001534268.1 3090391 R 398580 CDS YP_001534269.1 159045475 5710786 complement(3091833..3092705) 1 NC_009952.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is a regulatory subunit; F0F1 ATP synthase subunit gamma 3092705 atpG2 5710786 atpG2 Dinoroseobacter shibae DFL 12 = DSM 16493 F0F1 ATP synthase subunit gamma YP_001534269.1 3091833 R 398580 CDS YP_001534270.1 159045476 5710787 complement(3092718..3094256) 1 NC_009952.1 produces ATP from ADP in the presence of a proton gradient across the membrane; the alpha chain is a catalytic subunit; F0F1 ATP synthase subunit alpha 3094256 atpA1 5710787 atpA1 Dinoroseobacter shibae DFL 12 = DSM 16493 F0F1 ATP synthase subunit alpha YP_001534270.1 3092718 R 398580 CDS YP_001534271.1 159045477 5710788 complement(3094257..3094817) 1 NC_009952.1 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 3094817 atpH 5710788 atpH Dinoroseobacter shibae DFL 12 = DSM 16493 ATP synthase subunit delta YP_001534271.1 3094257 R 398580 CDS YP_001534272.1 159045478 5710789 complement(3095104..3095874) 1 NC_009952.1 hypothetical protein 3095874 5710789 Dshi_2938 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534272.1 3095104 R 398580 CDS YP_001534273.1 159045479 5710790 3096331..3098658 1 NC_009952.1 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 3098658 clpA 5710790 clpA Dinoroseobacter shibae DFL 12 = DSM 16493 ATP-dependent Clp protease ATP-binding subunit YP_001534273.1 3096331 D 398580 CDS YP_001534274.1 159045480 5710791 complement(3098707..3100653) 1 NC_009952.1 COG: COG1360 - Flagellar motor protein; PFAM: PF00691; PROSITE: PS51123; related to OmpA; hypothetical protein 3100653 5710791 Dshi_2940 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534274.1 3098707 R 398580 CDS YP_001534275.1 159045481 5710792 complement(3100657..3101940) 1 NC_009952.1 hypothetical protein 3101940 5710792 Dshi_2941 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534275.1 3100657 R 398580 CDS YP_001534276.1 159045482 5710793 complement(3102031..3102573) 1 NC_009952.1 PFAM: PF04752 - ChaC-like protein; SWISSPROT P39163: Cation transport protein chaC; COG: COG3703 - Uncharacterized protein involved in cation transport; putative cation transport protein 3102573 5710793 Dshi_2942 Dinoroseobacter shibae DFL 12 = DSM 16493 putative cation transport protein YP_001534276.1 3102031 R 398580 CDS YP_001534277.1 159045483 5710794 3102640..3103638 1 NC_009952.1 hypothetical protein 3103638 5710794 Dshi_2943 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534277.1 3102640 D 398580 CDS YP_001534278.1 159045484 5710795 complement(3103635..3104450) 1 NC_009952.1 COG: COG3921 - Uncharacterized protein conserved in bacteria; PFAM: PF06904; related to extensin; hypothetical protein 3104450 5710795 Dshi_2944 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534278.1 3103635 R 398580 CDS YP_001534279.1 159045485 5710796 complement(3104447..3105388) 1 NC_009952.1 dual function enzyme catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate and the formation of tyrosine from arogenate; cyclohexadienyl dehydrogenase 3105388 tyrC 5710796 tyrC Dinoroseobacter shibae DFL 12 = DSM 16493 cyclohexadienyl dehydrogenase YP_001534279.1 3104447 R 398580 CDS YP_001534280.1 159045486 5710797 complement(3105385..3106470) 1 NC_009952.1 catalyzes the formation of L-histidinol phosphate from imidazole-acetol phosphate and glutamate in histidine biosynthesis; histidinol-phosphate aminotransferase 3106470 hisC 5710797 hisC Dinoroseobacter shibae DFL 12 = DSM 16493 histidinol-phosphate aminotransferase YP_001534280.1 3105385 R 398580 CDS YP_001534281.1 159045487 5710798 complement(3106547..3107965) 1 NC_009952.1 SWISSPROT O32323: Homospermidine synthase; PFAM: PF06408 - Homospermidine synthase; COG: COG5310 - Homospermidine synthase; homospermidine synthase 3107965 hss 5710798 hss Dinoroseobacter shibae DFL 12 = DSM 16493 homospermidine synthase YP_001534281.1 3106547 R 398580 CDS YP_001534282.1 159045488 5710799 complement(3108054..3108674) 1 NC_009952.1 primary rRNA binding protein; nucleates 30S assembly; involved in translational accuracy with proteins S5 and S12; interacts with protein S5; involved in autogeneously regulating ribosomal proteins by binding to pseudoknot structures in the polycistronic mRNA; interacts with transcription complex and functions similar to protein NusA in antitermination; 30S ribosomal protein S4 3108674 rpsD 5710799 rpsD Dinoroseobacter shibae DFL 12 = DSM 16493 30S ribosomal protein S4 YP_001534282.1 3108054 R 398580 CDS YP_001534283.1 159045489 5710800 complement(3109029..3111326) 1 NC_009952.1 TIGRFAM: TIGR02504 ribonucleoside-diphosphate reductase, adenosylcobalamin-dependent; COG: COG0209 - Ribonucleotide reductase, alpha subunit; putative Vitamin B12-dependent ribonucleotide reductase 3111326 5710800 Dshi_2949 Dinoroseobacter shibae DFL 12 = DSM 16493 putative Vitamin B12-dependent ribonucleotide reductase YP_001534283.1 3109029 R 398580 CDS YP_001534284.1 159045490 5710801 3111468..3111923 1 NC_009952.1 PFAM: PF07370 - Protein of unknown function (DUF1489); COG: COG5458 - Uncharacterized conserved protein; hypothetical protein 3111923 5710801 Dshi_2950 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534284.1 3111468 D 398580 CDS YP_001534285.1 159045491 5710802 complement(3112137..3113279) 1 NC_009952.1 COG: COG0031 - Cysteine synthase; PFAM: PF00291; PROSITE: PS00216; similar to cysteine synthase; hypothetical protein 3113279 5710802 Dshi_2951 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534285.1 3112137 R 398580 CDS YP_001534286.1 159045492 5710803 complement(3113286..3114131) 1 NC_009952.1 TIGRFAM: TIGR00018 pantoate--beta-alanine ligase; COG: COG0414 - Panthothenate synthetase; PFAM: PF02569 - Pantoate-beta-alanine ligase; pantothenate synthase 3114131 panC 5710803 panC Dinoroseobacter shibae DFL 12 = DSM 16493 pantothenate synthase YP_001534286.1 3113286 R 398580 CDS YP_001534287.1 159045493 5710804 complement(3114128..3114847) 1 NC_009952.1 short form of enzyme; requires HisZ for function; catalyzes the formation of N'-5'-phosphoribosyl-ATP from phosphoribosyl pyrophosphate; crucial role in histidine biosynthesis; forms heteromultimer of HisG and HisZ; ATP phosphoribosyltransferase catalytic subunit 3114847 hisG 5710804 hisG Dinoroseobacter shibae DFL 12 = DSM 16493 ATP phosphoribosyltransferase catalytic subunit YP_001534287.1 3114128 R 398580 CDS YP_001534288.1 159045494 5710805 complement(3114844..3115950) 1 NC_009952.1 May allow the feedback regulation of ATP phosphoribosyltransferase activity by histidine; ATP phosphoribosyltransferase regulatory subunit 3115950 hisZ 5710805 hisZ Dinoroseobacter shibae DFL 12 = DSM 16493 ATP phosphoribosyltransferase regulatory subunit YP_001534288.1 3114844 R 398580 CDS YP_001534289.1 159045495 5710806 complement(3115954..3117447) 1 NC_009952.1 catalyzes a two-step reaction, first charging a histidine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; class II aminoacyl-tRNA synthetase; forms homodimers; some organisms have a paralogous gene, hisZ, that is similar to hisS and produces a protein that performs the first step in histidine biosynthesis along with HisG; histidyl-tRNA synthetase 3117447 hisS 5710806 hisS Dinoroseobacter shibae DFL 12 = DSM 16493 histidyl-tRNA synthetase YP_001534289.1 3115954 R 398580 CDS YP_001534290.1 159045496 5710807 3117536..3117745 1 NC_009952.1 PFAM: PF04102- SlyX; similar to slyX; hypothetical protein 3117745 5710807 Dshi_2956 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534290.1 3117536 D 398580 CDS YP_001534291.1 159045497 5710808 complement(3117972..3121466) 1 NC_009952.1 catalyzes DNA-template-directed extension of the 3'- end of a DNA strand by one nucleotide at a time; main replicative polymerase; DNA polymerase III subunit alpha 3121466 dnaE 5710808 dnaE Dinoroseobacter shibae DFL 12 = DSM 16493 DNA polymerase III subunit alpha YP_001534291.1 3117972 R 398580 CDS YP_001534292.1 159045498 5710809 3121712..3123163 1 NC_009952.1 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 3123163 xghB 5710809 xghB Dinoroseobacter shibae DFL 12 = DSM 16493 putative xanthine dehydrogenase YP_001534292.1 3121712 D 398580 CDS YP_001534293.1 159045499 5710810 3123160..3125505 1 NC_009952.1 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 3125505 xdhA 5710810 xdhA Dinoroseobacter shibae DFL 12 = DSM 16493 xanthine dehydrogenase molybdenum-binding subunit YP_001534293.1 3123160 D 398580 CDS YP_001534294.1 159045500 5710811 3125502..3126464 1 NC_009952.1 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 3126464 xdhC 5710811 xdhC Dinoroseobacter shibae DFL 12 = DSM 16493 putative xanthine dehydrogenase accessory protein YP_001534294.1 3125502 D 398580 CDS YP_001534295.1 159045501 5710812 3126461..3127996 1 NC_009952.1 COG: COG3845 - ABC-type uncharacterized transport systems, ATPase components; PFAM: PF00005; PROSITE: PS00211, PS50893; SMART: SM00382; ABC transporter ATP-binding protein 3127996 5710812 Dshi_2961 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC transporter ATP-binding protein YP_001534295.1 3126461 D 398580 CDS YP_001534296.1 159045502 5710813 3128219..3129304 1 NC_009952.1 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 3129304 5710813 Dshi_2962 Dinoroseobacter shibae DFL 12 = DSM 16493 putative ABC type branched chain amino acid transport system YP_001534296.1 3128219 D 398580 CDS YP_001534297.1 159045503 5710814 3129327..3130253 1 NC_009952.1 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 3130253 5710814 Dshi_2963 Dinoroseobacter shibae DFL 12 = DSM 16493 putative ABC type branched chain amino acid transport system YP_001534297.1 3129327 D 398580 CDS YP_001534298.1 159045504 5710815 3130346..3131509 1 NC_009952.1 PFAM: PF02608; SUPERFAMILY: SSF53822; putative basic membrane protein 3131509 5710815 Dshi_2964 Dinoroseobacter shibae DFL 12 = DSM 16493 putative basic membrane protein YP_001534298.1 3130346 D 398580 CDS YP_001534299.1 159045505 5710816 complement(3131594..3131788) 1 NC_009952.1 hypothetical protein 3131788 5710816 Dshi_2965 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534299.1 3131594 R 398580 CDS YP_001534300.1 159045506 5710817 complement(3131957..3132778) 1 NC_009952.1 TIGRFAM: TIGR00222 3-methyl-2-oxobutanoate hydroxymethyltransferase; COG: COG0413 - Ketopantoate hydroxymethyltransferase; PFAM: PF02548 Ketopantoate hydroxymethyltransferase; 3-methyl-2-oxobutanoate hydroxymethyltransferase 3132778 panB 5710817 panB Dinoroseobacter shibae DFL 12 = DSM 16493 3-methyl-2-oxobutanoate hydroxymethyltransferase YP_001534300.1 3131957 R 398580 CDS YP_001534301.1 159045507 5710818 3133015..3135510 1 NC_009952.1 COG: COG0404 - Glycine cleavage system T protein (aminomethyltransferase); PFAM: PF01266, PF01571, PF08669; bifunctional enzyme involved in glycine degradation 3135510 5710818 Dshi_2967 Dinoroseobacter shibae DFL 12 = DSM 16493 bifunctional enzyme involved in glycine degradation YP_001534301.1 3133015 D 398580 CDS YP_001534302.1 159045508 5710819 3135780..3136373 1 NC_009952.1 hypothetical protein 3136373 5710819 Dshi_2968 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534302.1 3135780 D 398580 CDS YP_001534303.1 159045509 5710820 complement(3136386..3136724) 1 NC_009952.1 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 3136724 5710820 Dshi_2969 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534303.1 3136386 R 398580 CDS YP_001534304.1 159045510 5710821 complement(3136810..3137796) 1 NC_009952.1 COG: COG1052 - Lactate dehydrogenase and related dehydrogenases; PFAM: PF00389, PF02826; PROSITE: PS00065, PS00671; glyoxylate reductase 3137796 gyaR 5710821 gyaR Dinoroseobacter shibae DFL 12 = DSM 16493 glyoxylate reductase YP_001534304.1 3136810 R 398580 CDS YP_001534305.1 159045511 5710822 3137930..3138544 1 NC_009952.1 PFAM: PF06347; COG: COG3807 - Uncharacterized protein conserved in bacteria; hypothetical protein 3138544 5710822 Dshi_2971 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534305.1 3137930 D 398580 CDS YP_001534306.1 159045512 5710823 complement(3138517..3139428) 1 NC_009952.1 PFAM: PF00989, PROSITE: PS50112, SMART: SM00091; hypothetical protein 3139428 5710823 Dshi_2972 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534306.1 3138517 R 398580 CDS YP_001534307.1 159045513 5710824 complement(3139524..3141545) 1 NC_009952.1 SWISSPROT P27236: Peptidyl-dipeptidase dcp; COG: COG0339 - Zn-dependent oligopeptidases; PFAM: PF01432; PROSITE: PS00142; peptidyl-dipeptidase 3141545 dcp 5710824 dcp Dinoroseobacter shibae DFL 12 = DSM 16493 peptidyl-dipeptidase YP_001534307.1 3139524 R 398580 CDS YP_001534308.1 159045514 5710825 complement(3141645..3142685) 1 NC_009952.1 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 3142685 moeB 5710825 moeB Dinoroseobacter shibae DFL 12 = DSM 16493 molydopterin biosynthesis protein YP_001534308.1 3141645 R 398580 CDS YP_001534309.1 159045515 5710826 complement(3142690..3143157) 1 NC_009952.1 PFAM: PF00692- dUTPase; TIGRFAM: TIGR00576 deoxyuridine 5-triphosphate nucleotidohydrolase (dut); COG: COG0756 - dUTPase; deoxyuridine 5'-triphosphate nucleotidohydrolase 3143157 dut 5710826 dut Dinoroseobacter shibae DFL 12 = DSM 16493 deoxyuridine 5'-triphosphate nucleotidohydrolase YP_001534309.1 3142690 R 398580 CDS YP_001534310.1 159045516 5710827 complement(3143154..3144347) 1 NC_009952.1 catalyzes the conjugation of cysteine to 4'-phosphopantothenate to form 4-phosphopantothenoylcysteine, which is then decarboxylated to form 4'-phosphopantotheine; bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase 3144347 coaBC 5710827 coaBC Dinoroseobacter shibae DFL 12 = DSM 16493 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase YP_001534310.1 3143154 R 398580 CDS YP_001534311.1 159045517 5710828 complement(3144414..3145166) 1 NC_009952.1 PFAM: PF04187 - Protein of unknown function DUF399; COG: COG3016 - Uncharacterized iron-regulated protein; hypothetical protein 3145166 5710828 Dshi_2977 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534311.1 3144414 R 398580 CDS YP_001534312.1 159045518 5710829 complement(3145214..3146095) 1 NC_009952.1 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 3146095 rpoH2 5710829 rpoH2 Dinoroseobacter shibae DFL 12 = DSM 16493 RNA polymerase factor sigma-32 YP_001534312.1 3145214 R 398580 CDS YP_001534313.1 159045519 5710830 3146213..3146737 1 NC_009952.1 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 3146737 5710830 Dshi_2979 Dinoroseobacter shibae DFL 12 = DSM 16493 putative bifunctional adenosylcobalamin biosynthesis protein YP_001534313.1 3146213 D 398580 CDS YP_001534314.1 159045520 5710831 3146734..3147306 1 NC_009952.1 PFAM: PF00300; related to phosphoglycerate mutase; hypothetical protein 3147306 5710831 Dshi_2980 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534314.1 3146734 D 398580 CDS YP_001534315.1 159045521 5710832 3147482..3148744 1 NC_009952.1 COG: COG2041 - Sulfite oxidase and related enzymes; PFAM: PF00174, PF03404; PRINTS: PR00407; SUPERFAMILY: SSF56524, SSF81296; putative molydopterin-binding oxidoreductase 3148744 5710832 Dshi_2981 Dinoroseobacter shibae DFL 12 = DSM 16493 putative molydopterin-binding oxidoreductase YP_001534315.1 3147482 D 398580 CDS YP_001534316.1 159045522 5710833 3148819..3149169 1 NC_009952.1 PROSITE: PS51257; SUPERFAMILY: SSF46626; related to cytochrome c; hypothetical protein 3149169 5710833 Dshi_2982 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534316.1 3148819 D 398580 CDS YP_001534317.1 159045523 5710834 3149233..3150231 1 NC_009952.1 COG:COG2130 - Putative NADP-dependent oxidoreductases; PFAM: PF00107; SUPERFAMILY: SSF50129; PANTHER: Alcohol dehydrogenase related; related to zinc-binding dehydrogenase; hypothetical protein 3150231 5710834 Dshi_2983 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534317.1 3149233 D 398580 CDS YP_001534318.1 159045524 5710835 3150311..3151009 1 NC_009952.1 COG: COG0625 - Glutathione S-transferase; SUPERFAMILY: SSF52833, SSF47616; Gene3D: G3DSA:3.40.30.10; similar to glutathione S-transferase; hypothetical protein 3151009 5710835 Dshi_2984 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534318.1 3150311 D 398580 CDS YP_001534319.1 159045525 5710836 complement(3151506..3152165) 1 NC_009952.1 COG: COG1802 - Transcriptional regulators; PFAM: PF00392, PF07729; PROSITE: PS50949; Gene3D: G3DSA:1.10.10.10; GntR type; HTH-type transcriptional regulator 3152165 5710836 Dshi_2985 Dinoroseobacter shibae DFL 12 = DSM 16493 HTH-type transcriptional regulator YP_001534319.1 3151506 R 398580 CDS YP_001534320.1 159045526 5710837 complement(3152197..3152889) 1 NC_009952.1 COG: COG1451 - Predicted metal-dependent hydrolase; PFAM: PF01863 - Protein of unknown function DUF45; PROSITE: PS00142; hypothetical protein 3152889 5710837 Dshi_2986 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534320.1 3152197 R 398580 CDS YP_001534321.1 159045527 5710838 3152992..3153318 1 NC_009952.1 TIGRFAM: TIGR02300 conserved hypothetical protein; PROSITE: PS00018; hypothetical protein 3153318 5710838 Dshi_2987 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534321.1 3152992 D 398580 CDS YP_001534322.1 159045528 5710840 3153753..3154094 1 NC_009952.1 PFAM: PF01906; COG: COG0393 - Uncharacterized conserved protein; hypothetical protein 3154094 5710840 Dshi_2988 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534322.1 3153753 D 398580 CDS YP_001534323.1 159045529 5710841 complement(3154359..3154565) 1 NC_009952.1 PROSITE: PS51257; related to membrane lipoprotein; hypothetical protein 3154565 5710841 Dshi_2989 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534323.1 3154359 R 398580 CDS YP_001534324.1 159045530 5710842 3154721..3155620 1 NC_009952.1 COG: COG4333 - Uncharacterized protein conserved in bacteria; PFAM: PF00126, PF03466; PROSITE: PS5093; Gene3D: G3DSA:1.10.10.10; LysR family; HTH-type transcriptional regulator 3155620 5710842 Dshi_2990 Dinoroseobacter shibae DFL 12 = DSM 16493 HTH-type transcriptional regulator YP_001534324.1 3154721 D 398580 CDS YP_001534325.1 159045531 5710843 3155748..3156266 1 NC_009952.1 PFAM: PF07799-Protein of unknown function (DUF1643); COG: COG4333 - Uncharacterized protein conserved in bacteria; hypothetical protein 3156266 5710843 Dshi_2991 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534325.1 3155748 D 398580 CDS YP_001534326.1 159045532 5710844 3156259..3157146 1 NC_009952.1 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 3157146 dehH 5710844 dehH Dinoroseobacter shibae DFL 12 = DSM 16493 Haloacetate dehalogenase H-1 YP_001534326.1 3156259 D 398580 CDS YP_001534327.1 159045533 5710845 complement(3157143..3157856) 1 NC_009952.1 hypothetical protein 3157856 5710845 Dshi_2993 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534327.1 3157143 R 398580 CDS YP_001534328.1 159045534 5710846 3158099..3158368 1 NC_009952.1 primary rRNA binding protein; helps nucleate assembly of 30S; binds directly to the 16S rRNA and an intersubunit bridge to the 23S rRNA; autoregulates translation through interactions with the mRNA leader sequence; 30S ribosomal protein S15 3158368 rpsO 5710846 rpsO Dinoroseobacter shibae DFL 12 = DSM 16493 30S ribosomal protein S15 YP_001534328.1 3158099 D 398580 CDS YP_001534329.1 159045535 5710847 complement(3158467..3158823) 1 NC_009952.1 hypothetical protein 3158823 5710847 Dshi_2995 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534329.1 3158467 R 398580 CDS YP_001534330.1 159045536 5710848 complement(3158863..3159771) 1 NC_009952.1 COG: COG3568 - Metal-dependent hydrolase; PFAM: PF03372; PROSITE: PS51257; SUPERFAMILY: SSF56219; similar to Endonuclease/Exonuclease/Phosphatase family; hypothetical protein 3159771 5710848 Dshi_2996 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534330.1 3158863 R 398580 CDS YP_001534331.1 159045537 5710849 3159996..3162131 1 NC_009952.1 SWISSPROT P05055: Polyribonucleotide nucleotidyltransferase; COG: COG1185 - Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase); PFAM: PF01138, PF00575, PF00013, PF03725, PF03726; SMART: SM00322; polynucleotide phosphorylase/polyadenylase 3162131 pnp 5710849 pnp Dinoroseobacter shibae DFL 12 = DSM 16493 polynucleotide phosphorylase/polyadenylase YP_001534331.1 3159996 D 398580 CDS YP_001534332.1 159045538 5710850 3162333..3164813 1 NC_009952.1 COG: COG0668 - Small-conductance mechanosensitive channel; PFAM: PF00924; SUPERFAMILY: SSF82689, SSF82861, SSF50182; putative mechanosensitive ion channel 3164813 5710850 Dshi_2998 Dinoroseobacter shibae DFL 12 = DSM 16493 putative mechanosensitive ion channel YP_001534332.1 3162333 D 398580 CDS YP_001534333.1 159045539 5710851 complement(3164958..3166478) 1 NC_009952.1 catalyzes the formation of malonyl-CoA from malonate and CoA; malonyl-CoA synthase 3166478 fadD1 5710851 fadD1 Dinoroseobacter shibae DFL 12 = DSM 16493 malonyl-CoA synthase YP_001534333.1 3164958 R 398580 CDS YP_001534334.1 159045540 5710852 complement(3166482..3167735) 1 NC_009952.1 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 3167735 mcd 5710852 mcd Dinoroseobacter shibae DFL 12 = DSM 16493 malonyl-CoA decarboxylase YP_001534334.1 3166482 R 398580 CDS YP_001534335.1 159045541 5710853 complement(3167732..3169048) 1 NC_009952.1 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 3169048 dctM2 5710853 dctM2 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP dicarboxylate transporter subunit DctM YP_001534335.1 3167732 R 398580 CDS YP_001534336.1 159045542 5710854 complement(3169048..3169599) 1 NC_009952.1 PFAM: Tripartite ATP-independent periplasmic transporter DctQ component . BLAST hit to Proteobacteria; TRAP dicarboxylate transporter subunit DctQ 3169599 dctQ4 5710854 dctQ4 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP dicarboxylate transporter subunit DctQ YP_001534336.1 3169048 R 398580 CDS YP_001534337.1 159045543 5710855 complement(3169667..3170650) 1 NC_009952.1 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 3170650 dctP4 5710855 dctP4 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP dicarboxylate transporter subunit DctP YP_001534337.1 3169667 R 398580 CDS YP_001534338.1 159045544 5710856 3170785..3171441 1 NC_009952.1 PFAM: regulatory protein GntR HTH; GntR domain protein KEGG: rde:RD1_1479 GntR-family transcription regulator, putative; GntR family; transcriptional regulator 3171441 5710856 Dshi_3004 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001534338.1 3170785 D 398580 CDS YP_001534339.1 159045545 5710857 3171549..3171857 1 NC_009952.1 hypothetical protein 3171857 5710857 Dshi_3005 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534339.1 3171549 D 398580 CDS YP_001534340.1 159045546 5710858 complement(3171858..3172556) 1 NC_009952.1 PFAM: ribulose-phosphate 3-epimerase KEGG: rsp:RSP_2864 pentose-5-phosphate-3-epimerase; ribulose-phosphate 3-epimerase 3172556 rpe 5710858 rpe Dinoroseobacter shibae DFL 12 = DSM 16493 ribulose-phosphate 3-epimerase YP_001534340.1 3171858 R 398580 CDS YP_001534341.1 159045547 5710859 complement(3172670..3175837) 1 NC_009952.1 PFAM: glycoside hydrolase family 38; glycosyl hydrolase 38 domain protein; Glycoside hydrolase family 38 central region KEGG: jan:Jann_2057 alpha-mannosidase; alpha-mannosidase 3175837 ybgG 5710859 ybgG Dinoroseobacter shibae DFL 12 = DSM 16493 alpha-mannosidase YP_001534341.1 3172670 R 398580 CDS YP_001534342.1 159045548 5710860 complement(3175881..3177611) 1 NC_009952.1 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 3177611 5710860 Dshi_3008 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC transporter-like protein YP_001534342.1 3175881 R 398580 CDS YP_001534343.1 159045549 5710861 complement(3177623..3178567) 1 NC_009952.1 contain signal peptide und Transmembrane Helices; MSD; ABC transporter-like protein 3178567 5710861 Dshi_3009 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC transporter-like protein YP_001534343.1 3177623 R 398580 CDS YP_001534344.1 159045550 5710862 complement(3178564..3179583) 1 NC_009952.1 contain signal peptide und Transmembrane Helices; MSD; ABC transporter-like protein 3179583 5710862 Dshi_3010 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC transporter-like protein YP_001534344.1 3178564 R 398580 CDS YP_001534345.1 159045551 5710863 complement(3179758..3181491) 1 NC_009952.1 contain signal peptide, RBS 5nt upstream; periplasmic component; ABC transporter-like protein 3181491 5710863 Dshi_3011 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC transporter-like protein YP_001534345.1 3179758 R 398580 CDS YP_001534346.1 159045552 5710864 complement(3181609..3182298) 1 NC_009952.1 KEGG: jan:Jann_2052 Zn-dependent hydrolase of the beta-lactamase fold; putative Zn-dependent hydrolase of the beta-lactamase fold family 3182298 5710864 Dshi_3012 Dinoroseobacter shibae DFL 12 = DSM 16493 putative Zn-dependent hydrolase of the beta-lactamase fold family YP_001534346.1 3181609 R 398580 CDS YP_001534347.1 159045553 5710865 3182474..3182914 1 NC_009952.1 PFAM: protein of unknown function DUF606 KEGG: jan:Jann_1137 protein of unknown function DUF606 ; TMH; hypothetical protein 3182914 5710865 Dshi_3013 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534347.1 3182474 D 398580 CDS YP_001534348.1 159045554 5710866 complement(3182924..3183751) 1 NC_009952.1 PFAM: Phytanoyl-CoA dioxygenase KEGG: jan:Jann_2051 phytanoyl-CoA dioxygenase; phytanoyl-CoA dioxygenase 3183751 5710866 Dshi_3014 Dinoroseobacter shibae DFL 12 = DSM 16493 phytanoyl-CoA dioxygenase YP_001534348.1 3182924 R 398580 CDS YP_001534349.1 159045555 5710867 3183841..3184692 1 NC_009952.1 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 3184692 5710867 Dshi_3015 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001534349.1 3183841 D 398580 CDS YP_001534350.1 159045556 5710868 3184761..3185780 1 NC_009952.1 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 3185780 deoC 5710868 deoC Dinoroseobacter shibae DFL 12 = DSM 16493 deoxyribose-phosphate aldolase YP_001534350.1 3184761 D 398580 CDS YP_001534351.1 159045557 5710869 3185825..3188167 1 NC_009952.1 PFAM: aldehyde dehydrogenase KEGG: sil:SPO3368 aldehyde dehydrogenase family protein; aldehyde dehydrogenase 3188167 ald 5710869 ald Dinoroseobacter shibae DFL 12 = DSM 16493 aldehyde dehydrogenase YP_001534351.1 3185825 D 398580 CDS YP_001534352.1 159045558 5710870 complement(3188327..3188980) 1 NC_009952.1 PFAM: protein of unknown function DUF1523; hypothetical protein 3188980 5710870 Dshi_3018 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534352.1 3188327 R 398580 CDS YP_001534353.1 159045559 5710871 complement(3188982..3189224) 1 NC_009952.1 hypothetical protein 3189224 5710871 Dshi_3019 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534353.1 3188982 R 398580 CDS YP_001534354.1 159045560 5710872 3189351..3190646 1 NC_009952.1 dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase (DapE), catalyzes the hydrolysis of N-succinyl-L,Ldiaminopimelate L,L-SDAP to L,L-diaminopimelate and succinate. It is a metalloprotease containing dinuclear active sites. Its structure is similar to the carboxypeptidase G2 from Pseudomonas sp. strain RS-16 and the aminopeptidase from Aeromonas proteolytica.; succinyl-diaminopimelate desuccinylase 3190646 dapE2 5710872 dapE2 Dinoroseobacter shibae DFL 12 = DSM 16493 succinyl-diaminopimelate desuccinylase YP_001534354.1 3189351 D 398580 CDS YP_001534355.1 159045561 5710873 3190673..3192130 1 NC_009952.1 PFAM: aldehyde dehydrogenase KEGG: sil:SPO0097 aldehyde dehydrogenase family protein; Gamma-Glu-gamma-aminobutyraldehyde dehydrogenase; gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase 3192130 puuC 5710873 puuC Dinoroseobacter shibae DFL 12 = DSM 16493 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase YP_001534355.1 3190673 D 398580 CDS YP_001534356.1 159045562 5710874 complement(3192313..3193314) 1 NC_009952.1 PFAM: PfkB domain protein KEGG: jan:Jann_1671 PfkB; rde:RD1_0962 PfkB family kinase, putative; PfkB domain-containing protein 3193314 5710874 Dshi_3022 Dinoroseobacter shibae DFL 12 = DSM 16493 PfkB domain-containing protein YP_001534356.1 3192313 R 398580 CDS YP_001534357.1 159045563 5710875 complement(3193311..3193955) 1 NC_009952.1 KEGG: sil:SPO3581 endonuclease III TIGRFAM: endonuclease III PFAM: helix-hairpin-helix motif; HhH-GPD family protein SMART: iron-sulfur cluster loop; endonuclease III 3193955 nth 5710875 nth Dinoroseobacter shibae DFL 12 = DSM 16493 endonuclease III YP_001534357.1 3193311 R 398580 CDS YP_001534358.1 159045564 5710876 3194067..3194930 1 NC_009952.1 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 3194930 ada 5710876 ada Dinoroseobacter shibae DFL 12 = DSM 16493 ADA regulatory protein YP_001534358.1 3194067 D 398580 CDS YP_001534359.1 159045565 5710877 3195037..3195663 1 NC_009952.1 PFAM: OmpA/MotB domain protein; 17 kDa surface antigen KEGG: rsq:Rsph17025_0195 OmpA/MotB domain protein; OmpA/MotB domain-containing protein 3195663 5710877 Dshi_3025 Dinoroseobacter shibae DFL 12 = DSM 16493 OmpA/MotB domain-containing protein YP_001534359.1 3195037 D 398580 CDS YP_001534360.1 159045566 5710878 3195719..3196486 1 NC_009952.1 PFAM: regulatory protein GntR HTH; GntR domain protein KEGG: rde:RD1_1326 pdhR; pyruvate dehydrogenase complex repressor; pyruvate dehydrogenase complex repressor 3196486 pdhR 5710878 pdhR Dinoroseobacter shibae DFL 12 = DSM 16493 pyruvate dehydrogenase complex repressor YP_001534360.1 3195719 D 398580 CDS YP_001534361.1 159045567 5710879 complement(3196549..3197109) 1 NC_009952.1 produces ATP from ADP in the presence of a proton gradient across the membrane; subunit B is part of the membrane proton channel.; F0F1 ATP synthase subunit B 3197109 atpF2 5710879 atpF2 Dinoroseobacter shibae DFL 12 = DSM 16493 F0F1 ATP synthase subunit B YP_001534361.1 3196549 R 398580 CDS YP_001534362.1 159045568 5710880 complement(3197114..3197638) 1 NC_009952.1 produces ATP from ADP in the presence of a proton gradient across the membrane; subunit B' is part of the membrane proton channel.; F0F1 ATP synthase subunit B' 3197638 atpX 5710880 atpX Dinoroseobacter shibae DFL 12 = DSM 16493 F0F1 ATP synthase subunit B' YP_001534362.1 3197114 R 398580 CDS YP_001534363.1 159045569 5710881 complement(3197716..3197940) 1 NC_009952.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit C is part of the membrane proton channel F0; F0F1 ATP synthase subunit C 3197940 atpE2 5710881 atpE2 Dinoroseobacter shibae DFL 12 = DSM 16493 F0F1 ATP synthase subunit C YP_001534363.1 3197716 R 398580 CDS YP_001534364.1 159045570 5710882 complement(3198004..3198750) 1 NC_009952.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit A is part of the membrane proton channel F0; F0F1 ATP synthase subunit A 3198750 atpB1 5710882 atpB1 Dinoroseobacter shibae DFL 12 = DSM 16493 F0F1 ATP synthase subunit A YP_001534364.1 3198004 R 398580 CDS YP_001534365.1 159045571 5710883 complement(3198754..3199086) 1 NC_009952.1 KEGG: rde:RD1_1321 ATP synthase F0, subunit I; I subunit; ATP synthase F0 3199086 atpI 5710883 atpI Dinoroseobacter shibae DFL 12 = DSM 16493 ATP synthase F0 YP_001534365.1 3198754 R 398580 CDS YP_001534366.1 159045572 5710884 complement(3199429..3201147) 1 NC_009952.1 PFAM: Heparinase II/III family protein KEGG: rde:RD1_0654 hypothetical protein; sit:TM1040_0090 heparinase II/III-like; heparinase II/III family protein 3201147 5710884 Dshi_3032 Dinoroseobacter shibae DFL 12 = DSM 16493 heparinase II/III family protein YP_001534366.1 3199429 R 398580 CDS YP_001534367.1 159045573 5710885 complement(3201216..3202547) 1 NC_009952.1 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 3202547 rsmB1 5710885 rsmB1 Dinoroseobacter shibae DFL 12 = DSM 16493 ribosomal RNA small subunit methyltransferase B YP_001534367.1 3201216 R 398580 CDS YP_001534368.1 159045574 5710886 3202651..3202875 1 NC_009952.1 PFAM: protein of unknown function DUF1674; hypothetical protein 3202875 5710886 Dshi_3034 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534368.1 3202651 D 398580 CDS YP_001534369.1 159045575 5710887 complement(3202894..3203289) 1 NC_009952.1 KEGG: jan:Jann_4038 hypothetical protein; hypothetical protein 3203289 5710887 Dshi_3035 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534369.1 3202894 R 398580 CDS YP_001534370.1 159045576 5710888 complement(3203392..3206619) 1 NC_009952.1 colocated with MFP subunit; pfam00873,; RND family, RND subunit; efflux transporter 3206619 5710888 Dshi_3036 Dinoroseobacter shibae DFL 12 = DSM 16493 efflux transporter YP_001534370.1 3203392 R 398580 CDS YP_001534371.1 159045577 5710889 complement(3206616..3207824) 1 NC_009952.1 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 3207824 5710889 Dshi_3037 Dinoroseobacter shibae DFL 12 = DSM 16493 efflux transporter YP_001534371.1 3206616 R 398580 CDS YP_001534372.1 159045578 5710890 3207941..3208633 1 NC_009952.1 PFAM: regulatory protein TetR KEGG: rpb:RPB_3412 transcriptional regulator, TetR family; TetR family; transcriptional regulator 3208633 5710890 Dshi_3038 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001534372.1 3207941 D 398580 CDS YP_001534373.1 159045579 5710891 complement(3208637..3209044) 1 NC_009952.1 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 3209044 5710891 Dshi_3039 Dinoroseobacter shibae DFL 12 = DSM 16493 BLUF domain-containing protein YP_001534373.1 3208637 R 398580 CDS YP_001534374.1 159045580 5710892 complement(3209163..3209972) 1 NC_009952.1 catalyzes the reduction of 2,3-dihydrodipicolinate to 2,3,4,5-tetrahydrodipicolinate in lysine and diaminopimelate biosynthesis; dihydrodipicolinate reductase 3209972 dapB 5710892 dapB Dinoroseobacter shibae DFL 12 = DSM 16493 dihydrodipicolinate reductase YP_001534374.1 3209163 R 398580 CDS YP_001534375.1 159045581 5710893 3210091..3210498 1 NC_009952.1 associates with free 30S ribosomal subunits; essential for efficient processing of 16S rRNA; in Escherichia coli rbfA is induced by cold shock; ribosome-binding factor A 3210498 rbfA 5710893 rbfA Dinoroseobacter shibae DFL 12 = DSM 16493 ribosome-binding factor A YP_001534375.1 3210091 D 398580 CDS YP_001534376.1 159045582 5710894 3210502..3211416 1 NC_009952.1 catalyzes isomerization of specific uridines in RNA to pseudouridine; responsible for residues in T loops of many tRNAs; tRNA pseudouridine synthase B 3211416 truB 5710894 truB Dinoroseobacter shibae DFL 12 = DSM 16493 tRNA pseudouridine synthase B YP_001534376.1 3210502 D 398580 CDS YP_001534377.1 159045583 5710895 3211416..3211694 1 NC_009952.1 PFAM: protein of unknown function DUF1294 KEGG: ret:RHE_CH01861 putative inner membrane protein, predicted 3TMH; hypothetical protein 3211694 5710895 Dshi_3043 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534377.1 3211416 D 398580 CDS YP_001534378.1 159045584 5710896 3211817..3213247 1 NC_009952.1 PFAM: Tannase and feruloyl esterase KEGG: psa:PST_1665 tannase precursor; BLAST hit to Rhodobacteraceae, RBS 5nt upstream; feruloyl esterase 3213247 5710896 Dshi_3044 Dinoroseobacter shibae DFL 12 = DSM 16493 feruloyl esterase YP_001534378.1 3211817 D 398580 CDS YP_001534379.1 159045585 5710897 3213310..3214326 1 NC_009952.1 PFAM: glycosyl transferase family 2 KEGG: rde:RD1_0635 glycosyl transferase, putative; putative glycosyl transferase 3214326 5710897 Dshi_3045 Dinoroseobacter shibae DFL 12 = DSM 16493 putative glycosyl transferase YP_001534379.1 3213310 D 398580 CDS YP_001534380.1 159045586 5710898 complement(3214330..3215577) 1 NC_009952.1 PFAM: MOFRL domain protein KEGG: rso:RSp1449 probable hydroxypyruvate reductase oxidoreductase protein; hydroxypyruvate reductase 3215577 ttuD 5710898 ttuD Dinoroseobacter shibae DFL 12 = DSM 16493 hydroxypyruvate reductase YP_001534380.1 3214330 R 398580 CDS YP_001534381.1 159045587 5710899 complement(3215574..3216458) 1 NC_009952.1 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 3216458 glxR 5710899 glxR Dinoroseobacter shibae DFL 12 = DSM 16493 2-hydroxy-3-oxopropionate reductase YP_001534381.1 3215574 R 398580 CDS YP_001534382.1 159045588 5710900 3216579..3217361 1 NC_009952.1 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 3217361 5710900 Dshi_3048 Dinoroseobacter shibae DFL 12 = DSM 16493 GntR family transcriptional regulator YP_001534382.1 3216579 D 398580 CDS YP_001534383.1 159045589 5710901 complement(3217365..3218309) 1 NC_009952.1 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 3218309 5710901 Dshi_3049 Dinoroseobacter shibae DFL 12 = DSM 16493 NAD-dependent epimerase/dehydratase YP_001534383.1 3217365 R 398580 CDS YP_001534384.1 159045590 5710902 complement(3218553..3219509) 1 NC_009952.1 PFAM: HpcH/HpaI aldolase KEGG: rsq:Rsph17025_2481 citrate (pro-3S)-lyase; citrate lyase subunit beta 3219509 citE2 5710902 citE2 Dinoroseobacter shibae DFL 12 = DSM 16493 citrate lyase subunit beta YP_001534384.1 3218553 R 398580 CDS YP_001534385.1 159045591 5710903 complement(3219781..3220143) 1 NC_009952.1 hypothetical protein 3220143 5710903 Dshi_3051 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534385.1 3219781 R 398580 CDS YP_001534386.1 159045592 5710904 complement(3220290..3220997) 1 NC_009952.1 N-terminal elongation? Mu phage related?; Mu-like prophage I protein 3220997 5710904 Dshi_3052 Dinoroseobacter shibae DFL 12 = DSM 16493 Mu-like prophage I protein YP_001534386.1 3220290 R 398580 CDS YP_001534387.1 159045593 5710905 complement(3221433..3222143) 1 NC_009952.1 rde:RD1_0339 transposase, putative; putative transposase 3222143 5710905 Dshi_3053 Dinoroseobacter shibae DFL 12 = DSM 16493 putative transposase YP_001534387.1 3221433 R 398580 CDS YP_001534388.1 159045594 5710906 complement(3222427..3223182) 1 NC_009952.1 PFAM: phospholipid/glycerol acyltransferase KEGG: sit:TM1040_3500 phospholipid/glycerol acyltransferas,COG0204; phospholipid/glycerol acyltransferase 3223182 5710906 Dshi_3054 Dinoroseobacter shibae DFL 12 = DSM 16493 phospholipid/glycerol acyltransferase YP_001534388.1 3222427 R 398580 CDS YP_001534389.1 159045595 5710907 complement(3223182..3224075) 1 NC_009952.1 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 3224075 5710907 Dshi_3055 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534389.1 3223182 R 398580 CDS YP_001534390.1 159045596 5710908 complement(3224072..3224743) 1 NC_009952.1 PFAM: ABC transporter related SMART: AAA ATPase KEGG: rde:RD1_1599 ftsE; cell division ATP-binding protein, putative; ABC transporter-like protein 3224743 ftsE 5710908 ftsE Dinoroseobacter shibae DFL 12 = DSM 16493 ABC transporter-like protein YP_001534390.1 3224072 R 398580 CDS YP_001534391.1 159045597 5710909 3224908..3225654 1 NC_009952.1 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 3225654 5710909 Dshi_3057 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534391.1 3224908 D 398580 CDS YP_001534392.1 159045598 5710910 complement(3225943..3228627) 1 NC_009952.1 TIGRFAM: conserved hypothetical protein TIGR02302 KEGG: sil:SPO0335 hypothetical protein; hypothetical protein 3228627 5710910 Dshi_3058 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534392.1 3225943 R 398580 CDS YP_001534393.1 159045599 5710911 complement(3228631..3229926) 1 NC_009952.1 TIGRFAM: diaminopimelate decarboxylase PFAM: Orn/DAP/Arg decarboxylase 2 KEGG: jan:Jann_0481 diaminopimelate decarboxylase; DAP decarboxylase; diaminopimelate decarboxylase 3229926 lysA 5710911 lysA Dinoroseobacter shibae DFL 12 = DSM 16493 diaminopimelate decarboxylase YP_001534393.1 3228631 R 398580 CDS YP_001534394.1 159045600 5710912 complement(3230005..3230340) 1 NC_009952.1 KEGG: rsq:Rsph17025_2447 hypothetical protein, RBS; hypothetical protein 3230340 5710912 Dshi_3060 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534394.1 3230005 R 398580 CDS YP_001534395.1 159045601 5710913 complement(3230492..3230662) 1 NC_009952.1 hypothetical protein 3230662 5710913 Dshi_3061 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534395.1 3230492 R 398580 CDS YP_001534396.1 159045602 5710914 complement(3230659..3232050) 1 NC_009952.1 catalyzes the formation of arginine from (N-L-arginino)succinate; argininosuccinate lyase 3232050 argH 5710914 argH Dinoroseobacter shibae DFL 12 = DSM 16493 argininosuccinate lyase YP_001534396.1 3230659 R 398580 CDS YP_001534397.1 159045603 5710915 3232085..3232660 1 NC_009952.1 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 3232660 tlpA 5710915 tlpA Dinoroseobacter shibae DFL 12 = DSM 16493 Thiol:disulfide interchange protein TlpA YP_001534397.1 3232085 D 398580 CDS YP_001534398.1 159045604 5710916 complement(3232657..3233226) 1 NC_009952.1 KEGG: rsq:Rsph17025_2464 DNA-3-methyladenine glycosylase I TIGRFAM: DNA-3-methyladenine glycosylase I PFAM: methyladenine glycosylase; DNA-3-methyladenine glycosylase 1 3233226 tag 5710916 tag Dinoroseobacter shibae DFL 12 = DSM 16493 DNA-3-methyladenine glycosylase 1 YP_001534398.1 3232657 R 398580 CDS YP_001534399.1 159045605 5710917 3233338..3234183 1 NC_009952.1 PFAM: EAL domain protein KEGG: pde:Pden_2025 diguanylate phosphodiesterase , DUF2; EAL domain-containing protein 3234183 5710917 Dshi_3065 Dinoroseobacter shibae DFL 12 = DSM 16493 EAL domain-containing protein YP_001534399.1 3233338 D 398580 CDS YP_001534400.1 159045606 5710918 3234503..3235678 1 NC_009952.1 Catalyzes the synthesis of acetoacetyl coenzyme A from two molecules of acetyl coenzyme A. It can also act as a thiolase, catalyzing the reverse reaction and generating two-carbon units from the four-carbon product of fatty acid oxidation; in Rhizobia and Ralstonia is involved in PHB biosynthesis; acetyl-CoA acetyltransferase 3235678 atoB 5710918 atoB Dinoroseobacter shibae DFL 12 = DSM 16493 acetyl-CoA acetyltransferase YP_001534400.1 3234503 D 398580 CDS YP_001534401.1 159045607 5710919 3235779..3236501 1 NC_009952.1 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 3236501 fabG1 5710919 fabG1 Dinoroseobacter shibae DFL 12 = DSM 16493 acetoacetyl-CoA reductase YP_001534401.1 3235779 D 398580 CDS YP_001534402.1 159045608 5710920 3236804..3237751 1 NC_009952.1 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 3237751 5710920 Dshi_3068 Dinoroseobacter shibae DFL 12 = DSM 16493 DNA-binding transcriptional activator GcvA YP_001534402.1 3236804 D 398580 CDS YP_001534403.1 159045609 5710921 complement(3237811..3237978) 1 NC_009952.1 PFAM: protein of unknown function DUF465 KEGG: pde:Pden_2028 protein of unknown function DUF465, COG5570; hypothetical protein 3237978 5710921 Dshi_3069 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534403.1 3237811 R 398580 CDS YP_001534404.1 159045610 5710922 complement(3238074..3238844) 1 NC_009952.1 KEGG: rsp:RSP_0748 N-6 adenine-specific DNA methylase ;pfam05175 MTS Methyltransferase small domain; COG4123 Predicted O-methyltransferase; type 11 methyltransferase 3238844 5710922 Dshi_3070 Dinoroseobacter shibae DFL 12 = DSM 16493 type 11 methyltransferase YP_001534404.1 3238074 R 398580 CDS YP_001534405.1 159045611 5710923 complement(3238844..3239071) 1 NC_009952.1 pfam09413 Protein of unknown function (DUF2007) KEGG: rde:RD1_3400 hypothetical protein; hypothetical protein 3239071 5710923 Dshi_3071 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534405.1 3238844 R 398580 CDS YP_001534406.1 159045612 5710924 3239127..3240131 1 NC_009952.1 PFAM: Polyprenyl synthetase KEGG: rsh:Rsph17029_2406 trans-hexaprenyltranstransferase; octaprenyl-diphosphate synthase 3240131 ispB 5710924 ispB Dinoroseobacter shibae DFL 12 = DSM 16493 octaprenyl-diphosphate synthase YP_001534406.1 3239127 D 398580 CDS YP_001534407.1 159045613 5710925 complement(3240124..3240987) 1 NC_009952.1 An essential enzyme in the nonmevalonate pathway of isopentenyl diphosphate and dimethylallyl diphosphate biosynthesis; 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase 3240987 ispE 5710925 ispE Dinoroseobacter shibae DFL 12 = DSM 16493 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase YP_001534407.1 3240124 R 398580 CDS YP_001534408.1 159045614 5710926 complement(3240971..3242725) 1 NC_009952.1 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 3242725 5710926 Dshi_3074 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534408.1 3240971 R 398580 CDS YP_001534409.1 159045615 5710927 complement(3242821..3244470) 1 NC_009952.1 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 3244470 ydiS 5710927 ydiS Dinoroseobacter shibae DFL 12 = DSM 16493 electron transfer flavoprotein-ubiquinone oxidoreductase YP_001534409.1 3242821 R 398580 CDS YP_001534410.1 159045616 5710928 3244630..3245145 1 NC_009952.1 necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites; arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by cleavage factors such as GreA or GreB allows the resumption of elongation from the new 3'terminus; transcription elongation factor GreA 3245145 greA 5710928 greA Dinoroseobacter shibae DFL 12 = DSM 16493 transcription elongation factor GreA YP_001534410.1 3244630 D 398580 CDS YP_001534411.1 159045617 5710929 3245223..3246209 1 NC_009952.1 KEGG: sil:SPO0311 hypothetical protein; hypothetical protein 3246209 5710929 Dshi_3077 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534411.1 3245223 D 398580 CDS YP_001534412.1 159045618 5710930 3246273..3246977 1 NC_009952.1 PFAM: AzlC family protein KEGG: rsq:Rsph17025_2457 AzlC family protein; AzlC family protein 3246977 5710930 Dshi_3078 Dinoroseobacter shibae DFL 12 = DSM 16493 AzlC family protein YP_001534412.1 3246273 D 398580 CDS YP_001534413.1 159045619 5710931 3246974..3247306 1 NC_009952.1 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 3247306 5710931 Dshi_3079 Dinoroseobacter shibae DFL 12 = DSM 16493 AzlD branched-chain amino acid transport YP_001534413.1 3246974 D 398580 CDS YP_001534414.1 159045620 5710932 3247400..3248863 1 NC_009952.1 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 3248863 5710932 Dshi_3080 Dinoroseobacter shibae DFL 12 = DSM 16493 efflux transporter YP_001534414.1 3247400 D 398580 CDS YP_001534415.1 159045621 5710933 3248865..3252272 1 NC_009952.1 colocated with MFP subunit; pfam00873,; RND family, RND subunit; efflux transporter 3252272 5710933 Dshi_3081 Dinoroseobacter shibae DFL 12 = DSM 16493 efflux transporter YP_001534415.1 3248865 D 398580 CDS YP_001534416.1 159045622 5710934 complement(3252382..3253191) 1 NC_009952.1 KEGG: rsh:Rsph17029_2660 hypothetical protein ,COG4233; hypothetical protein 3253191 5710934 Dshi_3082 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534416.1 3252382 R 398580 CDS YP_001534417.1 159045623 5710935 3253311..3253889 1 NC_009952.1 pfam02622,DUF179,COG1678 Putative transcriptional regulator; KEGG: rde:RD1_3419 hypothetical protein; hypothetical protein 3253889 5710935 Dshi_3083 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534417.1 3253311 D 398580 CDS YP_001534418.1 159045624 5710936 complement(3253947..3254924) 1 NC_009952.1 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 3254924 5710936 Dshi_3084 Dinoroseobacter shibae DFL 12 = DSM 16493 Sua5/YciO/YrdC/YwlC family protein YP_001534418.1 3253947 R 398580 CDS YP_001534419.1 159045625 5710937 3255050..3256765 1 NC_009952.1 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 3256765 5710937 Dshi_3085 Dinoroseobacter shibae DFL 12 = DSM 16493 putative acyl-CoA dehydrogenase family protein YP_001534419.1 3255050 D 398580 CDS YP_001534420.1 159045626 5710938 3256765..3257814 1 NC_009952.1 PFAM: beta-lactamase domain protein KEGG: rsh:Rsph17029_2397 beta-lactamase domain protein; metallo-beta-lactamase family protein 3257814 5710938 Dshi_3086 Dinoroseobacter shibae DFL 12 = DSM 16493 metallo-beta-lactamase family protein YP_001534420.1 3256765 D 398580 CDS YP_001534421.1 159045627 5710939 3257905..3258042 1 NC_009952.1 45aa protein PFAM: aa3 type cytochrome c oxidase subunit IV; hypothetical protein 3258042 5710939 Dshi_3087 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534421.1 3257905 D 398580 CDS YP_001534422.1 159045628 5710940 3258055..3258663 1 NC_009952.1 KEGG: rsh:Rsph17029_2395 hypothetical protein; hypothetical protein 3258663 5710940 Dshi_3088 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534422.1 3258055 D 398580 CDS YP_001534423.1 159045629 5710941 complement(3258688..3259230) 1 NC_009952.1 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 3259230 moaB 5710941 moaB Dinoroseobacter shibae DFL 12 = DSM 16493 molybdenum cofactor biosynthesis protein B YP_001534423.1 3258688 R 398580 CDS YP_001534424.1 159045630 5710942 complement(3259227..3260024) 1 NC_009952.1 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 3260024 udgA 5710942 udgA Dinoroseobacter shibae DFL 12 = DSM 16493 uracil-DNA glycosylase YP_001534424.1 3259227 R 398580 CDS YP_001534425.1 159045631 5710943 3260134..3261084 1 NC_009952.1 catalyzes the transfer of the carbamoyl moiety from carbamoyl phosphate to L- aspartate in pyrimidine biosynthesis; aspartate carbamoyltransferase catalytic subunit 3261084 pyrB 5710943 pyrB Dinoroseobacter shibae DFL 12 = DSM 16493 aspartate carbamoyltransferase catalytic subunit YP_001534425.1 3260134 D 398580 CDS YP_001534426.1 159045632 5710944 3261081..3261506 1 NC_009952.1 hypothetical protein 3261506 5710944 Dshi_3092 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534426.1 3261081 D 398580 CDS YP_001534427.1 159045633 5710945 3261503..3262081 1 NC_009952.1 hypothetical protein 3262081 5710945 Dshi_3093 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534427.1 3261503 D 398580 CDS YP_001534428.1 159045634 5710946 3262081..3263379 1 NC_009952.1 KEGG: rsh:Rsph17029_2663 dihydroorotase, multifunctional complex type TIGRFAM: dihydroorotase, multifunctional complex type PFAM: amidohydrolase; DHOase; dihydroorotase 3263379 pyrC1 5710946 pyrC1 Dinoroseobacter shibae DFL 12 = DSM 16493 dihydroorotase YP_001534428.1 3262081 D 398580 CDS YP_001534429.1 159045635 5710947 3263379..3263990 1 NC_009952.1 PFAM: protein of unknown function DUF205 KEGG: jan:Jann_3906 protein of unknown function DUF205 , COG0344, COG0344; hypothetical protein 3263990 5710947 Dshi_3095 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534429.1 3263379 D 398580 CDS YP_001534430.1 159045636 5710948 3263993..3264499 1 NC_009952.1 PFAM: protein of unknown function DUF805 KEGG: jan:Jann_3908 protein of unknown function DUF805,COG3152 - Predicted membrane protein; hypothetical protein 3264499 5710948 Dshi_3096 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534430.1 3263993 D 398580 CDS YP_001534431.1 159045637 5710949 complement(3264516..3265886) 1 NC_009952.1 KEGG: sil:SPO3626 glutamate-cysteine ligase TIGRFAM: glutamate--cysteine ligase PFAM: glutamate--cysteine ligase GCS2; glutamate--cysteine ligase 3265886 gsh 5710949 gsh Dinoroseobacter shibae DFL 12 = DSM 16493 glutamate--cysteine ligase YP_001534431.1 3264516 R 398580 CDS YP_001534432.1 159045638 5710950 complement(3265922..3266470) 1 NC_009952.1 hypothetical protein 3266470 5710950 Dshi_3098 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534432.1 3265922 R 398580 CDS YP_001534433.1 159045639 5710951 complement(3266467..3267216) 1 NC_009952.1 in Escherichia coli RsmE methylates the N3 position of the U1498 base in 16S rRNA; cells lacking this function can grow, but are outcompeted by wild-type; SAM-dependent m(3)U1498 methyltransferase; 16S ribosomal RNA methyltransferase RsmE 3267216 5710951 Dshi_3099 Dinoroseobacter shibae DFL 12 = DSM 16493 16S ribosomal RNA methyltransferase RsmE YP_001534433.1 3266467 R 398580 CDS YP_001534434.1 159045640 5710952 3267233..3268201 1 NC_009952.1 UbiA prenyltransferase family catalyzes the transfer of a prenyl group to various acceptors with hydrophobic ring structures in the biosynthesis of respiratory quinones, hemes, chlorophylls, vitamin E, and shikonin; 4-hydroxybenzoate polyprenyltransferase 3268201 ubiA 5710952 ubiA Dinoroseobacter shibae DFL 12 = DSM 16493 4-hydroxybenzoate polyprenyltransferase YP_001534434.1 3267233 D 398580 CDS YP_001534435.1 159045641 5710953 3268262..3270115 1 NC_009952.1 PFAM: OmpA/MotB domain protein KEGG: sit:TM1040_3081 OmpA/MotB. Annotation was derived from R. denitrificans; OmpA domain-containing protein 3270115 5710953 Dshi_3101 Dinoroseobacter shibae DFL 12 = DSM 16493 OmpA domain-containing protein YP_001534435.1 3268262 D 398580 CDS YP_001534436.1 159045642 5710954 3270112..3270444 1 NC_009952.1 KEGG: rsh:Rsph17029_2670 hypothetical protein; hypothetical protein 3270444 5710954 Dshi_3102 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534436.1 3270112 D 398580 CDS YP_001534437.1 159045643 5710955 complement(3270452..3270895) 1 NC_009952.1 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 3270895 moaE 5710955 moaE Dinoroseobacter shibae DFL 12 = DSM 16493 molybdopterin-converting factor subunit 2 YP_001534437.1 3270452 R 398580 CDS YP_001534438.1 159045644 5710956 complement(3270897..3271148) 1 NC_009952.1 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 3271148 moaD 5710956 moaD Dinoroseobacter shibae DFL 12 = DSM 16493 molybdopterin-converting factor subunit 1 YP_001534438.1 3270897 R 398580 CDS YP_001534439.1 159045645 5710957 complement(3271145..3271810) 1 NC_009952.1 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 3271810 pgsA 5710957 pgsA Dinoroseobacter shibae DFL 12 = DSM 16493 CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase YP_001534439.1 3271145 R 398580 CDS YP_001534440.1 159045646 5710958 complement(3272254..3272913) 1 NC_009952.1 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 3272913 rluA 5710958 rluA Dinoroseobacter shibae DFL 12 = DSM 16493 ribosomal large subunit pseudouridine synthase A YP_001534440.1 3272254 R 398580 CDS YP_001534441.1 159045647 5710959 3273004..3273621 1 NC_009952.1 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 3273621 rhtB 5710959 rhtB Dinoroseobacter shibae DFL 12 = DSM 16493 homoserine/homoserine lactone efflux protein YP_001534441.1 3273004 D 398580 CDS YP_001534442.1 159045648 5710960 3273755..3274522 1 NC_009952.1 PFAM: DSBA oxidoreductase KEGG: rde:RD1_0191 protein-disulfide isomerase, putative; putative protein-disulfide isomerase 3274522 5710960 Dshi_3108 Dinoroseobacter shibae DFL 12 = DSM 16493 putative protein-disulfide isomerase YP_001534442.1 3273755 D 398580 CDS YP_001534443.1 159045649 5710961 complement(3274527..3276476) 1 NC_009952.1 KEGG: rde:RD1_0522 hypothetical protein; hypothetical protein 3276476 5710961 Dshi_3109 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534443.1 3274527 R 398580 CDS YP_001534444.1 159045650 5710962 complement(3276494..3277162) 1 NC_009952.1 PFAM: cyclic nucleotide-binding KEGG: rsq:Rsph17025_3179 hypothetical protein; cyclic nucleotide-binding protein 3277162 5710962 Dshi_3110 Dinoroseobacter shibae DFL 12 = DSM 16493 cyclic nucleotide-binding protein YP_001534444.1 3276494 R 398580 CDS YP_001534445.1 159045651 5710963 3277491..3279092 1 NC_009952.1 PFAM: sulfatase KEGG: rde:RD1_0531 arylsulfatase; Aryl-sulfate sulphohydrolase; AS; arylsulfatase 3279092 aslA 5710963 aslA Dinoroseobacter shibae DFL 12 = DSM 16493 arylsulfatase YP_001534445.1 3277491 D 398580 CDS YP_001534446.1 159045652 5710964 3279170..3280126 1 NC_009952.1 KEGG: rde:RD1_0530 nonspecific acid phosphatase; nonspecific acid phosphatase 3280126 5710964 Dshi_3112 Dinoroseobacter shibae DFL 12 = DSM 16493 nonspecific acid phosphatase YP_001534446.1 3279170 D 398580 CDS YP_001534447.1 159045653 5710965 3280195..3281160 1 NC_009952.1 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 3281160 5710965 Dshi_3113 Dinoroseobacter shibae DFL 12 = DSM 16493 putative MoxR-like ATPase YP_001534447.1 3280195 D 398580 CDS YP_001534448.1 159045654 5710966 3281172..3282107 1 NC_009952.1 PFAM: protein of unknown function DUF58 KEGG: rde:RD1_0528 hypothetical protein, COG1721; hypothetical protein 3282107 5710966 Dshi_3114 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534448.1 3281172 D 398580 CDS YP_001534449.1 159045655 5710967 3282104..3282577 1 NC_009952.1 KEGG: rde:RD1_0527 hypothetical protein; hypothetical protein 3282577 5710967 Dshi_3115 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534449.1 3282104 D 398580 CDS YP_001534450.1 159045656 5710968 3282574..3283560 1 NC_009952.1 PFAM:VWA von Willebrand factor type A domain KEGG: rde:RD1_0526 hypothetical protein,TMH; von Willebrand factor type A domain-containing protein 3283560 5710968 Dshi_3116 Dinoroseobacter shibae DFL 12 = DSM 16493 von Willebrand factor type A domain-containing protein YP_001534450.1 3282574 D 398580 CDS YP_001534451.1 159045657 5710969 3283557..3285068 1 NC_009952.1 KEGG: rde:RD1_0525 hypothetical protein; hypothetical protein 3285068 5710969 Dshi_3117 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534451.1 3283557 D 398580 CDS YP_001534452.1 159045658 5710970 3285065..3286309 1 NC_009952.1 KEGG: rde:RD1_0524 hypothetical protein; hypothetical protein 3286309 5710970 Dshi_3118 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534452.1 3285065 D 398580 CDS YP_001534453.1 159045659 5710971 complement(3286328..3287092) 1 NC_009952.1 KEGG: sit:TM1040_2728 citrate synthase; citrate synthase 3287092 gltA1 5710971 gltA1 Dinoroseobacter shibae DFL 12 = DSM 16493 citrate synthase YP_001534453.1 3286328 R 398580 CDS YP_001534454.1 159045660 5710972 complement(3287089..3288279) 1 NC_009952.1 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 3288279 yfdW2 5710972 yfdW2 Dinoroseobacter shibae DFL 12 = DSM 16493 formyl-coenzyme A transferase YP_001534454.1 3287089 R 398580 CDS YP_001534455.1 159045661 5710973 complement(3288269..3289786) 1 NC_009952.1 PFAM: protein of unknown function DUF112 transmembrane COG3333 - Uncharacterized protein conserved in bacteria; hypothetical protein 3289786 5710973 Dshi_3121 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534455.1 3288269 R 398580 CDS YP_001534456.1 159045662 5710974 complement(3289790..3290278) 1 NC_009952.1 KEGG: rde:RD1_2947 hypothetical protein; hypothetical protein 3290278 5710974 Dshi_3122 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534456.1 3289790 R 398580 CDS YP_001534457.1 159045663 5710975 complement(3290359..3291339) 1 NC_009952.1 COG3181 Uncharacterized protein conserved in bacteria KEGG: rde:RD1_2946 hypothetical protein; hypothetical protein 3291339 5710975 Dshi_3123 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534457.1 3290359 R 398580 CDS YP_001534458.1 159045664 5710976 3291441..3292106 1 NC_009952.1 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 3292106 qseB 5710976 qseB Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulatory protein QseB YP_001534458.1 3291441 D 398580 CDS YP_001534459.1 159045665 5710977 3292103..3293476 1 NC_009952.1 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 3293476 qseC 5710977 qseC Dinoroseobacter shibae DFL 12 = DSM 16493 sensor protein QseC YP_001534459.1 3292103 D 398580 CDS YP_001534460.1 159045666 5710978 3293446..3294447 1 NC_009952.1 KEGG: sil:SPO0189 putative iron(III) transport system substrate-binding protein. Annotation was derived from R. denitrificans; putative periplasmic iron-binding protein 3294447 5710978 Dshi_3126 Dinoroseobacter shibae DFL 12 = DSM 16493 putative periplasmic iron-binding protein YP_001534460.1 3293446 D 398580 CDS YP_001534461.1 159045667 5710979 3294602..3296341 1 NC_009952.1 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 3296341 ugpB2 5710979 ugpB2 Dinoroseobacter shibae DFL 12 = DSM 16493 sugar ABC transporter YP_001534461.1 3294602 D 398580 CDS YP_001534462.1 159045668 5710980 3296414..3297475 1 NC_009952.1 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 3297475 ugpC5 5710980 ugpC5 Dinoroseobacter shibae DFL 12 = DSM 16493 sugar ABC transporter YP_001534462.1 3296414 D 398580 CDS YP_001534463.1 159045669 5710981 3297477..3298550 1 NC_009952.1 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 3298550 ugpC1 5710981 ugpC1 Dinoroseobacter shibae DFL 12 = DSM 16493 sugar ABC transporter YP_001534463.1 3297477 D 398580 CDS YP_001534464.1 159045670 5710982 3298547..3299410 1 NC_009952.1 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 3299410 ugpA2 5710982 ugpA2 Dinoroseobacter shibae DFL 12 = DSM 16493 sugar ABC transporter YP_001534464.1 3298547 D 398580 CDS YP_001534465.1 159045671 5710983 3299407..3300204 1 NC_009952.1 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 3300204 ugpE1 5710983 ugpE1 Dinoroseobacter shibae DFL 12 = DSM 16493 sugar ABC transporter YP_001534465.1 3299407 D 398580 CDS YP_001534466.1 159045672 5710984 3300204..3300602 1 NC_009952.1 TMH; hypothetical protein 3300602 5710984 Dshi_3132 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534466.1 3300204 D 398580 CDS YP_001534467.1 159045673 5710985 3300641..3301048 1 NC_009952.1 PFAM: Penicillinase repressor KEGG: rde:RD1_4115 transcriptional regulator, putative; putative transcriptional regulator 3301048 5710985 Dshi_3133 Dinoroseobacter shibae DFL 12 = DSM 16493 putative transcriptional regulator YP_001534467.1 3300641 D 398580 CDS YP_001534468.1 159045674 5710986 3301023..3302168 1 NC_009952.1 PFAM: peptidase M56 BlaR1 KEGG: rde:RD1_4114 BlaR1 peptidase M56 domain protein; Motif HEXXH; BlaR1 peptidase M56 domain-containing protein 3302168 5710986 Dshi_3134 Dinoroseobacter shibae DFL 12 = DSM 16493 BlaR1 peptidase M56 domain-containing protein YP_001534468.1 3301023 D 398580 CDS YP_001534469.1 159045675 5710987 3302652..3303122 1 NC_009952.1 hypothetical protein 3303122 5710987 Dshi_3135 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534469.1 3302652 D 398580 CDS YP_001534470.1 159045676 5710988 3303263..3304162 1 NC_009952.1 LipoP1.0 KEGG: jan:Jann_1313 lipoprotein, putative; putative lipoprotein 3304162 5710988 Dshi_3136 Dinoroseobacter shibae DFL 12 = DSM 16493 putative lipoprotein YP_001534470.1 3303263 D 398580 CDS YP_001534471.1 159045677 5710989 complement(3304170..3304880) 1 NC_009952.1 hypothetical protein 3304880 5710989 Dshi_3137 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534471.1 3304170 R 398580 CDS YP_001534472.1 159045678 5710990 complement(3304846..3305598) 1 NC_009952.1 KEGG: smd:Smed_4297 alpha/beta hydrolase fold; hypothetical protein 3305598 5710990 Dshi_3138 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534472.1 3304846 R 398580 CDS YP_001534473.1 159045679 5712195 complement(3305602..3306732) 1 NC_009952.1 KEGG: jan:Jann_1112 cupin 2 protein; cupin domain-containing protein 3306732 5712195 Dshi_3139 Dinoroseobacter shibae DFL 12 = DSM 16493 cupin domain-containing protein YP_001534473.1 3305602 R 398580 CDS YP_001534474.1 159045680 5712196 complement(3306735..3307787) 1 NC_009952.1 PFAM: regulatory protein LacI; periplasmic binding protein/LacI transcriptional regulator KEGG: rde:RD1_3944 transcriptional regulatory protein, LacI family, putative; LacI family; transcriptional regulator 3307787 5712196 Dshi_3140 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001534474.1 3306735 R 398580 CDS YP_001534475.1 159045681 5712197 complement(3307792..3308850) 1 NC_009952.1 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 3308850 ugpC3 5712197 ugpC3 Dinoroseobacter shibae DFL 12 = DSM 16493 sugar ABC transporter YP_001534475.1 3307792 R 398580 CDS YP_001534476.1 159045682 5712198 complement(3308891..3309718) 1 NC_009952.1 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 3309718 ugpE2 5712198 ugpE2 Dinoroseobacter shibae DFL 12 = DSM 16493 sugar ABC transporter YP_001534476.1 3308891 R 398580 CDS YP_001534477.1 159045683 5712199 complement(3309722..3310594) 1 NC_009952.1 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 3310594 ugpA3 5712199 ugpA3 Dinoroseobacter shibae DFL 12 = DSM 16493 sugar ABC transporter YP_001534477.1 3309722 R 398580 CDS YP_001534478.1 159045684 5712200 complement(3310655..3312037) 1 NC_009952.1 PFAM: extracellular solute-binding protein family 1 COG1653 - ABC-type sugar transport system, periplasmic component; sugar ABC transporter periplasmic sugar-binding protein 3312037 ugpB3 5712200 ugpB3 Dinoroseobacter shibae DFL 12 = DSM 16493 sugar ABC transporter periplasmic sugar-binding protein YP_001534478.1 3310655 R 398580 CDS YP_001534479.1 159045685 5712201 3312119..3312880 1 NC_009952.1 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 3312880 garL 5712201 garL Dinoroseobacter shibae DFL 12 = DSM 16493 2-dehydro-3-deoxyglucarate aldolase YP_001534479.1 3312119 D 398580 CDS YP_001534480.1 159045686 5712202 3312960..3313922 1 NC_009952.1 catalyzes the carboxylation of acetyl-CoA to malonyl-CoA; forms a tetramer composed of two alpha (AccA) and two beta (AccD) subunits; one of the two catalytic subunits that can form the acetyl CoA carboxylase enzyme together with a carrier protein; acetyl-CoA carboxylase carboxyltransferase subunit alpha 3313922 accA 5712202 accA Dinoroseobacter shibae DFL 12 = DSM 16493 acetyl-CoA carboxylase carboxyltransferase subunit alpha YP_001534480.1 3312960 D 398580 CDS YP_001534481.1 159045687 5712203 3313957..3314697 1 NC_009952.1 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 3314697 5712203 Dshi_3147 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534481.1 3313957 D 398580 CDS YP_001534482.1 159045688 5712204 complement(3314700..3315176) 1 NC_009952.1 hypothetical protein 3315176 5712204 Dshi_3148 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534482.1 3314700 R 398580 CDS YP_001534483.1 159045689 5712205 complement(3315173..3315985) 1 NC_009952.1 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 3315985 ddpX 5712205 ddpX Dinoroseobacter shibae DFL 12 = DSM 16493 putative D-alanyl-d-alanine dipeptidase YP_001534483.1 3315173 R 398580 CDS YP_001534484.1 159045690 5712206 3316090..3316944 1 NC_009952.1 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 3316944 dat 5712206 dat Dinoroseobacter shibae DFL 12 = DSM 16493 D-alanine aminotransferase YP_001534484.1 3316090 D 398580 CDS YP_001534485.1 159045691 5712207 3316985..3317893 1 NC_009952.1 PFAM: regulatory protein LysR; LysR substrate-binding KEGG: sil:SPO1110 transcriptional regulator, LysR family COG0583 - Transcriptional regulator; LysR family; transcriptional regulator 3317893 5712207 Dshi_3151 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001534485.1 3316985 D 398580 CDS YP_001534486.1 159045692 5712208 3317939..3318841 1 NC_009952.1 PFAM: protein of unknown function DUF1445 KEGG: sil:SPO1111 hypothetical protein; hypothetical protein 3318841 5712208 Dshi_3152 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534486.1 3317939 D 398580 CDS YP_001534487.1 159045693 5712209 3318825..3319859 1 NC_009952.1 PFAM: TRAP dicarboxylate transporter- DctP subunit KEGG: sil:SPO1112 TRAP transporter, periplasmic protein; TRAP dicarboxylate transporter subunit DctP 3319859 5712209 Dshi_3153 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP dicarboxylate transporter subunit DctP YP_001534487.1 3318825 D 398580 CDS YP_001534488.1 159045694 5712210 3319882..3320430 1 NC_009952.1 KEGG: sil:SPO1113 TRAP transporter, transmembrane protein, putative,TMH; TRAP dicarboxylate transporter subunit DctQ 3320430 5712210 Dshi_3154 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP dicarboxylate transporter subunit DctQ YP_001534488.1 3319882 D 398580 CDS YP_001534489.1 159045695 5712211 3320427..3321716 1 NC_009952.1 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 3321716 5712211 Dshi_3155 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP dicarboxylate transporter subunit DctM YP_001534489.1 3320427 D 398580 CDS YP_001534490.1 159045696 5712212 3321720..3322373 1 NC_009952.1 hypothetical protein 3322373 5712212 Dshi_3156 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534490.1 3321720 D 398580 CDS YP_001534491.1 159045697 5712213 3322458..3323468 1 NC_009952.1 PFAM: TRAP dicarboxylate transporter- DctP subunit KEGG: csa:Csal_2479 TRAP dicarboxylate transporter, DctP subunit; TRAP dicarboxylate transporter subunit DctP 3323468 5712213 Dshi_3157 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP dicarboxylate transporter subunit DctP YP_001534491.1 3322458 D 398580 CDS YP_001534492.1 159045698 5712214 3323471..3323968 1 NC_009952.1 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 3323968 5712214 Dshi_3158 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP dicarboxylate transporter subunit DctQ YP_001534492.1 3323471 D 398580 CDS YP_001534493.1 159045699 5712215 3323968..3325263 1 NC_009952.1 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 3325263 5712215 Dshi_3159 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP dicarboxylate transporter subunit DctM YP_001534493.1 3323968 D 398580 CDS YP_001534494.1 159045700 5712216 complement(3325448..3325705) 1 NC_009952.1 TMH; hypothetical protein 3325705 5712216 Dshi_3160 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534494.1 3325448 R 398580 CDS YP_001534495.1 159045701 5712217 complement(3325753..3326466) 1 NC_009952.1 PFAM: NapC/NirT cytochrome c domain protein KEGG: rsq:Rsph17025_3218 4Fe-4S ferredoxin, iron-sulfur binding domain protein; cytochrome c-type protein NapC 3326466 napC 5712217 napC Dinoroseobacter shibae DFL 12 = DSM 16493 cytochrome c-type protein NapC YP_001534495.1 3325753 R 398580 CDS YP_001534496.1 159045702 5712218 complement(3326494..3326937) 1 NC_009952.1 PFAM: Nitrate reductase cytochrome c-type subunit (NapB) KEGG: rsq:Rsph17025_3219 polyferredoxin-like protein; cytochrome c-type protein NapB 3326937 napB 5712218 napB Dinoroseobacter shibae DFL 12 = DSM 16493 cytochrome c-type protein NapB YP_001534496.1 3326494 R 398580 CDS YP_001534497.1 159045703 5712219 complement(3326957..3327865) 1 NC_009952.1 part of NapHG quinol dehydrogenase; couples electron transfer from ubiquinone-ubiquinol couple via NapC/B to NapA; quinol dehydrogenase membrane component 3327865 napH 5712219 napH Dinoroseobacter shibae DFL 12 = DSM 16493 quinol dehydrogenase membrane component YP_001534497.1 3326957 R 398580 CDS YP_001534498.1 159045704 5712220 complement(3327862..3328674) 1 NC_009952.1 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 3328674 napG 5712220 napG Dinoroseobacter shibae DFL 12 = DSM 16493 ferredoxin-type protein NapG YP_001534498.1 3327862 R 398580 CDS YP_001534499.1 159045705 5712221 complement(3328696..3331191) 1 NC_009952.1 periplasmic; catalytic subunit; with NapBC catalyzes the reduction of nitrate to nitrite; NapAB receives electrons from NapC; nitrate reductase catalytic subunit 3331191 napA 5712221 napA Dinoroseobacter shibae DFL 12 = DSM 16493 nitrate reductase catalytic subunit YP_001534499.1 3328696 R 398580 CDS YP_001534500.1 159045706 5712222 complement(3331178..3331480) 1 NC_009952.1 PFAM: NapD family protein KEGG: rsq:Rsph17025_3223 hypothetical protein; periplasmic nitrate reductase NapD 3331480 napD 5712222 napD Dinoroseobacter shibae DFL 12 = DSM 16493 periplasmic nitrate reductase NapD YP_001534500.1 3331178 R 398580 CDS YP_001534501.1 159045707 5712223 complement(3331477..3331989) 1 NC_009952.1 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 3331989 napF 5712223 napF Dinoroseobacter shibae DFL 12 = DSM 16493 ferredoxin-type protein napF YP_001534501.1 3331477 R 398580 CDS YP_001534502.1 159045708 5712224 3332404..3333345 1 NC_009952.1 PFAM: ApbE family lipoprotein KEGG: pde:Pden_2485 ApbE family lipoprotein; ApbE family lipoprotein 3333345 apbE1 5712224 apbE1 Dinoroseobacter shibae DFL 12 = DSM 16493 ApbE family lipoprotein YP_001534502.1 3332404 D 398580 CDS YP_001534503.1 159045709 5712225 3333379..3333759 1 NC_009952.1 PFAM: cytochrome c class I KEGG: sil:SPOA0055 cytochrome c family protein; cytochrome c2 3333759 cycA1 5712225 cycA1 Dinoroseobacter shibae DFL 12 = DSM 16493 cytochrome c2 YP_001534503.1 3333379 D 398580 CDS YP_001534504.1 159045710 5712226 complement(3333779..3334027) 1 NC_009952.1 hypothetical protein 3334027 5712226 Dshi_3170 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534504.1 3333779 R 398580 CDS YP_001534505.1 159045711 5712227 complement(3334024..3334740) 1 NC_009952.1 PFAM: cobalamin (vitamin B12) biosynthesis CbiX protein KEGG: rde:RD1_1574 cbiX; CbiX protein, putative; cobalamin (vitamin B12) biosynthesis CbiX protein 3334740 cbiX1 5712227 cbiX1 Dinoroseobacter shibae DFL 12 = DSM 16493 cobalamin (vitamin B12) biosynthesis CbiX protein YP_001534505.1 3334024 R 398580 CDS YP_001534506.1 159045712 5712228 complement(3334742..3336295) 1 NC_009952.1 PFAM: cytochrome d1 heme region KEGG: sil:SPOA0228 nitrite reductase protein N; nitrite reductase protein N 3336295 nirN 5712228 nirN Dinoroseobacter shibae DFL 12 = DSM 16493 nitrite reductase protein N YP_001534506.1 3334742 R 398580 CDS YP_001534507.1 159045713 5712229 complement(3336270..3337484) 1 NC_009952.1 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 3337484 nirJ 5712229 nirJ Dinoroseobacter shibae DFL 12 = DSM 16493 putative nitrite reductase heme biosynthesis J protein YP_001534507.1 3336270 R 398580 CDS YP_001534508.1 159045714 5712230 complement(3337486..3337971) 1 NC_009952.1 KEGG: sil:SPOA0226 nitrite reductase heme biosynthesis H protein, COG1522 - Transcriptional regulators; putative nitrite reductase heme biosynthesis H protein 3337971 nirH 5712230 nirH Dinoroseobacter shibae DFL 12 = DSM 16493 putative nitrite reductase heme biosynthesis H protein YP_001534508.1 3337486 R 398580 CDS YP_001534509.1 159045715 5712231 complement(3337968..3338417) 1 NC_009952.1 SMART: regulatory protein AsnC/Lrp family KEGG: rde:RD1_1570 nitrite reductase heme biosynthesis G; nitrite reductase heme biosynthesis G 3338417 nirG 5712231 nirG Dinoroseobacter shibae DFL 12 = DSM 16493 nitrite reductase heme biosynthesis G YP_001534509.1 3337968 R 398580 CDS YP_001534510.1 159045716 5712232 complement(3338414..3339409) 1 NC_009952.1 KEGG: sil:SPOA0224 nitrite reductase heme biosynthesis D/L protein, putative; nitrite reductase heme biosynthesis D protein 3339409 nirD 5712232 nirD Dinoroseobacter shibae DFL 12 = DSM 16493 nitrite reductase heme biosynthesis D protein YP_001534510.1 3338414 R 398580 CDS YP_001534511.1 159045717 5712233 complement(3339414..3340580) 1 NC_009952.1 PFAM: cytochrome d1 heme region KEGG: rde:RD1_1568 cytochrome cd1; cytochrome cd1 3340580 nirF 5712233 nirF Dinoroseobacter shibae DFL 12 = DSM 16493 cytochrome cd1 YP_001534511.1 3339414 R 398580 CDS YP_001534512.1 159045718 5712234 complement(3340585..3340896) 1 NC_009952.1 KEGG: sil:SPOA0222 cytochrome c55X , neighborhood; c55X; putative cytochrome c 3340896 nirC 5712234 nirC Dinoroseobacter shibae DFL 12 = DSM 16493 putative cytochrome c YP_001534512.1 3340585 R 398580 CDS YP_001534513.1 159045719 5712235 complement(3340889..3341683) 1 NC_009952.1 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 3341683 nirE 5712235 nirE Dinoroseobacter shibae DFL 12 = DSM 16493 uroporphyrinogen-III C-methyltransferase YP_001534513.1 3340889 R 398580 CDS YP_001534514.1 159045720 5712236 complement(3341772..3343523) 1 NC_009952.1 PFAM: cytochrome d1 heme region KEGG: rde:RD1_1565 nitrite reductase; Hydroxylamine reductase; Cytochrome oxidase; Cytochrome cd1; nitrite reductase 3343523 nirS 5712236 nirS Dinoroseobacter shibae DFL 12 = DSM 16493 nitrite reductase YP_001534514.1 3341772 R 398580 CDS YP_001534515.1 159045721 5712237 3343637..3345700 1 NC_009952.1 PFAM: FMN-binding domain protein KEGG: pde:Pden_2486 FMN-binding domain protein; nitrous oxide reductase regulatory protein NosR 3345700 nosR2 5712237 nosR2 Dinoroseobacter shibae DFL 12 = DSM 16493 nitrous oxide reductase regulatory protein NosR YP_001534515.1 3343637 D 398580 CDS YP_001534516.1 159045722 5712238 3345697..3346887 1 NC_009952.1 PFAM: NnrS family protein KEGG: sil:SPOA0219 NnrS, putative; NnrS family protein 3346887 5712238 Dshi_3182 Dinoroseobacter shibae DFL 12 = DSM 16493 NnrS family protein YP_001534516.1 3345697 D 398580 CDS YP_001534517.1 159045723 5712239 3346997..3347449 1 NC_009952.1 KEGG: sil:SPOA0217 nitric oxide reductase, small subunit; NOR small subunit; Nitric oxide reductase cytochrome c subunit; nitric-oxide reductase subunit C 3347449 norC 5712239 norC Dinoroseobacter shibae DFL 12 = DSM 16493 nitric-oxide reductase subunit C YP_001534517.1 3346997 D 398580 CDS YP_001534518.1 159045724 5712240 3347463..3348842 1 NC_009952.1 KEGG: sil:SPOA0216 nitric oxide reductase, large subunit rde:RD1_1561 norB; nitric-oxide reductase subunit B; nitric oxide reductase subunit B 3348842 norB 5712240 norB Dinoroseobacter shibae DFL 12 = DSM 16493 nitric oxide reductase subunit B YP_001534518.1 3347463 D 398580 CDS YP_001534519.1 159045725 5712241 3348848..3349654 1 NC_009952.1 KEGG: sil:SPOA0215 nitric oxide reductase Q protein; nitric oxide reductase Q protein 3349654 norQ 5712241 norQ Dinoroseobacter shibae DFL 12 = DSM 16493 nitric oxide reductase Q protein YP_001534519.1 3348848 D 398580 CDS YP_001534520.1 159045726 5712242 3349663..3351597 1 NC_009952.1 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 3351597 norD 5712242 norD Dinoroseobacter shibae DFL 12 = DSM 16493 nitric oxide reductase D protein YP_001534520.1 3349663 D 398580 CDS YP_001534521.1 159045727 5712243 3351594..3352148 1 NC_009952.1 PFAM: cytochrome c oxidase subunit III KEGG:rde:RD1_1558 norE; NorE protein; nitric oxide reductase E protein 3352148 norE 5712243 norE Dinoroseobacter shibae DFL 12 = DSM 16493 nitric oxide reductase E protein YP_001534521.1 3351594 D 398580 CDS YP_001534522.1 159045728 5712244 3352145..3352414 1 NC_009952.1 hypothetical protein 3352414 5712244 Dshi_3188 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534522.1 3352145 D 398580 CDS YP_001534523.1 159045729 5712245 complement(3352427..3353137) 1 NC_009952.1 PFAM: cyclic nucleotide-binding KEGG: sil:SPOA0323 cyclic nucleotide-binding protein; similar to DnrD; transcriptional regulator 3353137 5712245 Dshi_3189 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001534523.1 3352427 R 398580 CDS YP_001534524.1 159045730 5712246 complement(3353217..3354440) 1 NC_009952.1 catalyzes the formation of 5-aminolevulinate from succinyl-CoA and glycine; 5-aminolevulinate synthase 3354440 hemA3 5712246 hemA3 Dinoroseobacter shibae DFL 12 = DSM 16493 5-aminolevulinate synthase YP_001534524.1 3353217 R 398580 CDS YP_001534525.1 159045731 5712247 3354578..3355261 1 NC_009952.1 PFAM: cyclic nucleotide-binding SMART: regulatory protein Crp KEGG: sil:SPOA0323 cyclic nucleotide-binding protein; transcriptional regulator Dnr 3355261 dnr 5712247 dnr Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator Dnr YP_001534525.1 3354578 D 398580 CDS YP_001534526.1 159045732 5712248 3355274..3355933 1 NC_009952.1 hypothetical protein 3355933 5712248 Dshi_3192 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534526.1 3355274 D 398580 CDS YP_001534527.1 159045733 5712249 3355930..3358116 1 NC_009952.1 KEGG:rde:RD1_1546 nosR; nitrous-oxide reductase regulatory protein NosR PFAM: FMN-binding domain protein; nitrous oxide reductase regulatory protein NosR 3358116 nosR3 5712249 nosR3 Dinoroseobacter shibae DFL 12 = DSM 16493 nitrous oxide reductase regulatory protein NosR YP_001534527.1 3355930 D 398580 CDS YP_001534528.1 159045734 5712250 3358128..3360071 1 NC_009952.1 reduces nitrous oxide to nitrogen; nitrous-oxide reductase 3360071 nosZ 5712250 nosZ Dinoroseobacter shibae DFL 12 = DSM 16493 nitrous-oxide reductase YP_001534528.1 3358128 D 398580 CDS YP_001534529.1 159045735 5712251 3360074..3361411 1 NC_009952.1 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 3361411 nosD 5712251 nosD Dinoroseobacter shibae DFL 12 = DSM 16493 nitrous oxide maturation protein YP_001534529.1 3360074 D 398580 CDS YP_001534530.1 159045736 5712252 3361377..3362273 1 NC_009952.1 PFAM: ABC transporter related SMART: AAA ATPase KEGG: rde:RD1_1549 nosF; copper transport ATP-binding protein NosF; copper transport ATP-binding protein NosF 3362273 nosF 5712252 nosF Dinoroseobacter shibae DFL 12 = DSM 16493 copper transport ATP-binding protein NosF YP_001534530.1 3361377 D 398580 CDS YP_001534531.1 159045737 5712253 3362270..3363094 1 NC_009952.1 KEGG: pde:Pden_4216 nitrous oxide maturation protein NosY; nitrous oxide maturation protein NosY 3363094 nosY 5712253 nosY Dinoroseobacter shibae DFL 12 = DSM 16493 nitrous oxide maturation protein NosY YP_001534531.1 3362270 D 398580 CDS YP_001534532.1 159045738 5712254 3363091..3363660 1 NC_009952.1 PFAM: NosL family protein KEGG: pde:Pden_4215 NosL family protein; nitrous oxide reductase accessory protein NosL 3363660 nosL 5712254 nosL Dinoroseobacter shibae DFL 12 = DSM 16493 nitrous oxide reductase accessory protein NosL YP_001534532.1 3363091 D 398580 CDS YP_001534533.1 159045739 5712255 3363665..3364573 1 NC_009952.1 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 3364573 nosX 5712255 nosX Dinoroseobacter shibae DFL 12 = DSM 16493 putative nitrous-oxide reductase protein NosX YP_001534533.1 3363665 D 398580 CDS YP_001534534.1 159045740 5712256 3364993..3365862 1 NC_009952.1 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 3365862 5712256 Dshi_3200 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534534.1 3364993 D 398580 CDS YP_001534535.1 159045741 5712257 3366067..3366408 1 NC_009952.1 PFAM: Endoribonuclease L-PSP KEGG: rde:RD1_1044 endoribonuclease L-PSP family protein, putative; endoribonuclease L-PSP 3366408 5712257 Dshi_3201 Dinoroseobacter shibae DFL 12 = DSM 16493 endoribonuclease L-PSP YP_001534535.1 3366067 D 398580 CDS YP_001534536.1 159045742 5712258 complement(3366483..3367907) 1 NC_009952.1 TIGRFAM: uracil-xanthine permease PFAM: Xanthine/uracil/vitamin C permease KEGG: rde:RD1_4153 xanthine/uracil permease, putative,10xTHM; Uracil transporter; uracil permease 3367907 uraA 5712258 uraA Dinoroseobacter shibae DFL 12 = DSM 16493 uracil permease YP_001534536.1 3366483 R 398580 CDS YP_001534537.1 159045743 5712259 complement(3367958..3368452) 1 NC_009952.1 PFAM: Ureidoglycolate hydrolase KEGG: rsh:Rsph17029_0204 ureidoglycolate hydrolase; ureidoglycolatehydrolase 3368452 allA 5712259 allA Dinoroseobacter shibae DFL 12 = DSM 16493 ureidoglycolatehydrolase YP_001534537.1 3367958 R 398580 CDS YP_001534538.1 159045744 5712260 complement(3368449..3369861) 1 NC_009952.1 PFAM: polysaccharide deacetylase; pfam09349, OHCU_decarbox, OHCU decarboxylase. KEGG: jan:Jann_2608 polysaccharide deacetylase; polysaccharide deacetylase 3369861 5712260 Dshi_3204 Dinoroseobacter shibae DFL 12 = DSM 16493 polysaccharide deacetylase YP_001534538.1 3368449 R 398580 CDS YP_001534539.1 159045745 5712261 3370012..3370365 1 NC_009952.1 TIGRFAM: Hydroxyisourate hydrolase PFAM: Transthyretin KEGG: rde:RD1_4150 hypothetical protein; hydroxyisourate hydrolase 3370365 5712261 Dshi_3205 Dinoroseobacter shibae DFL 12 = DSM 16493 hydroxyisourate hydrolase YP_001534539.1 3370012 D 398580 CDS YP_001534540.1 159045746 5712262 complement(3370362..3371345) 1 NC_009952.1 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 3371345 5712262 Dshi_3206 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001534540.1 3370362 R 398580 CDS YP_001534541.1 159045747 5712263 3371394..3372626 1 NC_009952.1 PFAM: protein of unknown function DUF989 KEGG: rde:RD1_4148 hypothetical protein; hypothetical protein 3372626 5712263 Dshi_3207 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534541.1 3371394 D 398580 CDS YP_001534542.1 159045748 5712264 3372902..3374383 1 NC_009952.1 hypothetical protein 3374383 5712264 Dshi_3208 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534542.1 3372902 D 398580 CDS YP_001534543.1 159045749 5712265 complement(3374380..3375372) 1 NC_009952.1 hypothetical protein 3375372 5712265 Dshi_3209 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534543.1 3374380 R 398580 CDS YP_001534544.1 159045750 5712266 3375531..3377120 1 NC_009952.1 PFAM: phospholipase D/Transphosphatidylase KEGG: bpe:BP3092 putative phospholipase D protein; putative phospholipase D protein 3377120 ymdC 5712266 ymdC Dinoroseobacter shibae DFL 12 = DSM 16493 putative phospholipase D protein YP_001534544.1 3375531 D 398580 CDS YP_001534545.1 159045751 5712267 complement(3377373..3377993) 1 NC_009952.1 KEGG: mpt:Mpe_A0912 putative sulfite oxidase cytochrome subunit; putative sulfite oxidase cytochrome subunit 3377993 5712267 Dshi_3211 Dinoroseobacter shibae DFL 12 = DSM 16493 putative sulfite oxidase cytochrome subunit YP_001534545.1 3377373 R 398580 CDS YP_001534546.1 159045752 5712268 complement(3377980..3379251) 1 NC_009952.1 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 3379251 5712268 Dshi_3212 Dinoroseobacter shibae DFL 12 = DSM 16493 molybdopterin-binding oxidoreductase YP_001534546.1 3377980 R 398580 CDS YP_001534547.1 159045753 5712269 3379874..3381040 1 NC_009952.1 PFAM: integrase family protein KEGG: nwi:Nwi_0831 phage integrase; integrase family protein 3381040 5712269 Dshi_3213 Dinoroseobacter shibae DFL 12 = DSM 16493 integrase family protein YP_001534547.1 3379874 D 398580 CDS YP_001534548.1 159045754 5712270 complement(3381532..3384105) 1 NC_009952.1 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 3384105 cas3 5712270 cas3 Dinoroseobacter shibae DFL 12 = DSM 16493 CRISPR-associated protein Cas3 YP_001534548.1 3381532 R 398580 CDS YP_001534549.1 159045755 5712271 3384277..3385797 1 NC_009952.1 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 3385797 cse1 5712271 cse1 Dinoroseobacter shibae DFL 12 = DSM 16493 Cse1 family CRISPR-associated protein YP_001534549.1 3384277 D 398580 CDS YP_001534550.1 159045756 5712272 3385790..3386365 1 NC_009952.1 hypothetical protein 3386365 5712272 Dshi_3216 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534550.1 3385790 D 398580 CDS YP_001534551.1 159045757 5712273 3386358..3387479 1 NC_009952.1 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 3387479 cse3 5712273 cse3 Dinoroseobacter shibae DFL 12 = DSM 16493 CRISPR-associated protein YP_001534551.1 3386358 D 398580 CDS YP_001534552.1 159045758 5712274 3387476..3388162 1 NC_009952.1 TIGRFAM: CRISPR-associated protein Cas5 family; CRISPR-associated protein Cas5 KEGG: rru:Rru_A0345 CRISPR-associated CT1976 family protein; Cas5 family CRISPR-associated protein 3388162 cas5 5712274 cas5 Dinoroseobacter shibae DFL 12 = DSM 16493 Cas5 family CRISPR-associated protein YP_001534552.1 3387476 D 398580 CDS YP_001534553.1 159045759 5712275 3388159..3388950 1 NC_009952.1 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 3388950 cse2 5712275 cse2 Dinoroseobacter shibae DFL 12 = DSM 16493 CRISPR-associated protein YP_001534553.1 3388159 D 398580 CDS YP_001534554.1 159045760 5712276 3388955..3389830 1 NC_009952.1 TIGRFAM: CRISPR-associated protein Cas1 KEGG: mca:MCA0930 CRISPR-associated protein Cas1; CRISPR-associated protein Cas1 3389830 cas1 5712276 cas1 Dinoroseobacter shibae DFL 12 = DSM 16493 CRISPR-associated protein Cas1 YP_001534554.1 3388955 D 398580 CDS YP_001534555.1 159045761 5712277 3389862..3390155 1 NC_009952.1 TIGRFAM: CRISPR-associated protein Cas2 KEGG: rru:Rru_A0348 CRISPR-associated protein, Cas2; CRISPR-associated protein Cas2 3390155 cas2 5712277 cas2 Dinoroseobacter shibae DFL 12 = DSM 16493 CRISPR-associated protein Cas2 YP_001534555.1 3389862 D 398580 CDS YP_001534556.1 159045762 5712278 3392485..3392688 1 NC_009952.1 hypothetical protein 3392688 5712278 Dshi_3222 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534556.1 3392485 D 398580 CDS YP_001534557.1 159045763 5712279 3392688..3393194 1 NC_009952.1 TIGRFAM: DNA binding domain, excisionase family KEGG: she:Shewmr4_2783 hypothetical protein; hypothetical protein 3393194 5712279 Dshi_3223 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534557.1 3392688 D 398580 CDS YP_001534558.1 159045764 5712280 3393172..3394230 1 NC_009952.1 PFAM: integrase family protein KEGG: mpt:Mpe_A3816 site-specific recombinase XerD-like protein; integrase family protein 3394230 5712280 Dshi_3224 Dinoroseobacter shibae DFL 12 = DSM 16493 integrase family protein YP_001534558.1 3393172 D 398580 CDS YP_001534559.1 159045765 5712281 complement(3394234..3395673) 1 NC_009952.1 hypothetical protein 3395673 5712281 Dshi_3225 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534559.1 3394234 R 398580 CDS YP_001534560.1 159045766 5712282 complement(3395713..3395988) 1 NC_009952.1 hypothetical protein 3395988 5712282 Dshi_3226 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534560.1 3395713 R 398580 CDS YP_001534561.1 159045767 5712283 complement(3396008..3396778) 1 NC_009952.1 hypothetical protein 3396778 5712283 Dshi_3227 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534561.1 3396008 R 398580 CDS YP_001534562.1 159045768 5712285 3397087..3397935 1 NC_009952.1 PFAM: diaminopimelate epimerase KEGG: sil:SPO0278 diaminopimelate epimerase; DAP epimerase; diaminopimelate epimerase 3397935 dapF 5712285 dapF Dinoroseobacter shibae DFL 12 = DSM 16493 diaminopimelate epimerase YP_001534562.1 3397087 D 398580 CDS YP_001534563.1 159045769 5712286 3397932..3399182 1 NC_009952.1 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 3399182 5712286 Dshi_3229 Dinoroseobacter shibae DFL 12 = DSM 16493 MiaB-like tRNA modifying enzyme YP_001534563.1 3397932 D 398580 CDS YP_001534564.1 159045770 5712287 3399206..3399451 1 NC_009952.1 hypothetical protein 3399451 5712287 Dshi_3230 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534564.1 3399206 D 398580 CDS YP_001534565.1 159045771 5712288 3399663..3401321 1 NC_009952.1 rsp:RSP_1458 putative DNA repair enzyme; putative DNA repair enzyme 3401321 5712288 Dshi_3231 Dinoroseobacter shibae DFL 12 = DSM 16493 putative DNA repair enzyme YP_001534565.1 3399663 D 398580 CDS YP_001534566.1 159045772 5712289 3401706..3402056 1 NC_009952.1 KEGG: sil:SPO3807 hypothetical protein; hypothetical protein 3402056 5712289 Dshi_3232 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534566.1 3401706 D 398580 CDS YP_001534567.1 159045773 5712290 complement(3402060..3402899) 1 NC_009952.1 PFAM: NLP/P60 protein KEGG: jan:Jann_0105 NLP/P60; NLP/P60 protein 3402899 5712290 Dshi_3233 Dinoroseobacter shibae DFL 12 = DSM 16493 NLP/P60 protein YP_001534567.1 3402060 R 398580 CDS YP_001534568.1 159045774 5712291 complement(3402896..3404287) 1 NC_009952.1 PFAM: peptidase M17 leucyl aminopeptidase domain protein KEGG: sil:SPO3717 cytosol aminopeptidase family protein; (LAP) (Leucyl aminopeptidase); leucine aminopeptidase 3404287 pepA2 5712291 pepA2 Dinoroseobacter shibae DFL 12 = DSM 16493 leucine aminopeptidase YP_001534568.1 3402896 R 398580 CDS YP_001534569.1 159045775 5712292 complement(3404838..3405260) 1 NC_009952.1 hypothetical protein 3405260 5712292 Dshi_3235 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534569.1 3404838 R 398580 CDS YP_001534570.1 159045776 5712293 3405407..3406057 1 NC_009952.1 PFAM: carbonic anhydrase KEGG: sil:SPO3715 carbonic anhydrase, putative ; rde:RD1_0312 cynT; carbonate anhydratase; carbonate anhydratase 3406057 cynT 5712293 cynT Dinoroseobacter shibae DFL 12 = DSM 16493 carbonate anhydratase YP_001534570.1 3405407 D 398580 CDS YP_001534571.1 159045777 5712294 3406143..3407117 1 NC_009952.1 PFAM: protein of unknown function DUF897 KEGG: jan:Jann_0109 protein of unknown function DUF897; hypothetical protein 3407117 5712294 Dshi_3237 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534571.1 3406143 D 398580 CDS YP_001534572.1 159045778 5712295 3407128..3407439 1 NC_009952.1 KEGG: jan:Jann_0110 hypothetical protein; hypothetical protein 3407439 5712295 Dshi_3238 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534572.1 3407128 D 398580 CDS YP_001534573.1 159045779 5712296 3407481..3407954 1 NC_009952.1 KEGG: sil:SPO3714 hypothetical protein; hypothetical protein 3407954 5712296 Dshi_3239 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534573.1 3407481 D 398580 CDS YP_001534574.1 159045780 5712297 complement(3407961..3408983) 1 NC_009952.1 catalyzes the formation of 4-aspartyl phosphate from aspartate 4-semialdehyde; aspartate-semialdehyde dehydrogenase 3408983 asd 5712297 asd Dinoroseobacter shibae DFL 12 = DSM 16493 aspartate-semialdehyde dehydrogenase YP_001534574.1 3407961 R 398580 CDS YP_001534575.1 159045781 5712298 complement(3409201..3410250) 1 NC_009952.1 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 3410250 lpcC 5712298 lpcC Dinoroseobacter shibae DFL 12 = DSM 16493 lipopolysaccharide core biosynthesis mannosyltransferase YP_001534575.1 3409201 R 398580 CDS YP_001534576.1 159045782 5712299 3410436..3411863 1 NC_009952.1 PFAM: protein of unknown function DUF404; protein of unknown function DUF407 KEGG: sit:TM1040_2114 protein of unknown function DUF404; DUF407; hypothetical protein 3411863 5712299 Dshi_3242 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534576.1 3410436 D 398580 CDS YP_001534577.1 159045783 5712300 3411868..3412809 1 NC_009952.1 PFAM: protein of unknown function DUF403 KEGG: jan:Jann_2677 protein of unknown function DUF403; hypothetical protein 3412809 5712300 Dshi_3243 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534577.1 3411868 D 398580 CDS YP_001534578.1 159045784 5712301 3412814..3413650 1 NC_009952.1 PFAM: transglutaminase domain protein; transglutaminase domain protein KEGG: hne:HNE_2679 transglutaminase family protein; putative transglutaminase-like superfamily protein 3413650 5712301 Dshi_3244 Dinoroseobacter shibae DFL 12 = DSM 16493 putative transglutaminase-like superfamily protein YP_001534578.1 3412814 D 398580 CDS YP_001534579.1 159045785 5712302 3413789..3414574 1 NC_009952.1 PFAM: 20S proteasome A and B subunits KEGG: rde:RD1_4009 proteasome-type protease, putative; putative proteasome-type protease 3414574 5712302 Dshi_3245 Dinoroseobacter shibae DFL 12 = DSM 16493 putative proteasome-type protease YP_001534579.1 3413789 D 398580 CDS YP_001534580.1 159045786 5712303 complement(3414677..3416029) 1 NC_009952.1 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 3416029 fliI 5712303 fliI Dinoroseobacter shibae DFL 12 = DSM 16493 flagellum-specific ATP synthase YP_001534580.1 3414677 R 398580 CDS YP_001534581.1 159045787 5712304 3416124..3416504 1 NC_009952.1 with FlgF and C makes up the proximal portion of the flagellar basal body rod; flagellar basal body rod protein FlgB 3416504 flgB 5712304 flgB Dinoroseobacter shibae DFL 12 = DSM 16493 flagellar basal body rod protein FlgB YP_001534581.1 3416124 D 398580 CDS YP_001534582.1 159045788 5712305 3416511..3416903 1 NC_009952.1 with FlgF and B makes up the proximal portion of the flagellar basal body rod; flagellar basal body rod protein FlgC 3416903 flgC 5712305 flgC Dinoroseobacter shibae DFL 12 = DSM 16493 flagellar basal body rod protein FlgC YP_001534582.1 3416511 D 398580 CDS YP_001534583.1 159045789 5712306 3416918..3417196 1 NC_009952.1 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 3417196 fliE 5712306 fliE Dinoroseobacter shibae DFL 12 = DSM 16493 flagellar hook-basal body protein FliE YP_001534583.1 3416918 D 398580 CDS YP_001534584.1 159045790 5712307 3417196..3417462 1 NC_009952.1 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 3417462 fliQ 5712307 fliQ Dinoroseobacter shibae DFL 12 = DSM 16493 flagellar biosynthetic protein FliQ YP_001534584.1 3417196 D 398580 CDS YP_001534585.1 159045791 5712308 3417469..3418185 1 NC_009952.1 FlgF, with FlgB and C, makes up the proximal portion of the flagellar basal body rod; Rhodobacter sphaeroides has 2 copies of this and other flagella genes; flagellar basal body rod protein FlgF 3418185 flgF 5712308 flgF Dinoroseobacter shibae DFL 12 = DSM 16493 flagellar basal body rod protein FlgF YP_001534585.1 3417469 D 398580 CDS YP_001534586.1 159045792 5712309 3418207..3418992 1 NC_009952.1 makes up the distal portion of the flagellar basal body rod; Bradyrhizobium has one thick flagellum and several thin flagella; the Bradyrhizobium protein in this cluster is associated with the thick flagella; flagellar basal body rod protein FlgG 3418992 flgG 5712309 flgG Dinoroseobacter shibae DFL 12 = DSM 16493 flagellar basal body rod protein FlgG YP_001534586.1 3418207 D 398580 CDS YP_001534587.1 159045793 5712310 3418989..3419414 1 NC_009952.1 required for the assembly of the flagellar basal body P-ring; flagellar basal body P-ring biosynthesis protein FlgA 3419414 flgA 5712310 flgA Dinoroseobacter shibae DFL 12 = DSM 16493 flagellar basal body P-ring biosynthesis protein FlgA YP_001534587.1 3418989 D 398580 CDS YP_001534588.1 159045794 5712311 3419427..3420155 1 NC_009952.1 part of the flagellar basal body which consists of four rings L,P, S and M mounted on a central rod; flagellar basal body L-ring protein 3420155 flgH 5712311 flgH Dinoroseobacter shibae DFL 12 = DSM 16493 flagellar basal body L-ring protein YP_001534588.1 3419427 D 398580 CDS YP_001534589.1 159045795 5712312 3420164..3420655 1 NC_009952.1 PFAM: flagellar basal body-associated protein FliL; flagellar basal body-associated protein FliL 3420655 fliL1 5712312 fliL1 Dinoroseobacter shibae DFL 12 = DSM 16493 flagellar basal body-associated protein FliL YP_001534589.1 3420164 D 398580 CDS YP_001534590.1 159045796 5712313 complement(3421032..3422120) 1 NC_009952.1 membrane protein responsible for substrate specificity switching from rod/hook-type export to filament-type export; flagellar biosynthesis protein FlhB 3422120 flhB 5712313 flhB Dinoroseobacter shibae DFL 12 = DSM 16493 flagellar biosynthesis protein FlhB YP_001534590.1 3421032 R 398580 CDS YP_001534591.1 159045797 5712314 complement(3422117..3422890) 1 NC_009952.1 PFAM: type III secretion system inner membrane R protein KEGG: jan:Jann_4187 flagellar biosynthetic protein FliR; flagellar biosynthesis protein FliR 3422890 fliR 5712314 fliR Dinoroseobacter shibae DFL 12 = DSM 16493 flagellar biosynthesis protein FliR YP_001534591.1 3422117 R 398580 CDS YP_001534592.1 159045798 5712315 complement(3422887..3424983) 1 NC_009952.1 membrane protein involved in the flagellar export apparatus; flagellar biosynthesis protein FlhA 3424983 flhA 5712315 flhA Dinoroseobacter shibae DFL 12 = DSM 16493 flagellar biosynthesis protein FlhA YP_001534592.1 3422887 R 398580 CDS YP_001534593.1 159045799 5712316 complement(3424994..3426859) 1 NC_009952.1 KEGG: rsh:Rsph17029_2977 hypothetical protein; hypothetical protein 3426859 5712316 Dshi_3259 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534593.1 3424994 R 398580 CDS YP_001534594.1 159045800 5712317 complement(3426856..3427725) 1 NC_009952.1 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 3427725 motA 5712317 motA Dinoroseobacter shibae DFL 12 = DSM 16493 flagellar motor protein MotA YP_001534594.1 3426856 R 398580 CDS YP_001534595.1 159045801 5712318 complement(3427775..3428380) 1 NC_009952.1 KEGG: rsh:Rsph17029_2975 hypothetical protein; hypothetical protein 3428380 5712318 Dshi_3261 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534595.1 3427775 R 398580 CDS YP_001534596.1 159045802 5712319 complement(3428380..3428760) 1 NC_009952.1 KEGG: rde:RD1_0271 hypothetical protein; hypothetical protein 3428760 5712319 Dshi_3262 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534596.1 3428380 R 398580 CDS YP_001534597.1 159045803 5712320 complement(3428769..3429269) 1 NC_009952.1 PFAM: flagellar basal body-associated protein FliL KEGG: rsh:Rsph17029_2973 flagellar basal body-associated protein FliL; flagellar basal body-associated protein FliL 3429269 fliL2 5712320 fliL2 Dinoroseobacter shibae DFL 12 = DSM 16493 flagellar basal body-associated protein FliL YP_001534597.1 3428769 R 398580 CDS YP_001534598.1 159045804 5712321 3429384..3431060 1 NC_009952.1 the MS-ring anchors the flagellum to the cytoplasmic membrane; part of the flagellar basal body which consists of four rings L, P, S, and M mounted on a central rod; flagellar MS-ring protein 3431060 fliF 5712321 fliF Dinoroseobacter shibae DFL 12 = DSM 16493 flagellar MS-ring protein YP_001534598.1 3429384 D 398580 CDS YP_001534599.1 159045805 5712322 3431060..3431665 1 NC_009952.1 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 3431665 fliH 5712322 fliH Dinoroseobacter shibae DFL 12 = DSM 16493 flagellar biosynthesis protein FliH YP_001534599.1 3431060 D 398580 CDS YP_001534600.1 159045806 5712323 3431658..3431927 1 NC_009952.1 Swissprot: Q03593 Flagellar motor switch protein fliN COG: Flagellar motor switch/type III secretory pathway protein; flagellar motor switch protein FliN 3431927 fliN 5712323 fliN Dinoroseobacter shibae DFL 12 = DSM 16493 flagellar motor switch protein FliN YP_001534600.1 3431658 D 398580 CDS YP_001534601.1 159045807 5712324 3431930..3432658 1 NC_009952.1 FliP, with proteins FliQ and FliR, forms the core of the central channel in the flagella export apparatus; flagellar biosynthesis protein FliP 3432658 fliP 5712324 fliP Dinoroseobacter shibae DFL 12 = DSM 16493 flagellar biosynthesis protein FliP YP_001534601.1 3431930 D 398580 CDS YP_001534602.1 159045808 5712325 3432733..3433962 1 NC_009952.1 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 3433962 5712325 Dshi_3268 Dinoroseobacter shibae DFL 12 = DSM 16493 putative coenzyme F420 hydrogenase YP_001534602.1 3432733 D 398580 CDS YP_001534603.1 159045809 5712326 complement(3433959..3435065) 1 NC_009952.1 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 3435065 5712326 Dshi_3269 Dinoroseobacter shibae DFL 12 = DSM 16493 L-carnitine dehydratase/bile acid-inducible protein F YP_001534603.1 3433959 R 398580 CDS YP_001534604.1 159045810 5712327 complement(3435120..3435839) 1 NC_009952.1 hypothetical protein 3435839 5712327 Dshi_3270 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534604.1 3435120 R 398580 CDS YP_001534605.1 159045811 5712328 complement(3435991..3437064) 1 NC_009952.1 PFAM: protein of unknown function DUF59 KEGG: rde:RD1_2906 hypothetical protein; hypothetical protein 3437064 5712328 Dshi_3271 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534605.1 3435991 R 398580 CDS YP_001534606.1 159045812 5712329 complement(3437061..3437258) 1 NC_009952.1 KEGG: rde:RD1_2905 hypothetical protein; hypothetical protein 3437258 5712329 Dshi_3272 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534606.1 3437061 R 398580 CDS YP_001534607.1 159045813 5712330 3437544..3438491 1 NC_009952.1 hypothetical protein 3438491 5712330 Dshi_3273 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534607.1 3437544 D 398580 CDS YP_001534608.1 159045814 5712331 3438585..3439571 1 NC_009952.1 hypothetical protein 3439571 5712331 Dshi_3274 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534608.1 3438585 D 398580 CDS YP_001534609.1 159045815 5712332 complement(3439739..3440842) 1 NC_009952.1 catalyzes the formation of chorismate from 5-O-(1-carboxyvinyl)-3-phosphoshikimate in aromatic amino acid biosynthesis; chorismate synthase 3440842 aroC 5712332 aroC Dinoroseobacter shibae DFL 12 = DSM 16493 chorismate synthase YP_001534609.1 3439739 R 398580 CDS YP_001534610.1 159045816 5712333 complement(3441060..3441854) 1 NC_009952.1 PFAM: cytochrome c1 KEGG: rde:RD1_0565 cytochrome c1; cytochrome c1 3441854 petC 5712333 petC Dinoroseobacter shibae DFL 12 = DSM 16493 cytochrome c1 YP_001534610.1 3441060 R 398580 CDS YP_001534611.1 159045817 5712334 complement(3441879..3443228) 1 NC_009952.1 PFAM: Cytochrome b/b6 domain KEGG: jan:Jann_0326 cytochrome b/b6-like; cytochrome b 3443228 petB 5712334 petB Dinoroseobacter shibae DFL 12 = DSM 16493 cytochrome b YP_001534611.1 3441879 R 398580 CDS YP_001534612.1 159045818 5712335 complement(3443243..3443800) 1 NC_009952.1 TIGRFAM: ubiquinol-cytochrome c reductase, iron-sulfur subunit PFAM: Rieske [2Fe-2S] domain protein KEGG: sit:TM1040_2814 ubiquinol-cytochrome c reductase, iron-sulfur subunit; iron-sulfur subunit; ubiquinol-cytochrome c reductase 3443800 petA 5712335 petA Dinoroseobacter shibae DFL 12 = DSM 16493 ubiquinol-cytochrome c reductase YP_001534612.1 3443243 R 398580 CDS YP_001534613.1 159045819 5712336 complement(3444069..3444680) 1 NC_009952.1 PFAM: Glutathione S-transferase domain KEGG: rsp:RSP_1397 glutathione S-transferase; putative glutathione S-transferase family protein 3444680 5712336 Dshi_3279 Dinoroseobacter shibae DFL 12 = DSM 16493 putative glutathione S-transferase family protein YP_001534613.1 3444069 R 398580 CDS YP_001534614.1 159045820 5712337 complement(3444680..3444967) 1 NC_009952.1 KEGG: rsq:Rsph17025_2805 hypothetical protein; hypothetical protein 3444967 5712337 Dshi_3280 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534614.1 3444680 R 398580 CDS YP_001534615.1 159045821 5712338 complement(3445107..3448478) 1 NC_009952.1 PFAM: nucleic acid binding OB-fold tRNA/helicase-type; Endonuclease/exonuclease/phosphatase KEGG: syn:sll0656 extracellular nuclease; putative endonuclease/exonuclease/phosphatase 3448478 5712338 Dshi_3281 Dinoroseobacter shibae DFL 12 = DSM 16493 putative endonuclease/exonuclease/phosphatase YP_001534615.1 3445107 R 398580 CDS YP_001534616.1 159045822 5712339 3448790..3449674 1 NC_009952.1 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 3449674 fdhD 5712339 fdhD Dinoroseobacter shibae DFL 12 = DSM 16493 putative formate dehydrogenase accessory protein FdhD YP_001534616.1 3448790 D 398580 CDS YP_001534617.1 159045823 5712340 3449671..3450306 1 NC_009952.1 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 3450306 mobA 5712340 mobA Dinoroseobacter shibae DFL 12 = DSM 16493 molybdopterin-guanine dinucleotide biosynthesis protein MobA YP_001534617.1 3449671 D 398580 CDS YP_001534618.1 159045824 5712341 3450303..3452075 1 NC_009952.1 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 3452075 moeA3 5712341 moeA3 Dinoroseobacter shibae DFL 12 = DSM 16493 putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobB/MoeA YP_001534618.1 3450303 D 398580 CDS YP_001534619.1 159045825 5712342 complement(3452072..3452488) 1 NC_009952.1 PFAM: Thioredoxin domain KEGG: rde:RD1_0213 thioredoxin, putative; putative thioredoxin 3452488 trx 5712342 trx Dinoroseobacter shibae DFL 12 = DSM 16493 putative thioredoxin YP_001534619.1 3452072 R 398580 CDS YP_001534620.1 159045826 5712343 complement(3452504..3453217) 1 NC_009952.1 PFAM: cytochrome c biogenesis protein transmembrane region KEGG: rde:RD1_0214 cytochrome c biogenesis protein; cytochrome c biogenesis protein 3453217 ccdA 5712343 ccdA Dinoroseobacter shibae DFL 12 = DSM 16493 cytochrome c biogenesis protein YP_001534620.1 3452504 R 398580 CDS YP_001534621.1 159045827 5712344 complement(3453276..3454142) 1 NC_009952.1 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 3454142 5712344 Dshi_3287 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534621.1 3453276 R 398580 CDS YP_001534622.1 159045828 5712345 complement(3454254..3454544) 1 NC_009952.1 PFAM: histone family protein DNA-binding protein KEGG: rde:RD1_0603 DNA-binding protein HU; DNA-binding protein HU 3454544 hup 5712345 hup Dinoroseobacter shibae DFL 12 = DSM 16493 DNA-binding protein HU YP_001534622.1 3454254 R 398580 CDS YP_001534623.1 159045829 5712346 complement(3455298..3456767) 1 NC_009952.1 Catalyzes the hydrolysis of AMP to form adenine and ribose 5-phosphate using water as the nucleophile; AMP nucleosidase 3456767 amn 5712346 amn Dinoroseobacter shibae DFL 12 = DSM 16493 AMP nucleosidase YP_001534623.1 3455298 R 398580 CDS YP_001534624.1 159045830 5712347 3456894..3457313 1 NC_009952.1 KEGG: sil:SPO3747 hypothetical protein; hypothetical protein 3457313 5712347 Dshi_3290 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534624.1 3456894 D 398580 CDS YP_001534625.1 159045831 5712348 3457352..3458224 1 NC_009952.1 KEGG: jan:Jann_0273 NAD-dependent epimerase/dehydratase rde:RD1_0614 hypothetical protein; hypothetical protein 3458224 5712348 Dshi_3291 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534625.1 3457352 D 398580 CDS YP_001534626.1 159045832 5712349 complement(3458254..3459135) 1 NC_009952.1 hypothetical protein 3459135 5712349 Dshi_3292 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534626.1 3458254 R 398580 CDS YP_001534627.1 159045833 5712350 complement(3459141..3459959) 1 NC_009952.1 hypothetical protein 3459959 5712350 Dshi_3293 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534627.1 3459141 R 398580 CDS YP_001534628.1 159045834 5712351 complement(3459972..3461903) 1 NC_009952.1 catalyzes the formation of 1-deoxy-D-xylulose 5-phosphate from pyruvate and D-glyceraldehyde 3-phosphate; 1-deoxy-D-xylulose-5-phosphate synthase 3461903 dxs1 5712351 dxs1 Dinoroseobacter shibae DFL 12 = DSM 16493 1-deoxy-D-xylulose-5-phosphate synthase YP_001534628.1 3459972 R 398580 CDS YP_001534629.1 159045835 5712352 complement(3461924..3462799) 1 NC_009952.1 PFAM: Polyprenyl synthetase KEGG: rde:RD1_0549 ispA; geranyltranstransferase; FPP synthase; Farnesyl-diphosphate synthase; geranyltranstransferase 3462799 ispA 5712352 ispA Dinoroseobacter shibae DFL 12 = DSM 16493 geranyltranstransferase YP_001534629.1 3461924 R 398580 CDS YP_001534630.1 159045836 5712353 complement(3462803..3463045) 1 NC_009952.1 PFAM: histone deacetylase superfamily KEGG: rsp:RSP_1137 histone deacetylase family protein; Exonuclease VII small subunit; exodeoxyribonuclease 7 small subunit 3463045 xseB 5712353 xseB Dinoroseobacter shibae DFL 12 = DSM 16493 exodeoxyribonuclease 7 small subunit YP_001534630.1 3462803 R 398580 CDS YP_001534631.1 159045837 5712354 complement(3463042..3463983) 1 NC_009952.1 PFAM: histone deacetylase superfamily KEGG: rsp:RSP_1137 histone deacetylase family protein; histone deacetylase family protein 3463983 5712354 Dshi_3297 Dinoroseobacter shibae DFL 12 = DSM 16493 histone deacetylase family protein YP_001534631.1 3463042 R 398580 CDS YP_001534632.1 159045838 5712355 3464011..3464559 1 NC_009952.1 KEGG: mlo:mlr2044 hypothetical protein; hypothetical protein 3464559 5712355 Dshi_3298 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534632.1 3464011 D 398580 CDS YP_001534633.1 159045839 5712356 complement(3464567..3465280) 1 NC_009952.1 Swissprot: Protein petR PFAM: response regulator receiver; transcriptional regulator domain protein; DNA-binding response regulator PetR 3465280 petR 5712356 petR Dinoroseobacter shibae DFL 12 = DSM 16493 DNA-binding response regulator PetR YP_001534633.1 3464567 R 398580 CDS YP_001534634.1 159045840 5712357 complement(3465280..3465786) 1 NC_009952.1 PFAM: regulatory protein MarR KEGG: rde:RD1_0552 transcriptional regulator, MarR family; MarR family; transcriptional regulator 3465786 5712357 Dshi_3300 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001534634.1 3465280 R 398580 CDS YP_001534635.1 159045841 5712358 3465947..3466816 1 NC_009952.1 catalyzes the transamination of the branched-chain amino acids to their respective alpha-keto acids; branched-chain amino acid aminotransferase 3466816 ilvE 5712358 ilvE Dinoroseobacter shibae DFL 12 = DSM 16493 branched-chain amino acid aminotransferase YP_001534635.1 3465947 D 398580 CDS YP_001534636.1 159045842 5712359 3467100..3467408 1 NC_009952.1 KEGG: atc:AGR_L_2414 hypothetical protein; hypothetical protein 3467408 5712359 Dshi_3302 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534636.1 3467100 D 398580 CDS YP_001534637.1 159045843 5712360 complement(3467405..3468508) 1 NC_009952.1 REFSEQ: ref|ZP_01012112.1 membrane protein, putative [Rhodobacterale bacterium]; hypothetical protein 3468508 5712360 Dshi_3303 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534637.1 3467405 R 398580 CDS YP_001534638.1 159045844 5712361 3468555..3469358 1 NC_009952.1 KEGG: sil:SPO2058 hypothetical protein; hypothetical protein 3469358 5712361 Dshi_3304 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534638.1 3468555 D 398580 CDS YP_001534639.1 159045845 5712362 complement(3469362..3470303) 1 NC_009952.1 PFAM: integral membrane protein DUF6 KEGG: jan:Jann_3870 protein of unknown function DUF6, transmembrane; transmembrane; hypothetical protein 3470303 5712362 Dshi_3305 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534639.1 3469362 R 398580 CDS YP_001534640.1 159045846 5712363 complement(3470332..3470643) 1 NC_009952.1 hypothetical protein 3470643 5712363 Dshi_3306 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534640.1 3470332 R 398580 CDS YP_001534641.1 159045847 5712364 complement(3470805..3471839) 1 NC_009952.1 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 3471839 5712364 Dshi_3307 Dinoroseobacter shibae DFL 12 = DSM 16493 putative 4Fe-4S-binding domain-containing protein YP_001534641.1 3470805 R 398580 CDS YP_001534642.1 159045848 5712365 complement(3471836..3472501) 1 NC_009952.1 PFAM: Glutathione S-transferase domain KEGG: rsq:Rsph17025_2783 glutathione S-transferase, N-terminal domain; glutathione S-transferase 3472501 gst1 5712365 gst1 Dinoroseobacter shibae DFL 12 = DSM 16493 glutathione S-transferase YP_001534642.1 3471836 R 398580 CDS YP_001534643.1 159045849 5712366 complement(3472552..3473298) 1 NC_009952.1 TIGRFAM: monofunctional biosynthetic peptidoglycan transglycosylase PFAM: glycosyl transferase family 51 KEGG: rsh:Rsph17029_2806 monofunctional biosynthetic peptidoglycan transglycosylase; monofunctional biosynthetic peptidoglycan transglycosylase 3473298 mtgA 5712366 mtgA Dinoroseobacter shibae DFL 12 = DSM 16493 monofunctional biosynthetic peptidoglycan transglycosylase YP_001534643.1 3472552 R 398580 CDS YP_001534644.1 159045850 5712367 complement(3473352..3474155) 1 NC_009952.1 COG: RssA, Predicted esterase of the alpha-beta hydrolase superfamily PFAM: Patatin-like phospholipase; patatin-like phospholipase 3474155 rssA 5712367 rssA Dinoroseobacter shibae DFL 12 = DSM 16493 patatin-like phospholipase YP_001534644.1 3473352 R 398580 CDS YP_001534645.1 159045851 5712368 complement(3474155..3475375) 1 NC_009952.1 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 3475375 5712368 Dshi_3311 Dinoroseobacter shibae DFL 12 = DSM 16493 radical SAM protein YP_001534645.1 3474155 R 398580 CDS YP_001534646.1 159045852 5712369 3475522..3476199 1 NC_009952.1 KEGG: jan:Jann_2393 hypothetical protein; hypothetical protein 3476199 5712369 Dshi_3312 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534646.1 3475522 D 398580 CDS YP_001534647.1 159045853 5712370 complement(3476196..3476906) 1 NC_009952.1 KEGG: rsh:Rsph17029_0081 hypothetical protein; hypothetical protein 3476906 5712370 Dshi_3313 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534647.1 3476196 R 398580 CDS YP_001534648.1 159045854 5712371 complement(3477352..3477885) 1 NC_009952.1 KEGG: rde:RD1_0193 hypothetical protein; hypothetical protein 3477885 5712371 Dshi_3314 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534648.1 3477352 R 398580 CDS YP_001534649.1 159045855 5712372 3478272..3478583 1 NC_009952.1 hypothetical protein 3478583 5712372 Dshi_3315 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534649.1 3478272 D 398580 CDS YP_001534650.1 159045856 5712373 complement(3478598..3479476) 1 NC_009952.1 KEGG: sil:SPO3353 phosphoserine phosphatase TIGRFAM: phosphoserine phosphatase SerB; HAD-superfamily hydrolase, subfamily IB (PSPase-like) PFAM: Haloacid dehalogenase domain protein hydrolase; phosphoserine phosphatase 3479476 serB 5712373 serB Dinoroseobacter shibae DFL 12 = DSM 16493 phosphoserine phosphatase YP_001534650.1 3478598 R 398580 CDS YP_001534651.1 159045857 5712374 3479701..3480855 1 NC_009952.1 catalyzes the formation of 3-phosphonooxypyruvate and glutamate from O-phospho-L-serine and 2-oxoglutarate; phosphoserine aminotransferase 3480855 serC 5712374 serC Dinoroseobacter shibae DFL 12 = DSM 16493 phosphoserine aminotransferase YP_001534651.1 3479701 D 398580 CDS YP_001534652.1 159045858 5712375 3481012..3482607 1 NC_009952.1 catalyzes the formation of 3-phosphonooxypyruvate from 3-phospho-D-glycerate in serine biosynthesis; can also reduce alpha ketoglutarate to form 2-hydroxyglutarate; D-3-phosphoglycerate dehydrogenase 3482607 serA1 5712375 serA1 Dinoroseobacter shibae DFL 12 = DSM 16493 D-3-phosphoglycerate dehydrogenase YP_001534652.1 3481012 D 398580 CDS YP_001534653.1 159045859 5712376 3482662..3483396 1 NC_009952.1 PFAM: metallophosphoesterase KEGG: rsq:Rsph17025_0011 metallophosphoesterase; metallophosphoesterase 3483396 5712376 Dshi_3319 Dinoroseobacter shibae DFL 12 = DSM 16493 metallophosphoesterase YP_001534653.1 3482662 D 398580 CDS YP_001534654.1 159045860 5712377 complement(3483410..3483616) 1 NC_009952.1 KEGG: rde:RD1_1295 hypothetical protein; hypothetical protein 3483616 5712377 Dshi_3320 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534654.1 3483410 R 398580 CDS YP_001534655.1 159045861 5712378 3483814..3484269 1 NC_009952.1 PFAM: CreA family protein KEGG: rsh:Rsph17029_1167 CreA family protein; CreA family protein 3484269 5712378 Dshi_3321 Dinoroseobacter shibae DFL 12 = DSM 16493 CreA family protein YP_001534655.1 3483814 D 398580 CDS YP_001534656.1 159045862 5712379 complement(3484266..3485303) 1 NC_009952.1 PFAM: regulatory protein LacI; periplasmic binding protein/LacI transcriptional regulator KEGG: sil:SPO3684 transcriptional regulator, LacI family; LacI family; transcriptional regulator 3485303 5712379 Dshi_3322 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001534656.1 3484266 R 398580 CDS YP_001534657.1 159045863 5712380 complement(3485578..3486258) 1 NC_009952.1 PFAM: regulatory protein GntR HTH; GntR domain protein KEGG: jan:Jann_1164 transcriptional regulator, GntR family; GntR family; transcriptional regulator 3486258 5712380 Dshi_3323 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001534657.1 3485578 R 398580 CDS YP_001534658.1 159045864 5712381 complement(3486236..3489157) 1 NC_009952.1 PFAM: FAD binding domain, FAD linked oxidases KEGG: jan:Jann_1163 D-lactate dehydrogenase (cytochrome); D-lactate dehydrogenase 3489157 dld2 5712381 dld2 Dinoroseobacter shibae DFL 12 = DSM 16493 D-lactate dehydrogenase YP_001534658.1 3486236 R 398580 CDS YP_001534659.1 159045865 5712382 3489205..3490473 1 NC_009952.1 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 3490473 sgaA1 5712382 sgaA1 Dinoroseobacter shibae DFL 12 = DSM 16493 serine--glyoxylate aminotransferase YP_001534659.1 3489205 D 398580 CDS YP_001534660.1 159045866 5712383 3490512..3491489 1 NC_009952.1 TIGRFAM: TRAP dicarboxylate transporter, DctP subunit PFAM: TRAP dicarboxylate transporter- DctP subunit KEGG: pmu:PM1651 hypothetical E.coli; precursor; TRAP dicarboxylate transporter subunit DctP 3491489 dctP3 5712383 dctP3 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP dicarboxylate transporter subunit DctP YP_001534660.1 3490512 D 398580 CDS YP_001534661.1 159045867 5712384 3491612..3492154 1 NC_009952.1 PFAM: Tripartite ATP-independent periplasmic transporter DctQ component; TRAP dicarboxylate transporter subunit DctQ 3492154 dctQ1 5712384 dctQ1 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP dicarboxylate transporter subunit DctQ YP_001534661.1 3491612 D 398580 CDS YP_001534662.1 159045868 5712385 3492154..3493434 1 NC_009952.1 TIGRFAM: TRAP dicarboxylate transporter, DctM subunit PFAM: TRAP C4-dicarboxylate transport system permease DctM subunit; TRAP dicarboxylate transporter subunit DctM 3493434 dctM4 5712385 dctM4 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP dicarboxylate transporter subunit DctM YP_001534662.1 3492154 D 398580 CDS YP_001534663.1 159045869 5712386 3493431..3494204 1 NC_009952.1 Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA; enoyl-CoA hydratase 3494204 5712386 Dshi_3329 Dinoroseobacter shibae DFL 12 = DSM 16493 enoyl-CoA hydratase YP_001534663.1 3493431 D 398580 CDS YP_001534664.1 159045870 5712387 3494201..3495436 1 NC_009952.1 PFAM: CoA-transferase family III PRK: formyl-coenzyme A transferase; formyl-CoA transferase 3495436 yfdW1 5712387 yfdW1 Dinoroseobacter shibae DFL 12 = DSM 16493 formyl-CoA transferase YP_001534664.1 3494201 D 398580 CDS YP_001534665.1 159045871 5712389 3495749..3496933 1 NC_009952.1 catalyzes the formation of beta-ketovaleryl-CoA from acetyl-CoA and propionyl-CoA; beta-ketothiolase 3496933 bktB 5712389 bktB Dinoroseobacter shibae DFL 12 = DSM 16493 beta-ketothiolase YP_001534665.1 3495749 D 398580 CDS YP_001534666.1 159045872 5712390 3497022..3499481 1 NC_009952.1 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 3499481 5712390 Dshi_3332 Dinoroseobacter shibae DFL 12 = DSM 16493 sensor histidine kinase/response regulator YP_001534666.1 3497022 D 398580 CDS YP_001534667.1 159045873 5712391 complement(3499478..3500281) 1 NC_009952.1 PFAM: protein of unknown function DUF328 KEGG: sil:SPO0106 hypothetical protein; hypothetical protein 3500281 5712391 Dshi_3333 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534667.1 3499478 R 398580 CDS YP_001534668.1 159045874 5712392 complement(3500340..3502379) 1 NC_009952.1 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 3502379 recQ 5712392 recQ Dinoroseobacter shibae DFL 12 = DSM 16493 ATP-dependent DNA helicase RecQ YP_001534668.1 3500340 R 398580 CDS YP_001534669.1 159045875 5712393 complement(3502462..3502749) 1 NC_009952.1 PFAM: protein of unknown function YGGT KEGG: sil:SPO0122 YGGT family protein; transmembrane; hypothetical protein 3502749 5712393 Dshi_3335 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534669.1 3502462 R 398580 CDS YP_001534670.1 159045876 5712394 3502874..3503410 1 NC_009952.1 KEGG: sit:TM1040_2661 hypothetical protein; hypothetical protein 3503410 5712394 Dshi_3336 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534670.1 3502874 D 398580 CDS YP_001534671.1 159045877 5712395 3503472..3504803 1 NC_009952.1 PFAM: major facilitator superfamily MFS_1 KEGG: jan:Jann_0343 major facilitator superfamily MFS_1; major facilitator superfamily (MFS) transporter 3504803 5712395 Dshi_3337 Dinoroseobacter shibae DFL 12 = DSM 16493 major facilitator superfamily (MFS) transporter YP_001534671.1 3503472 D 398580 CDS YP_001534672.1 159045878 5712396 3504800..3505690 1 NC_009952.1 D-alanyl-D-alanine endopeptidase; functions in hydrolyzing cell wall peptidoglycan; similar to LAS metallopeptidases; forms a dimer in periplasm; penicillin-insensitive murein endopeptidase 3505690 mepA 5712396 mepA Dinoroseobacter shibae DFL 12 = DSM 16493 penicillin-insensitive murein endopeptidase YP_001534672.1 3504800 D 398580 CDS YP_001534673.1 159045879 5712397 3505663..3506544 1 NC_009952.1 KEGG: rsq:Rsph17025_0022 hypothetical protein; hypothetical protein 3506544 5712397 Dshi_3339 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534673.1 3505663 D 398580 CDS YP_001534674.1 159045880 5712398 3506634..3507257 1 NC_009952.1 TIGRFAM: conserved hypothetical integral membrane protein PFAM: protein of unknown function DUF165 KEGG: sit:TM1040_2665 protein of unknown function DUF165; hypothetical protein 3507257 5712398 Dshi_3340 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534674.1 3506634 D 398580 CDS YP_001534675.1 159045881 5712399 3507600..3509015 1 NC_009952.1 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 3509015 rimK 5712399 rimK Dinoroseobacter shibae DFL 12 = DSM 16493 ribosomal protein S6 modification protein YP_001534675.1 3507600 D 398580 CDS YP_001534676.1 159045882 5712400 3509061..3509483 1 NC_009952.1 PFAM: Class I peptide chain release factor KEGG: rde:RD1_0366 peptidyl-tRNA hydrolase, putative; peptidyl-tRNA hydrolase domain-containing protein 3509483 5712400 Dshi_3342 Dinoroseobacter shibae DFL 12 = DSM 16493 peptidyl-tRNA hydrolase domain-containing protein YP_001534676.1 3509061 D 398580 CDS YP_001534677.1 159045883 5712401 3509480..3510721 1 NC_009952.1 PFAM: aminotransferase class-III KEGG: sil:SPOA0354 aminotransferase, class III; class III aminotransferase 3510721 5712401 Dshi_3343 Dinoroseobacter shibae DFL 12 = DSM 16493 class III aminotransferase YP_001534677.1 3509480 D 398580 CDS YP_001534678.1 159045884 5712402 3510709..3511665 1 NC_009952.1 PFAM: aminoglycoside phosphotransferase; aminoglycoside phosphotransferase 3511665 5712402 Dshi_3344 Dinoroseobacter shibae DFL 12 = DSM 16493 aminoglycoside phosphotransferase YP_001534678.1 3510709 D 398580 CDS YP_001534679.1 159045885 5712403 complement(3511662..3512954) 1 NC_009952.1 catalyzes the formation of nictonate and 5-phospho-alpha-D-ribose 1-diphosphate from nicotinate D-ribonucleotide and diphosphate; nicotinate phosphoribosyltransferase 3512954 pncB 5712403 pncB Dinoroseobacter shibae DFL 12 = DSM 16493 nicotinate phosphoribosyltransferase YP_001534679.1 3511662 R 398580 CDS YP_001534680.1 159045886 5712404 complement(3513033..3515378) 1 NC_009952.1 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 3515378 5712404 Dshi_3346 Dinoroseobacter shibae DFL 12 = DSM 16493 multi-sensor hybrid histidine kinase YP_001534680.1 3513033 R 398580 CDS YP_001534681.1 159045887 5712405 complement(3515388..3515990) 1 NC_009952.1 KEGG: jan:Jann_0014 nicotinamidase; nicotinamidase 3515990 pncA 5712405 pncA Dinoroseobacter shibae DFL 12 = DSM 16493 nicotinamidase YP_001534681.1 3515388 R 398580 CDS YP_001534682.1 159045888 5712406 3516052..3516993 1 NC_009952.1 PFAM: Rhodanese domain protein KEGG: pde:Pden_0850 rhodanese domain protein; rhodanese domain-containing protein 3516993 5712406 Dshi_3348 Dinoroseobacter shibae DFL 12 = DSM 16493 rhodanese domain-containing protein YP_001534682.1 3516052 D 398580 CDS YP_001534683.1 159045889 5712407 3517036..3518097 1 NC_009952.1 PRK tRNA 2-selenouridine synthase; tRNA 2-selenouridine synthase 3518097 ybbB 5712407 ybbB Dinoroseobacter shibae DFL 12 = DSM 16493 tRNA 2-selenouridine synthase YP_001534683.1 3517036 D 398580 CDS YP_001534684.1 159045890 5712408 complement(3518104..3520233) 1 NC_009952.1 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 3520233 selD 5712408 selD Dinoroseobacter shibae DFL 12 = DSM 16493 selenide, water dikinase YP_001534684.1 3518104 R 398580 CDS YP_001534685.1 159045891 5712409 3520331..3521806 1 NC_009952.1 KEGG: bbt:BBta_2726 putative membrane protein of unknown function; hypothetical protein 3521806 5712409 Dshi_3351 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534685.1 3520331 D 398580 CDS YP_001534686.1 159045892 5712410 complement(3522370..3523434) 1 NC_009952.1 KEGG: jan:Jann_0255 hypothetical protein; hypothetical protein 3523434 5712410 Dshi_3352 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534686.1 3522370 R 398580 CDS YP_001534687.1 159045893 5712411 complement(3523424..3525826) 1 NC_009952.1 PFAM: Predicted permease KEGG: rsq:Rsph17025_3021 protein of unknown function DUF214; protein of unknown function DUF214; putative permease FtsX 3525826 5712411 Dshi_3353 Dinoroseobacter shibae DFL 12 = DSM 16493 putative permease FtsX YP_001534687.1 3523424 R 398580 CDS YP_001534688.1 159045894 5712412 complement(3525826..3526482) 1 NC_009952.1 PFAM: FtsE, Predicted ATPase involved in cell division; putative ATPase involved in cell division FtsE 3526482 5712412 Dshi_3354 Dinoroseobacter shibae DFL 12 = DSM 16493 putative ATPase involved in cell division FtsE YP_001534688.1 3525826 R 398580 CDS YP_001534689.1 159045895 5712413 3526685..3529102 1 NC_009952.1 negatively supercoils closed circular double-stranded DNA; DNA gyrase subunit B 3529102 gyrB 5712413 gyrB Dinoroseobacter shibae DFL 12 = DSM 16493 DNA gyrase subunit B YP_001534689.1 3526685 D 398580 CDS YP_001534690.1 159045896 5712414 3530095..3530361 1 NC_009952.1 PFAM: Transposase KEGG: mag:amb0646 insertion element ISR1 hypothetical 10 kDa protein A3; insertion element ISR1 10 kDa protein A3 3530361 5712414 Dshi_3356 Dinoroseobacter shibae DFL 12 = DSM 16493 insertion element ISR1 10 kDa protein A3 YP_001534690.1 3530095 D 398580 CDS YP_001534691.1 159045897 5712415 3530385..3531194 1 NC_009952.1 PFAM: Integrase catalytic region KEGG: bbt:BBta_7691 integrase, catalytic domain; integrase catalytic subunit 3531194 5712415 Dshi_3357 Dinoroseobacter shibae DFL 12 = DSM 16493 integrase catalytic subunit YP_001534691.1 3530385 D 398580 CDS YP_001534692.1 159045898 5712416 complement(3531547..3532338) 1 NC_009952.1 PFAM: protein of unknown function DUF1217 KEGG: sil:SPO3456 flagellar protein, putative; hypothetical protein 3532338 5712416 Dshi_3358 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534692.1 3531547 R 398580 CDS YP_001534693.1 159045899 5712417 complement(3532338..3532739) 1 NC_009952.1 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 3532739 flbT 5712417 flbT Dinoroseobacter shibae DFL 12 = DSM 16493 flagellar biosynthesis repressor FlbT YP_001534693.1 3532338 R 398580 CDS YP_001534694.1 159045900 5712418 complement(3532736..3533107) 1 NC_009952.1 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 3533107 flaF 5712418 flaF Dinoroseobacter shibae DFL 12 = DSM 16493 flagellar biosynthesis regulatory protein FlaF YP_001534694.1 3532736 R 398580 CDS YP_001534695.1 159045901 5712419 complement(3533170..3534720) 1 NC_009952.1 PFAM: flagellin domain protein KEGG: jan:Jann_4203 flagellin-like; flagellin 3534720 fliC 5712419 fliC Dinoroseobacter shibae DFL 12 = DSM 16493 flagellin YP_001534695.1 3533170 R 398580 CDS YP_001534696.1 159045902 5712420 complement(3534911..3535219) 1 NC_009952.1 hypothetical protein 3535219 5712420 Dshi_3362 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534696.1 3534911 R 398580 CDS YP_001534697.1 159045903 5712421 complement(3535242..3535544) 1 NC_009952.1 PRK: flgJ, peptidoglycan hydrolase KEGG: sit:TM1040_2976 flagellar protein FlgJ, putative; putative flagellar protein FlgJ 3535544 5712421 Dshi_3363 Dinoroseobacter shibae DFL 12 = DSM 16493 putative flagellar protein FlgJ YP_001534697.1 3535242 R 398580 CDS YP_001534698.1 159045904 5712422 3535667..3538003 1 NC_009952.1 PFAM: flagellar hook-length control protein; putative flagellar hook-length control protein 3538003 5712422 Dshi_3364 Dinoroseobacter shibae DFL 12 = DSM 16493 putative flagellar hook-length control protein YP_001534698.1 3535667 D 398580 CDS YP_001534699.1 159045905 5712423 3538012..3538674 1 NC_009952.1 acts as a scaffold for the assembly of hook proteins onto the flagellar basal body rod; Rhodobacter sphaeroides has 2 copies of many flagellar genes; the Rhodobacter protein in this cluster is associated with a set of flagellar genes acquired by lateral gene transfer; these genes are not normally expressed; flagellar basal body rod modification protein 3538674 flgD 5712423 flgD Dinoroseobacter shibae DFL 12 = DSM 16493 flagellar basal body rod modification protein YP_001534699.1 3538012 D 398580 CDS YP_001534700.1 159045906 5712424 3538823..3539614 1 NC_009952.1 PFAM: Phosphotransferase enzyme family Genbank: gb|ABF65711.1 aminoglycoside phosphotransferase (Silicibacter sp.); putative aminoglycoside phosphotransferase 3539614 5712424 Dshi_3366 Dinoroseobacter shibae DFL 12 = DSM 16493 putative aminoglycoside phosphotransferase YP_001534700.1 3538823 D 398580 CDS YP_001534701.1 159045907 5712425 complement(3539582..3541111) 1 NC_009952.1 TIGRFAM: 2-polyprenylphenol 6-hydroxylase PFAM: ABC-1 domain protein KEGG: rde:RD1_0202 ubiquinone biosynthesis protein UbiB; 2-polyprenylphenol 6-hydroxylase 3541111 ubiB 5712425 ubiB Dinoroseobacter shibae DFL 12 = DSM 16493 2-polyprenylphenol 6-hydroxylase YP_001534701.1 3539582 R 398580 CDS YP_001534702.1 159045908 5712426 complement(3541114..3541866) 1 NC_009952.1 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 3541866 ubiE 5712426 ubiE Dinoroseobacter shibae DFL 12 = DSM 16493 2-polyprenylmethoxybenozoquinol methylase YP_001534702.1 3541114 R 398580 CDS YP_001534703.1 159045909 5712427 3541951..3542805 1 NC_009952.1 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 3542805 mutM 5712427 mutM Dinoroseobacter shibae DFL 12 = DSM 16493 formamidopyrimidine-DNA glycosylase YP_001534703.1 3541951 D 398580 CDS YP_001534704.1 159045910 5712428 3542870..3543646 1 NC_009952.1 PFAM: Enoyl-CoA hydratase/isomerase KEGG: rsh:Rsph17029_0009 enoyl-CoA hydratase/isomerase; enoyl-CoA hydratase/isomerase 3543646 5712428 Dshi_3370 Dinoroseobacter shibae DFL 12 = DSM 16493 enoyl-CoA hydratase/isomerase YP_001534704.1 3542870 D 398580 CDS YP_001534705.1 159045911 5712429 3543739..3544005 1 NC_009952.1 binds directly to the 16S rRNA and is involved in post-translational inhibition of arginine and ornithine decarboxylase; 30S ribosomal protein S20 3544005 rpsT 5712429 rpsT Dinoroseobacter shibae DFL 12 = DSM 16493 30S ribosomal protein S20 YP_001534705.1 3543739 D 398580 CDS YP_001534706.1 159045912 5712430 3544233..3544682 1 NC_009952.1 PFAM: Rhodanese Homology Domain superfamily, subgroup 1 COG: PspE, Rhodanese-related sulfurtransferase; rhodanese-like sulfurtransferase 3544682 yibN 5712430 yibN Dinoroseobacter shibae DFL 12 = DSM 16493 rhodanese-like sulfurtransferase YP_001534706.1 3544233 D 398580 CDS YP_001534707.1 159045913 5712431 3544704..3546086 1 NC_009952.1 binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication; can also affect transcription of multiple genes including itself.; chromosomal replication initiation protein 3546086 dnaA 5712431 dnaA Dinoroseobacter shibae DFL 12 = DSM 16493 chromosomal replication initiation protein YP_001534707.1 3544704 D 398580 CDS YP_001534708.1 159045914 5712432 3546223..3547341 1 NC_009952.1 binds the polymerase to DNA and acts as a sliding clamp; DNA polymerase III subunit beta 3547341 dnaN 5712432 dnaN Dinoroseobacter shibae DFL 12 = DSM 16493 DNA polymerase III subunit beta YP_001534708.1 3546223 D 398580 CDS YP_001534709.1 159045915 5712433 3547348..3548433 1 NC_009952.1 Required for DNA replication; binds preferentially to single-stranded, linear DNA; recombination protein F 3548433 recF 5712433 recF Dinoroseobacter shibae DFL 12 = DSM 16493 recombination protein F YP_001534709.1 3547348 D 398580 CDS YP_001534710.1 159045916 5712434 complement(3548430..3549533) 1 NC_009952.1 part of the basal body which consists of four rings L, P, S, and M mounted on a central rod; Vibrio parahaemolyticus, Yersinia, Bradyrhizobium and other bacteria have two copies of this and other flagellar genes; the V. parahaemolyticus protein is associated with the polar flagella and the Bradyrhizobium protein is associated with the thick flagellum; flagellar basal body P-ring protein 3549533 flgI 5712434 flgI Dinoroseobacter shibae DFL 12 = DSM 16493 flagellar basal body P-ring protein YP_001534710.1 3548430 R 398580 CDS YP_001534711.1 159045917 5712435 complement(3549530..3550540) 1 NC_009952.1 PFAM: Putative flagellar hook-associated protein 3 (HAP3) KEGG: sil:SPO0194 flagellar hook-associated protein FlgL family protein; flagellar hook-associated protein FlgL 3550540 flgL 5712435 flgL Dinoroseobacter shibae DFL 12 = DSM 16493 flagellar hook-associated protein FlgL YP_001534711.1 3549530 R 398580 CDS YP_001534712.1 159045918 5712436 complement(3550543..3552000) 1 NC_009952.1 with FlgL acts as a hook filament junction protein to join the flagellar filament to the hook; flagellar hook-associated protein FlgK 3552000 flgK 5712436 flgK Dinoroseobacter shibae DFL 12 = DSM 16493 flagellar hook-associated protein FlgK YP_001534712.1 3550543 R 398580 CDS YP_001534713.1 159045919 5712437 complement(3552016..3553320) 1 NC_009952.1 PFAM: flagellar basal body rod protein; protein of unknown function DUF1078 domain protein Swissprot: Flagellar hook protein flgE; flagellar hook protein FlgE 3553320 flgE 5712437 flgE Dinoroseobacter shibae DFL 12 = DSM 16493 flagellar hook protein FlgE YP_001534713.1 3552016 R 398580 CDS YP_001534714.1 159045920 5712438 complement(3553404..3554222) 1 NC_009952.1 PRK: motB, flagellar motor protein MotB COG: MotB, Flagellar motor protein REFSEQ: chemotaxis protein MotB; chemotaxis protein MotB 3554222 motB 5712438 motB Dinoroseobacter shibae DFL 12 = DSM 16493 chemotaxis protein MotB YP_001534714.1 3553404 R 398580 CDS YP_001534715.1 159045921 5712439 3554408..3556192 1 NC_009952.1 PFAM: surface antigen (D15); surface antigen variable number repeat protein KEGG: rde:RD1_2329 outer membrane protein, putative; hypothetical protein 3556192 5712439 Dshi_3381 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534715.1 3554408 D 398580 CDS YP_001534716.1 159045922 5712440 3556189..3559443 1 NC_009952.1 PFAM: protein of unknown function DUF490 KEGG: jan:Jann_0244 protein of unknown function DUF490; hypothetical protein 3559443 5712440 Dshi_3382 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534716.1 3556189 D 398580 CDS YP_001534717.1 159045923 5712441 complement(3559437..3560141) 1 NC_009952.1 PFAM: Rhomboid family protein KEGG: jan:Jann_4233 rhomboid-like protein; rhomboid family protein 3560141 5712441 Dshi_3383 Dinoroseobacter shibae DFL 12 = DSM 16493 rhomboid family protein YP_001534717.1 3559437 R 398580 CDS YP_001534718.1 159045924 5712442 complement(3560203..3561804) 1 NC_009952.1 TIGRFAM: eight transmembrane protein EpsH; Methanolan biosynthesis EpsI KEGG: jan:Jann_4271 hypothetical protein; transmembrane exosortase 3561804 epsH 5712442 epsH Dinoroseobacter shibae DFL 12 = DSM 16493 transmembrane exosortase YP_001534718.1 3560203 R 398580 CDS YP_001534719.1 159045925 5712443 complement(3561914..3564349) 1 NC_009952.1 PFAM: Tetratricopeptide TPR_4; Tetratricopeptide TPR_2 repeat protein SMART: Tetratricopeptide domain protein KEGG: jan:Jann_4236 tetratricopeptide TPR_2; tetratricopeptide 3564349 5712443 Dshi_3385 Dinoroseobacter shibae DFL 12 = DSM 16493 tetratricopeptide YP_001534719.1 3561914 R 398580 CDS YP_001534720.1 159045926 5712444 complement(3564483..3564998) 1 NC_009952.1 PFAM: sugar transferase KEGG: rde:RD1_B0024 bacterial sugar transferase; Galactosyl-P-P-undecaprenol synthetase; undecaprenyl-phosphate galactose phosphotransferase 3564998 wcaJ 5712444 wcaJ Dinoroseobacter shibae DFL 12 = DSM 16493 undecaprenyl-phosphate galactose phosphotransferase YP_001534720.1 3564483 R 398580 CDS YP_001534721.1 159045927 5712445 3565730..3566584 1 NC_009952.1 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 3566584 exeA 5712445 exeA Dinoroseobacter shibae DFL 12 = DSM 16493 Type II secretory pathway YP_001534721.1 3565730 D 398580 CDS YP_001534722.1 159045928 5712446 3566584..3568110 1 NC_009952.1 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 3568110 5712446 Dshi_3388 Dinoroseobacter shibae DFL 12 = DSM 16493 polysaccharide chain length determinant protein YP_001534722.1 3566584 D 398580 CDS YP_001534723.1 159045929 5712447 3568158..3568988 1 NC_009952.1 KEGG: jan:Jann_4240 ATPases involved in chromosome partitioning-like; chromosome partitioning ATPase 3568988 5712447 Dshi_3389 Dinoroseobacter shibae DFL 12 = DSM 16493 chromosome partitioning ATPase YP_001534723.1 3568158 D 398580 CDS YP_001534724.1 159045930 5712448 complement(3568985..3569746) 1 NC_009952.1 PFAM: metallophosphoesterase KEGG: jan:Jann_3688 metallophosphoesterase; metallophosphoesterase 3569746 5712448 Dshi_3390 Dinoroseobacter shibae DFL 12 = DSM 16493 metallophosphoesterase YP_001534724.1 3568985 R 398580 CDS YP_001534725.1 159045931 5712449 complement(3569750..3570550) 1 NC_009952.1 PFAM: beta-lactamase domain protein KEGG: rde:RD1_3791 metallo-beta-lactamase family protein, putative; putative metallo-beta-lactamase family protein 3570550 5712449 Dshi_3391 Dinoroseobacter shibae DFL 12 = DSM 16493 putative metallo-beta-lactamase family protein YP_001534725.1 3569750 R 398580 CDS YP_001534726.1 159045932 5712450 complement(3570547..3570837) 1 NC_009952.1 PFAM: Antibiotic biosynthesis monooxygenase KEGG: rde:RD1_3790 hypothetical protein; hypothetical protein 3570837 5712450 Dshi_3392 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534726.1 3570547 R 398580 CDS YP_001534727.1 159045933 5712451 3570952..3572025 1 NC_009952.1 PFAM: isocitrate/isopropylmalate dehydrogenase KEGG: rde:RD1_3789 3-isopropylmalate dehydrogenase; 3-IPM-DH; IMDH; Beta-IPM dehydrogenase; 3-isopropylmalate dehydrogenase 3572025 leuB 5712451 leuB Dinoroseobacter shibae DFL 12 = DSM 16493 3-isopropylmalate dehydrogenase YP_001534727.1 3570952 D 398580 CDS YP_001534728.1 159045934 5712452 3572022..3573032 1 NC_009952.1 PFAM: oxidoreductase domain protein; Oxidoreductase domain; homoserine dehydrogenase NAD-binding KEGG: rde:RD1_3788 probable NADH-dependent dyhydrogenase; oxidoreductase domain-containing protein 3573032 5712452 Dshi_3394 Dinoroseobacter shibae DFL 12 = DSM 16493 oxidoreductase domain-containing protein YP_001534728.1 3572022 D 398580 CDS YP_001534729.1 159045935 5712453 complement(3573085..3574533) 1 NC_009952.1 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 3574533 dctM3 5712453 dctM3 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP dicarboxylate transporter subunit DctM YP_001534729.1 3573085 R 398580 CDS YP_001534730.1 159045936 5712454 complement(3574537..3575340) 1 NC_009952.1 PFAM: Tripartite ATP-independent periplasmic transporter DctQ component KEGG: maq:Maqu_0086 tripartite ATP-independent periplasmic transporter, DctQ component; TRAP dicarboxylate transporter subunit DctQ 3575340 dctQ2 5712454 dctQ2 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP dicarboxylate transporter subunit DctQ YP_001534730.1 3574537 R 398580 CDS YP_001534731.1 159045937 5712455 complement(3575429..3576475) 1 NC_009952.1 PFAM: TRAP dicarboxylate transporter- DctP subunit KEGG: cps:CPS_1264 extracellular solute-binding protein, family 7; precursor; TRAP dicarboxylate transporter subunit DctP 3576475 dctP2 5712455 dctP2 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP dicarboxylate transporter subunit DctP YP_001534731.1 3575429 R 398580 CDS YP_001534732.1 159045938 5712456 complement(3576583..3577113) 1 NC_009952.1 KEGG: nha:Nham_4013 ISSpo6, transposase OrfB; transposase OrfB; ISSpo6 3577113 orfB 5712456 orfB Dinoroseobacter shibae DFL 12 = DSM 16493 ISSpo6 YP_001534732.1 3576583 R 398580 CDS YP_001534733.1 159045939 5712457 complement(3577175..3577537) 1 NC_009952.1 KEGG: nha:Nham_4014 ISSpo6, transposase orf A; transposase OrfA; ISSpo6 3577537 orfA 5712457 orfA Dinoroseobacter shibae DFL 12 = DSM 16493 ISSpo6 YP_001534733.1 3577175 R 398580 CDS YP_001534734.1 159045940 5712458 complement(3577798..3578496) 1 NC_009952.1 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 3578496 ubiG2 5712458 ubiG2 Dinoroseobacter shibae DFL 12 = DSM 16493 3-demethylubiquinone-9 3-methyltransferase YP_001534734.1 3577798 R 398580 CDS YP_001534735.1 159045941 5712459 complement(3578510..3579325) 1 NC_009952.1 KEGG: rde:RD1_0738 hypothetical protein; hypothetical protein 3579325 5712459 Dshi_3401 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534735.1 3578510 R 398580 CDS YP_001534736.1 159045942 5712460 complement(3579372..3580727) 1 NC_009952.1 KEGG: rsp:RSP_0230 neutral zinc metallopeptidase CD: Zinc-dependent metalloprotease, serralysin_like subfamily; neutral zinc metallopeptidase 3580727 5712460 Dshi_3402 Dinoroseobacter shibae DFL 12 = DSM 16493 neutral zinc metallopeptidase YP_001534736.1 3579372 R 398580 CDS YP_001534737.1 159045943 5712461 complement(3580985..3582724) 1 NC_009952.1 PFAM: AMP-dependent synthetase and ligase KEGG: rde:RD1_1106 putative long chain fatty acid acyl-CoA ligase; acyl-CoA synthetase 3582724 5712461 Dshi_3403 Dinoroseobacter shibae DFL 12 = DSM 16493 acyl-CoA synthetase YP_001534737.1 3580985 R 398580 CDS YP_001534738.1 159045944 5712462 3582924..3583157 1 NC_009952.1 KEGG: mpt:Mpe_A3536 hypothetical protein; hypothetical protein 3583157 5712462 Dshi_3404 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534738.1 3582924 D 398580 CDS YP_001534739.1 159045945 5712463 complement(3583162..3583923) 1 NC_009952.1 PFAM: DSBA oxidoreductase; thiol:disulfide interchange protein DsbA 3583923 dsbA2 5712463 dsbA2 Dinoroseobacter shibae DFL 12 = DSM 16493 thiol:disulfide interchange protein DsbA YP_001534739.1 3583162 R 398580 CDS YP_001534740.1 159045946 5712464 3584144..3584692 1 NC_009952.1 PFAM: ErfK/YbiS/YcfS/YnhG family protein KEGG: mes:Meso_4112 ErfK/YbiS/YcfS/YnhG; ErfK/YbiS/YcfS/YnhG family protein 3584692 5712464 Dshi_3406 Dinoroseobacter shibae DFL 12 = DSM 16493 ErfK/YbiS/YcfS/YnhG family protein YP_001534740.1 3584144 D 398580 CDS YP_001534741.1 159045947 5712465 3584847..3586958 1 NC_009952.1 KEGG: mag:amb3382 thiol:disulfide interchange protein DsbD 1 precursor; thiol:disulfide interchange protein DsbD 3586958 dsbD 5712465 dsbD Dinoroseobacter shibae DFL 12 = DSM 16493 thiol:disulfide interchange protein DsbD YP_001534741.1 3584847 D 398580 CDS YP_001534742.1 159045948 5712466 complement(3586961..3588142) 1 NC_009952.1 PFAM: TPR repeat-containing protein SMART: Tetratricopeptide domain protein KEGG: ret:RHE_CH01289 cytochrome-C-type biogenesis protein; cytochrome c-type biogenesis protein CycH 3588142 cycH 5712466 cycH Dinoroseobacter shibae DFL 12 = DSM 16493 cytochrome c-type biogenesis protein CycH YP_001534742.1 3586961 R 398580 CDS YP_001534743.1 159045949 5712467 complement(3588139..3588624) 1 NC_009952.1 PFAM: cytochrome C biogenesis protein KEGG: rsh:Rsph17029_1291 cytochrome c biogenesis protein; cytochrome c-type biogenesis protein CycL 3588624 cycL 5712467 cycL Dinoroseobacter shibae DFL 12 = DSM 16493 cytochrome c-type biogenesis protein CycL YP_001534743.1 3588139 R 398580 CDS YP_001534744.1 159045950 5712468 complement(3588621..3589190) 1 NC_009952.1 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 3589190 dsbE 5712468 dsbE Dinoroseobacter shibae DFL 12 = DSM 16493 thiol:disulfide interchange protein DsbE YP_001534744.1 3588621 R 398580 CDS YP_001534745.1 159045951 5712469 complement(3589195..3591189) 1 NC_009952.1 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 3591189 cycK 5712469 cycK Dinoroseobacter shibae DFL 12 = DSM 16493 cytochrome c-type biogenesis protein CycK YP_001534745.1 3589195 R 398580 CDS YP_001534746.1 159045952 5712470 complement(3591397..3591816) 1 NC_009952.1 PFAM: protein of unknown function DUF55; hypothetical protein 3591816 5712470 Dshi_3412 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534746.1 3591397 R 398580 CDS YP_001534747.1 159045953 5712471 complement(3591816..3592088) 1 NC_009952.1 PFAM: YCII-related KEGG: rde:RD1_0468 YCII-related domain protein; YCII-like domain-containing protein 3592088 5712471 Dshi_3413 Dinoroseobacter shibae DFL 12 = DSM 16493 YCII-like domain-containing protein YP_001534747.1 3591816 R 398580 CDS YP_001534748.1 159045954 5712472 complement(3592090..3593052) 1 NC_009952.1 catalyzes the NAD(P)H-dependent reduction of glycerol 3-phosphate to glycerone phosphate; NAD(P)H-dependent glycerol-3-phosphate dehydrogenase 3593052 gpsA 5712472 gpsA Dinoroseobacter shibae DFL 12 = DSM 16493 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase YP_001534748.1 3592090 R 398580 CDS YP_001534749.1 159045955 5712473 complement(3593049..3594119) 1 NC_009952.1 in most organisms, only the N-terminal domain is present in a single polypeptide; in some archaea this domain is fused to a kinase domain; this gene is essential for growth in Escherichia coli and Bacillus subtilis; the secreted glycoprotease from Pasteurella haemolytica showed specificity for O-sialoglycosylated proteins; the Pyrococcus structure shows DNA-binding properties, iron-binding, ATP-binding, and AP endonuclease activity; putative DNA-binding/iron metalloprotein/AP endonuclease 3594119 gcp 5712473 gcp Dinoroseobacter shibae DFL 12 = DSM 16493 putative DNA-binding/iron metalloprotein/AP endonuclease YP_001534749.1 3593049 R 398580 CDS YP_001534750.1 159045956 5712474 3594171..3594887 1 NC_009952.1 PFAM: Uroporphyrinogen III synthase HEM4 KEGG: rsq:Rsph17025_2913 uroporphyrinogen III synthase HEM4; Hydroxymethylbilane hydrolyase [cyclizing]; Uroporphyrinogen-III cosynthetase; UROS; uroporphyrinogen-III synthase 3594887 hemD 5712474 hemD Dinoroseobacter shibae DFL 12 = DSM 16493 uroporphyrinogen-III synthase YP_001534750.1 3594171 D 398580 CDS YP_001534751.1 159045957 5712475 3594961..3596388 1 NC_009952.1 KEGG: jan:Jann_4082 hypothetical protein; hypothetical protein 3596388 5712475 Dshi_3417 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534751.1 3594961 D 398580 CDS YP_001534752.1 159045958 5712476 3596399..3597907 1 NC_009952.1 PFAM: HemY domain protein; hypothetical protein 3597907 5712476 Dshi_3418 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534752.1 3596399 D 398580 CDS YP_001534753.1 159045959 5712477 complement(3597982..3599307) 1 NC_009952.1 PFAM: Amidase KEGG: rsq:Rsph17025_3870 2-alkenal reductase; amidase 3599307 5712477 Dshi_3419 Dinoroseobacter shibae DFL 12 = DSM 16493 amidase YP_001534753.1 3597982 R 398580 CDS YP_001534754.1 159045960 5712478 3599365..3600924 1 NC_009952.1 TIGRFAM: glycerol kinase PFAM: carbohydrate kinase FGGY KEGG: rde:RD1_2883 glycerol kinase; GK; Glycerokinase; ATP:glycerol 3-phosphotransferase; glycerol kinase 3600924 glpK 5712478 glpK Dinoroseobacter shibae DFL 12 = DSM 16493 glycerol kinase YP_001534754.1 3599365 D 398580 CDS YP_001534755.1 159045961 5712479 complement(3601513..3603003) 1 NC_009952.1 Hydrolysis of proteins with broad specificity for peptide bonds, and a preference for a large uncharged residue in P1. Hydrolyses peptide amides; subtilisin DY 3603003 apr 5712479 apr Dinoroseobacter shibae DFL 12 = DSM 16493 subtilisin DY YP_001534755.1 3601513 R 398580 CDS YP_001534756.1 159045962 5712480 complement(3603000..3603596) 1 NC_009952.1 no hits to other proteins; hypothetical protein 3603596 5712480 Dshi_3422 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534756.1 3603000 R 398580 CDS YP_001534757.1 159045963 5712481 complement(3603596..3604171) 1 NC_009952.1 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 3604171 rpoE1 5712481 rpoE1 Dinoroseobacter shibae DFL 12 = DSM 16493 RNA polymerase sigma factor YP_001534757.1 3603596 R 398580 CDS YP_001534758.1 159045964 5712482 complement(3604171..3605991) 1 NC_009952.1 no significant BLAST hits, GC frame plot ok; hypothetical protein 3605991 5712482 Dshi_3424 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534758.1 3604171 R 398580 CDS YP_001534759.1 159045965 5712483 complement(3606501..3606842) 1 NC_009952.1 KEGG: sil:SPO3859 hypothetical protein; hypothetical protein 3606842 5712483 Dshi_3425 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534759.1 3606501 R 398580 CDS YP_001534760.1 159045966 5712484 complement(3607055..3608443) 1 NC_009952.1 catalyzes the formation of L-homocysteine from S-adenosyl-L-homocysteine; S-adenosyl-L-homocysteine hydrolase 3608443 ahcY 5712484 ahcY Dinoroseobacter shibae DFL 12 = DSM 16493 S-adenosyl-L-homocysteine hydrolase YP_001534760.1 3607055 R 398580 CDS YP_001534761.1 159045967 5712485 3608567..3609595 1 NC_009952.1 PFAM: glycosyl transferase family 8 KEGG: rde:RD1_0464 lipopolysaccharide 1,3-galactosyltransferase, putative; 3-galactosyltransferase, (Lipopolysaccharide 3-alpha-galactosyltransferase); lipopolysaccharide 1 3609595 rafI 5712485 rafI Dinoroseobacter shibae DFL 12 = DSM 16493 lipopolysaccharide 1 YP_001534761.1 3608567 D 398580 CDS YP_001534762.1 159045968 5712486 complement(3609608..3609898) 1 NC_009952.1 no hits to other proteins; hypothetical protein 3609898 5712486 Dshi_3428 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534762.1 3609608 R 398580 CDS YP_001534763.1 159045969 5712487 3610138..3610746 1 NC_009952.1 PFAM: HD domain KEGG: sit:TM1040_2836 metal dependent phosphohydrolase; metal dependent phosphohydrolase 3610746 5712487 Dshi_3429 Dinoroseobacter shibae DFL 12 = DSM 16493 metal dependent phosphohydrolase YP_001534763.1 3610138 D 398580 CDS YP_001534764.1 159045970 5712488 complement(3610863..3611417) 1 NC_009952.1 PFAM: response regulator receiver KEGG: sil:SPO3865 photosynthetic apparatus regulatory protein RegA; Response regulator PrrA; photosynthetic apparatus regulatory protein RegA 3611417 regA 5712488 regA Dinoroseobacter shibae DFL 12 = DSM 16493 photosynthetic apparatus regulatory protein RegA YP_001534764.1 3610863 R 398580 CDS YP_001534765.1 159045971 5712489 complement(3611501..3612121) 1 NC_009952.1 PFAM: electron transport protein SCO1/SenC KEGG: sit:TM1040_2839 electron transport protein SCO1/SenC; regulatory protein SenC 3612121 senC 5712489 senC Dinoroseobacter shibae DFL 12 = DSM 16493 regulatory protein SenC YP_001534765.1 3611501 R 398580 CDS YP_001534766.1 159045972 5712490 3612224..3613615 1 NC_009952.1 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 3613615 regB 5712490 regB Dinoroseobacter shibae DFL 12 = DSM 16493 sensor histidine kinase RegB YP_001534766.1 3612224 D 398580 CDS YP_001534767.1 159045973 5712491 3613670..3614974 1 NC_009952.1 TIGRFAM: PAS domain S-box REFSEQ: PAS domain containing protein; putative PAS/PAC sensor protein 3614974 5712491 Dshi_3433 Dinoroseobacter shibae DFL 12 = DSM 16493 putative PAS/PAC sensor protein YP_001534767.1 3613670 D 398580 CDS YP_001534768.1 159045974 5712492 3615034..3615531 1 NC_009952.1 PFAM: protein of unknown function UPF0079 KEGG: rsq:Rsph17025_2955 protein of unknown function UPF0079; hypothetical protein 3615531 5712492 Dshi_3434 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534768.1 3615034 D 398580 CDS YP_001534769.1 159045975 5712493 3615528..3616526 1 NC_009952.1 PFAM: aminoglycoside phosphotransferase KEGG: rsh:Rsph17029_0175 aminoglycoside phosphotransferase; aminoglycoside phosphotransferase 3616526 5712493 Dshi_3435 Dinoroseobacter shibae DFL 12 = DSM 16493 aminoglycoside phosphotransferase YP_001534769.1 3615528 D 398580 CDS YP_001534770.1 159045976 5712494 3616511..3617194 1 NC_009952.1 PFAM: Nucleotidyl transferase KEGG: pde:Pden_2796 nucleotidyl transferase; nucleotidyl transferase 3617194 5712494 Dshi_3436 Dinoroseobacter shibae DFL 12 = DSM 16493 nucleotidyl transferase YP_001534770.1 3616511 D 398580 CDS YP_001534771.1 159045977 5712495 3617191..3620157 1 NC_009952.1 TIGRFAM: Double-strand break repair protein AddB KEGG: rsq:Rsph17025_2952 RecB family exonuclease-like protein PMID: 15547262; double-strand break repair helicase AddB 3620157 addB 5712495 addB Dinoroseobacter shibae DFL 12 = DSM 16493 double-strand break repair helicase AddB YP_001534771.1 3617191 D 398580 CDS YP_001534772.1 159045978 5712496 3620154..3623531 1 NC_009952.1 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 3623531 addA 5712496 addA Dinoroseobacter shibae DFL 12 = DSM 16493 double-strand break repair helicase AddA YP_001534772.1 3620154 D 398580 CDS YP_001534773.1 159045979 5712497 3623597..3623917 1 NC_009952.1 TIGRFAM: thioredoxin PFAM: Thioredoxin domain KEGG: rde:RD1_0451 thioredoxin; Trx; thioredoxin 3623917 trxA1 5712497 trxA1 Dinoroseobacter shibae DFL 12 = DSM 16493 thioredoxin YP_001534773.1 3623597 D 398580 CDS YP_001534774.1 159045980 5712498 3624024..3624581 1 NC_009952.1 heat shock protein involved in degradation of misfolded proteins; ATP-dependent protease peptidase subunit 3624581 hslV 5712498 hslV Dinoroseobacter shibae DFL 12 = DSM 16493 ATP-dependent protease peptidase subunit YP_001534774.1 3624024 D 398580 CDS YP_001534775.1 159045981 5712499 3624650..3625963 1 NC_009952.1 heat shock protein involved in degradation of misfolded proteins; ATP-dependent protease ATP-binding subunit HslU 3625963 hslU 5712499 hslU Dinoroseobacter shibae DFL 12 = DSM 16493 ATP-dependent protease ATP-binding subunit HslU YP_001534775.1 3624650 D 398580 CDS YP_001534776.1 159045982 5712500 3626001..3627206 1 NC_009952.1 PFAM: major facilitator superfamily MFS_1 KEGG: sit:TM1040_0930 major facilitator superfamily MFS_1; major facilitator superfamily (MFS) transporter 3627206 5712500 Dshi_3442 Dinoroseobacter shibae DFL 12 = DSM 16493 major facilitator superfamily (MFS) transporter YP_001534776.1 3626001 D 398580 CDS YP_001534777.1 159045983 5712501 complement(3627203..3627796) 1 NC_009952.1 PFAM: Smr protein/MutS2 KEGG: rde:RD1_0446 Smr domain protein; Smr protein/MutS2 3627796 5712501 Dshi_3443 Dinoroseobacter shibae DFL 12 = DSM 16493 Smr protein/MutS2 YP_001534777.1 3627203 R 398580 CDS YP_001534778.1 159045984 5712502 complement(3627798..3628826) 1 NC_009952.1 PFAM: MltA domain protein; 3D domain protein KEGG: jan:Jann_0190 MltA; membrane-bound lytic murein transglycosylase A 3628826 mltA 5712502 mltA Dinoroseobacter shibae DFL 12 = DSM 16493 membrane-bound lytic murein transglycosylase A YP_001534778.1 3627798 R 398580 CDS YP_001534779.1 159045985 5712503 complement(3628823..3629488) 1 NC_009952.1 PFAM: import inner membrane translocase subunit Tim44 KEGG: jan:Jann_0191 import inner membrane translocase, subunit Tim44; subunit Tim44; import inner membrane translocase 3629488 5712503 Dshi_3445 Dinoroseobacter shibae DFL 12 = DSM 16493 import inner membrane translocase YP_001534779.1 3628823 R 398580 CDS YP_001534780.1 159045986 5712504 3629595..3630086 1 NC_009952.1 PFAM: FxsA cytoplasmic membrane protein KEGG: sil:SPO3887 FxsA; FxsA cytoplasmic membrane protein 3630086 fxsA 5712504 fxsA Dinoroseobacter shibae DFL 12 = DSM 16493 FxsA cytoplasmic membrane protein YP_001534780.1 3629595 D 398580 CDS YP_001534781.1 159045987 5712505 3630144..3630662 1 NC_009952.1 molecular chaperone that is required for the normal export of envelope proteins out of the cell cytoplasm; in Escherichia coli this proteins forms a homotetramer in the cytoplasm and delivers proteins to be exported to SecA; preprotein translocase subunit SecB 3630662 secB 5712505 secB Dinoroseobacter shibae DFL 12 = DSM 16493 preprotein translocase subunit SecB YP_001534781.1 3630144 D 398580 CDS YP_001534782.1 159045988 5712506 complement(3630667..3631359) 1 NC_009952.1 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 3631359 dnaQ1 5712506 dnaQ1 Dinoroseobacter shibae DFL 12 = DSM 16493 DNA polymerase III subunit epsilon YP_001534782.1 3630667 R 398580 CDS YP_001534783.1 159045989 5712507 complement(3631352..3631948) 1 NC_009952.1 KEGG: pde:Pden_2814 dephospho-CoA kinase TIGRFAM: dephospho-CoA kinase PFAM: Dephospho-CoA kinase; Dephosphocoenzyme A kinase; dephospho-CoA kinase 3631948 coaE 5712507 coaE Dinoroseobacter shibae DFL 12 = DSM 16493 dephospho-CoA kinase YP_001534783.1 3631352 R 398580 CDS YP_001534784.1 159045990 5712508 complement(3631945..3632781) 1 NC_009952.1 AroE; catalyzes the conversion of shikimate to 3-dehydroshikimate; shikimate 5-dehydrogenase 3632781 aroE 5712508 aroE Dinoroseobacter shibae DFL 12 = DSM 16493 shikimate 5-dehydrogenase YP_001534784.1 3631945 R 398580 CDS YP_001534785.1 159045991 5712509 complement(3632778..3633374) 1 NC_009952.1 TIGRFAM: maf protein PFAM: Maf family protein KEGG: sil:SPO3892 Maf; septum formation protein 3633374 maf 5712509 maf Dinoroseobacter shibae DFL 12 = DSM 16493 septum formation protein YP_001534785.1 3632778 R 398580 CDS YP_001534786.1 159045992 5712510 3633757..3634194 1 NC_009952.1 PFAM: Uncharacterized protein family (UPF0093) Swissprot: UPF0093 membrane protein; hypothetical protein 3634194 5712510 Dshi_3452 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534786.1 3633757 D 398580 CDS YP_001534787.1 159045993 5712511 3634311..3635582 1 NC_009952.1 An RNA-DNA helicase that actively releases nascent mRNAs from paused transcription complexes; transcription termination factor Rho 3635582 rho 5712511 rho Dinoroseobacter shibae DFL 12 = DSM 16493 transcription termination factor Rho YP_001534787.1 3634311 D 398580 CDS YP_001534788.1 159045994 5712512 3635603..3636892 1 NC_009952.1 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 3636892 trmE 5712512 trmE Dinoroseobacter shibae DFL 12 = DSM 16493 tRNA modification GTPase TrmE YP_001534788.1 3635603 D 398580 CDS YP_001534789.1 159045995 5712513 3636905..3638764 1 NC_009952.1 GidA; glucose-inhibited cell division protein A; involved in the 5-carboxymethylaminomethyl modification (mnm(5)s(2)U) of the wobble uridine base in some tRNAs; tRNA uridine 5-carboxymethylaminomethyl modification protein GidA 3638764 gidA 5712513 gidA Dinoroseobacter shibae DFL 12 = DSM 16493 tRNA uridine 5-carboxymethylaminomethyl modification protein GidA YP_001534789.1 3636905 D 398580 CDS YP_001534790.1 159045996 5712514 3638775..3639362 1 NC_009952.1 TIGRFAM: methyltransferase GidB PFAM: glucose inhibited division protein KEGG: acr:Acry_2405 methyltransferase GidB; Glucose-inhibited division protein B; methyltransferase GidB 3639362 gidB 5712514 gidB Dinoroseobacter shibae DFL 12 = DSM 16493 methyltransferase GidB YP_001534790.1 3638775 D 398580 CDS YP_001534791.1 159045997 5712515 3639355..3640161 1 NC_009952.1 PFAM: ParA family ATPase; chromosome partitioning protein ParA 3640161 parA1 5712515 parA1 Dinoroseobacter shibae DFL 12 = DSM 16493 chromosome partitioning protein ParA YP_001534791.1 3639355 D 398580 CDS YP_001534792.1 159045998 5712516 3640179..3641078 1 NC_009952.1 TIGRFAM: parB-like partition protein PFAM: ParB domain protein nuclease KEGG: rsp:RSP_1225 ParB-like partition protein; chromosome partitioning protein parB 3641078 parB 5712516 parB Dinoroseobacter shibae DFL 12 = DSM 16493 chromosome partitioning protein parB YP_001534792.1 3640179 D 398580 CDS YP_001534793.1 159045999 5712517 complement(3641075..3641428) 1 NC_009952.1 PFAM: protein of unknown function DUF454 KEGG: rsh:Rsph17029_2886 protein of unknown function DUF454; hypothetical protein 3641428 5712517 Dshi_3459 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534793.1 3641075 R 398580 CDS YP_001534794.1 159046000 5712518 complement(3641425..3642588) 1 NC_009952.1 catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III; coproporphyrinogen III oxidase 3642588 hemN3 5712518 hemN3 Dinoroseobacter shibae DFL 12 = DSM 16493 coproporphyrinogen III oxidase YP_001534794.1 3641425 R 398580 CDS YP_001534795.1 159046001 5712519 complement(3642591..3642968) 1 NC_009952.1 PFAM: Endoribonuclease L-PSP KEGG: rsp:RSP_1223 putative translation initiation inhibitor, YjgF family / putative endoribonuclease L-PSP; endoribonuclease L-PSP 3642968 5712519 Dshi_3461 Dinoroseobacter shibae DFL 12 = DSM 16493 endoribonuclease L-PSP YP_001534795.1 3642591 R 398580 CDS YP_001534796.1 159046002 5712520 complement(3642968..3643582) 1 NC_009952.1 HAM1-like protein; Rec-dependent growth; RgdB; yggV; it is suspected that this protein functions to remove misincorporated bases such as xanthine or hypoxanthine; putative deoxyribonucleotide triphosphate pyrophosphatase 3643582 ham1 5712520 ham1 Dinoroseobacter shibae DFL 12 = DSM 16493 putative deoxyribonucleotide triphosphate pyrophosphatase YP_001534796.1 3642968 R 398580 CDS YP_001534797.1 159046003 5712521 complement(3643582..3644295) 1 NC_009952.1 RNase PH; tRNA nucleotidyltransferase; forms hexamers in Bacillus subtilis; phosphoroltic 3'-5' exoribonuclease; involved in maturation of tRNA precursors and removes terminal nucleotides near CCA acceptor arms of mature tRNAs; ribonuclease PH 3644295 rph 5712521 rph Dinoroseobacter shibae DFL 12 = DSM 16493 ribonuclease PH YP_001534797.1 3643582 R 398580 CDS YP_001534798.1 159046004 5712522 3644431..3645495 1 NC_009952.1 Negative regulator of class I heat shock genes (grpE-dnaK-dnaJ and groELS operons). Prevents heat-shock induction of these operons; heat-inducible transcription repressor 3645495 hrcA 5712522 hrcA Dinoroseobacter shibae DFL 12 = DSM 16493 heat-inducible transcription repressor YP_001534798.1 3644431 D 398580 CDS YP_001534799.1 159046005 5712523 3645508..3646101 1 NC_009952.1 PFAM: GrpE protein KEGG: jan:Jann_0208 GrpE protein; HSP-70 cofactor; protein GrpE 3646101 grpE 5712523 grpE Dinoroseobacter shibae DFL 12 = DSM 16493 protein GrpE YP_001534799.1 3645508 D 398580 CDS YP_001534800.1 159046006 5712524 complement(3646135..3648768) 1 NC_009952.1 This protein performs the mismatch recognition step during the DNA repair process; DNA mismatch repair protein MutS 3648768 mutS 5712524 mutS Dinoroseobacter shibae DFL 12 = DSM 16493 DNA mismatch repair protein MutS YP_001534800.1 3646135 R 398580 CDS YP_001534801.1 159046007 5712525 3648901..3651159 1 NC_009952.1 NADP-dependent; catalyzes the oxidative decarboxylation of malate to form pyruvate; decarboxylates oxaloacetate; malic enzyme 3651159 maeB 5712525 maeB Dinoroseobacter shibae DFL 12 = DSM 16493 malic enzyme YP_001534801.1 3648901 D 398580 CDS YP_001534802.1 159046008 5712526 complement(3651291..3651971) 1 NC_009952.1 TIGRFAM: peptide methionine sulfoxide reductase PFAM: Methionine sulfoxide reductase A KEGG: rde:RD1_0419 methionine-S-sulfoxide reductase, putative; peptide methionine sulfoxide reductase 3651971 msrA1 5712526 msrA1 Dinoroseobacter shibae DFL 12 = DSM 16493 peptide methionine sulfoxide reductase YP_001534802.1 3651291 R 398580 CDS YP_001534803.1 159046009 5712527 3652180..3652893 1 NC_009952.1 REFSEQ: putative branched-chain amino acid aminotransferase; putative branched-chain amino acid aminotransferase 3652893 5712527 Dshi_3469 Dinoroseobacter shibae DFL 12 = DSM 16493 putative branched-chain amino acid aminotransferase YP_001534803.1 3652180 D 398580 CDS YP_001534804.1 159046010 5712528 complement(3652890..3653921) 1 NC_009952.1 PFAM: peptidase M48 Ste24p; peptidase M48 Ste24p 3653921 5712528 Dshi_3470 Dinoroseobacter shibae DFL 12 = DSM 16493 peptidase M48 Ste24p YP_001534804.1 3652890 R 398580 CDS YP_001534805.1 159046011 5712529 complement(3653928..3654965) 1 NC_009952.1 PFAM: protein of unknown function DUF898 transmembrane KEGG: sme:SMc00782 hypothetical protein; hypothetical protein 3654965 5712529 Dshi_3471 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534805.1 3653928 R 398580 CDS YP_001534806.1 159046012 5712530 complement(3655044..3656264) 1 NC_009952.1 catalyzes the formation of 2-N(omega)-(L-arginino)succinate from L-citrulline and L-aspartate in arginine biosynthesis, AMP-forming; argininosuccinate synthase 3656264 argG 5712530 argG Dinoroseobacter shibae DFL 12 = DSM 16493 argininosuccinate synthase YP_001534806.1 3655044 R 398580 CDS YP_001534807.1 159046013 5712531 3656372..3657613 1 NC_009952.1 catalyzes the formation of 2-oxobutanoate from L-threonine; biosynthetic; threonine dehydratase 3657613 ilvA 5712531 ilvA Dinoroseobacter shibae DFL 12 = DSM 16493 threonine dehydratase YP_001534807.1 3656372 D 398580 CDS YP_001534808.1 159046014 5712532 3657613..3658659 1 NC_009952.1 Catalyzes the cycloisomerization of cis,cis-muconate; 3-carboxy-cis,cis-muconate cycloisomerase 3658659 pcaB 5712532 pcaB Dinoroseobacter shibae DFL 12 = DSM 16493 3-carboxy-cis,cis-muconate cycloisomerase YP_001534808.1 3657613 D 398580 CDS YP_001534809.1 159046015 5712533 complement(3658656..3659495) 1 NC_009952.1 PFAM: protein of unknown function DUF849 KEGG: jan:Jann_4165 protein of unknown function DUF849; hypothetical protein 3659495 5712533 Dshi_3475 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534809.1 3658656 R 398580 CDS YP_001534810.1 159046016 5712534 complement(3659505..3660119) 1 NC_009952.1 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 3660119 pcaG 5712534 pcaG Dinoroseobacter shibae DFL 12 = DSM 16493 protocatechuate 3,4-dioxygenase subunit alpha YP_001534810.1 3659505 R 398580 CDS YP_001534811.1 159046017 5712535 complement(3660122..3660859) 1 NC_009952.1 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 3660859 pcaH 5712535 pcaH Dinoroseobacter shibae DFL 12 = DSM 16493 protocatechuate 3,4-dioxygenase subunit beta YP_001534811.1 3660122 R 398580 CDS YP_001534812.1 159046018 5713709 complement(3660856..3661242) 1 NC_009952.1 TIGRFAM: 4-carboxymuconolactone decarboxylase PFAM: Carboxymuconolactone decarboxylase KEGG: sit:TM1040_0559 4-carboxymuconolactone decarboxylase; CMD; 4-carboxymuconolactone decarboxylase 3661242 pcaC 5713709 pcaC Dinoroseobacter shibae DFL 12 = DSM 16493 4-carboxymuconolactone decarboxylase YP_001534812.1 3660856 R 398580 CDS YP_001534813.1 159046019 5713710 complement(3661252..3662421) 1 NC_009952.1 catalyzes the formation of protocatechuate from 4-hydroxybenzoate; 4-hydroxybenzoate 3-monooxygenase 3662421 pobA 5713710 pobA Dinoroseobacter shibae DFL 12 = DSM 16493 4-hydroxybenzoate 3-monooxygenase YP_001534813.1 3661252 R 398580 CDS YP_001534814.1 159046020 5713711 3662578..3662931 1 NC_009952.1 PFAM: regulatory protein LysR KEGG: pde:Pden_2664 putative transcriptional regulator, ModE family PMID 8550508; transcriptional regulator ModE 3662931 modE 5713711 modE Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator ModE YP_001534814.1 3662578 D 398580 CDS YP_001534815.1 159046021 5713712 3662924..3663676 1 NC_009952.1 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 3663676 modA 5713712 modA Dinoroseobacter shibae DFL 12 = DSM 16493 molybdate-binding periplasmic protein YP_001534815.1 3662924 D 398580 CDS YP_001534816.1 159046022 5713713 3663669..3664367 1 NC_009952.1 part of ModCBA molybdate transporter; member of ABC superfamily; inner membrane component; regulated by repressor protein ModE; molybdate ABC transporter permease 3664367 modB 5713713 modB Dinoroseobacter shibae DFL 12 = DSM 16493 molybdate ABC transporter permease YP_001534816.1 3663669 D 398580 CDS YP_001534817.1 159046023 5713714 3664364..3665446 1 NC_009952.1 KEGG: sil:SPO0697 molybdate ABC transporter, ATP-binding protein TIGRFAM: molybdate ABC transporter, ATPase subunit PFAM: ABC transporter related; TOBE domain protein SMART: AAA ATPase; molybdenum import ATP-binding protein modC 3665446 modC 5713714 modC Dinoroseobacter shibae DFL 12 = DSM 16493 molybdenum import ATP-binding protein modC YP_001534817.1 3664364 D 398580 CDS YP_001534818.1 159046024 5713715 complement(3665477..3665809) 1 NC_009952.1 PFAM: Hpt domain protein KEGG: sit:TM1040_2886 Hpt protein; Hpt domain-containing protein 3665809 5713715 Dshi_3484 Dinoroseobacter shibae DFL 12 = DSM 16493 Hpt domain-containing protein YP_001534818.1 3665477 R 398580 CDS YP_001534819.1 159046025 5713716 3665965..3667233 1 NC_009952.1 PFAM: response regulator receiver; Stage II sporulation E family protein SMART: protein phosphatase 2C domain protein KEGG: rde:RD1_0413 response regulator; response regulator 3667233 5713716 Dshi_3485 Dinoroseobacter shibae DFL 12 = DSM 16493 response regulator YP_001534819.1 3665965 D 398580 CDS YP_001534820.1 159046026 5713717 complement(3667262..3667714) 1 NC_009952.1 PFAM: NUDIX hydrolase KEGG: rsp:RSP_1208 NUDIX hydrolase; NUDIX hydrolase 3667714 5713717 Dshi_3486 Dinoroseobacter shibae DFL 12 = DSM 16493 NUDIX hydrolase YP_001534820.1 3667262 R 398580 CDS YP_001534821.1 159046027 5713718 3667814..3668812 1 NC_009952.1 PFAM: Hsp33 protein KEGG: jan:Jann_0079 HSP33 protein; HSP33; 33 kDa chaperonin 3668812 hslO 5713718 hslO Dinoroseobacter shibae DFL 12 = DSM 16493 33 kDa chaperonin YP_001534821.1 3667814 D 398580 CDS YP_001534822.1 159046028 5713719 3668799..3669398 1 NC_009952.1 PFAM: NUDIX hydrolase KEGG: sit:TM1040_2890 NUDIX hydrolase; NUDIX hydrolase 3669398 5713719 Dshi_3488 Dinoroseobacter shibae DFL 12 = DSM 16493 NUDIX hydrolase YP_001534822.1 3668799 D 398580 CDS YP_001534823.1 159046029 5713720 3669395..3670543 1 NC_009952.1 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 3670543 cca 5713720 cca Dinoroseobacter shibae DFL 12 = DSM 16493 CCA-adding enzyme YP_001534823.1 3669395 D 398580 CDS YP_001534824.1 159046030 5713721 3670604..3672448 1 NC_009952.1 PFAM: ABC transporter related SMART: AAA ATPase KEGG: sil:SPO0027 ABC transporter, transmembrane ATP-binding protein; ATPase 3672448 5713721 Dshi_3490 Dinoroseobacter shibae DFL 12 = DSM 16493 ATPase YP_001534824.1 3670604 D 398580 CDS YP_001534825.1 159046031 5713722 3672445..3674289 1 NC_009952.1 PFAM: ABC transporter transmembrane region; ABC transporter related SMART: AAA ATPase KEGG: rsq:Rsph17025_2641 ABC transporter related; ATPase 3674289 5713722 Dshi_3491 Dinoroseobacter shibae DFL 12 = DSM 16493 ATPase YP_001534825.1 3672445 D 398580 CDS YP_001534826.1 159046032 5713723 3674330..3675574 1 NC_009952.1 PFAM: (Uracil-5)-methyltransferase KEGG: sil:SPO0029 23S rRNA (uracil-5-)-methyltransferase RumA; 23S rRNA (uracil-5-)-methyltransferase RumA 3675574 rumA 5713723 rumA Dinoroseobacter shibae DFL 12 = DSM 16493 23S rRNA (uracil-5-)-methyltransferase RumA YP_001534826.1 3674330 D 398580 CDS YP_001534827.1 159046033 5713724 3675591..3676379 1 NC_009952.1 PFAM: Ion transport protein KEGG: rsq:Rsph17025_2848 ion transport protein REFSEQ: ref|ZP_01055369.1 voltage-gated sodium channel; voltage-gated sodium channel 3676379 5713724 Dshi_3493 Dinoroseobacter shibae DFL 12 = DSM 16493 voltage-gated sodium channel YP_001534827.1 3675591 D 398580 CDS YP_001534828.1 159046034 5713725 3676456..3676956 1 NC_009952.1 PFAM: ErfK/YbiS/YcfS/YnhG family protein KEGG: sil:SPO0031 ErfK/YbiS/YcfS/YnhG family protein PMID: 17098896; ErfK/YbiS/YcfS/YnhG family protein 3676956 5713725 Dshi_3494 Dinoroseobacter shibae DFL 12 = DSM 16493 ErfK/YbiS/YcfS/YnhG family protein YP_001534828.1 3676456 D 398580 CDS YP_001534829.1 159046035 5713726 complement(3676961..3677491) 1 NC_009952.1 PFAM: SCP-like extracellular KEGG: rsh:Rsph17029_2861 allergen V5/TPX-1 family protein; putative SCP-like extracellular protein 3677491 5713726 Dshi_3495 Dinoroseobacter shibae DFL 12 = DSM 16493 putative SCP-like extracellular protein YP_001534829.1 3676961 R 398580 CDS YP_001534830.1 159046036 5713727 3677660..3678262 1 NC_009952.1 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 3678262 5713727 Dshi_3496 Dinoroseobacter shibae DFL 12 = DSM 16493 ErfK/YbiS/YcfS/YnhG family protein YP_001534830.1 3677660 D 398580 CDS YP_001534832.1 159046038 5713729 complement(3678932..3680020) 1 NC_009952.1 protoheme ferro-lyase; catalyzes the insertion of a ferrous ion into protoporphyrin IX to form protoheme; involved in protoheme biosynthesis; in some organisms this protein is membrane-associated while in others it is cytosolic; ferrochelatase 3680020 hemH 5713729 hemH Dinoroseobacter shibae DFL 12 = DSM 16493 ferrochelatase YP_001534832.1 3678932 R 398580 CDS YP_001534833.1 159046039 5713730 complement(3680013..3680882) 1 NC_009952.1 KEGG: jan:Jann_0294 hypothetical protein PFAM Methyltransferase domain PMID: 17098896; SAM-dependent methyltransferase 3680882 5713730 Dshi_3499 Dinoroseobacter shibae DFL 12 = DSM 16493 SAM-dependent methyltransferase YP_001534833.1 3680013 R 398580 CDS YP_001534834.1 159046040 5713731 3680913..3681689 1 NC_009952.1 KEGG: sil:SPO0071 competence protein F, putative TIGR00201 comF family protein PMID 17098896; competence protein F 3681689 comF 5713731 comF Dinoroseobacter shibae DFL 12 = DSM 16493 competence protein F YP_001534834.1 3680913 D 398580 CDS YP_001534835.1 159046041 5713732 3681743..3682489 1 NC_009952.1 KEGG: rde:RD1_0121 spheroidene monooxygenase PMID: 17098896; spheroidene monooxygenase 3682489 crtA 5713732 crtA Dinoroseobacter shibae DFL 12 = DSM 16493 spheroidene monooxygenase YP_001534835.1 3681743 D 398580 CDS YP_001534836.1 159046042 5713733 3682486..3683490 1 NC_009952.1 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 3683490 bchI 5713733 bchI Dinoroseobacter shibae DFL 12 = DSM 16493 magnesium chelatase subunit I YP_001534836.1 3682486 D 398580 CDS YP_001534837.1 159046043 5713734 3683499..3685220 1 NC_009952.1 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 3685220 bchD 5713734 bchD Dinoroseobacter shibae DFL 12 = DSM 16493 magnesium chelatase subunit D YP_001534837.1 3683499 D 398580 CDS YP_001534838.1 159046044 5713735 3685217..3686125 1 NC_009952.1 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 3686125 bchO 5713735 bchO Dinoroseobacter shibae DFL 12 = DSM 16493 magnesium-chelatase 30 kDa subunit YP_001534838.1 3685217 D 398580 CDS YP_001534839.1 159046045 5713736 complement(3686122..3686574) 1 NC_009952.1 PFAM: regulatory protein MarR KEGG: rsh:Rsph17029_2853 transcriptional regulator, MarR family; MarR family; transcriptional regulator 3686574 5713736 Dshi_3505 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator YP_001534839.1 3686122 R 398580 CDS YP_001534840.1 159046046 5713737 complement(3686571..3687404) 1 NC_009952.1 PFAM: Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase KEGG: sil:SPO0069 hydrolase, carbon-nitrogen family; nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase 3687404 5713737 Dshi_3506 Dinoroseobacter shibae DFL 12 = DSM 16493 nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase YP_001534840.1 3686571 R 398580 CDS YP_001534841.1 159046047 5713738 complement(3687404..3687661) 1 NC_009952.1 TIGRFAM: glutaredoxin 3 PFAM: glutaredoxin KEGG: sil:SPO0070 glutaredoxin; Grx3; glutaredoxin-3 3687661 grxC 5713738 grxC Dinoroseobacter shibae DFL 12 = DSM 16493 glutaredoxin-3 YP_001534841.1 3687404 R 398580 CDS YP_001534842.1 159046048 5713739 3687777..3689351 1 NC_009952.1 TIGRFAM: Zeta-phytoene desaturase PFAM: amine oxidase; FAD dependent oxidoreductase KEGG: rde:RD1_0120 phytoene dehydrogenase PMID: 17098896; Phytoene desaturase; phytoene dehydrogenase 3689351 crtI 5713739 crtI Dinoroseobacter shibae DFL 12 = DSM 16493 phytoene dehydrogenase YP_001534842.1 3687777 D 398580 CDS YP_001534843.1 159046049 5713740 3689348..3690433 1 NC_009952.1 PFAM: Squalene/phytoene synthase KEGG: rde:RD1_0119 phytoene synthase PMID: 17098896; phytoene synthase 3690433 crtB 5713740 crtB Dinoroseobacter shibae DFL 12 = DSM 16493 phytoene synthase YP_001534843.1 3689348 D 398580 CDS YP_001534844.1 159046050 5713741 3690440..3690922 1 NC_009952.1 PFAM: TspO/MBR family protein KEGG: jan:Jann_0035 TspO and MBR like proteins PMID: 17098896; 10648776; tryptophan rich sensory protein 3690922 tspO 5713741 tspO Dinoroseobacter shibae DFL 12 = DSM 16493 tryptophan rich sensory protein YP_001534844.1 3690440 D 398580 CDS YP_001534845.1 159046051 5713742 complement(3690919..3691104) 1 NC_009952.1 KEGG: rsh:Rsph17029_2919 hypothetical protein; hypothetical protein 3691104 5713742 Dshi_3511 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534845.1 3690919 R 398580 CDS YP_001534846.1 159046052 5713743 complement(3691117..3691875) 1 NC_009952.1 PFAM: hydroxyneurosporene synthase KEGG: rde:RD1_0116 hydroxyneurosporene dehydrogenase PMID: 17098896; hydroxyneurosporene dehydrogenase 3691875 crtC 5713743 crtC Dinoroseobacter shibae DFL 12 = DSM 16493 hydroxyneurosporene dehydrogenase YP_001534846.1 3691117 R 398580 CDS YP_001534847.1 159046053 5713744 complement(3691944..3693542) 1 NC_009952.1 TIGRFAM: Zeta-phytoene desaturase PFAM: amine oxidase; FAD dependent oxidoreductase KEGG: jan:Jann_0183 amine oxidase Swissprot: P17059 PMID: 17098896; methoxyneurosporene dehydrogenase 3693542 crtD 5713744 crtD Dinoroseobacter shibae DFL 12 = DSM 16493 methoxyneurosporene dehydrogenase YP_001534847.1 3691944 R 398580 CDS YP_001534848.1 159046054 5713745 3693641..3694519 1 NC_009952.1 PFAM: Polyprenyl synthetase KEGG: jan:Jann_0182 polyprenyl synthetase COG0142 PMID: 17098896; Farnesyltranstransferase; GGPP synthetase; geranylgeranyl pyrophosphate synthetase 3694519 crtE 5713745 crtE Dinoroseobacter shibae DFL 12 = DSM 16493 geranylgeranyl pyrophosphate synthetase YP_001534848.1 3693641 D 398580 CDS YP_001534849.1 159046055 5713746 3694523..3695653 1 NC_009952.1 PFAM: O-methyltransferase family 2; Methyltransferase type 12 KEGG: jan:Jann_0181 O-methyltransferase, family 2 PMID: 17098896; O-methylase; hydroxyneurosporene methyltransferase 3695653 crtF 5713746 crtF Dinoroseobacter shibae DFL 12 = DSM 16493 hydroxyneurosporene methyltransferase YP_001534849.1 3694523 D 398580 CDS YP_001534850.1 159046056 5713747 3695777..3696715 1 NC_009952.1 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 3696715 bchC 5713747 bchC Dinoroseobacter shibae DFL 12 = DSM 16493 2-desacetyl-2-hydroxyethyl bacteriochlorophyllide A dehydrogenase YP_001534850.1 3695777 D 398580 CDS YP_001534851.1 159046057 5713748 3696712..3697719 1 NC_009952.1 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 3697719 bchX 5713748 bchX Dinoroseobacter shibae DFL 12 = DSM 16493 bacteriachlorophyllide reductase iron protein subunit X YP_001534851.1 3696712 D 398580 CDS YP_001534852.1 159046058 5713749 3697755..3699359 1 NC_009952.1 TIGRFAM: chlorophyllide reductase subunit Y KEGG: jan:Jann_0178 chlorophyllide reductase subunit Y PMID: 17098896; 10648776; 8468299; bacteriachlorophyllide reductase iron protein subunit Y 3699359 bchY 5713749 bchY Dinoroseobacter shibae DFL 12 = DSM 16493 bacteriachlorophyllide reductase iron protein subunit Y YP_001534852.1 3697755 D 398580 CDS YP_001534853.1 159046059 5713750 3699577..3701043 1 NC_009952.1 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 3701043 bchZ 5713750 bchZ Dinoroseobacter shibae DFL 12 = DSM 16493 bacteriachlorophyllide reductase iron protein subunit Z YP_001534853.1 3699577 D 398580 CDS YP_001534854.1 159046060 5713751 3701062..3701286 1 NC_009952.1 PFAM: PufQ cytochrome subunit KEGG: rde:RD1_0108 protein PufQ PMID: 17098896; protein pufQ 3701286 pufQ 5713751 pufQ Dinoroseobacter shibae DFL 12 = DSM 16493 protein pufQ YP_001534854.1 3701062 D 398580 CDS YP_001534855.1 159046061 5713752 3701410..3701559 1 NC_009952.1 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 3701559 pufB 5713752 pufB Dinoroseobacter shibae DFL 12 = DSM 16493 light-harvesting protein B-870 subunit beta YP_001534855.1 3701410 D 398580 CDS YP_001534856.1 159046062 5713753 3701573..3701734 1 NC_009952.1 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 3701734 pufA 5713753 pufA Dinoroseobacter shibae DFL 12 = DSM 16493 light-harvesting protein B-870 subunit alpha YP_001534856.1 3701573 D 398580 CDS YP_001534857.1 159046063 5713754 3701883..3702722 1 NC_009952.1 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 3702722 pufL 5713754 pufL Dinoroseobacter shibae DFL 12 = DSM 16493 photosynthetic reaction center subunit L YP_001534857.1 3701883 D 398580 CDS YP_001534858.1 159046064 5713755 3702726..3703718 1 NC_009952.1 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 3703718 pufM 5713755 pufM Dinoroseobacter shibae DFL 12 = DSM 16493 photosynthetic reaction center subunit M YP_001534858.1 3702726 D 398580 CDS YP_001534859.1 159046065 5713756 3703718..3704800 1 NC_009952.1 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 3704800 pufC 5713756 pufC Dinoroseobacter shibae DFL 12 = DSM 16493 photosynthetic reaction center cytochrome subunit C YP_001534859.1 3703718 D 398580 CDS YP_001534860.1 159046066 5713757 3704933..3706909 1 NC_009952.1 catalyzes the formation of 1-deoxy-D-xylulose 5-phosphate from pyruvate and D-glyceraldehyde 3-phosphate; 1-deoxy-D-xylulose-5-phosphate synthase 3706909 dxs2 5713757 dxs2 Dinoroseobacter shibae DFL 12 = DSM 16493 1-deoxy-D-xylulose-5-phosphate synthase YP_001534860.1 3704933 D 398580 CDS YP_001534861.1 159046067 5713758 complement(3707023..3707553) 1 NC_009952.1 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 3707553 idi 5713758 idi Dinoroseobacter shibae DFL 12 = DSM 16493 isopentenyl-diphosphate Delta-isomerase YP_001534861.1 3707023 R 398580 CDS YP_001534862.1 159046068 5713759 complement(3707550..3708734) 1 NC_009952.1 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 3708734 bchP 5713759 bchP Dinoroseobacter shibae DFL 12 = DSM 16493 geranylgeranyl reductase YP_001534862.1 3707550 R 398580 CDS YP_001534863.1 159046069 5713760 complement(3708748..3710049) 1 NC_009952.1 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 3710049 pucC2 5713760 pucC2 Dinoroseobacter shibae DFL 12 = DSM 16493 PucC protein YP_001534863.1 3708748 R 398580 CDS YP_001534864.1 159046070 5713761 complement(3710051..3710956) 1 NC_009952.1 TIGRFAM: bacteriochlorophyll/chlorophyll synthetase PFAM: UbiA prenyltransferase KEGG: jan:Jann_0165 bacteriochlorophyll/chlorophyll synthetase PMID: 17098896; bacteriochlorophyll/chlorophyll a synthase 3710956 bchG 5713761 bchG Dinoroseobacter shibae DFL 12 = DSM 16493 bacteriochlorophyll/chlorophyll a synthase YP_001534864.1 3710051 R 398580 CDS YP_001534865.1 159046071 5713762 complement(3711054..3712484) 1 NC_009952.1 TIGRFAM: PAS sensor protein; transcriptional regulator PpsR PMID: 10735869; 17098896; transcriptional regulator PpsR 3712484 ppsR 5713762 ppsR Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator PpsR YP_001534865.1 3711054 R 398580 CDS YP_001534866.1 159046072 5713763 complement(3712527..3713387) 1 NC_009952.1 REFSEQ: ref|ZP_01034604.1 regulatory protein PpaA PMID: 17098896; regulatory protein PpaA 3713387 ppaA 5713763 ppaA Dinoroseobacter shibae DFL 12 = DSM 16493 regulatory protein PpaA YP_001534866.1 3712527 R 398580 CDS YP_001534867.1 159046073 5713764 3713645..3714133 1 NC_009952.1 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 3714133 bchF 5713764 bchF Dinoroseobacter shibae DFL 12 = DSM 16493 2-oxoglutarate synthase subunit, 2-oxoacid-ferredoxin oxidoreductase subunit CD YP_001534867.1 3713645 D 398580 CDS YP_001534868.1 159046074 5713765 3714130..3715413 1 NC_009952.1 light-independent reduction of protochlorophyllide to form chlorophyllide a; light-independent protochlorophyllide reductase subunit N 3715413 bchN 5713765 bchN Dinoroseobacter shibae DFL 12 = DSM 16493 light-independent protochlorophyllide reductase subunit N YP_001534868.1 3714130 D 398580 CDS YP_001534869.1 159046075 5713766 3715410..3716996 1 NC_009952.1 light-independent reduction of protochlorophyllide to form chlorophyllide a; light-independent protochlorophyllide reductase subunit B 3716996 bchB 5713766 bchB Dinoroseobacter shibae DFL 12 = DSM 16493 light-independent protochlorophyllide reductase subunit B YP_001534869.1 3715410 D 398580 CDS YP_001534870.1 159046076 5713767 3716986..3720570 1 NC_009952.1 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 3720570 bchH 5713767 bchH Dinoroseobacter shibae DFL 12 = DSM 16493 magnesium chelatase subunit H YP_001534870.1 3716986 D 398580 CDS YP_001534871.1 159046077 5713768 3720602..3721501 1 NC_009952.1 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 3721501 chlL 5713768 chlL Dinoroseobacter shibae DFL 12 = DSM 16493 protochlorophyllide reductase iron-sulfur ATP-binding protein YP_001534871.1 3720602 D 398580 CDS YP_001534872.1 159046078 5713769 3721548..3722231 1 NC_009952.1 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 3722231 bchM 5713769 bchM Dinoroseobacter shibae DFL 12 = DSM 16493 Mg-protoporphyrin IX methyl transferase YP_001534872.1 3721548 D 398580 CDS YP_001534873.1 159046079 5713770 3722228..3723673 1 NC_009952.1 PFAM: PUCC protein; major facilitator superfamily MFS_1 KEGG: rde:RD1_0134 LhaA protein PMID: 17098896; PucC protein 3723673 lhaA 5713770 lhaA Dinoroseobacter shibae DFL 12 = DSM 16493 PucC protein YP_001534873.1 3722228 D 398580 CDS YP_001534874.1 159046080 5713771 3723698..3724468 1 NC_009952.1 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 3724468 puhA 5713771 puhA Dinoroseobacter shibae DFL 12 = DSM 16493 reaction center protein H chain YP_001534874.1 3723698 D 398580 CDS YP_001534875.1 159046081 5713772 3724493..3725170 1 NC_009952.1 KEGG: rde:RD1_0132 possible photosynthetic co REFSEQ: ref|ZP_01879036.1 putative photosynthetic complex assembly protein PMID: 17098896; putative photosynthetic complex assembly protein 3725170 puhB 5713772 puhB Dinoroseobacter shibae DFL 12 = DSM 16493 putative photosynthetic complex assembly protein YP_001534875.1 3724493 D 398580 CDS YP_001534876.1 159046082 5713773 3725184..3725663 1 NC_009952.1 KEGG: rde:RD1_0131 REFSEQ: ref|YP_680552.1 PuhC Protein PMID: 17098896; 17098896; PuhC protein 3725663 puhC 5713773 puhC Dinoroseobacter shibae DFL 12 = DSM 16493 PuhC protein YP_001534876.1 3725184 D 398580 CDS YP_001534877.1 159046083 5713774 3725667..3725963 1 NC_009952.1 KEGG: rde:RD1_0130 hypothetical protein; hypothetical protein 3725963 5713774 Dshi_3543 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534877.1 3725667 D 398580 CDS YP_001534878.1 159046084 5713775 3725960..3727081 1 NC_009952.1 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 3727081 acsF 5713775 acsF Dinoroseobacter shibae DFL 12 = DSM 16493 magnesium-protoporphyrin IX monomethyl ester cyclase YP_001534878.1 3725960 D 398580 CDS YP_001534879.1 159046085 5713776 3727081..3727878 1 NC_009952.1 KEGG: rde:RD1_0128 REFSEQ: ref|YP_680549.1 PuhE Protein PMID: 17098896; PuhE protein 3727878 puhE 5713776 puhE Dinoroseobacter shibae DFL 12 = DSM 16493 PuhE protein YP_001534879.1 3727081 D 398580 CDS YP_001534880.1 159046086 5713777 3728081..3729295 1 NC_009952.1 catalyzes the formation of 5-aminolevulinate from succinyl-CoA and glycine; 5-aminolevulinate synthase 3729295 hemA1 5713777 hemA1 Dinoroseobacter shibae DFL 12 = DSM 16493 5-aminolevulinate synthase YP_001534880.1 3728081 D 398580 CDS YP_001534881.1 159046087 5713778 3729391..3729831 1 NC_009952.1 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 3729831 cycA2 5713778 cycA2 Dinoroseobacter shibae DFL 12 = DSM 16493 cytochrome c2 YP_001534881.1 3729391 D 398580 CDS YP_001534882.1 159046088 5713779 3729973..3731778 1 NC_009952.1 PFAM: ABC transporter transmembrane region; ABC transporter related SMART: AAA ATPase KEGG: jan:Jann_4278 ABC transporter related; ATPase 3731778 5713779 Dshi_3548 Dinoroseobacter shibae DFL 12 = DSM 16493 ATPase YP_001534882.1 3729973 D 398580 CDS YP_001534883.1 159046089 5713780 3731871..3733085 1 NC_009952.1 PFAM: glycerophosphoryl diester phosphodiesterase KEGG: rde:RD1_1698 glycerophosphoryl diester phosphodiesterase family protein, putative PRK: glpQ; periplasmic; glycerophosphoryl diester phosphodiesterase 3733085 glpQ 5713780 glpQ Dinoroseobacter shibae DFL 12 = DSM 16493 glycerophosphoryl diester phosphodiesterase YP_001534883.1 3731871 D 398580 CDS YP_001534884.1 159046090 5713781 complement(3733252..3733998) 1 NC_009952.1 Involved in ubiquinone biosynthesis; 3-demethylubiquinone-9 3-methyltransferase 3733998 ubiG1 5713781 ubiG1 Dinoroseobacter shibae DFL 12 = DSM 16493 3-demethylubiquinone-9 3-methyltransferase YP_001534884.1 3733252 R 398580 CDS YP_001534885.1 159046091 5713782 3734063..3735049 1 NC_009952.1 KEGG: sil:SPO0066 proline iminopeptidase TIGRFAM: proline iminopeptidase PFAM: alpha/beta hydrolase fold; PAP; Prolyl aminopeptidase; PIP; proline iminopeptidase 3735049 pip 5713782 pip Dinoroseobacter shibae DFL 12 = DSM 16493 proline iminopeptidase YP_001534885.1 3734063 D 398580 CDS YP_001534886.1 159046092 5713783 3735027..3736508 1 NC_009952.1 PFAM: extracellular solute-binding protein family 5; family 5 extracellular solute-binding protein 3736508 5713783 Dshi_3552 Dinoroseobacter shibae DFL 12 = DSM 16493 family 5 extracellular solute-binding protein YP_001534886.1 3735027 D 398580 CDS YP_001534887.1 159046093 5713784 3736896..3738872 1 NC_009952.1 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 3738872 acs 5713784 acs Dinoroseobacter shibae DFL 12 = DSM 16493 acetyl-coenzyme A synthetase YP_001534887.1 3736896 D 398580 CDS YP_001534888.1 159046094 5713785 3738878..3739567 1 NC_009952.1 PFAM: adenylate kinase; adenylate kinase lid domain protein KEGG: sil:SPO1812 adenylate kinase; ATP-AMP transphosphorylase; adenylate kinase 3739567 adk1 5713785 adk1 Dinoroseobacter shibae DFL 12 = DSM 16493 adenylate kinase YP_001534888.1 3738878 D 398580 CDS YP_001534889.1 159046095 5713786 3739687..3739944 1 NC_009952.1 KEGG: psa:PST_3903 hypothetical protein; hypothetical protein 3739944 5713786 Dshi_3555 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534889.1 3739687 D 398580 CDS YP_001534890.1 159046096 5713787 3739962..3741758 1 NC_009952.1 PFAM: Na+/solute symporter KEGG: sil:SPO1810 sodium/solute symporter family protein; sodium/solute symporter family protein 3741758 5713787 Dshi_3556 Dinoroseobacter shibae DFL 12 = DSM 16493 sodium/solute symporter family protein YP_001534890.1 3739962 D 398580 CDS YP_001534891.1 159046097 5713788 3741883..3743700 1 NC_009952.1 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 3743700 5713788 Dshi_3557 Dinoroseobacter shibae DFL 12 = DSM 16493 putative CBS domain and cyclic nucleotide-regulated nucleotidyltransferase YP_001534891.1 3741883 D 398580 CDS YP_001534892.1 159046098 5713789 3743713..3744228 1 NC_009952.1 KEGG: sil:SPO1808 hypothetical protein; hypothetical protein 3744228 5713789 Dshi_3558 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534892.1 3743713 D 398580 CDS YP_001534893.1 159046099 5713790 3744249..3745706 1 NC_009952.1 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 3745706 dnaQ2 5713790 dnaQ2 Dinoroseobacter shibae DFL 12 = DSM 16493 DNA polymerase III subunit epsilon YP_001534893.1 3744249 D 398580 CDS YP_001534894.1 159046100 5713791 3745860..3746450 1 NC_009952.1 in Streptococcus pneumoniae this gene was found to be essential; structure determination of the Streptococcus protein shows that it is similar to a number of other proteins; hypothetical protein 3746450 5713791 Dshi_3560 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534894.1 3745860 D 398580 CDS YP_001534895.1 159046101 5713792 3746464..3748098 1 NC_009952.1 modifies transcription through interactions with RNA polymerase affecting elongation, readthrough, termination, and antitermination; transcription elongation factor NusA 3748098 nusA 5713792 nusA Dinoroseobacter shibae DFL 12 = DSM 16493 transcription elongation factor NusA YP_001534895.1 3746464 D 398580 CDS YP_001534896.1 159046102 5713793 3748122..3748760 1 NC_009952.1 PFAM: protein of unknown function DUF448; hypothetical protein 3748760 5713793 Dshi_3562 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534896.1 3748122 D 398580 CDS YP_001534897.1 159046103 5713794 3748757..3751255 1 NC_009952.1 Protects formylmethionyl-tRNA from spontaneous hydrolysis and promotes its binding to the 30S ribosomal subunits during initiation of protein synthesis. Also involved in the hydrolysis of GTP during the formation of the 70S ribosomal complex; translation initiation factor IF-2 3751255 infB 5713794 infB Dinoroseobacter shibae DFL 12 = DSM 16493 translation initiation factor IF-2 YP_001534897.1 3748757 D 398580 CDS YP_001534898.1 159046104 5713795 complement(3751598..3751996) 1 NC_009952.1 TIGRFAM: mutator MutT protein PFAM: NUDIX hydrolase KEGG: sil:SPO0060 mutator MutT protein; mutator MutT protein 3751996 mutT 5713795 mutT Dinoroseobacter shibae DFL 12 = DSM 16493 mutator MutT protein YP_001534898.1 3751598 R 398580 CDS YP_001534899.1 159046105 5713796 complement(3751993..3753216) 1 NC_009952.1 bifunctional arginine biosynthesis protein ArgJ; functions at the 1st and 5th steps in arginine biosynthesis; involved in synthesis of acetylglutamate from glutamate and acetyl-CoA and ornithine by transacetylation between acetylornithine and glutmate; bifunctional ornithine acetyltransferase/N-acetylglutamate synthase 3753216 argJ 5713796 argJ Dinoroseobacter shibae DFL 12 = DSM 16493 bifunctional ornithine acetyltransferase/N-acetylglutamate synthase YP_001534899.1 3751993 R 398580 CDS YP_001534900.1 159046106 5713797 complement(3753294..3754136) 1 NC_009952.1 PFAM: PpiC-type peptidyl-prolyl cis-trans isomerase KEGG: jan:Jann_0290 PpiC-type peptidyl-prolyl cis-trans isomerase; PpiC-type peptidyl-prolyl cis-trans isomerase 3754136 ppiC 5713797 ppiC Dinoroseobacter shibae DFL 12 = DSM 16493 PpiC-type peptidyl-prolyl cis-trans isomerase YP_001534900.1 3753294 R 398580 CDS YP_001534901.1 159046107 5713798 3754364..3757090 1 NC_009952.1 functions in protein export; can interact with acidic membrane phospholipids and the SecYEG protein complex; binds to preproteins; binds to ATP and undergoes a conformational change to promote membrane insertion of SecA/bound preprotein; ATP hydrolysis appears to drive release of the preprotein from SecA and deinsertion of SecA from the membrane; additional proteins SecD/F/YajC aid SecA recycling; exists in an equilibrium between monomers and dimers; may possibly form higher order oligomers; proteins in this cluster correspond SecA1; SecA2 is not essential and seems to play a role in secretion of a subset of proteins; preprotein translocase subunit SecA 3757090 secA 5713798 secA Dinoroseobacter shibae DFL 12 = DSM 16493 preprotein translocase subunit SecA YP_001534901.1 3754364 D 398580 CDS YP_001534902.1 159046108 5713799 3757069..3758595 1 NC_009952.1 no domains found, significant blast hits only to JGI projects, good GC frame plot; hypothetical protein 3758595 5713799 Dshi_3568 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534902.1 3757069 D 398580 CDS YP_001534903.1 159046109 5713800 complement(3758567..3759331) 1 NC_009952.1 TIGRFAM: DNA repair protein radc PFAM: DNA repair protein RadC KEGG: pde:Pden_2304 DNA repair protein RadC; DNA repair protein RadC 3759331 radC 5713800 radC Dinoroseobacter shibae DFL 12 = DSM 16493 DNA repair protein RadC YP_001534903.1 3758567 R 398580 CDS YP_001534904.1 159046110 5713801 complement(3759367..3760518) 1 NC_009952.1 chaperone Hsp40; co-chaperone with DnaK; Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins and by disaggregating proteins, also in an autonomous, dnaK-independent fashion; chaperone protein DnaJ 3760518 dnaJ 5713801 dnaJ Dinoroseobacter shibae DFL 12 = DSM 16493 chaperone protein DnaJ YP_001534904.1 3759367 R 398580 CDS YP_001534905.1 159046111 5713802 complement(3760594..3762513) 1 NC_009952.1 heat shock protein 70; assists in folding of nascent polypeptide chains; refolding of misfolded proteins; utilizes ATPase activity to help fold; co-chaperones are DnaJ and GrpE; multiple copies in some bacteria; molecular chaperone DnaK 3762513 dnaK 5713802 dnaK Dinoroseobacter shibae DFL 12 = DSM 16493 molecular chaperone DnaK YP_001534905.1 3760594 R 398580 CDS YP_001534906.1 159046112 5713803 3762679..3763314 1 NC_009952.1 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 3763314 alkB2 5713803 alkB2 Dinoroseobacter shibae DFL 12 = DSM 16493 alpha-ketoglutarate-dependent dioxygenase alkB YP_001534906.1 3762679 D 398580 CDS YP_001534907.1 159046113 5713804 complement(3763345..3764166) 1 NC_009952.1 PFAM: ABC-2 type transporter KEGG: sil:SPO0040 ABC transporter, permease protein; putative ABC-2 type transporter 3764166 5713804 Dshi_3573 Dinoroseobacter shibae DFL 12 = DSM 16493 putative ABC-2 type transporter YP_001534907.1 3763345 R 398580 CDS YP_001534908.1 159046114 5713805 3764320..3765117 1 NC_009952.1 TIGRFAM: 3(2),5-bisphosphate nucleotidase PFAM: inositol monophosphatase KEGG: sil:SPO0039 3(2),5-bisphosphate nucleotidase; 3'(2'),5'-bisphosphate nucleotidase 3765117 cysQ 5713805 cysQ Dinoroseobacter shibae DFL 12 = DSM 16493 3'(2'),5'-bisphosphate nucleotidase YP_001534908.1 3764320 D 398580 CDS YP_001534909.1 159046115 5713806 3765117..3765917 1 NC_009952.1 CMP-2-keto-3-deoxyoctulosonic acid synthetase; catalyzes the formation of CMP-3-deoxy-D-manno-octulosonate from CTP and 3-deoxy-D-manno-octulosonate which is incorporated into LPS; 3-deoxy-manno-octulosonate cytidylyltransferase 3765917 kdsB 5713806 kdsB Dinoroseobacter shibae DFL 12 = DSM 16493 3-deoxy-manno-octulosonate cytidylyltransferase YP_001534909.1 3765117 D 398580 CDS YP_001534910.1 159046116 5713807 3765914..3767146 1 NC_009952.1 PFAM: glycosyl transferase family 2 KEGG: pde:Pden_2298 glycosyl transferase, family 2; family 2; glycosyl transferase family protein 3767146 5713807 Dshi_3576 Dinoroseobacter shibae DFL 12 = DSM 16493 glycosyl transferase family protein YP_001534910.1 3765914 D 398580 CDS YP_001534911.1 159046117 5713808 3767288..3768184 1 NC_009952.1 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 3768184 galU 5713808 galU Dinoroseobacter shibae DFL 12 = DSM 16493 UTP-glucose-1-phosphate uridylyltransferase YP_001534911.1 3767288 D 398580 CDS YP_001534912.1 159046118 5713809 3768197..3769435 1 NC_009952.1 PFAM: glycosyl transferase group 1 KEGG: pde:Pden_2295 glycosyl transferase, group 1, COG0438 - Glycosyltransferase; group 1; glycosyl transferase family protein 3769435 5713809 Dshi_3578 Dinoroseobacter shibae DFL 12 = DSM 16493 glycosyl transferase family protein YP_001534912.1 3768197 D 398580 CDS YP_001534913.1 159046119 5713810 3769483..3770499 1 NC_009952.1 KEGG: sil:SPO0036 hypothetical protein; hypothetical protein 3770499 5713810 Dshi_3579 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534913.1 3769483 D 398580 CDS YP_001534914.1 159046120 5713811 3770718..3772205 1 NC_009952.1 KEGG: sil:SPO0035 core-2/I-branching enzyme family protein; core-2/I-branching enzyme family protein 3772205 5713811 Dshi_3580 Dinoroseobacter shibae DFL 12 = DSM 16493 core-2/I-branching enzyme family protein YP_001534914.1 3770718 D 398580 CDS YP_001534915.1 159046121 5713812 3772212..3773648 1 NC_009952.1 KEGG: jan:Jann_0222 hypothetical protein; hypothetical protein 3773648 5713812 Dshi_3581 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534915.1 3772212 D 398580 CDS YP_001534916.1 159046122 5713813 complement(3773660..3774124) 1 NC_009952.1 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 3774124 ptsN 5713813 ptsN Dinoroseobacter shibae DFL 12 = DSM 16493 PTS transporter subunit IIA-like nitrogen-regulatory protein PtsN YP_001534916.1 3773660 R 398580 CDS YP_001534917.1 159046123 5713814 complement(3774163..3774738) 1 NC_009952.1 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 3774738 5713814 Dshi_3583 Dinoroseobacter shibae DFL 12 = DSM 16493 30S ribosomal protein S30 YP_001534917.1 3774163 R 398580 CDS YP_001534918.1 159046124 5713815 complement(3774813..3776129) 1 NC_009952.1 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 3776129 rpoN 5713815 rpoN Dinoroseobacter shibae DFL 12 = DSM 16493 RNA polymerase sigma-54 factor YP_001534918.1 3774813 R 398580 CDS YP_001534919.1 159046125 5713816 complement(3776138..3776902) 1 NC_009952.1 pfam00005: ABC_tran, COG1137 - ABC-type (unclassified) transport system, ATPase component, BLAST hits to several ABC transporter, ATP-binding protein; ATPase 3776902 5713816 Dshi_3585 Dinoroseobacter shibae DFL 12 = DSM 16493 ATPase YP_001534919.1 3776138 R 398580 CDS YP_001534920.1 159046126 5713817 complement(3776899..3777411) 1 NC_009952.1 PFAM: OstA family protein KEGG: rsh:Rsph17029_2816 OstA family protein, COG1934 - Uncharacterized protein conserved in bacteria; OstA family protein 3777411 5713817 Dshi_3586 Dinoroseobacter shibae DFL 12 = DSM 16493 OstA family protein YP_001534920.1 3776899 R 398580 CDS YP_001534921.1 159046127 5713818 complement(3777425..3778027) 1 NC_009952.1 similar hit in Roseovarius, not conserved throughout many species; hypothetical protein 3778027 5713818 Dshi_3587 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534921.1 3777425 R 398580 CDS YP_001534922.1 159046128 5713819 complement(3778031..3778993) 1 NC_009952.1 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 3778993 yrbH 5713819 yrbH Dinoroseobacter shibae DFL 12 = DSM 16493 arabinose-5-phosphate isomerase YP_001534922.1 3778031 R 398580 CDS YP_001534923.1 159046129 5713820 complement(3779003..3779614) 1 NC_009952.1 PFAM: 3-5 exonuclease; 3'-5' exonuclease 3779614 5713820 Dshi_3589 Dinoroseobacter shibae DFL 12 = DSM 16493 3'-5' exonuclease YP_001534923.1 3779003 R 398580 CDS YP_001534924.1 159046130 5713822 3780019..3781002 1 NC_009952.1 pfam07993: NAD_binding_4 domain, COG0702 - Predicted nucleoside-diphosphate-sugar epimerases; ubiquinone dependent NADH dehydrogenase 3781002 5713822 Dshi_3590 Dinoroseobacter shibae DFL 12 = DSM 16493 ubiquinone dependent NADH dehydrogenase YP_001534924.1 3780019 D 398580 CDS YP_001534925.1 159046131 5713823 complement(3781025..3782716) 1 NC_009952.1 domain hit: Abi, transmembrane helices predicted, weak BLAST hits; CAAX amino terminal protease family protein 3782716 5713823 Dshi_3591 Dinoroseobacter shibae DFL 12 = DSM 16493 CAAX amino terminal protease family protein YP_001534925.1 3781025 R 398580 CDS YP_001534926.1 159046132 5713824 complement(3783102..3788285) 1 NC_009952.1 no domain hits, no BLAST hit, good GC frame plot over whole length; hypothetical protein 3788285 5713824 Dshi_3592 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001534926.1 3783102 R 398580 CDS YP_001534927.1 159046133 5713825 complement(3788688..3789491) 1 NC_009952.1 BacA; phosphatase activity in Escherichia coli not kinase; involved in bacitracin resistance as bacitracin supposedly sequesters undecaprenyl disphosphate which reduces the pool of lipid carrier available to the cell; undecaprenyl pyrophosphate phosphatase 3789491 uppP 5713825 uppP Dinoroseobacter shibae DFL 12 = DSM 16493 undecaprenyl pyrophosphate phosphatase YP_001534927.1 3788688 R 398580 CDS YP_001541808.1 159046136 5714321 complement(8..844) 1 NC_009955.1 PFAM: protein of unknown function DUF305; KEGG: rsh:Rsph17029_3677 protein of unknown function DUF305; hypothetical protein 844 5714321 Dshi_3594 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541808.1 8 R 398580 CDS YP_001541809.1 159046137 5714125 1024..1605 1 NC_009955.1 PFAM: ErfK/YbiS/YcfS/YnhG family protein; KEGG: mes:Meso_4112 ErfK/YbiS/YcfS/YnhG; ErfK/YbiS/YcfS/YnhG family protein 1605 5714125 Dshi_3595 Dinoroseobacter shibae DFL 12 = DSM 16493 ErfK/YbiS/YcfS/YnhG family protein YP_001541809.1 1024 D 398580 CDS YP_001541810.1 159046138 5714126 1689..2993 1 NC_009955.1 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 2993 5714126 Dshi_3596 Dinoroseobacter shibae DFL 12 = DSM 16493 multicopper oxidase type 3 YP_001541810.1 1689 D 398580 CDS YP_001541811.1 159046139 5714127 3107..3619 1 NC_009955.1 KEGG: sit:TM1040_1167 disulphide bond formation protein DsbB; disulfide bond formation protein DsbB 3619 5714127 Dshi_3597 Dinoroseobacter shibae DFL 12 = DSM 16493 disulfide bond formation protein DsbB YP_001541811.1 3107 D 398580 CDS YP_001541812.1 159046140 5714128 3662..4327 1 NC_009955.1 PFAM: ErfK/YbiS/YcfS/YnhG family protein; KEGG: rde:RD1_0492 ErfK/YbiS/YcfS/YnhG family protein; ErfK/YbiS/YcfS/YnhG family protein 4327 5714128 Dshi_3598 Dinoroseobacter shibae DFL 12 = DSM 16493 ErfK/YbiS/YcfS/YnhG family protein YP_001541812.1 3662 D 398580 CDS YP_001541813.1 159046141 5714129 complement(4404..4961) 1 NC_009955.1 KEGG: sil:SPO0304 lipoprotein, putative; putative lipoprotein 4961 5714129 Dshi_3599 Dinoroseobacter shibae DFL 12 = DSM 16493 putative lipoprotein YP_001541813.1 4404 R 398580 CDS YP_001541814.1 159046142 5714130 5359..5967 1 NC_009955.1 SMART: Calcium-binding EF-hand-containing protein; KEGG: rpb:RPB_2375 calcium-binding EF-hand protein; calcium-binding EF-hand-containing protein 5967 5714130 Dshi_3600 Dinoroseobacter shibae DFL 12 = DSM 16493 calcium-binding EF-hand-containing protein YP_001541814.1 5359 D 398580 CDS YP_001541815.1 159046143 5714131 6108..6494 1 NC_009955.1 PFAM: protein of unknown function DUF302; KEGG: mmr:Mmar10_2335 protein of unknown function DUF302; hypothetical protein 6494 5714131 Dshi_3601 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541815.1 6108 D 398580 CDS YP_001541816.1 159046144 5714132 6600..7520 1 NC_009955.1 transfers the N-acyl diglyceride moiety to the prospective N-terminal cysteine in prolipoprotein; prolipoprotein diacylglyceryl transferase 7520 5714132 Dshi_3602 Dinoroseobacter shibae DFL 12 = DSM 16493 prolipoprotein diacylglyceryl transferase YP_001541816.1 6600 D 398580 CDS YP_001541817.1 159046145 5714133 7599..9944 1 NC_009955.1 TIGRFAM: ATPase, P-type (transporting), HAD superfamily, subfamily IC; copper-translocating P-type ATPase; heavy metal translocating P-type ATPase; PFAM: Haloacid dehalogenase domain protein hydrolase; E1-E2 ATPase-associated domain protein; KEGG: sil:SPOA0365 copper-translocating P-type ATPase; heavy metal translocating P-type ATPase 9944 5714133 Dshi_3603 Dinoroseobacter shibae DFL 12 = DSM 16493 heavy metal translocating P-type ATPase YP_001541817.1 7599 D 398580 CDS YP_001541818.1 159046146 5714134 9993..11330 1 NC_009955.1 PFAM: amino acid permease-associated region; KEGG: sil:SPOA0366 amino acid permease; amino acid permease 11330 5714134 Dshi_3604 Dinoroseobacter shibae DFL 12 = DSM 16493 amino acid permease YP_001541818.1 9993 D 398580 CDS YP_001541819.1 159046147 5714135 complement(11338..11982) 1 NC_009955.1 hypothetical protein 11982 5714135 Dshi_3605 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541819.1 11338 R 398580 CDS YP_001541820.1 159046148 5714136 12199..12921 1 NC_009955.1 PFAM: cytochrome c biogenesis protein transmembrane region; KEGG: maq:Maqu_3250 cytochrome c biogenesis protein, transmembrane region; cytochrome c biogenesis protein transmembrane region 12921 5714136 Dshi_3606 Dinoroseobacter shibae DFL 12 = DSM 16493 cytochrome c biogenesis protein transmembrane region YP_001541820.1 12199 D 398580 CDS YP_001541821.1 159046149 5714137 13115..13780 1 NC_009955.1 PFAM: ErfK/YbiS/YcfS/YnhG family protein; KEGG: rde:RD1_0492 ErfK/YbiS/YcfS/YnhG family protein; ErfK/YbiS/YcfS/YnhG family protein 13780 5714137 Dshi_3607 Dinoroseobacter shibae DFL 12 = DSM 16493 ErfK/YbiS/YcfS/YnhG family protein YP_001541821.1 13115 D 398580 CDS YP_001541822.1 159046150 5714138 complement(13828..14100) 1 NC_009955.1 KEGG: rde:RD1_0491 hypothetical protein; hypothetical protein 14100 5714138 Dshi_3608 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541822.1 13828 R 398580 CDS YP_001541823.1 159046151 5714139 14461..16647 1 NC_009955.1 TIGRFAM: ATPase, P-type (transporting), HAD superfamily, subfamily IC; cadmium-translocating P-type ATPase; heavy metal translocating P-type ATPase; PFAM: Haloacid dehalogenase domain protein hydrolase; E1-E2 ATPase-associated domain protein; KEGG: mes:Meso_4212 heavy metal translocating P-type ATPase; heavy metal translocating P-type ATPase 16647 5714139 Dshi_3609 Dinoroseobacter shibae DFL 12 = DSM 16493 heavy metal translocating P-type ATPase YP_001541823.1 14461 D 398580 CDS YP_001541824.1 159046152 5714140 complement(16641..16916) 1 NC_009955.1 hypothetical protein 16916 5714140 Dshi_3610 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541824.1 16641 R 398580 CDS YP_001541825.1 159046153 5714141 17014..17472 1 NC_009955.1 PFAM: regulatory protein MarR; iron dependent repressor; SMART: regulatory protein Crp; KEGG: mlo:mll2499 hypothetical protein; DtxR family iron dependent repressor 17472 5714141 Dshi_3611 Dinoroseobacter shibae DFL 12 = DSM 16493 DtxR family iron dependent repressor YP_001541825.1 17014 D 398580 CDS YP_001541826.1 159046154 5714142 complement(17567..17734) 1 NC_009955.1 KEGG: sil:SPO2514 hypothetical protein; hypothetical protein 17734 5714142 Dshi_3612 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541826.1 17567 R 398580 CDS YP_001541827.1 159046155 5714143 complement(17734..19305) 1 NC_009955.1 TIGRFAM: apolipoprotein N-acyltransferase; PFAM: Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase; KEGG: nha:Nham_0025 apolipoprotein N-acyltransferase; apolipoprotein N-acyltransferase 19305 5714143 Dshi_3613 Dinoroseobacter shibae DFL 12 = DSM 16493 apolipoprotein N-acyltransferase YP_001541827.1 17734 R 398580 CDS YP_001541828.1 159046156 5714144 complement(19302..19775) 1 NC_009955.1 TIGRFAM: lipoprotein signal peptidase; PFAM: peptidase A8 signal peptidase II; KEGG: eli:ELI_04470 putative lipoprotein signal peptidase; lipoprotein signal peptidase 19775 5714144 Dshi_3614 Dinoroseobacter shibae DFL 12 = DSM 16493 lipoprotein signal peptidase YP_001541828.1 19302 R 398580 CDS YP_001541829.1 159046157 5714145 complement(19780..20562) 1 NC_009955.1 PFAM: zinc/iron permease; KEGG: gvi:glr4280 zinc transporter, ZIP family; zinc/iron permease 20562 5714145 Dshi_3615 Dinoroseobacter shibae DFL 12 = DSM 16493 zinc/iron permease YP_001541829.1 19780 R 398580 CDS YP_001541830.1 159046158 5714146 complement(20585..21043) 1 NC_009955.1 PFAM: protein of unknown function DUF411; KEGG: aav:Aave_1809 protein of unknown function DUF411; hypothetical protein 21043 5714146 Dshi_3616 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541830.1 20585 R 398580 CDS YP_001541831.1 159046159 5714147 complement(21047..22420) 1 NC_009955.1 PFAM: peptidase M23B; KEGG: hch:HCH_06239 membrane protein related to metalloendopeptidase; peptidase M23B 22420 5714147 Dshi_3617 Dinoroseobacter shibae DFL 12 = DSM 16493 peptidase M23B YP_001541831.1 21047 R 398580 CDS YP_001541832.1 159046160 5714148 complement(22417..23043) 1 NC_009955.1 PFAM: electron transport protein SCO1/SenC; KEGG: ccr:CC_3503 SCO1/2 family protein; electron transport protein SCO1/SenC 23043 5714148 Dshi_3618 Dinoroseobacter shibae DFL 12 = DSM 16493 electron transport protein SCO1/SenC YP_001541832.1 22417 R 398580 CDS YP_001541833.1 159046161 5714149 complement(23043..23513) 1 NC_009955.1 PFAM: protein of unknown function DUF461; KEGG: bra:BRADO4160 conserved hypothetical protein; putative signal peptide; hypothetical protein 23513 5714149 Dshi_3619 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541833.1 23043 R 398580 CDS YP_001541834.1 159046162 5714150 complement(23536..24195) 1 NC_009955.1 PFAM: DSBA oxidoreductase; KEGG: mes:Meso_4133 DsbA oxidoreductase; DSBA oxidoreductase 24195 5714150 Dshi_3620 Dinoroseobacter shibae DFL 12 = DSM 16493 DSBA oxidoreductase YP_001541834.1 23536 R 398580 CDS YP_001541835.1 159046163 5714151 complement(24192..24614) 1 NC_009955.1 PFAM: Disulphide bond formation protein DsbB; KEGG: psa:PST_0576 disulfide bond formation protein; disulfide bond formation protein DsbB 24614 5714151 Dshi_3621 Dinoroseobacter shibae DFL 12 = DSM 16493 disulfide bond formation protein DsbB YP_001541835.1 24192 R 398580 CDS YP_001541836.1 159046164 5714152 complement(24620..25222) 1 NC_009955.1 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 25222 5714152 Dshi_3622 Dinoroseobacter shibae DFL 12 = DSM 16493 electron transport protein SCO1/SenC YP_001541836.1 24620 R 398580 CDS YP_001541837.1 159046165 5714153 25400..25828 1 NC_009955.1 PFAM: regulatory protein MerR; Transcription regulator MerR DNA binding; KEGG: sil:SPOA0389 transcriptional regulator, MerR family; MerR family transcriptional regulator 25828 5714153 Dshi_3623 Dinoroseobacter shibae DFL 12 = DSM 16493 MerR family transcriptional regulator YP_001541837.1 25400 D 398580 CDS YP_001541838.1 159046166 5714154 25911..26531 1 NC_009955.1 PFAM: cation efflux protein; KEGG: mes:Meso_4424 cation efflux protein; cation efflux protein 26531 5714154 Dshi_3624 Dinoroseobacter shibae DFL 12 = DSM 16493 cation efflux protein YP_001541838.1 25911 D 398580 CDS YP_001541839.1 159046167 5714155 26601..27164 1 NC_009955.1 KEGG: ajs:Ajs_1334 hypothetical protein; hypothetical protein 27164 5714155 Dshi_3625 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541839.1 26601 D 398580 CDS YP_001541840.1 159046168 5714156 27154..28119 1 NC_009955.1 TIGRFAM: cation diffusion facilitator family transporter; PFAM: cation efflux protein; KEGG: maq:Maqu_3275 cation diffusion facilitator family transporter; cation diffusion facilitator family transporter 28119 5714156 Dshi_3626 Dinoroseobacter shibae DFL 12 = DSM 16493 cation diffusion facilitator family transporter YP_001541840.1 27154 D 398580 CDS YP_001541841.1 159046169 5714157 28091..28402 1 NC_009955.1 KEGG: gfo:GFO_1210 hypothetical protein; hypothetical protein 28402 5714157 Dshi_3627 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541841.1 28091 D 398580 CDS YP_001541842.1 159046170 5714158 28756..29451 1 NC_009955.1 KEGG: sit:TM1040_3830 hypothetical protein; hypothetical protein 29451 5714158 Dshi_3628 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541842.1 28756 D 398580 CDS YP_001541843.1 159046171 5714159 29691..30563 1 NC_009955.1 PFAM: integrase family protein; integrase domain protein SAM domain protein; KEGG: acr:Acry_2348 phage integrase family protein; integrase family protein 30563 5714159 Dshi_3629 Dinoroseobacter shibae DFL 12 = DSM 16493 integrase family protein YP_001541843.1 29691 D 398580 CDS YP_001541844.1 159046172 5714160 30576..31778 1 NC_009955.1 PFAM: putative transposase; KEGG: sal:Sala_0067 putative transposase; putative transposase 31778 5714160 Dshi_3630 Dinoroseobacter shibae DFL 12 = DSM 16493 putative transposase YP_001541844.1 30576 D 398580 CDS YP_001541845.1 159046173 5714161 complement(32223..33164) 1 NC_009955.1 PFAM: helix-turn-helix- domain containing protein AraC type; ThiJ/PfpI domain protein; KEGG: sil:SPO1704 transcriptional regulator, AraC family; AraC family transcriptional regulator 33164 5714161 Dshi_3631 Dinoroseobacter shibae DFL 12 = DSM 16493 AraC family transcriptional regulator YP_001541845.1 32223 R 398580 CDS YP_001541846.1 159046174 5714162 33247..35727 1 NC_009955.1 PFAM: L-carnitine dehydratase/bile acid-inducible protein F; KEGG: sil:SPO1703 CaiB/BaiF family protein; L-carnitine dehydratase/bile acid-inducible protein F 35727 5714162 Dshi_3632 Dinoroseobacter shibae DFL 12 = DSM 16493 L-carnitine dehydratase/bile acid-inducible protein F YP_001541846.1 33247 D 398580 CDS YP_001541847.1 159046175 5714163 35746..37389 1 NC_009955.1 KEGG: sil:SPO1702 hypothetical protein; hypothetical protein 37389 5714163 Dshi_3633 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541847.1 35746 D 398580 CDS YP_001541848.1 159046176 5714164 complement(37539..37766) 1 NC_009955.1 KEGG: sit:TM1040_3826 hypothetical protein; hypothetical protein 37766 5714164 Dshi_3634 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541848.1 37539 R 398580 CDS YP_001541849.1 159046177 5714165 complement(37936..38193) 1 NC_009955.1 PFAM: helix-turn-helix domain protein; KEGG: rsq:Rsph17025_0810 putative transcriptional regulator, XRE family; XRE family transcriptional regulator 38193 5714165 Dshi_3635 Dinoroseobacter shibae DFL 12 = DSM 16493 XRE family transcriptional regulator YP_001541849.1 37936 R 398580 CDS YP_001541850.1 159046178 5714166 complement(38318..38611) 1 NC_009955.1 KEGG: sit:TM1040_3824 hypothetical protein; hypothetical protein 38611 5714166 Dshi_3636 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541850.1 38318 R 398580 CDS YP_001541851.1 159046179 5714167 38780..39133 1 NC_009955.1 KEGG: sit:TM1040_3823 hypothetical protein; hypothetical protein 39133 5714167 Dshi_3637 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541851.1 38780 D 398580 CDS YP_001541852.1 159046180 5714168 39177..39797 1 NC_009955.1 PFAM: Lytic transglycosylase catalytic; KEGG: sit:TM1040_3822 lytic transglycosylase, catalytic; lytic transglycosylase 39797 5714168 Dshi_3638 Dinoroseobacter shibae DFL 12 = DSM 16493 lytic transglycosylase YP_001541852.1 39177 D 398580 CDS YP_001541853.1 159046181 5714169 39794..40087 1 NC_009955.1 PFAM: Conjugal transfer protein TrbC; KEGG: sit:TM1040_3821 VirB2 type IV secretion; conjugal transfer protein TrbC 40087 5714169 Dshi_3639 Dinoroseobacter shibae DFL 12 = DSM 16493 conjugal transfer protein TrbC YP_001541853.1 39794 D 398580 CDS YP_001541854.1 159046182 5714170 40080..40358 1 NC_009955.1 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 40358 5714170 Dshi_3640 Dinoroseobacter shibae DFL 12 = DSM 16493 type IV secretory pathway VirB3 family protein YP_001541854.1 40080 D 398580 CDS YP_001541855.1 159046183 5714171 40348..42723 1 NC_009955.1 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 42723 5714171 Dshi_3641 Dinoroseobacter shibae DFL 12 = DSM 16493 CagE TrbE VirB component of type IV transporter system YP_001541855.1 40348 D 398580 CDS YP_001541856.1 159046184 5714172 42720..42887 1 NC_009955.1 KEGG: sit:TM1040_3818 hypothetical protein; hypothetical protein 42887 5714172 Dshi_3642 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541856.1 42720 D 398580 CDS YP_001541857.1 159046185 5714173 42877..44031 1 NC_009955.1 PFAM: Lytic transglycosylase catalytic; KEGG: sit:TM1040_3817 lytic transglycosylase, catalytic; lytic transglycosylase catalytic 44031 5714173 Dshi_3643 Dinoroseobacter shibae DFL 12 = DSM 16493 lytic transglycosylase catalytic YP_001541857.1 42877 D 398580 CDS YP_001541858.1 159046186 5714174 44031..44840 1 NC_009955.1 KEGG: sit:TM1040_3816 hypothetical protein; hypothetical protein 44840 5714174 Dshi_3644 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541858.1 44031 D 398580 CDS YP_001541859.1 159046187 5714175 44855..45511 1 NC_009955.1 PFAM: VirB8 family protein; KEGG: sit:TM1040_3815 VirB8; VirB8 family protein 45511 5714175 Dshi_3645 Dinoroseobacter shibae DFL 12 = DSM 16493 VirB8 family protein YP_001541859.1 44855 D 398580 CDS YP_001541860.1 159046188 5714176 45513..46208 1 NC_009955.1 PFAM: Conjugal transfer protein TrbG/VirB9/CagX; KEGG: sit:TM1040_3814 conjugal transfer protein TrbG/VirB9/CagX; conjugal transfer protein TrbG/VirB9/CagX 46208 5714176 Dshi_3646 Dinoroseobacter shibae DFL 12 = DSM 16493 conjugal transfer protein TrbG/VirB9/CagX YP_001541860.1 45513 D 398580 CDS YP_001541861.1 159046189 5714177 46205..47584 1 NC_009955.1 PFAM: conjugation TrbI family protein; KEGG: sit:TM1040_3813 conjugation TrbI-like protein; conjugation TrbI family protein 47584 5714177 Dshi_3647 Dinoroseobacter shibae DFL 12 = DSM 16493 conjugation TrbI family protein YP_001541861.1 46205 D 398580 CDS YP_001541862.1 159046190 5714178 47589..48575 1 NC_009955.1 PFAM: type II secretion system protein E; KEGG: sit:TM1040_3812 type II secretion system protein E; type II secretion system protein E 48575 5714178 Dshi_3648 Dinoroseobacter shibae DFL 12 = DSM 16493 type II secretion system protein E YP_001541862.1 47589 D 398580 CDS YP_001541863.1 159046191 5714179 48572..48766 1 NC_009955.1 KEGG: sit:TM1040_3811 hypothetical protein; hypothetical protein 48766 5714179 Dshi_3649 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541863.1 48572 D 398580 CDS YP_001541864.1 159046192 5714180 48763..49173 1 NC_009955.1 KEGG: sit:TM1040_3810 hypothetical protein; hypothetical protein 49173 5714180 Dshi_3650 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541864.1 48763 D 398580 CDS YP_001541865.1 159046193 5714181 49186..50262 1 NC_009955.1 PFAM: TrbL/VirB6 plasmid conjugal transfer protein; KEGG: sit:TM1040_3809 TrbL/VirB6 plasmid conjugal transfer protein; TrbL/VirB6 plasmid conjugal transfer protein 50262 5714181 Dshi_3651 Dinoroseobacter shibae DFL 12 = DSM 16493 TrbL/VirB6 plasmid conjugal transfer protein YP_001541865.1 49186 D 398580 CDS YP_001541866.1 159046194 5714182 50623..51540 1 NC_009955.1 KEGG: mes:Meso_4413 hypothetical protein; hypothetical protein 51540 5714182 Dshi_3652 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541866.1 50623 D 398580 CDS YP_001541867.1 159046195 5714183 complement(51856..53406) 1 NC_009955.1 PFAM: DNA-directed DNA polymerase; KEGG: psp:PSPPH_4219 DNA polymerase I domain protein; DNA-directed DNA polymerase 53406 5714183 Dshi_3653 Dinoroseobacter shibae DFL 12 = DSM 16493 DNA-directed DNA polymerase YP_001541867.1 51856 R 398580 CDS YP_001541868.1 159046196 5714184 complement(53399..55099) 1 NC_009955.1 KEGG: pna:Pnap_3925 hypothetical protein; hypothetical protein 55099 5714184 Dshi_3654 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541868.1 53399 R 398580 CDS YP_001541869.1 159046197 5714185 complement(55361..57364) 1 NC_009955.1 PFAM: TRAG family protein; KEGG: sit:TM1040_3794 TraG protein; TRAG family protein 57364 5714185 Dshi_3655 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAG family protein YP_001541869.1 55361 R 398580 CDS YP_001541870.1 159046198 5714186 complement(57373..59706) 1 NC_009955.1 PFAM: Relaxase/mobilization nuclease family protein; KEGG: sit:TM1040_3793 relaxase/mobilization nuclease domain; relaxase/mobilization nuclease family protein 59706 5714186 Dshi_3656 Dinoroseobacter shibae DFL 12 = DSM 16493 relaxase/mobilization nuclease family protein YP_001541870.1 57373 R 398580 CDS YP_001541871.1 159046199 5714187 complement(59693..60274) 1 NC_009955.1 PFAM: transposase IS3/IS911 family protein; KEGG: sit:TM1040_3792 hypothetical protein; transposase IS3/IS911 family protein 60274 5714187 Dshi_3657 Dinoroseobacter shibae DFL 12 = DSM 16493 transposase IS3/IS911 family protein YP_001541871.1 59693 R 398580 CDS YP_001541872.1 159046200 5714188 complement(60838..61044) 1 NC_009955.1 KEGG: sit:TM1040_3791 hypothetical protein; hypothetical protein 61044 5714188 Dshi_3658 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541872.1 60838 R 398580 CDS YP_001541873.1 159046201 5714189 complement(61245..61547) 1 NC_009955.1 hypothetical protein 61547 5714189 Dshi_3659 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541873.1 61245 R 398580 CDS YP_001541874.1 159046202 5714190 complement(61583..62512) 1 NC_009955.1 KEGG: mes:Meso_4225 hypothetical protein; hypothetical protein 62512 5714190 Dshi_3660 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541874.1 61583 R 398580 CDS YP_001541875.1 159046203 5714191 63298..64170 1 NC_009955.1 PFAM: integrase family protein; integrase domain protein SAM domain protein; KEGG: acr:Acry_2348 phage integrase family protein; integrase family protein 64170 5714191 Dshi_3661 Dinoroseobacter shibae DFL 12 = DSM 16493 integrase family protein YP_001541875.1 63298 D 398580 CDS YP_001541876.1 159046204 5714192 64183..65385 1 NC_009955.1 PFAM: putative transposase; KEGG: sal:Sala_0067 putative transposase; putative transposase 65385 5714192 Dshi_3662 Dinoroseobacter shibae DFL 12 = DSM 16493 putative transposase YP_001541876.1 64183 D 398580 CDS YP_001541877.1 159046205 5714193 complement(65753..66727) 1 NC_009955.1 KEGG: bbt:BBta_1126 putative membrane protein of unknown function; hypothetical protein 66727 5714193 Dshi_3663 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541877.1 65753 R 398580 CDS YP_001541878.1 159046206 5714194 67147..67365 1 NC_009955.1 KEGG: acr:Acry_3183 hypothetical protein; hypothetical protein 67365 5714194 Dshi_3664 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541878.1 67147 D 398580 CDS YP_001541879.1 159046207 5714195 67356..67688 1 NC_009955.1 KEGG: gox:GOX2735 PemK-like protein; transcriptional modulator of MazE/toxin MazF 67688 5714195 Dshi_3665 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional modulator of MazE/toxin MazF YP_001541879.1 67356 D 398580 CDS YP_001541880.1 159046208 5714196 complement(68206..68370) 1 NC_009955.1 KEGG: rde:RD1_3456 hypothetical protein; hypothetical protein 68370 5714196 Dshi_3666 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541880.1 68206 R 398580 CDS YP_001541881.1 159046209 5714197 complement(68732..69094) 1 NC_009955.1 KEGG: reh:H16_B1492 hypothetical protein; hypothetical protein 69094 5714197 Dshi_3667 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541881.1 68732 R 398580 CDS YP_001541882.1 159046210 5714198 complement(69101..69835) 1 NC_009955.1 PFAM: protein of unknown function UPF0005; KEGG: rsh:Rsph17029_3820 protein of unknown function UPF0005; hypothetical protein 69835 5714198 Dshi_3668 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541882.1 69101 R 398580 CDS YP_001541883.1 159046211 5714199 complement(70079..70657) 1 NC_009955.1 PFAM: Exopolysaccharide synthesis ExoD; KEGG: jan:Jann_0449 exopolysaccharide synthesis, ExoD; exopolysaccharide synthesis ExoD 70657 5714199 Dshi_3669 Dinoroseobacter shibae DFL 12 = DSM 16493 exopolysaccharide synthesis ExoD YP_001541883.1 70079 R 398580 CDS YP_001541884.1 159046212 5714200 complement(70773..71738) 1 NC_009955.1 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 71738 5714200 Dshi_3670 Dinoroseobacter shibae DFL 12 = DSM 16493 CaCA family Na(+)/Ca(+) antiporter YP_001541884.1 70773 R 398580 CDS YP_001541885.1 159046213 5714201 complement(71864..72325) 1 NC_009955.1 PFAM: pentapeptide repeat protein; KEGG: tel:tlr0822 hypothetical protein; pentapeptide repeat-containing protein 72325 5714201 Dshi_3671 Dinoroseobacter shibae DFL 12 = DSM 16493 pentapeptide repeat-containing protein YP_001541885.1 71864 R 398580 CDS YP_001541886.1 159046214 5714202 complement(72650..73927) 1 NC_009955.1 PFAM: CBS domain containing protein; protein of unknown function DUF21; transporter-associated region; KEGG: pde:Pden_0723 protein of unknown function DUF21; hypothetical protein 73927 5714202 Dshi_3672 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541886.1 72650 R 398580 CDS YP_001541887.1 159046215 5714203 complement(74023..74991) 1 NC_009955.1 KEGG: rsp:RSP_0408 hypothetical protein; hypothetical protein 74991 5714203 Dshi_3673 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541887.1 74023 R 398580 CDS YP_001541888.1 159046216 5714204 complement(75225..77591) 1 NC_009955.1 PFAM: cyclic nucleotide-binding; sodium/hydrogen exchanger; KEGG: rde:RD1_3698 sodium/hydrogen exchanger family, putative; cyclic nucleotide-binding protein 77591 5714204 Dshi_3674 Dinoroseobacter shibae DFL 12 = DSM 16493 cyclic nucleotide-binding protein YP_001541888.1 75225 R 398580 CDS YP_001541889.1 159046217 5714205 complement(77607..77891) 1 NC_009955.1 KEGG: rde:RD1_3698 sodium/hydrogen exchanger family, putative; hypothetical protein 77891 5714205 Dshi_3675 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541889.1 77607 R 398580 CDS YP_001541890.1 159046218 5714206 complement(78020..80338) 1 NC_009955.1 PFAM: transposase Tn3 family protein; KEGG: psb:Psyr_2667 transposase Tn3; transposase Tn3 family protein 80338 5714206 Dshi_3676 Dinoroseobacter shibae DFL 12 = DSM 16493 transposase Tn3 family protein YP_001541890.1 78020 R 398580 CDS YP_001541891.1 159046219 5714207 complement(80378..80902) 1 NC_009955.1 KEGG: rsq:Rsph17025_4307 hypothetical protein; hypothetical protein 80902 5714207 Dshi_3677 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541891.1 80378 R 398580 CDS YP_001541892.1 159046220 5714208 complement(81019..81843) 1 NC_009955.1 KEGG: art:Arth_4384 ATP-binding protein; ATP-binding protein 81843 5714208 Dshi_3678 Dinoroseobacter shibae DFL 12 = DSM 16493 ATP-binding protein YP_001541892.1 81019 R 398580 CDS YP_001541893.1 159046221 5714209 complement(81840..83333) 1 NC_009955.1 PFAM: Integrase catalytic region; Transposase-like Mu; KEGG: art:Arth_4385 integrase, catalytic region; integrase catalytic region 83333 5714209 Dshi_3679 Dinoroseobacter shibae DFL 12 = DSM 16493 integrase catalytic region YP_001541893.1 81840 R 398580 CDS YP_001541894.1 159046222 5714210 83472..84071 1 NC_009955.1 PFAM: Resolvase domain; Resolvase helix-turn-helix domain protein; KEGG: gox:GOX2646 DNA integration/recombination/invertion protein; resolvase domain-containing protein 84071 5714210 Dshi_3680 Dinoroseobacter shibae DFL 12 = DSM 16493 resolvase domain-containing protein YP_001541894.1 83472 D 398580 CDS YP_001541895.1 159046223 5714211 84592..86400 1 NC_009955.1 required for the synthesis of the hydromethylpyrimidine moiety of thiamine; thiamine biosynthesis protein ThiC 86400 5714211 Dshi_3681 Dinoroseobacter shibae DFL 12 = DSM 16493 thiamine biosynthesis protein ThiC YP_001541895.1 84592 D 398580 CDS YP_001541896.1 159046224 5714212 complement(86804..88186) 1 NC_009955.1 PFAM: transposase IS4 family protein; KEGG: rde:RD1_3444 transposase, putative; transposase IS4 family protein 88186 5714212 Dshi_3682 Dinoroseobacter shibae DFL 12 = DSM 16493 transposase IS4 family protein YP_001541896.1 86804 R 398580 CDS YP_001541897.1 159046225 5714213 88435..89082 1 NC_009955.1 PFAM: Resolvase domain; KEGG: psb:Psyr_2668 helix-turn-helix, fis-type; resolvase domain-containing protein 89082 5714213 Dshi_3683 Dinoroseobacter shibae DFL 12 = DSM 16493 resolvase domain-containing protein YP_001541897.1 88435 D 398580 CDS YP_001541898.1 159046226 5714214 89186..90118 1 NC_009955.1 KEGG: pfl:PFL_2489 hypothetical protein; hypothetical protein 90118 5714214 Dshi_3684 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541898.1 89186 D 398580 CDS YP_001541899.1 159046227 5714215 90129..90698 1 NC_009955.1 PFAM: BioY protein; KEGG: bbk:BARBAKC583_1193 biotin transport protein BioY; BioY protein 90698 5714215 Dshi_3685 Dinoroseobacter shibae DFL 12 = DSM 16493 BioY protein YP_001541899.1 90129 D 398580 CDS YP_001541900.1 159046228 5714216 90714..91379 1 NC_009955.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sit:TM1040_3661 ABC transporter related; ABC transporter 91379 5714216 Dshi_3686 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC transporter YP_001541900.1 90714 D 398580 CDS YP_001541901.1 159046229 5714217 91376..91969 1 NC_009955.1 PFAM: cobalt transport protein; KEGG: sit:TM1040_3660 cobalt transport protein; cobalt transport protein 91969 5714217 Dshi_3687 Dinoroseobacter shibae DFL 12 = DSM 16493 cobalt transport protein YP_001541901.1 91376 D 398580 CDS YP_001541902.1 159046230 5714218 complement(92394..92966) 1 NC_009955.1 PFAM: BioY protein; KEGG: mlo:mlr7429 bioY protein; BioY protein 92966 5714218 Dshi_3688 Dinoroseobacter shibae DFL 12 = DSM 16493 BioY protein YP_001541902.1 92394 R 398580 CDS YP_001541903.1 159046231 5714219 93160..93360 1 NC_009955.1 KEGG: psb:Psyr_2668 helix-turn-helix, fis-type; hypothetical protein 93360 5714219 Dshi_3689 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541903.1 93160 D 398580 CDS YP_001541904.1 159046232 5714220 complement(93569..94297) 1 NC_009955.1 KEGG: jan:Jann_4220 ParB-like nuclease; ParB-like nuclease 94297 5714220 Dshi_3690 Dinoroseobacter shibae DFL 12 = DSM 16493 ParB-like nuclease YP_001541904.1 93569 R 398580 CDS YP_001541905.1 159046233 5714221 complement(94422..94724) 1 NC_009955.1 hypothetical protein 94724 5714221 Dshi_3691 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541905.1 94422 R 398580 CDS YP_001541906.1 159046234 5714222 complement(94825..95286) 1 NC_009955.1 KEGG: bbt:BBta_7341 hypothetical protein; hypothetical protein 95286 5714222 Dshi_3692 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541906.1 94825 R 398580 CDS YP_001541907.1 159046235 5714223 complement(95288..95674) 1 NC_009955.1 KEGG: sal:Sala_2657 hypothetical protein; hypothetical protein 95674 5714223 Dshi_3693 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541907.1 95288 R 398580 CDS YP_001541908.1 159046236 5714224 complement(95796..97667) 1 NC_009955.1 KEGG: ana:alr7089 hypothetical protein; hypothetical protein 97667 5714224 Dshi_3694 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541908.1 95796 R 398580 CDS YP_001541909.1 159046237 5714225 97825..100266 1 NC_009955.1 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 100266 5714225 Dshi_3695 Dinoroseobacter shibae DFL 12 = DSM 16493 type III restriction protein res subunit YP_001541909.1 97825 D 398580 CDS YP_001541910.1 159046238 5714226 complement(100305..101309) 1 NC_009955.1 PFAM: integrase family protein; integrase domain protein SAM domain protein; KEGG: sal:Sala_0440 phage integrase; integrase family protein 101309 5714226 Dshi_3696 Dinoroseobacter shibae DFL 12 = DSM 16493 integrase family protein YP_001541910.1 100305 R 398580 CDS YP_001541911.1 159046239 5714227 complement(101306..102217) 1 NC_009955.1 PFAM: integrase family protein; KEGG: sal:Sala_0439 phage integrase; integrase family protein 102217 5714227 Dshi_3697 Dinoroseobacter shibae DFL 12 = DSM 16493 integrase family protein YP_001541911.1 101306 R 398580 CDS YP_001541912.1 159046240 5714228 complement(102214..103740) 1 NC_009955.1 PFAM: integrase family protein; integrase domain protein SAM domain protein; KEGG: sal:Sala_0438 phage integrase; integrase family protein 103740 5714228 Dshi_3698 Dinoroseobacter shibae DFL 12 = DSM 16493 integrase family protein YP_001541912.1 102214 R 398580 CDS YP_001541913.1 159046241 5714229 complement(103864..106374) 1 NC_009955.1 KEGG: nar:Saro_2208 putative methylase/helicase; putative methylase/helicase 106374 5714229 Dshi_3699 Dinoroseobacter shibae DFL 12 = DSM 16493 putative methylase/helicase YP_001541913.1 103864 R 398580 CDS YP_001541914.1 159046242 5714230 107197..108084 1 NC_009955.1 PFAM: integrase family protein; integrase domain protein SAM domain protein; KEGG: nha:Nham_0858 phage integrase; integrase family protein 108084 5714230 Dshi_3700 Dinoroseobacter shibae DFL 12 = DSM 16493 integrase family protein YP_001541914.1 107197 D 398580 CDS YP_001541915.1 159046243 5714231 108097..109296 1 NC_009955.1 PFAM: putative transposase; KEGG: sal:Sala_0067 putative transposase; putative transposase 109296 5714231 Dshi_3701 Dinoroseobacter shibae DFL 12 = DSM 16493 putative transposase YP_001541915.1 108097 D 398580 CDS YP_001541916.1 159046244 5714232 complement(109817..110656) 1 NC_009955.1 PFAM: fatty acid hydroxylase; KEGG: pol:Bpro_3325 hypothetical protein; fatty acid hydroxylase 110656 5714232 Dshi_3702 Dinoroseobacter shibae DFL 12 = DSM 16493 fatty acid hydroxylase YP_001541916.1 109817 R 398580 CDS YP_001541917.1 159046245 5714234 complement(112171..113076) 1 NC_009955.1 PFAM: Integrase catalytic region; KEGG: pde:Pden_3846 integrase, catalytic region; integrase catalytic region 113076 5714234 Dshi_3705 Dinoroseobacter shibae DFL 12 = DSM 16493 integrase catalytic region YP_001541917.1 112171 R 398580 CDS YP_001541918.1 159046246 5714235 complement(113073..113405) 1 NC_009955.1 PFAM: transposase IS3/IS911 family protein; KEGG: psp:PSPPH_A0090 ISPsy21, transposase orfA; transposase IS3/IS911 family protein 113405 5714235 Dshi_3706 Dinoroseobacter shibae DFL 12 = DSM 16493 transposase IS3/IS911 family protein YP_001541918.1 113073 R 398580 CDS YP_001541919.1 159046247 5714236 complement(113417..113626) 1 NC_009955.1 KEGG: acr:Acry_0097 transposase, IS4 family protein; transposase, IS4 family protein 113626 5714236 Dshi_3707 Dinoroseobacter shibae DFL 12 = DSM 16493 transposase, IS4 family protein YP_001541919.1 113417 R 398580 CDS YP_001541920.1 159046248 5714237 113772..114608 1 NC_009955.1 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 114608 5714237 Dshi_3708 Dinoroseobacter shibae DFL 12 = DSM 16493 AraC family transcriptional regulator YP_001541920.1 113772 D 398580 CDS YP_001541921.1 159046249 5714238 complement(114610..115872) 1 NC_009955.1 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 115872 5714238 Dshi_3709 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP dicarboxylate transporter, DctM subunit YP_001541921.1 114610 R 398580 CDS YP_001541922.1 159046250 5714239 complement(115872..116441) 1 NC_009955.1 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 116441 5714239 Dshi_3710 Dinoroseobacter shibae DFL 12 = DSM 16493 tripartite ATP-independent periplasmic transporter DctQ YP_001541922.1 115872 R 398580 CDS YP_001541923.1 159046251 5714240 complement(116503..117483) 1 NC_009955.1 PFAM: TRAP dicarboxylate transporter- DctP subunit; KEGG: sit:TM1040_1591 TRAP dicarboxylate transporter-DctP subunit; TRAP dicarboxylate transporter- DctP subunit 117483 5714240 Dshi_3711 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP dicarboxylate transporter- DctP subunit YP_001541923.1 116503 R 398580 CDS YP_001541924.1 159046252 5714241 complement(117527..118285) 1 NC_009955.1 PFAM: short-chain dehydrogenase/reductase SDR; KR domain protein; KEGG: swi:Swit_3068 short-chain dehydrogenase/reductase SDR; short-chain dehydrogenase/reductase SDR 118285 5714241 Dshi_3712 Dinoroseobacter shibae DFL 12 = DSM 16493 short-chain dehydrogenase/reductase SDR YP_001541924.1 117527 R 398580 CDS YP_001541925.1 159046253 5714242 118469..118945 1 NC_009955.1 PFAM: conserved hypothetical protein; KEGG: ccr:CC_3289 hypothetical protein; hypothetical protein 118945 5714242 Dshi_3713 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541925.1 118469 D 398580 CDS YP_001541926.1 159046254 5714243 complement(118926..119519) 1 NC_009955.1 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 119519 5714243 Dshi_3714 Dinoroseobacter shibae DFL 12 = DSM 16493 3-octaprenyl-4-hydroxybenzoate carboxy-lyase YP_001541926.1 118926 R 398580 CDS YP_001541927.1 159046255 5714244 complement(119636..120550) 1 NC_009955.1 PFAM: regulatory protein LysR; LysR substrate-binding; KEGG: bxe:Bxe_A2070 transcriptional regulator, LysR family; LysR family transcriptional regulator 120550 5714244 Dshi_3715 Dinoroseobacter shibae DFL 12 = DSM 16493 LysR family transcriptional regulator YP_001541927.1 119636 R 398580 CDS YP_001541928.1 159046256 5714245 120678..122087 1 NC_009955.1 TIGRFAM: UbiD family decarboxylase; PFAM: Carboxylyase-related protein; KEGG: bja:blr3531 hypothetical protein; UbiD family decarboxylase 122087 5714245 Dshi_3716 Dinoroseobacter shibae DFL 12 = DSM 16493 UbiD family decarboxylase YP_001541928.1 120678 D 398580 CDS YP_001541929.1 159046257 5714246 122126..123583 1 NC_009955.1 PFAM: aldehyde dehydrogenase; KEGG: rpc:RPC_0853 aldehyde dehydrogenase; aldehyde dehydrogenase 123583 5714246 Dshi_3717 Dinoroseobacter shibae DFL 12 = DSM 16493 aldehyde dehydrogenase YP_001541929.1 122126 D 398580 CDS YP_001541930.1 159046258 5714247 123637..124554 1 NC_009955.1 SMART: helix-turn-helix- domain containing protein AraC type; KEGG: rpc:RPC_0847 transcriptional regulator, AraC family; AraC family transcriptional regulator 124554 5714247 Dshi_3718 Dinoroseobacter shibae DFL 12 = DSM 16493 AraC family transcriptional regulator YP_001541930.1 123637 D 398580 CDS YP_001541931.1 159046259 5714248 124654..127605 1 NC_009955.1 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 127605 5714248 Dshi_3719 Dinoroseobacter shibae DFL 12 = DSM 16493 molybdopterin binding aldehyde oxidase and xanthine dehydrogenase YP_001541931.1 124654 D 398580 CDS YP_001541932.1 159046260 5714249 127602..128429 1 NC_009955.1 PFAM: molybdopterin dehydrogenase FAD-binding; KEGG: acr:Acry_0669 molybdopterin dehydrogenase, FAD-binding; molybdopterin dehydrogenase FAD-binding 128429 5714249 Dshi_3720 Dinoroseobacter shibae DFL 12 = DSM 16493 molybdopterin dehydrogenase FAD-binding YP_001541932.1 127602 D 398580 CDS YP_001541933.1 159046261 5714250 128417..128926 1 NC_009955.1 PFAM: ferredoxin; [2Fe-2S]-binding domain protein; KEGG: rpc:RPC_0850 (2Fe-2S)-binding; 2Fe-2S iron-sulfur cluster binding domain-containing protein 128926 5714250 Dshi_3721 Dinoroseobacter shibae DFL 12 = DSM 16493 2Fe-2S iron-sulfur cluster binding domain-containing protein YP_001541933.1 128417 D 398580 CDS YP_001541934.1 159046262 5714251 128919..130454 1 NC_009955.1 PFAM: AMP-dependent synthetase and ligase; KEGG: rpc:RPC_0851 AMP-dependent synthetase and ligase; AMP-dependent synthetase and ligase 130454 5714251 Dshi_3722 Dinoroseobacter shibae DFL 12 = DSM 16493 AMP-dependent synthetase and ligase YP_001541934.1 128919 D 398580 CDS YP_001541935.1 159046263 5714252 130481..131284 1 NC_009955.1 PFAM: Enoyl-CoA hydratase/isomerase; KEGG: acr:Acry_0672 enoyl-CoA hydratase/isomerase; enoyl-CoA hydratase/isomerase 131284 5714252 Dshi_3723 Dinoroseobacter shibae DFL 12 = DSM 16493 enoyl-CoA hydratase/isomerase YP_001541935.1 130481 D 398580 CDS YP_001541936.1 159046264 5714253 131326..132480 1 NC_009955.1 PFAM: Extracellular ligand-binding receptor; KEGG: rpc:RPC_0836 extracellular ligand-binding receptor; extracellular ligand-binding receptor 132480 5714253 Dshi_3724 Dinoroseobacter shibae DFL 12 = DSM 16493 extracellular ligand-binding receptor YP_001541936.1 131326 D 398580 CDS YP_001541937.1 159046265 5714254 132501..133385 1 NC_009955.1 PFAM: inner-membrane translocator; KEGG: rpc:RPC_0837 inner-membrane translocator; inner-membrane translocator 133385 5714254 Dshi_3725 Dinoroseobacter shibae DFL 12 = DSM 16493 inner-membrane translocator YP_001541937.1 132501 D 398580 CDS YP_001541938.1 159046266 5714255 133378..134406 1 NC_009955.1 PFAM: inner-membrane translocator; KEGG: rpc:RPC_0838 inner-membrane translocator; inner-membrane translocator 134406 5714255 Dshi_3726 Dinoroseobacter shibae DFL 12 = DSM 16493 inner-membrane translocator YP_001541938.1 133378 D 398580 CDS YP_001541939.1 159046267 5714256 134403..135143 1 NC_009955.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rpc:RPC_0839 ABC transporter related; ABC transporter 135143 5714256 Dshi_3727 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC transporter YP_001541939.1 134403 D 398580 CDS YP_001541940.1 159046268 5714257 135136..135846 1 NC_009955.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: rpc:RPC_0840 ABC transporter related; ABC transporter 135846 5714257 Dshi_3728 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC transporter YP_001541940.1 135136 D 398580 CDS YP_001541941.1 159046269 5714258 complement(136657..137175) 1 NC_009955.1 KEGG: psa:PST_3459 hypothetical protein; hypothetical protein 137175 5714258 Dshi_3729 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541941.1 136657 R 398580 CDS YP_001541942.1 159046270 5714259 complement(137172..137498) 1 NC_009955.1 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 137498 5714259 Dshi_3730 Dinoroseobacter shibae DFL 12 = DSM 16493 putative regulator PrlF YP_001541942.1 137172 R 398580 CDS YP_001541943.1 159046271 5714260 complement(137625..138278) 1 NC_009955.1 KEGG: rde:RD1_A0106 RC187; hypothetical protein 138278 5714260 Dshi_3731 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541943.1 137625 R 398580 CDS YP_001541944.1 159046272 5714261 complement(138278..138871) 1 NC_009955.1 hypothetical protein 138871 5714261 Dshi_3732 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541944.1 138278 R 398580 CDS YP_001541945.1 159046273 5714262 complement(138944..140926) 1 NC_009955.1 TIGRFAM: parB-like partition protein; PFAM: ParB domain protein nuclease; KEGG: rde:RD1_A0072 plasmid stabilization protein, putative; parB-like partition protein 140926 5714262 Dshi_3733 Dinoroseobacter shibae DFL 12 = DSM 16493 parB-like partition protein YP_001541945.1 138944 R 398580 CDS YP_001541946.1 159046274 5714263 141254..142120 1 NC_009955.1 KEGG: swi:Swit_5197 transposase IS116/IS110/IS902 family protein; transposase IS116/IS110/IS902 family protein 142120 5714263 Dshi_3734 Dinoroseobacter shibae DFL 12 = DSM 16493 transposase IS116/IS110/IS902 family protein YP_001541946.1 141254 D 398580 CDS YP_001541947.1 159046275 5714265 complement(142349..143254) 1 NC_009955.1 PFAM: Integrase catalytic region; KEGG: pde:Pden_3846 integrase, catalytic region; integrase catalytic region 143254 5714265 Dshi_3736 Dinoroseobacter shibae DFL 12 = DSM 16493 integrase catalytic region YP_001541947.1 142349 R 398580 CDS YP_001541948.1 159046276 5714266 complement(143251..143583) 1 NC_009955.1 PFAM: transposase IS3/IS911 family protein; KEGG: psp:PSPPH_A0090 ISPsy21, transposase orfA; transposase IS3/IS911 family protein 143583 5714266 Dshi_3737 Dinoroseobacter shibae DFL 12 = DSM 16493 transposase IS3/IS911 family protein YP_001541948.1 143251 R 398580 CDS YP_001541949.1 159046277 5714267 143895..145256 1 NC_009955.1 PFAM: transposase IS116/IS110/IS902 family protein; KEGG: cph:Cpha266_0024 transposase; transposase IS116/IS110/IS902 family protein 145256 5714267 Dshi_3738 Dinoroseobacter shibae DFL 12 = DSM 16493 transposase IS116/IS110/IS902 family protein YP_001541949.1 143895 D 398580 CDS YP_001541950.1 159046278 5714268 145289..146146 1 NC_009955.1 PFAM: Integrase catalytic region; KEGG: bms:BRA1116 IS3 family element, transposase orfB; integrase catalytic region 146146 5714268 Dshi_3739 Dinoroseobacter shibae DFL 12 = DSM 16493 integrase catalytic region YP_001541950.1 145289 D 398580 CDS YP_001541951.1 159046279 5714269 complement(147054..147263) 1 NC_009955.1 hypothetical protein 147263 5714269 Dshi_3740 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541951.1 147054 R 398580 CDS YP_001541952.1 159046280 5714270 complement(147287..148219) 1 NC_009955.1 PFAM: domain of unknown function DUF1738; KEGG: nha:Nham_4029 peptidase M, neutral zinc metallopeptidases, zinc-binding site; hypothetical protein 148219 5714270 Dshi_3741 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541952.1 147287 R 398580 CDS YP_001541953.1 159046281 5714271 complement(148260..148730) 1 NC_009955.1 hypothetical protein 148730 5714271 Dshi_3742 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541953.1 148260 R 398580 CDS YP_001541954.1 159046282 5714272 complement(149105..150385) 1 NC_009955.1 PFAM: replication protein C; KEGG: rde:RD1_A0024 replication protein C; replication protein C 150385 5714272 Dshi_3743 Dinoroseobacter shibae DFL 12 = DSM 16493 replication protein C YP_001541954.1 149105 R 398580 CDS YP_001541955.1 159046283 5714273 complement(150613..151635) 1 NC_009955.1 KEGG: rde:RD1_A0023 RC101; hypothetical protein 151635 5714273 Dshi_3744 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541955.1 150613 R 398580 CDS YP_001541956.1 159046284 5714274 complement(151632..152987) 1 NC_009955.1 KEGG: rde:RD1_A0021 RC102; hypothetical protein 152987 5714274 Dshi_3745 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541956.1 151632 R 398580 CDS YP_001541957.1 159046285 5714275 153227..153460 1 NC_009955.1 hypothetical protein 153460 5714275 Dshi_3746 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541957.1 153227 D 398580 CDS YP_001541958.1 159046286 5714276 complement(153767..154930) 1 NC_009955.1 KEGG: mlo:mlr9349 hypothetical protein; hypothetical protein 154930 5714276 Dshi_3747 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541958.1 153767 R 398580 CDS YP_001541959.1 159046287 5714277 complement(155050..155931) 1 NC_009955.1 PFAM: Resolvase domain; KEGG: rsp:RSP_2482 TonB-dependent receptor protein; resolvase domain-containing protein 155931 5714277 Dshi_3748 Dinoroseobacter shibae DFL 12 = DSM 16493 resolvase domain-containing protein YP_001541959.1 155050 R 398580 CDS YP_001541960.1 159046288 5714278 156052..156297 1 NC_009955.1 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 156297 5714278 Dshi_3749 Dinoroseobacter shibae DFL 12 = DSM 16493 CopG/Arc/MetJ family addiction module antidote protein YP_001541960.1 156052 D 398580 CDS YP_001541961.1 159046289 5714279 156284..156592 1 NC_009955.1 PFAM: plasmid stabilization system; KEGG: nwi:Nwi_3092 plasmid stabilization system; plasmid stabilization system protein 156592 5714279 Dshi_3750 Dinoroseobacter shibae DFL 12 = DSM 16493 plasmid stabilization system protein YP_001541961.1 156284 D 398580 CDS YP_001541962.1 159046290 5714280 complement(156596..157705) 1 NC_009955.1 PFAM: integrase family protein; KEGG: rsq:Rsph17025_4239 hypothetical protein; integrase family protein 157705 5714280 Dshi_3751 Dinoroseobacter shibae DFL 12 = DSM 16493 integrase family protein YP_001541962.1 156596 R 398580 CDS YP_001541963.1 159046291 5714281 157819..158703 1 NC_009955.1 PFAM: protein of unknown function DUF1403; KEGG: sit:TM1040_3403 protein of unknown function DUF1403; hypothetical protein 158703 5714281 Dshi_3752 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541963.1 157819 D 398580 CDS YP_001541964.1 159046292 5714282 158706..159323 1 NC_009955.1 PFAM: chromosome segregation and condensation protein ScpB; KEGG: rsq:Rsph17025_4232 hypothetical protein; chromosome segregation and condensation protein ScpB 159323 5714282 Dshi_3753 Dinoroseobacter shibae DFL 12 = DSM 16493 chromosome segregation and condensation protein ScpB YP_001541964.1 158706 D 398580 CDS YP_001541965.1 159046293 5714283 159373..159636 1 NC_009955.1 PFAM: WGR domain protein; KEGG: mlo:msl9076 hypothetical protein; WGR domain-containing protein 159636 5714283 Dshi_3754 Dinoroseobacter shibae DFL 12 = DSM 16493 WGR domain-containing protein YP_001541965.1 159373 D 398580 CDS YP_001541966.1 159046294 5714284 159706..160824 1 NC_009955.1 PFAM: filamentation induced by cAMP protein Fic; KEGG: atc:AGR_pAT_503 hypothetical protein; filamentation induced by cAMP protein fic 160824 5714284 Dshi_3755 Dinoroseobacter shibae DFL 12 = DSM 16493 filamentation induced by cAMP protein fic YP_001541966.1 159706 D 398580 CDS YP_001541967.1 159046295 5714285 complement(160821..161543) 1 NC_009955.1 hypothetical protein 161543 5714285 Dshi_3756 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541967.1 160821 R 398580 CDS YP_001541968.1 159046296 5714286 161654..162001 1 NC_009955.1 KEGG: pde:Pden_2059 transposase orfA IS5 family element; IS5 family transposase OrfA 162001 5714286 Dshi_3757 Dinoroseobacter shibae DFL 12 = DSM 16493 IS5 family transposase OrfA YP_001541968.1 161654 D 398580 CDS YP_001541969.1 159046297 5714287 162022..162411 1 NC_009955.1 PFAM: transposase IS4 family protein; KEGG: pde:Pden_3333 transposase, IS4 family protein; transposase IS4 family protein 162411 5714287 Dshi_3758 Dinoroseobacter shibae DFL 12 = DSM 16493 transposase IS4 family protein YP_001541969.1 162022 D 398580 CDS YP_001541970.1 159046298 5714288 162514..163542 1 NC_009955.1 PFAM: transposase IS116/IS110/IS902 family protein; KEGG: rru:Rru_A0676 transposase IS116/IS110/IS902; transposase IS116/IS110/IS902 family protein 163542 5714288 Dshi_3759 Dinoroseobacter shibae DFL 12 = DSM 16493 transposase IS116/IS110/IS902 family protein YP_001541970.1 162514 D 398580 CDS YP_001541971.1 159046299 5714289 complement(163896..164078) 1 NC_009955.1 KEGG: rsq:Rsph17025_2803 ubiquinol-cytochrome c reductase, iron-sulfur subunit; hypothetical protein 164078 5714289 Dshi_3760 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541971.1 163896 R 398580 CDS YP_001541972.1 159046300 5714290 164408..164770 1 NC_009955.1 KEGG: nha:Nham_4014 ISSpo6, transposase orf A; ISSpo6, transposase orf A 164770 5714290 Dshi_3761 Dinoroseobacter shibae DFL 12 = DSM 16493 ISSpo6, transposase orf A YP_001541972.1 164408 D 398580 CDS YP_001541973.1 159046301 5714291 164832..165362 1 NC_009955.1 KEGG: nha:Nham_4013 ISSpo6, transposase OrfB; ISSpo6, transposase OrfB 165362 5714291 Dshi_3762 Dinoroseobacter shibae DFL 12 = DSM 16493 ISSpo6, transposase OrfB YP_001541973.1 164832 D 398580 CDS YP_001541974.1 159046302 5714292 complement(165334..165762) 1 NC_009955.1 KEGG: sru:SRU_1982 hypothetical protein; hypothetical protein 165762 5714292 Dshi_3763 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541974.1 165334 R 398580 CDS YP_001541975.1 159046303 5714293 165838..166404 1 NC_009955.1 PFAM: cyclic nucleotide-binding; KEGG: reh:H16_A1838 transcriptional regulator, NNR like; cyclic nucleotide-binding protein 166404 5714293 Dshi_3764 Dinoroseobacter shibae DFL 12 = DSM 16493 cyclic nucleotide-binding protein YP_001541975.1 165838 D 398580 CDS YP_001541976.1 159046304 5714294 complement(166410..166862) 1 NC_009955.1 PFAM: protein of unknown function DUF411; KEGG: rde:RD1_2307 hypothetical protein; hypothetical protein 166862 5714294 Dshi_3765 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541976.1 166410 R 398580 CDS YP_001541977.1 159046305 5714295 complement(166777..167769) 1 NC_009955.1 PFAM: fatty acid hydroxylase; KEGG: aeh:Mlg_0287 sterol desaturase-like protein; fatty acid hydroxylase 167769 5714295 Dshi_3766 Dinoroseobacter shibae DFL 12 = DSM 16493 fatty acid hydroxylase YP_001541977.1 166777 R 398580 CDS YP_001541978.1 159046306 5714296 complement(167776..168762) 1 NC_009955.1 TIGRFAM: cation diffusion facilitator family transporter; PFAM: cation efflux protein; KEGG: dge:Dgeo_0215 cation diffusion facilitator family transporter; cation diffusion facilitator family transporter 168762 5714296 Dshi_3767 Dinoroseobacter shibae DFL 12 = DSM 16493 cation diffusion facilitator family transporter YP_001541978.1 167776 R 398580 CDS YP_001541979.1 159046307 5714297 complement(168764..169426) 1 NC_009955.1 PFAM: SNARE associated Golgi protein; KEGG: sil:SPOA0363 hypothetical protein; SNARE associated Golgi protein 169426 5714297 Dshi_3768 Dinoroseobacter shibae DFL 12 = DSM 16493 SNARE associated Golgi protein YP_001541979.1 168764 R 398580 CDS YP_001541980.1 159046308 5714298 complement(169430..169879) 1 NC_009955.1 KEGG: ddi:DDBDRAFT_0184550 hypothetical protein; hypothetical protein 169879 5714298 Dshi_3769 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541980.1 169430 R 398580 CDS YP_001541981.1 159046309 5714299 complement(170041..170478) 1 NC_009955.1 KEGG: maq:Maqu_0306 ion transport 2 domain protein; ion transport 2 domain-containing protein 170478 5714299 Dshi_3770 Dinoroseobacter shibae DFL 12 = DSM 16493 ion transport 2 domain-containing protein YP_001541981.1 170041 R 398580 CDS YP_001541982.1 159046310 5714300 complement(170567..171040) 1 NC_009955.1 KEGG: rde:RD1_1666 hypothetical protein; hypothetical protein 171040 5714300 Dshi_3771 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541982.1 170567 R 398580 CDS YP_001541983.1 159046311 5714301 171229..171951 1 NC_009955.1 PFAM: response regulator receiver; transcriptional regulator domain protein; KEGG: sil:SPOA0357 DNA-binding response regulator; two component transcriptional regulator 171951 5714301 Dshi_3772 Dinoroseobacter shibae DFL 12 = DSM 16493 two component transcriptional regulator YP_001541983.1 171229 D 398580 CDS YP_001541984.1 159046312 5714302 171951..173417 1 NC_009955.1 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 173417 5714302 Dshi_3773 Dinoroseobacter shibae DFL 12 = DSM 16493 integral membrane sensor signal transduction histidine kinase YP_001541984.1 171951 D 398580 CDS YP_001541985.1 159046313 5714303 173467..173658 1 NC_009955.1 KEGG: aeh:Mlg_1384 hypothetical protein; hypothetical protein 173658 5714303 Dshi_3774 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541985.1 173467 D 398580 CDS YP_001541986.1 159046314 5714304 173724..175724 1 NC_009955.1 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 175724 5714304 Dshi_3775 Dinoroseobacter shibae DFL 12 = DSM 16493 cytochrome c-type biogenesis protein CcmF YP_001541986.1 173724 D 398580 CDS YP_001541987.1 159046315 5714305 175733..176299 1 NC_009955.1 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 176299 5714305 Dshi_3776 Dinoroseobacter shibae DFL 12 = DSM 16493 periplasmic protein thiol--disulfide oxidoreductase DsbE YP_001541987.1 175733 D 398580 CDS YP_001541988.1 159046316 5714306 176296..176769 1 NC_009955.1 PFAM: cytochrome C biogenesis protein; KEGG: atc:AGR_C_1789 cytochrome C-type biogenesis protein; cytochrome C biogenesis protein 176769 5714306 Dshi_3777 Dinoroseobacter shibae DFL 12 = DSM 16493 cytochrome C biogenesis protein YP_001541988.1 176296 D 398580 CDS YP_001541989.1 159046317 5714307 176766..177917 1 NC_009955.1 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 177917 5714307 Dshi_3778 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541989.1 176766 D 398580 CDS YP_001541990.1 159046318 5714308 complement(177946..180075) 1 NC_009955.1 KEGG: mag:amb3382 thiol:disulfide interchange protein DsbD 1 precursor; thiol:disulfide interchange protein DsbD 1 precursor 180075 5714308 Dshi_3779 Dinoroseobacter shibae DFL 12 = DSM 16493 thiol:disulfide interchange protein DsbD 1 precursor YP_001541990.1 177946 R 398580 CDS YP_001541991.1 159046319 5714309 complement(180359..180661) 1 NC_009955.1 hypothetical protein 180661 5714309 Dshi_3780 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001541991.1 180359 R 398580 CDS YP_001541992.1 159046320 5714310 180817..181377 1 NC_009955.1 PFAM: ErfK/YbiS/YcfS/YnhG family protein; KEGG: sil:SPO2205 ErfK/YbiS/YcfS/YnhG family protein; ErfK/YbiS/YcfS/YnhG family protein 181377 5714310 Dshi_3781 Dinoroseobacter shibae DFL 12 = DSM 16493 ErfK/YbiS/YcfS/YnhG family protein YP_001541992.1 180817 D 398580 CDS YP_001541993.1 159046321 5714311 181406..181864 1 NC_009955.1 PFAM: cytochrome c class I; KEGG: sil:SPOA0359 cytochrome c family protein; cytochrome c class I 181864 5714311 Dshi_3782 Dinoroseobacter shibae DFL 12 = DSM 16493 cytochrome c class I YP_001541993.1 181406 D 398580 CDS YP_001541994.1 159046322 5714312 182234..182827 1 NC_009955.1 KEGG: ret:RHE_CH02511 putative cytochrome c-like protein; putative cytochrome c-like protein 182827 5714312 Dshi_3783 Dinoroseobacter shibae DFL 12 = DSM 16493 putative cytochrome c-like protein YP_001541994.1 182234 D 398580 CDS YP_001541995.1 159046323 5714313 182830..183747 1 NC_009955.1 KEGG: psa:PST_0453 cytochrome c family protein; gluconate 2-dehydrogenase (acceptor) 183747 5714313 Dshi_3784 Dinoroseobacter shibae DFL 12 = DSM 16493 gluconate 2-dehydrogenase (acceptor) YP_001541995.1 182830 D 398580 CDS YP_001541996.1 159046324 5714314 183791..185185 1 NC_009955.1 PFAM: multicopper oxidase type 1; multicopper oxidase type 2; multicopper oxidase type 3; KEGG: sil:SPOA0360 multicopper oxidase, putative; multicopper oxidase type 3 185185 5714314 Dshi_3785 Dinoroseobacter shibae DFL 12 = DSM 16493 multicopper oxidase type 3 YP_001541996.1 183791 D 398580 CDS YP_001541997.1 159046325 5714315 185182..185664 1 NC_009955.1 PFAM: cytochrome c class I; KEGG: sil:SPOA0361 cytochrome c family protein; cytochrome c class I 185664 5714315 Dshi_3786 Dinoroseobacter shibae DFL 12 = DSM 16493 cytochrome c class I YP_001541997.1 185182 D 398580 CDS YP_001541998.1 159046326 5714316 185666..186397 1 NC_009955.1 PFAM: DSBA oxidoreductase; KEGG: sil:SPOA0362 27kDa outer membrane protein; DSBA oxidoreductase 186397 5714316 Dshi_3787 Dinoroseobacter shibae DFL 12 = DSM 16493 DSBA oxidoreductase YP_001541998.1 185666 D 398580 CDS YP_001541999.1 159046327 5714317 complement(186440..186640) 1 NC_009955.1 PFAM: Heavy metal transport/detoxification protein; KEGG: pen:PSEEN0671 copper-binding protein; heavy metal transport/detoxification protein 186640 5714317 Dshi_3788 Dinoroseobacter shibae DFL 12 = DSM 16493 heavy metal transport/detoxification protein YP_001541999.1 186440 R 398580 CDS YP_001542000.1 159046328 5714318 186794..189304 1 NC_009955.1 TIGRFAM: ATPase, P-type (transporting), HAD superfamily, subfamily IC; copper-translocating P-type ATPase; heavy metal translocating P-type ATPase; PFAM: Haloacid dehalogenase domain protein hydrolase; Heavy metal transport/detoxification protein; E1-E2 ATPase-associated domain protein; KEGG: sil:SPO0794 copper-translocating P-type ATPase; heavy metal translocating P-type ATPase 189304 5714318 Dshi_3789 Dinoroseobacter shibae DFL 12 = DSM 16493 heavy metal translocating P-type ATPase YP_001542000.1 186794 D 398580 CDS YP_001542001.1 159046329 5714319 189317..189715 1 NC_009955.1 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 189715 5714319 Dshi_3790 Dinoroseobacter shibae DFL 12 = DSM 16493 MerR family transcriptional regulator YP_001542001.1 189317 D 398580 CDS YP_001542002.1 159046330 5714320 complement(189737..190501) 1 NC_009955.1 PFAM: glutaredoxin; KEGG: eli:ELI_04570 hypothetical protein; glutaredoxin 190501 5714320 Dshi_3791 Dinoroseobacter shibae DFL 12 = DSM 16493 glutaredoxin YP_001542002.1 189737 R 398580 CDS YP_001542003.1 159046332 5714460 167..1822 1 NC_009956.1 PFAM: extracellular solute-binding protein family 5; KEGG: rme:Rmet_1932 extracellular solute-binding protein, family 5; extracellular solute-binding protein 1822 5714460 Dshi_3792 Dinoroseobacter shibae DFL 12 = DSM 16493 extracellular solute-binding protein YP_001542003.1 167 D 398580 CDS YP_001542004.1 159046333 5714322 1905..2858 1 NC_009956.1 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 2858 5714322 Dshi_3793 Dinoroseobacter shibae DFL 12 = DSM 16493 binding-protein-dependent transport systems inner membrane component YP_001542004.1 1905 D 398580 CDS YP_001542005.1 159046334 5714323 2862..3749 1 NC_009956.1 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 3749 5714323 Dshi_3794 Dinoroseobacter shibae DFL 12 = DSM 16493 binding-protein-dependent transport systems inner membrane component YP_001542005.1 2862 D 398580 CDS YP_001542006.1 159046335 5714324 3746..4741 1 NC_009956.1 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 4741 5714324 Dshi_3795 Dinoroseobacter shibae DFL 12 = DSM 16493 oligopeptide/dipeptide ABC transporter, ATPase subunit YP_001542006.1 3746 D 398580 CDS YP_001542007.1 159046336 5714325 4738..5739 1 NC_009956.1 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 5739 5714325 Dshi_3796 Dinoroseobacter shibae DFL 12 = DSM 16493 oligopeptide/dipeptide ABC transporter, ATPase subunit YP_001542007.1 4738 D 398580 CDS YP_001542008.1 159046337 5714326 5736..6419 1 NC_009956.1 PFAM: Asp/Glu racemase; KEGG: rsq:Rsph17025_3633 hypothetical protein; Asp/Glu racemase 6419 5714326 Dshi_3797 Dinoroseobacter shibae DFL 12 = DSM 16493 Asp/Glu racemase YP_001542008.1 5736 D 398580 CDS YP_001542009.1 159046338 5714327 complement(6416..6958) 1 NC_009956.1 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 6958 5714327 Dshi_3798 Dinoroseobacter shibae DFL 12 = DSM 16493 NADH:ubiquinone oxidoreductase complex I intermediate-associated protein 30 YP_001542009.1 6416 R 398580 CDS YP_001542010.1 159046339 5714328 7084..7680 1 NC_009956.1 PFAM: HupE/UreJ protein; KEGG: bra:BRADO6336 conserved hypothetical protein; putative [NiFe]-hydrogenase/urease accessory HupE/UreJ family protein; HupE/UreJ protein 7680 5714328 Dshi_3799 Dinoroseobacter shibae DFL 12 = DSM 16493 HupE/UreJ protein YP_001542010.1 7084 D 398580 CDS YP_001542011.1 159046340 5714329 7685..8299 1 NC_009956.1 KEGG: bbt:BBta_1289 putative membrane protein of unknown function; hypothetical protein 8299 5714329 Dshi_3800 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542011.1 7685 D 398580 CDS YP_001542012.1 159046341 5714330 complement(8358..10535) 1 NC_009956.1 TIGRFAM: catalase/peroxidase HPI; PFAM: Haem peroxidase; KEGG: rde:RD1_2195 catalase-peroxidase; catalase/peroxidase HPI 10535 5714330 Dshi_3801 Dinoroseobacter shibae DFL 12 = DSM 16493 catalase/peroxidase HPI YP_001542012.1 8358 R 398580 CDS YP_001542013.1 159046342 5714331 10649..11578 1 NC_009956.1 PFAM: regulatory protein LysR; LysR substrate-binding; KEGG: rde:RD1_2194 oxidative stress transcription regulator, OxyR, putative; LysR family transcriptional regulator 11578 5714331 Dshi_3802 Dinoroseobacter shibae DFL 12 = DSM 16493 LysR family transcriptional regulator YP_001542013.1 10649 D 398580 CDS YP_001542014.1 159046343 5714332 11636..11827 1 NC_009956.1 hypothetical protein 11827 5714332 Dshi_3803 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542014.1 11636 D 398580 CDS YP_001542015.1 159046344 5714333 11802..12791 1 NC_009956.1 PFAM: regulatory protein LuxR; KEGG: rle:RL1113 putative transcriptional regulator; LuxR family transcriptional regulator 12791 5714333 Dshi_3804 Dinoroseobacter shibae DFL 12 = DSM 16493 LuxR family transcriptional regulator YP_001542015.1 11802 D 398580 CDS YP_001542016.1 159046345 5714334 12918..15827 1 NC_009956.1 subunit A of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; in S. meliloti it is known to be involved with K+; putative monovalent cation/H+ antiporter subunit A 15827 5714334 Dshi_3805 Dinoroseobacter shibae DFL 12 = DSM 16493 putative monovalent cation/H+ antiporter subunit A YP_001542016.1 12918 D 398580 CDS YP_001542017.1 159046346 5714335 15829..16182 1 NC_009956.1 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 16182 5714335 Dshi_3806 Dinoroseobacter shibae DFL 12 = DSM 16493 putative monovalent cation/H+ antiporter subunit C YP_001542017.1 15829 D 398580 CDS YP_001542018.1 159046347 5714336 16179..17699 1 NC_009956.1 subunit D of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; contains an oxidoreductase domain; catalyzes the transfer of electrons from NADH to ubiquinone; putative monovalent cation/H+ antiporter subunit D 17699 5714336 Dshi_3807 Dinoroseobacter shibae DFL 12 = DSM 16493 putative monovalent cation/H+ antiporter subunit D YP_001542018.1 16179 D 398580 CDS YP_001542019.1 159046348 5714337 17704..18195 1 NC_009956.1 subunit E of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; in S. meliloti it is known to be involved specifically with K+ transport; putative monovalent cation/H+ antiporter subunit E 18195 5714337 Dshi_3808 Dinoroseobacter shibae DFL 12 = DSM 16493 putative monovalent cation/H+ antiporter subunit E YP_001542019.1 17704 D 398580 CDS YP_001542020.1 159046349 5714338 18192..18461 1 NC_009956.1 PFAM: multiple resistance and pH regulation protein F; KEGG: jan:Jann_3719 multiple resistance and pH regulation protein F; multiple resistance and pH regulation protein F 18461 5714338 Dshi_3809 Dinoroseobacter shibae DFL 12 = DSM 16493 multiple resistance and pH regulation protein F YP_001542020.1 18192 D 398580 CDS YP_001542021.1 159046350 5714339 18469..18858 1 NC_009956.1 TIGRFAM: monovalent cation/proton antiporter, MnhG/PhaG subunit; PFAM: Na+/H+ antiporter subunit; KEGG: jan:Jann_3720 Na+/H+ antiporter subunit; monovalent cation/proton antiporter, MnhG/PhaG subunit 18858 5714339 Dshi_3810 Dinoroseobacter shibae DFL 12 = DSM 16493 monovalent cation/proton antiporter, MnhG/PhaG subunit YP_001542021.1 18469 D 398580 CDS YP_001542022.1 159046351 5714340 complement(18901..20142) 1 NC_009956.1 KEGG: sit:TM1040_2622 fumarylacetoacetase; TIGRFAM: fumarylacetoacetase; PFAM: fumarylacetoacetate (FAA) hydrolase; Domain of unknown function DUF1969; fumarylacetoacetase 20142 5714340 Dshi_3811 Dinoroseobacter shibae DFL 12 = DSM 16493 fumarylacetoacetase YP_001542022.1 18901 R 398580 CDS YP_001542023.1 159046352 5714341 complement(20139..21494) 1 NC_009956.1 An oxygenase that acts to open the ring of homogentisate formingmaleylacetoacetate as part of the catabolism of L-tyrosine and L-phenylalanine; homogentisate 1,2-dioxygenase 21494 5714341 Dshi_3812 Dinoroseobacter shibae DFL 12 = DSM 16493 homogentisate 1,2-dioxygenase YP_001542023.1 20139 R 398580 CDS YP_001542024.1 159046353 5714342 complement(21527..21970) 1 NC_009956.1 PFAM: regulatory protein MarR; KEGG: pde:Pden_3546 transcriptional regulator, MarR family; MarR family transcriptional regulator 21970 5714342 Dshi_3813 Dinoroseobacter shibae DFL 12 = DSM 16493 MarR family transcriptional regulator YP_001542024.1 21527 R 398580 CDS YP_001542025.1 159046354 5714343 22097..23047 1 NC_009956.1 PFAM: beta-lactamase domain protein; KEGG: sil:SPO0683 metallo-beta-lactamase family protein; beta-lactamase domain-containing protein 23047 5714343 Dshi_3814 Dinoroseobacter shibae DFL 12 = DSM 16493 beta-lactamase domain-containing protein YP_001542025.1 22097 D 398580 CDS YP_001542026.1 159046355 5714344 23077..24702 1 NC_009956.1 PFAM: monooxygenase FAD-binding; FAD dependent oxidoreductase; KEGG: sil:SPO0682 monooxygenase family protein; FAD-dependent oxidoreductase 24702 5714344 Dshi_3815 Dinoroseobacter shibae DFL 12 = DSM 16493 FAD-dependent oxidoreductase YP_001542026.1 23077 D 398580 CDS YP_001542027.1 159046356 5714345 24705..24890 1 NC_009956.1 KEGG: sil:SPO0681 hypothetical protein; hypothetical protein 24890 5714345 Dshi_3816 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542027.1 24705 D 398580 CDS YP_001542028.1 159046357 5714346 25016..26218 1 NC_009956.1 KEGG: sil:SPO0758 acetyl-CoA acetyltransferase; TIGRFAM: acetyl-CoA acetyltransferase; beta-ketoadipyl CoA thiolase; PFAM: Thiolase; beta-ketoadipyl CoA thiolase 26218 5714346 Dshi_3817 Dinoroseobacter shibae DFL 12 = DSM 16493 beta-ketoadipyl CoA thiolase YP_001542028.1 25016 D 398580 CDS YP_001542029.1 159046358 5714347 26236..27213 1 NC_009956.1 with PaaBCDE catalyzes the hydroxylation of phenylacetyl-CoA; phenylacetate-CoA oxygenase subunit PaaA 27213 paaA 5714347 paaA Dinoroseobacter shibae DFL 12 = DSM 16493 phenylacetate-CoA oxygenase subunit PaaA YP_001542029.1 26236 D 398580 CDS YP_001542030.1 159046359 5714348 27210..27542 1 NC_009956.1 with PaaBCDE catalyzes the hydroxylation of phenylacetyl-CoA; involved in phenylacetate degradation; phenylacetate-CoA oxygenase subunit PaaB 27542 paaB 5714348 paaB Dinoroseobacter shibae DFL 12 = DSM 16493 phenylacetate-CoA oxygenase subunit PaaB YP_001542030.1 27210 D 398580 CDS YP_001542031.1 159046360 5714349 27542..28309 1 NC_009956.1 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 28309 5714349 Dshi_3820 Dinoroseobacter shibae DFL 12 = DSM 16493 phenylacetate-CoA oxygenase, PaaI subunit YP_001542031.1 27542 D 398580 CDS YP_001542032.1 159046361 5714350 28311..28769 1 NC_009956.1 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 28769 5714350 Dshi_3821 Dinoroseobacter shibae DFL 12 = DSM 16493 phenylacetate-CoA oxygenase, PaaJ subunit YP_001542032.1 28311 D 398580 CDS YP_001542033.1 159046362 5714351 28782..29852 1 NC_009956.1 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 29852 5714351 Dshi_3822 Dinoroseobacter shibae DFL 12 = DSM 16493 phenylacetate-CoA oxygenase/reductase, PaaK subunit YP_001542033.1 28782 D 398580 CDS YP_001542034.1 159046363 5714352 complement(29860..30456) 1 NC_009956.1 PFAM: regulatory protein TetR; KEGG: sil:SPO0743 transcriptional regulator, TetR family; TetR family transcriptional regulator 30456 5714352 Dshi_3823 Dinoroseobacter shibae DFL 12 = DSM 16493 TetR family transcriptional regulator YP_001542034.1 29860 R 398580 CDS YP_001542035.1 159046364 5714353 complement(30459..31769) 1 NC_009956.1 TIGRFAM: phenylacetate-CoA ligase; KEGG: sil:SPO0742 phenylacetate-CoA ligase; phenylacetate-CoA ligase 31769 5714353 Dshi_3824 Dinoroseobacter shibae DFL 12 = DSM 16493 phenylacetate-CoA ligase YP_001542035.1 30459 R 398580 CDS YP_001542036.1 159046365 5714354 complement(31792..32217) 1 NC_009956.1 TIGRFAM: phenylacetic acid degradation protein PaaD; PFAM: thioesterase superfamily protein; KEGG: sil:SPO0741 phenylacetic acid degradation protein PaaD; phenylacetic acid degradation protein PaaD 32217 5714354 Dshi_3825 Dinoroseobacter shibae DFL 12 = DSM 16493 phenylacetic acid degradation protein PaaD YP_001542036.1 31792 R 398580 CDS YP_001542037.1 159046366 5714355 32430..34451 1 NC_009956.1 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 34451 5714355 Dshi_3826 Dinoroseobacter shibae DFL 12 = DSM 16493 3-hydroxyacyl-CoA dehydrogenase YP_001542037.1 32430 D 398580 CDS YP_001542038.1 159046367 5714356 34493..36529 1 NC_009956.1 catalyzes the ring cleavage reaction in phenylacetate degradation and the formation of 3-hydroxyacyl-CoA from crotonyl-CoA; bifunctional aldehyde dehydrogenase/enoyl-CoA hydratase 36529 5714356 Dshi_3827 Dinoroseobacter shibae DFL 12 = DSM 16493 bifunctional aldehyde dehydrogenase/enoyl-CoA hydratase YP_001542038.1 34493 D 398580 CDS YP_001542039.1 159046368 5714357 36567..37361 1 NC_009956.1 PFAM: PaaX domain protein; KEGG: sil:SPO0734 PaaX domain protein; PaaX family transcriptional regulator 37361 5714357 Dshi_3828 Dinoroseobacter shibae DFL 12 = DSM 16493 PaaX family transcriptional regulator YP_001542039.1 36567 D 398580 CDS YP_001542040.1 159046369 5714358 37489..37941 1 NC_009956.1 hypothetical protein 37941 5714358 Dshi_3829 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542040.1 37489 D 398580 CDS YP_001542041.1 159046370 5714359 38247..39386 1 NC_009956.1 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)(+)) 39386 5714359 Dshi_3830 Dinoroseobacter shibae DFL 12 = DSM 16493 glycerol-3-phosphate dehydrogenase (NAD(P)(+)) YP_001542041.1 38247 D 398580 CDS YP_001542042.1 159046371 5714360 39383..40162 1 NC_009956.1 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 40162 5714360 Dshi_3831 Dinoroseobacter shibae DFL 12 = DSM 16493 sucrose-6F-phosphate phosphohydrolase YP_001542042.1 39383 D 398580 CDS YP_001542043.1 159046372 5714361 40174..41664 1 NC_009956.1 KEGG: tbd:Tbd_2626 glucosyl-glycerol-phosphate synthase; TIGRFAM: glucosylglycerol-phosphate synthase; PFAM: glycosyl transferase family 20; glucosylglycerol-phosphate synthase 41664 5714361 Dshi_3832 Dinoroseobacter shibae DFL 12 = DSM 16493 glucosylglycerol-phosphate synthase YP_001542043.1 40174 D 398580 CDS YP_001542044.1 159046373 5714362 complement(41763..43181) 1 NC_009956.1 PFAM: phospholipase D/Transphosphatidylase; KEGG: rde:RD1_2477 phospholipase D, putative; phospholipase D/transphosphatidylase 43181 5714362 Dshi_3833 Dinoroseobacter shibae DFL 12 = DSM 16493 phospholipase D/transphosphatidylase YP_001542044.1 41763 R 398580 CDS YP_001542045.1 159046374 5714363 complement(43171..44907) 1 NC_009956.1 PFAM: histidine kinase HAMP region domain protein; histidine kinase dimerisation/phosphoacceptor; KEGG: jan:Jann_3564 signal transduction histidine kinase; signal transduction histidine kinase 44907 5714363 Dshi_3834 Dinoroseobacter shibae DFL 12 = DSM 16493 signal transduction histidine kinase YP_001542045.1 43171 R 398580 CDS YP_001542046.1 159046375 5714364 complement(44882..45445) 1 NC_009956.1 Bacteria have multiple sigma factors which are active under specific conditions; the sigma factor binds with the catalytic core of RNA polymerase to produce the holoenzyme and directs bacterial core RNA polymerase to specific promoter elements to initiate transcription; RNA polymerase sigma factor 45445 5714364 Dshi_3835 Dinoroseobacter shibae DFL 12 = DSM 16493 RNA polymerase sigma factor YP_001542046.1 44882 R 398580 CDS YP_001542047.1 159046376 5714365 complement(45442..45621) 1 NC_009956.1 hypothetical protein 45621 5714365 Dshi_3836 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542047.1 45442 R 398580 CDS YP_001542048.1 159046377 5714366 45758..46573 1 NC_009956.1 in Caulobacter crescentus, CC3477 is differentially expressed in minimal salts media with glucose as compared to complex media; two-component response regulator 46573 5714366 Dshi_3837 Dinoroseobacter shibae DFL 12 = DSM 16493 two-component response regulator YP_001542048.1 45758 D 398580 CDS YP_001542049.1 159046378 5714367 complement(46686..48080) 1 NC_009956.1 KEGG: rde:RD1_4211 hypothetical protein; hypothetical protein 48080 5714367 Dshi_3838 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542049.1 46686 R 398580 CDS YP_001542050.1 159046379 5714368 complement(48216..48713) 1 NC_009956.1 PFAM: Ferritin Dps family protein; KEGG: sit:TM1040_2721 ferritin and Dps; Ferritin Dps family protein 48713 5714368 Dshi_3839 Dinoroseobacter shibae DFL 12 = DSM 16493 Ferritin Dps family protein YP_001542050.1 48216 R 398580 CDS YP_001542051.1 159046380 5714369 complement(48774..50414) 1 NC_009956.1 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 50414 5714369 Dshi_3840 Dinoroseobacter shibae DFL 12 = DSM 16493 thiamine pyrophosphate binding domain-containing protein YP_001542051.1 48774 R 398580 CDS YP_001542052.1 159046381 5714370 complement(50414..51757) 1 NC_009956.1 converts 2-oxoglutarate to glutamate; in Escherichia coli this enzyme plays a role in glutamate synthesis when the cell is under energy restriction; uses NADPH; forms a homohexamer; glutamate dehydrogenase 51757 5714370 Dshi_3841 Dinoroseobacter shibae DFL 12 = DSM 16493 glutamate dehydrogenase YP_001542052.1 50414 R 398580 CDS YP_001542053.1 159046382 5714371 complement(51857..52027) 1 NC_009956.1 PFAM: protein of unknown function DUF1328; KEGG: rso:RS02225 probable transmembrane protein; hypothetical protein 52027 5714371 Dshi_3842 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542053.1 51857 R 398580 CDS YP_001542054.1 159046383 5714372 complement(52170..52586) 1 NC_009956.1 hypothetical protein 52586 5714372 Dshi_3843 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542054.1 52170 R 398580 CDS YP_001542055.1 159046384 5714373 52616..53344 1 NC_009956.1 PFAM: cyclic nucleotide-binding; KEGG: rde:RD1_2451 nitrogen fixation regulatory protein FixK , putative; cyclic nucleotide-binding protein 53344 5714373 Dshi_3844 Dinoroseobacter shibae DFL 12 = DSM 16493 cyclic nucleotide-binding protein YP_001542055.1 52616 D 398580 CDS YP_001542056.1 159046385 5714376 54662..55786 1 NC_009956.1 SMART: ParB domain protein nuclease; KEGG: pde:Pden_2912 replication protein, putative; nuclease 55786 5714376 Dshi_3847 Dinoroseobacter shibae DFL 12 = DSM 16493 nuclease YP_001542056.1 54662 D 398580 CDS YP_001542057.1 159046386 5714377 complement(55886..56080) 1 NC_009956.1 KEGG: rsh:Rsph17029_2919 hypothetical protein; hypothetical protein 56080 5714377 Dshi_3848 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542057.1 55886 R 398580 CDS YP_001542058.1 159046387 5714378 complement(56108..56320) 1 NC_009956.1 KEGG: jan:Jann_2179 hypothetical protein; hypothetical protein 56320 5714378 Dshi_3849 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542058.1 56108 R 398580 CDS YP_001542059.1 159046388 5714379 complement(56328..56588) 1 NC_009956.1 KEGG: gfo:GFO_0298 hypothetical protein; hypothetical protein 56588 5714379 Dshi_3850 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542059.1 56328 R 398580 CDS YP_001542060.1 159046389 5714380 complement(56652..56915) 1 NC_009956.1 hypothetical protein 56915 5714380 Dshi_3851 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542060.1 56652 R 398580 CDS YP_001542061.1 159046390 5714381 complement(57076..58143) 1 NC_009956.1 KEGG: rsq:Rsph17025_2741 hypothetical protein; hypothetical protein 58143 5714381 Dshi_3852 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542061.1 57076 R 398580 CDS YP_001542062.1 159046391 5714382 58283..59263 1 NC_009956.1 PFAM: Resolvase domain; KEGG: rsp:RSP_2482 TonB-dependent receptor protein; resolvase domain-containing protein 59263 5714382 Dshi_3853 Dinoroseobacter shibae DFL 12 = DSM 16493 resolvase domain-containing protein YP_001542062.1 58283 D 398580 CDS YP_001542063.1 159046392 5714383 complement(59311..60357) 1 NC_009956.1 KEGG: sit:TM1040_3772 RepA; hypothetical protein 60357 5714383 Dshi_3854 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542063.1 59311 R 398580 CDS YP_001542064.1 159046393 5714384 60736..62127 1 NC_009956.1 PFAM: Cobyrinic acid ac-diamide synthase; KEGG: sit:TM1040_3773 cobyrinic acid a,c-diamide synthase; cobyrinic acid ac-diamide synthase 62127 5714384 Dshi_3855 Dinoroseobacter shibae DFL 12 = DSM 16493 cobyrinic acid ac-diamide synthase YP_001542064.1 60736 D 398580 CDS YP_001542065.1 159046394 5714385 62250..63425 1 NC_009956.1 SMART: ParB domain protein nuclease; KEGG: rsp:RSP_7084 ParB-like nuclease; nuclease 63425 5714385 Dshi_3856 Dinoroseobacter shibae DFL 12 = DSM 16493 nuclease YP_001542065.1 62250 D 398580 CDS YP_001542066.1 159046395 5714386 63834..65726 1 NC_009956.1 PFAM: NAD-dependent epimerase/dehydratase; short-chain dehydrogenase/reductase SDR; 3-beta hydroxysteroid dehydrogenase/isomerase; polysaccharide biosynthesis protein CapD; dTDP-4-dehydrorhamnose reductase; Male sterility domain; KEGG: rsh:Rsph17029_2850 polysaccharide biosynthesis protein CapD; polysaccharide biosynthesis protein CapD 65726 5714386 Dshi_3857 Dinoroseobacter shibae DFL 12 = DSM 16493 polysaccharide biosynthesis protein CapD YP_001542066.1 63834 D 398580 CDS YP_001542067.1 159046396 5714387 66007..68247 1 NC_009956.1 PFAM: protein of unknown function DUF940 membrane lipoprotein putative; KEGG: rsp:RSP_1187 hypothetical protein; hypothetical protein 68247 5714387 Dshi_3858 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542067.1 66007 D 398580 CDS YP_001542068.1 159046397 5714388 68244..69005 1 NC_009956.1 KEGG: rsh:Rsph17029_2848 hypothetical protein; hypothetical protein 69005 5714388 Dshi_3859 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542068.1 68244 D 398580 CDS YP_001542069.1 159046398 5714389 69139..69381 1 NC_009956.1 hypothetical protein 69381 5714389 Dshi_3860 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542069.1 69139 D 398580 CDS YP_001542070.1 159046399 5714390 69562..70758 1 NC_009956.1 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 70758 5714390 Dshi_3861 Dinoroseobacter shibae DFL 12 = DSM 16493 UDP-glucose 6-dehydrogenase YP_001542070.1 69562 D 398580 CDS YP_001542071.1 159046400 5714391 70763..72700 1 NC_009956.1 hypothetical protein 72700 5714391 Dshi_3862 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542071.1 70763 D 398580 CDS YP_001542072.1 159046401 5714392 complement(72755..73885) 1 NC_009956.1 KEGG: ter:Tery_3237 hypothetical protein; hypothetical protein 73885 5714392 Dshi_3863 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542072.1 72755 R 398580 CDS YP_001542073.1 159046402 5714393 complement(73902..74681) 1 NC_009956.1 PFAM: sulfotransferase; KEGG: rsh:Rsph17029_4075 sulfotransferase; sulfotransferase 74681 5714393 Dshi_3864 Dinoroseobacter shibae DFL 12 = DSM 16493 sulfotransferase YP_001542073.1 73902 R 398580 CDS YP_001542074.1 159046403 5714394 complement(74804..75793) 1 NC_009956.1 KEGG: ter:Tery_4433 hypothetical protein; hypothetical protein 75793 5714394 Dshi_3865 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542074.1 74804 R 398580 CDS YP_001542075.1 159046404 5714395 complement(75905..79813) 1 NC_009956.1 PFAM: glycosyl transferase group 1; KEGG: jan:Jann_4244 glycosyl transferase, group 1; glycosyl transferase group 1 79813 5714395 Dshi_3866 Dinoroseobacter shibae DFL 12 = DSM 16493 glycosyl transferase group 1 YP_001542075.1 75905 R 398580 CDS YP_001542076.1 159046405 5714396 complement(79818..80708) 1 NC_009956.1 KEGG: nar:Saro_0725 chromosome segregation ATPases-like; hypothetical protein 80708 5714396 Dshi_3867 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542076.1 79818 R 398580 CDS YP_001542077.1 159046406 5714397 complement(80804..81883) 1 NC_009956.1 TIGRFAM: UDP-glucose 4-epimerase; PFAM: NAD-dependent epimerase/dehydratase; short-chain dehydrogenase/reductase SDR; 3-beta hydroxysteroid dehydrogenase/isomerase; polysaccharide biosynthesis protein CapD; Male sterility domain; KEGG: mpt:Mpe_A1914 UDP-glucose 4-epimerase; UDP-glucose 4-epimerase 81883 5714397 Dshi_3868 Dinoroseobacter shibae DFL 12 = DSM 16493 UDP-glucose 4-epimerase YP_001542077.1 80804 R 398580 CDS YP_001542078.1 159046407 5714398 complement(81946..83121) 1 NC_009956.1 KEGG: ter:Tery_3237 hypothetical protein; hypothetical protein 83121 5714398 Dshi_3869 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542078.1 81946 R 398580 CDS YP_001542079.1 159046408 5714399 complement(83556..84359) 1 NC_009956.1 PFAM: peptidase S1 and S6 chymotrypsin/Hap; KEGG: rru:Rru_A0562 peptidase S1 and S6, chymotrypsin/Hap; peptidase S1 and S6 chymotrypsin/Hap 84359 5714399 Dshi_3870 Dinoroseobacter shibae DFL 12 = DSM 16493 peptidase S1 and S6 chymotrypsin/Hap YP_001542079.1 83556 R 398580 CDS YP_001542080.1 159046409 5714400 84768..88262 1 NC_009956.1 KEGG: pde:Pden_2124 hemolysin-type calcium-binding region; RTX toxins and related Ca2+-binding protein-like protein 88262 5714400 Dshi_3871 Dinoroseobacter shibae DFL 12 = DSM 16493 RTX toxins and related Ca2+-binding protein-like protein YP_001542080.1 84768 D 398580 CDS YP_001542081.1 159046410 5714401 88354..94041 1 NC_009956.1 PFAM: Hemolysin-type calcium-binding region; KEGG: rde:RD1_A0054 iron-regulated protein FrpC, putative; hemolysin-type calcium-binding region 94041 5714401 Dshi_3872 Dinoroseobacter shibae DFL 12 = DSM 16493 hemolysin-type calcium-binding region YP_001542081.1 88354 D 398580 CDS YP_001542082.1 159046411 5714402 complement(94097..94681) 1 NC_009956.1 KEGG: sil:SPOA0441 hypothetical protein; hypothetical protein 94681 5714402 Dshi_3873 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542082.1 94097 R 398580 CDS YP_001542083.1 159046412 5714403 complement(94737..95561) 1 NC_009956.1 KEGG: art:Arth_4384 ATP-binding protein; ATP-binding protein 95561 5714403 Dshi_3874 Dinoroseobacter shibae DFL 12 = DSM 16493 ATP-binding protein YP_001542083.1 94737 R 398580 CDS YP_001542084.1 159046413 5714404 complement(95558..97051) 1 NC_009956.1 PFAM: Integrase catalytic region; Transposase-like Mu; KEGG: art:Arth_4385 integrase, catalytic region; integrase catalytic region 97051 5714404 Dshi_3875 Dinoroseobacter shibae DFL 12 = DSM 16493 integrase catalytic region YP_001542084.1 95558 R 398580 CDS YP_001542085.1 159046414 5714405 97190..97789 1 NC_009956.1 PFAM: Resolvase domain; Resolvase helix-turn-helix domain protein; KEGG: gox:GOX2646 DNA integration/recombination/invertion protein; resolvase domain-containing protein 97789 5714405 Dshi_3876 Dinoroseobacter shibae DFL 12 = DSM 16493 resolvase domain-containing protein YP_001542085.1 97190 D 398580 CDS YP_001542086.1 159046415 5714406 98310..100118 1 NC_009956.1 required for the synthesis of the hydromethylpyrimidine moiety of thiamine; thiamine biosynthesis protein ThiC 100118 5714406 Dshi_3877 Dinoroseobacter shibae DFL 12 = DSM 16493 thiamine biosynthesis protein ThiC YP_001542086.1 98310 D 398580 CDS YP_001542087.1 159046416 5714407 complement(100522..101904) 1 NC_009956.1 PFAM: transposase IS4 family protein; KEGG: rde:RD1_3444 transposase, putative; transposase IS4 family protein 101904 5714407 Dshi_3878 Dinoroseobacter shibae DFL 12 = DSM 16493 transposase IS4 family protein YP_001542087.1 100522 R 398580 CDS YP_001542088.1 159046417 5714408 102305..103117 1 NC_009956.1 hypothetical protein 103117 5714408 Dshi_3879 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542088.1 102305 D 398580 CDS YP_001542089.1 159046418 5714409 103401..103925 1 NC_009956.1 hypothetical protein 103925 5714409 Dshi_3880 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542089.1 103401 D 398580 CDS YP_001542090.1 159046419 5714410 104842..105309 1 NC_009956.1 hypothetical protein 105309 5714410 Dshi_3881 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542090.1 104842 D 398580 CDS YP_001542091.1 159046420 5714411 105261..105971 1 NC_009956.1 KEGG: rde:RD1_A0058 transposase, putative; transposase, putative 105971 5714411 Dshi_3882 Dinoroseobacter shibae DFL 12 = DSM 16493 transposase, putative YP_001542091.1 105261 D 398580 CDS YP_001542092.1 159046421 5714412 complement(106070..106648) 1 NC_009956.1 KEGG: pat:Patl_4083 hypothetical protein; hypothetical protein 106648 5714412 Dshi_3883 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542092.1 106070 R 398580 CDS YP_001542093.1 159046422 5714413 complement(106635..108044) 1 NC_009956.1 PFAM: multi antimicrobial extrusion protein MatE; polysaccharide biosynthesis protein; KEGG: rde:RD1_2470 MatE efflux family protein; multi anti extrusion protein MatE 108044 5714413 Dshi_3884 Dinoroseobacter shibae DFL 12 = DSM 16493 multi anti extrusion protein MatE YP_001542093.1 106635 R 398580 CDS YP_001542094.1 159046423 5714414 108221..109795 1 NC_009956.1 PFAM: phospholipase D/Transphosphatidylase; KEGG: rde:RD1_2477 phospholipase D, putative; phospholipase D/transphosphatidylase 109795 5714414 Dshi_3885 Dinoroseobacter shibae DFL 12 = DSM 16493 phospholipase D/transphosphatidylase YP_001542094.1 108221 D 398580 CDS YP_001542095.1 159046424 5714415 110041..110658 1 NC_009956.1 KEGG: rpd:RPD_2508 hypothetical protein; hypothetical protein 110658 5714415 Dshi_3886 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542095.1 110041 D 398580 CDS YP_001542096.1 159046425 5714416 complement(110663..111094) 1 NC_009956.1 PFAM: cytochrome c class I; KEGG: psa:PST_1611 cytochrome c6; cytochrome c class I 111094 5714416 Dshi_3887 Dinoroseobacter shibae DFL 12 = DSM 16493 cytochrome c class I YP_001542096.1 110663 R 398580 CDS YP_001542097.1 159046426 5714417 complement(111091..112716) 1 NC_009956.1 PFAM: amine oxidase; KEGG: psa:PST_1610 flavin monoamine oxidase-related protein; L-amino-acid oxidase 112716 5714417 Dshi_3888 Dinoroseobacter shibae DFL 12 = DSM 16493 L-amino-acid oxidase YP_001542097.1 111091 R 398580 CDS YP_001542098.1 159046427 5714418 complement(112739..113458) 1 NC_009956.1 KEGG: nwi:Nwi_2311 hypothetical protein; hypothetical protein 113458 5714418 Dshi_3889 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542098.1 112739 R 398580 CDS YP_001542099.1 159046428 5714419 complement(113475..113804) 1 NC_009956.1 hypothetical protein 113804 5714419 Dshi_3890 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542099.1 113475 R 398580 CDS YP_001542100.1 159046429 5714420 complement(113801..116362) 1 NC_009956.1 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 116362 5714420 Dshi_3891 Dinoroseobacter shibae DFL 12 = DSM 16493 cytochrome c oxidase subunit I type YP_001542100.1 113801 R 398580 CDS YP_001542101.1 159046430 5714421 complement(116359..117396) 1 NC_009956.1 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 117396 5714421 Dshi_3892 Dinoroseobacter shibae DFL 12 = DSM 16493 cytochrome c oxidase subunit II YP_001542101.1 116359 R 398580 CDS YP_001542102.1 159046431 5714422 complement(117396..117893) 1 NC_009956.1 PFAM: cytochrome c class I; KEGG: eba:ebA4540 cytochrome c1, probably related to cytocrome c oxidase function; cytochrome c class I 117893 5714422 Dshi_3893 Dinoroseobacter shibae DFL 12 = DSM 16493 cytochrome c class I YP_001542102.1 117396 R 398580 CDS YP_001542103.1 159046432 5714423 complement(117901..118716) 1 NC_009956.1 KEGG: psa:PST_2844 cytochrome c type protein; cytochrome c553-like protein 118716 5714423 Dshi_3894 Dinoroseobacter shibae DFL 12 = DSM 16493 cytochrome c553-like protein YP_001542103.1 117901 R 398580 CDS YP_001542104.1 159046433 5714424 complement(118732..120516) 1 NC_009956.1 PFAM: FAD dependent oxidoreductase; KEGG: nha:Nham_4244 putative gluconate dehydrogenase; gluconate 2-dehydrogenase (acceptor) 120516 5714424 Dshi_3895 Dinoroseobacter shibae DFL 12 = DSM 16493 gluconate 2-dehydrogenase (acceptor) YP_001542104.1 118732 R 398580 CDS YP_001542105.1 159046434 5714425 complement(120509..121231) 1 NC_009956.1 KEGG: bvi:Bcep1808_4793 hypothetical protein; hypothetical protein 121231 5714425 Dshi_3896 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542105.1 120509 R 398580 CDS YP_001542106.1 159046435 5714426 complement(121309..121845) 1 NC_009956.1 PFAM: MgtC/SapB transporter; KEGG: mes:Meso_3446 MgtC/SapB transporter; MgtC/SapB transporter 121845 5714426 Dshi_3897 Dinoroseobacter shibae DFL 12 = DSM 16493 MgtC/SapB transporter YP_001542106.1 121309 R 398580 CDS YP_001542107.1 159046436 5714427 complement(121824..123404) 1 NC_009956.1 PFAM: alpha amylase catalytic region; SMART: alpha amylase catalytic sub domain; KEGG: xcb:XC_1642 alpha-glucosidase; alpha amylase 123404 5714427 Dshi_3898 Dinoroseobacter shibae DFL 12 = DSM 16493 alpha amylase YP_001542107.1 121824 R 398580 CDS YP_001542108.1 159046437 5714428 complement(123407..124261) 1 NC_009956.1 PFAM: short-chain dehydrogenase/reductase SDR; KR domain protein; KEGG: rru:Rru_A3667 short-chain dehydrogenase/reductase SDR; short-chain dehydrogenase/reductase SDR 124261 5714428 Dshi_3899 Dinoroseobacter shibae DFL 12 = DSM 16493 short-chain dehydrogenase/reductase SDR YP_001542108.1 123407 R 398580 CDS YP_001542109.1 159046438 5714429 complement(124299..125282) 1 NC_009956.1 PFAM: short-chain dehydrogenase/reductase SDR; KR domain protein; KEGG: psa:PST_3887 probable short-chain dehydrogenase; short-chain dehydrogenase/reductase SDR 125282 5714429 Dshi_3900 Dinoroseobacter shibae DFL 12 = DSM 16493 short-chain dehydrogenase/reductase SDR YP_001542109.1 124299 R 398580 CDS YP_001542110.1 159046439 5714430 complement(125343..128468) 1 NC_009956.1 PFAM: acriflavin resistance protein; KEGG: sru:SRU_0473 multidrug efflux transporter, AcrB/AcrD/AcrF family; acriflavin resistance protein 128468 5714430 Dshi_3901 Dinoroseobacter shibae DFL 12 = DSM 16493 acriflavin resistance protein YP_001542110.1 125343 R 398580 CDS YP_001542111.1 159046440 5714431 complement(128472..129650) 1 NC_009956.1 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 129650 5714431 Dshi_3902 Dinoroseobacter shibae DFL 12 = DSM 16493 RND family efflux transporter MFP subunit YP_001542111.1 128472 R 398580 CDS YP_001542112.1 159046441 5714432 complement(129663..130460) 1 NC_009956.1 PFAM: short-chain dehydrogenase/reductase SDR; KR domain protein; KEGG: cmi:CMM_2063 short chain dehydrogenase/oxidoreductase; short-chain dehydrogenase/reductase SDR 130460 5714432 Dshi_3903 Dinoroseobacter shibae DFL 12 = DSM 16493 short-chain dehydrogenase/reductase SDR YP_001542112.1 129663 R 398580 CDS YP_001542113.1 159046442 5714433 complement(130573..132153) 1 NC_009956.1 TIGRFAM: SSS sodium solute transporter superfamily; PFAM: Na+/solute symporter; KEGG: sru:SRU_0355 sodium/glucose cotransporter 2; SSS family solute/sodium (Na+) symporter 132153 5714433 Dshi_3904 Dinoroseobacter shibae DFL 12 = DSM 16493 SSS family solute/sodium (Na+) symporter YP_001542113.1 130573 R 398580 CDS YP_001542114.1 159046443 5714434 complement(132871..133992) 1 NC_009956.1 PFAM: MscS Mechanosensitive ion channel; KEGG: bra:BRADO5370 conserved hypothetical protein; putative membrane protein; putative small-conductance mechanosensitive channel; MscS mechanosensitive ion channel 133992 5714434 Dshi_3905 Dinoroseobacter shibae DFL 12 = DSM 16493 MscS mechanosensitive ion channel YP_001542114.1 132871 R 398580 CDS YP_001542115.1 159046444 5714435 complement(133997..135598) 1 NC_009956.1 TIGRFAM: SSS sodium solute transporter superfamily; PFAM: Na+/solute symporter; KEGG: sru:SRU_0355 sodium/glucose cotransporter 2; SSS family solute/sodium (Na+) symporter 135598 5714435 Dshi_3906 Dinoroseobacter shibae DFL 12 = DSM 16493 SSS family solute/sodium (Na+) symporter YP_001542115.1 133997 R 398580 CDS YP_001542116.1 159046445 5714436 complement(135680..136705) 1 NC_009956.1 PFAM: sodium/calcium exchanger membrane region; KEGG: eli:ELI_06950 cation antiporter (Na+/Ca2+); sodium/calcium exchanger membrane region 136705 5714436 Dshi_3907 Dinoroseobacter shibae DFL 12 = DSM 16493 sodium/calcium exchanger membrane region YP_001542116.1 135680 R 398580 CDS YP_001542117.1 159046446 5714437 136970..138121 1 NC_009956.1 PFAM: protein of unknown function UPF0118; KEGG: cps:CPS_2311 hypothetical protein; hypothetical protein 138121 5714437 Dshi_3908 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542117.1 136970 D 398580 CDS YP_001542118.1 159046447 5714438 complement(138124..138396) 1 NC_009956.1 KEGG: tcx:Tcr_1058 hypothetical protein; hypothetical protein 138396 5714438 Dshi_3909 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542118.1 138124 R 398580 CDS YP_001542119.1 159046448 5714439 complement(138528..138908) 1 NC_009956.1 hypothetical protein 138908 5714439 Dshi_3910 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542119.1 138528 R 398580 CDS YP_001542120.1 159046449 5714440 139092..140549 1 NC_009956.1 KEGG: rpe:RPE_2181 protease Do; TIGRFAM: protease Do; PFAM: peptidase S1 and S6 chymotrypsin/Hap; PDZ/DHR/GLGF domain protein; protease Do 140549 5714440 Dshi_3911 Dinoroseobacter shibae DFL 12 = DSM 16493 protease Do YP_001542120.1 139092 D 398580 CDS YP_001542121.1 159046450 5714441 complement(140779..141261) 1 NC_009956.1 PFAM: Ferritin Dps family protein; KEGG: pcr:Pcryo_0735 ferritin and Dps; Ferritin Dps family protein 141261 5714441 Dshi_3912 Dinoroseobacter shibae DFL 12 = DSM 16493 Ferritin Dps family protein YP_001542121.1 140779 R 398580 CDS YP_001542122.1 159046451 5714442 complement(141452..142111) 1 NC_009956.1 PFAM: TrkA-N domain protein; TrkA-C domain protein; KEGG: rde:RD1_2464 trk potassium uptake system protein; TrkA domain-containing protein 142111 5714442 Dshi_3913 Dinoroseobacter shibae DFL 12 = DSM 16493 TrkA domain-containing protein YP_001542122.1 141452 R 398580 CDS YP_001542123.1 159046452 5714443 complement(142116..143591) 1 NC_009956.1 PFAM: cation transporter; KEGG: rde:RD1_2465 trk potassium uptake system protein, transmembrane component; cation transporter 143591 5714443 Dshi_3914 Dinoroseobacter shibae DFL 12 = DSM 16493 cation transporter YP_001542123.1 142116 R 398580 CDS YP_001542124.1 159046453 5714444 143779..143946 1 NC_009956.1 PFAM: protein of unknown function UPF0057; KEGG: rxy:Rxyl_0694 protein of unknown function UPF0057; hypothetical protein 143946 5714444 Dshi_3915 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542124.1 143779 D 398580 CDS YP_001542125.1 159046454 5714445 143909..144319 1 NC_009956.1 KEGG: rde:RD1_2473 hypothetical protein; hypothetical protein 144319 5714445 Dshi_3916 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542125.1 143909 D 398580 CDS YP_001542126.1 159046455 5714446 144427..144894 1 NC_009956.1 KEGG: mlo:mlr3233 hypothetical protein; hypothetical protein 144894 5714446 Dshi_3917 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542126.1 144427 D 398580 CDS YP_001542127.1 159046456 5714447 complement(145009..145482) 1 NC_009956.1 KEGG: sde:Sde_3869 hypothetical protein; hypothetical protein 145482 5714447 Dshi_3918 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542127.1 145009 R 398580 CDS YP_001542128.1 159046457 5714448 145798..146166 1 NC_009956.1 PFAM: transposase IS3/IS911 family protein; KEGG: xac:XAC4322 ISxac3 transposase; transposase IS3/IS911 family protein 146166 5714448 Dshi_3919 Dinoroseobacter shibae DFL 12 = DSM 16493 transposase IS3/IS911 family protein YP_001542128.1 145798 D 398580 CDS YP_001542129.1 159046458 5714449 146299..146496 1 NC_009956.1 KEGG: ajs:Ajs_1844 integrase, catalytic region; integrase, catalytic region 146496 5714449 Dshi_3920 Dinoroseobacter shibae DFL 12 = DSM 16493 integrase, catalytic region YP_001542129.1 146299 D 398580 CDS YP_001542130.1 159046459 5714450 146523..146837 1 NC_009956.1 PFAM: Integrase catalytic region; KEGG: sfv:SFV_0556 ISEhe3 orfB; integrase catalytic region 146837 5714450 Dshi_3921 Dinoroseobacter shibae DFL 12 = DSM 16493 integrase catalytic region YP_001542130.1 146523 D 398580 CDS YP_001542131.1 159046460 5714451 147270..148109 1 NC_009956.1 KEGG: rde:RD1_2466 transport protein, putative; transport protein, putative 148109 5714451 Dshi_3922 Dinoroseobacter shibae DFL 12 = DSM 16493 transport protein, putative YP_001542131.1 147270 D 398580 CDS YP_001542132.1 159046461 5714452 complement(148170..148334) 1 NC_009956.1 KEGG: rde:RD1_2471 hypothetical protein; hypothetical protein 148334 5714452 Dshi_3923 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542132.1 148170 R 398580 CDS YP_001542133.1 159046462 5714453 complement(148360..148554) 1 NC_009956.1 hypothetical protein 148554 5714453 Dshi_3924 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542133.1 148360 R 398580 CDS YP_001542134.1 159046463 5714454 complement(148620..149342) 1 NC_009956.1 PFAM: glutamine amidotransferase class-I; peptidase C26; KEGG: csa:Csal_1160 peptidase C26; peptidase C26 149342 5714454 Dshi_3925 Dinoroseobacter shibae DFL 12 = DSM 16493 peptidase C26 YP_001542134.1 148620 R 398580 CDS YP_001542135.1 159046464 5714455 complement(149344..150306) 1 NC_009956.1 KEGG: ilo:IL1070 hypothetical protein; hypothetical protein 150306 5714455 Dshi_3926 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542135.1 149344 R 398580 CDS YP_001542136.1 159046465 5714456 complement(150369..150764) 1 NC_009956.1 KEGG: pnu:Pnuc_1656 hypothetical protein; hypothetical protein 150764 5714456 Dshi_3927 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542136.1 150369 R 398580 CDS YP_001542137.1 159046466 5714457 150931..151857 1 NC_009956.1 PFAM: homocysteine S-methyltransferase; KEGG: sil:SPO3398 homocysteine S-methyltransferase family protein; homocysteine S-methyltransferase 151857 5714457 Dshi_3928 Dinoroseobacter shibae DFL 12 = DSM 16493 homocysteine S-methyltransferase YP_001542137.1 150931 D 398580 CDS YP_001542138.1 159046467 5714458 151908..152129 1 NC_009956.1 KEGG: pna:Pnap_3267 hypothetical protein; hypothetical protein 152129 5714458 Dshi_3929 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542138.1 151908 D 398580 CDS YP_001542139.1 159046468 5714459 complement(152139..152852) 1 NC_009956.1 PFAM: regulatory protein GntR HTH; GntR domain protein; KEGG: rsp:RSP_3339 transcriptional regulator, GntR family; GntR family transcriptional regulator 152852 5714459 Dshi_3930 Dinoroseobacter shibae DFL 12 = DSM 16493 GntR family transcriptional regulator YP_001542139.1 152139 R 398580 CDS YP_001542140.1 159046470 5714596 complement(12..776) 1 NC_009957.1 PFAM: glutaredoxin; KEGG: eli:ELI_04570 hypothetical protein; glutaredoxin 776 5714596 Dshi_3931 Dinoroseobacter shibae DFL 12 = DSM 16493 glutaredoxin YP_001542140.1 12 R 398580 CDS YP_001542141.1 159046471 5714461 complement(789..1625) 1 NC_009957.1 PFAM: protein of unknown function DUF305; KEGG: rsh:Rsph17029_3677 protein of unknown function DUF305; hypothetical protein 1625 5714461 Dshi_3932 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542141.1 789 R 398580 CDS YP_001542142.1 159046472 5714462 1805..2386 1 NC_009957.1 PFAM: ErfK/YbiS/YcfS/YnhG family protein; KEGG: mes:Meso_4112 ErfK/YbiS/YcfS/YnhG; ErfK/YbiS/YcfS/YnhG family protein 2386 5714462 Dshi_3933 Dinoroseobacter shibae DFL 12 = DSM 16493 ErfK/YbiS/YcfS/YnhG family protein YP_001542142.1 1805 D 398580 CDS YP_001542143.1 159046473 5714463 2470..3774 1 NC_009957.1 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 3774 5714463 Dshi_3934 Dinoroseobacter shibae DFL 12 = DSM 16493 multicopper oxidase type 3 YP_001542143.1 2470 D 398580 CDS YP_001542144.1 159046474 5714464 3888..4400 1 NC_009957.1 KEGG: sit:TM1040_1167 disulphide bond formation protein DsbB; disulphide bond formation protein DsbB 4400 5714464 Dshi_3935 Dinoroseobacter shibae DFL 12 = DSM 16493 disulphide bond formation protein DsbB YP_001542144.1 3888 D 398580 CDS YP_001542145.1 159046475 5714465 4443..5108 1 NC_009957.1 PFAM: ErfK/YbiS/YcfS/YnhG family protein; KEGG: rde:RD1_0492 ErfK/YbiS/YcfS/YnhG family protein; ErfK/YbiS/YcfS/YnhG family protein 5108 5714465 Dshi_3936 Dinoroseobacter shibae DFL 12 = DSM 16493 ErfK/YbiS/YcfS/YnhG family protein YP_001542145.1 4443 D 398580 CDS YP_001542146.1 159046476 5714466 complement(5185..5742) 1 NC_009957.1 KEGG: sil:SPO0304 lipoprotein, putative; putative lipoprotein 5742 5714466 Dshi_3937 Dinoroseobacter shibae DFL 12 = DSM 16493 putative lipoprotein YP_001542146.1 5185 R 398580 CDS YP_001542147.1 159046477 5714467 6140..6748 1 NC_009957.1 SMART: Calcium-binding EF-hand-containing protein; KEGG: rpb:RPB_2375 calcium-binding EF-hand protein; calcium-binding EF-hand-containing protein 6748 5714467 Dshi_3938 Dinoroseobacter shibae DFL 12 = DSM 16493 calcium-binding EF-hand-containing protein YP_001542147.1 6140 D 398580 CDS YP_001542148.1 159046478 5714468 6889..7275 1 NC_009957.1 PFAM: protein of unknown function DUF302; KEGG: mmr:Mmar10_2335 protein of unknown function DUF302; hypothetical protein 7275 5714468 Dshi_3939 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542148.1 6889 D 398580 CDS YP_001542149.1 159046479 5714469 7381..8301 1 NC_009957.1 transfers the N-acyl diglyceride moiety to the prospective N-terminal cysteine in prolipoprotein; prolipoprotein diacylglyceryl transferase 8301 5714469 Dshi_3940 Dinoroseobacter shibae DFL 12 = DSM 16493 prolipoprotein diacylglyceryl transferase YP_001542149.1 7381 D 398580 CDS YP_001542150.1 159046480 5714470 8380..10725 1 NC_009957.1 TIGRFAM: ATPase, P-type (transporting), HAD superfamily, subfamily IC; copper-translocating P-type ATPase; heavy metal translocating P-type ATPase; PFAM: Haloacid dehalogenase domain protein hydrolase; E1-E2 ATPase-associated domain protein; KEGG: sil:SPOA0365 copper-translocating P-type ATPase; heavy metal translocating P-type ATPase 10725 5714470 Dshi_3941 Dinoroseobacter shibae DFL 12 = DSM 16493 heavy metal translocating P-type ATPase YP_001542150.1 8380 D 398580 CDS YP_001542151.1 159046481 5714471 10774..12111 1 NC_009957.1 PFAM: amino acid permease-associated region; KEGG: sil:SPOA0366 amino acid permease; amino acid permease 12111 5714471 Dshi_3942 Dinoroseobacter shibae DFL 12 = DSM 16493 amino acid permease YP_001542151.1 10774 D 398580 CDS YP_001542152.1 159046482 5714472 complement(12119..12763) 1 NC_009957.1 hypothetical protein 12763 5714472 Dshi_3943 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542152.1 12119 R 398580 CDS YP_001542153.1 159046483 5714473 12980..13702 1 NC_009957.1 PFAM: cytochrome c biogenesis protein transmembrane region; KEGG: maq:Maqu_3250 cytochrome c biogenesis protein, transmembrane region; cytochrome c biogenesis protein transmembrane region 13702 5714473 Dshi_3944 Dinoroseobacter shibae DFL 12 = DSM 16493 cytochrome c biogenesis protein transmembrane region YP_001542153.1 12980 D 398580 CDS YP_001542154.1 159046484 5714474 13896..14561 1 NC_009957.1 PFAM: ErfK/YbiS/YcfS/YnhG family protein; KEGG: rde:RD1_0492 ErfK/YbiS/YcfS/YnhG family protein; ErfK/YbiS/YcfS/YnhG family protein 14561 5714474 Dshi_3945 Dinoroseobacter shibae DFL 12 = DSM 16493 ErfK/YbiS/YcfS/YnhG family protein YP_001542154.1 13896 D 398580 CDS YP_001542155.1 159046485 5714475 complement(14609..14881) 1 NC_009957.1 KEGG: rde:RD1_0491 hypothetical protein; hypothetical protein 14881 5714475 Dshi_3946 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542155.1 14609 R 398580 CDS YP_001542156.1 159046486 5714476 15242..17428 1 NC_009957.1 TIGRFAM: ATPase, P-type (transporting), HAD superfamily, subfamily IC; cadmium-translocating P-type ATPase; heavy metal translocating P-type ATPase; PFAM: Haloacid dehalogenase domain protein hydrolase; E1-E2 ATPase-associated domain protein; KEGG: mes:Meso_4212 heavy metal translocating P-type ATPase; heavy metal translocating P-type ATPase 17428 5714476 Dshi_3947 Dinoroseobacter shibae DFL 12 = DSM 16493 heavy metal translocating P-type ATPase YP_001542156.1 15242 D 398580 CDS YP_001542157.1 159046487 5714477 complement(17422..17697) 1 NC_009957.1 hypothetical protein 17697 5714477 Dshi_3948 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542157.1 17422 R 398580 CDS YP_001542158.1 159046488 5714478 17795..18253 1 NC_009957.1 PFAM: regulatory protein MarR; iron dependent repressor; SMART: regulatory protein Crp; KEGG: mlo:mll2499 hypothetical protein; DtxR family iron dependent repressor 18253 5714478 Dshi_3949 Dinoroseobacter shibae DFL 12 = DSM 16493 DtxR family iron dependent repressor YP_001542158.1 17795 D 398580 CDS YP_001542159.1 159046489 5714479 complement(18348..18515) 1 NC_009957.1 KEGG: sil:SPO2514 hypothetical protein; hypothetical protein 18515 5714479 Dshi_3950 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542159.1 18348 R 398580 CDS YP_001542160.1 159046490 5714480 complement(18515..20086) 1 NC_009957.1 TIGRFAM: apolipoprotein N-acyltransferase; PFAM: Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase; KEGG: nha:Nham_0025 apolipoprotein N-acyltransferase; apolipoprotein N-acyltransferase 20086 5714480 Dshi_3951 Dinoroseobacter shibae DFL 12 = DSM 16493 apolipoprotein N-acyltransferase YP_001542160.1 18515 R 398580 CDS YP_001542161.1 159046491 5714481 complement(20083..20556) 1 NC_009957.1 TIGRFAM: lipoprotein signal peptidase; PFAM: peptidase A8 signal peptidase II; KEGG: eli:ELI_04470 putative lipoprotein signal peptidase; lipoprotein signal peptidase 20556 5714481 Dshi_3952 Dinoroseobacter shibae DFL 12 = DSM 16493 lipoprotein signal peptidase YP_001542161.1 20083 R 398580 CDS YP_001542162.1 159046492 5714482 complement(20561..21343) 1 NC_009957.1 PFAM: zinc/iron permease; KEGG: gvi:glr4280 zinc transporter, ZIP family; zinc/iron permease 21343 5714482 Dshi_3953 Dinoroseobacter shibae DFL 12 = DSM 16493 zinc/iron permease YP_001542162.1 20561 R 398580 CDS YP_001542163.1 159046493 5714483 complement(21366..21824) 1 NC_009957.1 PFAM: protein of unknown function DUF411; KEGG: aav:Aave_1809 protein of unknown function DUF411; hypothetical protein 21824 5714483 Dshi_3954 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542163.1 21366 R 398580 CDS YP_001542164.1 159046494 5714484 complement(21828..23201) 1 NC_009957.1 PFAM: peptidase M23B; KEGG: hch:HCH_06239 membrane protein related to metalloendopeptidase; peptidase M23B 23201 5714484 Dshi_3955 Dinoroseobacter shibae DFL 12 = DSM 16493 peptidase M23B YP_001542164.1 21828 R 398580 CDS YP_001542165.1 159046495 5714485 complement(23198..23824) 1 NC_009957.1 PFAM: electron transport protein SCO1/SenC; KEGG: ccr:CC_3503 SCO1/2 family protein; electron transport protein SCO1/SenC 23824 5714485 Dshi_3956 Dinoroseobacter shibae DFL 12 = DSM 16493 electron transport protein SCO1/SenC YP_001542165.1 23198 R 398580 CDS YP_001542166.1 159046496 5714486 complement(23824..24294) 1 NC_009957.1 PFAM: protein of unknown function DUF461; KEGG: bra:BRADO4160 conserved hypothetical protein; putative signal peptide; hypothetical protein 24294 5714486 Dshi_3957 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542166.1 23824 R 398580 CDS YP_001542167.1 159046497 5714487 complement(24317..24976) 1 NC_009957.1 PFAM: DSBA oxidoreductase; KEGG: mes:Meso_4133 DsbA oxidoreductase; DSBA oxidoreductase 24976 5714487 Dshi_3958 Dinoroseobacter shibae DFL 12 = DSM 16493 DSBA oxidoreductase YP_001542167.1 24317 R 398580 CDS YP_001542168.1 159046498 5714488 complement(24973..25395) 1 NC_009957.1 PFAM: Disulphide bond formation protein DsbB; KEGG: psa:PST_0576 disulfide bond formation protein; disulphide bond formation protein DsbB 25395 5714488 Dshi_3959 Dinoroseobacter shibae DFL 12 = DSM 16493 disulphide bond formation protein DsbB YP_001542168.1 24973 R 398580 CDS YP_001542169.1 159046499 5714489 complement(25401..26003) 1 NC_009957.1 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 26003 5714489 Dshi_3960 Dinoroseobacter shibae DFL 12 = DSM 16493 electron transport protein SCO1/SenC YP_001542169.1 25401 R 398580 CDS YP_001542170.1 159046500 5714490 26181..26609 1 NC_009957.1 PFAM: regulatory protein MerR; Transcription regulator MerR DNA binding; KEGG: sil:SPOA0389 transcriptional regulator, MerR family; MerR family transcriptional regulator 26609 5714490 Dshi_3961 Dinoroseobacter shibae DFL 12 = DSM 16493 MerR family transcriptional regulator YP_001542170.1 26181 D 398580 CDS YP_001542171.1 159046501 5714491 26692..27312 1 NC_009957.1 PFAM: cation efflux protein; KEGG: mes:Meso_4424 cation efflux protein; cation efflux protein 27312 5714491 Dshi_3962 Dinoroseobacter shibae DFL 12 = DSM 16493 cation efflux protein YP_001542171.1 26692 D 398580 CDS YP_001542172.1 159046502 5714492 27382..27945 1 NC_009957.1 KEGG: ajs:Ajs_1334 hypothetical protein; hypothetical protein 27945 5714492 Dshi_3963 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542172.1 27382 D 398580 CDS YP_001542173.1 159046503 5714493 27935..28900 1 NC_009957.1 TIGRFAM: cation diffusion facilitator family transporter; PFAM: cation efflux protein; KEGG: maq:Maqu_3275 cation diffusion facilitator family transporter; cation diffusion facilitator family transporter 28900 5714493 Dshi_3964 Dinoroseobacter shibae DFL 12 = DSM 16493 cation diffusion facilitator family transporter YP_001542173.1 27935 D 398580 CDS YP_001542174.1 159046504 5714494 28872..29183 1 NC_009957.1 KEGG: gfo:GFO_1210 hypothetical protein; hypothetical protein 29183 5714494 Dshi_3965 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542174.1 28872 D 398580 CDS YP_001542175.1 159046505 5714495 29536..30282 1 NC_009957.1 KEGG: sit:TM1040_3830 hypothetical protein; hypothetical protein 30282 5714495 Dshi_3966 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542175.1 29536 D 398580 CDS YP_001542176.1 159046506 5714496 complement(30471..30821) 1 NC_009957.1 PFAM: regulatory protein ArsR; KEGG: mkm:Mkms_5742 regulatory protein, ArsR; ArsR family transcriptional regulator 30821 5714496 Dshi_3967 Dinoroseobacter shibae DFL 12 = DSM 16493 ArsR family transcriptional regulator YP_001542176.1 30471 R 398580 CDS YP_001542177.1 159046507 5714497 30885..31736 1 NC_009957.1 PFAM: cation efflux protein; KEGG: sal:Sala_2560 hypothetical protein; cation efflux protein 31736 5714497 Dshi_3968 Dinoroseobacter shibae DFL 12 = DSM 16493 cation efflux protein YP_001542177.1 30885 D 398580 CDS YP_001542178.1 159046508 5714498 complement(31897..32124) 1 NC_009957.1 KEGG: sit:TM1040_3826 hypothetical protein; hypothetical protein 32124 5714498 Dshi_3969 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542178.1 31897 R 398580 CDS YP_001542179.1 159046509 5714499 complement(32292..32549) 1 NC_009957.1 PFAM: helix-turn-helix domain protein; KEGG: rsq:Rsph17025_0810 putative transcriptional regulator, XRE family; XRE family transcriptional regulator 32549 5714499 Dshi_3970 Dinoroseobacter shibae DFL 12 = DSM 16493 XRE family transcriptional regulator YP_001542179.1 32292 R 398580 CDS YP_001542180.1 159046510 5714500 complement(32674..32994) 1 NC_009957.1 KEGG: sit:TM1040_3824 hypothetical protein; hypothetical protein 32994 5714500 Dshi_3971 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542180.1 32674 R 398580 CDS YP_001542181.1 159046511 5714501 33138..33491 1 NC_009957.1 KEGG: sit:TM1040_3823 hypothetical protein; hypothetical protein 33491 5714501 Dshi_3972 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542181.1 33138 D 398580 CDS YP_001542182.1 159046512 5714502 33535..34149 1 NC_009957.1 PFAM: Lytic transglycosylase catalytic; KEGG: sit:TM1040_3822 lytic transglycosylase, catalytic; lytic transglycosylase 34149 5714502 Dshi_3973 Dinoroseobacter shibae DFL 12 = DSM 16493 lytic transglycosylase YP_001542182.1 33535 D 398580 CDS YP_001542183.1 159046513 5714503 34146..34439 1 NC_009957.1 PFAM: Conjugal transfer protein TrbC; KEGG: sit:TM1040_3821 VirB2 type IV secretion; conjugal transfer protein TrbC 34439 5714503 Dshi_3974 Dinoroseobacter shibae DFL 12 = DSM 16493 conjugal transfer protein TrbC YP_001542183.1 34146 D 398580 CDS YP_001542184.1 159046514 5714504 34432..34710 1 NC_009957.1 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 34710 5714504 Dshi_3975 Dinoroseobacter shibae DFL 12 = DSM 16493 type IV secretory pathway VirB3 family protein YP_001542184.1 34432 D 398580 CDS YP_001542185.1 159046515 5714505 34700..37063 1 NC_009957.1 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 37063 5714505 Dshi_3976 Dinoroseobacter shibae DFL 12 = DSM 16493 CagE TrbE VirB component of type IV transporter system YP_001542185.1 34700 D 398580 CDS YP_001542186.1 159046516 5714506 37060..37227 1 NC_009957.1 KEGG: sit:TM1040_3818 hypothetical protein; hypothetical protein 37227 5714506 Dshi_3977 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542186.1 37060 D 398580 CDS YP_001542187.1 159046517 5714507 37217..38371 1 NC_009957.1 PFAM: Lytic transglycosylase catalytic; KEGG: sit:TM1040_3817 lytic transglycosylase, catalytic; lytic transglycosylase catalytic 38371 5714507 Dshi_3978 Dinoroseobacter shibae DFL 12 = DSM 16493 lytic transglycosylase catalytic YP_001542187.1 37217 D 398580 CDS YP_001542188.1 159046518 5714508 38371..39180 1 NC_009957.1 KEGG: sit:TM1040_3816 hypothetical protein; hypothetical protein 39180 5714508 Dshi_3979 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542188.1 38371 D 398580 CDS YP_001542189.1 159046519 5714509 39197..39850 1 NC_009957.1 PFAM: VirB8 family protein; KEGG: sit:TM1040_3815 VirB8; VirB8 family protein 39850 5714509 Dshi_3980 Dinoroseobacter shibae DFL 12 = DSM 16493 VirB8 family protein YP_001542189.1 39197 D 398580 CDS YP_001542190.1 159046520 5714510 39853..40548 1 NC_009957.1 PFAM: Conjugal transfer protein TrbG/VirB9/CagX; KEGG: sit:TM1040_3814 conjugal transfer protein TrbG/VirB9/CagX; conjugal transfer protein TrbG/VirB9/CagX 40548 5714510 Dshi_3981 Dinoroseobacter shibae DFL 12 = DSM 16493 conjugal transfer protein TrbG/VirB9/CagX YP_001542190.1 39853 D 398580 CDS YP_001542191.1 159046521 5714511 40545..41924 1 NC_009957.1 PFAM: conjugation TrbI family protein; KEGG: sit:TM1040_3813 conjugation TrbI-like protein; conjugation TrbI family protein 41924 5714511 Dshi_3982 Dinoroseobacter shibae DFL 12 = DSM 16493 conjugation TrbI family protein YP_001542191.1 40545 D 398580 CDS YP_001542192.1 159046522 5714512 41929..42915 1 NC_009957.1 PFAM: type II secretion system protein E; KEGG: sit:TM1040_3812 type II secretion system protein E; type II secretion system protein E 42915 5714512 Dshi_3983 Dinoroseobacter shibae DFL 12 = DSM 16493 type II secretion system protein E YP_001542192.1 41929 D 398580 CDS YP_001542193.1 159046523 5714513 43103..43513 1 NC_009957.1 KEGG: sit:TM1040_3810 hypothetical protein; hypothetical protein 43513 5714513 Dshi_3984 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542193.1 43103 D 398580 CDS YP_001542194.1 159046524 5714514 43526..44602 1 NC_009957.1 PFAM: TrbL/VirB6 plasmid conjugal transfer protein; KEGG: sit:TM1040_3809 TrbL/VirB6 plasmid conjugal transfer protein; TrbL/VirB6 plasmid conjugal transfer protein 44602 5714514 Dshi_3985 Dinoroseobacter shibae DFL 12 = DSM 16493 TrbL/VirB6 plasmid conjugal transfer protein YP_001542194.1 43526 D 398580 CDS YP_001542195.1 159046525 5714515 complement(44763..46667) 1 NC_009957.1 KEGG: rru:Rru_A0809 hypothetical protein; hypothetical protein 46667 5714515 Dshi_3986 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542195.1 44763 R 398580 CDS YP_001542196.1 159046526 5714516 complement(47163..48227) 1 NC_009957.1 KEGG: ter:Tery_4988 hypothetical protein; hypothetical protein 48227 5714516 Dshi_3987 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542196.1 47163 R 398580 CDS YP_001542197.1 159046527 5714517 complement(48594..50606) 1 NC_009957.1 PFAM: TRAG family protein; KEGG: sit:TM1040_3794 TraG protein; TRAG family protein 50606 5714517 Dshi_3988 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAG family protein YP_001542197.1 48594 R 398580 CDS YP_001542198.1 159046528 5714518 complement(50603..52936) 1 NC_009957.1 PFAM: Relaxase/mobilization nuclease family protein; KEGG: sit:TM1040_3793 relaxase/mobilization nuclease domain; relaxase/mobilization nuclease family protein 52936 5714518 Dshi_3989 Dinoroseobacter shibae DFL 12 = DSM 16493 relaxase/mobilization nuclease family protein YP_001542198.1 50603 R 398580 CDS YP_001542199.1 159046529 5714519 complement(52923..53516) 1 NC_009957.1 KEGG: sit:TM1040_3792 hypothetical protein; hypothetical protein 53516 5714519 Dshi_3990 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542199.1 52923 R 398580 CDS YP_001542200.1 159046530 5714520 complement(54078..54284) 1 NC_009957.1 KEGG: sit:TM1040_3791 hypothetical protein; hypothetical protein 54284 5714520 Dshi_3991 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542200.1 54078 R 398580 CDS YP_001542201.1 159046531 5714522 complement(54824..55849) 1 NC_009957.1 KEGG: sit:TM1040_3771 hypothetical protein; hypothetical protein 55849 5714522 Dshi_3993 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542201.1 54824 R 398580 CDS YP_001542202.1 159046532 5714523 complement(55973..56902) 1 NC_009957.1 KEGG: mes:Meso_4225 hypothetical protein; hypothetical protein 56902 5714523 Dshi_3994 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542202.1 55973 R 398580 CDS YP_001542203.1 159046533 5714524 57594..58274 1 NC_009957.1 PFAM: protein of unknown function DUF159; KEGG: bbt:BBta_3432 hypothetical protein; hypothetical protein 58274 5714524 Dshi_3995 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542203.1 57594 D 398580 CDS YP_001542204.1 159046534 5714525 58264..58851 1 NC_009957.1 KEGG: sil:SPO0672 hypothetical protein; hypothetical protein 58851 5714525 Dshi_3996 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542204.1 58264 D 398580 CDS YP_001542205.1 159046535 5714526 58778..60277 1 NC_009957.1 KEGG: sil:SPO0671 hypothetical protein; hypothetical protein 60277 5714526 Dshi_3997 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542205.1 58778 D 398580 CDS YP_001542206.1 159046536 5714527 60274..63624 1 NC_009957.1 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 63624 5714527 Dshi_3998 Dinoroseobacter shibae DFL 12 = DSM 16493 DNA polymerase III subunit alpha YP_001542206.1 60274 D 398580 CDS YP_001542207.1 159046537 5714528 complement(63705..64433) 1 NC_009957.1 KEGG: jan:Jann_4220 ParB-like nuclease; ParB-like nuclease 64433 5714528 Dshi_3999 Dinoroseobacter shibae DFL 12 = DSM 16493 ParB-like nuclease YP_001542207.1 63705 R 398580 CDS YP_001542208.1 159046538 5714529 complement(64558..64860) 1 NC_009957.1 hypothetical protein 64860 5714529 Dshi_4000 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542208.1 64558 R 398580 CDS YP_001542209.1 159046539 5714530 complement(64961..65422) 1 NC_009957.1 KEGG: bbt:BBta_7341 hypothetical protein; hypothetical protein 65422 5714530 Dshi_4001 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542209.1 64961 R 398580 CDS YP_001542210.1 159046540 5714531 complement(65424..65810) 1 NC_009957.1 KEGG: sal:Sala_2657 hypothetical protein; hypothetical protein 65810 5714531 Dshi_4002 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542210.1 65424 R 398580 CDS YP_001542211.1 159046541 5714532 complement(65932..67803) 1 NC_009957.1 KEGG: ana:alr7089 hypothetical protein; hypothetical protein 67803 5714532 Dshi_4003 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542211.1 65932 R 398580 CDS YP_001542212.1 159046542 5714533 67841..69367 1 NC_009957.1 PFAM: integrase family protein; integrase domain protein SAM domain protein; KEGG: sal:Sala_0438 phage integrase; integrase family protein 69367 5714533 Dshi_4004 Dinoroseobacter shibae DFL 12 = DSM 16493 integrase family protein YP_001542212.1 67841 D 398580 CDS YP_001542213.1 159046543 5714534 69364..70275 1 NC_009957.1 PFAM: integrase family protein; KEGG: sal:Sala_0439 phage integrase; integrase family protein 70275 5714534 Dshi_4005 Dinoroseobacter shibae DFL 12 = DSM 16493 integrase family protein YP_001542213.1 69364 D 398580 CDS YP_001542214.1 159046544 5714535 70272..71276 1 NC_009957.1 PFAM: integrase family protein; integrase domain protein SAM domain protein; KEGG: sal:Sala_0440 phage integrase; integrase family protein 71276 5714535 Dshi_4006 Dinoroseobacter shibae DFL 12 = DSM 16493 integrase family protein YP_001542214.1 70272 D 398580 CDS YP_001542215.1 159046545 5714536 complement(71315..73756) 1 NC_009957.1 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 73756 5714536 Dshi_4007 Dinoroseobacter shibae DFL 12 = DSM 16493 type III restriction protein res subunit YP_001542215.1 71315 R 398580 CDS YP_001542216.1 159046546 5714537 complement(74000..76510) 1 NC_009957.1 KEGG: nar:Saro_2208 putative methylase/helicase; putative methylase/helicase 76510 5714537 Dshi_4008 Dinoroseobacter shibae DFL 12 = DSM 16493 putative methylase/helicase YP_001542216.1 74000 R 398580 CDS YP_001542217.1 159046547 5714538 complement(77303..78163) 1 NC_009957.1 PFAM: regulatory protein LysR; LysR substrate-binding; KEGG: pol:Bpro_1615 transcriptional regulator, LysR family; LysR family transcriptional regulator 78163 5714538 Dshi_4009 Dinoroseobacter shibae DFL 12 = DSM 16493 LysR family transcriptional regulator YP_001542217.1 77303 R 398580 CDS YP_001542218.1 159046548 5714539 78320..79039 1 NC_009957.1 KEGG: lpn:lpg1968 hypothetical protein; hypothetical protein 79039 5714539 Dshi_4010 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542218.1 78320 D 398580 CDS YP_001542219.1 159046549 5714540 complement(79361..79879) 1 NC_009957.1 KEGG: psa:PST_3459 hypothetical protein; hypothetical protein 79879 5714540 Dshi_4011 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542219.1 79361 R 398580 CDS YP_001542220.1 159046550 5714541 complement(79876..80202) 1 NC_009957.1 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 80202 5714541 Dshi_4012 Dinoroseobacter shibae DFL 12 = DSM 16493 putative regulator PrlF YP_001542220.1 79876 R 398580 CDS YP_001542221.1 159046551 5714542 complement(80329..80982) 1 NC_009957.1 KEGG: rde:RD1_A0106 RC187; hypothetical protein 80982 5714542 Dshi_4013 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542221.1 80329 R 398580 CDS YP_001542222.1 159046552 5714543 complement(80982..81674) 1 NC_009957.1 hypothetical protein 81674 5714543 Dshi_4014 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542222.1 80982 R 398580 CDS YP_001542223.1 159046553 5714544 complement(81749..83731) 1 NC_009957.1 TIGRFAM: parB-like partition protein; PFAM: ParB domain protein nuclease; KEGG: rde:RD1_A0072 plasmid stabilization protein, putative; parB-like partition protein 83731 5714544 Dshi_4015 Dinoroseobacter shibae DFL 12 = DSM 16493 parB-like partition protein YP_001542223.1 81749 R 398580 CDS YP_001542224.1 159046554 5714545 complement(83888..84277) 1 NC_009957.1 KEGG: jan:Jann_4219 hypothetical protein; hypothetical protein 84277 5714545 Dshi_4016 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542224.1 83888 R 398580 CDS YP_001542225.1 159046555 5714546 complement(84365..84574) 1 NC_009957.1 hypothetical protein 84574 5714546 Dshi_4017 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542225.1 84365 R 398580 CDS YP_001542226.1 159046556 5714547 complement(84598..85536) 1 NC_009957.1 PFAM: domain of unknown function DUF1738; KEGG: nha:Nham_4029 peptidase M, neutral zinc metallopeptidases, zinc-binding site; hypothetical protein 85536 5714547 Dshi_4018 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542226.1 84598 R 398580 CDS YP_001542227.1 159046557 5714548 complement(85577..86062) 1 NC_009957.1 hypothetical protein 86062 5714548 Dshi_4019 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542227.1 85577 R 398580 CDS YP_001542228.1 159046558 5714549 86341..87543 1 NC_009957.1 PFAM: filamentation induced by cAMP protein Fic; KEGG: rsq:Rsph17025_4217 hypothetical protein; filamentation induced by cAMP protein fic 87543 5714549 Dshi_4020 Dinoroseobacter shibae DFL 12 = DSM 16493 filamentation induced by cAMP protein fic YP_001542228.1 86341 D 398580 CDS YP_001542229.1 159046559 5714550 complement(87675..88910) 1 NC_009957.1 PFAM: replication protein C; KEGG: rsp:RSP_7387 replication initiator RepC; replication initiation protein RepC 88910 5714550 Dshi_4021 Dinoroseobacter shibae DFL 12 = DSM 16493 replication initiation protein RepC YP_001542229.1 87675 R 398580 CDS YP_001542230.1 159046560 5714551 complement(89088..90104) 1 NC_009957.1 TIGRFAM: parB-like partition protein; PFAM: ParB domain protein nuclease; KEGG: rsp:RSP_4185 RepB partitioning protein/ParB-like protein; parB-like partition protein 90104 5714551 Dshi_4022 Dinoroseobacter shibae DFL 12 = DSM 16493 parB-like partition protein YP_001542230.1 89088 R 398580 CDS YP_001542231.1 159046561 5714552 complement(90101..91288) 1 NC_009957.1 PFAM: regulatory protein MerR; Cobyrinic acid ac-diamide synthase; KEGG: rsp:RSP_4186 RepA partitioning protein/ATPase, ParA type; cobyrinic acid ac-diamide synthase 91288 5714552 Dshi_4023 Dinoroseobacter shibae DFL 12 = DSM 16493 cobyrinic acid ac-diamide synthase YP_001542231.1 90101 R 398580 CDS YP_001542232.1 159046562 5714553 91602..91829 1 NC_009957.1 PFAM: SpoVT/AbrB domain protein; KEGG: rsp:RSP_7280 SpoVT/AbrB-like cell growth regulatory protein; transcriptional regulator/antitoxin MazE 91829 5714553 Dshi_4024 Dinoroseobacter shibae DFL 12 = DSM 16493 transcriptional regulator/antitoxin MazE YP_001542232.1 91602 D 398580 CDS YP_001542233.1 159046563 5714554 91819..92214 1 NC_009957.1 KEGG: rsp:RSP_4188 hypothetical memebrane protein; hypothetical protein 92214 5714554 Dshi_4025 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542233.1 91819 D 398580 CDS YP_001542234.1 159046564 5714555 complement(92198..93094) 1 NC_009957.1 PFAM: Resolvase domain; KEGG: rsp:RSP_2482 TonB-dependent receptor protein; resolvase domain-containing protein 93094 5714555 Dshi_4026 Dinoroseobacter shibae DFL 12 = DSM 16493 resolvase domain-containing protein YP_001542234.1 92198 R 398580 CDS YP_001542235.1 159046565 5714556 complement(93153..94271) 1 NC_009957.1 PFAM: integrase family protein; KEGG: rsq:Rsph17025_4239 hypothetical protein; integrase family protein 94271 5714556 Dshi_4027 Dinoroseobacter shibae DFL 12 = DSM 16493 integrase family protein YP_001542235.1 93153 R 398580 CDS YP_001542236.1 159046566 5714557 94398..95282 1 NC_009957.1 PFAM: protein of unknown function DUF1403; KEGG: sit:TM1040_3403 protein of unknown function DUF1403; hypothetical protein 95282 5714557 Dshi_4028 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542236.1 94398 D 398580 CDS YP_001542237.1 159046567 5714558 95285..95902 1 NC_009957.1 PFAM: chromosome segregation and condensation protein ScpB; KEGG: rsq:Rsph17025_4232 hypothetical protein; chromosome segregation and condensation protein ScpB 95902 5714558 Dshi_4029 Dinoroseobacter shibae DFL 12 = DSM 16493 chromosome segregation and condensation protein ScpB YP_001542237.1 95285 D 398580 CDS YP_001542238.1 159046568 5714559 95952..96215 1 NC_009957.1 PFAM: WGR domain protein; KEGG: mlo:msl9076 hypothetical protein; WGR domain-containing protein 96215 5714559 Dshi_4030 Dinoroseobacter shibae DFL 12 = DSM 16493 WGR domain-containing protein YP_001542238.1 95952 D 398580 CDS YP_001542239.1 159046569 5714560 96285..97403 1 NC_009957.1 PFAM: filamentation induced by cAMP protein Fic; KEGG: atc:AGR_pAT_503 hypothetical protein; filamentation induced by cAMP protein fic 97403 5714560 Dshi_4031 Dinoroseobacter shibae DFL 12 = DSM 16493 filamentation induced by cAMP protein fic YP_001542239.1 96285 D 398580 CDS YP_001542240.1 159046570 5714561 complement(97400..98122) 1 NC_009957.1 hypothetical protein 98122 5714561 Dshi_4032 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542240.1 97400 R 398580 CDS YP_001542241.1 159046571 5714562 98233..98580 1 NC_009957.1 KEGG: pde:Pden_2059 transposase orfA IS5 family element; IS5 family transposase OrfA 98580 5714562 Dshi_4033 Dinoroseobacter shibae DFL 12 = DSM 16493 IS5 family transposase OrfA YP_001542241.1 98233 D 398580 CDS YP_001542242.1 159046572 5714563 98601..98990 1 NC_009957.1 PFAM: transposase IS4 family protein; KEGG: pde:Pden_3333 transposase, IS4 family protein; transposase IS4 family protein 98990 5714563 Dshi_4034 Dinoroseobacter shibae DFL 12 = DSM 16493 transposase IS4 family protein YP_001542242.1 98601 D 398580 CDS YP_001542243.1 159046573 5714564 99093..100121 1 NC_009957.1 PFAM: transposase IS116/IS110/IS902 family protein; KEGG: rru:Rru_A0676 transposase IS116/IS110/IS902; transposase IS116/IS110/IS902 family protein 100121 5714564 Dshi_4035 Dinoroseobacter shibae DFL 12 = DSM 16493 transposase IS116/IS110/IS902 family protein YP_001542243.1 99093 D 398580 CDS YP_001542244.1 159046574 5714565 complement(100475..100657) 1 NC_009957.1 KEGG: rsq:Rsph17025_2803 ubiquinol-cytochrome c reductase, iron-sulfur subunit; hypothetical protein 100657 5714565 Dshi_4036 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542244.1 100475 R 398580 CDS YP_001542245.1 159046575 5714566 100987..101349 1 NC_009957.1 KEGG: nha:Nham_4014 ISSpo6, transposase orf A; ISSpo6, transposase orf A 101349 5714566 Dshi_4037 Dinoroseobacter shibae DFL 12 = DSM 16493 ISSpo6, transposase orf A YP_001542245.1 100987 D 398580 CDS YP_001542246.1 159046576 5714567 101411..101941 1 NC_009957.1 KEGG: nha:Nham_4013 ISSpo6, transposase OrfB; ISSpo6, transposase OrfB 101941 5714567 Dshi_4038 Dinoroseobacter shibae DFL 12 = DSM 16493 ISSpo6, transposase OrfB YP_001542246.1 101411 D 398580 CDS YP_001542247.1 159046577 5714568 complement(101913..102341) 1 NC_009957.1 KEGG: sru:SRU_1982 hypothetical protein; hypothetical protein 102341 5714568 Dshi_4039 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542247.1 101913 R 398580 CDS YP_001542248.1 159046578 5714569 102417..102983 1 NC_009957.1 PFAM: cyclic nucleotide-binding; KEGG: reh:H16_A1838 transcriptional regulator, NNR like; cyclic nucleotide-binding protein 102983 5714569 Dshi_4040 Dinoroseobacter shibae DFL 12 = DSM 16493 cyclic nucleotide-binding protein YP_001542248.1 102417 D 398580 CDS YP_001542249.1 159046579 5714570 complement(102989..103441) 1 NC_009957.1 PFAM: protein of unknown function DUF411; KEGG: rde:RD1_2307 hypothetical protein; hypothetical protein 103441 5714570 Dshi_4041 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542249.1 102989 R 398580 CDS YP_001542250.1 159046580 5714571 complement(103356..104348) 1 NC_009957.1 PFAM: fatty acid hydroxylase; KEGG: aeh:Mlg_0287 sterol desaturase-like protein; fatty acid hydroxylase 104348 5714571 Dshi_4042 Dinoroseobacter shibae DFL 12 = DSM 16493 fatty acid hydroxylase YP_001542250.1 103356 R 398580 CDS YP_001542251.1 159046581 5714572 complement(104355..105341) 1 NC_009957.1 TIGRFAM: cation diffusion facilitator family transporter; PFAM: cation efflux protein; KEGG: dge:Dgeo_0215 cation diffusion facilitator family transporter; cation diffusion facilitator family transporter 105341 5714572 Dshi_4043 Dinoroseobacter shibae DFL 12 = DSM 16493 cation diffusion facilitator family transporter YP_001542251.1 104355 R 398580 CDS YP_001542252.1 159046582 5714573 complement(105343..106005) 1 NC_009957.1 PFAM: SNARE associated Golgi protein; KEGG: sil:SPOA0363 hypothetical protein; SNARE associated Golgi protein 106005 5714573 Dshi_4044 Dinoroseobacter shibae DFL 12 = DSM 16493 SNARE associated Golgi protein YP_001542252.1 105343 R 398580 CDS YP_001542253.1 159046583 5714574 complement(106009..106458) 1 NC_009957.1 KEGG: ddi:DDBDRAFT_0184550 hypothetical protein; hypothetical protein 106458 5714574 Dshi_4045 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542253.1 106009 R 398580 CDS YP_001542254.1 159046584 5714575 complement(106620..107057) 1 NC_009957.1 KEGG: maq:Maqu_0306 ion transport 2 domain protein; ion transport 2 domain-containing protein 107057 5714575 Dshi_4046 Dinoroseobacter shibae DFL 12 = DSM 16493 ion transport 2 domain-containing protein YP_001542254.1 106620 R 398580 CDS YP_001542255.1 159046585 5714576 complement(107146..107619) 1 NC_009957.1 KEGG: rde:RD1_1666 hypothetical protein; hypothetical protein 107619 5714576 Dshi_4047 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542255.1 107146 R 398580 CDS YP_001542256.1 159046586 5714577 107808..108530 1 NC_009957.1 PFAM: response regulator receiver; transcriptional regulator domain protein; KEGG: sil:SPOA0357 DNA-binding response regulator; two component transcriptional regulator 108530 5714577 Dshi_4048 Dinoroseobacter shibae DFL 12 = DSM 16493 two component transcriptional regulator YP_001542256.1 107808 D 398580 CDS YP_001542257.1 159046587 5714578 108530..109996 1 NC_009957.1 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 109996 5714578 Dshi_4049 Dinoroseobacter shibae DFL 12 = DSM 16493 integral membrane sensor signal transduction histidine kinase YP_001542257.1 108530 D 398580 CDS YP_001542258.1 159046588 5714579 110046..110237 1 NC_009957.1 KEGG: aeh:Mlg_1384 hypothetical protein; hypothetical protein 110237 5714579 Dshi_4050 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542258.1 110046 D 398580 CDS YP_001542259.1 159046589 5714580 110303..112303 1 NC_009957.1 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 112303 5714580 Dshi_4051 Dinoroseobacter shibae DFL 12 = DSM 16493 cytochrome c-type biogenesis protein CcmF YP_001542259.1 110303 D 398580 CDS YP_001542260.1 159046590 5714581 112312..112878 1 NC_009957.1 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 112878 5714581 Dshi_4052 Dinoroseobacter shibae DFL 12 = DSM 16493 periplasmic protein thiol--disulphide oxidoreductase DsbE YP_001542260.1 112312 D 398580 CDS YP_001542261.1 159046591 5714582 112875..113348 1 NC_009957.1 PFAM: cytochrome C biogenesis protein; KEGG: atc:AGR_C_1789 cytochrome C-type biogenesis protein; cytochrome C biogenesis protein 113348 5714582 Dshi_4053 Dinoroseobacter shibae DFL 12 = DSM 16493 cytochrome C biogenesis protein YP_001542261.1 112875 D 398580 CDS YP_001542262.1 159046592 5714583 113345..114496 1 NC_009957.1 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 114496 5714583 Dshi_4054 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542262.1 113345 D 398580 CDS YP_001542263.1 159046593 5714584 complement(114525..116654) 1 NC_009957.1 KEGG: mag:amb3382 thiol:disulfide interchange protein DsbD 1 precursor; thiol:disulfide interchange protein DsbD 1 precursor 116654 5714584 Dshi_4055 Dinoroseobacter shibae DFL 12 = DSM 16493 thiol:disulfide interchange protein DsbD 1 precursor YP_001542263.1 114525 R 398580 CDS YP_001542264.1 159046594 5714585 complement(116938..117240) 1 NC_009957.1 hypothetical protein 117240 5714585 Dshi_4056 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542264.1 116938 R 398580 CDS YP_001542265.1 159046595 5714586 117396..117956 1 NC_009957.1 PFAM: ErfK/YbiS/YcfS/YnhG family protein; KEGG: sil:SPO2205 ErfK/YbiS/YcfS/YnhG family protein; ErfK/YbiS/YcfS/YnhG family protein 117956 5714586 Dshi_4057 Dinoroseobacter shibae DFL 12 = DSM 16493 ErfK/YbiS/YcfS/YnhG family protein YP_001542265.1 117396 D 398580 CDS YP_001542266.1 159046596 5714587 117985..118443 1 NC_009957.1 PFAM: cytochrome c class I; KEGG: sil:SPOA0359 cytochrome c family protein; cytochrome c class I 118443 5714587 Dshi_4058 Dinoroseobacter shibae DFL 12 = DSM 16493 cytochrome c class I YP_001542266.1 117985 D 398580 CDS YP_001542267.1 159046597 5714588 118813..119406 1 NC_009957.1 KEGG: ret:RHE_CH02511 putative cytochrome c-like protein; putative cytochrome c-like protein 119406 5714588 Dshi_4059 Dinoroseobacter shibae DFL 12 = DSM 16493 putative cytochrome c-like protein YP_001542267.1 118813 D 398580 CDS YP_001542268.1 159046598 5714589 119409..120326 1 NC_009957.1 KEGG: psa:PST_0453 cytochrome c family protein; gluconate 2-dehydrogenase (acceptor) 120326 5714589 Dshi_4060 Dinoroseobacter shibae DFL 12 = DSM 16493 gluconate 2-dehydrogenase (acceptor) YP_001542268.1 119409 D 398580 CDS YP_001542269.1 159046599 5714590 120370..121764 1 NC_009957.1 PFAM: multicopper oxidase type 1; multicopper oxidase type 2; multicopper oxidase type 3; KEGG: sil:SPOA0360 multicopper oxidase, putative; multicopper oxidase type 3 121764 5714590 Dshi_4061 Dinoroseobacter shibae DFL 12 = DSM 16493 multicopper oxidase type 3 YP_001542269.1 120370 D 398580 CDS YP_001542270.1 159046600 5714591 121761..122243 1 NC_009957.1 PFAM: cytochrome c class I; KEGG: sil:SPOA0361 cytochrome c family protein; cytochrome c class I 122243 5714591 Dshi_4062 Dinoroseobacter shibae DFL 12 = DSM 16493 cytochrome c class I YP_001542270.1 121761 D 398580 CDS YP_001542271.1 159046601 5714592 122245..122976 1 NC_009957.1 PFAM: DSBA oxidoreductase; KEGG: sil:SPOA0362 27kDa outer membrane protein; DSBA oxidoreductase 122976 5714592 Dshi_4063 Dinoroseobacter shibae DFL 12 = DSM 16493 DSBA oxidoreductase YP_001542271.1 122245 D 398580 CDS YP_001542272.1 159046602 5714593 complement(123019..123219) 1 NC_009957.1 PFAM: Heavy metal transport/detoxification protein; KEGG: pen:PSEEN0671 copper-binding protein; heavy metal transport/detoxification protein 123219 5714593 Dshi_4064 Dinoroseobacter shibae DFL 12 = DSM 16493 heavy metal transport/detoxification protein YP_001542272.1 123019 R 398580 CDS YP_001542273.1 159046603 5714594 123373..125883 1 NC_009957.1 TIGRFAM: ATPase, P-type (transporting), HAD superfamily, subfamily IC; copper-translocating P-type ATPase; heavy metal translocating P-type ATPase; PFAM: Haloacid dehalogenase domain protein hydrolase; Heavy metal transport/detoxification protein; E1-E2 ATPase-associated domain protein; KEGG: sil:SPO0794 copper-translocating P-type ATPase; heavy metal translocating P-type ATPase 125883 5714594 Dshi_4065 Dinoroseobacter shibae DFL 12 = DSM 16493 heavy metal translocating P-type ATPase YP_001542273.1 123373 D 398580 CDS YP_001542274.1 159046604 5714595 125896..126294 1 NC_009957.1 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 126294 5714595 Dshi_4066 Dinoroseobacter shibae DFL 12 = DSM 16493 MerR family transcriptional regulator YP_001542274.1 125896 D 398580 CDS YP_001542275.1 159046606 5714613 complement(42..731) 1 NC_009958.1 hypothetical protein 731 5714613 Dshi_4067 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542275.1 42 R 398580 CDS YP_001542276.1 159046607 5714623 3168..6497 1 NC_009958.1 SMART: Parallel beta-helix repeat; KEGG: tcx:Tcr_0105 VCBS; parallel beta-helix repeat-containing protein 6497 5714623 Dshi_4071 Dinoroseobacter shibae DFL 12 = DSM 16493 parallel beta-helix repeat-containing protein YP_001542276.1 3168 D 398580 CDS YP_001542277.1 159046608 5714620 complement(7492..7764) 1 NC_009958.1 PFAM: transposase IS3/IS911 family protein; KEGG: xac:XAC4322 ISxac3 transposase; transposase IS3/IS911 family protein 7764 5714620 Dshi_4074 Dinoroseobacter shibae DFL 12 = DSM 16493 transposase IS3/IS911 family protein YP_001542277.1 7492 R 398580 CDS YP_001542278.1 159046609 5714618 8880..9245 1 NC_009958.1 hypothetical protein 9245 5714618 Dshi_4075 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542278.1 8880 D 398580 CDS YP_001542279.1 159046610 5714621 9370..10845 1 NC_009958.1 KEGG: rsp:RSP_3838 capsule polysaccharide export protein; capsule polysaccharide export protein 10845 5714621 Dshi_4076 Dinoroseobacter shibae DFL 12 = DSM 16493 capsule polysaccharide export protein YP_001542279.1 9370 D 398580 CDS YP_001542280.1 159046611 5714615 10862..11521 1 NC_009958.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: pde:Pden_5037 ABC transporter related; ABC transporter related 11521 5714615 Dshi_4077 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC transporter related YP_001542280.1 10862 D 398580 CDS YP_001542281.1 159046612 5714606 11557..11931 1 NC_009958.1 hypothetical protein 11931 5714606 Dshi_4078 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542281.1 11557 D 398580 CDS YP_001542282.1 159046613 5714602 12125..13507 1 NC_009958.1 PFAM: transposase IS4 family protein; KEGG: rde:RD1_3444 transposase, putative; transposase IS4 family protein 13507 5714602 Dshi_4079 Dinoroseobacter shibae DFL 12 = DSM 16493 transposase IS4 family protein YP_001542282.1 12125 D 398580 CDS YP_001542283.1 159046614 5714635 complement(13911..15719) 1 NC_009958.1 required for the synthesis of the hydromethylpyrimidine moiety of thiamine; thiamine biosynthesis protein ThiC 15719 5714635 Dshi_4080 Dinoroseobacter shibae DFL 12 = DSM 16493 thiamine biosynthesis protein ThiC YP_001542283.1 13911 R 398580 CDS YP_001542284.1 159046615 5714632 complement(16240..16839) 1 NC_009958.1 PFAM: Resolvase domain; Resolvase helix-turn-helix domain protein; KEGG: gox:GOX2646 DNA integration/recombination/invertion protein; resolvase domain-containing protein 16839 5714632 Dshi_4081 Dinoroseobacter shibae DFL 12 = DSM 16493 resolvase domain-containing protein YP_001542284.1 16240 R 398580 CDS YP_001542285.1 159046616 5714658 16978..18471 1 NC_009958.1 PFAM: Integrase catalytic region; Transposase-like Mu; KEGG: art:Arth_4385 integrase, catalytic region; integrase catalytic region 18471 5714658 Dshi_4082 Dinoroseobacter shibae DFL 12 = DSM 16493 integrase catalytic region YP_001542285.1 16978 D 398580 CDS YP_001542286.1 159046617 5714665 18468..19292 1 NC_009958.1 KEGG: art:Arth_4384 ATP-binding protein; ATP-binding protein 19292 5714665 Dshi_4083 Dinoroseobacter shibae DFL 12 = DSM 16493 ATP-binding protein YP_001542286.1 18468 D 398580 CDS YP_001542287.1 159046618 5714647 19415..19981 1 NC_009958.1 PFAM: Resolvase domain; Resolvase helix-turn-helix domain protein; KEGG: swi:Swit_5093 resolvase, N-terminal domain; resolvase domain-containing protein 19981 5714647 Dshi_4084 Dinoroseobacter shibae DFL 12 = DSM 16493 resolvase domain-containing protein YP_001542287.1 19415 D 398580 CDS YP_001542288.1 159046619 5714604 19968..20222 1 NC_009958.1 PFAM: WGR domain protein; KEGG: rsq:Rsph17025_4211 hypothetical protein; WGR domain-containing protein 20222 5714604 Dshi_4085 Dinoroseobacter shibae DFL 12 = DSM 16493 WGR domain-containing protein YP_001542288.1 19968 D 398580 CDS YP_001542289.1 159046620 5714600 20366..20572 1 NC_009958.1 KEGG: noc:Noc_2541 hypothetical protein; hypothetical protein 20572 5714600 Dshi_4086 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542289.1 20366 D 398580 CDS YP_001542290.1 159046621 5714633 20559..20852 1 NC_009958.1 PFAM: plasmid stabilization system; KEGG: pha:PSHAa2625 hypothetical protein; plasmid stabilization system protein 20852 5714633 Dshi_4087 Dinoroseobacter shibae DFL 12 = DSM 16493 plasmid stabilization system protein YP_001542290.1 20559 D 398580 CDS YP_001542291.1 159046622 5714643 20858..21250 1 NC_009958.1 hypothetical protein 21250 5714643 Dshi_4088 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542291.1 20858 D 398580 CDS YP_001542292.1 159046623 5714659 complement(21412..22221) 1 NC_009958.1 PFAM: Integrase catalytic region; KEGG: bbt:BBta_7691 integrase, catalytic domain; integrase catalytic region 22221 5714659 Dshi_4089 Dinoroseobacter shibae DFL 12 = DSM 16493 integrase catalytic region YP_001542292.1 21412 R 398580 CDS YP_001542293.1 159046624 5714634 complement(22245..22511) 1 NC_009958.1 PFAM: transposase IS3/IS911 family protein; KEGG: mag:amb0646 insertion element ISR1 hypothetical 10 kDa protein A3; transposase IS3/IS911 family protein 22511 5714634 Dshi_4090 Dinoroseobacter shibae DFL 12 = DSM 16493 transposase IS3/IS911 family protein YP_001542293.1 22245 R 398580 CDS YP_001542294.1 159046625 5714666 complement(22571..23200) 1 NC_009958.1 hypothetical protein 23200 5714666 Dshi_4091 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542294.1 22571 R 398580 CDS YP_001542295.1 159046626 5714644 complement(24188..25219) 1 NC_009958.1 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 25219 5714644 Dshi_4092 Dinoroseobacter shibae DFL 12 = DSM 16493 transposase IS116/IS110/IS902 family protein YP_001542295.1 24188 R 398580 CDS YP_001542296.1 159046627 5714645 complement(25327..25716) 1 NC_009958.1 PFAM: transposase IS4 family protein; KEGG: pde:Pden_3333 transposase, IS4 family protein; transposase IS4 family protein 25716 5714645 Dshi_4093 Dinoroseobacter shibae DFL 12 = DSM 16493 transposase IS4 family protein YP_001542296.1 25327 R 398580 CDS YP_001542297.1 159046628 5714641 complement(25737..26090) 1 NC_009958.1 KEGG: pde:Pden_2059 transposase orfA IS5 family element; IS5 family transposase OrfA 26090 5714641 Dshi_4094 Dinoroseobacter shibae DFL 12 = DSM 16493 IS5 family transposase OrfA YP_001542297.1 25737 R 398580 CDS YP_001542298.1 159046629 5714598 26734..27168 1 NC_009958.1 KEGG: bra:BRADO4296 putative insertion element (IS) transposase; putative insertion element (IS) transposase 27168 5714598 Dshi_4095 Dinoroseobacter shibae DFL 12 = DSM 16493 putative insertion element (IS) transposase YP_001542298.1 26734 D 398580 CDS YP_001542300.1 159046631 5714599 complement(30488..31699) 1 NC_009958.1 PFAM: replication protein C; KEGG: rsp:RSP_7387 replication initiator RepC; replication initiation protein RepC 31699 5714599 Dshi_4102 Dinoroseobacter shibae DFL 12 = DSM 16493 replication initiation protein RepC YP_001542300.1 30488 R 398580 CDS YP_001542301.1 159046632 5714640 complement(31914..32738) 1 NC_009958.1 TIGRFAM: parB-like partition protein; PFAM: ParB domain protein nuclease; KEGG: rsp:RSP_4185 RepB partitioning protein/ParB-like protein; parB-like partition protein 32738 5714640 Dshi_4103 Dinoroseobacter shibae DFL 12 = DSM 16493 parB-like partition protein YP_001542301.1 31914 R 398580 CDS YP_001542302.1 159046633 5714653 complement(32827..34020) 1 NC_009958.1 PFAM: regulatory protein MerR; Cobyrinic acid ac-diamide synthase; KEGG: rsp:RSP_4186 RepA partitioning protein/ATPase, ParA type; cobyrinic acid ac-diamide synthase 34020 5714653 Dshi_4104 Dinoroseobacter shibae DFL 12 = DSM 16493 cobyrinic acid ac-diamide synthase YP_001542302.1 32827 R 398580 CDS YP_001542303.1 159046634 5714630 complement(34155..35036) 1 NC_009958.1 PFAM: Resolvase domain; KEGG: rsp:RSP_2482 TonB-dependent receptor protein; resolvase domain-containing protein 35036 5714630 Dshi_4105 Dinoroseobacter shibae DFL 12 = DSM 16493 resolvase domain-containing protein YP_001542303.1 34155 R 398580 CDS YP_001542304.1 159046635 5714629 35263..36330 1 NC_009958.1 KEGG: rsh:Rsph17029_2968 hypothetical protein; hypothetical protein 36330 5714629 Dshi_4106 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542304.1 35263 D 398580 CDS YP_001542305.1 159046636 5714614 36463..37227 1 NC_009958.1 KEGG: smd:Smed_5442 transcriptional regulator; hypothetical protein 37227 5714614 Dshi_4107 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542305.1 36463 D 398580 CDS YP_001542306.1 159046637 5714612 37700..37960 1 NC_009958.1 hypothetical protein 37960 5714612 Dshi_4108 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542306.1 37700 D 398580 CDS YP_001542307.1 159046638 5714626 39318..39818 1 NC_009958.1 hypothetical protein 39818 5714626 Dshi_4109 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542307.1 39318 D 398580 CDS YP_001542308.1 159046639 5714611 39815..41992 1 NC_009958.1 hypothetical protein 41992 5714611 Dshi_4110 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542308.1 39815 D 398580 CDS YP_001542309.1 159046640 5714619 41989..44979 1 NC_009958.1 PFAM: integrase family protein; KEGG: shn:Shewana3_2354 phage integrase family protein; integrase family protein 44979 5714619 Dshi_4111 Dinoroseobacter shibae DFL 12 = DSM 16493 integrase family protein YP_001542309.1 41989 D 398580 CDS YP_001542310.1 159046641 5714617 45616..45843 1 NC_009958.1 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 45843 5714617 Dshi_4112 Dinoroseobacter shibae DFL 12 = DSM 16493 prevent-host-death family protein YP_001542310.1 45616 D 398580 CDS YP_001542311.1 159046642 5714652 45840..46232 1 NC_009958.1 TIGRFAM: death-on-curing family protein; PFAM: Death-on-curing protein; KEGG: hne:HNE_0348 putative addiction module toxin; death-on-curing family protein 46232 5714652 Dshi_4113 Dinoroseobacter shibae DFL 12 = DSM 16493 death-on-curing family protein YP_001542311.1 45840 D 398580 CDS YP_001542312.1 159046643 5714622 46419..46973 1 NC_009958.1 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 46973 5714622 Dshi_4114 Dinoroseobacter shibae DFL 12 = DSM 16493 dTDP-4-dehydrorhamnose 3,5-epimerase YP_001542312.1 46419 D 398580 CDS YP_001542313.1 159046644 5714616 46978..48018 1 NC_009958.1 TIGRFAM: dTDP-glucose 4,6-dehydratase; PFAM: NAD-dependent epimerase/dehydratase; short-chain dehydrogenase/reductase SDR; 3-beta hydroxysteroid dehydrogenase/isomerase; polysaccharide biosynthesis protein CapD; dTDP-4-dehydrorhamnose reductase; Male sterility domain; KEGG: rde:RD1_B0019 dTDP-glucose 4,6-dehydratase; dTDP-glucose 4,6-dehydratase 48018 5714616 Dshi_4115 Dinoroseobacter shibae DFL 12 = DSM 16493 dTDP-glucose 4,6-dehydratase YP_001542313.1 46978 D 398580 CDS YP_001542314.1 159046645 5714597 48022..48855 1 NC_009958.1 hypothetical protein 48855 5714597 Dshi_4116 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542314.1 48022 D 398580 CDS YP_001542315.1 159046646 5714607 48852..49709 1 NC_009958.1 PFAM: NAD-dependent epimerase/dehydratase; dTDP-4-dehydrorhamnose reductase; Male sterility domain; KEGG: rsp:RSP_3845 dTDP-4-dehydrorhamnose reductase; dTDP-4-dehydrorhamnose reductase 49709 5714607 Dshi_4117 Dinoroseobacter shibae DFL 12 = DSM 16493 dTDP-4-dehydrorhamnose reductase YP_001542315.1 48852 D 398580 CDS YP_001542316.1 159046647 5714605 49744..50616 1 NC_009958.1 TIGRFAM: glucose-1-phosphate thymidylyltransferase; PFAM: Nucleotidyl transferase; KEGG: sit:TM1040_3859 glucose-1-phosphate thymidylyltransferase; glucose-1-phosphate thymidylyltransferase 50616 5714605 Dshi_4118 Dinoroseobacter shibae DFL 12 = DSM 16493 glucose-1-phosphate thymidylyltransferase YP_001542316.1 49744 D 398580 CDS YP_001542317.1 159046648 5714663 50748..51629 1 NC_009958.1 PFAM: NAD-dependent epimerase/dehydratase; dTDP-4-dehydrorhamnose reductase; KEGG: rsq:Rsph17025_2629 NAD-dependent epimerase/dehydratase; NAD-dependent epimerase/dehydratase 51629 5714663 Dshi_4119 Dinoroseobacter shibae DFL 12 = DSM 16493 NAD-dependent epimerase/dehydratase YP_001542317.1 50748 D 398580 CDS YP_001542318.1 159046649 5714657 51626..52234 1 NC_009958.1 PFAM: sugar transferase; KEGG: rsh:Rsph17029_2851 sugar transferase; sugar transferase 52234 5714657 Dshi_4120 Dinoroseobacter shibae DFL 12 = DSM 16493 sugar transferase YP_001542318.1 51626 D 398580 CDS YP_001542319.1 159046650 5714667 52382..54934 1 NC_009958.1 PFAM: glycosyl transferase family 2; KEGG: aav:Aave_4142 glycosyl transferase, family 2; glycosyl transferase family protein 54934 5714667 Dshi_4121 Dinoroseobacter shibae DFL 12 = DSM 16493 glycosyl transferase family protein YP_001542319.1 52382 D 398580 CDS YP_001542320.1 159046651 5714662 54931..55707 1 NC_009958.1 hypothetical protein 55707 5714662 Dshi_4122 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542320.1 54931 D 398580 CDS YP_001542321.1 159046652 5714603 57015..59051 1 NC_009958.1 hypothetical protein 59051 5714603 Dshi_4125 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542321.1 57015 D 398580 CDS YP_001542322.1 159046653 5714636 60093..60374 1 NC_009958.1 KEGG: acr:Acry_3373 IstB domain protein ATP-binding protein; hypothetical protein 60374 5714636 Dshi_4128 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542322.1 60093 D 398580 CDS YP_001542323.1 159046654 5714668 complement(60514..61947) 1 NC_009958.1 PFAM: polysaccharide biosynthesis protein; KEGG: bvi:Bcep1808_6521 polysaccharide biosynthesis protein; polysaccharide biosynthesis protein 61947 5714668 Dshi_4129 Dinoroseobacter shibae DFL 12 = DSM 16493 polysaccharide biosynthesis protein YP_001542323.1 60514 R 398580 CDS YP_001542324.1 159046655 5714664 62343..64739 1 NC_009958.1 SMART: Parallel beta-helix repeat; parallel beta-helix repeat-containing protein 64739 5714664 Dshi_4130 Dinoroseobacter shibae DFL 12 = DSM 16493 parallel beta-helix repeat-containing protein YP_001542324.1 62343 D 398580 CDS YP_001542325.1 159046656 5714637 65809..66255 1 NC_009958.1 PFAM: Oligosaccharide biosynthesis protein Alg14 like; KEGG: mjl:Mjls_0958 oligosaccharide biosynthesis protein Alg14 like; oligosaccharide biosynthesis protein Alg14-like protein 66255 5714637 Dshi_4133 Dinoroseobacter shibae DFL 12 = DSM 16493 oligosaccharide biosynthesis protein Alg14-like protein YP_001542325.1 65809 D 398580 CDS YP_001542326.1 159046657 5714648 66252..66728 1 NC_009958.1 PFAM: Glycosyltransferase 28 domain; KEGG: rle:RL3655 putative glycosyltransferase; glycosyltransferase family 28 protein 66728 5714648 Dshi_4134 Dinoroseobacter shibae DFL 12 = DSM 16493 glycosyltransferase family 28 protein YP_001542326.1 66252 D 398580 CDS YP_001542327.1 159046658 5714650 66718..68040 1 NC_009958.1 KEGG: psa:PST_2497 hypothetical protein; hypothetical protein 68040 5714650 Dshi_4135 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542327.1 66718 D 398580 CDS YP_001542328.1 159046659 5714646 68033..69217 1 NC_009958.1 PFAM: polysaccharide pyruvyl transferase; KEGG: mfa:Mfla_2020 polysaccharide pyruvyl transferase; polysaccharide pyruvyl transferase 69217 5714646 Dshi_4136 Dinoroseobacter shibae DFL 12 = DSM 16493 polysaccharide pyruvyl transferase YP_001542328.1 68033 D 398580 CDS YP_001542329.1 159046660 5714639 complement(69126..70604) 1 NC_009958.1 KEGG: smd:Smed_4799 hypothetical protein; hypothetical protein 70604 5714639 Dshi_4137 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542329.1 69126 R 398580 CDS YP_001542330.1 159046661 5714649 complement(70715..71707) 1 NC_009958.1 hypothetical protein 71707 5714649 Dshi_4138 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542330.1 70715 R 398580 CDS YP_001542331.1 159046662 5714601 complement(71700..72764) 1 NC_009958.1 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 72764 5714601 Dshi_4139 Dinoroseobacter shibae DFL 12 = DSM 16493 GDP-mannose 4,6-dehydratase YP_001542331.1 71700 R 398580 CDS YP_001542332.1 159046663 5714656 complement(72811..73542) 1 NC_009958.1 PFAM: sulfotransferase; KEGG: bta:282485 sulfotransferase family, cytosolic, 1A, phenol-preferring, member 1; sulfotransferase 73542 5714656 Dshi_4140 Dinoroseobacter shibae DFL 12 = DSM 16493 sulfotransferase YP_001542332.1 72811 R 398580 CDS YP_001542333.1 159046664 5714660 complement(73755..74459) 1 NC_009958.1 KEGG: ava:Ava_1042 methyltransferase FkbM; hypothetical protein 74459 5714660 Dshi_4141 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542333.1 73755 R 398580 CDS YP_001542334.1 159046665 5714627 74668..75609 1 NC_009958.1 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 75609 5714627 Dshi_4142 Dinoroseobacter shibae DFL 12 = DSM 16493 NAD-dependent epimerase/dehydratase YP_001542334.1 74668 D 398580 CDS YP_001542335.1 159046666 5714628 75619..76494 1 NC_009958.1 PFAM: glycosyl transferase family 2; KEGG: nha:Nham_3045 glycosyl transferase, family 2; glycosyl transferase family protein 76494 5714628 Dshi_4143 Dinoroseobacter shibae DFL 12 = DSM 16493 glycosyl transferase family protein YP_001542335.1 75619 D 398580 CDS YP_001542336.1 159046667 5714610 complement(76612..77184) 1 NC_009958.1 PFAM: transferase hexapeptide repeat containing protein; KEGG: dde:Dde_3680 acetyltransferase (isoleucine patch superfamily)-like; hexapaptide repeat-containing transferase 77184 5714610 Dshi_4144 Dinoroseobacter shibae DFL 12 = DSM 16493 hexapaptide repeat-containing transferase YP_001542336.1 76612 R 398580 CDS YP_001542337.1 159046668 5714625 complement(77191..78195) 1 NC_009958.1 PFAM: glycosyl transferase family 2; KEGG: nar:Saro_3226 glycosyl transferase, family 2; glycosyl transferase family protein 78195 5714625 Dshi_4145 Dinoroseobacter shibae DFL 12 = DSM 16493 glycosyl transferase family protein YP_001542337.1 77191 R 398580 CDS YP_001542338.1 159046669 5714671 complement(78217..79641) 1 NC_009958.1 KEGG: sit:TM1040_3778 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; TIGRFAM: mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; PFAM: mannose-6-phosphate isomerase type II; Nucleotidyl transferase; Cupin 2 conserved barrel domain protein; mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase 79641 5714671 Dshi_4146 Dinoroseobacter shibae DFL 12 = DSM 16493 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase YP_001542338.1 78217 R 398580 CDS YP_001542339.1 159046670 5714672 complement(79830..80822) 1 NC_009958.1 PFAM: glycosyl transferase family 2; KEGG: rsh:Rsph17029_4080 glycosyl transferase, family 2; glycosyl transferase family protein 80822 5714672 Dshi_4147 Dinoroseobacter shibae DFL 12 = DSM 16493 glycosyl transferase family protein YP_001542339.1 79830 R 398580 CDS YP_001542340.1 159046671 5714673 complement(80815..81660) 1 NC_009958.1 PFAM: ABC-2 type transporter; KEGG: rsh:Rsph17029_4086 ABC-2 type transporter; ABC-2 type transporter 81660 5714673 Dshi_4148 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC-2 type transporter YP_001542340.1 80815 R 398580 CDS YP_001542341.1 159046672 5714674 81926..82657 1 NC_009958.1 PFAM: transferase hexapeptide repeat containing protein; KEGG: mag:amb0878 acetyltransferase; hexapaptide repeat-containing transferase 82657 5714674 Dshi_4149 Dinoroseobacter shibae DFL 12 = DSM 16493 hexapaptide repeat-containing transferase YP_001542341.1 81926 D 398580 CDS YP_001542342.1 159046673 5714675 82654..83457 1 NC_009958.1 hypothetical protein 83457 5714675 Dshi_4150 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542342.1 82654 D 398580 CDS YP_001542344.1 159046675 5714677 complement(84463..85098) 1 NC_009958.1 PFAM: autoinducer synthesis protein; KEGG: rde:RD1_1639 autoinducer synthesis protein TraL, putative; autoinducer synthesis protein 85098 5714677 Dshi_4152 Dinoroseobacter shibae DFL 12 = DSM 16493 autoinducer synthesis protein YP_001542344.1 84463 R 398580 CDS YP_001542345.1 159046677 5714694 complement(24..977) 1 NC_009959.1 PFAM: beta-lactamase domain protein; KEGG: sil:SPO1523 metallo-beta-lactamase family protein; beta-lactamase domain-containing protein 977 5714694 Dshi_4154 Dinoroseobacter shibae DFL 12 = DSM 16493 beta-lactamase domain-containing protein YP_001542345.1 24 R 398580 CDS YP_001542346.1 159046678 5714725 complement(977..1759) 1 NC_009959.1 KEGG: sil:SPO1524 hypothetical protein; hypothetical protein 1759 5714725 Dshi_4155 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542346.1 977 R 398580 CDS YP_001542347.1 159046679 5714726 1936..3684 1 NC_009959.1 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 3684 5714726 Dshi_4156 Dinoroseobacter shibae DFL 12 = DSM 16493 Fis family GAF modulated sigma54 specific transcriptional regulator YP_001542347.1 1936 D 398580 CDS YP_001542348.1 159046680 5714727 3833..5632 1 NC_009959.1 KEGG: rde:RD1_3706 monooxygenase; monooxygenase 5632 5714727 Dshi_4157 Dinoroseobacter shibae DFL 12 = DSM 16493 monooxygenase YP_001542348.1 3833 D 398580 CDS YP_001542349.2 251833004 5714728 5711..6484 1 NC_009959.1 TIGRFAM: acetoin reductase; PFAM: short-chain dehydrogenase/reductase SDR; KR domain protein; KEGG: rha:RHA1_ro05279 acetoin dehydrogenase; acetoin reductase 6484 5714728 Dshi_4158 Dinoroseobacter shibae DFL 12 = DSM 16493 acetoin reductase YP_001542349.2 5711 D 398580 CDS YP_001542350.1 159046682 5714729 6606..7658 1 NC_009959.1 PFAM: Alcohol dehydrogenase zinc-binding domain protein; Alcohol dehydrogenase GroES domain protein; KEGG: bha:BH3949 L-iditol 2-dehydrogenase; alcohol dehydrogenase 7658 5714729 Dshi_4159 Dinoroseobacter shibae DFL 12 = DSM 16493 alcohol dehydrogenase YP_001542350.1 6606 D 398580 CDS YP_001542351.1 159046683 5714730 complement(7713..8699) 1 NC_009959.1 Converts chlorophyllide a into protochlorophyllide; light dependent; protochlorophyllide oxidoreductase 8699 5714730 Dshi_4160 Dinoroseobacter shibae DFL 12 = DSM 16493 protochlorophyllide oxidoreductase YP_001542351.1 7713 R 398580 CDS YP_001542352.1 159046684 5714731 8902..9714 1 NC_009959.1 PFAM: MltA-interacting MipA family protein; KEGG: reu:Reut_A3319 MltA-interacting MipA; MltA-interacting MipA family protein 9714 5714731 Dshi_4161 Dinoroseobacter shibae DFL 12 = DSM 16493 MltA-interacting MipA family protein YP_001542352.1 8902 D 398580 CDS YP_001542353.1 159046685 5714732 complement(9725..10768) 1 NC_009959.1 PFAM: glycosyl transferase group 1; KEGG: pde:Pden_4362 glycosyl transferase, group 1; glycosyl transferase group 1 10768 5714732 Dshi_4162 Dinoroseobacter shibae DFL 12 = DSM 16493 glycosyl transferase group 1 YP_001542353.1 9725 R 398580 CDS YP_001542354.1 159046686 5714733 complement(10765..12342) 1 NC_009959.1 PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: jan:Jann_0308 binding-protein-dependent transport systems inner membrane component; binding-protein-dependent transport systems inner membrane component 12342 5714733 Dshi_4163 Dinoroseobacter shibae DFL 12 = DSM 16493 binding-protein-dependent transport systems inner membrane component YP_001542354.1 10765 R 398580 CDS YP_001542355.1 159046687 5714679 complement(12339..13145) 1 NC_009959.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: jan:Jann_0307 ABC transporter related; ABC transporter related 13145 5714679 Dshi_4164 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC transporter related YP_001542355.1 12339 R 398580 CDS YP_001542356.1 159046688 5714680 complement(13135..14130) 1 NC_009959.1 PFAM: NMT1/THI5 like domain protein; KEGG: jan:Jann_0306 twin-arginine translocation pathway signal; NMT1/THI5-like domain-containing protein 14130 5714680 Dshi_4165 Dinoroseobacter shibae DFL 12 = DSM 16493 NMT1/THI5-like domain-containing protein YP_001542356.1 13135 R 398580 CDS YP_001542357.1 159046689 5714681 complement(14227..15177) 1 NC_009959.1 KEGG: jan:Jann_0305 hypothetical protein; hypothetical protein 15177 5714681 Dshi_4166 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542357.1 14227 R 398580 CDS YP_001542358.1 159046690 5714682 complement(15174..16799) 1 NC_009959.1 PFAM: sulfatase; KEGG: jan:Jann_0304 hypothetical protein; sulfatase 16799 5714682 Dshi_4167 Dinoroseobacter shibae DFL 12 = DSM 16493 sulfatase YP_001542358.1 15174 R 398580 CDS YP_001542359.1 159046691 5714683 complement(16796..17545) 1 NC_009959.1 PFAM: CDP-alcohol phosphatidyltransferase; KEGG: pde:Pden_4357 CDP-alcohol phosphatidyltransferase; CDP-alcohol phosphatidyltransferase 17545 5714683 Dshi_4168 Dinoroseobacter shibae DFL 12 = DSM 16493 CDP-alcohol phosphatidyltransferase YP_001542359.1 16796 R 398580 CDS YP_001542360.1 159046692 5714684 17646..18203 1 NC_009959.1 PFAM: cytochrome B561; KEGG: jan:Jann_0302 cytochrome b561; cytochrome B561 18203 5714684 Dshi_4169 Dinoroseobacter shibae DFL 12 = DSM 16493 cytochrome B561 YP_001542360.1 17646 D 398580 CDS YP_001542361.1 159046693 5714685 18287..19852 1 NC_009959.1 necessary for biosynthesis of osmoregulated periplasmic glucans possibly involved in the transfer to the periplasmic space; glucosyltransferase MdoH 19852 5714685 Dshi_4170 Dinoroseobacter shibae DFL 12 = DSM 16493 glucosyltransferase MdoH YP_001542361.1 18287 D 398580 CDS YP_001542362.1 159046694 5714686 19852..21336 1 NC_009959.1 involved in the control of the structural glucose backbone of osmoregulated periplasmic glucans; glucan biosynthesis protein D 21336 mdoD 5714686 mdoD Dinoroseobacter shibae DFL 12 = DSM 16493 glucan biosynthesis protein D YP_001542362.1 19852 D 398580 CDS YP_001542363.1 159046695 5714687 21403..22290 1 NC_009959.1 PFAM: helix-turn-helix- domain containing protein AraC type; KEGG: rde:RD1_0248 transcriptional regulator, AraC family; AraC family transcriptional regulator 22290 5714687 Dshi_4172 Dinoroseobacter shibae DFL 12 = DSM 16493 AraC family transcriptional regulator YP_001542363.1 21403 D 398580 CDS YP_001542364.1 159046696 5714688 22428..23387 1 NC_009959.1 KEGG: jan:Jann_1319 hypothetical protein; hypothetical protein 23387 5714688 Dshi_4173 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542364.1 22428 D 398580 CDS YP_001542365.1 159046697 5714689 23458..24015 1 NC_009959.1 KEGG: jan:Jann_1320 hypothetical protein; hypothetical protein 24015 5714689 Dshi_4174 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542365.1 23458 D 398580 CDS YP_001542366.2 251833005 5714690 complement(24079..25098) 1 NC_009959.1 PFAM: protein of unknown function UPF0118; KEGG: rde:RD1_2476 hypothetical protein; hypothetical protein 25098 5714690 Dshi_4175 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542366.2 24079 R 398580 CDS YP_001542367.1 159046699 5714691 25262..25924 1 NC_009959.1 PFAM: oxidoreductase FAD/NAD(P)-binding domain protein; KEGG: eli:ELI_11485 oxidoreductase; oxidoreductase FAD/NAD(P)-binding subunit 25924 5714691 Dshi_4176 Dinoroseobacter shibae DFL 12 = DSM 16493 oxidoreductase FAD/NAD(P)-binding subunit YP_001542367.1 25262 D 398580 CDS YP_001542368.1 159046700 5714692 complement(26016..27332) 1 NC_009959.1 PFAM: Acetamidase/Formamidase; KEGG: rsh:Rsph17029_3153 acetamidase/formamidase; acetamidase/formamidase 27332 5714692 Dshi_4177 Dinoroseobacter shibae DFL 12 = DSM 16493 acetamidase/formamidase YP_001542368.1 26016 R 398580 CDS YP_001542369.1 159046701 5714693 complement(27466..28224) 1 NC_009959.1 KEGG: rde:RD1_2481 hypothetical protein; hypothetical protein 28224 5714693 Dshi_4178 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542369.1 27466 R 398580 CDS YP_001542370.1 159046702 5714710 complement(28217..28627) 1 NC_009959.1 PFAM: protein of unknown function DUF1469; KEGG: rde:RD1_2479 hypothetical protein; hypothetical protein 28627 5714710 Dshi_4179 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542370.1 28217 R 398580 CDS YP_001542371.1 159046703 5714711 complement(28620..29135) 1 NC_009959.1 KEGG: rde:RD1_2478 hypothetical protein; hypothetical protein 29135 5714711 Dshi_4180 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542371.1 28620 R 398580 CDS YP_001542372.1 159046704 5714712 complement(29307..29495) 1 NC_009959.1 KEGG: jan:Jann_3633 hypothetical protein; hypothetical protein 29495 5714712 Dshi_4181 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542372.1 29307 R 398580 CDS YP_001542373.1 159046705 5714713 29547..30521 1 NC_009959.1 PFAM: MscS Mechanosensitive ion channel; KEGG: rde:RD1_2453 hypothetical protein; MscS mechanosensitive ion channel 30521 5714713 Dshi_4182 Dinoroseobacter shibae DFL 12 = DSM 16493 MscS mechanosensitive ion channel YP_001542373.1 29547 D 398580 CDS YP_001542374.1 159046706 5714714 complement(30634..30933) 1 NC_009959.1 hypothetical protein 30933 5714714 Dshi_4183 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542374.1 30634 R 398580 CDS YP_001542375.1 159046707 5714715 complement(31088..31285) 1 NC_009959.1 PFAM: CsbD family protein; KEGG: jan:Jann_3572 CsbD-like; CsbD family protein 31285 5714715 Dshi_4184 Dinoroseobacter shibae DFL 12 = DSM 16493 CsbD family protein YP_001542375.1 31088 R 398580 CDS YP_001542376.1 159046708 5714716 31537..32229 1 NC_009959.1 PFAM: regulatory protein GntR HTH; GntR domain protein; KEGG: ent:Ent638_0750 GntR domain protein; GntR family transcriptional regulator 32229 5714716 Dshi_4185 Dinoroseobacter shibae DFL 12 = DSM 16493 GntR family transcriptional regulator YP_001542376.1 31537 D 398580 CDS YP_001542377.1 159046709 5714717 32317..33138 1 NC_009959.1 PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sme:SMc02346 ATP-binding ABC transporter protein; ABC transporter related 33138 5714717 Dshi_4186 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC transporter related YP_001542377.1 32317 D 398580 CDS YP_001542378.1 159046710 5714718 33135..33890 1 NC_009959.1 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 33890 5714718 Dshi_4187 Dinoroseobacter shibae DFL 12 = DSM 16493 binding-protein-dependent transport systems inner membrane component YP_001542378.1 33135 D 398580 CDS YP_001542379.1 159046711 5714719 33904..34665 1 NC_009959.1 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 34665 5714719 Dshi_4188 Dinoroseobacter shibae DFL 12 = DSM 16493 binding-protein-dependent transport systems inner membrane component YP_001542379.1 33904 D 398580 CDS YP_001542380.1 159046712 5714720 34761..35777 1 NC_009959.1 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 35777 5714720 Dshi_4189 Dinoroseobacter shibae DFL 12 = DSM 16493 ABC-type nitrate/sulfonate/bicarbonate transport systems periplasmic components-like protein YP_001542380.1 34761 D 398580 CDS YP_001542381.1 159046713 5714721 35941..37218 1 NC_009959.1 KEGG: mac:MA1904 hypothetical protein; hypothetical protein 37218 5714721 Dshi_4190 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542381.1 35941 D 398580 CDS YP_001542382.1 159046714 5714722 37297..38292 1 NC_009959.1 TIGRFAM: TRAP dicarboxylate transporter, DctP subunit; PFAM: TRAP dicarboxylate transporter- DctP subunit; KEGG: sit:TM1040_3319 TRAP dicarboxylate transporter, DctP subunit; TRAP dicarboxylate transporter, DctP subunit 38292 5714722 Dshi_4191 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP dicarboxylate transporter, DctP subunit YP_001542382.1 37297 D 398580 CDS YP_001542383.1 159046715 5714723 38385..38972 1 NC_009959.1 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 38972 5714723 Dshi_4192 Dinoroseobacter shibae DFL 12 = DSM 16493 tripartite ATP-independent periplasmic transporter DctQ YP_001542383.1 38385 D 398580 CDS YP_001542384.1 159046716 5714724 38969..40258 1 NC_009959.1 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 40258 5714724 Dshi_4193 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP dicarboxylate transporter, DctM subunit YP_001542384.1 38969 D 398580 CDS YP_001542385.1 159046717 5714695 complement(40279..41874) 1 NC_009959.1 PFAM: gamma-glutamyltranspeptidase; KEGG: rde:RD1_2179 gamma-glutamyltranspeptidase; gamma-glutamyltransferase 41874 5714695 Dshi_4194 Dinoroseobacter shibae DFL 12 = DSM 16493 gamma-glutamyltransferase YP_001542385.1 40279 R 398580 CDS YP_001542386.1 159046718 5714696 complement(41874..43385) 1 NC_009959.1 PFAM: protein of unknown function DUF112 transmembrane; KEGG: oih:OB3268 hypothetical protein; hypothetical protein 43385 5714696 Dshi_4195 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542386.1 41874 R 398580 CDS YP_001542387.1 159046719 5714697 complement(43389..43895) 1 NC_009959.1 KEGG: oih:OB3269 hypothetical protein; hypothetical protein 43895 5714697 Dshi_4196 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542387.1 43389 R 398580 CDS YP_001542388.1 159046720 5714698 complement(43895..44845) 1 NC_009959.1 PFAM: conserved hypothetical protein; KEGG: oih:OB3270 hypothetical protein; hypothetical protein 44845 5714698 Dshi_4197 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542388.1 43895 R 398580 CDS YP_001542389.1 159046721 5714699 44976..45887 1 NC_009959.1 PFAM: regulatory protein LysR; LysR substrate-binding; KEGG: pde:Pden_3415 transcriptional regulator, LysR family; LysR family transcriptional regulator 45887 5714699 Dshi_4198 Dinoroseobacter shibae DFL 12 = DSM 16493 LysR family transcriptional regulator YP_001542389.1 44976 D 398580 CDS YP_001542390.1 159046722 5714700 complement(45953..46597) 1 NC_009959.1 PFAM: regulatory protein TetR; KEGG: rle:pRL80035 TetR family transcriptional regulator; TetR family transcriptional regulator 46597 5714700 Dshi_4199 Dinoroseobacter shibae DFL 12 = DSM 16493 TetR family transcriptional regulator YP_001542390.1 45953 R 398580 CDS YP_001542391.1 159046723 5714701 46743..47576 1 NC_009959.1 PFAM: molybdopterin dehydrogenase FAD-binding; CO dehydrogenase flavoprotein domain protein; KEGG: bja:bll6239 probable carbon monoxide dehydrogenase medium chain; carbon-monoxide dehydrogenase (acceptor) 47576 5714701 Dshi_4200 Dinoroseobacter shibae DFL 12 = DSM 16493 carbon-monoxide dehydrogenase (acceptor) YP_001542391.1 46743 D 398580 CDS YP_001542392.1 159046724 5714702 47573..48073 1 NC_009959.1 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 48073 5714702 Dshi_4201 Dinoroseobacter shibae DFL 12 = DSM 16493 2Fe-2S iron-sulfur cluster binding domain-containing protein YP_001542392.1 47573 D 398580 CDS YP_001542393.1 159046725 5714703 48070..50451 1 NC_009959.1 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) 50451 5714703 Dshi_4202 Dinoroseobacter shibae DFL 12 = DSM 16493 carbon-monoxide dehydrogenase (acceptor) YP_001542393.1 48070 D 398580 CDS YP_001542394.1 159046726 5714704 50499..51551 1 NC_009959.1 PFAM: TRAP dicarboxylate transporter- DctP subunit; KEGG: jan:Jann_0870 TRAP dicarboxylate transporter-DctP subunit; TRAP dicarboxylate transporter- DctP subunit 51551 5714704 Dshi_4203 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP dicarboxylate transporter- DctP subunit YP_001542394.1 50499 D 398580 CDS YP_001542395.1 159046727 5714705 51618..52199 1 NC_009959.1 KEGG: jan:Jann_2036 hypothetical protein; hypothetical protein 52199 5714705 Dshi_4204 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542395.1 51618 D 398580 CDS YP_001542396.1 159046728 5714706 52196..53524 1 NC_009959.1 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 53524 5714706 Dshi_4205 Dinoroseobacter shibae DFL 12 = DSM 16493 TRAP dicarboxylate transporter, DctM subunit YP_001542396.1 52196 D 398580 CDS YP_001542397.1 159046729 5714707 53586..54509 1 NC_009959.1 PFAM: aminotransferase class IV; KEGG: jan:Jann_2852 aminotransferase, class IV; aminotransferase class IV 54509 5714707 Dshi_4206 Dinoroseobacter shibae DFL 12 = DSM 16493 aminotransferase class IV YP_001542397.1 53586 D 398580 CDS YP_001542398.1 159046730 5714708 54580..55551 1 NC_009959.1 PFAM: protein of unknown function DUF900 hydrolase family protein; KEGG: rde:RD1_3768 hypothetical protein; hypothetical protein 55551 5714708 Dshi_4207 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542398.1 54580 D 398580 CDS YP_001542399.1 159046731 5714709 complement(55567..56109) 1 NC_009959.1 KEGG: sil:SPO0302 hypothetical protein; hypothetical protein 56109 5714709 Dshi_4208 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542399.1 55567 R 398580 CDS YP_001542400.1 159046732 5714738 complement(56106..57956) 1 NC_009959.1 PFAM: glycerophosphoryl diester phosphodiesterase; KEGG: rde:RD1_0308 glycerophosphoryl diester phosphodiesterase family protein; glycerophosphoryl diester phosphodiesterase 57956 5714738 Dshi_4209 Dinoroseobacter shibae DFL 12 = DSM 16493 glycerophosphoryl diester phosphodiesterase YP_001542400.1 56106 R 398580 CDS YP_001542401.1 159046733 5714739 complement(58042..58482) 1 NC_009959.1 PFAM: PilT protein domain protein; KEGG: gvi:glr1678 plasmid stabilization protein StbB homolog; twitching motility protein PilT 58482 5714739 Dshi_4210 Dinoroseobacter shibae DFL 12 = DSM 16493 twitching motility protein PilT YP_001542401.1 58042 R 398580 CDS YP_001542402.1 159046734 5714740 complement(58479..58724) 1 NC_009959.1 KEGG: gvi:gsr1677 hypothetical protein; hypothetical protein 58724 5714740 Dshi_4211 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542402.1 58479 R 398580 CDS YP_001542403.1 159046735 5714741 complement(58898..60001) 1 NC_009959.1 PFAM: ParB domain protein nuclease; KEGG: rsq:Rsph17025_3691 hypothetical protein; nuclease 60001 5714741 Dshi_4212 Dinoroseobacter shibae DFL 12 = DSM 16493 nuclease YP_001542403.1 58898 R 398580 CDS YP_001542404.1 159046736 5714742 complement(59994..61394) 1 NC_009959.1 PFAM: Cobyrinic acid ac-diamide synthase; KEGG: sit:TM1040_3406 cobyrinic acid a,c-diamide synthase; cobyrinic acid ac-diamide synthase 61394 5714742 Dshi_4213 Dinoroseobacter shibae DFL 12 = DSM 16493 cobyrinic acid ac-diamide synthase YP_001542404.1 59994 R 398580 CDS YP_001542405.1 159046737 5714743 61901..63073 1 NC_009959.1 PFAM: initiator RepB protein; KEGG: rsq:Rsph17025_3693 hypothetical protein; initiator RepB protein 63073 5714743 Dshi_4214 Dinoroseobacter shibae DFL 12 = DSM 16493 initiator RepB protein YP_001542405.1 61901 D 398580 CDS YP_001542406.1 159046738 5714744 63125..63772 1 NC_009959.1 KEGG: sru:SRU_1591 hypothetical protein; hypothetical protein 63772 5714744 Dshi_4215 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542406.1 63125 D 398580 CDS YP_001542407.1 159046739 5714745 63812..65134 1 NC_009959.1 PFAM: ABC-1 domain protein; KEGG: rpb:RPB_4322 ABC-1; hypothetical protein 65134 5714745 Dshi_4216 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542407.1 63812 D 398580 CDS YP_001542408.1 159046740 5714746 complement(65138..66145) 1 NC_009959.1 PFAM: regulatory protein LacI; periplasmic binding protein/LacI transcriptional regulator; KEGG: acr:Acry_2432 alanine racemase; LacI family transcription regulator 66145 5714746 Dshi_4217 Dinoroseobacter shibae DFL 12 = DSM 16493 LacI family transcription regulator YP_001542408.1 65138 R 398580 CDS YP_001542409.1 159046741 5714747 66272..67225 1 NC_009959.1 PFAM: conserved hypothetical protein; KEGG: bbr:BB4749 hypothetical protein; hypothetical protein 67225 5714747 Dshi_4218 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542409.1 66272 D 398580 CDS YP_001542410.1 159046742 5714748 67292..67747 1 NC_009959.1 hypothetical protein 67747 5714748 Dshi_4219 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542410.1 67292 D 398580 CDS YP_001542411.1 159046743 5714749 67749..69233 1 NC_009959.1 PFAM: protein of unknown function DUF112 transmembrane; KEGG: jan:Jann_1159 protein of unknown function DUF112, transmembrane; hypothetical protein 69233 5714749 Dshi_4220 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542411.1 67749 D 398580 CDS YP_001542412.1 159046744 5714750 69235..70116 1 NC_009959.1 PFAM: 6-phosphogluconate dehydrogenase NAD-binding; KEGG: rde:RD1_3786 3-hydroxyisobutyrate dehydrogenase; 2-hydroxy-3-oxopropionate reductase 70116 5714750 Dshi_4221 Dinoroseobacter shibae DFL 12 = DSM 16493 2-hydroxy-3-oxopropionate reductase YP_001542412.1 69235 D 398580 CDS YP_001542413.1 159046745 5714751 70201..70617 1 NC_009959.1 KEGG: rde:RD1_0908 hypothetical protein; hypothetical protein 70617 5714751 Dshi_4222 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542413.1 70201 D 398580 CDS YP_001542414.1 159046746 5714734 70690..71160 1 NC_009959.1 PFAM: Ferritin Dps family protein; KEGG: rde:RD1_0909 hypothetical protein; Ferritin Dps family protein 71160 5714734 Dshi_4223 Dinoroseobacter shibae DFL 12 = DSM 16493 Ferritin Dps family protein YP_001542414.1 70690 D 398580 CDS YP_001542415.1 159046747 5714735 complement(71161..71427) 1 NC_009959.1 KEGG: rde:RD1_0910 hypothetical protein; hypothetical protein 71427 5714735 Dshi_4224 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542415.1 71161 R 398580 CDS YP_001542416.1 159046748 5714736 complement(71437..71592) 1 NC_009959.1 hypothetical protein 71592 5714736 Dshi_4225 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542416.1 71437 R 398580 CDS YP_001542417.2 251833006 5714737 71714..72295 1 NC_009959.1 KEGG: sil:SPO1522 hypothetical protein; hypothetical protein 72295 5714737 Dshi_4226 Dinoroseobacter shibae DFL 12 = DSM 16493 hypothetical protein YP_001542417.2 71714 D 398580 CDS