Dinoroseobacter shibae DFL 12 = DSM 16493 plasmid pDSHI02, complete sequence.
Dinoroseobacter shibae DFL 12 = DSM 16493
Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodobacterales; Roseobacteraceae; Dinoroseobacter.
Complete sequence of chromosome of Dinoroseobacter shibae DFL 12
The Roseobacter - microalgae symbiosis: Adaptation to viral pressure, horizontal gene transfer, and ability to synthesize vitamine B12 under all conditions are revealed by the genome sequence
Submitted (06-JUL-2009) HZI-Braunschweig, Braunschweig, Germany
Submitted (21-SEP-2007) US DOE Joint Genome Institute, 2800 Mitchell Drive B100, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP000832.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4002768\nSource DNA and bacteria available from Irene Wagner-Dobler\n(Irene.Wagner-Doebler@helmholtz-hzi.de)\nContacts: Irene Wagner-Dobler\n(Irene.Wagner-Doebler@helmholtz-hzi.de)\n Paul Richardson (microbes@cuba.jgi-psf.org)\nQuality assurance done by JGI-Stanford\nAnnotation done by JGI-ORNL and JGI-PGF\nFinishing done by JGI-LANL\nFinished microbial genomes have been curated to close all gaps with\ngreater than 98% coverage of at least two independent clones. Each\nbase pair has a minimum q (quality) value of 30 and the total error\nrate is less than one per 50000.\nThe JGI and collaborators endorse the principles for the\ndistribution and use of large scale sequencing data adopted by the\nlarger genome sequencing community and urge users of this data to\nfollow them. It is our intention to publish the work of this\nproject in a timely fashion and we welcome collaborative\ninteraction on the project and analysis.\n(http://www.genome.gov/page.cfm?pageID=10506376).\nThe annotation was added by the NCBI Prokaryotic Genome Annotation\nPipeline (PGAP). Information about PGAP can be found here:\nhttps://www.ncbi.nlm.nih.gov/genome/annotation_prok/\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 05/02/2023 02:01:02\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.5\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 4,328\nCDSs (total) :: 4,274\nGenes (coding) :: 4,219\nCDSs (with protein) :: 4,219\nGenes (RNA) :: 54\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 44\nncRNAs :: 4\nPseudo Genes (total) :: 55\nCDSs (without protein) :: 55\nPseudo Genes (ambiguous residues) :: 0 of 55\nPseudo Genes (frameshifted) :: 20 of 55\nPseudo Genes (incomplete) :: 37 of 55\nPseudo Genes (internal stop) :: 17 of 55\nPseudo Genes (multiple problems) :: 19 of 55\nCRISPR Arrays :: 2\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_012115356.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_012746005.1
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007813805.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019966206.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011156322.1
COORDINATES: similar to AA sequence:RefSeq:WP_008885454.1
GO:0036361 - racemase activity, acting on amino acids and derivatives [Evidence IEA]
GO:0006807 - nitrogen compound metabolic process [Evidence IEA]
aspartate/glutamate racemase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013067202.1
COORDINATES: similar to AA sequence:RefSeq:WP_009806178.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_012187194.1
GO:0004096 - catalase activity [Evidence IEA]; GO:0004601 - peroxidase activity [Evidence IEA]
GO:0006979 - response to oxidative stress [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003505612.1
hydrogen peroxide-inducible genes activator
COORDINATES: similar to AA sequence:RefSeq:WP_008233805.1
COORDINATES: similar to AA sequence:RefSeq:WP_019402136.1
GO:0051139 - metal cation:proton antiporter activity [Evidence IEA]
GO:0098662 - inorganic cation transmembrane transport [Evidence IEA]
monovalent cation/H+ antiporter subunit A
COORDINATES: similar to AA sequence:RefSeq:WP_011456833.1
COORDINATES: similar to AA sequence:RefSeq:WP_007815049.1
monovalent cation/H+ antiporter subunit D
COORDINATES: similar to AA sequence:RefSeq:WP_009816488.1
GO:0008324 - monoatomic cation transmembrane transporter activity [Evidence IEA]
GO:0006812 - monoatomic cation transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011456836.1
GO:0015075 - monoatomic ion transmembrane transporter activity [Evidence IEA]
GO:0034220 - monoatomic ion transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009806006.1
COORDINATES: similar to AA sequence:RefSeq:WP_014878843.1
GO:0004334 - fumarylacetoacetase activity [Evidence IEA]
GO:0006559 - L-phenylalanine catabolic process [Evidence IEA]; GO:0006572 - tyrosine catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008229445.1
GO:0004411 - homogentisate 1,2-dioxygenase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008887683.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010437560.1
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005857204.1
COORDINATES: similar to AA sequence:RefSeq:WP_018304763.1
COORDINATES: similar to AA sequence:RefSeq:WP_011046507.1
GO:0016747 - acyltransferase activity, transferring groups other than amino-acyl groups [Evidence IEA]
GO:0019619 - 3,4-dihydroxybenzoate catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014879085.1
GO:0097266 - phenylacetyl-CoA 1,2-epoxidase activity [Evidence IEA]
GO:0010124 - phenylacetate catabolic process [Evidence IEA]
1,2-phenylacetyl-CoA epoxidase subunit PaaA
COORDINATES: similar to AA sequence:RefSeq:WP_011046505.1
1,2-phenylacetyl-CoA epoxidase subunit PaaB
COORDINATES: similar to AA sequence:RefSeq:WP_007118521.1
1,2-phenylacetyl-CoA epoxidase subunit PaaC
COORDINATES: similar to AA sequence:RefSeq:WP_008756374.1
1,2-phenylacetyl-CoA epoxidase subunit PaaD
COORDINATES: similar to AA sequence:RefSeq:WP_009831495.1
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0051536 - iron-sulfur cluster binding [Evidence IEA]
2Fe-2S iron-sulfur cluster-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_019297692.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_005978269.1
GO:0047475 - phenylacetate-CoA ligase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014880891.1
hydroxyphenylacetyl-CoA thioesterase PaaI
COORDINATES: similar to AA sequence:RefSeq:WP_011046488.1
GO:0070403 - NAD+ binding [Evidence IEA]
GO:0006631 - fatty acid metabolic process [Evidence IEA]
3-hydroxyacyl-CoA dehydrogenase NAD-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014875584.1
phenylacetic acid degradation bifunctional protein PaaZ
COORDINATES: protein motif:HMM:NF019463.2
PaaX family transcriptional regulator C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014748234.1
GO:0009331 - glycerol-3-phosphate dehydrogenase complex [Evidence IEA]
GO:0047952 - glycerol-3-phosphate dehydrogenase [NAD(P)+] activity [Evidence IEA]; GO:0051287 - NAD binding [Evidence IEA]
GO:0046167 - glycerol-3-phosphate biosynthetic process [Evidence IEA]
NAD(P)H-dependent glycerol-3-phosphate dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_007198558.1
COORDINATES: protein motif:HMM:NF013173.2
GO:0033828 - glucosylglycerol-phosphate synthase activity [Evidence IEA]
GO:0006970 - response to osmotic stress [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005858332.1
COORDINATES: protein motif:HMM:NF019174.2
COORDINATES: similar to AA sequence:RefSeq:WP_008553468.1
COORDINATES: similar to AA sequence:RefSeq:WP_008283222.1
COORDINATES: similar to AA sequence:RefSeq:WP_002721808.1
COORDINATES: similar to AA sequence:RefSeq:WP_015135366.1
COORDINATES: similar to AA sequence:RefSeq:WP_005622789.1
DNA starvation/stationary phase protection protein
COORDINATES: similar to AA sequence:RefSeq:WP_005982054.1
GO:0003824 - catalytic activity [Evidence IEA]; GO:0000287 - magnesium ion binding [Evidence IEA]; GO:0030976 - thiamine pyrophosphate binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017628608.1
GO:0016639 - oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor [Evidence IEA]
GO:0006520 - amino acid metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013173747.1
COORDINATES: similar to AA sequence:RefSeq:WP_011456685.1
GO:0030552 - cAMP binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
Crp/Fnr family transcriptional regulator
COORDINATES: protein motif:HMM:NF023069.2
DnaA N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008209744.1
COORDINATES: similar to AA sequence:RefSeq:WP_011749186.1
ParB N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008235471.1
PLD nuclease N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008688216.1
COORDINATES: similar to AA sequence:RefSeq:WP_008231986.1
GO:0006353 - DNA-templated transcription termination [Evidence IEA]
Rho termination factor N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF014171.2
TrkA C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008335981.1
COORDINATES: similar to AA sequence:RefSeq:WP_009503864.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011536551.1
COORDINATES: similar to AA sequence:RefSeq:WP_020043761.1
COORDINATES: protein motif:HMM:NF014273.2
COORDINATES: similar to AA sequence:RefSeq:WP_009175289.1
GO:0000271 - polysaccharide biosynthetic process [Evidence IEA]
nucleoside-diphosphate sugar epimerase/dehydratase
COORDINATES: similar to AA sequence:RefSeq:WP_020041627.1
COORDINATES: protein motif:HMM:NF022552.2
COORDINATES: similar to AA sequence:RefSeq:WP_008994567.1
GO:0051287 - NAD binding [Evidence IEA]; GO:0016616 - oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor [Evidence IEA]; GO:0003979 - UDP-glucose 6-dehydrogenase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF019552.2
GO:0016829 - lyase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF016145.2
GO:0016757 - glycosyltransferase activity [Evidence IEA]
polysaccharide pyruvyl transferase family protein
COORDINATES: protein motif:HMM:NF012888.2
GO:0008146 - sulfotransferase activity [Evidence IEA]
sulfotransferase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017933424.1
COORDINATES: protein motif:HMM:NF024831.2
COORDINATES: similar to AA sequence:RefSeq:WP_008186594.1
GO:0003978 - UDP-glucose 4-epimerase activity [Evidence IEA]
GO:0006012 - galactose metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF012318.2
GO:0004252 - serine-type endopeptidase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012573.2
RTX toxins and related Ca2+-binding protein-like protein
GO:0005509 - calcium ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007406871.1
COORDINATES: similar to AA sequence:RefSeq:WP_003939267.1
Mu transposase C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013635075.1
COORDINATES: nucleotide motif:Rfam:14.4:RF00059
TPP riboswitch; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: similar to AA sequence:RefSeq:WP_020042767.1
GO:0051536 - iron-sulfur cluster binding [Evidence IEA]
GO:0009228 - thiamine biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009824789.1
COORDINATES: similar to AA sequence:RefSeq:WP_005859586.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011568652.1
GO:0015297 - antiporter activity [Evidence IEA]; GO:0042910 - xenobiotic transmembrane transporter activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF024491.2
phospholipase D-like domain-containing protein
COORDINATES: protein motif:HMM:NF015674.2
COORDINATES: protein motif:HMM:NF012264.2
COORDINATES: similar to AA sequence:RefSeq:WP_016846403.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012522144.1
COORDINATES: protein motif:HMM:TIGR02891.1
GO:0004129 - cytochrome-c oxidase activity [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR02866.1
COORDINATES: similar to AA sequence:RefSeq:WP_008973019.1
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0020037 - heme binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008382400.1
COORDINATES: similar to AA sequence:RefSeq:WP_009824247.1
gluconate 2-dehydrogenase subunit 3 family protein
COORDINATES: similar to AA sequence:RefSeq:WP_005848748.1
GO:0005886 - plasma membrane [Evidence IEA]
COORDINATES: protein motif:HMM:NF012356.2
GO:0003824 - catalytic activity [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007426955.1
COORDINATES: similar to AA sequence:RefSeq:WP_007426954.1
COORDINATES: protein motif:HMM:NF013069.2
GO:0022857 - transmembrane transporter activity [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR01730.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_014437566.1
COORDINATES: protein motif:HMM:TIGR00813.1
COORDINATES: similar to AA sequence:RefSeq:WP_007256757.1
GO:0008381 - mechanosensitive monoatomic ion channel activity [Evidence IEA]
mechanosensitive ion channel family protein
COORDINATES: similar to AA sequence:RefSeq:WP_008332312.1
COORDINATES: protein motif:HMM:NF013740.2
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]
GO:1905887 - autoinducer AI-2 transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011370480.1
COORDINATES: protein motif:HMM:TIGR02037.1
GO:0030288 - outer membrane-bounded periplasmic space [Evidence IEA]
GO:0005515 - protein binding [Evidence IEA]; GO:0004252 - serine-type endopeptidase activity [Evidence IEA]
GO:0006508 - proteolysis [Evidence IEA]; GO:0006950 - response to stress [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018304646.1
GO:0016722 - oxidoreductase activity, acting on metal ions [Evidence IEA]
DNA starvation/stationary phase protection protein Dps
COORDINATES: similar to AA sequence:RefSeq:WP_011568647.1
GO:0006813 - potassium ion transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011568648.1
GO:0006812 - monoatomic cation transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020040189.1
COORDINATES: similar to AA sequence:RefSeq:WP_011455327.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120166.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120710.1
GO:0042314 - bacteriochlorophyll binding [Evidence IEA]
GO:0019684 - photosynthesis, light reaction [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076611345.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011568649.1
GO:0015499 - formate transmembrane transporter activity [Evidence IEA]
GO:0015724 - formate transport [Evidence IEA]
formate/nitrite transporter family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011568653.1
COORDINATES: similar to AA sequence:RefSeq:WP_005858321.1
Members of this family of hydrolases with an active site Cys residue belong to MEROPS family C26; Derived by automated computational analysis using gene prediction method: Protein Homology.
gamma-glutamyl-gamma-aminobutyrate hydrolase family protein
COORDINATES: protein motif:HMM:NF023645.2
COORDINATES: similar to AA sequence:RefSeq:WP_015421741.1
GO:0004150 - dihydroneopterin aldolase activity [Evidence IEA]
GO:0046656 - folic acid biosynthetic process [Evidence IEA]; GO:0006760 - folic acid-containing compound metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020675052.1
homocysteine S-methyltransferase family protein
COORDINATES: protein motif:HMM:NF022577.2
COORDINATES: similar to AA sequence:RefSeq:WP_009502778.1