Dinoroseobacter shibae DFL 12 = DSM 16493 plasmid pDSHI03, 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\nCP000833.1.\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_009808021.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_018303301.1
COORDINATES: similar to AA sequence:RefSeq:WP_017927528.1
GO:0016746 - acyltransferase activity [Evidence IEA]; GO:0071972 - peptidoglycan L,D-transpeptidase activity [Evidence IEA]
GO:0018104 - peptidoglycan-protein cross-linking [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008327307.1
COORDINATES: similar to AA sequence:RefSeq:WP_007254433.1
COORDINATES: similar to AA sequence:RefSeq:WP_009503854.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803430.1
COORDINATES: similar to AA sequence:RefSeq:WP_018065800.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803435.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803438.1
GO:0008961 - phosphatidylglycerol-prolipoprotein diacylglyceryl transferase activity [Evidence IEA]
GO:0009249 - protein lipoylation [Evidence IEA]
prolipoprotein diacylglyceryl transferase
COORDINATES: similar to AA sequence:RefSeq:WP_011242142.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803442.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007803445.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611948.1
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_007803446.1
GO:0017004 - cytochrome complex assembly [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005613342.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807971.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803452.1
COORDINATES: similar to AA sequence:RefSeq:WP_008327326.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0046983 - protein dimerization activity [Evidence IEA]; GO:0046914 - transition metal ion binding [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
manganese-binding transcriptional regulator MntR
COORDINATES: similar to AA sequence:RefSeq:WP_009807490.1
GO:0016410 - N-acyltransferase activity [Evidence IEA]
GO:0042158 - lipoprotein biosynthetic process [Evidence IEA]; GO:0006497 - protein lipidation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007803461.1
GO:0005886 - plasma membrane [Evidence IEA]
GO:0004190 - aspartic-type endopeptidase activity [Evidence IEA]
GO:0009306 - protein secretion [Evidence IEA]; GO:0006508 - proteolysis [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007803463.1
GO:0046873 - metal ion transmembrane transporter activity [Evidence IEA]
GO:0030001 - metal ion transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007803465.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803467.1
GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007803468.1
GO:0031966 - mitochondrial membrane [Evidence IEA]
GO:0033617 - mitochondrial cytochrome c oxidase assembly [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005647556.1
GO:0016531 - copper chaperone activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018001721.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803474.1
GO:0015035 - protein-disulfide reductase activity [Evidence IEA]
GO:0006457 - protein folding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009827282.1
COORDINATES: similar to AA sequence:RefSeq:WP_018303599.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_005645239.1
GO:0008324 - monoatomic cation transmembrane transporter activity [Evidence IEA]
GO:0006812 - monoatomic cation transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007803479.1
transglutaminase-like domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009807491.1
cation diffusion facilitator family transporter
COORDINATES: similar to AA sequence:RefSeq:WP_012187173.1
COORDINATES: similar to AA sequence:RefSeq:WP_009808043.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803330.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_007803328.1
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]; GO:0008324 - monoatomic cation transmembrane transporter activity [Evidence IEA]
GO:0006812 - monoatomic cation transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007120687.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120686.1
COORDINATES: similar to AA sequence:RefSeq:WP_009803698.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187165.1
COORDINATES: similar to AA sequence:RefSeq:WP_008327370.1
GO:0016798 - hydrolase activity, acting on glycosyl bonds [Evidence IEA]
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009808058.1
COORDINATES: similar to AA sequence:RefSeq:WP_008327373.1
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_009807508.1
type IV secretion system DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009815545.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120678.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820232.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807512.1
COORDINATES: similar to AA sequence:RefSeq:WP_009808065.1
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_008327387.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820228.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187154.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120671.1
COORDINATES: similar to AA sequence:RefSeq:WP_009808070.1
COORDINATES: protein motif:HMM:NF024867.2
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_009807937.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_009807938.1
relaxase/mobilization nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007120663.1
COORDINATES: similar to AA sequence:RefSeq:WP_011536569.1
COORDINATES: similar to AA sequence:RefSeq:WP_009815535.1
GSU2403 family nucleotidyltransferase fold protein
COORDINATES: similar to AA sequence:RefSeq:WP_009820257.1
COORDINATES: similar to AA sequence:RefSeq:WP_012043539.1
GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0006974 - cellular response to DNA damage stimulus [Evidence IEA]; GO:0018142 - protein-DNA covalent cross-linking [Evidence IEA]
SOS response-associated peptidase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_009808718.1
COORDINATES: similar to AA sequence:RefSeq:WP_011046421.1
GO:0008408 - 3'-5' exonuclease activity [Evidence IEA]; GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012187346.1
COORDINATES: similar to AA sequence:RefSeq:WP_009819680.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187348.1
COORDINATES: similar to AA sequence:RefSeq:WP_008327427.1
COORDINATES: similar to AA sequence:RefSeq:WP_009503768.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
strawberry notch C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008877989.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010408889.1
COORDINATES: similar to AA sequence:RefSeq:WP_010967849.1
COORDINATES: similar to AA sequence:RefSeq:WP_007424858.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014131757.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014131758.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120648.1
type II toxin-antitoxin system YhaV family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_012187077.1
type II toxin-antitoxin system PrlF family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_012187076.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820261.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807539.1
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_012187358.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120641.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807542.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008282917.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807962.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187363.1
COORDINATES: similar to AA sequence:RefSeq:WP_009815512.1
COORDINATES: similar to AA sequence:RefSeq:WP_008558667.1
COORDINATES: similar to AA sequence:RefSeq:WP_009503866.1
AbrB/MazE/SpoVT family DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011331447.1
COORDINATES: similar to AA sequence:RefSeq:WP_010138187.1
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_009807854.1
COORDINATES: similar to AA sequence:RefSeq:WP_009819736.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820064.1
COORDINATES: similar to AA sequence:RefSeq:WP_011930898.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803314.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611905.1
GO:0004803 - transposase activity [Evidence IEA]
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_005859550.1
COORDINATES: similar to AA sequence:RefSeq:WP_002722009.1
GO:0008121 - ubiquinol-cytochrome-c reductase activity [Evidence IEA]
ubiquinol-cytochrome c reductase iron-sulfur subunit N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015886710.1
COORDINATES: protein motif:HMM:NF033545.0
COORDINATES: similar to AA sequence:RefSeq:WP_009824462.1
GO:0030552 - cAMP binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
Crp/Fnr family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_012187045.1
COORDINATES: similar to AA sequence:RefSeq:WP_009570513.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
GO:0006629 - lipid metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009807997.1
COORDINATES: similar to AA sequence:RefSeq:WP_008327266.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803357.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187040.1
COORDINATES: similar to AA sequence:RefSeq:WP_009808001.1
rhodanese-like domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007803380.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008327277.1
COORDINATES: similar to AA sequence:RefSeq:WP_020042978.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803387.1
COORDINATES: similar to AA sequence:RefSeq:WP_009808006.1
GO:0030288 - outer membrane-bounded periplasmic space [Evidence IEA]
GO:0015036 - disulfide oxidoreductase activity [Evidence IEA]
DsbE family thiol:disulfide interchange protein
COORDINATES: similar to AA sequence:RefSeq:WP_007803391.1
cytochrome c-type biogenesis protein CcmH
COORDINATES: similar to AA sequence:RefSeq:WP_009808008.1
GO:0051082 - unfolded protein binding [Evidence IEA]
c-type cytochrome biogenesis protein CcmI
COORDINATES: similar to AA sequence:RefSeq:WP_007803395.1
protein-disulfide reductase DsbD family protein
COORDINATES: similar to AA sequence:RefSeq:WP_008327290.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807486.1
GO:0042834 - peptidoglycan binding [Evidence IEA]; GO:0071972 - peptidoglycan L,D-transpeptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007803401.1
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0020037 - heme binding [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007803403.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803405.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803406.1
COORDINATES: similar to AA sequence:RefSeq:WP_008327301.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807488.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803412.1
heavy-metal-associated domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012187038.1
GO:0042625 - ATPase-coupled ion transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007803416.1
GO:0006878 - cellular copper ion homeostasis [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
Cu(I)-responsive transcriptional regulator