Dinoroseobacter shibae DFL 12 = DSM 16493 plasmid pDSHI05, 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\nCP000835.1.\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_010394426.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
quinoprotein relay system zinc metallohydrolase 1
COORDINATES: similar to AA sequence:RefSeq:WP_011047261.1
quinoprotein dehydrogenase-associated SoxYZ-like carrier
COORDINATES: similar to AA sequence:RefSeq:WP_013960689.1
sigma-54-dependent Fis family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011569789.1
COORDINATES: similar to AA sequence:RefSeq:WP_005565102.1
GO:0019152 - acetoin dehydrogenase activity [Evidence IEA]
GO:0045150 - acetoin catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018001415.1
COORDINATES: similar to AA sequence:RefSeq:WP_011056423.1
GO:0016630 - protochlorophyllide reductase activity [Evidence IEA]
GO:0015995 - chlorophyll biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF018352.2
COORDINATES: similar to AA sequence:RefSeq:WP_011453435.1
GO:0016757 - glycosyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011453434.1
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012640787.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008887891.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_019955712.1
lysylphosphatidylglycerol synthase transmembrane domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011453430.1
GO:0008484 - sulfuric ester hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008887912.1
CDP-alcohol phosphatidyltransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011750582.1
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0020037 - heme binding [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
GO:0022904 - respiratory electron transport chain [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007818211.1
glucans biosynthesis glucosyltransferase MdoH
COORDINATES: similar to AA sequence:RefSeq:WP_007818209.1
COORDINATES: similar to AA sequence:RefSeq:WP_013964106.1
GO:0043565 - sequence-specific DNA binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008232814.1
COORDINATES: similar to AA sequence:RefSeq:WP_011454444.1
nuclear transport factor 2 family protein
COORDINATES: similar to AA sequence:RefSeq:WP_014880911.1
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]
GO:1905887 - autoinducer AI-2 transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009807159.1
oxidoreductase FAD/NAD(P)-binding subunit
COORDINATES: similar to AA sequence:RefSeq:WP_009564143.1
COORDINATES: similar to AA sequence:RefSeq:WP_011568662.1
COORDINATES: protein motif:HMM:NF018980.2
GO:0016020 - membrane [Evidence IEA]; GO:0005886 - plasma membrane [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013960077.1
COORDINATES: similar to AA sequence:RefSeq:WP_008189426.1
PLDc N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014878952.1
GO:0008381 - mechanosensitive monoatomic ion channel activity [Evidence IEA]
mechanosensitive ion channel family protein
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_019296333.1
COORDINATES: similar to AA sequence:RefSeq:WP_012179200.1
COORDINATES: protein motif:HMM:NF012235.2
COORDINATES: protein motif:HMM:NF012738.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0022857 - transmembrane transporter activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF020650.2
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]
GO:0140359 - ABC-type transporter activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF015445.2
TRAP transporter substrate-binding protein
COORDINATES: protein motif:HMM:NF016200.2
GO:0005886 - plasma membrane [Evidence IEA]; GO:0031317 - tripartite ATP-independent periplasmic transporter complex [Evidence IEA]
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0015740 - C4-dicarboxylate transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018389699.1
GO:0008643 - carbohydrate transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005848685.1
GO:0016787 - hydrolase activity [Evidence IEA]
gamma-glutamyltransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007088644.1
tripartite tricarboxylate transporter permease
COORDINATES: similar to AA sequence:RefSeq:WP_008191458.1
GO:0005215 - transporter activity [Evidence IEA]
tripartite tricarboxylate transporter TctB family protein
COORDINATES: similar to AA sequence:RefSeq:WP_005848679.1
GO:0042597 - periplasmic space [Evidence IEA]
tripartite tricarboxylate transporter substrate binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_008195543.1
COORDINATES: similar to AA sequence:RefSeq:WP_005859930.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_007803811.1
xanthine dehydrogenase family protein subunit M
COORDINATES: similar to AA sequence:RefSeq:WP_007803810.1
GO:0051537 - 2 iron, 2 sulfur cluster binding [Evidence IEA]; GO:0051536 - iron-sulfur cluster binding [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007803808.1
xanthine dehydrogenase family protein molybdopterin-binding subunit
COORDINATES: similar to AA sequence:RefSeq:WP_009515214.1
C4-dicarboxylate TRAP transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_007803805.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803802.1
COORDINATES: similar to AA sequence:RefSeq:WP_011455973.1
GO:0003824 - catalytic activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013960645.1
COORDINATES: similar to AA sequence:RefSeq:WP_005979050.1
COORDINATES: similar to AA sequence:RefSeq:WP_013964053.1
GO:0008081 - phosphoric diester hydrolase activity [Evidence IEA]
GO:0006629 - lipid metabolic process [Evidence IEA]
glycerophosphodiester phosphodiesterase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_003608677.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_011141676.1
COORDINATES: similar to AA sequence:RefSeq:WP_020043035.1
ParB N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018001450.1
COORDINATES: similar to AA sequence:RefSeq:WP_013368559.1
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006270 - DNA replication initiation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007814457.1
COORDINATES: similar to AA sequence:RefSeq:WP_013960670.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016301 - kinase activity [Evidence IEA]
GO:0016310 - phosphorylation [Evidence IEA]
COORDINATES: protein motif:HMM:NF012742.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0043565 - sequence-specific DNA binding [Evidence IEA]; GO:0000976 - transcription cis-regulatory region binding [Evidence IEA]
GO:0006351 - DNA-templated transcription [Evidence IEA]; GO:0045892 - negative regulation of DNA-templated transcription [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
LacI family DNA-binding transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_008236123.1
COORDINATES: protein motif:HMM:NF018979.2
COORDINATES: similar to AA sequence:RefSeq:WP_005029895.1
COORDINATES: similar to AA sequence:RefSeq:WP_008192297.1
GO:0050661 - NADP binding [Evidence IEA]
NAD(P)-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008232096.1
DNA starvation/stationary phase protection protein
COORDINATES: similar to AA sequence:RefSeq:WP_011456394.1
COORDINATES: similar to AA sequence:RefSeq:WP_014537955.1
COORDINATES: similar to AA sequence:RefSeq:WP_011047259.1
rhodanese-like domain-containing protein