Dinoroseobacter shibae DFL 12 = DSM 16493 plasmid pDSHI04, 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\nCP000834.1.\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: protein motif:HMM:NF015437.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
autoinducer binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007635327.1
GO:0004803 - transposase activity [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_076611905.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF024627.2
COORDINATES: similar to AA sequence:RefSeq:WP_076611345.1
programmed frameshift; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_020039273.1
COORDINATES: similar to AA sequence:RefSeq:WP_017999661.1
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_009824789.1
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: 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_013635075.1
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_003939267.1
Mu transposase C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007406871.1
COORDINATES: similar to AA sequence:RefSeq:WP_009469706.1
COORDINATES: similar to AA sequence:RefSeq:WP_009503743.1
COORDINATES: protein motif:HMM:NF015640.2
type II toxin-antitoxin system ParD family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_013455559.1
GO:0008657 - DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) inhibitor activity [Evidence IEA]; GO:0042803 - protein homodimerization activity [Evidence IEA]
GO:0030541 - plasmid partitioning [Evidence IEA]; GO:0051290 - protein heterotetramerization [Evidence IEA]
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_076611844.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012177568.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011983025.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611612.1
COORDINATES: similar to AA sequence:RefSeq:WP_009574206.1
ParB N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012187387.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820070.1
COORDINATES: similar to AA sequence:RefSeq:WP_009827042.1
COORDINATES: similar to AA sequence:RefSeq:WP_010138187.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187243.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611960.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
frameshifted; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF014643.2
GO:0110001 - toxin-antitoxin complex [Evidence IEA]
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_005848694.1
GO:0016301 - kinase activity [Evidence IEA]
type II toxin-antitoxin system death-on-curing family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_020041597.1
GO:0008830 - dTDP-4-dehydrorhamnose 3,5-epimerase activity [Evidence IEA]
GO:0019305 - dTDP-rhamnose biosynthetic process [Evidence IEA]; GO:0009243 - O antigen biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014876615.1
GO:0008460 - dTDP-glucose 4,6-dehydratase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF015527.2
GO:0008146 - sulfotransferase activity [Evidence IEA]
sulfotransferase family 2 domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014889398.1
GO:0008831 - dTDP-4-dehydrorhamnose reductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007812014.1
GO:0008879 - glucose-1-phosphate thymidylyltransferase activity [Evidence IEA]
glucose-1-phosphate thymidylyltransferase RfbA
COORDINATES: similar to AA sequence:RefSeq:WP_011909577.1
COORDINATES: similar to AA sequence:RefSeq:WP_007256743.1
GO:0016740 - transferase activity [Evidence IEA]
GO:0006486 - protein glycosylation [Evidence IEA]
COORDINATES: protein motif:HMM:NF012745.2
COORDINATES: similar to AA sequence:RefSeq:WP_012187429.1
COORDINATES: protein motif:HMM:NF015038.2
internal stop; incomplete; partial in the middle of a contig; missing N-terminus and C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF025189.2
COORDINATES: similar to AA sequence:RefSeq:WP_012778787.1
incomplete; partial in the middle of a contig; missing N-terminus and C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF024832.2
right-handed parallel beta-helix repeat-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017366008.1
COORDINATES: protein motif:HMM:NF016027.2
GO:0016758 - hexosyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009506832.1
Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C-terminal domain
COORDINATES: similar to AA sequence:RefSeq:WP_009506831.1
GO:0016757 - glycosyltransferase activity [Evidence IEA]
polysaccharide pyruvyl transferase family protein
GO:0009103 - lipopolysaccharide biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008229977.1
COORDINATES: similar to AA sequence:RefSeq:WP_012556676.1
GO:0008446 - GDP-mannose 4,6-dehydratase activity [Evidence IEA]
GO:0000271 - polysaccharide biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF012888.2
sulfotransferase domain-containing protein
COORDINATES: protein motif:HMM:NF024775.2
COORDINATES: similar to AA sequence:RefSeq:WP_012977883.1
COORDINATES: similar to AA sequence:RefSeq:WP_013959954.1
COORDINATES: similar to AA sequence:RefSeq:WP_009506838.1
GO:0016746 - acyltransferase activity [Evidence IEA]; GO:0120225 - coenzyme A binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008209683.1
COORDINATES: similar to AA sequence:RefSeq:WP_013959937.1
GO:0004476 - mannose-6-phosphate isomerase activity [Evidence IEA]
mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase
COORDINATES: protein motif:HMM:NF025025.2
COORDINATES: similar to AA sequence:RefSeq:WP_009506806.1
COORDINATES: similar to AA sequence:RefSeq:WP_020039275.1
GO:0016746 - acyltransferase activity [Evidence IEA]
GO:0046677 - response to antibiotic [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012187407.1
COORDINATES: protein motif:HMM:NF012967.2
COORDINATES: similar to AA sequence:RefSeq:WP_011112884.1
internal stop; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.