Solidesulfovibrio carbinolicus strain DSM 3852 plasmid pDCAR1, complete sequence.
Bacteria; Proteobacteria; Deltaproteobacteria; Desulfovibrionales; Desulfovibrionaceae; Solidesulfovibrio.
Genome sequence of Desulfovibrio carbinolicus DSM 3852
Submitted (01-FEB-2018) Division of Geological and Planetary Sciences, California Institute of Technology, 1200 East California Blvd, Pasadena, CA 91125, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP026539.1.\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-Assembly-Data-START##\nAssembly Date :: MAR-2015\nAssembly Method :: HGAP v. v3\nAssembly Name :: DvCab\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 200.0x\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/14/2022 17:50:02\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.3\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 4,215\nCDSs (total) :: 4,143\nGenes (coding) :: 4,108\nCDSs (with protein) :: 4,108\nGenes (RNA) :: 72\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 54\nncRNAs :: 9\nPseudo Genes (total) :: 35\nCDSs (without protein) :: 35\nPseudo Genes (ambiguous residues) :: 0 of 35\nPseudo Genes (frameshifted) :: 6 of 35\nPseudo Genes (incomplete) :: 31 of 35\nPseudo Genes (internal stop) :: 2 of 35\nPseudo Genes (multiple problems) :: 4 of 35\nCRISPR Arrays :: 2\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Desulfovibrio carbinolicus
COORDINATES: similar to AA sequence:RefSeq:WP_009182986.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012750604.1
COORDINATES: protein motif:HMM:NF024831.2
COORDINATES: similar to AA sequence:RefSeq:WP_011236098.1
GO:0004803 - transposase activity [Evidence IEA]
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF025080.2
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF012744.2
COORDINATES: protein motif:HMM:NF026041.2
COORDINATES: similar to AA sequence:RefSeq:WP_021234579.1
COORDINATES: similar to AA sequence:RefSeq:WP_011939721.1
COORDINATES: similar to AA sequence:RefSeq:WP_009106364.1
COORDINATES: similar to AA sequence:RefSeq:WP_005994204.1
COORDINATES: protein motif:HMM:NF024912.2
COORDINATES: protein motif:HMM:TIGR01536.1
GO:0004066 - asparagine synthase (glutamine-hydrolyzing) activity [Evidence IEA]
GO:0006529 - asparagine biosynthetic process [Evidence IEA]
asparagine synthase (glutamine-hydrolyzing)
COORDINATES: protein motif:HMM:NF013245.2
COORDINATES: protein motif:HMM:NF012235.2
ATP-binding cassette domain-containing protein
COORDINATES: protein motif:HMM:NF040425.1
COORDINATES: protein motif:HMM:NF033517.1
COORDINATES: protein motif:HMM:NF013753.2
COORDINATES: protein motif:HMM:NF013227.2
DegT/DnrJ/EryC1/StrS family aminotransferase
COORDINATES: similar to AA sequence:RefSeq:WP_012704725.1
GO:0003824 - catalytic activity [Evidence IEA]; GO:0051536 - iron-sulfur cluster binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF024967.2
COORDINATES: protein motif:HMM:NF020463.2
COORDINATES: protein motif:HMM:NF024880.2
COORDINATES: protein motif:HMM:NF024751.2
COORDINATES: similar to AA sequence:RefSeq:WP_012750623.1
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_021138877.1
COORDINATES: similar to AA sequence:RefSeq:WP_010025401.1
COORDINATES: similar to AA sequence:RefSeq:WP_015197255.1
COORDINATES: similar to AA sequence:RefSeq:WP_014834018.1
COORDINATES: similar to AA sequence:RefSeq:WP_019897068.1
COORDINATES: similar to AA sequence:RefSeq:WP_012976042.1
TnpB, as the term is used for proteins encoded by IS66 family insertion elements, is considered an accessory protein, since TnpC, encoded by a neighboring gene, is a DDE family transposase.; TnpB, as the term is used for proteins encoded by IS66 family insertion elements, is considered an accessory protein, since TnpC, encoded by a neighboring gene, is a DDE family transposase; Derived by automated computational analysis using gene prediction method: Protein Homology.
IS66 family insertion sequence element accessory protein TnpB
COORDINATES: similar to AA sequence:RefSeq:WP_002811120.1
COORDINATES: similar to AA sequence:RefSeq:WP_086558308.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009798194.1
TnpB, as the term is used for proteins encoded by IS66 family insertion elements, is considered an accessory protein, since TnpC, encoded by a neighboring gene, is a DDE family transposase; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF025063.2
GO:0015074 - DNA integration [Evidence IEA]
integrase core domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010941222.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011235977.1
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: similar to AA sequence:RefSeq:WP_011235976.1
DDE-type integrase/transposase/recombinase
COORDINATES: protein motif:HMM:NF015038.2
COORDINATES: protein motif:HMM:NF024863.2
COORDINATES: protein motif:HMM:NF033581.1
COORDINATES: similar to AA sequence:RefSeq:WP_015961146.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_009183034.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220837.1
COORDINATES: similar to AA sequence:RefSeq:WP_010967405.1
COORDINATES: similar to AA sequence:RefSeq:WP_005994207.1
GO:0003824 - catalytic activity [Evidence IEA]
NAD-dependent epimerase/dehydratase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007192445.1
COORDINATES: protein motif:HMM:NF012745.2
COORDINATES: protein motif:HMM:NF015983.2
COORDINATES: protein motif:HMM:NF015585.2
COORDINATES: protein motif:HMM:NF027579.2
COORDINATES: similar to AA sequence:RefSeq:WP_015336054.1
COORDINATES: similar to AA sequence:RefSeq:WP_015336053.1
COORDINATES: similar to AA sequence:RefSeq:WP_015336052.1
COORDINATES: similar to AA sequence:RefSeq:WP_015850450.1
COORDINATES: similar to AA sequence:RefSeq:WP_011340858.1
GO:0016051 - carbohydrate biosynthetic process [Evidence IEA]
N-acetylneuraminate synthase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_018606558.1
GO:0070567 - cytidylyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015336191.1
COORDINATES: similar to AA sequence:RefSeq:WP_015850461.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014063365.1
COORDINATES: similar to AA sequence:RefSeq:WP_015850459.1
COORDINATES: similar to AA sequence:RefSeq:WP_015850457.1
COORDINATES: similar to AA sequence:RefSeq:WP_015850456.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015336199.1
COORDINATES: similar to AA sequence:RefSeq:WP_015336200.1
UDP-N-acetylglucosamine 4,6-dehydratase (inverting)
COORDINATES: similar to AA sequence:RefSeq:WP_015336201.1
UDP-4-amino-4, 6-dideoxy-N-acetyl-beta-L-altrosamine transaminase
aminoglycoside phosphotransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013514895.1
COORDINATES: similar to AA sequence:RefSeq:WP_015336058.1
COORDINATES: similar to AA sequence:RefSeq:WP_006655330.1
COORDINATES: similar to AA sequence:RefSeq:WP_015336062.1
COORDINATES: protein motif:HMM:NF016228.2
COORDINATES: protein motif:HMM:TIGR04372.1
GO:0016757 - glycosyltransferase activity [Evidence IEA]
radical SAM/SPASM domain-containing protein
COORDINATES: protein motif:HMM:NF014075.2
GO:0046872 - metal ion binding [Evidence IEA]
Presence of a B(12) (cobalamin)-binding domain implies dependence on cobalamin itself, in one of its several forms, or in some unusual lineages, dependence on a cobalamin-like analog; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_015863177.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_015863176.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012805330.1
phosphocholine cytidylyltransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012750658.1
GO:0047355 - CDP-glycerol glycerophosphotransferase activity [Evidence IEA]
CDP-glycerol glycerophosphotransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_005994214.1
COORDINATES: similar to AA sequence:RefSeq:WP_012750661.1
amino acid adenylation domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012750662.1
COORDINATES: similar to AA sequence:RefSeq:WP_012750663.1
COORDINATES: protein motif:HMM:NF014571.2
GO:0046353 - aminoglycoside 3-N-acetyltransferase activity [Evidence IEA]
GO:0046677 - response to antibiotic [Evidence IEA]