Solidesulfovibrio carbinoliphilus subsp. oakridgensis strain FW-101-2B plasmid pFW10101, whole genome shotgun sequence.
Solidesulfovibrio carbinoliphilus subsp. oakridgensis
Bacteria; Thermodesulfobacteriota; Desulfovibrionia; Desulfovibrionales; Desulfovibrionaceae; Solidesulfovibrio.
High-Quality Draft Genome Sequence of Desulfovibrio carbinoliphilus FW-101-2B, an Organic Acid-Oxidizing Sulfate-Reducing Bacterium Isolated from Uranium(VI)-Contaminated Groundwater
Complete sequence of chromosome Desulfovibrio sp. FW1012B
Submitted (14-JUN-2011) US DOE Joint Genome Institute, 2800 Mitchell Drive B310, Walnut Creek, CA 94598-1698, USA
Submitted (07-DEC-2009) US DOE Joint Genome Institute, 2800 Mitchell Drive B310, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCM001369.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4086280\nSource DNA and organism available from Terry C. Hazen\n(TCHazen@lbl.gov)\nContacts: Terry C. Hazen (TCHazen@lbl.gov)\n Tanja Woyke (microbe@cuba.jgi-psf.org)\nAnnotation done by JGI-ORNL and JGI-PGF\nFinishing done by JGI-LANL\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##MIGS-Data-START##\ninvestigation_type :: bacteria_archaea\nproject_name :: Desulfovibrio sp. FW1012B\ncollection_date :: Missing\nlat_lon :: Missing\ndepth :: Missing\nalt_elev :: Missing\ncountry :: Missing\nenvironment :: Fresh water, Animal intestinal microflora,\n Mud, Sea water, Soil\nnum_replicons :: 3\nref_biomaterial :: Missing\nbiotic_relationship :: Free living\ntrophic_level :: Missing\nrel_to_oxygen :: Obligate anaerobe\nisol_growth_condt :: Missing\nsequencing_meth :: WGS\nassembly :: Newbler v. 2.3 (pre-release)\nfinishing_strategy :: Finished\nGOLD Stamp ID :: Gi03938\nFunding Program :: DOE-GTL 2007\nGene Calling Method :: Prodigal 1.4, GenePRIMP\nIsolation Site :: ORFRC groundwater during biostimulation for\n uranium bioreduction.\nCell Shape :: Rod-shaped\nMotility :: Motile\nSporulation :: Sporulating\nTemperature Range :: Mesophile\nTemperature Optimum :: 37C\nGram Staining :: Gram-\nDiseases :: None\n##MIGS-Data-END##\n\n##Genome-Assembly-Data-START##\nFinishing Goal :: Noncontiguous Finished\nCurrent Finishing Status :: Noncontiguous Finished\nAssembly Method :: Newbler v. 2.3\nGenome Coverage :: 30x\nSequencing Technology :: 454; Illumina\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/10/2023 13:40:39\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.4\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 3,815\nCDSs (total) :: 3,745\nGenes (coding) :: 3,729\nCDSs (with protein) :: 3,729\nGenes (RNA) :: 70\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 55\nncRNAs :: 6\nPseudo Genes (total) :: 16\nCDSs (without protein) :: 16\nPseudo Genes (ambiguous residues) :: 0 of 16\nPseudo Genes (frameshifted) :: 3 of 16\nPseudo Genes (incomplete) :: 14 of 16\nPseudo Genes (internal stop) :: 1 of 16\nPseudo Genes (multiple problems) :: 2 of 16\nCRISPR Arrays :: 2\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
ORFRC groundwater during biostimulation for uranium bioreduction
reference strain of Desulfovibrio carbinoliphilus subsp. oakridgensis
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF025025.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_010403212.1
COORDINATES: protein motif:HMM:NF012235.2
COORDINATES: similar to AA sequence:RefSeq:WP_011940617.1
COORDINATES: protein motif:HMM:NF012360.2
COORDINATES: protein motif:HMM:NF024967.2
COORDINATES: protein motif:HMM:NF024949.2
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_009105715.1
COORDINATES: similar to AA sequence:RefSeq:WP_009105710.1
GO:0030253 - protein secretion by the type I secretion system [Evidence IEA]
HlyD family type I secretion periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_009105712.1
peptidase domain-containing ABC transporter
COORDINATES: similar to AA sequence:RefSeq:WP_009105709.1
GO:0031012 - extracellular matrix [Evidence IEA]
GO:0004222 - metalloendopeptidase activity [Evidence IEA]; GO:0008270 - zinc ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009105721.1
COORDINATES: similar to AA sequence:RefSeq:WP_009182986.1
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_015336188.1
phosphocholine cytidylyltransferase family protein
COORDINATES: protein motif:HMM:NF025217.2
COORDINATES: protein motif:HMM:NF013257.2
GO:0016757 - glycosyltransferase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF017522.2
TylF/MycF/NovP-related O-methyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_018914061.1
GO:0016051 - carbohydrate biosynthetic process [Evidence IEA]
N-acetylneuraminate synthase family protein
COORDINATES: protein motif:HMM:NF016228.2
COORDINATES: similar to AA sequence:RefSeq:WP_012869430.1
GO:0030170 - pyridoxal phosphate binding [Evidence IEA]; GO:0008483 - transaminase activity [Evidence IEA]
aminotransferase class III-fold pyridoxal phosphate-dependent enzyme
COORDINATES: protein motif:HMM:NF012472.2
COORDINATES: similar to AA sequence:RefSeq:WP_006391960.1
COORDINATES: protein motif:HMM:NF012744.2
COORDINATES: similar to AA sequence:RefSeq:WP_009148799.1
UDP-N-acetylglucosamine 4,6-dehydratase (inverting)
COORDINATES: protein motif:HMM:TIGR01855.1
GO:0016884 - carbon-nitrogen ligase activity, with glutamine as amido-N-donor [Evidence IEA]; GO:0000107 - imidazoleglycerol-phosphate synthase activity [Evidence IEA]
GO:0000105 - histidine biosynthetic process [Evidence IEA]
imidazole glycerol phosphate synthase subunit HisH
COORDINATES: similar to AA sequence:RefSeq:WP_015131473.1
imidazole glycerol phosphate synthase cyclase subunit
COORDINATES: protein motif:HMM:NF024880.2
methyltransferase domain-containing protein
COORDINATES: protein motif:HMM:TIGR03573.1
COORDINATES: protein motif:HMM:NF025017.2
COORDINATES: protein motif:HMM:NF012888.2
COORDINATES: protein motif:HMM:NF015983.2
COORDINATES: similar to AA sequence:RefSeq:WP_009105580.1
phosphoadenosine phosphosulfate reductase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_009183012.1
type II toxin-antitoxin system PemK/MazF family toxin
COORDINATES: protein motif:HMM:NF022894.2
COORDINATES: similar to AA sequence:RefSeq:WP_009105586.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
PAS domain-containing hybrid sensor histidine kinase/response regulator
COORDINATES: similar to AA sequence:RefSeq:WP_009105588.1
COORDINATES: similar to AA sequence:RefSeq:WP_009105590.1
COORDINATES: similar to AA sequence:RefSeq:WP_009105592.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_009105594.1
COORDINATES: similar to AA sequence:RefSeq:WP_009105595.1
COORDINATES: similar to AA sequence:RefSeq:WP_012749875.1
COORDINATES: similar to AA sequence:RefSeq:WP_009105599.1
COORDINATES: similar to AA sequence:RefSeq:WP_009105602.1
COORDINATES: similar to AA sequence:RefSeq:WP_009105603.1
COORDINATES: similar to AA sequence:RefSeq:WP_009105606.1
COORDINATES: similar to AA sequence:RefSeq:WP_009105607.1
COORDINATES: similar to AA sequence:RefSeq:WP_012749871.1
COORDINATES: similar to AA sequence:RefSeq:WP_009105616.1
COORDINATES: similar to AA sequence:RefSeq:WP_009105617.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012824488.1
ribbon-helix-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015862886.1
COORDINATES: similar to AA sequence:RefSeq:WP_009105618.1
GO:0016779 - nucleotidyltransferase activity [Evidence IEA]
GO:0009244 - lipopolysaccharide core region biosynthetic process [Evidence IEA]
D-glycero-beta-D-manno-heptose 1-phosphate adenylyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_009183033.1
GO:0008712 - ADP-glyceromanno-heptose 6-epimerase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012750654.1
COORDINATES: protein motif:HMM:NF014691.2
COORDINATES: similar to AA sequence:RefSeq:WP_009105695.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009183037.1
COORDINATES: similar to AA sequence:RefSeq:WP_009183038.1
type II toxin-antitoxin system HigB family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_009105701.1
lysophospholipid acyltransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012749878.1
B12-binding domain-containing radical SAM protein
COORDINATES: similar to AA sequence:RefSeq:WP_009105704.1
COORDINATES: similar to AA sequence:RefSeq:WP_005994573.1
COORDINATES: similar to AA sequence:RefSeq:WP_009183043.1
COORDINATES: protein motif:HMM:NF025214.2
COORDINATES: protein motif:HMM:NF012573.2
COORDINATES: similar to AA sequence:RefSeq:WP_019425725.1
COORDINATES: similar to AA sequence:RefSeq:WP_009105717.1
GO:0008168 - methyltransferase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF021126.2