Allochromatium vinosum DSM 180 plasmid pALVIN02, complete sequence.
Bacteria; Proteobacteria; Gammaproteobacteria; Chromatiales; Chromatiaceae; Allochromatium.
Complete genome sequence of Allochromatium vinosum DSM 180(T)
Submitted (01-FEB-2010) US DOE Joint Genome Institute, 2800 Mitchell Drive B310, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP001898.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4084488\nSource DNA and bacteria available from Christiane Dahl\n(ChDahl@uni-bonn.de)\nContacts: Christiane Dahl (ChDahl@uni-bonn.de)\n Tanja Woyke (microbe@cuba.jgi-psf.org)\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##Metadata-START##\nOrganism Display Name :: Allochromatium vinosum DSM 180\nCulture Collection ID :: DSM 180, ATCC 17899\nGOLD Stamp ID :: Gi02104\nIsolation Site :: Ditch water\nOxygen Requirement :: Anaerobe\nCell Shape :: Rod-shaped\nMotility :: Motile\nSporulation :: Nonsporulating\nTemperature Range :: Mesophile\nTemperature Optimum :: 25C\nGram Staining :: gram-\nBiotic Relationship :: Free living\nDiseases :: None\nHabitat :: Fresh water\nEnergy Source :: Phototroph\n##Metadata-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 10/12/2022 01:20:53\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;\n repeat_region\nGenes (total) :: 3,348\nCDSs (total) :: 3,284\nGenes (coding) :: 3,245\nCDSs (with protein) :: 3,245\nGenes (RNA) :: 64\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 51\nncRNAs :: 4\nPseudo Genes (total) :: 39\nCDSs (without protein) :: 39\nPseudo Genes (ambiguous residues) :: 0 of 39\nPseudo Genes (frameshifted) :: 8 of 39\nPseudo Genes (incomplete) :: 31 of 39\nPseudo Genes (internal stop) :: 3 of 39\nPseudo Genes (multiple problems) :: 3 of 39\nCRISPR Arrays :: 3\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_020504303.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012972345.1
COORDINATES: protein motif:HMM:NF021558.2
COORDINATES: protein motif:HMM:NF013970.2
COORDINATES: similar to AA sequence:RefSeq:WP_017977244.1
class I SAM-dependent DNA methyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_011745144.1
COORDINATES: similar to AA sequence:RefSeq:WP_012879669.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_019396227.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_005240543.1
COORDINATES: similar to AA sequence:RefSeq:WP_005004485.1
COORDINATES: similar to AA sequence:RefSeq:WP_011791641.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004519 - endonuclease activity [Evidence IEA]
GO:0006304 - DNA modification [Evidence IEA]
COORDINATES: protein motif:HMM:NF013014.2
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
H-NS family nucleoid-associated regulatory protein
COORDINATES: similar to AA sequence:RefSeq:WP_019466989.1
GO:0006310 - DNA recombination [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: protein motif:HMM:NF023154.2
COORDINATES: similar to AA sequence:RefSeq:WP_017337807.1
COORDINATES: similar to AA sequence:RefSeq:WP_014777958.1
GO:0006259 - DNA metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR03033.1
COORDINATES: similar to AA sequence:RefSeq:WP_014777132.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007195073.1
COORDINATES: similar to AA sequence:RefSeq:WP_007195364.1
COORDINATES: similar to AA sequence:RefSeq:WP_007195365.1
COORDINATES: similar to AA sequence:RefSeq:WP_007195089.1
COORDINATES: protein motif:HMM:NF037877.2
COORDINATES: similar to AA sequence:RefSeq:WP_001172372.1
COORDINATES: similar to AA sequence:RefSeq:WP_006115896.1
COORDINATES: similar to AA sequence:RefSeq:WP_011518269.1
COORDINATES: similar to AA sequence:RefSeq:WP_018002176.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_012506989.1
COORDINATES: protein motif:HMM:NF012464.2
COORDINATES: protein motif:HMM:NF023168.2
COORDINATES: similar to AA sequence:RefSeq:WP_012969338.1
COORDINATES: protein motif:HMM:NF014180.2
COORDINATES: protein motif:HMM:NF013235.2
RepB family plasmid replication initiator protein