Allochromatium vinosum DSM 180 plasmid pALVIN01, 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\nCP001897.1.\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_006786737.1
GO:0003674 - molecular_function [Evidence IEA]
GO:0043571 - maintenance of CRISPR repeat elements [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_006786736.1
type III-B CRISPR module RAMP protein Cmr1
COORDINATES: similar to AA sequence:RefSeq:WP_006786735.1
type III-B CRISPR-associated protein Cas10/Cmr2
COORDINATES: similar to AA sequence:RefSeq:WP_006786733.1
type III-B CRISPR module-associated protein Cmr3
COORDINATES: similar to AA sequence:RefSeq:WP_015258281.1
type III-B CRISPR module RAMP protein Cmr4
COORDINATES: similar to AA sequence:RefSeq:WP_015258282.1
type III-B CRISPR module-associated protein Cmr5
COORDINATES: similar to AA sequence:RefSeq:WP_006786730.1
type III-B CRISPR module RAMP protein Cmr6
COORDINATES: protein motif:HMM:NF024980.2
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF033545.0
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006786729.1
GO:0003824 - catalytic activity [Evidence IEA]; GO:0051536 - iron-sulfur cluster binding [Evidence IEA]
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF015983.2
COORDINATES: similar to AA sequence:RefSeq:WP_010308382.1
COORDINATES: similar to AA sequence:RefSeq:WP_004359789.1
COORDINATES: similar to AA sequence:RefSeq:WP_018870790.1
COORDINATES: similar to AA sequence:RefSeq:WP_002708339.1
COORDINATES: protein motif:HMM:NF021378.2
COORDINATES: similar to AA sequence:RefSeq:WP_012972306.1
COORDINATES: protein motif:HMM:NF021356.2
GO:0004521 - endoribonuclease activity [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR00287.1
GO:0004520 - endodeoxyribonuclease activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF013014.2
COORDINATES: similar to AA sequence:RefSeq:WP_010969960.1
COORDINATES: similar to AA sequence:RefSeq:WP_019448797.1
GO:0016787 - hydrolase activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF024901.2
COORDINATES: similar to AA sequence:RefSeq:WP_013221953.1
COORDINATES: similar to AA sequence:RefSeq:WP_005220884.1
COORDINATES: protein motif:HMM:NF024787.2
COORDINATES: similar to AA sequence:RefSeq:WP_020562668.1
COORDINATES: similar to AA sequence:RefSeq:WP_015280558.1
COORDINATES: similar to AA sequence:RefSeq:WP_007195180.1
COORDINATES: similar to AA sequence:RefSeq:WP_007195761.1
COORDINATES: similar to AA sequence:RefSeq:WP_018199442.1
COORDINATES: protein motif:HMM:NF016255.2
COORDINATES: similar to AA sequence:RefSeq:WP_011418024.1
COORDINATES: similar to AA sequence:RefSeq:WP_015281308.1
COORDINATES: similar to AA sequence:RefSeq:WP_012970229.1
COORDINATES: similar to AA sequence:RefSeq:WP_020507791.1
COORDINATES: similar to AA sequence:RefSeq:WP_014779763.1
COORDINATES: similar to AA sequence:RefSeq:WP_007686527.1
type I restriction-modification system endonuclease
COORDINATES: similar to AA sequence:RefSeq:WP_007193806.1
COORDINATES: similar to AA sequence:RefSeq:WP_007193805.1
GO:0006304 - DNA modification [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018989344.1
GO:0004386 - helicase activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012970212.1
COORDINATES: similar to AA sequence:RefSeq:WP_012972342.1
COORDINATES: similar to AA sequence:RefSeq:WP_012701616.1
COORDINATES: similar to AA sequence:RefSeq:WP_012972344.1
COORDINATES: similar to AA sequence:RefSeq:WP_012979572.1
COORDINATES: protein motif:HMM:NF018178.2
COORDINATES: similar to AA sequence:RefSeq:WP_005375209.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020405267.1
COORDINATES: similar to AA sequence:RefSeq:WP_020503537.1
COORDINATES: protein motif:HMM:NF013540.2
helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:NF024252.2
COORDINATES: similar to AA sequence:RefSeq:WP_014777128.1
COORDINATES: similar to AA sequence:RefSeq:WP_013221925.1
COORDINATES: similar to AA sequence:RefSeq:WP_014777131.1
COORDINATES: protein motif:HMM:TIGR00621.2
GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]; GO:0006281 - DNA repair [Evidence IEA]; GO:0006260 - DNA replication [Evidence IEA]; GO:0006351 - DNA-templated transcription [Evidence IEA]
COORDINATES: protein motif:HMM:NF024949.2
COORDINATES: similar to AA sequence:RefSeq:WP_005375230.1
COORDINATES: similar to AA sequence:RefSeq:WP_004164104.1
COORDINATES: similar to AA sequence:RefSeq:WP_012969336.1
COORDINATES: similar to AA sequence:RefSeq:WP_012971484.1
COORDINATES: protein motif:HMM:NF012264.2
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0020037 - heme binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012972395.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611896.1
GO:0015074 - DNA integration [Evidence IEA]
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
integrase core domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_020810458.1
COORDINATES: similar to AA sequence:RefSeq:WP_018935906.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_018869217.1
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: protein motif:HMM:NF023168.2
COORDINATES: protein motif:HMM:NF012798.2
COORDINATES: similar to AA sequence:RefSeq:WP_009146522.1
COORDINATES: similar to AA sequence:RefSeq:WP_014777379.1
COORDINATES: similar to AA sequence:RefSeq:WP_015282516.1
COORDINATES: similar to AA sequence:RefSeq:WP_014777598.1
GO:0008757 - S-adenosylmethionine-dependent methyltransferase activity [Evidence IEA]
GO:0006400 - tRNA modification [Evidence IEA]
tRNA (N6-threonylcarbamoyladenosine(37)-N6)-methyltransferase TrmO
COORDINATES: similar to AA sequence:RefSeq:WP_014870871.1
GO:0015087 - cobalt ion transmembrane transporter activity [Evidence IEA]; GO:0015095 - magnesium ion transmembrane transporter activity [Evidence IEA]
GO:0006824 - cobalt ion transport [Evidence IEA]; GO:0015693 - magnesium ion transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020506093.1
chlororespiratory reduction 6 domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007193828.1
COORDINATES: similar to AA sequence:RefSeq:WP_007191794.1
COORDINATES: protein motif:HMM:NF012245.2
COORDINATES: protein motif:HMM:NF021759.2
COORDINATES: similar to AA sequence:RefSeq:WP_012969339.1
COORDINATES: similar to AA sequence:RefSeq:WP_015019184.1
COORDINATES: protein motif:HMM:NF013235.2
RepB family plasmid replication initiator protein
COORDINATES: similar to AA sequence:RefSeq:WP_012252452.1
COORDINATES: similar to AA sequence:RefSeq:WP_012969346.1
COORDINATES: similar to AA sequence:RefSeq:WP_012969347.1
COORDINATES: protein motif:HMM:NF021551.2
CRISPR system precrRNA processing endoribonuclease RAMP protein Cas6