Methylovorus glucosetrophus SIP3-4 plasmid pMsip02, complete sequence.
Bacteria; Pseudomonadota; Betaproteobacteria; Nitrosomonadales; Methylophilaceae; Methylovorus.
Genomes of three methylotrophs from a single niche reveal the genetic and metabolic divergence of the methylophilaceae
Complete sequence of plasmid 2 of Methylovorus sp. SIP3-4
Submitted (13-JUL-2009) US DOE Joint Genome Institute, 2800 Mitchell Drive B310, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP001676.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4086190\nSource DNA and bacteria available from Ludmila Chistoserdova\n(milachis@u.washington.edu)\nContacts: Ludmila Chistoserdova (milachis@u.washington.edu)\n David Bruce (microbe@cuba.jgi-psf.org)\nAnnotation done by JGI-ORNL and JGI-PGF\nFinishing done by JGI-PGF\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 :: Methylovorus sp. SIP3-4\nGOLD Stamp ID :: Gi03952\nFunding Program :: DOE-CSP 2009\nOxygen Requirement :: Aerobe\nCell Shape :: Rod-shaped\nMotility :: Motile\nSporulation :: Nonsporulating\nTemperature Range :: Mesophile\nGram Staining :: gram-\nBiotic Relationship :: Free living\nHabitat :: Fresh water\n##Metadata-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/22/2023 13:55:18\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) :: 2,952\nCDSs (total) :: 2,894\nGenes (coding) :: 2,887\nCDSs (with protein) :: 2,887\nGenes (RNA) :: 58\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 49\nncRNAs :: 3\nPseudo Genes (total) :: 7\nCDSs (without protein) :: 7\nPseudo Genes (ambiguous residues) :: 0 of 7\nPseudo Genes (frameshifted) :: 2 of 7\nPseudo Genes (incomplete) :: 6 of 7\nPseudo Genes (internal stop) :: 0 of 7\nPseudo Genes (multiple problems) :: 1 of 7\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF024700.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_019882331.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF014074.2
COORDINATES: protein motif:HMM:NF017518.2
zonular occludens toxin domain-containing protein
COORDINATES: protein motif:HMM:NF022194.2
COORDINATES: protein motif:HMM:NF017194.2
COORDINATES: similar to AA sequence:RefSeq:WP_015830056.1
COORDINATES: similar to AA sequence:RefSeq:WP_008955695.1