Methylovorus glucosetrophus SIP3-4 plasmid pMsip01, 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 1 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\nCP001675.1.\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: similar to AA sequence:RefSeq:WP_006889572.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_019366923.1
helix-turn-helix transcriptional regulator
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF013235.2
COORDINATES: protein motif:HMM:NF041292.1
COORDINATES: protein motif:HMM:NF037106.2
COORDINATES: protein motif:HMM:NF015397.2
TraI/MobA(P) family conjugative relaxase
COORDINATES: similar to AA sequence:RefSeq:WP_014707330.1
GO:0003684 - damaged DNA binding [Evidence IEA]
translesion error-prone DNA polymerase V subunit UmuC
COORDINATES: similar to AA sequence:RefSeq:WP_012667839.1
translesion error-prone DNA polymerase V autoproteolytic subunit
COORDINATES: similar to AA sequence:RefSeq:WP_013294328.1
GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0006974 - cellular response to DNA damage stimulus [Evidence IEA]; GO:0018142 - protein-DNA covalent cross-linking [Evidence IEA]
SOS response-associated peptidase family protein
COORDINATES: protein motif:HMM:NF012422.2
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
LuxR C-terminal-related transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_009522294.1
COORDINATES: similar to AA sequence:RefSeq:WP_017362440.1
COORDINATES: protein motif:HMM:NF014505.2
type II toxin-antitoxin system PemK/MazF family toxin
COORDINATES: protein motif:HMM:NF012772.2
bifunctional diguanylate cyclase/phosphodiesterase
COORDINATES: protein motif:HMM:TIGR01051.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003917 - DNA topoisomerase type I (single strand cut, ATP-independent) activity [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]; GO:0006265 - DNA topological change [Evidence IEA]
COORDINATES: protein motif:HMM:NF013618.2
lytic transglycosylase domain-containing protein
COORDINATES: protein motif:HMM:NF012372.2
GO:0008168 - methyltransferase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF014581.2
type IV secretory system conjugative DNA transfer family protein
COORDINATES: protein motif:HMM:NF037521.2
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011875688.1
COORDINATES: protein motif:HMM:NF037421.2
COORDINATES: protein motif:HMM:NF027824.2
COORDINATES: protein motif:HMM:NF016408.2
COORDINATES: protein motif:HMM:NF014044.2
COORDINATES: protein motif:HMM:TIGR00180.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: protein motif:HMM:NF018290.2
COORDINATES: protein motif:HMM:NF015688.2
COORDINATES: protein motif:HMM:TIGR02775.1
GO:0009291 - unidirectional conjugation [Evidence IEA]
P-type conjugative transfer protein TrbG
COORDINATES: protein motif:HMM:NF016238.2
COORDINATES: protein motif:HMM:TIGR02783.1
P-type conjugative transfer protein TrbL
COORDINATES: protein motif:HMM:TIGR02780.1
P-type conjugative transfer protein TrbJ
COORDINATES: protein motif:HMM:NF010404.0
COORDINATES: protein motif:HMM:NF016820.2
COORDINATES: similar to AA sequence:RefSeq:WP_011630639.1
COORDINATES: protein motif:HMM:NF012894.2
COORDINATES: protein motif:HMM:NF022136.2
toxin co-regulated pilus biosynthesis Q family protein
COORDINATES: protein motif:HMM:TIGR02520.1
GO:0019867 - outer membrane [Evidence IEA]
GO:0009297 - pilus assembly [Evidence IEA]; GO:0009306 - protein secretion [Evidence IEA]
PilN family type IVB pilus formation outer membrane protein
COORDINATES: protein motif:HMM:NF018562.2
COORDINATES: protein motif:HMM:NF012652.2
COORDINATES: similar to AA sequence:RefSeq:WP_011486084.1
type II secretion system F family protein
COORDINATES: protein motif:HMM:NF020384.2
COORDINATES: similar to AA sequence:RefSeq:WP_011486086.1
COORDINATES: protein motif:HMM:NF019064.2
COORDINATES: protein motif:HMM:NF016785.2
shufflon system plasmid conjugative transfer pilus tip adhesin PilV