Methylobacterium nodulans ORS 2060 plasmid pMNOD07, complete sequence.
type: Entry
definition: Methylobacterium nodulans ORS 2060 plasmid pMNOD07, complete sequence.
sequence version: NC_011890.1
sequence date: 2023-04-24
sequence: sequence
division: CON
label: NC_011890.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN00000043
keyword: RefSeq
source: Methylobacterium nodulans ORS 2060
organism: Methylobacterium nodulans ORS 2060
taxonomy: Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales; Methylobacteriaceae; Methylobacterium.
reference: 1
references: 22887658
reference: 2
reference: 3
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP001356.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4003783\nSource DNA and bacteria available from Christopher J. Marx\n(cmarx@oeb.harvard.edu)\nContacts: Christopher J. Marx (cmarx@oeb.harvard.edu)\n David Bruce (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##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/24/2023 02:07:41\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.5\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 8,718\nCDSs (total) :: 8,621\nGenes (coding) :: 8,153\nCDSs (with protein) :: 8,153\nGenes (RNA) :: 97\nrRNAs :: 7, 7, 7 (5S, 16S, 23S)\ncomplete rRNAs :: 7, 7, 7 (5S, 16S, 23S)\ntRNAs :: 72\nncRNAs :: 4\nPseudo Genes (total) :: 468\nCDSs (without protein) :: 468\nPseudo Genes (ambiguous residues) :: 0 of 468\nPseudo Genes (frameshifted) :: 194 of 468\nPseudo Genes (incomplete) :: 372 of 468\nPseudo Genes (internal stop) :…

sequence
subclass of: SO_0000155
sequence length: 9829
topology: circular
so has quality: SO_0000988
location: 1..9829
location: region:1-9829:1
RO_0002162: 460265

NC_011890
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN00000043
type: BioSample
SIO_000068: biosample

1
title: Complete genome sequences of six strains of the genus Methylobacterium
author: Marx, C.J.
author: Bringel, F.
author: Chistoserdova, L.
author: Moulin, L.
author: Farhan Ul Haque, M.
author: Fleischman, D.E.
author: Gruffaz, C.
author: Jourand, P.
author: Knief, C.
author: Lee, M.C.
author: Muller, E.E.
author: Nadalig, T.
author: Peyraud, R.
author: Roselli, S.
author: Russ, L.
author: Goodwin, L.A.
author: Ivanova, N.
author: Kyrpides, N.
author: Lajus, A.
author: Land, M.L.
author: Medigue, C.
author: Mikhailova, N.
author: Nolan, M.
author: Woyke, T.
author: Stolyar, S.
author: Vorholt, J.A.
author: Vuilleumier, S.
journal: J Bacteriol
volume: 194
issue: 17
pages: 4746-4748
year: 2012
pubmed: 22887658

22887658
type: PubMed
SIO_000068: pubmed

2
title: Complete sequence of plasmid7 of Methylobacterium nodulans ORS 2060
author: Lucas, S.
author: Copeland, A.
author: Lapidus, A.
author: Glavina del Rio, T.
author: Dalin, E.
author: Tice, H.
author: Bruce, D.
author: Goodwin, L.
author: Pitluck, S.
author: Sims, D.
author: Brettin, T.
author: Detter, J.C.
author: Han, C.
author: Larimer, F.
author: Land, M.
author: Hauser, L.
author: Kyrpides, N.
author: Ivanova, N.
author: Marx, C.J.
author: Richardson, P.
journal: Unpublished

3
title: Direct Submission
author: Lucas, S.
author: Copeland, A.
author: Lapidus, A.
author: Glavina del Rio, T.
author: Dalin, E.
author: Tice, H.
author: Bruce, D.
author: Goodwin, L.
author: Pitluck, S.
author: Sims, D.
author: Brettin, T.
author: Detter, J.C.
author: Han, C.
author: Larimer, F.
author: Land, M.
author: Hauser, L.
author: Kyrpides, N.
author: Ivanova, N.
author: Marx, C.J.
author: Richardson, P.
journal: Submitted (06-JAN-2009) US DOE Joint Genome Institute, 2800 Mitchell Drive B100, Walnut Creek, CA 94598-1698, USA

position:1:1
position: 1
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:9829:1
position: 9829
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-9829:1:source
so part of: sequence
organism: Methylobacterium nodulans ORS 2060
mol type: genomic DNA
strain: ORS 2060
type material: type strain of Methylobacterium nodulans
plasmid: pMNOD07

460265
type: Taxonomy
SIO_000068: taxonomy

MNOD_RS41140
type: Gene
subclass of: SO_0000704
RO_0002162: 460265
locus tag: MNOD_RS41140
old locus tag: Mnod_7765
so part of: sequence
location: complement(1114..1359)
location: region:1114-1359:-1
so has part: feature:1114-1359:-1:exon
subclass of: SO_0000010

position:1114:-1
position: 1114
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1359:-1
position: 1359
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1114-1359:-1:exon

MNOD_RS41140
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 460265
locus tag: MNOD_RS41140
old locus tag: Mnod_7765
inference: COORDINATES: similar to AA sequence:RefSeq:WP_018262702.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MTLPIVVAAAEAAVFTLGCAFIHSQKRLRAERLTVLLAAVAYAAFLALVVMSTPEDTTMAEVAAEMGSPLPLPGEPRLIEP
SIO_010081: MNOD_RS41140
subclass of: SO_0000673
so part of: MNOD_RS41140
location: complement(1114..1359)
location: region:1114-1359:-1
so has part: feature:1114-1359:-1:exon

WP_012631452.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1114-1359:-1:exon

MNOD_RS47865
type: Gene
subclass of: SO_0000704
RO_0002162: 460265
locus tag: MNOD_RS47865
so part of: sequence
location: complement(2373..2627)
location: region:2373-2627:-1
so has part: feature:2373-2627:-1:exon
subclass of: SO_0000010

position:2373:-1
position: 2373
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2627:-1
position: 2627
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2373-2627:-1:exon

MNOD_RS47865
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 460265
locus tag: MNOD_RS47865
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MKEAAQAYTLEMLAVLVRVAMDEGAPPAARVTAANAVLDRGHGKPTTNVDAKVATVDVTKLHLQALLDLSAPAPQPTGAERGAP
SIO_010081: MNOD_RS47865
subclass of: SO_0000673
so part of: MNOD_RS47865
location: complement(2373..2627)
location: region:2373-2627:-1
so has part: feature:2373-2627:-1:exon

WP_198157718.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2373-2627:-1:exon

MNOD_RS41150
type: Gene
subclass of: SO_0000704
RO_0002162: 460265
locus tag: MNOD_RS41150
old locus tag: Mnod_7767
so part of: sequence
location: complement(3014..5554)
location: region:3014-5554:-1
so has part: feature:3014-5554:-1:exon
subclass of: SO_0000010

position:3014:-1
position: 3014
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:5554:-1
position: 5554
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3014-5554:-1:exon

MNOD_RS41150
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 460265
locus tag: MNOD_RS41150
old locus tag: Mnod_7767
inference: COORDINATES: similar to AA sequence:RefSeq:WP_012631444.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: DUF5906 domain-containing protein
translation: MSAQSLHRLGARNKSGQPWRDYGDALRTNKWRAVHIQHGEKRPLLKEWPQRGVPTAAEVETWQRPERASMGLILGPQPSLPPDEHVVAVDADVFTPAAATAVNEILERRLPGAPHRLGNPAKVGTRFVRTKTADGSEPVRRQGRRFIFDGAPDTKENHNRVELLGQGQQSVVHGTHPCGVAYAWPSGTSIVEMHPSELPLIPIDELNAIIAECDTAMEAAGGVLVSGATFSRSGRNGGGADLTALVEANAEALLSGLADTRNDISSRNRWVMFTKAFAALCLPALGEDRVAEALFRFTDRWETAPGTADMEEIRRIIREEDKPAQMGLREVFHMMRERGAPLPGNFLARLDFEGVPVNDNDMPGATGRAPRAPKVAPADMPEHVSALSAMNGRYAVARNGGSTVVLRFGPEGSVPSMMTKTAFMDLEAPNKITGPDARRHPIAPAWFGWSGRRTYPEGVAMWPQGVTGEGLPVPEGALNTWQGFVSTPAAAGSDWPTIRAYLRDVICAGDQSLFAWLMNWLAHAAQRPHEKPGTAPIFKGPQGSGKTTFTNLLRAIFHPAHVVSAERPEALLGKHNAHLREALFVMADEAVFAGDPAANNRLKAMVTDATLTIEPKGIDAVSVPSFHRFVMTSNEDHVIRAEADARRWAVFDVSGEQVGNVAYFRELYAVLKPETPEVRAFLRDLAVMEIDEAAVRRAPTTSALVGQIVQSLPAPQQWLYELLRGCLPASKPLTAREAATAIPYHPEFEDGDGEWPEFATKEALSASFKAWTTGRPYLRGAGTNAFGKLLTIFGPPTQVTFSDDSRRRVVCLGTLDAARAAFAAAYLRGVNDASVWGRGEGDETPE
SIO_010081: MNOD_RS41150
subclass of: SO_0000673
so part of: MNOD_RS41150
location: complement(3014..5554)
location: region:3014-5554:-1
so has part: feature:3014-5554:-1:exon

WP_012631454.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3014-5554:-1:exon

MNOD_RS41155
type: Gene
subclass of: SO_0000704
RO_0002162: 460265
locus tag: MNOD_RS41155
old locus tag: Mnod_7768
so part of: sequence
location: complement(5683..6603)
location: region:5683-6603:-1
so has part: feature:5683-6603:-1:exon
subclass of: SO_0000010

position:5683:-1
position: 5683
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:6603:-1
position: 6603
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5683-6603:-1:exon

MNOD_RS41155
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 460265
locus tag: MNOD_RS41155
old locus tag: Mnod_7768
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MTPRAHIAGLGLDEPIAETSALRVDEALRAFDLLRGGVTVTSREHAAQLGPNGGRIINSYRSDKQARQRCREDLLEVFSKADPQDFVMVLNEAPYTLRIPRKEEVTGIRAVAVRLTFDHQARELCRINPGAAALDFMVRVAQPLLARAIRAGTRPFYISDPAHYSVILLWTFEEPIPVETERDRNAFRDETLRLVRTVRAAGVQGANIAGCPLTQTVPVPGVVRLRNGVEHIGVLSYDPRDDNPGLPESNGRTFADIVRLVDRIERTPPVSPAEVLSDLADVGLYQKVNDRIVDCGGRPLHEARPC
SIO_010081: MNOD_RS41155
subclass of: SO_0000673
so part of: MNOD_RS41155
location: complement(5683..6603)
location: region:5683-6603:-1
so has part: feature:5683-6603:-1:exon

WP_012631455.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5683-6603:-1:exon

MNOD_RS41160
type: Gene
subclass of: SO_0000704
RO_0002162: 460265
locus tag: MNOD_RS41160
old locus tag: Mnod_7769
so part of: sequence
location: complement(6600..6803)
location: region:6600-6803:-1
so has part: feature:6600-6803:-1:exon
subclass of: SO_0000010

position:6600:-1
position: 6600
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:6803:-1
position: 6803
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6600-6803:-1:exon

MNOD_RS41160
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 460265
locus tag: MNOD_RS41160
old locus tag: Mnod_7769
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MEDELMTQRQLAAKLKVCLRTLERELATAKDGPPEIRPSPRRILYRSTDVNRWLEARTVRRNQGISQ
SIO_010081: MNOD_RS41160
subclass of: SO_0000673
so part of: MNOD_RS41160
location: complement(6600..6803)
location: region:6600-6803:-1
so has part: feature:6600-6803:-1:exon

WP_012631456.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6600-6803:-1:exon

MNOD_RS41165
type: Gene
subclass of: SO_0000704
RO_0002162: 460265
locus tag: MNOD_RS41165
old locus tag: Mnod_7770
pseudo: true
so part of: sequence
location: 7803..8448
location: region:7803-8448:1
so has part: feature:7803-8448:1:exon
subclass of: SO_0000010

position:7803:1
position: 7803
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:8448:1
position: 8448
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:7803-8448:1:exon

MNOD_RS41165
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 460265
locus tag: MNOD_RS41165
old locus tag: Mnod_7770
inference: COORDINATES: similar to AA sequence:RefSeq:WP_012631439.1
GO function: GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO process: GO:0006310 - DNA recombination [Evidence IEA]
note: frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
pseudo: true
codon start: 1
transl table: 11
product: recombinase family protein
SIO_010081: MNOD_RS41165
subclass of: SO_0000673
so part of: MNOD_RS41165
location: 7803..8448
location: region:7803-8448:1
so has part: feature:7803-8448:1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:7803-8448:1:exon

MNOD_RS41170
type: Gene
subclass of: SO_0000704
RO_0002162: 460265
locus tag: MNOD_RS41170
old locus tag: Mnod_7771
so part of: sequence
location: complement(8517..9008)
location: region:8517-9008:-1
so has part: feature:8517-9008:-1:exon
subclass of: SO_0000010

position:8517:-1
position: 8517
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:9008:-1
position: 9008
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:8517-9008:-1:exon

MNOD_RS41170
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 460265
locus tag: MNOD_RS41170
old locus tag: Mnod_7771
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MADDVQWMTYAELAEALGIGGDSARNLVRRKRWARQLGNDGMARVGVPIEHLQEGRGSEPPADPPADGGSDGDDDGASVVSVLTNHICRLERDLHALKEEHAAERSRLRDEAEVLRQERDAERLRATQVEVLQAVLDEIRQDRDRWHATATARRSWWPWRRTG
SIO_010081: MNOD_RS41170
subclass of: SO_0000673
so part of: MNOD_RS41170
location: complement(8517..9008)
location: region:8517-9008:-1
so has part: feature:8517-9008:-1:exon

WP_012631457.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:8517-9008:-1:exon