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Overview

StatusReference proteome
Proteinsi <p>Number of protein entries associated with this proteome: UniProtKB entries for regular proteomes or UniParc entries for redundant proteomes (<a href="/help/proteome%5Fredundancy">more...</a>)</p> 8,128
Gene counti <p>This is the total number of unique genes found in the proteome set, algorithmically computed. For each gene, a single representative protein sequence is chosen from the proteome. Where possible, reviewed (Swiss-Prot) protein sequences are chosen as the representatives.</p> - Download one protein sequence per gene (FASTA)
Proteome IDi <p>The proteome identifier (UPID) is the unique identifier assigned to the set of proteins that constitute the <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">proteome</a>. It consists of the characters 'UP' followed by 9 digits, is stable across releases and can therefore be used to cite a UniProt proteome.<p><a href='/help/proteome_id' target='_top'>More...</a></p>UP000008207
Taxonomy460265 - Methylobacterium nodulans (strain LMG 21967 / CNCM I-2342 / ORS 2060)
StrainLMG 21967 / CNCM I-2342 / ORS 2060
Last modifiedFebruary 26, 2021
Genome assembly and annotationi <p>Identifier for the genome assembly (<a href="https://www.ensembl.org/Help/Faq?id=216">more...</a>)</p> GCA_000022085.1 from ENA/EMBL full
Buscoi <p>The Benchmarking Universal Single-Copy Ortholog (BUSCO) assessment tool is used, for eukaryotic and bacterial proteomes, to provide quantitative measures of UniProt proteome data completeness in terms of expected gene content. BUSCO scores include percentages of complete (C) single-copy (S) genes, complete (C) duplicated (D) genes, fragmented (F) and missing (F) genes, as well as the total number of orthologous clusters (n) used in the BUSCO assessment.</p> C:99.8%[S:98.7%,D:1.1%],F:0%,M:0.2%,n:639 rhizobiales_odb10
Completenessi <p>Complete Proteome Detector (CPD) is an algorithm which employs statistical evaluation of the completeness and quality of proteomes in UniProt, by looking at the sizes of taxonomically close proteomes. Possible values are 'Standard', 'Close to Standard' and 'Outlier'.</p> Outlier (high value)

In 2001 Methylobacterium, which had been hitherto found associated non-symbiotically with plants, was discovered to nodulate Crotalaria, a large Fabaceae group found in Africa. Strain ORS 2060 (also known as CNCM I 2342T=LMG 21967T), the type strain for this species, was isolated from nodules on C. podocarpa from the Bel-Air area, Dakar, Senegal. It is able to use C1 compounds such as methanol, formate and formaldehyde but not methylamine as its sole carbon source, as well as more complex carbon sources such as succinate, citrate, pyruvate, glutamate and ethanol. It grows as short asporogenous Gram-negative rods that occur singly or occasionally in pairs; some are motile with one or more polar flagella. Optimal growth occurs at pH 6.8-7.5 and at 30-37 degrees C. It is strictly aerobic and unpigmented (adapted from PubMed 15545469 and genome.jgi-psf.org/finished_microbes/metno/metno.home.html).

Componentsi <p>Genomic components encoding the proteome</p>

Component nameGenome Accession(s)
Component representationProteins
Chromosome7224
Plasmid pMNOD01395
Plasmid pMNOD02398
Plasmid pMNOD0353
Plasmid pMNOD0448
Plasmid pMNOD0521
Plasmid pMNOD0613
Plasmid pMNOD077

Publications

  1. "Complete sequence of chromosome of Methylobacterium nodulans ORS 2060."
    US DOE Joint Genome Institute
    Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H., Bruce D., Goodwin L., Pitluck S., Sims D., Brettin T., Detter J.C., Han C., Larimer F., Land M., Hauser L., Kyrpides N., Ivanova N., Marx C.J., Richardson P.
    Submitted (JAN-2009) to the EMBL/GenBank/DDBJ databases
  2. "Complete sequence of plasmid 1 of Methylobacterium nodulans ORS 2060."
    US DOE Joint Genome Institute
    Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H., Bruce D., Goodwin L., Pitluck S., Sims D., Brettin T., Detter J.C., Han C., Larimer F., Land M., Hauser L., Kyrpides N., Ivanova N., Marx C.J., Richardson P.
    Submitted (JAN-2009) to the EMBL/GenBank/DDBJ databases
  3. "Complete sequence of plasmid 2 of Methylobacterium nodulans ORS 2060."
    US DOE Joint Genome Institute
    Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H., Bruce D., Goodwin L., Pitluck S., Sims D., Brettin T., Detter J.C., Han C., Larimer F., Land M., Hauser L., Kyrpides N., Ivanova N., Marx C.J., Richardson P.
    Submitted (JAN-2009) to the EMBL/GenBank/DDBJ databases
  4. "Complete sequence of plasmid 3 of Methylobacterium nodulans ORS 2060."
    US DOE Joint Genome Institute
    Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H., Bruce D., Goodwin L., Pitluck S., Sims D., Brettin T., Detter J.C., Han C., Larimer F., Land M., Hauser L., Kyrpides N., Ivanova N., Marx C.J., Richardson P.
    Submitted (JAN-2009) to the EMBL/GenBank/DDBJ databases
  5. "Complete sequence of plasmid 4 of Methylobacterium nodulans ORS 2060."
    US DOE Joint Genome Institute
    Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H., Bruce D., Goodwin L., Pitluck S., Sims D., Brettin T., Detter J.C., Han C., Larimer F., Land M., Hauser L., Kyrpides N., Ivanova N., Marx C.J., Richardson P.
    Submitted (JAN-2009) to the EMBL/GenBank/DDBJ databases
  6. "Complete sequence of plasmid 5 of Methylobacterium nodulans ORS 2060."
    US DOE Joint Genome Institute
    Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H., Bruce D., Goodwin L., Pitluck S., Sims D., Brettin T., Detter J.C., Han C., Larimer F., Land M., Hauser L., Kyrpides N., Ivanova N., Marx C.J., Richardson P.
    Submitted (JAN-2009) to the EMBL/GenBank/DDBJ databases
  7. "Complete sequence of plasmid 6 of Methylobacterium nodulans ORS 2060."
    US DOE Joint Genome Institute
    Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H., Bruce D., Goodwin L., Pitluck S., Sims D., Brettin T., Detter J.C., Han C., Larimer F., Land M., Hauser L., Kyrpides N., Ivanova N., Marx C.J., Richardson P.
    Submitted (JAN-2009) to the EMBL/GenBank/DDBJ databases
  8. "Complete sequence of plasmid 7 of Methylobacterium nodulans ORS 2060."
    US DOE Joint Genome Institute
    Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H., Bruce D., Goodwin L., Pitluck S., Sims D., Brettin T., Detter J.C., Han C., Larimer F., Land M., Hauser L., Kyrpides N., Ivanova N., Marx C.J., Richardson P.
    Submitted (JAN-2009) to the EMBL/GenBank/DDBJ databases
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