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Overview

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> 5,740
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>UP000008070
Taxonomy661410 - Methylorubrum extorquens (strain DSM 6343 / CIP 106787 / DM4)
StrainDSM 6343 / CIP 106787 / DM4
Last modifiedAugust 21, 2020
Genome assembly and annotationi <p>Identifier for the genome assembly (<a href="https://www.ensembl.org/Help/Faq?id=216">more...</a>)</p> GCA_000083545.1 from ENA/EMBL full
Pan proteomei <p>A pan proteome is the full set of proteins thought to be expressed by a group of highly related organisms (e.g. multiple strains of the same bacterial species).<p><a href='/help/pan_proteomes' target='_top'>More...</a></p> This proteome is part of the Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1) (Methylobacterium extorquens) pan proteome (fasta)
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:100%[S:99.2%,D:0.8%],F:0%,M:0%,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> Standard

Methylobacterium extorquens is a pink-pigmented facultative methylotrophic Gram-negative bacterium first isolated in 1960 in Oxford as an airborne contaminant growing on methylamine. The trait common to all Methylobacterium species is the ability to grow on one or several reduced one carbon (C1) compounds other than methane, most prominently methanol. They are often found associated with plants. It has been used as a workhorse to characterize the serine cycle for assimilation of the C1-unit of methylene tetrahydrofolate, a central intermediate in methylotrophic metabolism, and more recently the ethylmalonyl-CoA pathway for glyoxylate regeneration.

Methylobacterium strain DM4 was isolated from industrial wastewater sludge in Switzerland, as part of efforts to characterize microorganisms able to degrade the organohalogenated pollutant dichloromethane (DCM). Unlike methanol and methylamine, which are mainly produced naturally, DCM is a highly produced synthetic compound which is rated as potentially carcinogenic for humans. It is highly volatile and water-soluble, making it a widespread contaminant in the environment. Most of the genomic determinants associated with methylotrophy are nearly identical in all strains with exceptions that illustrate the metabolic and genomic versatility of Methylobacterium species. M.extorquens (strain ATCC 14718 / DSM 1338 / AM1, METEA) possesses a unique methylamine dehydrogenase and accessory functions gene cluster (mau), indicating that strain DSM 5838 / DM4 employs an alternative system for growth with methylamine, while the dcm (dichloromethane degradation) gene region is present only in strain DM4. M. extorquens contains large sets of insertion elements, many of them strain-specific, suggesting an important potential for genomic plasticity (adapted from PMID 19440302).

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

Component nameGenome Accession(s)
Component representationProteins
Chromosome5590
Plasmid p1METDI116
Plasmid p2METDI37
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Main funding by: National Institutes of Health

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