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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> 5,937
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>UP000008917
Taxonomy595537 - Variovorax paradoxus (strain EPS)
StrainEPS
Last modifiedMarch 31, 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_000184745.1 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 Variovorax paradoxus pan proteome (fasta)
BuscoC:100%[S:99.4%,D:0.6%],F:0%,M:0%,n:688

Variovorax paradoxus is a ubiquitous, aerobic, gram negative bacterium present in diverse environments. This organism has been associated with a number of interesting biotransformations, including atrazine degradation, nitrotyrosine assimilation, and mineralization of acyl-homoserine lactone signals. It is able to grow autotrophically using hydrogen gas and carbon dioxide for energy and carbon and has been implicated in plant growth promotion, as part of the rhizosphere consortium with nodulating diazotrophs. This microorganism was also recently identified as a member of methylotrophic community in the human oral cavity (adapted from PMID 19523213).

Strain EPS was cultivated from the soil in the Land Lab at CSU San Bernardino. It is one of 2 (December 2010) sequenced V.paradoxus strains. This strain has only 1 chromosome, whereas the other strain, S110, has 2 chromosomes.

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

Component nameGenome Accession(s)
Component representationProteins
Chromosome5937

Publications

  1. "Genome of the Root-Associated Plant Growth-Promoting Bacterium Variovorax paradoxus Strain EPS."
    Han J.I., Spain J.C., Leadbetter J.R., Ovchinnikova G., Goodwin L.A., Han C.S., Woyke T., Davenport K.W., Orwin P.M.
    Genome Announc 1:e00843-13(2013) [PubMed] [Europe PMC] [Abstract]
  2. "Complete sequence of Variovorax paradoxus EPS."
    US DOE Joint Genome Institute
    Lucas S., Copeland A., Lapidus A., Cheng J.-F., Goodwin L., Pitluck S., Teshima H., Detter J.C., Han C., Tapia R., Land M., Hauser L., Kyrpides N., Ivanova N., Ovchinnikova G., Orwin P., Han J.-I.G., Woyke T.
    Submitted (DEC-2010) to the EMBL/GenBank/DDBJ databases
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Main funding by: National Institutes of Health

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