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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> 3,071
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>UP000000663
Taxonomy351160 - Methanocella arvoryzae (strain DSM 22066 / NBRC 105507 / MRE50)
StrainDSM 22066 / NBRC 105507 / MRE50
Last modifiedAugust 19, 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_000063445.1 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:94.4%[S:92.5%,D:1.9%],F:0%,M:5.6%,n:588 methanomicrobia_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

A large part of the emitted methane is produced by methanogenic archaea and released through the gas vascular system of the rice plant. Rice Cluster I (RC-I) methanogens in the rice rhizosphere were found to play the key role in methane production from plant-derived carbon. They were identified as the predominant methanogens in rice paddy soils of geographically diverse regions. Several attempts have been made to isolate RC-I representatives in pure culture. Although isolation failed, one of these attempts with rice paddy soil as the inoculum resulted in the methanogenic consortium MRE50, in which RC-I methanogens constituted the only archaeal components. The complete genome sequence of a single RC-I representative was unambiguously reconstructed. The genome of the Uncultured methanogenic archaeon RC-I is made up of a single circular chromosome of 3,179,916 base pairs with 3103 coding sequences. The central energy metabolism of RC-I is H2/CO2-dependent methanogenesis. It can use formate and formaldehyde for methanogenic growth. It encodes only an incomplete methanol-coenzyme M methyltransferase system. It appears to use the Embden-Meyerhof-Parnas pathway for carbohydrate metabolism, thus involving bacterial-type enzymes not yet identified in archaea. The biosynthetic pathways for all amino acids except glutamate appear to be complete. Two mechanisms for nitrogen acquisition exist besides glutamate uptake: ammonium assimilation (glutamine synthetase, glutamate synthase and glutamate dehydrogenase) and dinitrogen fixation (nitrogenase). Sulfur assimilation is predicted to occur thanks to the reduction of sulfate to sulfide.

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

Component nameGenome Accession(s)
Component representationProteins
Chromosome3071

Publications

  1. "Genome of rice cluster I archaea -- the key methane producers in the rice rhizosphere."
    Erkel C., Kube M., Reinhardt R., Liesack W.
    Science 313:370-372(2006) [PubMed] [Europe PMC] [Abstract]
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