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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> 4,864
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>UP000001948
Taxonomy316056 - Rhodopseudomonas palustris (strain BisB18)
StrainBisB18
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_000013745.1 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:100%[S:99.4%,D:0.6%],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> Close to standard (low value)

Rhodopseudomonas palustris are phototrophic, purple non-sulfur bacteria commonly found in soils and water. They fix carbon dioxide and nitrogen, produce hydrogen, and degrade diverse biomass-associated aromatic compounds under anaerobic (phototrophic) and aerobic (heterotrophic) conditions. Against the background of general metabolic versatility of the R. palustris species there is considerable strain-to-strain diversity. The JGI has sequenced 5 strains in all of R. palustris. These additional genome sequences will provide a basis for defining the genetic and functional differences that can exist within the species Rhodopseudomonas palustris. The 16S rRNA sequence of each of the strains differs from that of the already sequenced strain (CGA009 / ATCC BAA-98, RHOPA) by about 2%. The more recently sequenced strains were isolated by direct plating from two different sites, one pristine and one polluted. The strains were frozen immediately following their isolation and have had minimal exposure to the laboratory environment. The strains to be sequenced differ from each other in BOX-PCR genomic DNA fingerprints. Although the strains have not been extensively characterized phenotypically, they have some obvious differences. They differ in pigmentation, in growth on benzoate, and the cells of each strain have slightly different shapes and sizes, although they all have the distinctive appearance of R. palustris.

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

Component nameGenome Accession(s)
Component representationProteins
Chromosome4864
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Main funding by: National Institutes of Health

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