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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_redundancy">more...</a>)</p> 2,657
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_manual">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>UP000002717
Taxonomy1140 - Synechococcus elongatus (strain PCC 7942 / FACHB-805)
StrainPCC 7942 / FACHB-805
Last modifiedMay 24, 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_000012525.1 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 Synechococcus elongatus (strain PCC 7942 / FACHB-805) (Anacystis nidulans R2) 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 (M) genes, as well as the total number of orthologous clusters (n) used in the BUSCO assessment, and the name of the taxonomic lineage dataset used.</p> C:99.7%[S:99.7%,D:0%],F:0%,M:0.3%,n:788 synechococcales_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

The freshwater cyanobacterium Synechococcus PCC 7942 (previously known as Anacystis nidulans R2) was the first cyanobacterium demonstrated to be reliably transformable by exogenously added DNA. Over the decades many genetic tools have been developed for Synechococcus and applied to other transformable cyanobacteria. Strain PCC 7942 is an obligate photoautotroph with a genome of approximately 2.7 Mb. It has been extensively studied by a multi-national research community with respect to: acquisition of inorganic carbon, transport and regulation of nitrogen compounds, response to iron deprivation, acclimation to a variety of nutrient stresses, adaptation to environmental variations in temperature and light intensity and photosynthesis. In recent years, Synechococcus PCC 7942 has taken a pioneering position as the only developed model system for exploring the mechanism of the prokaryotic circadian clock. Gene organization and sequence are nearly identical to another freshwater cyanobacterium Synechococcus elongatus PCC 6301 (SYNP6) except for a large inversion of 187 kb. The endpoints of this inversion are found in genes that may encode outer membrane porins, and thus the two proteins in question are polymorphic with respect to one another. These differences may explain the fact that SYNE7 is naturally competent for transformation while SYNP6 is not.

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

Component nameGenome Accession(s)
Component representationProteins
Chromosome2607
Plasmid pANL50

Publications

  1. "Complete sequence of chromosome 1 of Synechococcus elongatus PCC 7942."
    US DOE Joint Genome Institute
    Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina T., Hammon N., Israni S., Pitluck S., Schmutz J., Larimer F., Land M., Kyrpides N., Lykidis A., Richardson P.
    Submitted (AUG-2005) to the EMBL/GenBank/DDBJ databases
  2. "Complete sequence of plasmid 1 of Synechococcus elongatus PCC 7942."
    US DOE Joint Genome Institute
    Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina T., Hammon N., Israni S., Pitluck S., Schmutz J., Larimer F., Land M., Kyrpides N., Lykidis A., Richardson P.
    Submitted (AUG-2005) to the EMBL/GenBank/DDBJ databases
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Main funding by: National Institutes of Health

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