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Proteomes - Synechocystis sp. (strain PCC 6803 / Kazusa)

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> 3,507
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>UP000001425
Taxonomy1111708 - Synechocystis sp. (strain PCC 6803 / Kazusa)
StrainPCC 6803 / Kazusa
Last modifiedMarch 7, 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_000009725.1 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 Synechocystis sp. (strain PCC 6803 / Kazusa) 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:96.2%[S:95.9%,D:0.3%],F:0.9%,M:2.9%,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> Close to standard (high value)

Model cyanobacterium that carries a complete set of genes for oxygenic photosynthesis, Synechocystis is also studied for its stress response and metabolism. The first glucose-tolerant strain was sequenced in 1996 (this strain Kazusa, SYNY3),while a second glucose tolerant strain, Synechocystis GT-S, and has been maintained as frozen glycerol stocks since the late 1980s. Careful comparison reveals that there is a single nucleotide change and two IS insertions between the Kazusa strain and the GT-S strain, with some changes to the sequence of the Kazusa strain also noticed. Although they have not been resubmitted strain GT-S also encodes the 4 plasmids sound in SYNY3 (adapted from PMID 21803841).

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

Component nameGenome Accession(s)
Component representationProteins
Chromosome
BA000022
3140
Plasmid pSYSM
AP004310
132
Plasmid pSYSA
AP004311
106
Plasmid pSYSG
AP004312
47
Plasmid pSYSX
AP006585
85

Publications

  1. "Structural analysis of four large plasmids harboring in a unicellular cyanobacterium, Synechocystis sp. PCC 6803."
    Kaneko T., Nakamura Y., Sasamoto S., Watanabe A., Kohara M., Matsumoto M., Shimpo S., Yamada M., Tabata S.
    DNA Res. 10:221-228(2003) [PubMed] [Europe PMC] [Abstract]
  2. "Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions."
    Kaneko T., Sato S., Kotani H., Tanaka A., Asamizu E., Nakamura Y., Miyajima N., Hirosawa M., Sugiura M., Sasamoto S., Kimura T., Hosouchi T., Matsuno A., Muraki A., Nakazaki N., Naruo K., Okumura S., Shimpo S.
    Tabata S.
    DNA Res. 3:109-136(1996) [PubMed] [Europe PMC] [Abstract]
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