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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> 4,336
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>UP000002350
Taxonomy637905 - Shewanella violacea (strain JCM 10179 / CIP 106290 / LMG 19151 / DSS12)
StrainJCM 10179 / CIP 106290 / LMG 19151 / DSS12
Last modifiedNovember 5, 2019
Genome assembly and annotationi <p>Identifier for the genome assembly (<a href="https://www.ensembl.org/Help/Faq?id=216">more...</a>)</p> GCA_000091325.1 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 Shewanella violacea (strain JCM 10179 / CIP 106290 / LMG 19151 / DSS12) pan proteome (fasta)
BuscoC:98.2%[S:97.8%,D:0.4%],F:1.1%,M:0.7%,n:452
CompletenessStandard

Shewanella are facultatively anaerobic, Gram-negative bacteria, motile by polar flagella, rod-like, and generally associated with aquatic or marine environments. They are capable of using a variety of compounds as electron acceptors, including oxygen, iron, manganese, uranium, nitrate, nitrite, fumarate, to name but a few. This ability makes Shewanella important for bioremediation of contaminated metals and radioactive wastes. The genus Shewanella comprises 36 recognized and hundreds of uncharacterized cultivable species.

S.violacea strain DSS12 is a psychrophilic and piezophilic bacterium isolated from the surface layer of sediments in the Ryuku Trench at a depth of 5110m. As befits its habitat, it grows optimally at 8 degrees Celsius and at 30 MPa. The genome of S.violacea when compared to S.oneidensis reflects adaptations to the environment in the surface layer of deep-sea sediments. It can secrete a wide variety of enzymes which enables it to decompose a wide variety of organic compounds, suggesting that it contributes substantially to remineralization of organic matter in deep-sea sediments. S.violacea strongly depends on oxygen as a terminal electron acceptor, indicating that a steady supply of oxygen to the deep-sea floor through the global thermohaline circulation (when cold salty water sinks from the surface near the poles and flows at depth to all the ocean basins) is very important for maintaining adequate remineralization of deep-sea sediments. The finding that S. violacea is likely to utilize nitrate as a nitrogen source suggests that the contribution of deep-sea sediment bacteria to nitrate assimilation processes in the oceanic nitrogen cycle may need to be considered. The genome analysis has also revealed the involvement of phosphatidylethanolamine and cadiolipin in adaptation to the cold, deep-sea environment (adapted from PMID 20458400).

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

Component nameGenome Accession(s)
Component representationProteins
Chromosome4336

Publications

  1. "Complete genome sequence and comparative analysis of Shewanella violacea, a psychrophilic and piezophilic bacterium from deep sea floor sediments."
    Aono E., Baba T., Ara T., Nishi T., Nakamichi T., Inamoto E., Toyonaga H., Hasegawa M., Takai Y., Okumura Y., Baba M., Tomita M., Kato C., Oshima T., Nakasone K., Mori H.
    Mol. Biosyst. 6:1216-1226(2010) [PubMed] [Europe PMC] [Abstract]
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