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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> 3,849
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>UP000000636
Taxonomy292414 - Ruegeria sp. (strain TM1040)
StrainTM1040
Last modifiedSeptember 28, 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_000014065.1 from ENA/EMBL
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 Ruegeria sp. (strain TM1040) (Silicibacter sp.) pan proteome (fasta)

Ruegeria sp. (strain TM1040) (formerly Silicibacter sp.) belongs to the Roseobacter clade of the alpha-proteobacteria, which is among the most abundant and ecologically relevant marine bacterial groups. It was originally isolated as part of an investigation to understand the role of the bacteria in the physiology and toxigenesis of the dinoflagellate Pfiesteria piscicida. Ruegeria sp. (strain TM1040) is found within the phycosphere or physically attached to the surface of the dinoflagellate cell. Axenic cultures of P.piscicida grow poorly (and ultimately die) compared to cultures with associated bacterial assemblages. Although P.piscicida is a heterotrophic dinoflagellate, the Pfiesteria /TM1040 association is the only known "obligate" association between a dinoflagellate and a culturable bacterium. In addition, Ruegeria sp. (strain TM1040) metabolizes the dinoflagellate secondary metabolite dimethylsulfoniopropionate (DMSP) via demethylation to methylmercaptopropionic acid (MMPA). DMSP is the major source of organic sulfur in the world's oceans and plays a significant role in the global sulfur cycle. The genome of Ruegeria sp. (strain TM1040) is made up of one chromosome, one megaplasmid and one plasmid.

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

Component nameGenome Accession(s)
Proteins
Chromosome3024
Plasmid megaplasmid TM1040722
Plasmid pTM1040103

Publications

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