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Overview

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> 4,757
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>UP000001866
Taxonomy454169 - Salmonella heidelberg (strain SL476)
StrainSL476
Last modifiedJuly 17, 2020
Genome assembly and annotationi <p>Identifier for the genome assembly (<a href="https://www.ensembl.org/Help/Faq?id=216">more...</a>)</p> GCA_000020705.1 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 Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) 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:98.6%[S:98.4%,D:0.2%],F:0%,M:1.4%,n:440 enterobacterales_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)

Salmonella species belong to the group of Enterobactericiae. These bacteria were named after the scientist Dr. Daniel Salmon who isolated the first organism, Salmonella choleraesuis, from the intestine of a pig. The majority of the components of these bacteria are identical, and at the DNA level, they are between 95% and 99% identical. Many Salmonella enterica are involved in causing diseases of the intestine (enteric means pertaining to the intestine). The nontyphoidal Salmonella are the leading cause of bacterial food borne illness in humans, making these pathogens an immediate biomedical, public health, and biodefense concern. The presence of several pathogenicity islands (PAIs) that encode various virulence factors allows Salmonella spp. to colonize and infect host organisms. There are two important PAIs, Salmonella pathogenicity island 1 and 2 (SPI-1 and SPI-2) that encode two different type III secretion systems for the delivery of effector molecules into the host cell that result in internalization of the bacteria, which then leads to systemic spread.

In recent years, Salmonella heidelberg (strain SL476) has been the third or fourth most common Salmonella serotype causing disease in the U.S., estimated at 84,000 cases of illness annually. Epidemic outbreaks of S. heidelberg present a significant economic burden to healthcare systems in the United States and elsewhere, although studies have failed to elucidate the genetic factors of S. heidelberg that make it a particularly virulent serovar. The recent rise in S. heidelberg in the United States is accompanied by a concomitant increase in antimicrobial resistance. MDR strain SL476 (NARMS alternate designations: CVMN418, CVM30485) and antibiotic susceptible strain SL486 were chosen from this serotype.

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

Component nameGenome Accession(s)
Component representationProteins
Chromosome4628
Plasmid pSL476_91125
Plasmid pSL476_34

Publications

  1. "Comparative genomics of 28 Salmonella enterica isolates: evidence for CRISPR-mediated adaptive sublineage evolution."
    Fricke W.F., Mammel M.K., McDermott P.F., Tartera C., White D.G., Leclerc J.E., Ravel J., Cebula T.A.
    J. Bacteriol. 193:3556-3568(2011) [PubMed] [Europe PMC] [Abstract]
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