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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> 1,998
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>UP000006559
Taxonomy362948 - Lactobacillus salivarius (strain UCC118)
StrainUCC118
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_000008925.1 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 Lactobacillus salivarius (strain UCC118) pan proteome (fasta)

Lactobacillus salivarius subsp. salivarius (strain UCC118) was isolated from the terminal ileum of a healthy patient undergoing urinary tract reconstruction surgery. This strain has been extensively studied for its probiotic properties in human trials and animal models. Its genome is made up of one circular chromosome, a megaplasmid pMP118 and two smaller plasmids pSF118-20 and pSF118-44. No single-copy essential genes are located on the megaplasmid. However, it harbors the gene for the Abp118 bacteriocin. Four regions of bacteriophage-related DNA have been detected in the genome. Two seem to be intact prophages and two are remnants of prophages. Seventy-three pseudogenes have been found in the genome, a large part (27%) being located on the megaplasmid. Frameshifts are the main cause of gene inactivation. L. salivarius possesses both the highest number and diversity of IS elements in Lactobacillus genomes sequenced so far. Sixteen different IS elements, present in a total of 43 copies, have been identified. The megaplasmid harbors almost 25% of the IS elements of the genome. L.salivarius seems to lack the genes required for synthesis of tryptophan and related amino acids. It can synthesize de novo or by interconversion nine amino acids, can convert glutamine to three more and is theoretically auxotrophic for eight amino acids. A complete pathway for the biosynthesis of UMP (that can be further converted to UTP and CTP) as well as a complete pathway for biosynthesis of IMP (that branches AMP and GMP) are present. Currently L.salivarius is considered homofermentative. This means that sugars can be fermented only via the Embden-Meyerhof-Parnas pathway. However, genes for the pentose phosphate pathway have been found, suggesting that it could be grouped among the facultatively heterofermentative lactobacilli. This has been confirmed by the ability of L.salivarius to grow on ribose as a sole carbon source and by the detection of lactate, acetate and ethanol in the culture medium.

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

Component nameGenome Accession(s)
Proteins
Plasmid pMP118222
Chromosome1703
Plasmid pSF118-4448
Plasmid pSF118-2027
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Main funding by: National Institutes of Health

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