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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_redundancy">more...</a>)</p> 5,841
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>UP000006503
Taxonomy1196325 - Pseudomonas putida (strain DOT-T1E)
StrainDOT-T1E
Last modifiedJuly 21, 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_000281215.1 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 Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440) 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 (M) genes, as well as the total number of orthologous clusters (n) used in the BUSCO assessment, and the name of the taxonomic lineage dataset used.</p> C:98%[S:97.6%,D:0.4%],F:1.2%,M:0.9%,n:782 pseudomonadales_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> Standard

Members of the genus Pseudomonas are characterized by their ability to grow in simple media at the expense of a great variety of organic compounds. They have a strict respiratory metabolism and are motile by one or several polar flagella. They are common inhabitants of soil and water and can also be found on the surfaces of plants and animals. They are are found in nature in a biofilm or in planktonic form.

Strain DOT-T1E is one of a handful of P.putida strains able to thrive in the presence of toxic solvents (e.g. decanol, octanol, toluene, styrene), and is thus considered an extremophile microorganism with great potential in bioremediation and in biocatalysis in biphasic systems. Its ability to survive these toxic components resides in its chromosomally and plasmid-encoded RND (resistance-nodulation-cell division) efflux pumps and its chromosomally-encoded ABC efflux transporters (adapted from PMID 23815283).

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

Component nameGenome Accession(s)
Component representationProteins
Chromosome5719
Plasmid pGRT1122

Publications

  1. "The pGRT1 plasmid of Pseudomonas putida DOT-T1E encodes functions relevant for survival under harsh conditions in the environment."
    Molina L., Duque E., Gomez M.J., Krell T., Lacal J., Garcia-Puente A., Garcia V., Matilla M.A., Ramos J.L., Segura A.
    Environ. Microbiol. 13:2315-2327(2011) [PubMed] [Europe PMC] [Abstract]
  2. "Metabolic potential of the organic-solvent tolerant Pseudomonas putida DOT-T1E deduced from its annotated genome."
    Udaondo Z., Molina L., Daniels C., Gomez M.J., Molina-Henares M.A., Matilla M.A., Roca A., Fernandez M., Duque E., Segura A., Ramos J.L.
    Microb. Biotechnol. 6:598-611(2013) [PubMed] [Europe PMC] [Abstract]
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