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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> 4,484
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>UP000006626
Taxonomy596153 - Alicycliphilus denitrificans (strain DSM 18852 / JCM 14587 / BC)
StrainJCM 14587 / BC
Last modifiedJuly 15, 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_000179015.2 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 Alicycliphilus denitrificans (strain DSM 14773 / CIP 107495 / K601) 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:99.7%[S:99.6%,D:0.1%],F:0%,M:0.3%,n:688 burkholderiales_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

Chlorate contamination of groundwater is a big problem that is often associated with the manufacture and use of explosives and munitions. To clean up chlorate-contaminated areas, some researchers turn to bacteria that can break down these compounds. These microbes can produce oxygen in anaerobic conditions, which can speed up the process of breaking down other compounds that do not degrade quickly in anaerobic environments such as the hydrocarbon benzene. Adding chlorate-reducing bacteria to contaminated, oxygen-poor environments could therefore encourage the growth of other bacteria that need oxygen to break down other compounds found at these sites. Microbes usually need oxygen to break down benzene; in anaerobic environments, the process is very slow. Alicycliphilus denitrificans (strain JCM 14587 / BC) is Gram-negative bacterium which can break down both chlorates and benzene. It produces oxygen while breaking down chlorates, and the oxygen is used to speed up the degradation of benzene in anaerobic conditions. (Adapted from: www.ncbi.nlm.nih.gov/genomeprj/41663).

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

Component nameGenome Accession(s)
Component representationProteins
Chromosome4284
Plasmid pALIDE01121
Plasmid pALIDE0287

Publications

  1. "Complete sequence of chromosome of Alicycliphilus denitrificans BC."
    US DOE Joint Genome Institute
    Lucas S., Copeland A., Lapidus A., Cheng J.-F., Goodwin L., Pitluck S., Daligault H., Detter J.C., Han C., Tapia R., Land M., Hauser L., Kyrpides N., Ivanova N., Mikhailova N., Oosterkamp M.J., Veuskens T., Weelink S.A.
    Woyke T.
    Submitted (JAN-2011) to the EMBL/GenBank/DDBJ databases
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

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