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Proteomes - Acidiphilium cryptum (strain JF-5)

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%5Fredundancy">more...</a>)</p> 3,521
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>UP000000245
Taxonomy349163 - Acidiphilium cryptum (strain JF-5)
StrainJF-5
Last modifiedOctober 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_000016725.1 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 Acidiphilium cryptum (strain JF-5) 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:98.2%[S:97.9%,D:0.3%],F:0.3%,M:1.5%,n:617 rhodospirillales_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

Acidiphilium cryptum (strain JF-5) is an acidophilic dissimilatory iron-reducing bacterium (DIRB) of the alpha subdivision of the Proteobacteria. This bacteria is detected in a variety of extreme low pH, radionuclide- and heavy-metal contaminated habitats where Fe(III) reduction is taking place, and may represent a significant proportion of metal-transforming organisms in these environments. Strain JF-5 serves as a model organism for facultative iron-respiring Alphaproteobacterium. It utilizes glucose as an electron donor with the concomitant reduction of soluble and solid-phase Fe(III). Major findings for this bacterium are a novel outer-membrane cytochrome c involved in iron respiration and a Cr(VI) reductase enzyme.

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

Component nameGenome Accession(s)
Component representationProteins
Chromosome
CP000697
3053
Plasmid pACRY01
CP000689
160
Plasmid pACRY02
CP000690
169
Plasmid pACRY03
CP000691
77
Plasmid pACRY04
CP000692
32
Plasmid pACRY05
CP000693
28
Plasmid pACRY06
CP000694
9
Plasmid pACRY07
CP000695
5
Plasmid pACRY08
CP000696
5

Publications

  1. "Complete sequence of plasmid6 pACRY06 of Acidiphilium cryptum JF-5."
    US DOE Joint Genome Institute
    Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S., Sims D., Brettin T., Bruce D., Han C., Schmutz J., Larimer F., Land M.
    Richardson P.
    Submitted (MAY-2007) to the EMBL/GenBank/DDBJ databases
  2. "Complete sequence of plasmid7 pACRY07 of Acidiphilium cryptum JF-5."
    US DOE Joint Genome Institute
    Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S., Sims D., Brettin T., Bruce D., Han C., Schmutz J., Larimer F., Land M.
    Richardson P.
    Submitted (MAY-2007) to the EMBL/GenBank/DDBJ databases
  3. "Complete sequence of plasmid4 pACRY04 of Acidiphilium cryptum JF-5."
    US DOE Joint Genome Institute
    Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S., Sims D., Brettin T., Bruce D., Han C., Schmutz J., Larimer F., Land M.
    Richardson P.
    Submitted (MAY-2007) to the EMBL/GenBank/DDBJ databases
  4. "Complete sequence of plasmid2 pACRY02 of Acidiphilium cryptum JF-5."
    US DOE Joint Genome Institute
    Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S., Sims D., Brettin T., Bruce D., Han C., Schmutz J., Larimer F., Land M.
    Richardson P.
    Submitted (MAY-2007) to the EMBL/GenBank/DDBJ databases
  5. "Complete sequence of plasmid3 pACRY03 of Acidiphilium cryptum JF-5."
    US DOE Joint Genome Institute
    Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S., Sims D., Brettin T., Bruce D., Han C., Schmutz J., Larimer F., Land M.
    Richardson P.
    Submitted (MAY-2007) to the EMBL/GenBank/DDBJ databases
  7. "Complete sequence of plasmid1 pACRY01 of Acidiphilium cryptum JF-5."
    US DOE Joint Genome Institute
    Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S., Sims D., Brettin T., Bruce D., Han C., Schmutz J., Larimer F., Land M.
    Richardson P.
    Submitted (MAY-2007) to the EMBL/GenBank/DDBJ databases
  8. "Complete sequence of plasmid8 pACRY08 of Acidiphilium cryptum JF-5."
    US DOE Joint Genome Institute
    Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S., Sims D., Brettin T., Bruce D., Han C., Schmutz J., Larimer F., Land M.
    Richardson P.
    Submitted (MAY-2007) to the EMBL/GenBank/DDBJ databases
  9. "Complete sequence of plasmid5 pACRY05 of Acidiphilium cryptum JF-5."
    US DOE Joint Genome Institute
    Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S., Sims D., Brettin T., Bruce D., Han C., Schmutz J., Larimer F., Land M.
    Richardson P.
    Submitted (MAY-2007) to the EMBL/GenBank/DDBJ databases
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