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Proteomes - Dictyostelium discoideum (Slime mold)

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> 12,746
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>UP000002195
Taxonomy44689 - Dictyostelium discoideum
StrainAX4
Last modifiedAugust 24, 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_000004695.1 from ENA/EMBL full
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:93.7%[S:89.8%,D:3.9%],F:1.6%,M:4.7%,n:255 eukaryota_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

Dictyostelium discoideum, commonly known as slime mold, is a species of soil-living amoeba. It has the remarkable ability to switch from a solitary to a multicellular form. Under certain conditions, such as starvation, individuals aggregate and differentiate to generate a spore-releasing fruiting body. Since it is relatively easy to cultivate and manipulate in the laboratory, D. discoideum is a popular eukaryote model organism for researchers studying basic cellular processes such as chemotaxis, phagocytosis, apoptosis, signal transduction and cell differentiation.

The genome was sequenced in 2005, has a size of 34 Mb, and contains approximately 12,500 protein-coding genes. It has an unusually high repeat number and is also AT-rich (approximately 78%), making sequencing and assembly particularly challenging.

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

Component nameGenome Accession(s)
Component representationProteins
Chromosome 1
CM000150
1893
Chromosome 2
CM000151
2957
Chromosome 3
CM000152
2427
Chromosome 4
CM000153
2074
Chromosome 5
CM000154
1920
Chromosome 6
CM000155
1354
Unassembled WGS sequence
AAFI02000000
4196
Mitochondrion
AB000109
42

Publications

  2. "The genome of the social amoeba Dictyostelium discoideum."
    Eichinger L., Pachebat J.A., Gloeckner G., Rajandream M.A., Sucgang R., Berriman M., Song J., Olsen R., Szafranski K., Xu Q., Tunggal B., Kummerfeld S., Madera M., Konfortov B.A., Rivero F., Bankier A.T., Lehmann R., Hamlin N.
    Kuspa A.
    Nature 435:43-57(2005) [PubMed] [Europe PMC] [Abstract]
  3. "The mitochondrial DNA of Dictyostelium discoideum: complete sequence, gene content and genome organization."
    Ogawa S., Yoshino R., Angata K., Iwamoto M., Pi M., Kuroe K., Matsuo K., Morio T., Urushihara H., Yanagisawa K., Tanaka Y.
    Mol. Gen. Genet. 263:514-519(2000) [PubMed] [Europe PMC] [Abstract]
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