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S. pombe

S. pombe. Unicellular archiascomycete Diverged from S. cerevisiae 330- 1144 Ma Size ~14 Mb, 3 chromosomes No synteny Data stored in GeneDB. Areas of interest. Nomenclature Evolutionary relationships (orthology, paralogy, protein family and domain)

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S. pombe

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  1. S. pombe • Unicellular archiascomycete • Diverged from S. cerevisiae 330- 1144 Ma • Size ~14 Mb, 3 chromosomes • No synteny • Data stored in GeneDB

  2. Areas of interest Nomenclature Evolutionary relationships (orthology, paralogy, protein family and domain) Functional annotation (Using GO, from literature curation, functional transfer from orthologs, inferred electronically from protein family/domain) Genetic mapping data (minimal, small amount, mostly linked to physical sequence data)

  3. Areas of expertise/collaborations • Literature curation • Ontology development (GO consortium) • Ortholog/paralog resolution (and functional inference) • Protein family identification (Pfam/Interpro) • Functional mappings (e.g. Interpro2GO) • Physical and genetic interactions (GO & BioGRID consortiums) • Functional prediction (Daniel Barker)

  4. Dataflow Links Sequence analysis User submission Literature curation Data mining SPKW2GO 3 Orthologs 1 4 GO associations GO curation 5 Domain /family Family identification 2 Sequence and annotation updates Interpro2Go 6 GOA

  5. Biological process 101 494 537 2681 318 124 106 Cellular component Molecular function Gene count 4990 Dubious 67 No GO S. pombe 567 11.5% (c.f. S. cerevisiae 612 10.5%)

  6. GO terms Gene count 4990 Unassigned 456 Dubious 67 Conserved 57 No GO/Pf/Ort 341 No orthologs Of which 74 272 484 No S. cerevisiae ortholog 532 3161 41 27 38 S. cerevisiae orthologs Pfam families ** Distant ortholog detection Pfam coverage S. pombe 75% c.f.S. cerevisiae 65% ** Submitted to Pfam ** DUF mainly eukaryotic/fungal

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