S. pombe
• Unicellular archiascomycete• Diverged from S. cerevisiae 330- 1144 Ma • Size ~14 Mb, 3 chromosomes • No synteny• Data stored in GeneDB
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)
Areas of interest
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)
Orthologs
Sequence and annotation updates
GO curationGO associations
Domain /family Family identification
DataflowLinks
Interpro2Go
GOASPKW2GO
1
2
3
5
4
6
User submissionSequence analysis
Literature curation
Data mining
Biological process
Cellular component Molecular function
101
124318
2681
494 537
106
Gene count 4990Dubious 67No GO S. pombe 567 11.5% (c.f. S. cerevisiae 612 10.5%)
GO terms
S. cerevisiae orthologs
Pfam families
** Submitted to Pfam
484
3161
272
41
3827
532
** DUF mainly eukaryotic/fungal
No orthologsOf which 74
No S. cerevisiae ortholog
Gene count 4990
Unassigned 456 Dubious 67Conserved 57No GO/Pf/Ort 341
** Distant ortholog detectionPfam coverageS. pombe 75%c.f.S. cerevisiae 65%