The HAMAP (High-Quality Automated and Manual Annotation of Microbial Proteomes) project at the Swiss Institute of Bioinformatics (SIB) aims to annotate Swiss-Prot proteins originating from bacterial and archaeal genome sequencing projects. It is also used to annotate proteins encoded by complete plant and algal plastid genomes (e.g. chloroplasts, cyanelles, apicoplasts, non-photosynthetic plastids).
GO terms are manually assigned to each HAMAP family rule by HAMAP curators. HAMAP family rules are a collection of orthologous microbial protein families, from bacteria, archaea and plastids, generated manually by expert curators. The assigned GO terms are then transferred to all the proteins that belong to each HAMAP family. Only GO terms from the molecular function and biological process ontologies are assigned. GO annotations using this technique will receive the evidence code Inferred from Electronic Annotation (IEA). These annotations are updated monthly by HAMAP and are available for download on both GO and UniProt-GOA EBI ftp sites.
The HAMAP2GO mapping file is available at:
For further information, please see:
Example. proS from Neisseria meningitidis (UniProtKB accession A1KUG4) is part of the HAMAP family rule MF_01569. This family rule has been manually mapped to the GO term ‘proline-tRNA ligase activity’ (GO:0004827), therefore proS, and any other member of MF_01569, will automatically be assigned this GO term.
The annotations created by HAMAP2GO mapping are displayed in the UniProt-GOA gene association files (Fig. 1), the HAMAP family rule will be indicated in column 8 ('With') and column 6 (DB:Reference) will indicate that this method has the GO reference: GO_REF:0000020. HAMAP2GO annotations can also be viewed in QuickGO .
Figure 1. Representation of a HAMAP2GO annotation in the gene association file.
|Database||Object ID||Object Symbol||Qualifier||GO ID||Reference||Evidence||'With' Column|
|Aspect||Object Name||Object Synonym||Object Type||Taxon ID||Date||Source DB|
|F||proS, NMC1277: Prolyl-tRNA synthetase||protein||taxon:272831||20080521||UniProtKB|