Enzyme Commission numbers EC2GO

Method

Enzyme Commission (EC) numbers are manually curated into the description line of Swiss-Prot entries and added automatically to TrEMBL entries.

Mappings between EC and the corresponding GO terms are automatically made using the EC cross-references in the GO Molecular Function ontology. Also see Hill et al. (2001).

The mappings are then transitively assigned at each UniProtKB-GOA release. GO annotations using this technique will receive the evidence code Inferred from Electronic Annotation (IEA). This method has been evaluated at up to 100% accurate (Camon et. al. 2005)

GO Reference

The GO reference for this method is GO_REF:0000003. Abstracts for all GO references can be seen here.

Mapping file

The EC2GO mapping file is available at: http://www.geneontology.org/external2go/ec2go.

Example

EC 6.4.1.2 is the Enzyme Commission number for Acetyl-CoA carboxylase and has therefore been mapped to the GO term ‘acetyl-CoA carboxylase activity’ (GO:0003989).

The alpha subunit of acetyl-coenzyme A carboxylase carboxyl transferase (UniProtKB accession A0AJ21, see Fig. 1) is associated with EC 6.4.1.2 within UniProtKB, therefore because of the mapping between the EC number and the GO term this protein (and any protein assigned EC 6.4.1.2) will be automatically associated with the GO term ‘acetyl-CoA carboxylase activity’.

Annotations

The annotations created by EC2GO mapping are displayed in the UniProtKB-GOA gene association files (Fig. 1), the EC identifier will be indicated in column 8 ('With') and column 6 (DB:Reference) will indicate that this method has the GO reference: GO_REF:0000003. EC2GO annotations can also be viewed in QuickGO.

Figure 1. Representation of an EC2GO annotation in the gene association file.

References

Hill et al. (2001) Program description: Strategies for biological annotation of mammalian systems: implementing gene ontologies in mouse genome informatics. Genomics 74:121-128.

Camon et al. (2005) An evaluation of GO annotation retrieval for BioCreAtIvE and GOA. BMC Bioinformatics 6 Suppl. 1:S17