We examined 383 enzyme superfamilies in CATH/Gene 3D v4.2 that contain well-known (experimentally-validated) catalytic domains, and identified the proportion of functional families that have enzyme annotations and compared them to those that lack any enzyme annotation. These are highly populated superfamilies accounting for 64% of sequences in all CATH enzyme superfamilies and 60% of all sequences in CATH.

A functional family was considered to have enzyme annotations if it has at least one relative that has an EC annotation in UniProtKB and an experimental Gene Ontology (GO) annotation for ‘catalytic activity’. For a third of these enzyme superfamilies, all functional families were annotated as enzymes. However, approximately 252 enzyme superfamilies (two-thirds) had varying proportions of functional families that had no enzyme annotations in the EC classification or GO, suggesting that these are very likely to be pseudoenzymes.



Summary of 383 superfamilies in CATH (v4.2) that may contain pseudoenzyme Functional Families (FunFams)
Superfamily ID FunFams Sequences FunFams With Annotations FunFams Without Annotations Uniq EC Uniq GO
Superfamily ID FunFams Sequences FunFams With Annotations FunFams Without Annotations Uniq EC Uniq GO