Twenty-five years of nomenclature and classification of proteolytic enzymes

Proteolytic enzymes and their homologues have been classified into clans by comparing the tertiary structures of the peptidase domains, into families by comparing the protein sequences of the peptidase domains, and into protein-species by comparing various attributes including domain architecture, substrate preference, inhibitor interactions, subcellular location, and phylogeny. The results are compared with the earlier classification (Rawlings and Barrett, 1993 [1]). The numbers of sequences, protein-species, families, clans and even catalytic type have substantially increased during the intervening 26 years. The alternative classifications by catalytic type and/or activity are shown not to reflect evolutionary relationships.