A large and accurate collection of peptidase cleavages in the MEROPS database

Rawlings, Neil D.

The MEROPS cleavage collection contains 39 118 cleavages (as of 7 August 2009). The number of cleavages that can be mapped to entries in the UniProt database is 34 606, the remaining 4512 consisting mainly of synthetic substrates. The number of different entries in the UniProt database to which cleavages are mapped is 10513. The number of cleavages that are designated as 'physiological' is 13 307; whereas 20 187 cleavages are designated 'nonphysiological' and 2677 cleavages are designated 'synthetic'. The remaining 2947 are cleavages in peptides that can not be mapped to UniProt because: they are too short; they are significantly modified, such as the non-alpha peptide bond between ubiquitin and its target protein; they are derived from phage displays; they are theoretical cleavages or because it is unclear whether the cleavage is physiological or not. The data are derived from 6095 publications. The number of cleavages in common between the MEROPS and CutDB collections is 5876, of which 3424 were originally found in the literature by the CutDB researchers. The number of cleavages from the CutDB database that failed to make the MEROPS collection, excluding 892 isoforms and 35 duplicates, was 560 (9.5%), mostly due to being mapped to the wrong residue or sequence. The CutDB curators have been informed of these discrepancies. Because the CutDB database includes only cleavages thought to be of physiological relevance and those that can be included in their proteolytic pathways, it has fewer cleavages than in the MEROPS collection. It does not include cleavages in synthetic substrates and those peptides used solely to map peptidase specificities, or general purpose processing enzymes such as signal peptidases and methionyl aminopeptidases.