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

Rawlings, Neil D.

The MEROPS website has two displays to show peptidase specificity. Both use the data from natural and synthetic substrates, but show only naturally occurring amino acids. The first display is a logo which uses the WebLogo software (27) . Residues P4-P4 0 from all the substrates for a peptidase are treated as an alignment. The observed frequency for each amino acid in each position is calculated as a bit score, the maximum possible being 4.32 bits. An amino acid is shown in the logo (in single-letter code) if the bit score exceeds 0.1. The logo is also shown as a text string, where if a single amino acid predominates at one position (i.e. the bit score exceeds 0.4) the letter is shown in uppercase, and if more than one amino acid predominates in any position a letter is shown in uppercase when the bit score exceeds 0.7 and in lower case if the bit score is between 0.1 and 0.7.