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

Rawlings, Neil D.

A substrate alignment is shown in Figure 3 . The density of residues highlighted in black is high, implying that this cleavage position is very poorly conserved and thus may not be physiologically relevant. The logo is shown at the top with the frequency matrix below. The cleavage pattern is a textual representation of the logo, where the scissile bond is shown as a red cross, and the binding pockets separated by forward slashes. The preferred residue is shown in uppercase if the preference is strong. The number of cleavages on which these data are based is given in parentheses. For the logo, the binding pockets S4-S4 0 are shown along the x-axis, where 1 is S4, 2 is S3, etc. The bit score is shown on the y-axis. The height of the letter is proportional to the bit score. The letters are coloured to indicate amino acid properties: blue for basic, red for acidic, black for hydrophobic and green for any other. In the frequency matrix below the logo, each cell shows the number of substrates with an amino acid occupying one of the positions P4-P4 0 . Cells in the matrix are highlighted in shades of green where the greater the preference, i.e. the more often an amino acid occurs at that position, the brighter the shade. Cells are highlighted in black if the amino acid is unknown at that position for any substrate.