Figure 6. Predicted high affinity MHC binding peptides following cleavage by cathepsin. (A) JL-5, (B) Iowa-06. Top left: cathepsin B, top right: cathepsin S, bottom: cathepsin L. Y Axis shows MHC-II alleles colored by cluster but ranked alphabetically. X axis shows peptide index positions from 260–475. The yellow baseline marginal bar shows the areas of high probability BEPI (orange) and high density MHC-II binding (blue) as in Figure 3. Peptides with high predicted binding affinity (-1 to -3 standard deviations below the mean) for each allele, that are between 15 and 20 amino acids in length and that are predicted to be excised by cathepsin cleavage are colored more intensely. The uniform background coloration indicates that there are no high affinity peptides in that region although there are numerous potential cleavages predicted. The difference in background colors are only to aid in identification of the operative peptidase. Peptides might be cut in any length ranging between 15 and 20 amino acids. They may have several different cut sites. The peptide pixel color intensity is indicative of the number of sites with > 0.5 probability of being cleaved i.e., the darkest colors might be cut in any one of six different positions. As the MHC-II binding groove accommodates multiple lengths of peptide any of the peptides is likely to bind. The arrows indicate the regions where most difference is seen at amino acid index positions 275 and 425.