Fig. 4

Processing signals found at N and C terminus positions in the DR15 Pm data set (located at upstream and downstream regions, respectively), grouped by peptide flanking region (PFR) length. For the upstream part of the ligands (top row), the processing signal is always centered at the N terminal position, extending three positions beyond the cleavage site (upstream “context,” symbolized as blue bars) and one to six positions towards the binding core, depending on the PFR length (orange bars). For the downstream region (bottom row), the disposition of elements is mirrored: the proposed processing signal is centered at C terminus and extends three positions beyond the cleavage site (downstream “context” region, pink bars) and one to six positions towards the binding core (green bars), depending on the PFR length. Amino acid background frequencies were calculated using the antigenic source protein of all the ligands present in the data set. Motifs were generated using Seq2logo, as described in the “Methods” section