FIG. 5.

MHC class I and II haplotype epitope mapping of PmpFs from both A/HAR-13 and D/UW-3. PmpF is indicated as an open box (top) and is 1,034 aa in size in both strains. The protein is predicted to be a member of a family of autotransporter proteins (15). As such, the predicted passenger domain, translocation unit, and site of signal sequence cleavage (SS↓) are indicated above the open box. The PmpF sequences from both strains were aligned, and the location of each amino acid substitution is indicated with a vertical line within the open box. Two regions were identified via this alignment as containing a disproportionate number of the amino acid substitutions. Region I (87 aa) is located within the vertical dashed lines, while region II (378 aa) is located within the shaded region. The sequence of each protein was analyzed with the algorithm SYFPEITHI (33) to predict the locations of the MHC class I and II epitopes. The haplotypes included in this analysis are indicated on the right, with predicted epitopes identified for each haplotype located in the same row. Only epitopes giving a predictive score of 25 or greater are shown. Class I epitopes ranged in size from 8 to 10 aa, while class II epitopes were 15 aa in size. Epitopes that were found within conserved regions of the protein are indicated in blue. Epitopes found in regions shown to contain amino acid substitutions are indicated in red.