Figure 2

Clustal W Alignment and Boxshade display of the deduced full-length amino acid sequences of (A) representative class I pilins from cc32, cc41/44 and cc269 and (B) the 15 class II pilin proteins encoded by 77 meningococcal isolates. For class I pilins, isolate ID and name are indicated. For class II pilins, sequence numbers correspond to the pilE allele number assigned by PubMLST. The phenylalanine (F) residue which is the start of mature pilin is shown by an arrow. The SM1 motif at the end of the putative N-terminal α-helical region is indicated. Black background highlights different residues. Grey background text indicates similar residues. The N-terminal region is highly conserved, as for all meningococcal type IV pilins. The D-region (highlighted) is defined by two conserved C-terminal cysteine residues. The hypervariable region of class I pilins is within the D-region. In class II pilins, sequence variation is found over the entire C-terminal domain.