Figure 4

Extended motif for H. ducreyi and H. influenzae. (a) A sequence logo [26,27] created from the regions surrounding occurrences of USS motifs in H. influenzae. Position +1 is the first position following the USS motif. The previously reported extended motif is shown above the letters. (b) A sequence logo created from the regions surrounding occurrences of the conjectured USS motif in H. ducreyi. A gap of two nucleotides has been introduced to align the H. ducreyi motif with the H. influenzae motif. (An alternative alignment places position -4 in H. ducreyi across from position -6 in H. influenzae.) Examining the frequencies, we can derive a consensus pattern as follows. We mark a position with a 'w' if more than 70% of the occurrences contain an A or a T (expected frequency of an A or T = 60%). We mark a column with a 'y' or 'r' if more than 60% of the occurrences have a T or a C (for 'y') or A or a G (for 'r'). The expected frequency for either case is 50%. The 'rwwwwnnnn' from positions +2 to +11 matches the previously identified extended motif for H. influenzae, though the rwwww motif is not as clear. The subsequent 'nnrwwwww' from the extended H. influenzae motif is not exactly matched in H. ducreyi but there is a general bias toward A and T residues extending to about +25.