Figure 4

DUS degeneracy. (a) Histogram of the degeneracy of DNA uptake sequence (DUS) elements in Neisseria gonorrhoeae that are exact DUSs (nondegenerate) in all of the other five genomes. These DUSs have most likely degenerated in the N. gonorrhoeae lineage. The number of substitutions (blue striped bars) and gaps (red striped bars) present in each degenerate DUS site in N. gonorrhoeae were calculated. The x-axis labels are the number of each type of mutation for each case, for example 1 to 10 substitutions or gaps. (b) The same analysis as shown in panel a but for DUSs that are present in at least one strain of Neisseria meningitidis but are absent in both N. gonorrhoeae and Neisseria lactamica. Most of these DUSs are not expected to be ancestral. The degeneracy in this case was measured in the N. lactamica sequences facing the N. meningitidis DUS, and is similar when N. gonorrhoeae is used instead. (c) Weblogo [87] of the degeneracy of DUS sites in one N. meningitidis strain. A weblogo is a graphical representation of a multiple sequence alignment in which the height of the bases in each position indicates their relative frequency, whereas the overall weight of the stack indicates the conservation of that position in the motif. Similar weblogos are found for the other genomes.