FIG 5.

Sequence logo of the H. ducreyi RpoE promoter motifs. (A) Sequence logo of the H. ducreyi RpoE promoter motifs. The logo was generated by the MEME algorithm using the 100-bp upstream sequences from the TSSs of 44 of 73 RpoE-dependent TUs for which the TSSs could be predicted based on the RNA-Seq data. The putative TSS is indicated, and the putative −10 and −35 regions are boxed. (B) Multiple-sequence alignment of the RpoE promoter region in the eight putative RpoE-dependent promoters that contained the most significant matches. Name, gene in which the motif was identified; Strand, strand in which the gene is located (+, sense strand; −, antisense strand); Start, start position of the binding site relative to the TSS; P value, P value for the predicted promoter motifs; −35 and −10 regions of the predicted promoter are highlighted in bold.