Figure 1.

Alignment of predicted Motif 1 (A) and Motif 2 (B) binding sites in intergenic regions of V. cholerae. Genes for which predicted binding sites are on the complementary strand are indicated with gray shading. Loci labeled in orange indicate the first of two divergently transcribed genes that contain a HapR binding site in the intergenic region. The 22-bp-binding regions are shown for each binding site. While the predicted binding site length is seen to be variable for Motif 1 genes, Motif 2-binding sites show very weak conservation beyond 16 bp. The alignment demonstrates the distinctions between the two proposed motifs in terms of concluding sequences and binding site lengths.