FIG. 5.
Alignment of the promoter sequences of ORFs positively regulated by response regulator HP166. The alignment shows the promoter sequences of ORFs HP1408 (upper part) and HP119 (lower part) and their orthologs derived from different H. pylori strains. The HP and JHP designations indicate sequences derived from the previously published genomes of H. pylori 26695 and J99, respectively. The promoter sequences of the HP1408 orthologs in strains G46, G50, G27, and G25 were obtained by performing PCR with primer pair Prom5-Prom3. The promoter sequences of the HP119 orthologs in H. pylori G27 were derived from the DNA inserts in plasmids pGG2 (G27a) and pGG3 (G27b). The numbers above the sequences indicate positions relative to the transcriptional start point. The −10 promoter elements are italicized. The bars indicate the regions which are protected from DNase I digestion in footprint experiments with His6-HP166 and the PHP1408 and PHP119 promoter probes. Nucleotides in the response regulator binding site which are identical in all of the sequences aligned are indicated by black shading, and nucleotides which are different in a single promoter sequence are indicated by gray shading. The sequences below the upper part of the promoter alignment (G25-M1, G25-M2, and G25-M3) represent the mutated response regulator binding sites in the PHP1408 promoter which were analyzed in DNase I footprint experiments (see text for details).