FIG. 7.

Alignment of the nucleotide sequences of the three LmrA-binding sites. The 36-bp nucleotide sequences of both strands of the three LmrA-binding sites (lmrA site, yxaG site 1, and yxaG site 2) are aligned. To optimize the alignment, the sequences of the lmrA site are oriented so that transcription occurs from left to right, while those of yxaG site 1 and yxaG site 2 are in the opposite orientation. The nucleotide positions conserved in two of the three sites are indicated by asterisks on the lines labeled lmrA vs site2 (between the lmrA site and yxaG site 2), lmrA vs site1 (between the lmrA site and yxaG site 1), and site2 vs site1 (between yxaG site 2 and yxaG site 1). Beneath the alignment, the 18-bp consensus sequence for the three sites is indicated by asterisks that indicate the positions conserved in the three sites. The protected areas found in the DNase I footprinting experiments are enclosed in boxes. The pair of horizontal arrows facing each other above the sequence of the lmrA site indicates the incomplete palindrome sequence. The dotted line beneath the upper sequence of yxaG site 2 indicates that this sequence was predicted to be a putative LmrA-binding site during the GRASP-DNA search. The vertical arrows indicate the mutation points found in strains PLR1 and 1A221.