FIG. 6.

SoxS and OxyR binding in the grx-ybjC intergenic region. SoxS and OxyR binding sites are indicated by square brackets above and below the sequence, respectively. The −35 sequences of the ybjC-nfsA and grxA promoters are indicated by lines above and below the sequence, respectively. The SoxS sequence logo is above the sequence in the 5′-3′ orientation and corresponds to the upper DNA strand. The OxyR sequence logo is below the sequence in the 3′-5′ orientation and corresponds to the lower DNA strand. Both logos were generated by using the web-based program available online (http://www.bio.cam.ac.uk/seqlogo/). The SoxS logo was generated from an alignment of the ybjC-nfsA sequence and 14 other sequences taken from Wood et al. (55). The OxyR logo was generated from an alignment of the grxA sequence and its complement and seven other OxyR binding sites and their complement taken from Schneider (44). The OxyR logo was generated from both strands of DNA sequence due to the symmetrical nature of the binding site (45). A dotted line represents the helical nature of the DNA strand. Peaks corresponding to nucleotides in major grooves (containing >1 bit of information) in each logo are spaced ca. 10 bases apart; peaks of the SoxS logos correspond to the troughs of the OxyR logo.