(A and B) DNase I footprinting of BphR2 binding site in sense (A) and antisense (B) strands. Lane 1, DNase I-digested DNA fragment without BphR2 protein; lane 2, DNase I-digested DNA fragment with 1 μg of BphR2; lane 3, DNase I-digested DNA fragment with 1 μg of BphR2 plus 1 mM HMSA. The 5′-end-labeled sense strand includes the salA promoter/operator and its coding sequence, and the 5′-end-labeled antisense strand includes the bphR2 promoter/operator and its coding sequence. The regions protected from DNase I digestion are indicated by BS1, BS2, and BS3, respectively. (C) BphR2 binding stretches of BS1, BS2, and BS3 are enclosed in boxes. The numbers indicate the distances from the transcriptional start site. (D) Multiple alignment of BphR2 and NahR binding sequences. Conserved bases are indicated by a black background. RBS (AN10) is the regulator binding site of nahG in P. stutzeri AN10.