Validation of predicted binding site motifs using EMSAs. The sequences tested are in Table S6 in Additional file 1. The RRs are shown by their DVU#. For each RR, a wild type motif (w) and a modified motif (m) were tested. RRs DVU0946 and DVU0539 bind to the same sequence and are shown in one panel. We used 10 μl of the RR prep in the assay, except for RRs DVU3023 (2 μl), DVU3381 (5 μl) and DVU1083 (5 μl). The gel shift observed using the wild-type motif was titrated away using unlabeled wild-type motif but not the modified motif (shown for RR DVU2934 in Figure S5 in Additional file 3). RR, response regulator.