Determination of a positive target for each RR. Target numbers indicate the gene DVU# whose upstream region was shifted. RRs are shown by their DVU#. (a) RRs whose target was identified upstream of its own gene or operon. (b) RRs whose target was identified upstream of adjacent operons. (c) RRs whose target was identified based on regulon/promoter predictions (Additional file 2). Arrows indicate shifted DNA. Primers used to amplify the DNA substrates and the sizes of the substrates used are listed in Table S2 in Additional file 1. We used 10 μl of RR in the assay except for RRs DVU621 (5 μl), DVU1083 (4 μl), and DVU3023 (0.5 μl). RR, response regulator.