Single RR regulatory units. Each box includes one two component system and its targets as determined in this study using DAP-chip. Objects are not drawn to scale. This is a conservative list of the most likely targets, and the complete list of peaks is available in Table S4 in Additional file 1. Where present, predicted σ54-dependent promoters and experimentally validated binding site motifs are indicated. Open boxes indicate missing annotations for sRNAs or ORFs based on the location of the DAP-chip peak and predicted σ54-promoter locations (Figure S1 in Additional file 3). Note that for RR DVU3220, the DAP-chip has not been done, and the target determined using EMSA is shown. AT, acetyltransferase; CBS, cystathionine betasynthase domain; DBD, DNA binding domain; exo, exonuclease; HK, histidine kinase; Hpt, histidine phosphotransfer domain; mp, membrane protein; reg, transcriptional regulator; RR, response regulator; sRNA, small RNA; TPR, tetratricopeptide repeat domain; Tr, transporter; UspA, universal stress family protein domain. Gene names are italicized. For more description see Table S5 in Additional file 1.