Promoter predictions in S. meliloti and rpoE2 -dependent genes/intergenic regions (IGRs). (a) Number of predicted σ70, σH, σE2, and σ54 promoter sequences assigned to each TSS category. The number of promoter sequences used in the initial promoter search (IPS) is shown above the total number of newly identified promoters, and includes model, but not virtual promoters (Methods; Additional file 5: Table S23). Numbers in red represent promoter sequences that were assigned independently to at least two σ factors. The asterisk denotes 6 promoters that were used in the IPS for RpoH, but were also predicted for RpoD. (b) Venn diagram showing overlap among σH1, σH2, and σH1/H2 promoter predictions. Each column of numbers represents the number of promoters assigned to each of the six transcript categories and are listed in the same order as in Figure 1a. (c) Plot of genes (green circles) and IGRs (purple circles) by replicon and position, showing decreased or increased expression with rpoE2 overexpression. Black, trans-encoded sRNA; light green, cis-encoded antisense sRNA; red, gene and corresponding 5′-UTR; orange, gene and corresponding putative 5′-UTR; light blue, new ORF; purple, putative 5′-UTR only.