Fig. 2

PProCoM analysis of the gcvA-gcvB intergenic regions in Gammaproteobacteria. a Profile of multiple consensus sequences of increasing length positioned relative to the E. coli K12 gcvA-gcvB intergenic region. In the left column, separated by a pipe, the window width used in each MEME analysis, the E-value obtained for each motif and the number of organisms presenting the identified motif (out of 150 Gammaproteobacteria used in our analysis) are indicated. The last of these consensus sequences is indicated as dm and corresponds to the default motif without forcing the size of the analysis window (see the Methods section). The consensus motifs of the IR sequences (IR1 and IR2) are displayed at the top of the figure and are represented with inverted black arrows. b TFBSs with experimental reported evidence, with references cited on the left side of the figure. c Each one of the identified motifs was mapped into the E. coli K12 gcvA-gcvB intergenic region and was used as a reference. Black arrows indicate TSSs that had been previously identified or proposed in our study. The -35 and -10 promoter boxes are indicated with yellow boxes. TSSs and -35 and -10 promoter boxes are indicated with solid lines if these elements had been previously reported and with dashed lines if these elements were identified based on our PProCoM analysis. The center positions of the IR motifs related to the beginnings of transcription of the genes coding for the TF or TG are indicated. The nucleotides of the E. coli IR1 sequence, matching the consensus, are underlined with red lines. d A LOGO corresponding to a representative consensus was selected from the profile of a consensus of the section (marked with a red asterisk) and is shown. This LOGO includes all of the regulatory motifs of the intergenic region of study