Figure 3.

Prediction of rnTrpL targets in Enterobacteriaceae reveals dnaA mRNA as most conserved candidate. (A) Heatmap showing the predicted target and interaction site conservation for the four investigated targets. The columns are clustered based on a 16S rRNA tree. Matching colours within a row indicate the same predicted interaction site, grey indicates no site conservation and white that no homolog was detected in the respective organism. A fill in the lower triangle corresponds to the optimal predicted interaction and in the upper triangle to the first suboptimal prediction. (B) Interaction probability landscape for the most likely dnaA/rnTrpL nucleotide pairs. A distinct peak represents a conserved interaction site starting 29 nt 3ʹ of the first nucleotide of the start codon indicated by an arrow. The landscape is drawn based on the individual organism IntaRNA predictions mapped to the multiple sequence alignments of dnaA and rnTrpL. (C) Partial multiple sequence alignment of the investigated dnaA homologs. The predicted interaction regions are highlighted in green if belonging to the conserved site, otherwise in grey