E. coli Crp and PurR binding sites that have been experimentally identified by DNase I footprinting were extracted from the literature and available databases, RegulonDB [47] and DPInteract [48]. The 87 Crp sites (from 65 E. coli intergenic regions) and 22 PurR sites (from 20 E. coli intergenic regions), were aligned using the Gibbs Recursive Sampler [49] specifying palindromic models (total width of 16–24 bp), to generate a PurR motif (Figure 7) and a Crp motif (Figure 1). These figures show both the nucleotide equilibrium and the information content for each position of the motif [9].