Figure 1

Crp Binding Site Motif and Generation of Weaker Versions. The logo in panel A indicates the Crp motif used to scan for Crp binding sites. It is also used to generate a pair of full-strength Crp sites in the synthetic sequence data. The binding site equilibria were calculated from sequence data aligned by the Gibbs Recursive Sampler [49], and were plotted using publicly available software [27]. The logo in panel B indicates the motif used to generate 1/2-strength Crp sites. It was generated by raising each probability of a nucleotide to its 0.637^th power, with subsequent scaling so that the probabilities of the four nucleotides for any motif column sum to 1.0. The exponent was chosen so that the average information content (i.e., "bits") would be half that value for the full-strength sites. The logo in panel C is the 1/3-strength Crp motif, generated with an exponent of 0.507 so that average information content would be one-third of the full-strength value.