Figure 3.

Affinity (ΔΔG) versus weight score (W_s) comparison of all 10 published endogenous SyCrp1 binding sites validating the PSSM #3 model. Traditional (open symbols) and Ψ-plots (closed symbols) for both dyad and dyad (+13)bend His-SyCrp1/DNA conformers are shown. Substrate ΔΔG values relative to ΔG for ICAP were obtained from experiments performed by Omagari et al. (20). PSSM #3 was the scanning matrix for calculating all scores. The highest score fitting to PSSM #3 (either strand orientation) is shown using all 10 input sequences as the background p_i. (A) PSSM #3 used to calculate W_s for all known SyCrp1 sequence-specific binding substrates (open circles). (B) PSSM #3 calculated ψ-scores (W_ψs) of ψ_His-SyCrp1 (closed circles and crosses) by application of a HS algorithm. Specific ψ-sequences, ΔΔG values and PSSM #3 calculated ψ-scores are clearly listed in Supplementary Table S35. Outliers (crosses) are labeled vertically and not included in the R² value because they are distinct from the major mode trendline. The R² value for the major mode trendline (dotted) was obtained by fitting to y = y₀ + alnx. ΔΔG is the same for any given substrate in each plot. Substrates are labeled as previously (20). Here, 4 = slr1351 and 2 = sll1268 substrates from Figure 1A. Note logarithmic scaling of the abscissa.