Figure 6. RNAP-DNA binding energy cannot be accurately predicted from sequence.

(A) The PSAM for RNAP-DNA binding inferred by Kinney et al. (2010). This model assumes that the DNA base pair at each position in the RNAP binding site contributes independently to $\mathrm{\Delta }{G}_P$. Shown are the $\mathrm{\Delta }\mathrm{\Delta }{G}_P$ values assigned by this model to mutations away from the lac* RNAP site. The sequence of the lac* RNAP site is indicated by gray vertical bars; see also Appendix 1—figure 1. A sequence logo representation for this PSAM is provided for reference. (B) PSAM predictions plotted against the values ${\displaystyle \mathrm{\Delta }{G}_P=-k_{B}T\log P}$ inferred by fitting the allelic manifolds in Figure 5C. Error bars on these measurements represent 68% confidence intervals. Note that measured $\mathrm{\Delta }{G}_P$ values are absolute, whereas the $\mathrm{\Delta }\mathrm{\Delta }{G}_P$ predictions of the PSAM are relative to the lac* RNAP site, which thus corresponds to $\mathrm{\Delta }\mathrm{\Delta }{G}_P=0$ kcal/mol. The dashed line, provided for reference, has slope 1 and passes through this lac* data point.