Figure 5

DNA binding specificity of Hac1. (a) Alignment of the Hac1 basic region against the basic regions of the eight bZIP proteins shown in Figure 3. Hac1 is most similar to Gcn4 in terms of DNA-contacting residues. The font color scheme is the same as in Figure 3; residues indicated in gray are not part of the basic region (of either bZIP or bHLH proteins). (b) PBM-derived motifs for Gcn4, Hac1, and Cbf1. Despite the fact that Hac1 belongs to the bZIP structural class, the Hac1 motif barely matches the motif of the bZIP protein Gcn4. Instead, the Hac1 motif resembles E-box motifs bound by bHLH proteins (such as Cbf1). (c, d) In-depth comparison of the DNA binding specificities of Hac1 and Cbf1. The scatter plots show 8-mer E-scores.