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Fig. 4 | Genome Biology

Fig. 4

From: Non-base-contacting residues enable kaleidoscopic evolution of metazoan C2H2 zinc finger DNA binding

Fig. 4

Limited diversity of non-metazoan C2H2-ZF proteins. a Triplets that appear at least once in the PBM motifs of fungal proteins (black bars at the bottom) are among those with the highest predicted frequencies based on the recognition code (Mann–Whitney U test P < 0.001). The x-axis represents the 64 triplets, sorted by their predicted frequency. b Correlation of the predicted and observed frequencies for DNA triplets that are observed at least once in the PBM motifs. The top three triplets with the highest predicted and observed frequencies are highlighted in blue. c Percent identity of contact residues between pairs of proteins is highly predictive of similarity of their motifs. Each dot represents one pair of non-metazoan C2H2-ZF proteins, with the x-axis corresponding to the similarity of the entire set of their contact residues and the y-axis showing the similarity of their motifs as determined by PBMs (motif similarity was measured as correlation in predicted affinity to different sequences, as previously described [46]). C2H2-ZF proteins with 100% identical base-contacting residues have motif similarity of 0.76 ± 0.12. d Of 4349 non-metazoan C2H2-ZF proteins that have at least two C2H2-ZF domains, 1116 have base-contacting residues that are identical to at least one of the 43 proteins we analyzed by PBM and therefore recognize motifs that are nearly identical to their matching PBM motifs

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