FIGURE 2 

Analysis of cognate pairs for the HisKA and H3 kinase classes. Top left panel: The red line shows the tail of the reverse cumulative distribution of log(R_ij) (dependency) values for pairs of positions in cognate HisKA kinase/receiver pairs. The blue line shows the tail of the log(R_ij) distribution after randomizing kinase/receiver assignments in such a way that all phylogenetic relationships are maintained. Top right panel: The cumulative distribution of estimated (see the text) distances between the amino acids in the co-crystal for the 50 pairs with highest R values (red line) versus all other pairs (green line). Bottom left panel: Sensitivities and positive predictive values of the predictions for cognate HisKA kinases and regulators. The red curves show the performance of the model in which P(D|a, T) is averaged over all dependence trees, the blue curve shows the performance of the model P(D|a, T^*) that uses only the best dependence tree, and the green line shows the performance of random predictions. All pairs of curves show estimated PPVone standard error. Bottom right panel: Performance results as in the bottom left panel for cognate H3 kinases and regulators.