Comparative Genomics and Disorder Prediction Identify Biologically Relevant SH3 Protein Interactions
Figure 4
Optimal Divergence Time to Search for Conservation of Target Motif of SH3 Domains
We designated seven groups of species with an increasing average divergence time from S. cerevisiae and calculated for each group the highest accuracy obtained for restricted windows of coverage. We used the gold positive and the negative set to calculate the accuracy and coverage (see Materials and Methods). The seven groups of species are as follows: (1) S. bayanus, S. paradoxus, S. mikatae, and C. glabrata (average divergence of 112.5 My from S. cerevisiae); (2) S. paradoxus, S. mikatae, C. glabrata, and K. lactis (average divergence of 200 My from S. cerevisiae); (3) S. mikatae, C. glabrata, K. lactis, and C. albicans (average divergence of 387.5 My from S. cerevisiae); (4) C. glabrata, K. lactis, C. albicans, and D. hansenii (average divergence of 575 My from S. cerevisiae); (5) K. lactis, C. albicans, D. hansenii, and Y. lipolytica (average divergence of 725 My from S. cerevisiae); (6) C. albicans, D. hansenii, Y. lipolytica, and N. crassa (average divergence of 875 My from S. cerevisiae); and (7) D. hansenii, Y. lipolytica, N. crassa, and Sch. pombe (average divergence of 950 My from S. cerevisiae). The individual values for the divergence time from S. cerevisiae were taken from the literature [32,42,43]. Although we tried to create groups that would not have genomes of species with very different separation dates from S. cerevisiae, it should be noted that because of the small number of available genomes, the groups are not homogenous. Also, the values of the divergence time of each species were not always obtained with the same method. Therefore, this range of values should be viewed critically.