Structural Evolution of the Protein Kinase–Like Superfamily
Figure 4
Proposed Phylogeny for the Kinase-Like Superfamily, Based on a Unified Bayesian Analysis of Both the Sequence Alignment in Figure 3 and the Structural Character Matrix in Table 2
Structures are labeled by their PDB IDs, followed by the abbreviated name of the structure. TPKs are to the left of the figure, and are labeled with their group membership. TPKs labeled with a black asterisk are classified differently in our tree compared with the classification produced by Manning et al. [7]. The AKs are highlighted with an orange oval. Major branches are labeled with their posterior probabilities. Gray ovals represent areas of doubt in the tree, based on the tree itself and other aspects of our analysis (see text). The left-hand oval represents uncertainty as to the closest TPK relative to the AKs; it is unclear where precisely the AKs should link to the TPKs (note that this uncertainty does not include the branching of most of the TPK groups in this region, as these are generally well supported). The right-hand oval represents uncertainty as to the proper placement of ChaK and PIPKIIβ. These kinases are difficult to place with high confidence because of their extreme divergence. They are labeled with red asterisks to denote the speculative nature of the current placement (see text).