Figure 5
From: Predicting functional sites with an automated algorithm suitable for heterogeneous datasets
Triosephosphate isomerase phylogenetic motifs identified at the two different PSZ thresholds. Colored spheres indicate phylogenetic motif α-carbons identified past the (A) -1.83 and (B) -2.75 thresholds, which correspond to gap ranges of {-1.0: -2.0} and {-1.0, -3.0}, respectively. The {-1.0: -2.5} gap range identifies the same threshold as (A). The substrate analog is colored white. Making the threshold more stringent fails to identify residues (the red phylogenetic motif) involved in two stabilizing enzyme-substrate interactions (a salt bridge and an H-bond).