Figure 3.

JEvTrace analysis of the YbaK protein family. The three major subclades are labeled S₁, S₂ and S₃, and the location of H. influenzae YbaK (PDB 1DBX) in the phylogeny is shown. The 3D structure of YbaK viewed from the top and the side is given to the right of each phylogeny. (a) Results of parent tracing through seven consecutive parent subclades. Color coding corresponds to the colors of the subclades in the phylogeny. (b) Partition trace results for six partitions of the phylogeny, ranging from 7-50% average sequence identity. Coloring of residues in the 3D structures in (a) and (b) corresponds to the color-coded scores in Figure 4. Black circles in the top views of (a) and (b) represent the approximate location of the putative binding site. Graphics of the molecular surfaces were created with Chimera [49] and MSMS [56] using the SCF format to import JEvTrace results. Graphics of the phylogeny were created with JEvTrace.