Figure 5.

Key residue prediction using SCI-PHY subfamily-specific and family-wide conservation patterns. Shown above is the PDB structure for the Pyrococcus furiosus Argonaute protein (PDB structure 1Z26A), from the PhyloFacts book Argonaute III (Archaea-Eukarya). The structure has been colored to predict functional residues. Residues colored yellow are conserved within both subfamilies and across the family as a whole. Positions conserved only within individual subfamilies but not across the family are colored dark blue. Positions having sufficient conservation across the family, but potentially variable within one or more subfamilies are colored light blue. These conservation patterns are predicted for each book in the PhyloFacts resource; where homologous PDB structures can be identified, these patterns are plotted on the structure. Users can modify cutoffs for determining significance using the boxes at right. Most of the residues highlighted automatically by our conservation analyses, based on the default cutoffs, have been determined experimentally to be part of the active site [80-82] (labeled manually for this figure): R627, D628, G629, D558, Y743, H745). Y221 and W222 represent a prediction by this server. Structure viewing and interaction is enabled by the Jmol software.