Figure 3.

Examples of similarities found using merged profiles. (A) A typical example from our profile searches using mergers of SMART domains of Helix-Turn-Helix fold. Domains with white boxes are from the starting sets. The solid black bars represent merged families. Domains in gray ovals are structurally uncharacterized and those in white ovals are structurally characterized (but not included in starting set). The gray dotted lines starting from the black bars represent the merged pair that brings out the “bridging” family. The relationships described here are a complex web where the same resultant families may be picked up by more than one different profile. (B) A similar figure for mergers of different Pfam families of the Methyltransferase fold.