Fig. 6.

Structural phylogeny of palm domains from the reverse polymerase Thg1 and canonical forward polymerases. For the identification of palm domains, we used the classification scheme provided by the structural classification of the protein database. Structures were downloaded from the protein database and aligned using the STAMP algorithm as implemented in Visual Molecular Dynamics (VMD) (31). The palm domains display a classical star phylogeny, with palm domains clustering according to their enzymatic function. All structures within a group are labeled with the organism name. One representative structure for each group (organism underlined) is displayed and color-coded by structural conservation (from blue indicating highly conserved to red indicating little structural conservation).