Compilation, alignment, and phylogenetic relationships of DNA polymerases

This is an update of an earlier compilation and alignment of DNA polymerase sequences (Ito and Braithwaite, 1991). As in the previous compilation, we attempted to compile complete sequences, to facilitate the identification of conserved and viable regions of the DNA polymerases (1). This update includes, for the first time, three DNA polymerase sequences from Archaea (2); two new members of the Family A DNA polymerases; and 19 new members of the Family B DNA polymerases. In addition, we included nucleases that have related amino acid sequences to E.coli DNA polymerase I, and the sequence of E.coli DNA polymerase HI (e-subunit) was aligned to Family C due to its homology to Bacillus subtilis DNA polymerase HI. As in the previous compilation (1), Family A DNA polymerases are named for their homology to the product of the polA gene specifying E.coli DNA polymerase I; Family B DNA polymerases are named for their homology to the product of the polB gene encoding E.coli DNA polymerase II; and Family C DNA polymerases are named for their homology to the product of the polC encoding E. coli DNA polymerase HI alpha subunit. Table 1 summarizes the molecular weights and isoelectric points of each DNA polymerase and nuclease. Table 1 also serves as a reference guide to the sequences shown in Figures 1A, IB, and 1C. Since no new sequences were published for the Family X DNA polymerases (/Mike), we have excluded them from this compilation.