Logo representation of DNA polymerase domains from representative polymerase sequences. The sequences were extracted from SwissProt links in Prosite [3] to the DNA polymerase type A (PS00447) and DNA polymerase type B (PS00116) families. The families were initially found using 'DNA polymerase' as keyword. Sequence logos show the relative representation of the different amino acids at each sequence position in terms of the size of the appropriate letter in the single-letter amino acid code; the largest letters are the most conserved. They were constructed using the online server WebLogo [17]. Type A DNA polymerases (10 sequences) were from E. coli (polA), Bacillus subtilis, Thermus aquaticus, Aquifex aeolicus, Mycobacterium tuberculosis, phage T3, phage T5, phage T7, mitochondrial Saccharomyces cerevisiae DNA polymerase and mitochondrial Homo sapiens DNA polymerases. Type B DNA polymerases (15 sequences) were from H. sapiens (α and δ), S. cerevisiae (α and δ), Drosophila melanogaster (α), phage T4, phage RB69, Chlorella virus NY-2A, Zea mays plasmid S-1, herpes simplex virus 1, vaccinia virus, African swine fever virus, Archaeoglobus fulgidus, Pyrococcus horikoshii, E. coli (polB).

DNA polymerase protein structures. The figures were generated with the free software Rasmol (RasWin Molecular Graphics, Windows Version 2.4) and files extracted from the Protein Data Bank (PDB) [18]. (a) Bacteriophage T7 DNA polymerase (type A; PDB code: 1t7p) [9]. Blue, catalytic domain; green, 3'-to-5' exonuclease domain. (b)Thermococcus gorgorianus type B DNA polymerase [11] (PDB code: 1tgo). Blue, catalytic domain; green, 3'-to-5' exonuclease domain; orange, amino-terminal domain; yellow, linker region.