Taq polymerase sequences useful for incorporating analogs of nucleoside triphosphates

This patent applications concerns compositions of matter that are DNA polymerases, where those polymerases have had one or more of their amino acids replaced at sites chosen by an analysis of patterns of conservation and replacement within homologous protein sequences. Disclosed here are sites within Family A DNA polymerases where amino acid replacement creates polymerases having utility, in an example where DNA nucleotides are incorporated having modified or unnatural nucleobases, and/or nucleotides whose sugar is unnatural or derivatized, including 3′-O-amino-2′-deoxyribonucleoside triphosphates. The claimed compositions include polymerases that hold amino acid replacements at claimed sites in Taq polymerase, and are prepared by site-directed mutagenesis that modifies a gene encoding a parent Taq gene (natural or already mutated) to change the codon encoding the amino acid at the claimed site, giving a variant gene that encodes a Taq polymerase protein that has a different amino acid at the claimed site.