71 trees containing 1,572 exchanges were used. Different protein families manifest different PAM rates. Back to Table of Contents . The matrix has compositional information in it, since it depends on the relative frequencies of amino acids in the pool of sequences from which the tallies were drawn. Back to Table of Contents .
Many sequences depart from average composition.
This implies that replacement is not equally probable over entire sequence. Back to Table of Contents . Amino acid substitution matrices from protein blocks. Starting data is conserved blocks from Blocks database . The expected frequency of each pair is essentially the product of the frequencies of each residue in the data set.