Point accepted mutation

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Point Accepted Mutation (PAM) or Percent Accepted Mutation, is a set of peptide mutation matrices calculated by Margaret Dayhoff. Each matrix is twenty-by-twenty (for the twenty standard amino acids); the value in a given cell represents the probability of a substitution of one amino acid for another, known as a point mutation. This type of matrix is commonly known as a substitution matrix, and is used in sequence alignment and multiple sequence alignment.

There are multiple PAM matrices. PAM1 is calculated from sequences with one point mutation per hundred amino acids. Other PAM matrices are derived from the multiplication of the PAM1 matrix. PAM250 is equivalent to 250 substitutions per hundred amino acids.