A 1-PAM mutation matrix describes an amount of evolution which
will change, on the average, 1% of the amino acids.
In mathematical terms this is expressed as a matrix M such that
If we have a probability or frequency vector p, the product Mp gives the probability vector or the expected frequency of p after an evolution equivalent to 1-PAM unit. Or, if we start with amino acid i (a probability vector which contains a 1 in position i and 0s in all others) M*i (the ith column of M) is the corresponding probability vector after one unit of random evolution. Similarly, after k units of evolution (what is called k-PAM evolution) a frequency vector p will be changed into the frequency vector Mk p. Notice that chronological time is not linearly dependent on PAM distance. Evolution rates may be very different for different species and different proteins.