Figure 1

Profile-pair specific estimates of λ. The histogram of estimates of λ for 500 pairs of profiles selected at random from the set of profiles built for representative sequences in the FSSP database. For each pair of profiles, the distribution parameters were fit to 10,000 optimal alignment scores between the profiles' shuffles. The standard error in each estimate of λ is 0.78%. The mean and standard deviation of λ are: (a) μ = 0.244, σ = 0.093 (b) μ = 0.353, σ = 0.139 (c) 0.238, σ = 0.067 (d) μ = 0.283 σ = 0.089. For sequence only comparisons, μ = 0.307 and σ = 0.048.