Figure 5:

A learned pHMM for the Bowman–Birk serine protease inhibitor family in the HomFam collection with Viterbi paths for 3 different sequences: A single domain hit (blue), a multihit (brown) and, a partial hit (cyan). Numbers on edges are transition probabilities, numbers on nodes are self-loop probabilities. For each match states, the top 3 amino acids and their probabilities are printed, along with the probability of entering and exiting at the respective match.