Figure 2

Partial logo (positions 172–209) of the Pfam pkinase model. Positions with narrow match state stacks are likely to be deleted in typical family members. The total width of a red-shaded (dark+light) stack visualizes the expected number of inserted letters. The left dark-shaded part of the stack's width represents the probability that at least one letter is inserted. The difference is illustrated by comparing I₁₇₃ with I₁₇₆: Both states have approximately the same expected contribution, but the hitting probability of I₁₇₆ is higher. The insertion stack height is zero for all shown examples because the emission probabilities correspond to the background frequencies.