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.
Schuster-Böckler et al. BMC Bioinformatics 2004 5:7 doi:10.1186/1471-2105-5-7