Figure 2.

Profile HMM for the following sequences. In MSA, conserved regions are identified based on a threshold of more than 75% similarity, shown in green and yellow. In Figure 2, there is a gap in a conserved region, which is indicated by a delete state. Delete states in a profile HMM account for deletions (nucleotides or amino acids) in conserved regions, while insert states account for insertions in non-conserved regions. This distinction is crucial for accurately modeling sequence variability and conservation.