Figure 3.

Pairwise sequence alignments for the α₃ (top) and β₂ (bottom) amino acids of the target sequence (rat nAChR) with the template sequence (2BG9 – Tm-nAChR). An asterisk (*) is used to represent conserved residues, colon (:) for similar amino acids, and a period (.) for dissimilar residues. The boxed segments indicate regions of the protein sequences that share the same secondary structure. The alignment was created based on the Needleman-Wunsch alignment algorithm using the Matchmaker module in the UCSF Chimera package.