Structure-Based Sequence Alignment of the Transmembrane Domains of All Human GPCRs: Phylogenetic, Structural and Functional Implications
Fig 3
Testing the robustness of the alignment of the Vomeronasal receptors with the other groups.
The table shows similarity between TMs averaged over all pairs of sequences formed from the two groups (red denotes high similarity, blue low similarity). For most TMs the optimal choices agree with the optimal alignment to Aα (full table in S5 Fig); all combinations are shown only for TM5. The same table but using the GPCRtm substitution matrix [74] instead of BLOSUM62 is shown in S7 Fig. GPCRtm was developed in particular for GPCR proteins, but in this case both matrices result in the same alignment.