[AndrewC]

Since, evolutionary theory suggests that critical functions are more likely to be conserved than non-critical functions, mutations are less likely to accumulate there, and so you look for correspondences in the important bits of the gene

So 11 amino acids in a range of 50 or so out of a total of about 250 define the "functions" of MOTA?

[general_re]

So 11 amino acids in a range of 50 or so out of a total of about 250 define the "functions" of MOTA?

No. 11 out of 55 is the number of correspondences between ALL of the following: ExbB (V. cholerae), ExbB (D. radiodurans), MTH1022 (M. thermoautotrophicum), motA (A. aeolicus), motA (D. vulgaris). 23 out of the 55 are correspondences between motA in A. aeolicus and MTH1022. 22 of the 55 are correspondences between motA in D. vulgaris and MTH1022.

This sequence of 55 residues is not the sum total of motA, but it is a substring known to be important to the functioning of motA. Or, to put it another way:

Pro and Asp residues important for function and conserved in both systems are shown....The arrow indicates a Pro residue that is conserved in both systems and known to be important for function of MotA.