And those are the critical "functions" as you described. Otherwise you must count all of the things. In fact you have reduced the "functionality" of MOTA to 2 aa. This is with respect to what to count.
Not 11, because the idea was to compare MTH1022 to motA as you did. If you compare strictly those two things, there are 23 (or 22) correspondences in this substring known to contain parts critical to functionality. There are 11 correspondences only when you compare motA, MTH1022, and ExbB. There are 18 correspondences if you compare motA (D. vulgaris) directly to ExbB (V. cholerae), for example.