Well, as a check of your test, I went to the journals for the relevant excerpt. Hopefully the graphic will show up for you, but if not, I'll grab it and put it somewhere where it will. I count 55 residues, of which 23 are common to both motA in A. aeolicus and MTH1022 in M. thermoautotrophicum, or 42%. Which beats both your comparisons handily ;)
Conformational Change in the Stator of the Bacterial Flagellar MotorSeiji Kojima and David F. Blair*
Department of Biology, University of Utah, Salt Lake City, Utah 84112
The occurrence of significant conformational change in the stator has implications not only for the present-day mechanism but also for the evolution of the flagellar motor. A membrane complex that undergoes proton-driven conformational changes could perform useful work in contexts other than (and simpler than) the flagellar motor, and ancestral forms of the MotA/MotB complex might have arisen independently of any part of the rotor. We queried the sequence database using the sequence of the best-conserved part of MotA (the segment containing membrane segments 3 and 4) from Aquifex aeolicus, a species whose lineage is deeply branched from other bacteria. In addition to the expected MotA homologues, the search returned a protein sequence from the archaeal species Methanobacterium thermoautotrophicum (protein MTH1022) that shows significant sequence similarity not only to MotA but also to the protein ExbB (Figure 9). ExbB is a cytoplasmic-membrane protein that functions in conjunction with ExbD, TonB, and outer-membrane receptors to drive active transport of certain essential nutrients across the outer membrane of Gram-negative bacteria. The energy for this transport comes from the proton gradient across the inner membrane. Thus, MotA and ExbB are both components of systems that tap the proton gradient to do work some distance away (at either the rotor-stator interface or the outer membrane; Figure 9).
Figure 9 Correspondences between the MotA/MotB and ExbB/ExbD complexes. (A) Functions of the complexes. Both use the membrane proton gradient as a source of energy to drive processes occurring outside of the membrane (either the application of force to the flagellar rotor, or active transport of nutrients across the outer membrane). As shown here very diagrammatically, the complexes are hypothesized to do work by undergoing conformational changes as protons move on and off critical Asp residues in MotB and ExbD, respectively. (B) Membrane topologies. The ExbB/ExbD complex also contains the protein TonB, which has a single membrane segment with topology (N-terminus in) like that of segment 1 of MotA. Pro and Asp residues important for function and conserved in both systems are shown. (C) Alignment of a ca. 50-residue segment from selected MotA and ExbB sequences. Shown below are approximate positions of membrane segments (segments 3 and 4 of MotA, or segments 2 and 3 of ExbB). The arrow indicates a Pro residue that is conserved in both systems and known to be important for function of MotA (Pro173 in MotA of E. coli). V. chol., Vibrio cholerae; D. rad., Deinococcus radiodurans; M. ther., Methanobacterium thermoautotrophicum; A. ael., Aquifex aeolicus; D. vulg., Desulfovibrio vulgaris. Using the M. thermoautotrophicum MTH1022 sequence fragment to query the database of finished and unfinished bacterial genomes (National Center for Biotechnology Information, 5/21/01), pairwise BLAST E-values for these alignments are for V. cholerae [ExbB], 1E-6; for D. radiodurans [ExbB], 9E-5; for A. aeolicus [MotA], 0.004; and for D. vulgaris [MotA], 0.002.
Other features also point to a connection between the Mot and Exb systems. MotA functions in a complex with MotB, which as noted contains the critical residue Asp32 near the cytoplasmic end of its single membrane segment. ExbB functions in a complex with ExbD, which likewise has a single membrane segment with a critical Asp residue near its cytoplasmic end (Asp25 in ExbD of E. coli; ref 59). Although ExbB has only three membrane segments in contrast to the four in MotA, the membrane segments that show sequence similarity have the same topology. The protein TonB is also present in the complex with ExbB and ExbD (59, 60) and would provide an additional membrane segment to round out the topological correspondence (Figure 9). ExbB contains a well-conserved Pro residue (Pro141 in E. coli ExbB) that is the counterpart of Pro173 of MotA. Although MotB and ExbD do not share close sequence similarity apart from the critical Asp residue, in certain positions in the membrane segment the residues most common in MotB proteins are also common in ExbD proteins. Finally, like the MotA/MotB complex the ExbB/ExbD complex contains multiple copies of each protein (61). Together, these facts make a reasonable case for an evolutionary connection between the Mot proteins of the flagellar motor and the Exb proteins of outer-membrane transport (and by extension the TolQ/TolR proteins, which are related to ExbB/ExbD but whose functions are less understood).
