Bioinformatics Question:

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After analyzing numerous multicomponent transport systems phylogenetically, we found little evidence for shuffling of protein constituents during their late evolutionary divergence. We included several protein secretion systems, such as types I, II, III, and IV as well as ABC-type solute uptake systems. The protein secretion systems consist of many proteins that were often transferred laterally among gram-negative bacteria. Although several such multicomponent systems may be found within a single bacterial cell, the systems apparently did not exchange protein constituents, even though they can be exchanged experimentally by genetic manipulation. One important caveat: phylogenetic analyses may overlook constituent shuffling between closely related systems.
These observations suggest to us that complex multicomponent transport systems depend on extensive protein-protein interactions, which probably arose through coevolution of the protein constituents. Once any two systems have diverged appreciably in sequence, the constituents in one system no longer can interact properly with those in another, effectively preventing shuffling between the two.