Over the past decade, our laboratory and others have been concerned
with molecular archaeological studies aimed at revealing the
origins and evolutionary histories of permeases (1). These studies
have revealed that several different families, defined on the basis
of sequence similarities, arose independently of each other, at
different times in evolutionary history, following different
routes. When complete microbial genomes first became available for
analysis, we adapted p- existing software and designed new programs
that allowed us quickly to identify probable transmembrane
proteins, estimate their topologies and determine the likelihood
that they function in transport (2). This work allowed us to expand
previously-recognized families and to identify dozens of new
families. All of this work then led us to attempt to design a
rational but comprehensive classification system that would be
applicable to the complete complement of transport systems found in
all living organisms (3). The classification system that we have
devised is based primarily on mode of transport and energy coupling
mechanism, secondarily on molecular phylogeny, and lastly on the
substrate specificities of the individual permeases (4).
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