As a result of recent genome sequencing projects as well as detailed bioche
mical, molecular genetic and physiological experimentation on representativ
e transport proteins, we have come to realize that all organisms possess an
extensive but limited array of transport protein types that allow the upta
ke of nutrients and excretion of toxic substances. These proteins fall into
phylogenetic families that presumably reflect their evolutionary histories
. Some of these families are restricted to a single phylogenetic group of o
rganisms and may have arisen recently in evolutionary time while others are
found ubiquitously and may be ancient. In this study we conduct systematic
phylogenetic analyses of 26 families of transport systems that either had
not been characterized previously or were in need of updating. Among the fa
milies analyzed are some that are bacterial-specific, others that are eukar
yotic-specific, and others that are ubiquitous. They can function by either
a channel-type or a carrier-type mechanism, and in the latter case, they a
re frequently energized by coupling solute transport to the flux of an ion
down its electrochemical gradient. We tabulate the currently sequenced memb
ers of the 26 families analyzed, describe the properties of these families,
and present partial multiple alignments, signature sequences and phylogene
tic trees for them all. (C) 1999 Elsevier Science B.V. All rights reserved.