Phylogenetic characterization of novel transport protein families revealed by genome analyses

Biochim Biophys Acta. 1999 Feb 25;1422(1):1-56. doi: 10.1016/s0304-4157(98)00023-9.


As a result of recent genome sequencing projects as well as detailed biochemical, molecular genetic and physiological experimentation on representative transport proteins, we have come to realize that all organisms possess an extensive but limited array of transport protein types that allow the uptake 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 organisms 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 families analyzed are some that are bacterial-specific, others that are eukaryotic-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 are frequently energized by coupling solute transport to the flux of an ion down its electrochemical gradient. We tabulate the currently sequenced members of the 26 families analyzed, describe the properties of these families, and present partial multiple alignments, signature sequences and phylogenetic trees for them all.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.
  • Review

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Bacterial Proteins / chemistry
  • Carrier Proteins / chemistry
  • Carrier Proteins / classification*
  • Carrier Proteins / genetics*
  • Conserved Sequence*
  • Genome*
  • Humans
  • Membrane Transport Proteins / chemistry
  • Molecular Sequence Data
  • Phylogeny*
  • Sequence Alignment
  • Software
  • Substrate Specificity


  • Bacterial Proteins
  • Carrier Proteins
  • Membrane Transport Proteins