Amino acid permeases are integral membrane proteins involved in the transport of amino acids into the cell. A number of such proteins have been found to be evolutionary related [1,2,3]. These proteins are:

• Yeast general amino acid permeases (genes GAP1, AGP2 and AGP3).
• Yeast basic amino acid permease (gene ALP1).
• Yeast Leu/Val/Ile permease (gene BAP2).
• Yeast arginine permease (gene CAN1).
• Yeast dicarboxylic amino acid permease (gene DIP5).
• Yeast asparagine/glutamine permease (gene AGP1).
• Yeast glutamine permease (gene GNP1).
• Yeast histidine permease (gene HIP1).
• Yeast lysine permease (gene LYP1).
• Yeast proline permease (gene PUT4).
• Yeast valine and tyrosine permease (gene VAL1/TAT1).
• Yeast tryptophan permease (gene TAT2/SCM2).
• Yeast choline transport protein (gene HNM1/CTR1).
• Yeast GABA permease (gene UGA4).
• Yeast hypothetical protein YKL174c.
• Fission yeast protein isp5.
• Fission yeast hypothetical protein SpAC8A4.11
• Fission yeast hypothetical protein SpAC11D3.08c.
• Emericella nidulans proline transport protein (gene prnB).
• Trichoderma harzianum amino acid permease INDA1.
• Salmonella typhimurium L-asparagine permease (gene ansP).
• Escherichia coli aromatic amino acid transport protein (gene aroP).
• Escherichia coli D-serine/D-alanine/glycine transporter (gene cycA).
• Escherichia coli GABA permease (gene gabP).
• Escherichia coli lysine-specific permease (gene lysP).
• Escherichia coli phenylalanine-specific permease (gene pheP).
• Salmonella typhimurium proline-specific permease (gene proY).
• Escherichia coli and Klebsiella pneumoniae hypothetical protein yeeF.
• Escherichia coli and Salmonella typhimurium hypothetical protein yifK.
• Bacillus subtilis permeases rocC and rocE which probably transports arginine or ornithine.

These proteins seem to contain up to 12 transmembrane segments. As a signature for this family of proteins we selected the best conserved region which is located in the second transmembrane segment.