A family of eukaryotic and prokaryotic proteins that seem to be mainly involved in the intake of small peptides with the concomitant uptake of a proton has been recently characterized [1,2]. Proteins that belong to this family are:

• Fungal peptide transporter PTR2.
• Mammalian intestine proton-dependent oligopeptide transporter PeptT1.
• Mammalian kidney proton-dependent oligopeptide transporter PeptT2.
• Drosophila opt1.
• Arabidopsis thaliana peptide transporters PTR2-A and PTR2-B (also known as the histidine transporting protein NTR1).
• Arabidopsis thaliana proton-dependent nitrate/chlorate transporter CHL1.
• Lactococcus proton-dependent di- and tri-peptide transporter dtpT.
• Caenorhabditis elegans hypothetical protein C06G8.2.
• Caenorhabditis elegans hypothetical protein F56F4.5.
• Caenorhabditis elegans hypothetical protein K04E7.2.
• Escherichia coli hypothetical protein ybgH.
• Escherichia coli hypothetical protein ydgR.
• Escherichia coli hypothetical protein yhiP.
• Escherichia coli hypothetical protein yjdL.
• Bacillus subtilis hypothetical protein yclF.

These integral membrane proteins are predicted to comprise twelve transmembrane regions. As signature patterns, we selected two of the best conserved regions. The first is a region that includes the end of the second transmembrane region, a cytoplasmic loop as well as the third transmembrane region. The second pattern corresponds to the core of the fifth transmembrane region.