ATP synthase (proton-translocating ATPase) (EC 3.6.3.14) [1,2] is a component of the cytoplasmic membrane of eubacteria, the inner membrane of mitochondria, and the thylakoid membrane of chloroplasts. The ATPase complex is composed of an oligomeric transmembrane sector, called CF(0), which acts as a proton channel, and a catalytic core, termed coupling factor CF(1).

The CF(0) a subunit, also called protein 6, is a key component of the proton channel; it may play a direct role in translocating protons across the membrane. It is a highly hydrophobic protein that has been predicted to contain 8 transmembrane regions [3].

Sequence comparison of a subunits from all available sources reveals very few conserved regions. The best conserved region is located in what is predicted to be the fifth transmembrane domain. This region contains three perfectly conserved residues: an arginine, a leucine and an asparagine. Mutagenesis experiments carried out in Escherichia coli [4] have shown that the arginine is necessary for proton translocation and that its replacement by another amino acid results in loss of ATPase activity. We selected this region as a signature pattern.