Phylogeny of Na+-translocating and proton-translocating F/V-ATPases in Archaea (A), Bacteria (B) and Eukarya (E). The maximum-likelihood phylogenetic tree was constructed on the basis of a sequence alignment of β-subunits of F-ATPases and A subunits of V-ATPases (see Additional File 2). The names of organisms with experimentally characterized ATPases are shown in bold and colored red for Na+-dependent enzymes and blue for H+-dependent enzymes. The ATPases whose c subunits carry all Na+-ligands and are hence predicted to translocate sodium are denoted by red circles, and those lacking one or more of these ligands (and so predicted to translocate protons only) are denoted by blue circles. The numbers at internal branches indicate the RELL bootstrap probabilities (expressed as percentage points). The root position was forced between the F- and V-ATPases.