Positions of inteins and introns along the protein sequence (panel A) and in the structure of vacuolar/archaeal ATPase catalytic subunit (panel B). Panel A shows the conservation profiles of subunit A of the V/A ATPase and the beta subunit of the F-type ATPase. The abscissa shows the amino acid position along the alignment; the ordinate designates the number of different amino acids present in that position averaged over a window of size 11. The dark grey line is the conservation profile of all three domains. The medium gray line is the conservation profile of Eukaryotes and Archaea. The light gray line is the conservation profile of the Archaea. The positions of inteins are indicated as blue dots with arrows. Positions of spliceosomal introns from are indicated as green dots without arrows. Panel B shows the structure of ATPase catalytic subunit A structure from Pyrococcus horikoshii OT3 (PDB ID: 1VDZ) colored according to sequence conservation. The arrows indicate "a" and "b" intein insertion sites. "b" is the archaeal intein insertion site between Lys240 and Thr241 (both amino acids are shown with space-filled model) and "a" is the eukaryotic intein insertion site between Gly260 and Cys261 (space-filled model).