A – ML tree of FBA protein sequences. Maximum likelihood (ML) tree of class II type B FBAs based on 268 aligned aa positions. Amitochondriate protists are labelled pink and eubacteria black. The numbers at the bipartitions are ML distance bootstrap values (left: puzzleboot) and ML bootstrap values (right: phyml). Bootstrap values below 50% are omitted. The asterisk and the dot mark indel events in FBA amino acid sequences as shown in the alignment in (1B), supporting indirectly the grouping of Trimastix with the diplomonads to the exclusion of the remaining amitochondriates. For display purposes the tree was arbitrarily rooted. B – FBA amino acid alignment sections showing indel events. Two separate sections from the FBA alignment which was used to calculate the tree from 1A are shown. The dot marks a 4–7 amino acid insertion: the amitochondriate protists Trichomonas, Mastigamoeba and Entamoeba have a 7 aa insertion; Treponema (not shown in the alignment) and Chlorobium have a 4 aa insertion and Bacteroides has a 5 aa insertion. The insertion event is supported by high bootstrap support in the ML tree (100%). The asterisk marks another indel event, where the three amitochondriate protists Trimastix, Spironucleus and Giardia have a characteristic deletion followed by a phenylalanin seen also in the clade with Ralstonia, Synechococcus and Caulobacter. This deletion separates these two clades from the remaining part of the tree.