Protein maximum likelihood trees of the short and long versions of glucosamine-6-phosphate isomerase ( nagB gene). ML tree based on 229 unambiguously aligned aa positions from the N-terminal part of the alignment of the glucosamine-6-phosphate isomerase protein. The grey boxes A and B indicate strongly separated groups which include eukaryotic sequences. The sequences in the B box (with the exception of the R. baltica 3 sequence) have an approximately 500 aa long conserved C-terminal extension of the protein which is absent from all other sequences in the alignment. The sequences in box B, together with the sequences indicated with asterisks were excluded in a separate analysis shown in Additional File 5, to test the influence of the removal of the long version of the protein and long branches on the relative positions of eukaryotic sequences. The tree is arbitrarily rooted. Details about the phylogenetic analyses are found in the Methods section and Additional File 2. Labelling as in Figure 2.