Fig. 1
Annotated multiple alignment of representative RABL2 proteins sequences. The figure shows a subset of RABL2 sequences from a complete alignment provided as Additional file 3. The five conserved functionally important motifs of the Ras superfamily (G1 to G5 [45]) are marked on the top. Regions corresponding to secondary structure elements – α-helices and β-sheets – predicted for the RABL2 GTPase are indicated by series of letters “h” and “e”, respectively. The figure shows the prediction of α-helices and β-sheets as provided by PROMALS [113], but predictions using other tools were generally congruent with some differences in exact delimitation of the different elements. Note the predicted extra helix at the C-terminus that does not belong to the conserved core of a GTPase domain (comprised of the region from strand 1 to helix 5). The seven intron positions inferred to be ancestral for the RABL2 gene (see main text) are marked by consecutive numbers above the amino acid residues whose codon is located immediately upstream of the intron (phase 0) or is interrupted by the intron at the second or third position (phases 2 and 3). The phase of each intron is indicated by the number in superscript. The sequences of the extremely variable C-terminal tail encoded by the terminal ancestral exon (downstream of the 7th ancestral intron) are not aligned, as no meaningful alignment can be produced for the sequences from different major eukaryotic groups. Species abbreviations used to label the RABL2 sequences: Hsa – Homo sapiens; Bde – Batrachochytrium dendrobatidis; Ttr – Thecamonas trahens; Mba – Mastigamoeba balamuthi; Pmi – Planomonas micra; Mca – Malawimonas californiana; Tva – Trichomonas vaginalis; Ngr – Naegleria gruberi; Cre – Chlamydomonas reinhardtii; Cpx – Cyanophora paradoxa; Gth – Guillardia theta; Ehu – Emiliania huxleyi; Pso – Phytophthora sojae; Otr – Oxytricha trifallax; Bna – Bigelowiella natans. Sequence identifiers are available in Additional file 1: Table S1