Examples of phylogenetic trees supporting the contribution of interkingdom horizontal gene transfer to the emergence of interkingdom domain fusions. The names of proteins from different primary kingdoms are color-coded: black, bacterial; pink, archaeal; green, eukaryotic; the domains involved in the apparent IKF are shown in red. Red circles show nodes with bootstrap support >70%, and yellow circles show nodes with 50-70% support. The bar unit corresponds to 0.1 substitutions per site (10 PAM). (a) IKF: Rv1683 (gi| 7476858) from M. tuberculosis. Fusion of a bacterial poly(3-hydroxy-butyrate) (PHB) synthase and eukaryotic very long chain acyl-CoA synthetase. Note the absence of eukaryotic homologs in the PHB synthase tree and of bacterial homologs other than the two from M. leprae in the acyl-CoA synthetase tree. (b) IKF: yeast YOL066c (gi|6324506). Fusion of a eukaryotic pesudouridylate synthetase with a bacterial pyrimidine deaminase. Note the absence of eukaryotic homologs, other than that from S. pombe, in the pyrimidine deaminase tree. (c) IKF: aq_2060 (gi|2984285) from Aquifex aeolicus. This protein is a fusion of a PHP superfamily hydrolase of apparent bacterial origin and a pyruvate formate-lyase activating enzyme of archaeal origin. (d) IKF: yeast YOL055c (gi|1419865), YPL258c (gi|2132251) and YPR121w (gi|2132289) from S. cerevisiae. Fusion of a eukaryotic phosphomethylpyrimidine kinase and a bacterial transcriptional activator. Species abbreviations: Bac.meg., Bacillus megaterium; Chr.vin., Chromatium vinosum; Thi.vi., Thiocystis violacea; Am.med., Amycolatopsis mediterranei; Coch.het., Cochliobolus heterostrophus; Dme, Drosophila melanogaster; Cel, Caenorhabditis elegans; Mus, Mus musculus; Spo, Schizosaccharomyces pombe; Ath, Arabidopsis thaliana; Strep.co., Streptomyces coelicolor; The.nea., Thermotoga neapolitana; Bac. am, Bacillus amyloliquefaciens; Shi.fl., Shigella flexneri; Hsa, Homo sapiens.