Fig. 3

Multiple amino acid sequence alignment of different types of RNHs. The names of RNH sequences corresponding to oomycete and plant lineages are emphasized in bold and highlighted in blue and green, respectively. Archaeal RNHs, Fungi/Metazoa RNHs, and original RNHs of LTR retrotransposons are designated as aRNH, fmRNH, and LTR-RTs, respectively. Apart from RIRE2 and Ogre gRNH that were retrieved from GyDB, all the sequences are available in the Additional file 8. Conserved catalytic residues (D-E-D-R/H-D) are indicated by asterisks at the top of the alignment. The semiconservative (R/H)-residue varying between the aRNH and fmRNH is additionally denoted by the bigger font at position 166 of the alignment. The conserved residues are highlighted in shades of gray. The secondary structure of Escherichia coli fmRNH (PDB: 1g15_A) is shown at the bottom of the alignment. The secondary structures of oomycete Chronos-1_PInfe LTR gRNH (predicted, this study) and Sulfolobus tokodaii aRNH (PDB: 3aly_A) are shown at the top of the alignment. The α-helices are depicted as helices, and the β-sheets are shown as arrows