Figure 2

Multiple sequence alignment and contextual information of the pPIWI-RE family. (A) An alignment along with representatives of the classical PIWI module is shown. Regions of poor conservation are replaced with numbers representing the length of the excision. Consensus sequence is provided on the bottom line. Strongly-conserved residues are shaded red and colored white. Residues involved in catalytic RNase H activity are shaded red and colored yellow. Columns in alignment are color-coded based on conservation of shared chemical properties: yellow, hydrophobic/aliphatic (h/l); green, small/tiny (s/u); purple, charged (c/+/−); blue, polar (p); orange, hydroxyl group-containing (o); grey, large (b). Conserved residues involved in nucleotide binding across classical and pPIWI-RE PIWI modules or residues contributing to nuclease activity are denoted above columns by “*” and “^”, respectively. Predicted salt bridge-forming arginine and glutamate residues unique to pPIWI-RE are denoted by “&”. Residues conserved in classical PIWI modules but not in the pPIWI-RE module are denoted by “%”. Boundaries of the MID and PIWI domains are noted above the secondary structure. Sequences are labeled to the left of the alignment with gene name, organism abbreviation, and gene identifier number (gi number), demarcated by underscores. (B) Representative domain architectures and conserved gene neighborhoods involving the pPIWI-RE module. Genes within a conserved neighborhood are depicted as arrows with the arrowhead pointing 5′ to 3′. Labels below each architecture or neighborhood provide gene name, organism abbreviation, and gi number for a representative protein. Characteristic C-rich and helical regions of the DinG-type helicase are represented by yellow lettering and purple coils, respectively. Domain abbreviations: ZR, zinc ribbon; X, conserved globular region N-terminal to MID and pPIWI-RE domains; Y, conserved, largely α-helical domain with conserved arginine residue N-terminal to ZR and REase domains; Z, largely α-helical domain N-terminal to DinG-type helicase. Organism abbreviations in Additional file 1.