Figure 1

Multiple sequenced alignment of the conserved RDRP module from eukaryotic RNA-dependent RNA polymerases and their bacteriophage homologs. The sequences are denoted by gene names, abbreviated species names and Gene Identification (GI) numbers from the GenBank database. Species name abbreviations: At: Arabidopsis thaliana, Cac: Clostridium acetobutylicum, Ce: Caenorhabditis elegans, Cpe: Clostridium perfringens, Ddi: Dictyostelium discoideum, Diam: Diaporthe ambigua, Diper: Diaporthe perjuncta, Giin: Giardia intestinalis, Lyes: Lycopersicon esculentum, Nc: Neurospora crassa, Nt: Nicotiana tabacum, Os: Oryza sativa, Pethy: Petunia hybrida, Phsp: Phomopsis sp., Sp: Schizosaccharomyces pombe, Spbc2: Bacteriophage Spβc2. The positions of the first and the last residue of the aligned region in the corresponding protein are indicated before and after each sequence, respectively. The numbers between aligned blocks represent poorly conserved inserts that are not shown. The coloring is based on the 95% consensus shown underneath the alignment; h indicates hydrophobic residues (ACFILMVWY), a indicates aromatic residues (FYW), l indicates aliphatic residues (ILVA), p indicates polar residues (STEDKRNQHC), c indicates charged residues (DEKR), bi indicates bulky residue (ILFYWMKREQ), s indicates small residues (AGSVCDN). The predicted secondary structure elements are shown below the alignment; H indicates α-helix and E indicate extended conformation (β-strand). The predicted helices are marked H1-16 and the predicted strands S1-20. The signature motif DbDGD, which is predicted to form part of the catalytic site, is shown in reverse shading. The three sequences at the bottom are those of bacteriophage homologs of the RDRPs (the YRH proteins); the remaining are RDRP sequences.