The N-terminal domains of Flexiviridae and Tymoviridae are methyltransferases As described above the Pfam methyltransferase motif (Vmethyltransf) did not match any of the putative methyltransferase domains of Flexiviridae and Tymoviridae, despite the fact that they had been identified via PSI-Blast searches starting with known methyltransferases. Therefore an additional Pfam-type profile was generated. It is obviously a possibility that these domains in Flexiviridae and Tymoviridae are not methyltransferases, and that they are false positives from PSI-Blast. However, the essential residues of a typical viral methyltransferase motif are conserved in the alignment of these domains (data not shown) [16] . In Bamboo mosaic virus, which belongs to Flexiviridae, the residues H68, D122, R125 and Y213 have been identified as putative active site residues with similarity to the Sindbis virus-like methyltransferase [17] , and it has been demonstrated that this region of the Bamboo mosaic virus has methyltransferase activity, as it catalyses the transfer of a methyl group from S-adenosylmethionine (AdoMet) to GTP or guanylylimidodiphosphate (GIDP). The corresponding sequence positions are almost completely conserved in the alignment of Flexiviridae and Tymoviridae N-terminal domains. This is most likely significant, as only 7 positions in total are completely conserved in this alignment, which means that the majority of the conserved positions are known to be essential for methyltransferase activity. Work e.g. by Hataya et al. seems to support the assumption that this sequence region is a methyltransferase domain [18] . It therefore seems likely that all the sequences with AlkB domains also contain functional MT, HEL and RdRp domains. The MT Location of Pfam domains in the variable region of Flexiviridae 2 sequences Figure 5 Location of Pfam domains in the variable region of Flexiviridae 2 sequences. The regions have been extracted directly from Pfam output, and sequences and regions are drawn to scale. The black bar at each end of a motif indicates that a fulllength motif has been found, for partial motifs the bar at the truncated end would be missing. domains are probably involved in capping of genomic and subgenomic RNA [19] .