As seen in Figures 2 and 5 , some closely related sequences are lacking specific domains in the sense that HMMER does not find a significant similarity to the Pfam entries for these domains. In order to understand the degree of sequence variation associated with this domain loss, as well as the general sequence variation in conserved vs. non-conserved regions of typical polyproteins, several dot plots were generated. The dot plot for two Carlavirus sequences, Potato virus M (NCBI gi9626090) and Aconitum latent virus (NCBI gi14251191), is shown in Figure 6 . The dot plot confirms that these two sequences are closely related in the MT, HEL and RdRp domains. However, there are significant differences in the region between MT and HEL. Potato virus M is lacking the AlkB domain whereas Aconitum latent virus is lacking the OTU domain. As seen from the dot plot, short regions of similarity close to the diagonal shows that both domains may have been present in an ancestral sequence. However, this region shows a high degree of sequence variation, and as indicated by the dot plot they are almost exclusively mutations. Non-essential or non-functional domains are probably rapidly lost. In this particular case, none of the typical AlkB motifs seem to be conserved in Potato virus M, indicating that this indeed is a non-functional AlkB domain.