As seen in Figure 4 , the range of score values is generally smaller for the AlkB domains than e.g. the RdRp domains, particularly if we exclude a couple of very high-scoring cases (see figure caption) . On the other hand, the degree of sequence variation within the collection of AlkB domains is significant, average sequence identity for pairwise alignments is 38%, and only 10% of the positions are totally conserved. This can be consistent with a recent integration if we assume that several different AlkB-type vectors have been used for integration (see below for details). An increased mutation rate after integration could also have contributed to sequence diversity in this region. Moving the AlkB domain into a novel structural and functional context would have removed many of the original evolutionarily constraints, as well as introduced some new ones. This could have created a "punctuated equilibrium" type of situation, potentially leading to a very rapid evolution that could have introduced significant differences between the AlkB domains, independent of the evolution in the other domains. A high mutation rate seems to be the case for this region in general, as indi-cated in Figure 6 . Although the MT, HEL and RdRp domains seem to be well conserved from the dot plot, there are very large sequence variations in the intervening region. One sequence in Figure 6 has a well conserved AlkB domain, the other an OTU domain. The fact that there are very weak sequence similarities in these two domains in the dot plot indicates that both sequences originally had both domains. However, the fact that this similarity now is very weak and without any of the typical AlkB active site motifs also indicates a high mutation rate where non-essential domains are rapidly lost. Therefore the conservation of AlkB domains is a strong indication that they are functional, as already mentioned.