However, two of the new phages described here – Angelica and CrimD –have evident sequence similarity to TM4 (Fig. 1, Fig. 2B).
The most evident sequence divergence is located at the N-terminus of ERK1 where a sequence of about 39 residues has not been associated previously to any specific function.
The enzymatic activity of the other four domains is questionable, due to their evident sequence divergence.
Sequence alignments in the NTRs and CTRs revealed evident sequence conservation for most proteins in each clade.
There is no evident sequence similarity among HK97, Epsilon 15 and Phi 29 (Jiang et al., 2008; Morais et al., 2005).
Although in many cases aberrant IC1 methylation has not been associated with any evident sequence change, several microdeletions within IC1 were described in BWS and Wilms' tumour cases (10– 10).
Although there are no evident sequence data on FAD-binding in prokaryotic molybdo-iron-flavoproteins, the medium subunit of MhyADH should contain an FAD cofactor as other molybdenum-containing oxidoreductases.
These conserved folds extracted from bacteriophages HK97, Epsilon 15 and Phi 29 confirm the high structural similarity between the phages, even with no evident sequence similarity between them, suggesting the possibility of a common ancestor between them (Jiang et al., 2006; Morais et al., 2005).
Dehydrins are now classified in Class IIa and Class IIb of LEA proteins, corresponding to the previous D11 family or Group 2. LEA proteins belonging to different classes do not share any evident sequence similarity, even if Garay-Arroyo et al. [ 13] found that they are characterized by high hydrophilicity and high percentage of glycines, leading to their denomination as "hydrophilins".
Since LEA proteins belonging to different classes have no evident sequence similarity but only common structural and physicochemical characteristics, the hypothesis of an independent evolution in different organisms under dehydration conditions is more likely than the hypothesis that they share a common ancestor [ 13].
Moreover, the reported effects are evident in sequences with no shifting and balanced shifting between consistent and violation sequences (Suppl. Fig. S6).
