(A) The CheckV database of complete viral genomes was searched for viruses which contain a cap M7MTase domain using hmmsearch and the PFAM profile PF03291. The 83 identified viruses were clustered by proteome similarity using the vContact2 program. The program was run using DIAMOND (Buchfink et al. 2021) for the all-vs-all protein alignment, and the figure was prepared by excluding the reference virus database. (B) A subset of the 83 capping enzymes was selected to represent the diversity of the data set, aligned and used to construct a phylogenetic tree. The tree is built from an MAFFT alignment of the N7MTase domains; for viruses which contain separate genes from TPase, GTase and N7MTase domains, only the N7MTase protein was used. The viruses were mapped to the clustering in (A) (color dots), showing that the clustering based on the whole proteome is consistent with the phylogeny of the cap N7MTase genes. On the right, putative TPase (TP), GTase (GT), and N7MTase (MT) domains, as well as homologs of the regulatory subunit (D12L) of VCE are shown as white hexagons. Domains attached by solid lines are found within one gene.
