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The brand new ensuing BAM data had been up coming processed and reviewed to spot methylation patterns using the ipdSummary and motifMaker sales regarding the unmarried-molecule, real-go out (SMRT) connect research computer software (v11.0, PacBio). The fresh phylogenetic classification try predicted according to genome-broad similarities having fun with ViPTree entire-proteome-dependent similarity out of MGE away from Atabeyarchaeia or other Asgardarchaeota (Supplemental Desk S8). The brand new Opia virus proteomes exhibit similarities (elizabeth.grams., capsid, tube and you will end healthy protein) to those from tailed worms, which commonly simulate inside the bacterial and you may archaeal computers of hypersaline surroundings (Senčilo and you can Roine 2014). Considering phylogenetic analysis, these proteins people with Arf GTPases off their Asgardarchaeota and you may eukaryotes (Extra Fig. S10). The brand new Yucahu-i system is analogous on the MmeI family members, and therefore usually understands a great 6–7 bp theme which have adenine as the penultimate foot (Morgan et al. 2009).
The new pairwise matrix taken from the fresh mTM-line-up techniques (Supplemental Desk S12) was utilized to choose proteins right for three dimensional reconstruction of its alignments (Supplemental Fig. S11B). Proteins structures to possess Opia virus hallmark protein (capsid, terminase highest subunit, and you can PCNA) were predicted having fun with AlphaFold step 3 (Abramson et al. 2024). Sequences was aligned which have MAFFT (v7.490) (Katoh and Standley 2013), cut which have TrimAl -gt 0.5 (v1.4.rev22) (Capella-Gutiérrez et al. 2009), and you can used to do an optimum opportunities tree which have IQ-Forest (v1.six.12) (Nguyen et al. 2015).
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