Alignment and sequence analysis
Multiple Sequence Alignment was implemented by the MEGA service
(https://www.megasoftware.net)
(ClustalW). In our work, we used the standard parameters of this
program. The sequence logos were created by the WebLogo 3 server
(http://weblogo.threeplusone.com)24. To calculate the PID (percent sequence identity),
each pair of amino acid sequences was aligned using the
Bio.pairwise2.align.globalds function with the
Bio.SubsMat.MatrixInfo.blosum62 matrix (Biopython).The PID was
calculated as described in 9. The Bio.codonalign.build
and Bio.codonalign.codonseq.cal_dn_ds modules (using the Goldman and
Yang model 25) were used to calculate dN/dS (ratio of
non-synonymous to synonymous substitutions).
Bio.SeqUtils.ProtParam.ProteinAnalysis was used to count the number of
amino acids in a protein sequence.