Mutation predictions using the
EVcouplings model (Hopf et al. 2017). Pairwise interaction terms capture how surrounding amino acids impact mutation effect.
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legend
Column: position in protein sequence. Row: amino acid substituted at position. x-labels show the wild-type SARS-CoV-2 amino acid followed by position (e.g. “A100”). Where SARS-CoV-2 is different than the SARS-CoV (2003) sequence, magenta x-labels include the SARS-CoV amino acid after the position (e.g. “A100K” for A in SARS-CoV-2 and K in SARS-CoV). Black “x”s show the SARS-CoV-2 amino acid at each position. Magenta “x”s show the SARS-CoV amino acid at each position, when different from SARS-CoV-2.
Black lines show regions excluded due to low alignment coverage, these may be insertions largely unique to SARS-CoV-2. Magenta lines show deletions relative to SARS-CoV.
Mutation predictions using a simple model with only sitewise terms, not context specific.
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legend
Column: position in protein sequence. Row: amino acid substituted at position. x-labels show the wild-type SARS-CoV-2 amino acid followed by position (e.g. “A100”). Where SARS-CoV-2 is different than the SARS-CoV (2003) sequence, magenta x-labels include the SARS-CoV amino acid after the position (e.g. “A100K” for A in SARS-CoV-2 and K in SARS-CoV). Black “x”s show the SARS-CoV-2 amino acid at each position. Magenta “x”s show the SARS-CoV amino acid at each position, when different from SARS-CoV-2.
Black lines show regions excluded due to low alignment coverage, these may be insertions largely unique to SARS-CoV-2. Magenta lines show deletions relative to SARS-CoV.
This is a
visualization of the pairwise interactions learned by the
EVcouplings model (Hopf et al. 2017) from the variation in our natural sequence alignment.
Gray dots show the pairs of residues that interact most strongly, each is sized according to the total magnitude of interaction. Mousing over a dot shows the matrix of interaction terms for pairs of amino acids at those two positions.
Purple shows less fit interactions,
yellow shows favorable interactions. The matrix shows only amino acids that appear in the alignment. The frequency of amino acids at each site is shown along the plot edges.