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Authors' response: The revised version of the manuscript includes a comprehensive test for stability using LOCBIF.
Author response: The revised version of the Methods section clarifies that the values t j have not been used as adjustable parameters but as a concept to formally unify Gaussian-type physical property terms and fixed penalties.
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Response: In the revised version, we have discussed the previous studies as suggested by reviewer.
Author's response : In the revised version of the article, this review section has been deleted.
Response: In the revised version, I've rephrased the "improving biological interpretation" statement as "to help researchers to focus their attention on genes that may be biologically informative".
Authors' response: In the revised version of the manuscript we included a sentence stating that efp was found in all 725 genomes analyzed.
Authors' response: In the revised version we provided an additional figure (Fig. 1B) that shows that the EF-P Lys-34 residue is nearly strictly conserved in all the organisms that have the yjeA/yjeK pair.
Authors' response: In the revised version of the manuscript, we added a caveat emptor (in the discussion section) where we emphasize that we, essentially, explore a toy model of the code's evolution that ignores the expansion of the number of amino acids and involves only codon series swaps.
As described in response to comment #2, in the revised version we considered both phosphosrylated and non-phosphorylated serines from disordered and regular regions separately.
Authors' response: We have adjusted it in the revised version.
Authors' response: Thanks, we corrected it in the revised version.
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CEO of Professional Science Editing for Scientists @ prosciediting.com