Because the reference strains NCTC8325 and N315 presented 54 and 25% of their coding sequences (CDSs) annotated as “hypothetical proteins,” we reannotated the genes identified in our analysis using InterProScan (www.ebi.ac.uk/interpro/) and BLAST searches against the Conserved Domain Database (www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml) or Pfam protein families database (https://pfam.xfam.org/). In addition, we assigned clusters of orthologous groups to mutated genes using the eggnog mapper (58).

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