Viral adaptation to host: a proteome-based analysis of codon usage and amino acid preferences

Bahir, Iris; Fromer, Menachem; Prat, Yosef; Linial, Michal

We divided all mammalian virus proteins into one of four classes: (i) recognition receptors on the surface, for example, coat, spike, glycoprotein, or envelope (Figure 7 , orange frames); (ii) enzymes (as annotated by the EC classification according to UniProt-mostly polymerases, purple frames); (iii) capsomers and structural units, including tegument, nucleoproteins, and capsids in enveloped viruses (Figure 7 , blue frame); and (iv) proteins that are either unknown or cannot be uniquely assigned to the other three functional sets (see Supplementary Table S4 ). This assignment was performed manually, addressing the proteins with multiple functions or non-exclusive functional assignments (mainly in filamentous phage and other bacteriophages).