TABLE 1.
Amino acid replacements by capsid functional domain
| Capsid region | Proportion of variable residue positions | No. of replacements/variable residue positiona | No. of alternative replacement residues/variable residue position | Weighted avg Miyata distance/variable residueb | Weighted avg LG distance/ variable residuec |
Replacement rate (no. of replacements/ site/lineage/yr) (10−3) |
Relative replacement rate |
|---|---|---|---|---|---|---|---|
| Total capsid | 0.217 | 4.07 | 1.60 | 1.32 | 3.86 | 3.06 | 2.88 |
| Capsid without N termini | 0.200 | 3.82 | 1.51 | 1.34 | 3.86 | 2.64 | 2.48 |
| Structural core | 0.125 | 2.46 | 1.10 | 1.06 | 5.63 | 1.06 | 1.00 |
| β-Strands | 0.127 | 1.97 | 1.13 | 1.07 | 6.15 | 0.95 | 0.89 |
| α-Helices | 0.115 | 4.11 | 1.00 | 1.05 | 4.63 | 1.64 | 1.54 |
| Loops and C termini | 0.271 | 4.58 | 1.74 | 1.42 | 3.33 | 4.29 | 4.04 |
| NAg sites | 0.860 | 6.24 | 2.19 | 1.33 | 2.75 | 18.57 | 17.47 |
| PVR-binding sites | 0.318 | 3.21 | 1.57 | 1.35 | 3.56 | 4.76 | 4.47 |
| PVR-binding sites without NAg sites | 0.231 | 1.67 | 1.11 | 1.36 | 5.07 | 1.81 | 1.70 |
| VP1 1–32 | 0.844 | 8.11 | 2.59 | 1.36 | 3.67 | 23.66 | 22.25 |
a
Mixed-base positions were counted as a single replacement.
b
Theoretical range, 0.47 to 5.38 (mean, 2.256); observed range, 0.47 to 2.69; a low value indicates frequent replacement.
c
Theoretical range, 0.008705 to 10.64911 (mean, 1.022213); observed range, 0.037967 to 10.64911; a high value indicates frequent replacement.