FIG 5.

Amino acid (AA) sequence conservation in the RNA-binding protein and PKR antagonist US11. The amino acid alignment of US11 shows it to be 89.5% identical across the 26 strains analyzed. Gray in the bar across the top indicates identical residues in all strains; orange indicates nonidentity. The median divergence of all strains versus the consensus (top line) is 1.2% (98.8% similarity to the consensus) (see Table 3; see also Table S3 in the supplemental material). Green-shaded blocks above the alignment indicate known functional regions of the protein (146–152). The variations in US11 illustrate those commonly seen among HSV-1 strains. Boxes indicate strain-specific SNPs (e.g., P12S, V22M, V66I, and P112S), variations shared by a group of strains (e.g., G13C, R40H, P45S, and E162K), and SSR-related indels (PRX repeat beginning at residue 130).