Analysis of amino acids of the HVR-VP2 region of Cuban IBDV strains.

<p><b>Panel (A)</b> Amino acid entropy rates plot, x-axis: amino acid position; y-axis: entropy. The measure of entropy (Hi) for each position of amino acid was obtained using DAMBE software. The position with the highest value of entropy is indicated. <b>Panel (B)</b> Difference between non-synonymous and synonymous rates (dN-dS). Codon-specific nonsynonymous (dN) and synonymous (dS) substitution rates were obtained via a website (WEBSNAP); position 299 was denoted. <b>Panel (C)</b> Amino acid sequence alignment of the Cuban field strains of IBDV. Those residues under purifying selection as detected by SLAC and FEL analyses are indicated with black arrows. The secondary structure that belongs to each residue of the alignment is also denoted: β indicates β-sheets (in sky blue), λ indicates loops (in dark blue) and α indicates α-helices (in orange). The residue at position 299 is highlighted using a black rectangle. <b>Panel (D)</b> X-ray crystal structures of a monomer of VP2, crystal structure <i>2DF7</i> was downloaded from Protein Data Bank; only the monomer A was used for clarity. Chimera software v1.6.2 was used for visualisation. Residues Y206 and T350, respectively indicating the beginning and end of HVR, are shown. The HVR is annotated using the same colours as panel (C): β-sheets in sky blue, loops in dark blue and α-helices in orange. The remaining domains (S and B) are denoted in yellow. The β-hairpin AA′ involved in the stabilisation of the trimer conformation of VP2 (Coulibaly et al., 2005) is indicated. The distance between residues 299 and 194 is shown.