FIG 2 .

Mutant EMCVs harbor single amino acid substitutions in nonstructural protein 3A. The locations of the acquired mutations in 3A in the context of sequence conservation and putative structural features of this protein are shown. A multiple-sequence alignment (MSA) of 3A of four picornaviruses forming a monophyletic cluster was obtained as specified in Materials and Methods. The name of each MSA entry includes the acronym of the virus name and the GenBank accession number of the respective sequence. SenV, Seneca virus; BoCV, Boone cardiovirus; TMEV, Theiler’s murine encephalomyelitis virus; EMCV, encephalomyocarditis virus. Amino acid conservation is highlighted with shadows using the conserved panel in default mode, which produces a consensus line featuring the invariant residues (uppercase letters) and the most frequent residues (lowercase letters), as well as 6 groups of physicochemically similar residues (digits from 1 to 6). SecStructConf and SecStructPred, confidence and state (C, coil; H, helix; E, strand) of predicted secondary structure of EMCV 3A according to PsiPred analysis of the MSA. CoiledCoil, elements of coiled-coil heptads in EMCV 3A protein as assigned by Paircoil2 with a window length of 21 under the P score cutoff of 0.025 (range, 0.0223 to 0.0041). The hydrophobic a and d positions are contrasted with background shading. Transmembrane residues of EMCV 3A whose data were above the TMHMM2 threshold of 0.4 to form transmembrane helix are indicated with an asterisk (*).