Figure 9

Consensus structures and loop sequences for HRVA and HRVB minimal CREs. A. Consensus secondary structure and sequence of HRVA minimal CRE derived from alignment of publicly available HRV prototype sequences in the region of the 2A gene (Laine et al., 2005) identified to be the minimal functional CRE in HRV2 (Gerber et al., 2001). B. Consensus secondary structure and sequence of HRVB minimal CRE derived from an alignment of sequence from all HRVB prototypes in the region of the 1D gene (Ledford et al., 2004; Laine et al., 2005) shown to function as the minimal CRE in HRV14 (McKnight and Lemon, 1998; Yang et al., 2002). Circled residues, positions where compensatory substitutions are detected in the alignment. Gray residues indicate positions where substitutions that disrupt basepairing potential are detected in the alignment. Weblogo (Schneider and Stephens, 1990; Crook et al., 2004) of consensus sequence of loop region is provided above to provide a quantitative view of the conservation of this element. The height of each letter is proportional to the fraction of the observed frequency relative to the expected frequency at each position.