Fig. 1.

Sequence relationships of the Orf3a-M protein superfamily. (a): Pictorial representation of the reference alignment: sequence logo displayed at the bottom, bars signify gaps and conservation; secondary structure elements of Orf3a are shown at the top (helices in yellow, strands in green) and labeled; conserved positions are marked by circles, red for those present and pink for those unavailable in the structure. (b): Similarity matrix for the superfamily, annotated on the right, and color-coded with a vertical bar as follows: blue for M protein in the beta group, green for M protein in the alpha and gamma groups and orange for Orf3a member; bar sections with a brush stroke correspond to homologs within the SARS lineage for M protein (blue) and Orf3a (orange). (c): Structure of the sequence alignment depicted in MView color scheme, white sections correspond to gap regions. (d): Sequence space embedding of the reference alignment and annotations: color-coding as in (b) with the exception of the gamma group members; ‘sars-1′/‘sars-2′ denote SARS-CoV-1/-2, for brevity. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)