SI and SII PSSM for yeast paralog alignment (28 domains) and example ortholog alignments for Fus1 (16 species) and Bud14 (29 species).

<p>Total occurrence for each amino acid group for each position is indicated and colored as yellow (low) to red (high). Residues are grouped into SI (left) and SII (right). Dark outlined regions indicate most common preference for the family (≥ 20 occurrences). Overall, for SI there is a family preference for aromatic residues except the less conserved positions 9, 52 and 53. Notable exceptions include Fus1 that has cysteines at positions 37 and 54 (which are usually in the FWYH group). For SII, there is a loose family preference for polar/acidic residues except at position 49 where hydrophobic residues are found. The extent of conservation in the orthlog alignments in SI and SII vary, with a much greater variation seen in SII PSSMs. PSSMs for all domains (showing both complete domain sequence and only surface I/II) can be found in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0193128#pone.0193128.s008" target="_blank">S4 File</a>.