Structure-Based Sequence Alignment of QDE-1 ΔN and DdRPs

<p>Alignment of QDE1 ΔN (top sequence), bacterial (middle sequence, orange), and yeast (bottom sequence, green) polymerases is based on structurally equivalent residues, as determined by SHP [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0040434#pbio-0040434-b041" target="_blank">41</a>]. Residues structurally equivalent in all polymerases are shaded purple, green (light for Rbp1, dark for Rp2) if equivalent in yeast DdRP and QDE1 ΔN, and orange if only equivalent in QDE1 ΔN and bacterial DdRP. Invariant residues are shaded in red. Conserved sequence motifs identified in cRdRPs are represented as in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0040434#pbio-0040434-sg001" target="_blank">Figure S1</a>, marked on QDE1 sequence. QDE1 secondary structure elements are shown on top, coloured according to domain definition (slab, blue; catalytic, deep purple; neck, pink; and head, red). DPBB1 and DPBB2 are outlined by deep purple boxes. The flap sub-domain and the potential “bridge helix” are also represented by boxes, coloured light purple and grey, respectively.