Alignment of CCD domain for Ty3, PFV, and HIV-1 IN proteins.

<p>PFV and HIV-1 sequence and secondary structure alignments were adapted from Hare, et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0063957#pone.0063957-Hare1" target="_blank">[13]</a> and Valkov, et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0063957#pone.0063957-Valkov1" target="_blank">[11]</a>. Ty3 sequence and secondary structure alignments are the consensus of several methods as described in the text. “H” denotes both 3–10 and alpha helices. “E” denotes extended (beta strand). “cons TP” denotes conservation between Ty3 and PFV, and “cons TPH” conservation between Ty3, PFV, and HIV-1, using the ClustalW conservation groups <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0063957#pone.0063957-Thompson1" target="_blank">[32]</a>. Note that PFV sequence numbering is according to NCBI but the actual chimeric IN starts at the fourth residue in the PFV sequence. Conserved D,D X₃₅E catalytic residues as numbered in the alignment are Ty3 IN: D164, D225, E 261; PFV: D128, D185, E221; HIV-1: D64, D116, E152.