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Figure 5 | BMC Evolutionary Biology

Figure 5

From: Relationships of gag-pol diversity between Ty3/Gypsy and RetroviridaeLTR retroelements and the three kings hypothesis

Figure 5

Retroviridae protease isoforms. Retroviridae PRs dimerize in their active form and each lobe of this enzyme usually has a structural flap (the two β-hairpin loops enclosed in a circle covering the catalytic DT/SG dyad). Retroviridae differentiation into the 3 classes reveals 3 different isoforms of the same enzyme, each exhibiting a particular flap motif. A) Sequence logo describing class II PRs, the flap correspondence on sequence in this PR is a GIGG amino acid motif included in a box. B) Sequence logo describing class I PRs; this variant preserves a GATG motif at the same flap sequence position. C) Sequence logo built based on class III PRs revealing a TIHG motif in this position. To improve the visualization on amino acidic architecture, we have used the HFV and SFV-1 sequences (see methods) plus FFV (Genbank accession CAA70075), FSV (AAC58531), SFV-3 (AAA47796), and EFV (AAF64414), to build the logo.

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