Figure 3

Functional divergence in reverse transcriptase. (A) The SplitTester output for the reverse transcriptase dataset. Windows supporting the functional split are shown as colored lines in the plot. The X-axis represents the length of the aligned sequences; the Y-axis represents increasing window size (see legend to Fig. 2 for additional detail). (B) The X-ray structure of the HIV reverse transcriptase/primer/template complex (1RTD). The reverse transcriptase protein is represented by the yellow strand. The two green regions are domains identified by SplitTester. All residue numbers correspond to HIV sequence positions in 1RTD. Residues 166–215 and 280–311 in the aligned retrotransposon sequences correspond to 167–210 and 267–297 in the HIV 1RTD sequence, respectively.