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. Author manuscript; available in PMC: 2022 Aug 1.
Published in final edited form as: Prog Biophys Mol Biol. 2020 Oct 6;163:87–108. doi: 10.1016/j.pbiomolbio.2020.09.010

Fig. 8. Evolutionary Trace analysis of the DNA-PKcs protein family.

Fig. 8.

Panel A: The evolutionary importance of the DNA-PKcs residues was estimated by the Evolutionary Trace (ET) algorithm using as input the sequences alignment of Supplementary Fig. 9 (selected metazoan/vertebrates plus invertebrates and putative archaeon). The results are represented by a color scale from red (most important) to green (least important). The three viewpoints differ for about 90° and show the FAT-kinase-FATC domain (crown) on the top.

Panel B: The phylogenetic tree of the sequences found in Supplementary Fig. 9. A branch of closely related metazoan sequences was highlighted cyan. The phylogenetic tree was output of the ET algorithm and it was visualized using Archaeopteryx (version 0.9901).

Panel C: The correlation of ET ranks generated for all sequences shown in panel B versus the ET ranks generated for the metazoan branch highlighted in panel B. The Pearson’s correlation coefficient r was calculated to be 0.84.

Panel D: The ET ranks of the DNA-PKcs residues using as input the sequence alignment of the metazoan branch highlighted in panel B (same color scale and viewpoints as in panel A).

The figure panels A and D were generated by PyMol, using the PyETV plugin (Lua and Lichtarge, 2010) and chain C of the 5y3r pdb structure.