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Figure 4 | BMC Structural Biology

Figure 4

From: Revealing divergent evolution, identifying circular permutations and detecting active-sites by protein structure comparison

Figure 4

The comparison result of protein pair 1TPO/223 (β-trysin) and 2ACT/218 (actinidin) by SAMO. Subfigure (a) illustrates the aligned result after the optimal superimposing by different colors. The red chain is 1TPO and the blue chain is 2ACT. There are 122 amino-acid matching pairs with RMSD = 2.02. Also the active site region on 1TPO is highlighted in yellow and the active site region on 2act is drawn in green. Subfigure (b) is the detail match of the active sites between 1TPO(red) and 2ACT(blue). As indicated in the figure, the superposition of C α s found by SAMO brings the catalytic triads close together. In the matched active sites, the amino acids come from different fragments of each protein chain. Some segments contain contiguous residues. The actual matching of these segments is, for 2ACT: 24–25, 151–152, 132–137, 158–167, 177–183, 191–198; for 1TPO: 194–195, 85–86, 31–36, 39–48, 50–56, 101–108. The actual matching of the residues formed the active sites is listed in Subfigure (c).

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