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Figure 2 | Genome Biology

Figure 2

From: Determinants of protein function revealed by combinatorial entropy optimization

Figure 2

Typical results and predictive power of the CEO method illustrated in the family of small GTPases (G-domains). The analysis used 126 distinct human sequences of the Ras superfamily of GTPase domains obtained after removing redundant identical copies and gappy (>30% gaps relative to rasH) sequences from the 284 protein domain sequences in the PFAM Protein Family Database (version 20), which includes ras, rab, and rho subfamilies. (a) Alignments of 22 specificity residues (numbered as in RasH) in the two largest ras and rho subfamilies; these residues (out of a total of about 190) carry most of the information for the distinction between functional subfamilies; note the conservation of residue type within each subfamily and nonconservation between subfamilies. (b) Presence of the computed specificity residues in known molecular interfaces (marked '#') of three GTPases (RasH, RhoA, and CDC42). Seventeen of the 22 specificity residues are in these interfaces (yellow numbers). Nine of the specificity residues are in the functionally important switch I (magenta numbers) and switch II (orange numbers) regions, which are involved in sensing and/or communicating the differences between the GTP and GDP states. CEO, combinatorial entropy optimization.

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