Abstract
Abstract To predict the protein binding domain or active site residues of an enzyme always helps offering useful information for protein and enzyme researches.A strategy called “Evolutionary Trace Method (denoted to ET)” is developed by Lichtarge et al. (1996). We try to use ET to investigate TIM barrel glycosidase superfamily. The diversity within the samples is so enormous that many gaps occur during MSA. To handle this problem, we modify Evolutionary Trace by tracing consensus of protein groups belonged to “the same ancestor” by each level of tree instead of according “PICs”, partition identity cutoffs (PICs) that are used to define partitions. Our Evolutionary Trace Method is compared to traditional one by repeat experiment made by Mathew E. Sowa et al. . Six residues with PDEγ effects identified by Mathew E. Sowa et al. are identified on branch 12 in our studies, too. No false negative result occurs in our study. Then we investigate beta-glycanases TIM-barrel in glycosidases superfamily. Among 313 residues of Cellulose/Xylan Specificity of the beta-1,4-Glycanase Cex from Cellulomonas fimi[1exp], we can eliminate 281 unnecessary residues from 313 residues of Cellulose/Xylan Specificity of the beta-1,4- Glycanase Cex from ellulomonas fimi and pick up 32 critical residues on branch 39. Ten of picked up residues are considered to play a role in hydrolase activities. In contrast, traditional Evolutionary Trace can get no information. This is helpful to biologists, and they can save a lot of time and money. This is the contribution of our modified Evolutionary Trace Method.