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Microorganisms produce enzymes which have the ability convert a given substrate into a desired product. Enzyme became essential components of industries and often called as biocatalyst. Maintaining enzymes and obtaining desired product is a costly affair. In order to overcome such short coming bioinformatics has entered into the field of industrial enzymology. In this study xylanases enzyme from different extremophilic bacteria was selected for which protein were built by homology modeling each of receptors bears partial structural similarity which was also highlighted by similar active site residues but were positioned at different locations. In silico binding affinity of these enzyme shows is multi-substrate activity and among the twenty amino acids Glutamate, Lysine, Arginine, Serine, Aspartic acid, Glutamine and Thereonine were found to be effective in binding to different type of ligands.