A bioinformatics method was used to search the responsible dipeptides for optimum pH in the G/11 xylanase, for dipeptides can provide position information of the related residues for rational protein design. The responsible dipeptides were found as negative YS and positive SY, GR, MR, and KR. The minimum and maximum optimum pH was calculated as 2.33 and 14.29, respectively. Compared with the known crystal structures of the G/11 xylanase, YS was found mostly in the turn area of beta-strands of S/T surface; and SY was found in the inner part of beta-strands of the S/T area near to the active site of proton donor; and the GR, MR, and KR in the coil region connecting "finger" to the alpha-helix. The result clearly explained the success of shifting of pH 0.5 U to alkaline by the introduction of arginines into S/T area of a xylanase. The result would be useful for xylanase engineering, and the adaptation mechanism to high alkaline was also discussed. (C) 2004 Elsevier Inc. All rights reserved.