Detecting the boundaries of protein domains is an important and challenging task in both experimental and computational structural biology. In this paper, a promising method for detecting the domain structure of a protein from sequence information alone is presented. The method is based on analyzing multiple sequence alignments derived from a database search. Multiple measures are defined to quantify the domain information content of each position along the sequence. Then they are combined into a single predictor using support vector machine. What is more important, the domain detection is first taken as an imbalanted data learning problem. A novel undersampling method is proposed on distance-based maximal entropy in the feature space of Support Vector Machine (SVM). The overall precision is about 80%. Simulation results demonstrate that the method can help not only in predicting the complete 3D structure of a protein but also in the machine learning system on general imbalanced datasets.