Analyzing protein sequence data becomes increasingly important recently. Most previous work on this area has mainly focused on building classification models. In this paper, we investigate in the problem of automatic clustering of unlabeled protein sequences. As a widely recognized technique in statistics and computer science, clustering has been proven very useful in detecting unknown object categories and revealing hidden correlations among objects. One difficulty that prevents clustering from being performed directly on protein sequence is the lack of an effective similarity measure that can be computed efficiently. Therefore, we propose a novel model for protein sequence cluster by exploring significant statistical properties possessed by the sequences. The concept of imprecise probabilities are introduced to the original probabilistic suffix tree to monitor the convergence of the empirical measurement and to guide the clustering process. It has been demonstrated that the proposed method can successfully discover meaningful families without the necessity of learning models of different families from pre-labeled "training data".