Motivation: Several methods in genetic information have recently been developed to estimate classification of protein sequences through their sequence similarity. These methods are essential for understanding the function of predicted open reading frames (ORFs) and their molecular evolutionary processes. However, since many protein sequences consist of a number of independently evolved structural units (we refer to these units as components), the combinatorial nature of the components makes it difficult to classify the sequences. Results: This paper presents a new method for classifying uncharacterized protein sequences. As the measure of sequence similarity, we use similarity score computed by a method based on the Smith-Waterman local alignment algorithm. Here we introduce how this method cope when sequences have multi-component structure. This method was applied to predicted ORFs on the Escherichia coli genome and we discuss the algorithm and experimental results.