Remote homology detection between protein sequences is a central problem in computational biology. The discriminative method such as the support vector machine (SVM) is one of the most effective methods. Many of the SVM-based methods focus on finding useful representations of protein sequence, using either explicit feature vector representations or kernel functions. Such representations may suffer from the peaking phenomenon in many machine-learning methods because the features are usually very large and noise data may be introduced. Based on these observations, this research focuses on feature extraction and efficient representation of protein vectors for SVM protein classification.