A large number of newly sequenced proteins are generated by the next-generation sequencing technologies and the biochemical function assignment of the proteins is an important task. However, biological experiments are too expensive to characterize such a large number of protein sequences, thus protein function prediction is primarily done by computational modeling methods, such as profile Hidden Markov Model (pHMM) and k-mer based methods. Nevertheless, existing methods have some limitations, k-mer based methods are not accurate enough to assign protein functions and pHMM is not fast enough to handle large number of protein sequences from numerous genome projects. Therefore, a more accurate and faster protein function prediction method is needed.