Evolutionary information, one of the most important types of information in assessing functionality in biological analysis, has been successfully used to encode protein in many applications, such as our previous work of lysine ubiquitylation site prediction [32] , transmembrane protein topology prediction [33] and malaria parasite mitochondrial protein prediction [34] . To extract the evolutionary information, the profile of each protein sequence is generated by running Position Specific Iterated BLAST (PSI-BLAST) program [35, 36] . Then this information can be represented as a two dimensional matrix which is known as the PSSM of the protein.