The definition of the automatic protein function means designating the function with the automation by utilizing the data that already revealed unknown protein function. The demand for analysis on the sequencing technology such as the next generation genome analysis (NGS) and the subsequent genome are on the rise; thus, the need for the method of predicting the protein function automatically has been more and more highlighted. As for the existing methods, the studies on the definition of function between the similar species based on the similarities of sequence have been primarily conducted. However, this paper aims to designate by automatically predicting the function of genome by utilizing InterPro (IPR) that can represent the properties of the protein family, which similarly groups the protein function. Moreover, the gene ontology (GO), which is the controlled vocabulary to describe the protein function comprehensively, is to be used. As for the data used in the experiment, the analysis on properties was conducted in the sparse state that is deflected to one side. Thus, this paper aims to analyze the prediction method for protein function automatically through selecting the features, assigning the data processing and weights and applying a variety of classification methods to overcome that property.