Domain-based approaches are used in phylogenetic reconstruction and functional identification. Two groups of ionotropic glutamate receptors (iGluR???s) were identified with the topology of the binding core and pore-loop of the eukaryotic iGluR???s. Group 1 has a potassium-like selectivity filter and Group 2 is most closely related to eukaryotic iGluR???s. The relationship among them was investigated in this research. Then, the domain complexity of proteins was analysed on a comprehensive basis. Our results showed that bacterial and archaeal proteins are as complex as eukaryotic proteins in domain abundance, but more promiscuous. Proteins emerged in early stage are also more promiscuous, but with low domain abundance. The possible application of protein comparison based on domain content was also suggested in this research and could be used to help the identification of function and orthology. Therefore, domain-based approaches are proved to be useful in many areas of proteome research, including functional annotation, evolutionary illustration, and protein-protein network construction
