A growing body of research has concentrated on the identification and definition of conserved sequence motifs. It is widely recognized that these conserved sequence and structural units often mediate protein functions and interactions. The continuing advancements in high-throughput experiments necessitate the development of computational methods to critically assess the results. In this work, we analyzed high-throughput protein complexes using the domain composition of their protein constituents. Domains that mediate similar or related functions may consistently co-occur in protein complexes.