Detailed analysis of function divergence in a large and diverse domain superfamily: toward a refined protocol of function classification.

Some superfamilies contain large numbers of protein domains with very different functions. The ability to refine the functional classification of domains within these superfamilies is necessary for better understanding the evolution of functions and to guide function prediction of new relatives. To achieve this, a suitable starting point is the detailed analysis of functional divisions and mechanisms of functional divergence in a single superfamily. Here, we present such a detailed analysis in the superfamily of HUP domains. A biologically meaningful functional classification of HUP domains is obtained manually. Mechanisms of function diversification are investigated in detail using this classification. We observe that structural motifs play an important role in shaping broad functional divergence, whereas residue-level changes shape diversity at a more specific level. In parallel we examine the ability of an automated protocol to capture the biologically meaningful classification, with a view to automatically extending this classification in the future.