From protein sequence space to elementary protein modules.

The formatted protein sequence space is built from identical size fragments of prokaryotic proteins (112 complete proteomes). Connecting sequence-wise similar fragments (points in the space) results in the formation of numerous networks, that combine sometimes different types of proteins sharing, though, fragments with similar or distantly related sequences. The networks are mapped on individual protein sequences revealing distinct regions (modules) associated with prominent networks with well-defined functional identities. Presence of multiple sites of sequence conservation (modules) in a given protein sequence suggests that the annotated protein function may be decomposed in "elementary" subfunctions of the respective modules. The modules correspond to previously discovered conserved closed loop structures and their sequence prototypes.