Figure 4

CP relationship between GTPase and hypothetical protein YlqF. Rab3A ([PDB:1ZBD], chain A) is a small G protein with GTPase activity [49] while YlqF ([PDB:1PUJ], chain A) is a conserved hypothetical protein from B. subtilis. (a) These two proteins can be structurally aligned by DALI [36] only partially (left); however, CPSARST detects their CP relationship (right). If the 64 residue amino-terminal region of Rab3A (in cyan text) is permuted to the carboxul terminus, it can be extensively aligned to YlqF with an RMSD of 3.2 Å (right). The transparent cyan and pink arrows indicate the amino termini of Rab3A and YlqF, respectively. (b) The superimposition of Rab3A and YlqF made by CPSARST (cross-eye stereo view). Colors are the same as in (a). Residues shown as cyan/pink and blue/red spacefill models are the amino and carboxyl termini, respectively.