Structural features of Rab GTPases. (a) Ribbon drawing of Rab3A complexed with the GTP analog GppNHp (reproduced with permission from ). Purple, bound nucleotide; orange sphere, Mg2+ ion; blue, switch I and II regions; green, α helices and β sheets; yellow, loops. (b) A profile amino-acid sequence of the Rab GTPase subfamily generated using the hidden Markov model (HMM) method (modified from ). The uppercase/lowercase coding represents outcome of the profile HMM method. Upper-case characters, residues found in the profile with a probability of p > 0.5; red, Rab-specific residues (RabF1-5); dark blue, subfamily-specific motifs (RabSF1-4); cyan, highly conserved nucleotide-binding motifs; G, guanine-base-binding motif; PM, phosphate/magnesium-binding motif. The secondary structure units (α helices, β strands, and loops, λ) are indicated above the sequence.