PFRMAT TS 
TARGET T0056 
AUTHOR 7397-8542-2481 
METHOD ADDITIONAL INFORMATION 
METHOD From target information:  6 alpha helices, residues: 30(I)-41(M),  
METHOD 47(W)-51(A),  
METHOD 64(H)-76(E), 84(I)-92(R), 103(A)-110(K),118(I)-134(M) 
METHOD  
METHOD -The protein has a C-terminal domain belonging to the RecA/Rad family of 
METHOD P-loop NTPases. 
METHOD -The N-terminal domain (which we have to predict) contains six helices  
METHOD and is connected to the C-terminal domain by about sixty residues or so. 
METHOD -Most P-loop NTP-ases require an 'arginine finger' for full activity.  
METHOD This is either provided in a separate polypeptide (RasGAP, RhoGAP) or in 
METHOD the same polypeptide (G-alpha, DEAD-box helicases, clamp loader  
METHOD subunits). 
METHOD -The N-terminal domain of DnaB contains an invariant Arg at the end of  
METHOD the last helix (the only invariant residue in the domain). This 
METHOD Arg is the 'arginine finger' and the helical domain is the scaffold. 
METHOD -The 'arginine finger' scaffolds are mostly all helical (RasGAP, RhoGAP, 
METHOD G-alpha, clamp loader subunits), but only RasGAP and RhoGAP have a  
METHOD similar fold, and the arginine is in a completely wrong place for us.  
METHOD The clamp loader scaffold has only three helices, so it is out too. G- 
METHOD alpha has an inserted domain of six helices with the arginine at the end 
METHOD of the last helix, just like DnaB, but the helices and the connecting  
METHOD loops don't have matching lengths. 1TAD (transducin alpha) is 94th in  
METHOD our MAP list. 
METHOD -The top 10 hits of our MAP list belong to 7 different folds. 
METHOD -We found no indications of a similar function in RuvA and DnaB domains. 
METHOD -Our conclusion: it is probably a novel fold. 
MODEL  1 
PARENT NONE 
TER 
END 
