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Molecule Parameter List for GAP

The statistics table lists the distribution of a molecule acting either as a substrate, product, enzyme or as a molecule within the network.
The text color of a molecule is highlighted by

color.

Statistics

*GAP* participated as	Molecule	Sum total of	Enzyme	Substrate of an enzyme	Product of an enzyme	Substrate in Reaction	Product in Reaction
No. of occurrences	1	0	1	1	0	0	1

Accession and Pathway Details

Accession Name	Accession No.	Accession Type	Pathway Link
3d_fold_model	8	Network	Shared_Object_3d_fold_model, PKC, MAPK, PLA2, Ras
This model is an annotated version of the synaptic signaling network. The primary reference is Bhalla US and Iyengar R. Science (1999) 283(5400):381-7 but several of the model pathways have been updated Bhalla US, Ram PT, Iyengar R. Science. 2002 Aug 9;297(5583):1018-23.

GAP acting as a Molecule in 3d_fold_model Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
GAP	3d_fold_model Accession No. : 8	Ras Pathway No. : 58	0.002	1000	No
GTPase-activating proteins. See Boguski and McCormick. Turn off Ras by helping to hydrolyze bound GTP. This one is probably NF1, ie., Neurofibromin as it is inhibited by AA and lipids, and expressed in neural cells. p120-GAP is also a possible candidate, but is less regulated. Both may exist at similar levels. See Eccleston et al JBC 268(36) pp27012-19 Level=.002

GAP acting as an Enzyme in 3d_fold_model Network

Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
GAP / GAP-inact-ras	3d_fold_model Accession No. : 8	Ras Pathway No. : 58	1.0104	10	100	explicit E-S complex	Substrate GTP-Ras Product GDP-Ras
From Eccleston et al JBC 268(36)pp27012-19 get Kd < 2uM, kcat - 10/sec From Martin et al Cell 63 843-849 1990 get Kd ~ 250 nM, kcat = 20/min I will go with the Eccleston figures as there are good error bars (10%). In general the values are reasonably close. k1 = 1.666e-3/sec, k2 = 1000/sec, k3 = 10/sec (note k3 is rate-limiting)

GAP acting as a Substrate for an Enzyme in 3d_fold_model Network

Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
PKC-active / PKC-inact-GAP	3d_fold_model Accession No. : 8	Shared_Object_ 3d_fold_model Pathway No. : 54	3.33333	4	4	explicit E-S complex	Substrate GAP Product GAP*
Rate consts copied from PCK-act-raf This reaction inactivates GAP. The idea is from the Boguski and McCormick review.

GAP acting as a Product in a reaction in 3d_fold_model Network

Kd is calculated only for second order reactions, like nA+nB <->nC or nA<->nC+nD, where n is number and A,B,C,D are molecules, where as for first order reactions Keq is calculated. Kd for higher order reaction are not consider.

Name	Accession Name	Pathway Name	Kf	Kb	Kd	tau	Reagents
dephosph-GAP	3d_fold_model Accession No. : 8	Ras Pathway No. : 58	0.1 (s^-1)	0 (s^-1)	-	-	Substrate GAP* Product GAP
Assume a reasonably good rate for dephosphorylating it, 1/sec

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