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Name Notes Model

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
Differential syn thesis of mRNA	95	Network	kinetics,  compartment_1,  compartment_2
The model consists of three major pathways: Calcium-calmodulin dependent protein kinase IV (CaMKIV), Mitogen-activated protein kinase (MAPK) and Protein Phosphatase 1 (PP1). Each of these converged on CREB activation. We also modeled further interactions with Transducer of regulated CREB activity 1 (TORC1) and the protein kinase A (PKA) pathway.

GAP acting as a Molecule in  Differential synthesis of mRNA Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
GAP	Differential syn thesis of mRNA Accession No. : 95	kinetics Pathway No. : 1115	0.01	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 16 May 2003: Increased level to 0.0036, in line with other concentration raises at the synapse.

GAP acting as an Enzyme in  Differential synthesis of mRNA Network

Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
GAP / GAP_dash_inact_ dash_ras	Differential syn thesis of mRNA Accession No. : 95	kinetics Pathway No. : 1115	1.0104	10	4	explicit E-S complex	Substrate GTP_dash_Ras Product GDP_dash_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) 5 Nov 2002: Changed ratio term to 4 from 100. Now we have k1=8.25e-5; k2=40, k3=10. k3 is still rate-limiting.

GAP acting as a Substrate for an Enzyme in  Differential synthesis of mRNA Network

Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
PKC_dash_active  / PKC_dash_inact_ dash_GAP	Differential syn thesis of mRNA Accession No. : 95	kinetics Pathway No. : 1115	3.3333	4	4	explicit E-S complex	Substrate GAP Product GAP_star
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  Differential synthesis of mRNA 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_dash_ GAP	Differential syn thesis of mRNA Accession No. : 95	kinetics Pathway No. : 1115	0.1 (s^-1)	0 (s^-1)	-	-	Substrate GAP_star Product GAP
Assume a reasonably good rate for dephosphorylating it, 1/sec