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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 asMoleculeSum total ofEnzymeSubstrate of an enzymeProduct of an enzymeSubstrate in ReactionProduct in Reaction
No. of occurrences1011001

Accession and Pathway Details
Accession NameAccession No.Accession TypePathway Link
  • Ajay_Bhalla_
    2004_PKM_MKP3_
    Tuning
  • 77Network
    Shared_Object_Ajay_Bhalla_2004_PKM_MKP3_Tuning PKC PLA2 
    PLCbeta Ras Gq 
    MAPK EGFR Sos 
    PLC_g CaMKII CaM 
    PP1 PP2B PKA 
    AC MKP3 PKM 
    This model is based on Ajay SM, Bhalla US. Eur J Neurosci. 2004 Nov;20(10):2671-80. This is the feedforward model with MPK3 from figure 8a.

    GAP acting as a Molecule in  
    Ajay_Bhalla_2004_PKM_MKP3_Tuning Network
    NameAccession NamePathway NameInitial Conc.
    (uM)
    Volume
    (fL)
    Buffered
    GAP
  • Ajay_Bhalla_
    2004_PKM_MKP3_
    Tuning

    Accession No. : 77
  • Ras
    Pathway No. : 333
    0.011.5No
    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  
    Ajay_Bhalla_2004_PKM_MKP3_Tuning Network
    Enzyme Molecule /
    Enzyme Activity
    Accession NamePathway NameKm (uM)kcat (s^-1)RatioEnzyme TypeReagents
    GAP /
    GAP-inact-ras
  • Ajay_Bhalla_
    2004_PKM_MKP3_
    Tuning

    Accession No. : 77
  • Ras
    Pathway No. : 333
    1.01039104explicit E-S complexSubstrate
    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) 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  
    Ajay_Bhalla_2004_PKM_MKP3_Tuning Network
    Enzyme Molecule /
    Enzyme Activity
    Accession NamePathway NameKm (uM)kcat (s^-1)RatioEnzyme TypeReagents
    PKC-active  /
    PKC-inact-GAP
  • Ajay_Bhalla_
    2004_PKM_MKP3_
    Tuning

    Accession No. : 77
  • Shared_Object_
    Ajay_Bhalla_
    2004_PKM_MKP3_
    Tuning

    Pathway No. : 329
  • 3.3333244explicit E-S complexSubstrate
    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  
    Ajay_Bhalla_2004_PKM_MKP3_Tuning 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.
    NameAccession NamePathway NameKfKbKdtauReagents
    dephosph-GAP
  • Ajay_Bhalla_
    2004_PKM_MKP3_
    Tuning

    Accession No. : 77
  • Ras
    Pathway No. : 333
    0.1
    (s^-1)
    0
    (s^-1)
    --Substrate
    GAP*

    Product
    GAP
    Assume a reasonably good rate for dephosphorylating it, 1/sec



    Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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