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Molecule Parameter List for degraded_PKM | 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 |
| degraded_PKM participated as | Molecule | Sum total of | Enzyme | Substrate of an enzyme | Product of an enzyme | Substrate in Reaction | Product in Reaction | | No. of occurrences | 40 | 0 | 0 | 0 | 0 | 0 | 40 |
Accession and Pathway Details | |
| Accession Name | Accession No. | Accession Type | Pathway Link | Ajay_Bhalla_
2007_ReacDiff2 | 83 | Network | Shared_Object_Ajay_Bhalla_2007_ReacDiff, PKC, MAPK,
Ras, CaM, PKM, chain, kinetics, PKC, MAPK, Ras, CaM, PKM, kinetics[1],
PKC, MAPK, Ras, kinetics[3], CaM, PKM, kinetics[2], PKC, MAPK, Ras,
CaM, PKM, PKC, MAPK, Ras, CaM, PKM, kinetics[4], PKC, MAPK, Ras, CaM,
PKM, kinetics[5], PKC, MAPK, Ras, CaM, PKM, kinetics[6], PKC, MAPK,
Ras, CaM, PKM, kinetics[7], PKC, MAPK, Ras, CaM, PKM, kinetics[8],
PKC, MAPK, Ras, CaM, PKM, kinetics[9], PKC, MAPK, Ras, CaM, PKM, kinetics[10],
PKC, MAPK, Ras, CaM, PKM, kinetics[11], PKC, MAPK, Ras, CaM, PKM, kinetics[12],
PKC, MAPK, Ras, CaM, PKM, kinetics[13], PKC, MAPK, Ras, CaM, PKM, kinetics[14],
PKC, MAPK, Ras, CaM, PKM, kinetics[15], PKC, MAPK, Ras, CaM, PKM, kinetics[16],
PKC, MAPK, Ras, CaM, PKM, kinetics[17], PKC, MAPK, Ras, CaM, PKM, kinetics[18],
PKC, MAPK, Ras, CaM, PKM, kinetics[19], PKC, MAPK, Ras, CaM, PKM, kinetics[20],
PKC, MAPK, Ras, CaM, PKM, kinetics[21], PKC, MAPK, Ras, CaM, PKM, kinetics[22],
PKC, MAPK, Ras, CaM, PKM, kinetics[23], PKC, MAPK, Ras, CaM, PKM, kinetics[24],
PKC, MAPK, Ras, CaM, PKM, kinetics[25], PKC, MAPK, Ras, CaM, PKM, kinetics[26],
PKC, MAPK, Ras, CaM, PKM, kinetics[27], PKC, MAPK, Ras, CaM, PKM, kinetics[28],
PKC, MAPK, Ras, CaM, PKM, kinetics[29], PKC, MAPK, Ras, CaM, PKM, kinetics[30],
PKC, MAPK, Ras, CaM, PKM, kinetics[31], PKC, MAPK, Ras, CaM, PKM, kinetics[32],
PKC, MAPK, Ras, CaM, PKM, kinetics[33], PKC, MAPK, Ras, CaM, PKM, kinetics[34],
PKC, MAPK, Ras, CaM, PKM, kinetics[35], PKC, MAPK, Ras, CaM, PKM, kinetics[36],
PKC, MAPK, Ras, CaM, PKM, kinetics[37], PKC, MAPK, Ras, CaM, PKM, kinetics[38],
PKC, MAPK, Ras, CaM, PKM | This is a 40-compartment reaction-diffusion-transport version of the Ajay_Bhalla_2007_PKM model. The original single-compartment model is repeated 40 times. In addition, a subset (27 out of 42) molecules can diffuse between compartments. Diffusion is implemented as a reaction between corresponding molecules in neighboring compartments. For D = 1e-12 m^2/sec (i.e., 1 micron^2/sec ) the kf and kb of this reaction for these 10 micron compartments are both 0.01/sec In addition, we have a forward (dendrite to soma) transport term of 1 microns/sec. This converts to a rate of 0.1/sec, but applies only to the kf. So the total kf of the diffusion 'reaction' is 0.11 for D = 1 micron^2/sec, and kb is 0.01. If D=0.1 micron^2/sec then kf = 0.101 and kb = 0.001. In addition this model has all molecules buffered in the first and last compartments. This boundary conditions says that the molecules are not drained out of the first compartment, nor do they all pile up in the last one.
The stimulus file pkm_mapk22_transp_endbuf_D1e-13_Fig4CD which was used for the model to replicate Figure 4C and 4D from the paper.
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degraded_PKM acting as a Molecule in Ajay_Bhalla_2007_ReacDiff2 Network
degraded_PKM acting as a Product in a reaction in Ajay_Bhalla_2007_ReacDiff2 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. |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
This Copyright is applied to ensure that the contents of this database remain freely available. Please see FAQ for details. |
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