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Molecule Parameter List for PPX | 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 |
Accession and Pathway Details | |
| Accession Name | Accession No. | Accession Type | Pathway Link | Mammalian_cell_
cycle | 85 | Network |
Growth, CELLDIV, Rb_grp,
IE_GRP, CycB_Grp, Cdc20_Grp,
Cdh1_grp, E2F, CycA_Grp,
CycE_grp, Early_Response_Genes, Delayed_Response_Genes,
CycD_Grp | | This is a fairly complete mass-action reimplementation of the Novak and Tyson mammalian cell cycle model. It is inexact on two counts. First, it replaces many rather abstracted equations with mass action and Michaelis-Menten forms of enzymes. Second, it does not handle the halving of cellular volume at the division point. Within these limitations, the model does most of what the original paper shows including oscillation of the relevant molecules. |
PPX acting as a Molecule in Mammalian_cell_cycle Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | PPX | Mammalian_cell_
cycle
Accession No. : 85 | IE_GRP
Pathway No. : 1072 | 1 | 200 | No | | From the notes on the equations: We assuem that the activity of this phosphatase (in the nucleus, where it opposes the action of CycB/Cdk1) is proportional to translational efficiency epsilon. Hence, when epsilon drops to 05, both kinase and phosphatase acting on IE are halved. |
PPX acting as an Enzyme in Mammalian_cell_cycle Network
Enzyme Molecule /
Enzyme Activity | Accession Name | Pathway Name | Km (uM) | kcat (s^-1) | Ratio | Enzyme Type | Reagents | PPX /
k32
| Mammalian_cell_
cycle
Accession No. : 85 | IE_GRP
Pathway No. : 1072 | 0.01 | 1.8 | 4 | explicit E-S complex | Substrate
IEP
Product
IE
| | Represented as k32.[PPx].[IEP] / (J32 + [IEP]) k32 = 1.8 J32 = 0.01 |
PPX acting as a Substrate in a reaction in Mammalian_cell_cycle 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. |
PPX acting as a Product in a reaction in Mammalian_cell_cycle 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
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