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Molecule Parameter List for RibRBS | 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 | | Kierzek_LacZ | 29 | Pathway |
LacZ | | An approximation to the Kierzek AM. et al. J Biol Chem. (2001) 276(11):8165-72 model of LacZ gene expression in E. coli. They use stochastic simulation and model cell growth. Despite these discrepancies, the continuous fixed size model is within a factor of 3 of their results. Parameter values are identical. |
RibRBS acting as a Molecule in Kierzek_LacZ Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | RibRBS | Kierzek_LacZ
Accession No. : 29 | LacZ
Pathway No. : 141 | 0 | 0.99997 | No | | This is the ribosome binding site protected by the bound ribosome. |
RibRBS acting as a Substrate in a reaction in Kierzek_LacZ 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 | | Clearance | Kierzek_LacZ
Accession No. : 29 | LacZ
Pathway No. : 141 | 0.5
(s^-1) | 0
(uM^-1 s^-1) | - | - | Substrate
RibRBS
Product
RBS
elRIB
| | Equation 7 from Kierzek et al. Based on Draper , DE 1996 E coli and Salmonella 2nd Ed pp 902-908 ASM Press, Washington DC. This is the rate at which the RBS is cleared. |
RibRBS acting as a Product in a reaction in Kierzek_LacZ 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 | Ribosome_
binding | Kierzek_LacZ
Accession No. : 29 | LacZ
Pathway No. : 141 | 99.9927
(uM^-1 s^-1) | 2.25
(s^-1) | Kd(bf) = 0.0225(uM) | - | Substrate
RBS
Ribosome
Product
RibRBS
| | Equations 5 and 6 from Kierzek et al. Association rate set to order of magnitude of diffusion-limited aggregation. Dissociation rate set to reproduce translation initiation frequency. |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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