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Molecule Parameter List for elRIB | 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. |
elRIB acting as a Molecule in Kierzek_LacZ Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | elRIB | Kierzek_LacZ
Accession No. : 29 | LacZ
Pathway No. : 141 | 0 | 0.99997 | No | | Ribosome elongating protein chain. |
elRIB 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 | | Prot_elongation | Kierzek_LacZ
Accession No. : 29 | LacZ
Pathway No. : 141 | 0.015
(s^-1) | 0
(uM^-1 s^-1) | - | - | Substrate
elRIB
Product
Protein
Ribosome
| | Equation 9 from Kierzek et al. They say that this step should be RibRBS-> Protein, but based on text and the logic of the synthesis, it should really be ElRIB, the Ribosome elongating protein chain, that should give rise to the protein. The calculation is: ribosome moves at 15 AAs /sec. The protein is 1024 AAs long. So protein is formed at 0.015/sec. |
elRIB 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 | | 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. |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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