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Molecule Parameter List for nucleotides | 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 |
| nucleotides participated as | Molecule | Sum total of | Enzyme | Substrate of an enzyme | Product of an enzyme | Substrate in Reaction | Product in Reaction | | No. of occurrences | 1 | 0 | 0 | 0 | 0 | 0 | 2 |
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. |
nucleotides acting as a Molecule in Kierzek_LacZ Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | nucleotides | Kierzek_LacZ
Accession No. : 29 | LacZ
Pathway No. : 141 | 0 | 0.99997 | Yes | | |
nucleotides 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 | | 1 | RBS_degradation | Kierzek_LacZ
Accession No. : 29 | LacZ
Pathway No. : 141 | 0.3
(s^-1) | 0
(s^-1) | - | - | Substrate
RBS
Product
nucleotides
| | | Equation 8 from Kierzek et al, set equal to transcription initiaton frequency. This is the decay rate of unprotected RBS. | | 2 | mRNA_
degradation | Kierzek_LacZ
Accession No. : 29 | LacZ
Pathway No. : 141 | 0.3
(s^-1) | 0
(s^-1) | - | - | Substrate
ElRNAP
Product
nucleotides
| | | Also equation 8 from Kierzek et al. Since RBS is assumed to be the rate-limiting part of the protein synthesis, we don't really need to worry about the fate of the ElRNAP. For balance we degrade it at the same rate as the RBS. |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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