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Molecule Parameter List for TA | 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 | | Chemotaxis | 57 | Pathway |
Chemotaxis | Reactions feeding into TnWa, TaWA and TWA are scaled by 10 Binding reaction of Tar with Aspartate has been scaled by 10 Phosphotransfer from CheAp to CheY has Kb = 0.263/sec/uM instead of 0.2/sec/uM used in BCT1.1.
All remaining parameters are from the .BCT files for BCT1.1 provided by Matthew Levin from the Computational Biology Group in the Department of Zoology at the University of Cambridge.
The June 2003 version of the BCT program is BCT4.3 and is available at the computational biology site of the Zoology department at Cambridge University.
Citation: Bray et al. Mol.Biol.Cell (1993) 4(5): 469-482. |
TA acting as a Molecule in Chemotaxis Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | Ta | Chemotaxis
Accession No. : 57 | Chemotaxis
Pathway No. : 228 | 0 | 1.41 | No | | Aspartate bound Tar Ta = 0.0 M As per Signal 3 in 1SIG_B.BCT provided by Matthew Levin Cell volume = 1.41e-15 L Table 1 pp.474 Bray et al 1993, Mol.Biol.Cell 4: 469-482 | | TA | Chemotaxis
Accession No. : 57 | Chemotaxis
Pathway No. : 228 | 1.55 | 1.41 | No | | Tar-CheA complex TA = 1.55e-06 M = 1.55 uM As per Signal entry 9 in 1SIG_B.BCT provided by Matthew Levin Cell volume = 1.41e-15 L Table 1 pp.474 Bray et al 1993, Mol.Biol.Cell 4: 469-482 |
TA acting as a Substrate in a reaction in Chemotaxis 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 | Complexing[2] | Chemotaxis
Accession No. : 57 | Chemotaxis
Pathway No. : 228 | 0.1
(uM^-1 s^-1) | 1
(s^-1) | Kd(bf) = 10.0003(uM) | - | Substrate
CheW
TA
Product
TaW
| | | Complex formation of aspartate bound Tar and CheW Kf = 1 * 10e+05 /sec/M = 0.1 /sec/uM Kb = 1 /sec Bray et al 1993, Mol.Biol.Cell 4: 469-482; Table 3 pp.476 Reaction Scheme 3 Footnote states that ligands do not have any effect on the formation of complexes so same rates are used for Aspartate or Ni associated Tar complexes. | | 2 | Complexing[7] | Chemotaxis
Accession No. : 57 | Chemotaxis
Pathway No. : 228 | 4
(uM^-1 s^-1) | 10
(s^-1) | Kd(bf) = 2.5(uM) | - | Substrate
CheW
TA
Product
TWA
| | | TA and CheW complex formation Kf = 4*10e+05 /sec/M = 0.4 /sec/uM Kb = 1 /sec Table 3 pp.476 Reaction Scheme 7 Bray et al 1993, Mol.Biol.Cell 4: 469-482 Rates used here are 10 times that stated, to allow for faster time courses seen during the drop of bias on removal of stimulus. | | 3 | Binding[7] | Chemotaxis
Accession No. : 57 | Chemotaxis
Pathway No. : 228 | 0.05
(uM^-1 s^-1) | 1
(s^-1) | Kd(bf) = 19.9999(uM) | - | Substrate
CheA
TA
Product
TaA
| | | Binding of Tar-Aspartate and CheA Kf = 0.05 /sec/uM as per Reaction 3 in 1REACT.BCT Kf = 1e+04 /sec/M = 0.01 /sec/uM Kb = 1 /sec Bray et al 1993, Mol.Biol.Cell 4: 469-482 Table 3 pp.476 Reaction Scheme 4 Footnote states that ligands do not have any effect on the formation of complexes so same rates are used for Aspartate or Ni associated Tar complexes. | | 4 | Binding[11] | Chemotaxis
Accession No. : 57 | Chemotaxis
Pathway No. : 228 | 4
(uM^-1 s^-1) | 10
(s^-1) | Kd(bf) = 2.5(uM) | - | Substrate
TA
WA
Product
TaWA
| | | Binding of Ta and CheW-CheA complex Kf = 4e+05 /sec/M = 0.4 /sec/uM Kb = 1 /sec Bray et al 1993, Mol.Biol.Cell 4: 469-482 Table 3 pp.476 Reaction Scheme 8 Rates used here are 10 times that stated, to allow for faster time courses seen during the drop of bias on removal of stimulus. Footnote states that ligands do not have any effect on the the formation of complexes so same rates are used for Aspartate or Ni associated Tar complexes. |
TA acting as a Product in a reaction in Chemotaxis 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 | Binding[1] | Chemotaxis
Accession No. : 57 | Chemotaxis
Pathway No. : 228 | 12.8
(uM^-1 s^-1) | 10
(s^-1) | Kd(bf) = 0.7813(uM) | - | Substrate
Aspartate
Tar
Product
TA
| | | Binding of Aspartate with Tar Kd = 0.78 uM Dunten and Koshland, 1991 Kf = 1.28e+06 /sec/M = 1.28 /sec/uM here scaled by 5 As per Reaction 0 in 1REACT.BCT provided by Matthew Levin Kf = 1.0e+06 /sec/M = 1 /sec/uM; Kb = 1 /sec Bray et al 1993, Mol.Biol.Cell 4: 469-482 Table 3 pp.476 Reaction Scheme 1 | | 2 | Binding[3] | Chemotaxis
Accession No. : 57 | Chemotaxis
Pathway No. : 228 | 0.05
(uM^-1 s^-1) | 1
(s^-1) | Kd(bf) = 19.9999(uM) | - | Substrate
CheA
Tar
Product
TA
| | | Binding of T and CheA Kf = 0.05 /sec/uM as per Reaction 3 in 1REACT.BCT Kf = 1*10e+04 /sec/M = 0.01 /sec/uM Kb = 1 /sec Bray et al 1993, Mol.Biol.Cell 4: 469-482 Table 3 pp.476 Reaction Scheme 4 |
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