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Molecule Parameter List for Tar

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

Tar 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	5	0

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.

Tar acting as a Molecule in  Chemotaxis Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
Tar	Chemotaxis Accession No. : 57	Chemotaxis Pathway No. : 228	1.37	1.41	No
Tar = 1.37e-06 M = 1.37 uM As per Signal 2 in 1SIG_B.BCT provided by Matthew Levin Tar = 4250 molecules per cell As per Enzyme entry 0 in 1ENZ.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

Tar 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	Chemotaxis Accession No. : 57	Chemotaxis Pathway No. : 228	0.1 (uM^-1 s^-1)	1 (s^-1)	Kd(bf) = 10.0003(uM)	-	Substrate CheW Tar Product TW
	Tar and CheW complex formation Kf = 1 * 10e5 /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
2	Binding	Chemotaxis Accession No. : 57	Chemotaxis Pathway No. : 228	0.001 (uM^-1 s^-1)	1 (s^-1)	Kd(bf) = 1000.028(uM)	-	Substrate Ni Tar Product Tn
	Binding of Tar and Ni Kf = 1 * 10e+03 /sec/M = 0.001 /sec/uM Kb = 1 /sec Bray et al 1993, Mol.Biol.Cell 4: 469-482 Table 3 pp.476 Reaction Scheme 2
3	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
4	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
5	Binding[9]	Chemotaxis Accession No. : 57	Chemotaxis Pathway No. : 228	4 (uM^-1 s^-1)	10 (s^-1)	Kd(bf) = 2.5(uM)	-	Substrate Tar WA Product TWA
	Binding of Tar and CheW-CheA complex Kd = 2 uM and therefore Kf also suggested as 0.5 /sec/uM 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.