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Reaction List for pathway Ras (Pathway Number 76) in Accession Synaptic_Network (Accession Number 16) |
Entries are grouped according to Pathway Number and they are alternately color coded using  and  color.
Further ordering can be done to the table header.   indicates that ordering is done according to ascending or descending order.Keq is calculated only for first order reactions. Kd is calculated only for second order reactions. [nA+nB <->nC or nA<->nC+nD, where n is number and A,B,C,D are molecules] |
| Reaction Name | Pathway Name / Pathway No. | Kf | Kb | Kd | tau | Reagents | |
| 1 | bg-act-GEF | Ras Pathway No. 76 | 6 (uM^-1 s^-1) | 1 (s^-1) | Kd(bf) = 0.1667(uM) | - | Substrate: BetaGamma inact-GEF Products: GEF-Gprot-bg | SoS/GEF is present at 50 nM ie 3e4/cell. BetaGamma maxes out at 9e4. Assume we have 1/3 of the GEF active when the BetaGamma is 1.5e4. so 1e4 * kb = 2e4 * 1.5e4 * kf, so kf/kb = 3e-5. The rate of this equil should be reasonably fast, say 1/sec |
| 2 | dephosph-GEF | Ras Pathway No. 76 | 1 (s^-1) | 0 (s^-1) | - | - | Substrate: GEF* Products: inact-GEF | This rate is based on the known ratio of GDP-Ras to GTP-Ras. Basal: Ras.GTP = 7% Stimulated 15% Time course is within 10 min, probably much faster as not all early data points are there. See Gibbs et al JBC 265(33):20437-20422 |
| 3 | Pase | Ras Pathway No. 76 | 0.0001 (s^-1) | 0 (s^-1) | - | - | Substrate: GTP-Ras Products: GDP-Ras | This is extremely slow (kf = 1e-4), but it is significant as so little GAP actually gets complexed with it that the total GTP turnover rises only by 2-3 X (see Gibbs et al, JBC 265(33) 20437-20422) and Eccleston et al JBC 268(36) 27012-27019 There is no back reaction as we assume this to be a regular irreversible Michaelis-Menten zeroth order hydrolysis. |
| 4 | dephosph-GAP | Ras Pathway No. 76 | 0.1 (s^-1) | 0 (s^-1) | - | - | Substrate: GAP* Products: GAP | Assume a reasonably good rate for dephosphorylating it, 0.1/sec. This fits well with resting levels of active kinase and the degree of activation as well as time-course of turnoff of Ras activation, but data is quite indirect. |
| 5 | CaM-bind-GEF | Ras Pathway No. 76 | 60 (uM^-1 s^-1) | 1 (s^-1) | Kd(bf) = 0.0167(uM) | - | Substrate: inact-GEF CaM-Ca4 Products: CaM-GEF | We have no numbers for this. It is probably between the two extremes represented by the CaMKII phosph states, and I have used guesses based on this. kf=1e-4 kb=1 The reaction is based on Farnsworth et al Nature 376 524-527 1995 |
| 6 | EF* | Ras Pathway No. 76 | 1 (s^-1) | 0 (s^-1) | - | - | Substrate: inact-GEF* Products: inact-GEF |