MetNetComp Database [1] / Minimal gene deletions

Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : iML1515 [2].
Target metabolite : 12ppd__R_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (51 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3553 b1478 b3942 b1732 b1241 b0351 b3844 b1004 b3713 b1109 b0046 b1779 b2463 b2210 b1033 b3551 b1602 b4219 b1832 b1778 b0529 b1380 b1710 b2480 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.597238 (mmol/gDw/h)
  Minimum Production Rate : 0.105026 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 33.791509
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.450118
  EX_pi_e : 0.576099
  EX_so4_e : 0.150396
  EX_k_e : 0.116577
  EX_fe2_e : 0.009592
  EX_mg2_e : 0.005181
  EX_ca2_e : 0.003109
  EX_cl_e : 0.003109
  EX_cu2_e : 0.000423
  EX_mn2_e : 0.000413
  EX_zn2_e : 0.000204
  EX_ni2_e : 0.000193
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 50.837426
  EX_co2_e : 35.171052
  EX_h_e : 5.487660
  EX_12ppd__R_e : 0.105026
  DM_5drib_c : 0.000134
  DM_4crsol_c : 0.000133

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].
  3. Select "Data > Load reaction data" and apply the downloaded file.

References
[1] Tamura, T. MetNetComp: Database for minimal and maximal gene deletion strategies for growth-coupled production of genome-scale metabolic networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press.
[2] Norsigian, C. J., Pusarla, N., McConn, J. L., Yurkovich, J. T., Dräger, A., Palsson, B. O., & King, Z. (2020). BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. Nucleic acids research, 48(D1), D402-D406.
[3] King, Z. A., Dräger, A., Ebrahim, A., Sonnenschein, N., Lewis, N. E., & Palsson, B. O. (2015). Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways. PLoS computational biology, 11(8), e1004321.

Last updated: 21-Sep-2023
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