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 : nadphx__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (84 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 51
  Gene deletion: b3553 b3399 b1241 b0351 b4069 b2744 b3708 b2297 b2458 b2779 b3617 b0160 b3844 b1238 b1004 b3713 b1109 b0046 b3236 b1982 b2797 b3117 b1814 b4471 b1033 b4374 b0675 b2361 b0261 b1602 b0153 b2913 b4381 b2406 b1727 b0114 b0584 b0509 b3125 b2366 b2492 b0904 b1533 b3825 b1380 b0494 b1771 b4141 b1798 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.366944 (mmol/gDw/h)
  Minimum Production Rate : 0.204905 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.984621
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.463619
  EX_pi_e : 0.968670
  EX_so4_e : 0.092404
  EX_k_e : 0.071625
  EX_fe2_e : 0.005893
  EX_mg2_e : 0.003183
  EX_ca2_e : 0.001910
  EX_cl_e : 0.001910
  EX_cu2_e : 0.000260
  EX_mn2_e : 0.000254
  EX_zn2_e : 0.000125
  EX_ni2_e : 0.000119

Product: (mmol/gDw/h)
  EX_h2o_e : 51.487378
  EX_co2_e : 34.402885
  EX_h_e : 6.676103
  EX_etoh_e : 0.836631
  EX_his__L_e : 0.688227
  EX_ac_e : 0.213630
  Auxiliary production reaction : 0.204905
  EX_hxan_e : 0.000411
  DM_5drib_c : 0.000246
  DM_4crsol_c : 0.000082

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.

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Last updated: 21-Sep-2023
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