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__S_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (51 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b3553 b4069 b4384 b2744 b3752 b3115 b1849 b2296 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b1982 b1033 b0261 b0411 b2799 b3945 b1602 b4381 b3915 b1727 b0114 b0529 b2492 b0904 b3927 b1380 b2660 b3662 b0606 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.386584 (mmol/gDw/h)
  Minimum Production Rate : 0.349625 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.844785
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.624610
  EX_pi_e : 1.421777
  EX_so4_e : 0.097349
  EX_k_e : 0.075458
  EX_fe3_e : 0.006209
  EX_mg2_e : 0.003354
  EX_ca2_e : 0.002012
  EX_cl_e : 0.002012
  EX_cu2_e : 0.000274
  EX_mn2_e : 0.000267
  EX_zn2_e : 0.000132
  EX_ni2_e : 0.000125

Product: (mmol/gDw/h)
  EX_h2o_e : 51.998588
  EX_co2_e : 35.309916
  EX_h_e : 5.533646
  EX_etoh_e : 0.513660
  Auxiliary production reaction : 0.349625
  EX_ac_e : 0.225064
  EX_ade_e : 0.000433
  DM_5drib_c : 0.000259
  DM_4crsol_c : 0.000086

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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