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 : nadph_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (59 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b4467 b1478 b4382 b1241 b4069 b4384 b3752 b2297 b2458 b2779 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1638 b0937 b1982 b4139 b1623 b4015 b0261 b0411 b2799 b3945 b1602 b2913 b0529 b2492 b0904 b2954 b3029 b1380 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.443841 (mmol/gDw/h)
  Minimum Production Rate : 0.186276 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.870318
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.097384
  EX_pi_e : 0.986961
  EX_so4_e : 0.111768
  EX_k_e : 0.086635
  EX_mg2_e : 0.003850
  EX_fe2_e : 0.003663
  EX_fe3_e : 0.003466
  EX_cl_e : 0.002310
  EX_ca2_e : 0.002310
  EX_cu2_e : 0.000315
  EX_mn2_e : 0.000307
  EX_zn2_e : 0.000151
  EX_ni2_e : 0.000143
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 52.983455
  EX_co2_e : 37.352759
  EX_h_e : 5.271438
  EX_ac_e : 0.258398
  Auxiliary production reaction : 0.186276
  DM_5drib_c : 0.000298
  DM_4crsol_c : 0.000099

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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