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 : nad_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (50 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b4467 b4069 b4384 b2744 b3115 b1849 b2296 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b0937 b1982 b0261 b0411 b2799 b3945 b1602 b2913 b4381 b1727 b2975 b0114 b3603 b0529 b2492 b0904 b3927 b1380 b3662 b0606 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.389759 (mmol/gDw/h)
  Minimum Production Rate : 0.353123 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.799088
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.683403
  EX_pi_e : 1.082210
  EX_so4_e : 0.098149
  EX_k_e : 0.076078
  EX_fe2_e : 0.006260
  EX_mg2_e : 0.003381
  EX_ca2_e : 0.002029
  EX_cl_e : 0.002029
  EX_cu2_e : 0.000276
  EX_mn2_e : 0.000269
  EX_zn2_e : 0.000133
  EX_ni2_e : 0.000126

Product: (mmol/gDw/h)
  EX_h2o_e : 52.282863
  EX_co2_e : 35.090225
  EX_h_e : 5.222843
  EX_etoh_e : 0.519757
  Auxiliary production reaction : 0.353123
  EX_ac_e : 0.226912
  EX_ade_e : 0.000436
  DM_5drib_c : 0.000262
  DM_4crsol_c : 0.000087

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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