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 : nadh_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (56 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b4467 b1054 b1478 b1241 b4069 b4384 b3752 b3115 b1849 b2296 b2407 b1004 b3713 b1109 b0046 b3236 b1779 b1982 b0261 b0411 b2799 b3945 b1602 b2913 b2223 b4381 b3915 b0529 b2492 b0904 b1380 b0606 b2285 b1010 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.466883 (mmol/gDw/h)
  Minimum Production Rate : 0.148706 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.685157
  EX_o2_e : 286.541227
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.085334
  EX_pi_e : 0.747771
  EX_so4_e : 0.117571
  EX_k_e : 0.091132
  EX_mg2_e : 0.004050
  EX_ca2_e : 0.002430
  EX_cl_e : 0.002430
  EX_cu2_e : 0.000331
  EX_mn2_e : 0.000323
  EX_zn2_e : 0.000159
  EX_ni2_e : 0.000151
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992501
  EX_h2o_e : 552.470649
  EX_co2_e : 37.166473
  EX_ac_e : 0.271813
  Auxiliary production reaction : 0.148706
  EX_hxan_e : 0.000522
  DM_5drib_c : 0.000313
  DM_4crsol_c : 0.000104

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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