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 : his__L_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (61 of 76: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b3399 b4382 b1241 b0351 b4069 b2744 b3708 b2297 b2458 b2883 b1779 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b0675 b2361 b0411 b4381 b2406 b0112 b0114 b1539 b2492 b0904 b1533 b0515 b1517 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.398987 (mmol/gDw/h)
  Minimum Production Rate : 1.173577 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.034124
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.872594
  EX_pi_e : 0.384866
  EX_so4_e : 0.100473
  EX_k_e : 0.077880
  EX_fe2_e : 0.006408
  EX_mg2_e : 0.003461
  EX_ca2_e : 0.002077
  EX_cl_e : 0.002077
  EX_cu2_e : 0.000283
  EX_mn2_e : 0.000276
  EX_zn2_e : 0.000136
  EX_ni2_e : 0.000129

Product: (mmol/gDw/h)
  EX_h2o_e : 52.332442
  EX_co2_e : 34.679870
  EX_h_e : 8.158791
  Auxiliary production reaction : 1.173577
  EX_ac_e : 0.929172
  EX_alltn_e : 0.010708
  DM_mththf_c : 0.000179
  DM_5drib_c : 0.000090
  DM_4crsol_c : 0.000089

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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