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 (57 of 76: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b1241 b0351 b4069 b4384 b3752 b0512 b3115 b1849 b2296 b2779 b2407 b3236 b3962 b1982 b3616 b3589 b4267 b2913 b4381 b2406 b0112 b0114 b0529 b2492 b0904 b0325 b0508 b4266 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.398849 (mmol/gDw/h)
  Minimum Production Rate : 1.526723 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 32.713617
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.896508
  EX_pi_e : 0.384732
  EX_so4_e : 0.100438
  EX_k_e : 0.077852
  EX_fe2_e : 0.006406
  EX_mg2_e : 0.003460
  EX_ca2_e : 0.002076
  EX_cl_e : 0.002076
  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 : 51.744839
  EX_co2_e : 32.034663
  EX_h_e : 9.462086
  Auxiliary production reaction : 1.529301
  EX_ac_e : 1.208328
  EX_alltn_e : 0.000268
  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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