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 : 2omph_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (45 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b1241 b0351 b4069 b2930 b4232 b3697 b3925 b0512 b3115 b1849 b2296 b3617 b1612 b1611 b4122 b1779 b2690 b3945 b4381 b0114 b0529 b2492 b0904 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.334979 (mmol/gDw/h)
  Minimum Production Rate : 0.160280 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.445062
  EX_glc__D_e : 10.000000
  EX_nh4_e : 3.622975
  EX_pi_e : 0.323123
  EX_so4_e : 0.084354
  EX_k_e : 0.065386
  EX_fe2_e : 0.005380
  EX_mg2_e : 0.002906
  EX_cl_e : 0.001744
  EX_ca2_e : 0.001744
  EX_cu2_e : 0.000238
  EX_mn2_e : 0.000231
  EX_zn2_e : 0.000114
  EX_ni2_e : 0.000108

Product: (mmol/gDw/h)
  EX_h2o_e : 43.849475
  EX_co2_e : 32.530131
  EX_h_e : 5.773140
  EX_ac_e : 1.988747
  EX_fum_e : 0.350621
  DM_mththf_c : 0.160430
  Auxiliary production reaction : 0.160280
  EX_alltn_e : 0.001308
  DM_5drib_c : 0.000075
  DM_4crsol_c : 0.000075

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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