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 : ametam_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (21 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b3399 b4069 b2502 b2744 b3708 b3008 b3115 b1849 b2296 b1982 b2797 b3117 b1814 b4471 b3449 b0675 b2361 b0261 b4381 b2406 b0114 b1539 b2492 b0904 b1533 b3927 b0494   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.741854 (mmol/gDw/h)
  Minimum Production Rate : 0.176902 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.209029
  EX_o2_e : 274.091233
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.073374
  EX_pi_e : 0.715597
  EX_so4_e : 0.363715
  EX_k_e : 0.144805
  EX_mg2_e : 0.006436
  EX_cl_e : 0.003861
  EX_ca2_e : 0.003861
  EX_cu2_e : 0.000526
  EX_mn2_e : 0.000513
  EX_zn2_e : 0.000253
  EX_ni2_e : 0.000240
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_fe3_e : 999.988085
  EX_h2o_e : 547.738498
  EX_co2_e : 25.854411
  EX_ac_e : 0.608799
  Auxiliary production reaction : 0.176902
  DM_5drib_c : 0.000498
  DM_4crsol_c : 0.000165

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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