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 : 25drapp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (45 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b3553 b3399 b1241 b0351 b4069 b2502 b2744 b3115 b1849 b2296 b2779 b2926 b3617 b0907 b1982 b1033 b4374 b0675 b2361 b2291 b0261 b0112 b2789 b3127 b0114 b0529 b2492 b0904   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.399317 (mmol/gDw/h)
  Minimum Production Rate : 1.530562 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 27.326423
  EX_nh4_e : 11.965853
  EX_glc__D_e : 10.000000
  EX_pi_e : 1.915746
  EX_so4_e : 0.100556
  EX_k_e : 0.077944
  EX_fe2_e : 0.006413
  EX_mg2_e : 0.003464
  EX_cl_e : 0.002078
  EX_ca2_e : 0.002078
  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 : 50.202884
  EX_co2_e : 24.351498
  EX_h_e : 14.063549
  EX_ac_e : 2.740578
  Auxiliary production reaction : 1.530562
  DM_oxam_c : 0.000447
  DM_5drib_c : 0.000268
  EX_glyclt_e : 0.000178
  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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