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 : trp__L_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (51 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b2836 b3553 b3399 b4382 b0586 b4069 b2744 b1278 b3708 b3008 b3115 b1849 b2296 b2779 b2925 b2097 b0160 b2690 b1982 b2688 b2797 b3117 b1814 b4471 b1033 b0675 b2361 b0261 b0822 b0507 b4381 b2406 b0112 b1727 b0114 b1539 b2492 b0904 b2578 b1533 b3927   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.597786 (mmol/gDw/h)
  Minimum Production Rate : 0.354200 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 26.413463
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.180751
  EX_pi_e : 0.576628
  EX_so4_e : 0.150535
  EX_k_e : 0.116684
  EX_fe2_e : 0.009601
  EX_mg2_e : 0.005186
  EX_ca2_e : 0.003111
  EX_cl_e : 0.003111
  EX_cu2_e : 0.000424
  EX_mn2_e : 0.000413
  EX_zn2_e : 0.000204
  EX_ni2_e : 0.000193
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 46.494021
  EX_co2_e : 27.841919
  EX_h_e : 8.079494
  EX_ac_e : 1.845775
  EX_trp__L_e : 0.354200
  DM_oxam_c : 0.016311
  DM_5drib_c : 0.000401
  DM_4crsol_c : 0.000133

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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