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 : adphep_DD_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (81 of 99: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b2836 b3399 b1241 b0351 b4069 b2744 b3708 b3614 b0910 b3115 b1849 b2296 b2781 b3617 b0160 b1779 b1759 b1982 b2797 b3117 b1814 b4471 b4374 b0675 b2361 b0261 b4381 b2406 b0112 b0114 b2366 b2492 b0904 b1533 b3918 b1912   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.485900 (mmol/gDw/h)
  Minimum Production Rate : 0.676628 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 25.288734
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.781365
  EX_pi_e : 1.821957
  EX_so4_e : 0.122359
  EX_k_e : 0.094844
  EX_fe2_e : 0.007804
  EX_mg2_e : 0.004215
  EX_ca2_e : 0.002529
  EX_cl_e : 0.002529
  EX_cu2_e : 0.000345
  EX_mn2_e : 0.000336
  EX_zn2_e : 0.000166
  EX_ni2_e : 0.000157
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 47.239351
  EX_co2_e : 24.558919
  EX_h_e : 8.453572
  EX_ac_e : 1.808499
  Auxiliary production reaction : 0.676628
  EX_thym_e : 0.075274
  DM_5drib_c : 0.000326
  DM_4crsol_c : 0.000108

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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