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 (43 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b1241 b0351 b4069 b4384 b3752 b3115 b1849 b2296 b2925 b2097 b3617 b2407 b2690 b1982 b0261 b3945 b4388 b4381 b0114 b0755 b3612 b0529 b2492 b0904 b1813   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.505503 (mmol/gDw/h)
  Minimum Production Rate : 0.025532 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 25.903627
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.798926
  EX_pi_e : 0.487612
  EX_so4_e : 0.127296
  EX_k_e : 0.098671
  EX_fe2_e : 0.008119
  EX_mg2_e : 0.004385
  EX_cl_e : 0.002631
  EX_ca2_e : 0.002631
  EX_cu2_e : 0.000358
  EX_mn2_e : 0.000349
  EX_zn2_e : 0.000172
  EX_ni2_e : 0.000163
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 46.857896
  EX_co2_e : 24.892315
  EX_h_e : 10.421488
  EX_ac_e : 2.411091
  EX_xtsn_e : 0.828359
  DM_oxam_c : 0.026098
  Auxiliary production reaction : 0.025532
  DM_5drib_c : 0.000339
  DM_4crsol_c : 0.000113

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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