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 : pg160_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (72 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b0474 b2518 b2744 b1278 b4152 b2925 b2097 b2926 b2781 b3844 b1232 b1612 b1611 b4122 b1759 b3946 b0825 b4374 b4161 b0675 b4138 b4123 b0621 b4381 b2406 b0452 b2197 b2835 b3918 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.413838 (mmol/gDw/h)
  Minimum Production Rate : 0.187981 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.770872
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.056363
  EX_fe3_e : 0.611054
  EX_pi_e : 0.587171
  EX_so4_e : 0.104213
  EX_k_e : 0.080778
  EX_mg2_e : 0.003590
  EX_ca2_e : 0.002154
  EX_cl_e : 0.002154
  EX_cu2_e : 0.000293
  EX_mn2_e : 0.000286
  EX_zn2_e : 0.000141
  EX_ni2_e : 0.000134
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 45.868169
  EX_co2_e : 32.970501
  EX_h_e : 5.675625
  EX_fe2_e : 0.604408
  EX_succ_e : 0.431547
  EX_ura_e : 0.293473
  Auxiliary production reaction : 0.187981
  DM_5drib_c : 0.000093
  DM_4crsol_c : 0.000092

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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