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 : dmpp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (92 of 111: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b4467 b1478 b0469 b0474 b1241 b4069 b3115 b1849 b2296 b2926 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b1638 b2799 b3945 b1602 b2913 b4381 b3915 b2492 b0904 b3029 b1380 b0221 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.465211 (mmol/gDw/h)
  Minimum Production Rate : 0.272746 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.003371
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.024244
  EX_pi_e : 0.994238
  EX_so4_e : 0.117150
  EX_k_e : 0.090806
  EX_fe3_e : 0.007472
  EX_mg2_e : 0.004036
  EX_ca2_e : 0.002421
  EX_cl_e : 0.002421
  EX_cu2_e : 0.000330
  EX_mn2_e : 0.000321
  EX_zn2_e : 0.000159
  EX_ni2_e : 0.000150
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 50.855638
  EX_co2_e : 37.058070
  EX_h_e : 5.250977
  EX_fum_e : 0.485432
  Auxiliary production reaction : 0.272746
  EX_ac_e : 0.270840
  DM_5drib_c : 0.000105
  DM_4crsol_c : 0.000104

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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