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 : acetol_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (22 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b4467 b1478 b1241 b4069 b3115 b1849 b2296 b2926 b3844 b1004 b3713 b1109 b0046 b3236 b3945 b1602 b3915 b2975 b3603 b2492 b0904 b1380 b2660 b1511 b0606 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.502111 (mmol/gDw/h)
  Minimum Production Rate : 0.441158 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.187313
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.422752
  EX_pi_e : 0.484339
  EX_so4_e : 0.126441
  EX_k_e : 0.098008
  EX_fe3_e : 0.008064
  EX_mg2_e : 0.004356
  EX_ca2_e : 0.002613
  EX_cl_e : 0.002613
  EX_cu2_e : 0.000356
  EX_mn2_e : 0.000347
  EX_zn2_e : 0.000171
  EX_ni2_e : 0.000162
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 50.736743
  EX_co2_e : 37.481423
  EX_h_e : 4.913979
  Auxiliary production reaction : 0.441158
  EX_ac_e : 0.292322
  EX_mththf_e : 0.000225
  DM_5drib_c : 0.000113
  DM_4crsol_c : 0.000112

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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