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 : glyc_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (50 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b3553 b0474 b1241 b0351 b4069 b3926 b3115 b1849 b2296 b2925 b2097 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b2690 b0477 b1033 b3945 b1602 b2492 b0904 b1380 b2660 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.446268 (mmol/gDw/h)
  Minimum Production Rate : 0.979558 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 32.075904
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.819652
  EX_pi_e : 0.430472
  EX_so4_e : 0.112379
  EX_k_e : 0.087108
  EX_fe2_e : 0.007168
  EX_mg2_e : 0.003871
  EX_ca2_e : 0.002323
  EX_cl_e : 0.002323
  EX_cu2_e : 0.000316
  EX_mn2_e : 0.000308
  EX_zn2_e : 0.000152
  EX_ni2_e : 0.000144
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 43.968994
  EX_co2_e : 34.614617
  EX_h_e : 4.360295
  EX_glyc_e : 1.687894
  EX_etoh_e : 0.742422
  EX_ac_e : 0.259811
  DM_5drib_c : 0.000100
  DM_4crsol_c : 0.000100

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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