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 : mnl1p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (26 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b4467 b1478 b1241 b4069 b3115 b1849 b2296 b2926 b3844 b1004 b3713 b1109 b0046 b3236 b0207 b3012 b0261 b2799 b1602 b2913 b4381 b3915 b0529 b2492 b0904 b1781 b3001 b1380 b0325 b1771 b0606 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.429798 (mmol/gDw/h)
  Minimum Production Rate : 0.951800 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.255607
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.437395
  EX_pi_e : 1.366386
  EX_so4_e : 0.108232
  EX_k_e : 0.083894
  EX_fe3_e : 0.006903
  EX_mg2_e : 0.003729
  EX_ca2_e : 0.002237
  EX_cl_e : 0.002237
  EX_cu2_e : 0.000305
  EX_mn2_e : 0.000297
  EX_zn2_e : 0.000147
  EX_ni2_e : 0.000139
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 48.289450
  EX_co2_e : 35.153357
  EX_h_e : 5.001893
  Auxiliary production reaction : 0.951800
  EX_ac_e : 0.250223
  EX_hxan_e : 0.198541
  EX_ade_e : 0.000289
  DM_5drib_c : 0.000097
  DM_4crsol_c : 0.000096

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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