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 : adphep_LD_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (40 of 49: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b4467 b4069 b4384 b3752 b3115 b1849 b2296 b2407 b1004 b3713 b1109 b0046 b3236 b1779 b1982 b0261 b2799 b3945 b1602 b2913 b4381 b2406 b3915 b1727 b0114 b0529 b2492 b0904 b3927 b1380 b3662 b0606 b2285 b1010 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.460258 (mmol/gDw/h)
  Minimum Production Rate : 0.215401 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.435852
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.050333
  EX_pi_e : 0.874771
  EX_so4_e : 0.115902
  EX_k_e : 0.089839
  EX_fe3_e : 0.007392
  EX_mg2_e : 0.003993
  EX_ca2_e : 0.002396
  EX_cl_e : 0.002396
  EX_cu2_e : 0.000326
  EX_mn2_e : 0.000318
  EX_zn2_e : 0.000157
  EX_ni2_e : 0.000149
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.051437
  EX_co2_e : 36.889199
  EX_h_e : 5.153165
  EX_ac_e : 0.267956
  Auxiliary production reaction : 0.215401
  EX_etoh_e : 0.008986
  EX_ade_e : 0.000515
  DM_5drib_c : 0.000309
  DM_4crsol_c : 0.000103

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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