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 : hisp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (46 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b4467 b1478 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b2744 b3752 b0871 b3617 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1982 b0261 b0411 b1602 b2913 b4381 b0114 b0529 b2492 b0904 b1380 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.377058 (mmol/gDw/h)
  Minimum Production Rate : 1.225726 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.077930
  EX_o2_e : 284.054008
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.749375
  EX_pi_e : 1.589439
  EX_so4_e : 0.094951
  EX_k_e : 0.073599
  EX_mg2_e : 0.003271
  EX_cl_e : 0.001963
  EX_ca2_e : 0.001963
  EX_cu2_e : 0.000267
  EX_mn2_e : 0.000261
  EX_zn2_e : 0.000129
  EX_ni2_e : 0.000122

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993944
  EX_h2o_e : 552.630258
  EX_co2_e : 35.321864
  Auxiliary production reaction : 1.225726
  EX_acald_e : 0.923215
  DM_5drib_c : 0.000253
  DM_4crsol_c : 0.000084

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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