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 : eig3p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (58 of 89: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b3399 b1241 b0351 b4069 b2744 b2297 b2458 b2926 b0160 b1851 b3236 b3962 b1982 b3616 b3589 b4267 b0675 b2361 b2291 b2799 b4381 b0112 b2868 b0114 b0509 b3125 b0529 b0306 b3605 b2492 b0904 b1380 b4266 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.386944 (mmol/gDw/h)
  Minimum Production Rate : 1.483654 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.998867
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.147573
  EX_pi_e : 1.856903
  EX_so4_e : 0.097440
  EX_k_e : 0.075529
  EX_fe2_e : 0.006215
  EX_mg2_e : 0.003357
  EX_ca2_e : 0.002014
  EX_cl_e : 0.002014
  EX_cu2_e : 0.000274
  EX_mn2_e : 0.000267
  EX_zn2_e : 0.000132
  EX_ni2_e : 0.000125

Product: (mmol/gDw/h)
  EX_h2o_e : 51.721133
  EX_co2_e : 34.082135
  EX_h_e : 7.089755
  Auxiliary production reaction : 1.483654
  EX_ac_e : 0.565748
  EX_ade_e : 0.000260
  DM_mththf_c : 0.000173
  DM_5drib_c : 0.000087
  DM_4crsol_c : 0.000086

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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