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 : dudp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (60 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b4467 b1478 b1241 b4069 b4384 b3752 b3115 b1849 b2296 b1004 b3713 b1109 b0046 b3236 b1779 b0207 b3012 b1982 b0261 b2799 b1602 b2913 b4381 b2406 b3915 b4064 b4464 b0529 b2492 b0904 b1781 b3001 b1380 b0325 b1771 b3662 b0606 b0221 b2285 b1009 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.368605 (mmol/gDw/h)
  Minimum Production Rate : 1.157645 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.585566
  EX_o2_e : 283.419097
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.298256
  EX_pi_e : 2.670848
  EX_so4_e : 0.092822
  EX_k_e : 0.071949
  EX_mg2_e : 0.003198
  EX_cl_e : 0.001919
  EX_ca2_e : 0.001919
  EX_cu2_e : 0.000261
  EX_mn2_e : 0.000255
  EX_zn2_e : 0.000126
  EX_ni2_e : 0.000119

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994080
  EX_h2o_e : 551.721099
  EX_co2_e : 32.724935
  Auxiliary production reaction : 1.157645
  EX_glyclt_e : 0.647319
  EX_ac_e : 0.214597
  EX_ade_e : 0.000412
  DM_5drib_c : 0.000247
  DM_4crsol_c : 0.000082

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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