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 : dimp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (58 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b3399 b3942 b1732 b1241 b0351 b4069 b2744 b3115 b1849 b2296 b2779 b3617 b3236 b2883 b0517 b2210 b0261 b0505 b2913 b4381 b0511 b4064 b4464 b0114 b0529 b2492 b0904 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.384843 (mmol/gDw/h)
  Minimum Production Rate : 0.485095 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.159166
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.137966
  EX_pi_e : 0.856317
  EX_so4_e : 0.096911
  EX_k_e : 0.075119
  EX_fe2_e : 0.006181
  EX_mg2_e : 0.003339
  EX_ca2_e : 0.002003
  EX_cl_e : 0.002003
  EX_cu2_e : 0.000273
  EX_mn2_e : 0.000266
  EX_zn2_e : 0.000131
  EX_ni2_e : 0.000124

Product: (mmol/gDw/h)
  EX_h2o_e : 51.570893
  EX_co2_e : 35.979252
  EX_h_e : 7.178847
  EX_ac_e : 1.661062
  Auxiliary production reaction : 0.485095
  EX_xan_e : 0.010329
  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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