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 : 2h3oppan_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (55 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3399 b2744 b3708 b3008 b0871 b2925 b2097 b0517 b2690 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b0822 b4381 b1727 b0114 b2366 b2492 b0904 b1533 b3821 b1912   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.797277 (mmol/gDw/h)
  Minimum Production Rate : 0.103250 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.558246
  EX_o2_e : 275.364337
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.610523
  EX_pi_e : 0.769058
  EX_so4_e : 0.200770
  EX_k_e : 0.155623
  EX_mg2_e : 0.006916
  EX_ca2_e : 0.004150
  EX_cl_e : 0.004150
  EX_cu2_e : 0.000565
  EX_mn2_e : 0.000551
  EX_zn2_e : 0.000272
  EX_ni2_e : 0.000258
  EX_cobalt2_e : 0.000020

Product: (mmol/gDw/h)
  EX_fe3_e : 999.987195
  EX_h2o_e : 548.116421
  EX_co2_e : 26.965694
  Auxiliary production reaction : 0.103250
  DM_5drib_c : 0.000179
  DM_4crsol_c : 0.000178

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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