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 : thmnp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (47 of 87: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b2836 b3399 b4069 b2502 b2744 b3708 b3008 b3115 b1849 b2296 b2779 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b0261 b4381 b2406 b0114 b2366 b0529 b2492 b0904 b1533 b3927 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.642109 (mmol/gDw/h)
  Minimum Production Rate : 0.382714 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.844630
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.848289
  EX_pi_e : 0.619382
  EX_so4_e : 0.161696
  EX_k_e : 0.125335
  EX_mg2_e : 0.005570
  EX_fe2_e : 0.005299
  EX_fe3_e : 0.005014
  EX_ca2_e : 0.003342
  EX_cl_e : 0.003342
  EX_cu2_e : 0.000455
  EX_mn2_e : 0.000444
  EX_zn2_e : 0.000219
  EX_ni2_e : 0.000207
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 49.849108
  EX_co2_e : 29.450873
  EX_h_e : 8.192361
  Auxiliary production reaction : 0.382714
  EX_ac_e : 0.373827
  DM_5drib_c : 0.000431
  DM_4crsol_c : 0.000143

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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