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 : 5mthf_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (114 of 120: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 61
  Gene deletion: b3399 b3846 b0586 b2341 b1241 b0351 b4069 b2502 b2744 b1278 b3708 b1479 b3115 b1849 b2296 b2779 b3236 b3962 b1982 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b4374 b0675 b2361 b2291 b1014 b4014 b0261 b2976 b0822 b0507 b3709 b1907 b2913 b3161 b0112 b0452 b0511 b2975 b0114 b3603 b0306 b1539 b3605 b2492 b0904 b1533 b1380 b0325 b0508 b1473 b0516 b4266 b2842 b1985   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.248865 (mmol/gDw/h)
  Minimum Production Rate : 0.528860 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 32.666730
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.606690
  EX_so4_e : 0.278506
  EX_pi_e : 0.240056
  EX_k_e : 0.048577
  EX_fe2_e : 0.003997
  EX_mg2_e : 0.002159
  EX_ca2_e : 0.001295
  EX_cl_e : 0.001295
  EX_cu2_e : 0.000176
  EX_mn2_e : 0.000172
  EX_zn2_e : 0.000085
  EX_ni2_e : 0.000080

Product: (mmol/gDw/h)
  EX_h2o_e : 48.939882
  EX_co2_e : 32.414390
  EX_h_e : 8.365549
  EX_ac_e : 1.533695
  EX_dxylnt_e : 0.529027
  Auxiliary production reaction : 0.528860
  EX_met__L_e : 0.215837
  EX_xan_e : 0.000278
  DM_5drib_c : 0.000167
  DM_4crsol_c : 0.000055

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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