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 : gua_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (111 of 123: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b4467 b3399 b4069 b2744 b3115 b1849 b2296 b2779 b3844 b1004 b3713 b1109 b0046 b3236 b2883 b1638 b1982 b4139 b0675 b2361 b0261 b1602 b4381 b1727 b4064 b4464 b0114 b0529 b2492 b0904 b3029 b1380 b2660 b1771 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.467499 (mmol/gDw/h)
  Minimum Production Rate : 0.203515 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 38.860210
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.066529
  EX_pi_e : 0.450953
  EX_so4_e : 0.117726
  EX_k_e : 0.091253
  EX_mg2_e : 0.004056
  EX_fe2_e : 0.003858
  EX_fe3_e : 0.003650
  EX_ca2_e : 0.002433
  EX_cl_e : 0.002433
  EX_cu2_e : 0.000331
  EX_mn2_e : 0.000323
  EX_zn2_e : 0.000159
  EX_ni2_e : 0.000151
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 53.627027
  EX_co2_e : 39.248335
  EX_h_e : 5.588968
  EX_ac_e : 0.272172
  Auxiliary production reaction : 0.203515
  DM_5drib_c : 0.000314
  DM_4crsol_c : 0.000104

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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