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 : glyclt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (56 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b4467 b3399 b4069 b2744 b3115 b1849 b2296 b2926 b3844 b1004 b3713 b1109 b0046 b3236 b1982 b0675 b2361 b0261 b3945 b1602 b0507 b2913 b4381 b1727 b2975 b0114 b3603 b0529 b2492 b0904 b1380 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.456001 (mmol/gDw/h)
  Minimum Production Rate : 0.198713 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 38.844439
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.985960
  EX_fe3_e : 2.424399
  EX_pi_e : 0.439861
  EX_so4_e : 0.114830
  EX_k_e : 0.089008
  EX_mg2_e : 0.003956
  EX_ca2_e : 0.002373
  EX_cl_e : 0.002373
  EX_cu2_e : 0.000323
  EX_mn2_e : 0.000315
  EX_zn2_e : 0.000155
  EX_ni2_e : 0.000147
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 51.245600
  EX_co2_e : 40.293701
  EX_h_e : 7.139697
  EX_fe2_e : 2.417075
  EX_ac_e : 0.265477
  Auxiliary production reaction : 0.198713
  EX_ade_e : 0.012239
  DM_5drib_c : 0.000103
  DM_4crsol_c : 0.000102

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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