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 : frdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (76 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b3399 b4382 b4384 b2744 b3708 b2930 b4232 b3697 b3925 b0871 b3115 b1849 b2296 b2407 b3236 b1779 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b0452 b2868 b0114 b2366 b0529 b2492 b0904 b1533 b1380   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.583543 (mmol/gDw/h)
  Minimum Production Rate : 0.134334 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 27.170371
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.304176
  EX_pi_e : 0.831557
  EX_so4_e : 0.146948
  EX_k_e : 0.113903
  EX_fe2_e : 0.009372
  EX_mg2_e : 0.005062
  EX_ca2_e : 0.003037
  EX_cl_e : 0.003037
  EX_cu2_e : 0.000414
  EX_mn2_e : 0.000403
  EX_zn2_e : 0.000199
  EX_ni2_e : 0.000188
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 46.133819
  EX_co2_e : 28.258568
  EX_h_e : 7.153689
  EX_pyr_e : 1.924235
  Auxiliary production reaction : 0.134334
  EX_ade_e : 0.000393
  DM_5drib_c : 0.000131
  DM_4crsol_c : 0.000130

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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