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 : trp__L_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (17 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b3399 b2744 b3708 b3008 b0871 b2779 b2926 b0160 b0121 b1982 b2797 b3117 b1814 b4471 b4374 b0675 b2361 b2291 b0261 b0112 b0114 b0886 b2366 b2492 b0904 b0591 b2578 b1533 b3927 b3821 b0516 b4141 b1798   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.679555 (mmol/gDw/h)
  Minimum Production Rate : 0.233973 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 27.964070
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.810128
  EX_pi_e : 0.655503
  EX_so4_e : 0.171126
  EX_k_e : 0.132644
  EX_fe2_e : 0.010914
  EX_mg2_e : 0.005895
  EX_cl_e : 0.003537
  EX_ca2_e : 0.003537
  EX_cu2_e : 0.000482
  EX_mn2_e : 0.000470
  EX_zn2_e : 0.000232
  EX_ni2_e : 0.000219
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 49.351398
  EX_co2_e : 29.529112
  EX_h_e : 6.715014
  EX_trp__L_e : 0.233973
  EX_alltn_e : 0.000760
  DM_5drib_c : 0.000456
  DM_4crsol_c : 0.000152

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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