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 (18 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b2836 b4384 b2744 b3708 b3008 b0871 b0030 b2407 b0583 b0120 b1982 b2797 b3117 b1814 b4471 b4374 b2361 b2291 b0261 b0411 b0507 b0114 b0886 b2366 b2492 b0904 b2578 b1533 b3927 b4141 b1798 b3662 b0221   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.756820 (mmol/gDw/h)
  Minimum Production Rate : 0.185100 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 24.324665
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.691378
  EX_pi_e : 0.730033
  EX_so4_e : 0.190583
  EX_k_e : 0.147726
  EX_fe2_e : 0.012155
  EX_mg2_e : 0.006565
  EX_cl_e : 0.003939
  EX_ca2_e : 0.003939
  EX_cu2_e : 0.000537
  EX_mn2_e : 0.000523
  EX_zn2_e : 0.000258
  EX_ni2_e : 0.000244
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 48.124419
  EX_co2_e : 26.067341
  EX_h_e : 7.476813
  EX_trp__L_e : 0.257414
  DM_oxam_c : 0.002955
  DM_5drib_c : 0.002616
  DM_4crsol_c : 0.002277
  EX_glyclt_e : 0.002108

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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