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 : forcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (62 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b3399 b4069 b4384 b2744 b3708 b3008 b2930 b4232 b3697 b3925 b3115 b1849 b2296 b2407 b2690 b1982 b2797 b3117 b1814 b4471 b4374 b0675 b2361 b2291 b0261 b3945 b0114 b1539 b2492 b0904 b3035 b2578 b1533 b3927 b3821 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.516592 (mmol/gDw/h)
  Minimum Production Rate : 0.130433 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.661718
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.494199
  EX_pi_e : 0.889607
  EX_so4_e : 0.260521
  EX_k_e : 0.100835
  EX_fe2_e : 0.008297
  EX_mg2_e : 0.004481
  EX_ca2_e : 0.002689
  EX_cl_e : 0.002689
  EX_cu2_e : 0.000366
  EX_mn2_e : 0.000357
  EX_zn2_e : 0.000176
  EX_ni2_e : 0.000167
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 46.088101
  EX_co2_e : 29.829321
  EX_h_e : 8.179471
  EX_ac_e : 3.037484
  Auxiliary production reaction : 0.130433
  DM_oxam_c : 0.002017
  DM_5drib_c : 0.001785
  DM_4crsol_c : 0.001554

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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