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 (27 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b2836 b3399 b4069 b2502 b2744 b3708 b3008 b2297 b2458 b1982 b2688 b2797 b3117 b1814 b4471 b4374 b0675 b2361 b2291 b0261 b0114 b1539 b2492 b0904 b3035 b2578 b1533 b3927 b0516 b4141 b1798 b0221   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.712712 (mmol/gDw/h)
  Minimum Production Rate : 0.181142 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 23.592837
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.968412
  EX_pi_e : 1.230912
  EX_so4_e : 0.360617
  EX_k_e : 0.139116
  EX_fe2_e : 0.011447
  EX_mg2_e : 0.006183
  EX_ca2_e : 0.003710
  EX_cl_e : 0.003710
  EX_cu2_e : 0.000505
  EX_mn2_e : 0.000492
  EX_zn2_e : 0.000243
  EX_ni2_e : 0.000230
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 47.651289
  EX_co2_e : 25.202116
  EX_h_e : 7.872513
  EX_ac_e : 0.777215
  Auxiliary production reaction : 0.181142
  EX_alltn_e : 0.000798
  DM_5drib_c : 0.000478
  DM_4crsol_c : 0.000159

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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