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 : glx_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (46 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b1241 b0351 b4069 b4384 b2744 b3752 b3115 b1849 b2296 b3617 b2883 b1982 b1623 b0261 b0411 b0507 b4381 b0112 b0114 b0529 b2492 b0904 b2954 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.516091 (mmol/gDw/h)
  Minimum Production Rate : 0.507821 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 20.097933
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.007159
  EX_pi_e : 0.497825
  EX_so4_e : 0.129962
  EX_k_e : 0.100737
  EX_fe2_e : 0.008289
  EX_mg2_e : 0.004477
  EX_ca2_e : 0.002686
  EX_cl_e : 0.002686
  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 : 42.915047
  EX_co2_e : 20.463366
  EX_h_e : 8.492150
  EX_thymd_e : 0.962509
  DM_oxam_c : 0.508399
  DM_5drib_c : 0.508167
  DM_4crsol_c : 0.507936
  Auxiliary production reaction : 0.507821
  EX_ac_e : 0.300461

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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