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 (48 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b2836 b3553 b1241 b0351 b4069 b4384 b2744 b3708 b2297 b2458 b0030 b2407 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b1033 b4374 b2361 b2291 b0261 b0411 b0112 b0114 b0509 b3125 b2366 b2492 b0904 b1533 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.508844 (mmol/gDw/h)
  Minimum Production Rate : 0.507538 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 20.202451
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.048807
  EX_pi_e : 2.013448
  EX_so4_e : 0.635675
  EX_k_e : 0.099323
  EX_fe2_e : 0.008173
  EX_mg2_e : 0.004414
  EX_ca2_e : 0.002649
  EX_cl_e : 0.002649
  EX_cu2_e : 0.000361
  EX_mn2_e : 0.000352
  EX_zn2_e : 0.000174
  EX_ni2_e : 0.000164
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 45.130253
  EX_co2_e : 21.541193
  EX_h_e : 9.401710
  EX_ac_e : 3.202155
  Auxiliary production reaction : 0.507538
  DM_oxam_c : 0.000569
  DM_5drib_c : 0.000341
  EX_glyclt_e : 0.000340
  DM_4crsol_c : 0.000113

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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