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 : dadp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (58 of 95: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b2836 b1241 b0351 b4384 b3708 b3008 b3752 b0871 b2297 b2458 b2779 b3617 b2407 b1982 b2797 b3117 b1814 b4471 b4381 b0114 b1539 b2492 b0904 b1533 b1511 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.493435 (mmol/gDw/h)
  Minimum Production Rate : 0.085140 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.116987
  EX_o2_e : 288.009411
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.755068
  EX_pi_e : 0.646242
  EX_so4_e : 0.124258
  EX_k_e : 0.096315
  EX_mg2_e : 0.004281
  EX_ca2_e : 0.002568
  EX_cl_e : 0.002568
  EX_cu2_e : 0.000350
  EX_mn2_e : 0.000341
  EX_zn2_e : 0.000168
  EX_ni2_e : 0.000159
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992073
  EX_h2o_e : 553.027349
  EX_co2_e : 38.893627
  Auxiliary production reaction : 0.085136
  DM_oxam_c : 0.000332
  DM_mththf_c : 0.000221
  DM_5drib_c : 0.000111
  DM_4crsol_c : 0.000110

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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