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 : q8h2_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (72 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b1478 b3399 b1241 b0351 b4069 b2502 b2744 b0512 b0871 b2297 b2458 b2925 b2097 b2690 b1982 b3616 b3589 b4374 b0675 b2361 b0822 b2913 b4381 b0511 b0114 b0529 b2492 b0904 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.406904 (mmol/gDw/h)
  Minimum Production Rate : 0.109921 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 27.298286
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.757258
  EX_pi_e : 0.392502
  EX_so4_e : 0.102466
  EX_k_e : 0.079425
  EX_fe2_e : 0.006535
  EX_mg2_e : 0.003530
  EX_ca2_e : 0.002118
  EX_cl_e : 0.002118
  EX_cu2_e : 0.000288
  EX_mn2_e : 0.000281
  EX_zn2_e : 0.000139
  EX_ni2_e : 0.000131
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 44.381745
  EX_co2_e : 28.665195
  EX_h_e : 7.700501
  EX_ac_e : 1.902903
  EX_pyr_e : 0.696072
  EX_xan_e : 0.340683
  DM_mththf_c : 0.329945
  Auxiliary production reaction : 0.109921
  DM_5drib_c : 0.000092
  DM_4crsol_c : 0.000091

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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