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 : coa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (83 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 61
  Gene deletion: b0945 b3553 b3399 b3846 b2341 b1241 b0351 b3831 b4069 b2502 b2744 b3708 b0910 b3115 b1849 b2296 b1238 b0907 b1779 b3962 b4139 b0104 b2797 b3117 b1814 b4471 b2498 b3616 b3589 b4267 b1033 b1623 b3665 b0675 b2361 b1748 b1415 b1014 b0411 b0822 b2799 b1907 b4381 b0112 b3654 b3714 b3664 b0114 b2366 b2492 b0904 b2954 b0591 b1533 b1380 b0723 b4266 b2842 b1985 b1517 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.378611 (mmol/gDw/h)
  Minimum Production Rate : 0.015253 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.789804
  EX_o2_e : 283.464031
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.451513
  EX_pi_e : 0.410971
  EX_so4_e : 0.110595
  EX_k_e : 0.073902
  EX_mg2_e : 0.003284
  EX_ca2_e : 0.001971
  EX_cl_e : 0.001971
  EX_cu2_e : 0.000268
  EX_mn2_e : 0.000262
  EX_zn2_e : 0.000129
  EX_ni2_e : 0.000122

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993919
  EX_h2o_e : 548.235882
  EX_co2_e : 33.514412
  EX_ac_e : 0.917402
  EX_succ_e : 0.753091
  EX_thymd_e : 0.544102
  EX_ura_e : 0.083783
  Auxiliary production reaction : 0.015253
  DM_mththf_c : 0.000170
  EX_dxylnt_e : 0.000169
  DM_5drib_c : 0.000085
  DM_4crsol_c : 0.000084

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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