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 : bwco1gdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (89 of 96: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 47
  Gene deletion: b2836 b3553 b1478 b3399 b1241 b4069 b4384 b2744 b3708 b3115 b1849 b2296 b2779 b2407 b1004 b3713 b1109 b0046 b3236 b1982 b2797 b3117 b1814 b4471 b1033 b4374 b0675 b2361 b2291 b0261 b2799 b3945 b1602 b2913 b3915 b1539 b2492 b0904 b1533 b1380 b4141 b1798 b0606 b0221 b2285 b1009 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.419676 (mmol/gDw/h)
  Minimum Production Rate : 0.099930 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.191408
  EX_o2_e : 287.688773
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.033253
  EX_pi_e : 0.704604
  EX_so4_e : 0.505393
  EX_tungs_e : 0.099927
  EX_k_e : 0.081918
  EX_mg2_e : 0.003641
  EX_ca2_e : 0.002184
  EX_cl_e : 0.002184
  EX_cu2_e : 0.000298
  EX_mn2_e : 0.000290
  EX_zn2_e : 0.000143
  EX_ni2_e : 0.000136
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993258
  EX_h2o_e : 553.965188
  EX_co2_e : 38.485050
  EX_ac_e : 0.644040
  Auxiliary production reaction : 0.099927
  EX_hxan_e : 0.000470
  DM_5drib_c : 0.000282
  DM_4crsol_c : 0.000094

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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