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 : gdpofuc_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (51 of 71: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b2836 b1478 b3399 b1241 b2744 b1278 b3708 b3008 b0871 b2925 b2097 b0160 b2690 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b0261 b0822 b4381 b2406 b2868 b0114 b2366 b0755 b3612 b0529 b2492 b0904 b2578 b1533 b3927 b2413 b3447 b1813 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.361858 (mmol/gDw/h)
  Minimum Production Rate : 0.073564 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.035915
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.315744
  EX_pi_e : 0.496173
  EX_so4_e : 0.091124
  EX_k_e : 0.070632
  EX_fe2_e : 0.005813
  EX_mg2_e : 0.003139
  EX_cl_e : 0.001883
  EX_ca2_e : 0.001883
  EX_cu2_e : 0.000257
  EX_mn2_e : 0.000250
  EX_zn2_e : 0.000123
  EX_ni2_e : 0.000117

Product: (mmol/gDw/h)
  EX_h2o_e : 43.978894
  EX_co2_e : 27.885687
  EX_h_e : 8.930326
  EX_pyr_e : 5.344845
  Auxiliary production reaction : 0.073561
  EX_xan_e : 0.009468
  EX_ade_e : 0.000405
  DM_5drib_c : 0.000243
  DM_4crsol_c : 0.000081

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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