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 : nadphx__S_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (57 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b4467 b4382 b4269 b0493 b3588 b3003 b3011 b4384 b3752 b0871 b2926 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b0937 b1982 b0261 b2799 b3945 b1602 b2913 b2406 b1727 b2975 b0114 b3603 b0529 b2492 b0904 b3927 b1380 b3662 b0606 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.413319 (mmol/gDw/h)
  Minimum Production Rate : 0.278217 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.494805
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.413638
  EX_pi_e : 1.233341
  EX_so4_e : 0.104082
  EX_k_e : 0.080677
  EX_fe2_e : 0.006638
  EX_mg2_e : 0.003586
  EX_cl_e : 0.002151
  EX_ca2_e : 0.002151
  EX_cu2_e : 0.000293
  EX_mn2_e : 0.000286
  EX_zn2_e : 0.000141
  EX_ni2_e : 0.000134
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 52.163798
  EX_co2_e : 36.183278
  EX_h_e : 5.191134
  EX_etoh_e : 0.503049
  Auxiliary production reaction : 0.278217
  EX_ade_e : 0.000463
  DM_5drib_c : 0.000277
  DM_4crsol_c : 0.000092

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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