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 : dimp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (51 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b4269 b0493 b3588 b3003 b3011 b1241 b0351 b2930 b4232 b3697 b3925 b0871 b2926 b2407 b3616 b3589 b3946 b0825 b0261 b4381 b2868 b0114 b0529 b2492 b0904 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.333158 (mmol/gDw/h)
  Minimum Production Rate : 0.197710 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.622051
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.370178
  EX_pi_e : 0.519075
  EX_so4_e : 0.083896
  EX_k_e : 0.065030
  EX_fe2_e : 0.005351
  EX_mg2_e : 0.002890
  EX_cl_e : 0.001734
  EX_ca2_e : 0.001734
  EX_cu2_e : 0.000236
  EX_mn2_e : 0.000230
  EX_zn2_e : 0.000114
  EX_ni2_e : 0.000108

Product: (mmol/gDw/h)
  EX_h2o_e : 45.558596
  EX_co2_e : 27.742340
  EX_h_e : 8.733171
  EX_pyr_e : 3.899882
  EX_thymd_e : 0.490633
  Auxiliary production reaction : 0.197710
  DM_5drib_c : 0.000075
  DM_4crsol_c : 0.000074

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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