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 : didp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (55 of 87: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b3399 b1241 b0351 b4069 b2502 b2744 b2930 b4232 b3697 b3925 b0512 b2297 b2458 b3617 b1779 b3946 b0825 b4374 b2361 b2291 b0261 b0511 b0114 b0529 b2492 b0904 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.349620 (mmol/gDw/h)
  Minimum Production Rate : 0.446796 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 31.521225
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.563997
  EX_pi_e : 1.230838
  EX_so4_e : 0.088041
  EX_k_e : 0.068243
  EX_fe2_e : 0.005615
  EX_mg2_e : 0.003033
  EX_ca2_e : 0.001820
  EX_cl_e : 0.001820
  EX_cu2_e : 0.000248
  EX_mn2_e : 0.000242
  EX_zn2_e : 0.000119
  EX_ni2_e : 0.000113

Product: (mmol/gDw/h)
  EX_h2o_e : 45.969204
  EX_co2_e : 31.373024
  EX_h_e : 9.457544
  EX_ac_e : 4.903763
  Auxiliary production reaction : 0.446796
  EX_xan_e : 0.000235
  DM_5drib_c : 0.000079
  DM_4crsol_c : 0.000078

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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