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 : nad_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (46 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b3553 b1478 b1241 b0351 b4069 b4384 b3752 b3115 b1849 b2296 b2926 b3844 b1004 b3713 b1109 b0046 b3236 b0937 b1982 b1033 b0261 b0411 b2799 b3945 b1602 b4381 b4064 b4464 b0529 b2492 b0904 b1380 b2660 b0606 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.347591 (mmol/gDw/h)
  Minimum Production Rate : 0.427213 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.472210
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.702128
  EX_pi_e : 1.189714
  EX_so4_e : 0.087530
  EX_k_e : 0.067847
  EX_fe2_e : 0.005583
  EX_mg2_e : 0.003015
  EX_ca2_e : 0.001809
  EX_cl_e : 0.001809
  EX_cu2_e : 0.000246
  EX_mn2_e : 0.000240
  EX_zn2_e : 0.000119
  EX_ni2_e : 0.000112

Product: (mmol/gDw/h)
  EX_h2o_e : 53.519327
  EX_co2_e : 33.214636
  EX_h_e : 7.035087
  EX_ac_e : 1.174746
  Auxiliary production reaction : 0.427213
  EX_xan_e : 0.238936
  EX_ade_e : 0.000389
  DM_5drib_c : 0.000233
  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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