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 (44 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b3553 b1478 b3399 b1241 b0351 b4069 b2744 b3115 b1849 b2296 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b1982 b1033 b0675 b2361 b0261 b2799 b3945 b1602 b0153 b2913 b4381 b0590 b0529 b2492 b0904 b1380 b0606 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.334480 (mmol/gDw/h)
  Minimum Production Rate : 0.287385 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.062336
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.279148
  EX_pi_e : 0.897412
  EX_so4_e : 0.084229
  EX_k_e : 0.065288
  EX_fe2_e : 0.005372
  EX_mg2_e : 0.002902
  EX_ca2_e : 0.001741
  EX_cl_e : 0.001741
  EX_cu2_e : 0.000237
  EX_mn2_e : 0.000231
  EX_zn2_e : 0.000114
  EX_ni2_e : 0.000108

Product: (mmol/gDw/h)
  EX_h2o_e : 51.839277
  EX_co2_e : 33.201456
  EX_h_e : 7.647650
  EX_ac_e : 1.769678
  Auxiliary production reaction : 0.287385
  EX_ade_e : 0.239050
  EX_thymd_e : 0.229923
  DM_5drib_c : 0.000224
  DM_4crsol_c : 0.000075

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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