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 : dudp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (36 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b1241 b0351 b4069 b2744 b2930 b4232 b3697 b3925 b0871 b2297 b2458 b3617 b3236 b2883 b3946 b2210 b0825 b2913 b4381 b3654 b2868 b3714 b3664 b4064 b4464 b0114 b0755 b3612 b0529 b2492 b0904 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.290568 (mmol/gDw/h)
  Minimum Production Rate : 1.114514 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.640952
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.367143
  EX_pi_e : 2.509312
  EX_so4_e : 0.073171
  EX_k_e : 0.056717
  EX_fe2_e : 0.004667
  EX_mg2_e : 0.002521
  EX_ca2_e : 0.001512
  EX_cl_e : 0.001512
  EX_cu2_e : 0.000206
  EX_mn2_e : 0.000201
  EX_zn2_e : 0.000099
  EX_ni2_e : 0.000094

Product: (mmol/gDw/h)
  EX_h2o_e : 46.362842
  EX_co2_e : 26.519413
  EX_h_e : 7.918674
  EX_pyr_e : 3.254208
  Auxiliary production reaction : 1.114514
  EX_ac_e : 0.880093
  DM_mththf_c : 0.000130
  DM_5drib_c : 0.000065
  DM_4crsol_c : 0.000065

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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