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 : air_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (76 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b4467 b3846 b2341 b1241 b0351 b4384 b0910 b0871 b2925 b2097 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b2690 b1982 b0261 b0411 b2799 b3945 b1602 b0507 b2913 b4381 b3915 b1727 b0755 b3612 b0529 b2492 b0904 b3927 b1380 b0606 b2285 b1009 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.431494 (mmol/gDw/h)
  Minimum Production Rate : 0.056187 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.155536
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.831043
  EX_pi_e : 0.472398
  EX_so4_e : 0.108660
  EX_k_e : 0.084225
  EX_fe3_e : 0.006932
  EX_mg2_e : 0.003743
  EX_ca2_e : 0.002246
  EX_cl_e : 0.002246
  EX_cu2_e : 0.000306
  EX_mn2_e : 0.000298
  EX_zn2_e : 0.000147
  EX_ni2_e : 0.000139
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 44.538112
  EX_co2_e : 32.748949
  EX_h_e : 8.686320
  EX_glyclt_e : 4.543705
  Auxiliary production reaction : 0.056175
  EX_ade_e : 0.000483
  DM_5drib_c : 0.000290
  DM_4crsol_c : 0.000096

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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