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 (69 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b1241 b0351 b3708 b3008 b0871 b2297 b2458 b2925 b2097 b3617 b0030 b2407 b2883 b1779 b2797 b3117 b1814 b4471 b3946 b0825 b2440 b4381 b2406 b3654 b2868 b3714 b3664 b4064 b4464 b0114 b2366 b0529 b2492 b0904 b1533 b3927 b1511 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.599820 (mmol/gDw/h)
  Minimum Production Rate : 0.207661 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 26.846495
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.100987
  EX_pi_e : 0.786251
  EX_so4_e : 0.151047
  EX_k_e : 0.117081
  EX_fe2_e : 0.009634
  EX_mg2_e : 0.005203
  EX_ca2_e : 0.003122
  EX_cl_e : 0.003122
  EX_cu2_e : 0.000425
  EX_mn2_e : 0.000414
  EX_zn2_e : 0.000205
  EX_ni2_e : 0.000194
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 46.371804
  EX_co2_e : 26.759130
  EX_h_e : 8.453830
  EX_pyr_e : 2.319463
  Auxiliary production reaction : 0.207661
  DM_mththf_c : 0.000269
  DM_5drib_c : 0.000135
  DM_4crsol_c : 0.000134

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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