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 (71 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b2836 b3553 b4384 b2744 b3708 b3008 b3752 b0871 b2779 b2925 b2097 b2926 b2407 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b1033 b0596 b4374 b2361 b2291 b0261 b0411 b0112 b2789 b3127 b2868 b0114 b0886 b0529 b1539 b2492 b0904 b2578 b1533 b3927 b1380 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.569146 (mmol/gDw/h)
  Minimum Production Rate : 0.130593 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 27.102930
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.064061
  EX_pi_e : 0.810188
  EX_so4_e : 0.143322
  EX_k_e : 0.111093
  EX_fe2_e : 0.009141
  EX_mg2_e : 0.004937
  EX_cl_e : 0.002962
  EX_ca2_e : 0.002962
  EX_cu2_e : 0.000404
  EX_mn2_e : 0.000393
  EX_zn2_e : 0.000194
  EX_ni2_e : 0.000184
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 46.896245
  EX_co2_e : 26.730649
  EX_h_e : 8.142303
  EX_pyr_e : 2.387210
  Auxiliary production reaction : 0.130593
  EX_ade_e : 0.000637
  DM_5drib_c : 0.000382
  DM_4crsol_c : 0.000127

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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