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 : nadhx__S_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (62 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b2836 b3399 b2744 b3708 b3008 b0871 b0160 b2797 b3117 b1814 b4471 b2440 b0596 b1623 b3665 b4374 b0675 b2361 b2291 b0411 b3709 b3161 b0112 b3654 b3714 b3664 b0114 b0886 b2366 b2492 b0904 b2578 b1533 b3927 b1473 b4141 b1798 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.557836 (mmol/gDw/h)
  Minimum Production Rate : 0.128721 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.530252
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.925675
  EX_pi_e : 0.795534
  EX_so4_e : 0.140474
  EX_k_e : 0.108886
  EX_fe2_e : 0.008959
  EX_mg2_e : 0.004839
  EX_ca2_e : 0.002904
  EX_cl_e : 0.002904
  EX_cu2_e : 0.000396
  EX_mn2_e : 0.000385
  EX_zn2_e : 0.000190
  EX_ni2_e : 0.000180
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 51.575515
  EX_co2_e : 34.398907
  EX_h_e : 5.769226
  Auxiliary production reaction : 0.128721
  DM_mththf_c : 0.000250
  DM_5drib_c : 0.000126
  DM_4crsol_c : 0.000124
  EX_etha_e : 0.000045

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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