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 : 4r5au_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (90 of 111: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b2066 b4384 b3708 b3008 b0910 b0871 b2779 b0030 b2407 b0120 b1982 b2797 b3117 b1814 b4471 b3449 b0261 b4381 b2239 b2406 b0114 b0886 b0529 b1539 b2492 b0904 b2578 b1533 b3927 b4141 b1798 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.486528 (mmol/gDw/h)
  Minimum Production Rate : 0.123482 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.773909
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.925058
  EX_pi_e : 0.469308
  EX_so4_e : 0.122517
  EX_k_e : 0.094967
  EX_fe2_e : 0.007814
  EX_mg2_e : 0.004221
  EX_ca2_e : 0.002532
  EX_cl_e : 0.002532
  EX_cu2_e : 0.000345
  EX_mn2_e : 0.000336
  EX_zn2_e : 0.000166
  EX_ni2_e : 0.000157
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.630071
  EX_co2_e : 38.476436
  EX_h_e : 5.141555
  Auxiliary production reaction : 0.123482
  EX_thym_e : 0.088063
  DM_oxam_c : 0.000544
  DM_5drib_c : 0.000326
  DM_4crsol_c : 0.000108

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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