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 : ade_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (67 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b3553 b4069 b3926 b2297 b2458 b2779 b3844 b1004 b3713 b1109 b0046 b3236 b1033 b0261 b3945 b1602 b4381 b3654 b3714 b3664 b4064 b4464 b0114 b0529 b2492 b0904 b1380 b2660 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.461768 (mmol/gDw/h)
  Minimum Production Rate : 0.211919 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 997.951407
  EX_h_e : 992.372653
  EX_o2_e : 288.479665
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.046649
  EX_pi_e : 0.445424
  EX_so4_e : 0.116282
  EX_k_e : 0.090134
  EX_mg2_e : 0.004006
  EX_ca2_e : 0.002404
  EX_cl_e : 0.002404
  EX_cu2_e : 0.000327
  EX_mn2_e : 0.000319
  EX_zn2_e : 0.000157
  EX_ni2_e : 0.000149
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 997.943991
  EX_h2o_e : 552.734488
  EX_co2_e : 39.449291
  EX_ac_e : 0.268835
  Auxiliary production reaction : 0.211919
  DM_5drib_c : 0.000104
  DM_4crsol_c : 0.000103

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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