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 : accoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (53 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b2836 b3399 b4069 b4384 b2744 b3708 b3008 b3752 b2297 b2458 b3844 b1238 b2883 b1982 b2688 b2797 b3117 b1814 b4471 b1623 b0261 b0411 b0507 b3709 b0153 b4381 b2406 b3161 b0112 b2975 b0114 b3603 b2366 b2492 b0904 b0591 b2578 b1533 b3927 b1473 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.694817 (mmol/gDw/h)
  Minimum Production Rate : 0.220700 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 23.448891
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.049640
  EX_pi_e : 1.332324
  EX_so4_e : 0.395669
  EX_k_e : 0.135623
  EX_fe2_e : 0.011159
  EX_mg2_e : 0.006028
  EX_ca2_e : 0.003617
  EX_cl_e : 0.003617
  EX_cu2_e : 0.000493
  EX_mn2_e : 0.000480
  EX_zn2_e : 0.000237
  EX_ni2_e : 0.000224
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 47.915078
  EX_co2_e : 25.151333
  EX_h_e : 7.673122
  EX_ac_e : 0.625213
  Auxiliary production reaction : 0.220700
  DM_oxam_c : 0.000778
  DM_5drib_c : 0.000466
  DM_4crsol_c : 0.000155

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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