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 : hisp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (66 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b4467 b4382 b1241 b0351 b4384 b3752 b0871 b2925 b2097 b2926 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b2690 b1982 b0261 b2799 b3945 b1602 b2913 b2406 b3915 b0452 b1727 b2975 b3603 b0529 b1539 b2492 b0904 b3927 b1380 b3662 b0606 b2285 b1008   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.367775 (mmol/gDw/h)
  Minimum Production Rate : 0.094506 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.292066
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.257088
  EX_pi_e : 0.449260
  EX_so4_e : 0.092614
  EX_k_e : 0.071787
  EX_fe3_e : 0.005908
  EX_mg2_e : 0.003190
  EX_ca2_e : 0.001914
  EX_cl_e : 0.001914
  EX_cu2_e : 0.000261
  EX_mn2_e : 0.000254
  EX_zn2_e : 0.000125
  EX_ni2_e : 0.000119

Product: (mmol/gDw/h)
  EX_h2o_e : 44.008553
  EX_co2_e : 28.425994
  EX_h_e : 8.878705
  EX_pyr_e : 5.302886
  Auxiliary production reaction : 0.094502
  EX_hxan_e : 0.000412
  DM_5drib_c : 0.000247
  DM_4crsol_c : 0.000082

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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