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 (44 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b4467 b1478 b1241 b0351 b4069 b4384 b3752 b2297 b2458 b2779 b3617 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1982 b0261 b0411 b3945 b1602 b0153 b4381 b0590 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 : 0.376833 (mmol/gDw/h)
  Minimum Production Rate : 1.444381 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.903089
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.405016
  EX_pi_e : 1.807876
  EX_so4_e : 0.094894
  EX_k_e : 0.073555
  EX_fe2_e : 0.006052
  EX_mg2_e : 0.003269
  EX_ca2_e : 0.001961
  EX_cl_e : 0.001961
  EX_cu2_e : 0.000267
  EX_mn2_e : 0.000260
  EX_zn2_e : 0.000129
  EX_ni2_e : 0.000122

Product: (mmol/gDw/h)
  EX_h2o_e : 53.327908
  EX_co2_e : 34.706288
  EX_h_e : 6.922895
  Auxiliary production reaction : 1.444381
  EX_ac_e : 0.551385
  EX_3hpp_e : 0.018148
  EX_ade_e : 0.000422
  DM_5drib_c : 0.000253
  DM_4crsol_c : 0.000084

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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