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 (41 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3553 b1241 b0351 b4069 b4384 b3752 b3926 b2297 b2458 b2407 b1004 b3713 b1109 b0046 b3236 b1982 b3616 b3589 b1033 b0261 b1602 b2913 b4381 b2406 b0114 b0529 b2492 b0904 b1380 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.375861 (mmol/gDw/h)
  Minimum Production Rate : 1.440656 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 32.847960
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.381238
  EX_pi_e : 1.803214
  EX_so4_e : 0.094649
  EX_k_e : 0.073365
  EX_fe2_e : 0.006037
  EX_mg2_e : 0.003261
  EX_ca2_e : 0.001956
  EX_cl_e : 0.001956
  EX_cu2_e : 0.000266
  EX_mn2_e : 0.000260
  EX_zn2_e : 0.000128
  EX_ni2_e : 0.000121

Product: (mmol/gDw/h)
  EX_h2o_e : 52.219532
  EX_co2_e : 33.650140
  EX_h_e : 7.473729
  Auxiliary production reaction : 1.440656
  EX_ac_e : 1.138854
  DM_5drib_c : 0.000252
  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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