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 : fpram_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (34 of 51: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b4467 b4382 b1241 b0351 b4069 b4384 b3926 b3115 b1849 b2296 b2779 b3617 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b3665 b1602 b2913 b2406 b3654 b3714 b3664 b0114 b0529 b2492 b0904 b1380 b1771 b1511 b3662 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.339013 (mmol/gDw/h)
  Minimum Production Rate : 0.512645 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.412208
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.562295
  EX_pi_e : 0.839659
  EX_so4_e : 0.085370
  EX_k_e : 0.066173
  EX_fe2_e : 0.005445
  EX_mg2_e : 0.002941
  EX_ca2_e : 0.001765
  EX_cl_e : 0.001765
  EX_cu2_e : 0.000240
  EX_mn2_e : 0.000234
  EX_zn2_e : 0.000116
  EX_ni2_e : 0.000110

Product: (mmol/gDw/h)
  EX_h2o_e : 49.589702
  EX_co2_e : 34.177668
  EX_h_e : 6.700694
  EX_etoh_e : 1.342328
  EX_his__L_e : 0.787684
  Auxiliary production reaction : 0.512645
  EX_ac_e : 0.197369
  DM_mththf_c : 0.000152
  DM_5drib_c : 0.000076
  DM_4crsol_c : 0.000076

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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