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 : pyr_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (112 of 114: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b4467 b3942 b1732 b1241 b0351 b3926 b2930 b4232 b3697 b3925 b0871 b3115 b1849 b2296 b1004 b3713 b1109 b0046 b2690 b1302 b2662 b2210 b0726 b3945 b1602 b0507 b2975 b3603 b2492 b0904 b1380 b1695 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.468694 (mmol/gDw/h)
  Minimum Production Rate : 3.081945 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 31.510567
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.061851
  EX_pi_e : 0.452105
  EX_so4_e : 0.118026
  EX_k_e : 0.091486
  EX_mg2_e : 0.004066
  EX_fe2_e : 0.003868
  EX_fe3_e : 0.003660
  EX_ca2_e : 0.002440
  EX_cl_e : 0.002440
  EX_cu2_e : 0.000332
  EX_mn2_e : 0.000324
  EX_zn2_e : 0.000160
  EX_ni2_e : 0.000151
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 46.427730
  EX_co2_e : 30.970712
  EX_h_e : 7.665015
  EX_pyr_e : 3.081945
  EX_ac_e : 0.272867
  DM_5drib_c : 0.000105
  DM_4crsol_c : 0.000105

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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