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 : ppgpp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (78 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 49
  Gene deletion: b4467 b3399 b4382 b4069 b4384 b2744 b2930 b4232 b3697 b3925 b0871 b2297 b2458 b2779 b1004 b3713 b1109 b0046 b3236 b2883 b1638 b0207 b3012 b1982 b4139 b3946 b0825 b0675 b2361 b0261 b0411 b2799 b1602 b2913 b4381 b1727 b0114 b0529 b2492 b0904 b1781 b3001 b3927 b3029 b1380 b0325 b1771 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.357109 (mmol/gDw/h)
  Minimum Production Rate : 0.061288 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.190286
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.163186
  EX_pi_e : 0.589621
  EX_so4_e : 0.089927
  EX_k_e : 0.069705
  EX_fe3_e : 0.005736
  EX_mg2_e : 0.003098
  EX_ca2_e : 0.001859
  EX_cl_e : 0.001859
  EX_cu2_e : 0.000253
  EX_mn2_e : 0.000247
  EX_zn2_e : 0.000122
  EX_ni2_e : 0.000115

Product: (mmol/gDw/h)
  EX_h2o_e : 43.824970
  EX_co2_e : 28.061370
  EX_h_e : 9.096051
  EX_pyr_e : 5.416889
  EX_ac_e : 0.207904
  Auxiliary production reaction : 0.061288
  EX_glyclt_e : 0.000400
  DM_5drib_c : 0.000240
  DM_4crsol_c : 0.000080

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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