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 : preq0_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (48 of 51: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 46
  Gene deletion: b4467 b2836 b4069 b4384 b2744 b3115 b1849 b2296 b2779 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b3908 b1656 b0207 b3012 b1982 b4139 b1623 b0261 b0411 b2799 b1602 b4381 b3915 b1727 b0114 b0529 b2492 b0904 b2954 b1781 b3001 b1380 b0325 b2660 b0515 b1771 b3662 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.435188 (mmol/gDw/h)
  Minimum Production Rate : 0.394762 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 39.119037
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.676238
  EX_pi_e : 0.419785
  EX_so4_e : 0.109589
  EX_k_e : 0.084946
  EX_fe3_e : 0.006990
  EX_mg2_e : 0.003775
  EX_ca2_e : 0.002265
  EX_cl_e : 0.002265
  EX_cu2_e : 0.000309
  EX_mn2_e : 0.000301
  EX_zn2_e : 0.000148
  EX_ni2_e : 0.000141
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 55.094706
  EX_co2_e : 38.864077
  EX_h_e : 6.235275
  Auxiliary production reaction : 0.394762
  EX_ac_e : 0.253360
  EX_ade_e : 0.000487
  DM_5drib_c : 0.000292
  DM_4crsol_c : 0.000097

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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