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 : adprib_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (63 of 97: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b4384 b3708 b3008 b0871 b0030 b2407 b1851 b1779 b0121 b1982 b2797 b3117 b1814 b4471 b3449 b0261 b4381 b2406 b0114 b0886 b2366 b2492 b0904 b2578 b1533 b3927 b1380 b0494 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.666782 (mmol/gDw/h)
  Minimum Production Rate : 0.153050 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.293989
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.966435
  EX_pi_e : 0.949282
  EX_so4_e : 0.167909
  EX_k_e : 0.130151
  EX_fe2_e : 0.010709
  EX_mg2_e : 0.005784
  EX_cl_e : 0.003471
  EX_ca2_e : 0.003471
  EX_cu2_e : 0.000473
  EX_mn2_e : 0.000461
  EX_zn2_e : 0.000227
  EX_ni2_e : 0.000215
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 50.084999
  EX_co2_e : 30.334438
  EX_h_e : 6.585806
  Auxiliary production reaction : 0.153050
  DM_5drib_c : 0.000447
  DM_4crsol_c : 0.000149

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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