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 : dgdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (29 of 41: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b4384 b3708 b3008 b3752 b2930 b4232 b3697 b3925 b0871 b2407 b3236 b1779 b2797 b3117 b1814 b4471 b3449 b3946 b2210 b0825 b3665 b4381 b0114 b1539 b2492 b0904 b1533 b3927 b0494   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.638226 (mmol/gDw/h)
  Minimum Production Rate : 0.110085 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.743861
  EX_o2_e : 276.764673
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.445363
  EX_pi_e : 0.835807
  EX_so4_e : 0.160718
  EX_k_e : 0.124577
  EX_mg2_e : 0.005537
  EX_ca2_e : 0.003322
  EX_cl_e : 0.003322
  EX_cu2_e : 0.000453
  EX_mn2_e : 0.000441
  EX_zn2_e : 0.000218
  EX_ni2_e : 0.000206
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_fe3_e : 999.989749
  EX_h2o_e : 547.106567
  EX_co2_e : 26.883376
  EX_pyr_e : 1.939122
  Auxiliary production reaction : 0.110085
  EX_ade_e : 0.000430
  DM_5drib_c : 0.000144
  DM_4crsol_c : 0.000142

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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