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 : 2tpr3dpcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (27 of 106: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b2836 b4069 b4384 b3708 b3008 b3752 b3115 b1849 b2296 b2407 b1982 b2797 b3117 b1814 b4471 b0261 b4381 b2406 b0114 b1539 b2492 b0904 b2578 b1533 b3927 b3662 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.730984 (mmol/gDw/h)
  Minimum Production Rate : 0.116094 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 24.215430
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.707227
  EX_pi_e : 1.285582
  EX_so4_e : 0.300171
  EX_k_e : 0.142683
  EX_mg2_e : 0.006341
  EX_fe2_e : 0.006033
  EX_fe3_e : 0.005708
  EX_ca2_e : 0.003805
  EX_cl_e : 0.003805
  EX_cu2_e : 0.000518
  EX_mn2_e : 0.000505
  EX_zn2_e : 0.000249
  EX_ni2_e : 0.000236
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 47.747540
  EX_co2_e : 25.893049
  EX_h_e : 7.380040
  EX_ac_e : 0.541663
  Auxiliary production reaction : 0.116094
  DM_5drib_c : 0.000490
  DM_4crsol_c : 0.000163

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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