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 : ametam_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (10 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b2836 b4069 b4384 b3708 b3008 b3752 b3115 b1849 b2296 b2407 b1982 b2797 b3117 b1814 b4471 b2440 b0261 b4381 b2406 b0114 b2366 b2492 b0904 b1533 b3927 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.734607 (mmol/gDw/h)
  Minimum Production Rate : 0.186683 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.250610
  EX_o2_e : 274.246212
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.053853
  EX_pi_e : 0.708607
  EX_so4_e : 0.371672
  EX_k_e : 0.143390
  EX_mg2_e : 0.006373
  EX_ca2_e : 0.003824
  EX_cl_e : 0.003824
  EX_cu2_e : 0.000521
  EX_mn2_e : 0.000508
  EX_zn2_e : 0.000251
  EX_ni2_e : 0.000237
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_fe3_e : 999.988201
  EX_h2o_e : 547.823632
  EX_co2_e : 26.003705
  EX_ac_e : 0.614361
  Auxiliary production reaction : 0.186683
  DM_5drib_c : 0.000493
  DM_4crsol_c : 0.000164
  EX_etha_e : 0.000059

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.

Last updated: 21-Sep-2023
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