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 : btn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (28 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b2836 b3399 b4069 b2502 b2744 b3708 b3008 b2297 b2458 b1779 b1982 b2797 b3117 b1814 b4471 b4374 b0675 b2361 b2291 b0261 b3453 b0114 b1539 b2492 b0904 b1533 b3927 b2240   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.651837 (mmol/gDw/h)
  Minimum Production Rate : 0.071443 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 28.329067
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.539889
  EX_pi_e : 0.642926
  EX_so4_e : 0.307031
  EX_k_e : 0.127234
  EX_fe2_e : 0.010469
  EX_mg2_e : 0.005655
  EX_cl_e : 0.003393
  EX_ca2_e : 0.003393
  EX_cu2_e : 0.000462
  EX_mn2_e : 0.000450
  EX_zn2_e : 0.000222
  EX_ni2_e : 0.000211
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 48.512293
  EX_co2_e : 29.941655
  EX_h_e : 6.797490
  EX_ac_e : 0.522376
  DM_5drib_c : 0.071880
  EX_meoh_e : 0.071444
  DM_amob_c : 0.071444
  Auxiliary production reaction : 0.071443
  EX_glyc3p_e : 0.014160
  DM_4crsol_c : 0.000145

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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