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 : adn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (41 of 87: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b4069 b4384 b3708 b3008 b3752 b2297 b2458 b2407 b2797 b3117 b1814 b4471 b3665 b4381 b2406 b3654 b3714 b3664 b0114 b1539 b2492 b0904 b1533 b3927 b3821 b3662 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.750910 (mmol/gDw/h)
  Minimum Production Rate : 0.319036 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.055926
  EX_o2_e : 274.304314
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.704949
  EX_pi_e : 0.724333
  EX_so4_e : 0.189094
  EX_k_e : 0.146572
  EX_mg2_e : 0.006514
  EX_cl_e : 0.003908
  EX_ca2_e : 0.003908
  EX_cu2_e : 0.000532
  EX_mn2_e : 0.000519
  EX_zn2_e : 0.000256
  EX_ni2_e : 0.000243
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_fe3_e : 999.987940
  EX_h2o_e : 548.445030
  EX_co2_e : 25.112197
  EX_ac_e : 0.437170
  Auxiliary production reaction : 0.319036
  DM_mththf_c : 0.000336
  DM_5drib_c : 0.000169
  DM_4crsol_c : 0.000167

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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