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 (35 of 87: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b1241 b0351 b4069 b4384 b2744 b3752 b3115 b1849 b2296 b1238 b2883 b1982 b3616 b3589 b0411 b4381 b2868 b4064 b4464 b0114 b0529 b2492 b0904 b1517 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.445434 (mmol/gDw/h)
  Minimum Production Rate : 0.853961 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 31.349493
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.081958
  EX_pi_e : 0.429669
  EX_so4_e : 0.112169
  EX_k_e : 0.086946
  EX_fe2_e : 0.007154
  EX_mg2_e : 0.003864
  EX_cl_e : 0.002318
  EX_ca2_e : 0.002318
  EX_cu2_e : 0.000316
  EX_mn2_e : 0.000308
  EX_zn2_e : 0.000152
  EX_ni2_e : 0.000144
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 51.323665
  EX_co2_e : 30.164406
  EX_h_e : 9.869361
  EX_ac_e : 1.505227
  Auxiliary production reaction : 0.853961
  EX_ade_e : 0.000300
  DM_mththf_c : 0.000200
  DM_5drib_c : 0.000100
  DM_4crsol_c : 0.000099

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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