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_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (40 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b2744 b3752 b0871 b2883 b1982 b3616 b3589 b0411 b2913 b4381 b2868 b4064 b4464 b0114 b0529 b2492 b0904 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.441594 (mmol/gDw/h)
  Minimum Production Rate : 0.706499 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 31.053900
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.360930
  EX_pi_e : 0.425964
  EX_so4_e : 0.111202
  EX_k_e : 0.086196
  EX_fe2_e : 0.007092
  EX_mg2_e : 0.003831
  EX_ca2_e : 0.002298
  EX_cl_e : 0.002298
  EX_cu2_e : 0.000313
  EX_mn2_e : 0.000305
  EX_zn2_e : 0.000151
  EX_ni2_e : 0.000143
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 50.656845
  EX_co2_e : 31.094011
  EX_h_e : 7.649295
  EX_acald_e : 1.798790
  Auxiliary production reaction : 0.706499
  EX_gsn_e : 0.011555
  EX_ade_e : 0.000297
  DM_mththf_c : 0.000198
  DM_5drib_c : 0.000099
  DM_4crsol_c : 0.000098

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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