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 : gsn_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (25 of 49: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b1241 b0351 b4069 b4384 b3708 b2297 b2458 b0030 b2407 b1238 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b0261 b0411 b4381 b2406 b0114 b2366 b2492 b0904 b1533   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.604640 (mmol/gDw/h)
  Minimum Production Rate : 0.904656 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 22.963526
  EX_nh4_e : 11.053335
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.583239
  EX_so4_e : 0.152260
  EX_k_e : 0.118021
  EX_fe2_e : 0.009711
  EX_mg2_e : 0.005245
  EX_ca2_e : 0.003147
  EX_cl_e : 0.003147
  EX_cu2_e : 0.000429
  EX_mn2_e : 0.000418
  EX_zn2_e : 0.000206
  EX_ni2_e : 0.000195
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 47.458081
  EX_co2_e : 21.540007
  EX_h_e : 12.376153
  EX_ac_e : 2.297204
  EX_gsn_e : 0.904656
  DM_5drib_c : 0.000406
  DM_4crsol_c : 0.000135

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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