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 (19 of 49: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b3942 b1732 b1241 b0351 b4069 b4384 b2744 b3115 b1849 b2296 b0030 b2407 b1982 b3616 b3589 b4374 b2361 b2291 b0114 b0529 b2492 b0904 b0516 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.583312 (mmol/gDw/h)
  Minimum Production Rate : 1.116409 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 23.042612
  EX_nh4_e : 11.890876
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.562667
  EX_so4_e : 0.146890
  EX_k_e : 0.113858
  EX_fe2_e : 0.009369
  EX_mg2_e : 0.005060
  EX_cl_e : 0.003036
  EX_ca2_e : 0.003036
  EX_cu2_e : 0.000414
  EX_mn2_e : 0.000403
  EX_zn2_e : 0.000199
  EX_ni2_e : 0.000188
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 48.631586
  EX_co2_e : 20.931484
  EX_h_e : 12.922008
  EX_ac_e : 1.971150
  EX_gsn_e : 1.116409
  EX_alltn_e : 0.002277
  DM_mththf_c : 0.001886
  DM_5drib_c : 0.000391
  DM_4crsol_c : 0.000130

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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