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 (30 of 49: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b4382 b0238 b0125 b1241 b0351 b4384 b0871 b2779 b2925 b2097 b2883 b0477 b3616 b3589 b3946 b0825 b1623 b0411 b4388 b2868 b0114 b0529 b2492 b0904 b2954 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.401967 (mmol/gDw/h)
  Minimum Production Rate : 0.064823 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.006540
  EX_o2_e : 279.764282
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.665321
  EX_pi_e : 0.387740
  EX_so4_e : 0.101223
  EX_k_e : 0.078461
  EX_mg2_e : 0.003487
  EX_ca2_e : 0.002092
  EX_cl_e : 0.002092
  EX_cu2_e : 0.000285
  EX_mn2_e : 0.000278
  EX_zn2_e : 0.000137
  EX_ni2_e : 0.000130
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993544
  EX_h2o_e : 539.269159
  EX_co2_e : 27.944504
  EX_glyc__R_e : 4.969459
  EX_gsn_e : 0.064823
  DM_5drib_c : 0.000090
  DM_4crsol_c : 0.000090

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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