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_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (64 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b4382 b2066 b4069 b4384 b3708 b0910 b3115 b1849 b2296 b0030 b2407 b1982 b2797 b3117 b1814 b4471 b2498 b0411 b2406 b2943 b3453 b0511 b0114 b2366 b0529 b2492 b0904 b1533 b3927 b3825 b2240 b0515 b1511   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.726695 (mmol/gDw/h)
  Minimum Production Rate : 0.308259 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.286308
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.654568
  EX_pi_e : 0.700975
  EX_so4_e : 0.182996
  EX_k_e : 0.141846
  EX_fe2_e : 0.011671
  EX_mg2_e : 0.006304
  EX_cl_e : 0.003782
  EX_ca2_e : 0.003782
  EX_cu2_e : 0.000515
  EX_mn2_e : 0.000502
  EX_zn2_e : 0.000248
  EX_ni2_e : 0.000235
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 48.956485
  EX_co2_e : 25.713547
  EX_h_e : 8.906559
  EX_ac_e : 0.423072
  Auxiliary production reaction : 0.308259
  EX_ura_e : 0.131534
  EX_xan_e : 0.000489
  DM_mththf_c : 0.000326
  DM_5drib_c : 0.000164
  DM_4crsol_c : 0.000162

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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