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 : frdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (51 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b1241 b0351 b4069 b3115 b1849 b2296 b2925 b2097 b2926 b1612 b1611 b0517 b4122 b2690 b2388 b3616 b3589 b3565 b3945 b4381 b0114 b0529 b2492 b0904 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.521630 (mmol/gDw/h)
  Minimum Production Rate : 0.068202 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.722391
  EX_o2_e : 278.393877
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.633560
  EX_pi_e : 0.639571
  EX_so4_e : 0.131357
  EX_k_e : 0.101819
  EX_mg2_e : 0.004525
  EX_ca2_e : 0.002715
  EX_cl_e : 0.002715
  EX_cu2_e : 0.000370
  EX_mn2_e : 0.000360
  EX_zn2_e : 0.000178
  EX_ni2_e : 0.000168
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991622
  EX_h2o_e : 545.403817
  EX_co2_e : 28.476311
  EX_ac_e : 1.660408
  EX_fum_e : 1.442040
  Auxiliary production reaction : 0.068202
  DM_mththf_c : 0.000234
  DM_5drib_c : 0.000117
  DM_4crsol_c : 0.000116

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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