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 : 10fthf_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (19 of 46: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b3399 b1241 b0351 b4069 b4384 b2744 b3115 b1849 b2296 b0030 b2883 b1982 b3616 b3589 b1623 b4014 b0261 b2976 b0411 b0507 b4381 b2406 b0112 b2975 b0114 b3603 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.313912 (mmol/gDw/h)
  Minimum Production Rate : 1.186781 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 20.582927
  EX_nh4_e : 11.706259
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.302802
  EX_so4_e : 0.079049
  EX_k_e : 0.061273
  EX_fe2_e : 0.005042
  EX_mg2_e : 0.002723
  EX_ca2_e : 0.001634
  EX_cl_e : 0.001634
  EX_cu2_e : 0.000223
  EX_mn2_e : 0.000217
  EX_zn2_e : 0.000107
  EX_ni2_e : 0.000101

Product: (mmol/gDw/h)
  EX_h2o_e : 48.535228
  EX_co2_e : 17.679701
  EX_h_e : 16.423607
  EX_ac_e : 2.841095
  Auxiliary production reaction : 1.186781
  DM_oxam_c : 0.008565
  DM_5drib_c : 0.000211
  DM_4crsol_c : 0.000070

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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