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 (4 of 46: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3553 b4382 b1241 b0351 b4069 b4384 b3752 b3115 b1849 b2296 b3617 b2407 b1982 b1033 b4014 b0261 b2976 b0507 b2406 b0112 b0114 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.318724 (mmol/gDw/h)
  Minimum Production Rate : 1.221654 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 20.260181
  EX_nh4_e : 11.994131
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.307444
  EX_so4_e : 0.080261
  EX_k_e : 0.062213
  EX_fe2_e : 0.005119
  EX_mg2_e : 0.002765
  EX_cl_e : 0.001659
  EX_ca2_e : 0.001659
  EX_cu2_e : 0.000226
  EX_mn2_e : 0.000220
  EX_zn2_e : 0.000109
  EX_ni2_e : 0.000103

Product: (mmol/gDw/h)
  EX_h2o_e : 48.292757
  EX_h_e : 16.833834
  EX_co2_e : 16.663986
  EX_ac_e : 1.687801
  EX_glyclt_e : 1.221867
  Auxiliary production reaction : 1.221654
  DM_oxam_c : 0.000357
  DM_5drib_c : 0.000214
  DM_4crsol_c : 0.000071

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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