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 (18 of 46: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b3553 b1241 b0351 b4069 b4384 b2744 b3752 b2297 b2458 b2883 b1982 b3616 b3589 b1033 b4014 b0261 b2976 b4381 b2406 b0112 b2868 b4064 b4464 b0114 b0509 b3125 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.318720 (mmol/gDw/h)
  Minimum Production Rate : 1.221637 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 20.260015
  EX_nh4_e : 11.995393
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.307439
  EX_so4_e : 0.080260
  EX_k_e : 0.062212
  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 : 48.294701
  EX_h_e : 16.834672
  EX_co2_e : 16.663513
  EX_ac_e : 1.687777
  EX_glyclt_e : 1.221850
  Auxiliary production reaction : 1.221637
  EX_ade_e : 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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