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 (46 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3399 b1241 b0351 b3831 b4069 b2744 b3115 b1849 b2296 b3617 b2883 b0907 b1779 b1982 b0675 b2361 b0261 b0507 b4381 b0112 b4064 b4464 b0114 b0529 b2492 b0904   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.497352 (mmol/gDw/h)
  Minimum Production Rate : 0.940148 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 27.014771
  EX_nh4_e : 10.085669
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.479749
  EX_so4_e : 0.125243
  EX_k_e : 0.097080
  EX_fe2_e : 0.007988
  EX_mg2_e : 0.004315
  EX_ca2_e : 0.002589
  EX_cl_e : 0.002589
  EX_cu2_e : 0.000353
  EX_mn2_e : 0.000344
  EX_zn2_e : 0.000170
  EX_ni2_e : 0.000161
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 48.737789
  EX_co2_e : 25.235331
  EX_h_e : 11.758212
  EX_ac_e : 2.460242
  Auxiliary production reaction : 0.940148
  DM_oxam_c : 0.013570
  DM_5drib_c : 0.000334
  EX_glyclt_e : 0.000222
  DM_4crsol_c : 0.000111

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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