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 : 5aizc_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (49 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b3553 b3399 b1241 b0351 b4069 b2502 b2744 b3115 b1849 b2296 b2926 b3617 b3124 b1982 b1033 b0675 b2361 b0261 b4388 b4381 b2406 b0112 b2789 b3127 b0114 b0755 b3612 b0529 b2492 b0904   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.415861 (mmol/gDw/h)
  Minimum Production Rate : 1.572211 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.344467
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.219247
  EX_pi_e : 1.973354
  EX_so4_e : 0.104722
  EX_k_e : 0.081173
  EX_fe2_e : 0.006679
  EX_mg2_e : 0.003608
  EX_ca2_e : 0.002165
  EX_cl_e : 0.002165
  EX_cu2_e : 0.000295
  EX_mn2_e : 0.000287
  EX_zn2_e : 0.000142
  EX_ni2_e : 0.000134
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 46.652564
  EX_co2_e : 23.070434
  EX_h_e : 12.976063
  EX_ac_e : 2.843146
  Auxiliary production reaction : 1.572211
  DM_oxam_c : 0.011347
  DM_5drib_c : 0.000279
  EX_glyclt_e : 0.000278
  DM_4crsol_c : 0.000093

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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