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 : 25aics_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (62 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b2836 b3553 b3399 b1241 b0351 b4069 b2502 b2744 b3708 b3115 b1849 b2296 b2779 b3617 b1982 b2797 b3117 b1814 b4471 b1033 b4374 b0675 b2361 b2291 b0261 b0112 b2789 b3127 b0114 b2366 b0755 b3612 b2492 b0904 b0591 b1533 b0514 b4141 b1798   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.416182 (mmol/gDw/h)
  Minimum Production Rate : 1.245341 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.166597
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.476556
  EX_pi_e : 1.646792
  EX_so4_e : 0.104803
  EX_k_e : 0.081236
  EX_fe2_e : 0.006684
  EX_mg2_e : 0.003610
  EX_ca2_e : 0.002166
  EX_cl_e : 0.002166
  EX_cu2_e : 0.000295
  EX_mn2_e : 0.000288
  EX_zn2_e : 0.000142
  EX_ni2_e : 0.000134
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 47.007858
  EX_co2_e : 22.317971
  EX_h_e : 13.501215
  EX_ac_e : 2.203918
  Auxiliary production reaction : 1.245341
  DM_oxam_c : 0.000466
  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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