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 : urdglyc_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (63 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b1241 b0351 b4069 b4384 b2744 b3708 b3115 b1849 b2296 b2407 b0521 b2797 b3117 b1814 b4471 b3616 b3589 b4374 b2361 b2291 b0507 b0511 b0114 b1539 b2492 b0904 b1511   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.675450 (mmol/gDw/h)
  Minimum Production Rate : 0.588281 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.899595
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.894593
  EX_pi_e : 0.651543
  EX_so4_e : 0.170092
  EX_k_e : 0.131843
  EX_fe2_e : 0.010848
  EX_mg2_e : 0.005860
  EX_ca2_e : 0.003516
  EX_cl_e : 0.003516
  EX_cu2_e : 0.000479
  EX_mn2_e : 0.000467
  EX_zn2_e : 0.000230
  EX_ni2_e : 0.000218
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 44.977458
  EX_co2_e : 24.529389
  EX_h_e : 11.384441
  EX_ac_e : 2.566386
  Auxiliary production reaction : 0.588281
  DM_oxam_c : 0.423228
  EX_glyclt_e : 0.000452
  DM_mththf_c : 0.000303
  DM_5drib_c : 0.000152
  DM_4crsol_c : 0.000151

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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