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 : 6hmhpt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (80 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 49
  Gene deletion: b2836 b0238 b0125 b1241 b0351 b4069 b4384 b2744 b3708 b3115 b1849 b2296 b2925 b2097 b3617 b0030 b3124 b2883 b2690 b2388 b1982 b0477 b2797 b3117 b1814 b4471 b4374 b2361 b2291 b3565 b0261 b3945 b2406 b0112 b2789 b3127 b2868 b4064 b4464 b2975 b0114 b3603 b2366 b2492 b0904 b0591 b1533 b0514 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.479449 (mmol/gDw/h)
  Minimum Production Rate : 0.052771 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 20.612958
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.826432
  EX_so4_e : 1.502619
  EX_pi_e : 0.462479
  EX_k_e : 0.093585
  EX_fe2_e : 0.007700
  EX_mg2_e : 0.004159
  EX_ca2_e : 0.002496
  EX_cl_e : 0.002496
  EX_cu2_e : 0.000340
  EX_mn2_e : 0.000331
  EX_zn2_e : 0.000163
  EX_ni2_e : 0.000155
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 40.888883
  EX_co2_e : 24.931112
  EX_h_e : 7.263955
  EX_ac_e : 3.920838
  EX_met__L_e : 1.381884
  EX_dxylnt_e : 0.053092
  Auxiliary production reaction : 0.052771
  EX_ade_e : 0.000537
  DM_5drib_c : 0.000322
  DM_4crsol_c : 0.000107

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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