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 : aicar_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (60 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b4467 b1478 b4382 b1241 b4069 b4384 b3752 b3115 b1849 b2296 b2779 b2407 b1004 b3713 b1109 b0046 b3236 b1982 b0261 b2799 b3945 b1602 b0507 b2406 b3915 b0452 b2975 b3603 b0529 b2492 b0904 b1380 b2660 b3662 b0606 b2285 b1009 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.322714 (mmol/gDw/h)
  Minimum Production Rate : 1.062062 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.914326
  EX_o2_e : 284.897557
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.735335
  EX_pi_e : 1.373354
  EX_so4_e : 0.081266
  EX_k_e : 0.062991
  EX_mg2_e : 0.002800
  EX_ca2_e : 0.001680
  EX_cl_e : 0.001680
  EX_cu2_e : 0.000229
  EX_mn2_e : 0.000223
  EX_zn2_e : 0.000110
  EX_ni2_e : 0.000104

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994817
  EX_h2o_e : 551.544129
  EX_co2_e : 33.462574
  EX_ac_e : 1.865214
  Auxiliary production reaction : 1.062062
  EX_ade_e : 0.000361
  DM_5drib_c : 0.000217
  DM_4crsol_c : 0.000072

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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