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 : sbzcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (46 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b3553 b1241 b0351 b4069 b4384 b2744 b3708 b3115 b1849 b2296 b0030 b2407 b3844 b3236 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b3449 b1033 b4374 b2361 b2291 b0261 b0411 b0507 b3709 b3161 b0112 b0452 b2868 b0114 b1539 b2492 b0904 b1533 b1473 b0594 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.387966 (mmol/gDw/h)
  Minimum Production Rate : 0.580455 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.820502
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.255355
  EX_pi_e : 2.115600
  EX_so4_e : 0.678153
  EX_k_e : 0.075728
  EX_fe2_e : 0.006231
  EX_mg2_e : 0.003366
  EX_ca2_e : 0.002019
  EX_cl_e : 0.002019
  EX_cu2_e : 0.000275
  EX_mn2_e : 0.000268
  EX_zn2_e : 0.000132
  EX_ni2_e : 0.000125

Product: (mmol/gDw/h)
  EX_h2o_e : 45.569036
  EX_co2_e : 20.227755
  EX_h_e : 8.523990
  EX_ac_e : 2.634954
  Auxiliary production reaction : 0.580455
  EX_ade_e : 0.000434
  DM_5drib_c : 0.000260
  EX_glyclt_e : 0.000260
  DM_4crsol_c : 0.000087

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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