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 : 5apru_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (99 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b3916 b1241 b0351 b4069 b4384 b3708 b3752 b2297 b2458 b1850 b3617 b2407 b1238 b1982 b1200 b2797 b3117 b1814 b4471 b0261 b0507 b4381 b2406 b0112 b0452 b0114 b2366 b1723 b2492 b0904 b1533 b3825 b3662 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.486215 (mmol/gDw/h)
  Minimum Production Rate : 1.367624 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.352558
  EX_nh4_e : 10.722121
  EX_glc__D_e : 10.000000
  EX_pi_e : 1.836630
  EX_fe3_e : 1.749323
  EX_so4_e : 0.122439
  EX_k_e : 0.094906
  EX_mg2_e : 0.004218
  EX_ca2_e : 0.002531
  EX_cl_e : 0.002531
  EX_cu2_e : 0.000345
  EX_mn2_e : 0.000336
  EX_zn2_e : 0.000166
  EX_ni2_e : 0.000157
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 46.682187
  EX_co2_e : 22.407550
  EX_h_e : 14.350830
  EX_ac_e : 2.662059
  EX_fe2_e : 1.741514
  Auxiliary production reaction : 1.367624
  DM_oxam_c : 0.000544
  DM_5drib_c : 0.000326
  EX_glyclt_e : 0.000325
  DM_4crsol_c : 0.000108

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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