MetNetComp Database [1] / Minimal gene deletions

Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : iPC815 [2].
Target metabolite : apg120_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (25 of 34: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: YPO1384 YPO4078 YPO3825 YPO3937 YPO3428 YPO0459 YPO1962 YPO3977 YPO0348 YPO0253 YPO3992 YPO0347 YPO3202 YPO0670 YPO2303 YPO3914 YPO3868 YPO3270 YPO1851 YPO3418 YPO2370 YPO0921 YPO1133 YPO0439 YPO2567   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.105710 (mmol/gDw/h)
  Minimum Production Rate : 0.089284 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_h_e : 8.700770
  EX_cit_e : 6.822206
  EX_o2_e : 3.705328
  EX_gly_e : 2.200000
  EX_cys__L_e : 1.000000
  EX_glc__D_e : 0.388989
  EX_pi_e : 0.315820
  EX_lys__L_e : 0.026427
  EX_phe__L_e : 0.020085
  EX_met__L_e : 0.014799
  EX_tyr__L_e : 0.013742

Product: (mmol/gDw/h)
  EX_co2_e : 13.658508
  EX_succ_e : 6.822206
  EX_h2o_e : 5.016628
  EX_nh4_e : 2.007040
  EX_h2s_e : 0.992277
  EX_ac_e : 0.410220
  EX_g3pg_e : 0.139989
  EX_glyald_e : 0.089841
  Auxiliary production reaction : 0.089284

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].

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: 27-Sep-2023
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