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 : h2o2_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (18 of 20: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: YPO4078 YPO3825 YPO3937 YPO3428 YPO0459 YPO1962 YPO0348 YPO3992 YPO0347 YPO3319 YPO1207 YPO1511 YPO1145 YPO3014 YPO0670 YPO2303 YPO3914 YPO3868 YPO3270 YPO2067 YPO0920 YPO1851 YPO0914 YPO0439 YPO2393   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.283558 (mmol/gDw/h)
  Minimum Production Rate : 0.884794 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_cit_e : 7.400000
  EX_o2_e : 7.057917
  EX_h_e : 5.894537
  EX_gly_e : 2.200000
  EX_glc__D_e : 2.000000
  EX_cys__L_e : 1.000000
  EX_pi_e : 0.232157
  EX_lys__L_e : 0.070890
  EX_phe__L_e : 0.053876
  EX_met__L_e : 0.039698
  EX_tyr__L_e : 0.036863
  EX_pnto__R_e : 0.000017

Product: (mmol/gDw/h)
  EX_co2_e : 14.818627
  EX_succ_e : 7.400000
  EX_h2o_e : 6.605098
  Auxiliary production reaction : 2.278543
  EX_dha_e : 1.749191
  EX_ac_e : 1.646228
  EX_h2s_e : 0.979284
  EX_glyc_e : 0.001494

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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