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 : 1agpe120_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (34 of 34: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: YPO4078 YPO3825 YPO3937 YPO2157 YPO3428 YPO0459 YPO3977 YPO0348 YPO1963 YPO3319 YPO1207 YPO1511 YPO0670 YPO2303 YPO3914 YPO3868 YPO3270 YPO0440 YPO3358 YPO2559 YPO2067 YPO1851 YPO0138 YPO2836 YPO0442   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.236771 (mmol/gDw/h)
  Minimum Production Rate : 0.528004 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_h_e : 16.213731
  EX_o2_e : 9.479352
  EX_cit_e : 7.400000
  EX_gly_e : 2.200000
  EX_cys__L_e : 1.000000
  EX_pi_e : 0.999435
  EX_glc__D_e : 0.799329
  EX_lys__L_e : 0.059193
  EX_phe__L_e : 0.044986
  EX_met__L_e : 0.033148
  EX_tyr__L_e : 0.030780
  EX_pnto__R_e : 0.000014

Product: (mmol/gDw/h)
  EX_co2_e : 22.027118
  EX_h2o_e : 15.842050
  EX_fum_e : 3.513698
  EX_h2s_e : 0.982702
  Auxiliary production reaction : 0.528004
  EX_ac_e : 0.410000
  EX_g3pg_e : 0.277581
  EX_glyald_e : 0.001248

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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