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 (33 of 34: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: YPO3371 YPO4078 YPO3825 YPO3937 YPO2157 YPO3428 YPO0459 YPO3095 YPO0348 YPO3225 YPO3408 YPO3319 YPO1207 YPO1511 YPO1965 YPO0670 YPO2303 YPO3914 YPO3868 YPO3270 YPO0440 YPO2067 YPO1389 YPO1851 YPO0138   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.250130 (mmol/gDw/h)
  Minimum Production Rate : 0.377243 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_h_e : 13.122552
  EX_o2_e : 8.067906
  EX_cit_e : 7.152777
  EX_gly_e : 2.200000
  EX_cys__L_e : 1.000000
  EX_pi_e : 0.784998
  EX_glc__D_e : 0.663877
  EX_lys__L_e : 0.062533
  EX_phe__L_e : 0.047525
  EX_met__L_e : 0.035018
  EX_tyr__L_e : 0.032517
  EX_pnto__R_e : 0.000015

Product: (mmol/gDw/h)
  EX_co2_e : 18.270909
  EX_h2o_e : 14.525736
  EX_fum_e : 4.503701
  EX_h2s_e : 0.981726
  EX_ac_e : 0.410000
  Auxiliary production reaction : 0.377243
  EX_g3pg_e : 0.202967
  EX_glyald_e : 0.001318

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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