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 (20 of 34: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 21
  Gene deletion: YPO4078 YPO3825 YPO3937 YPO2157 YPO3428 YPO0459 YPO3977 YPO0348 YPO1511 YPO1964 YPO0670 YPO2303 YPO3914 YPO3868 YPO3270 YPO2067 YPO1851 YPO2370 YPO0138 YPO0439 YPO0442   (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
Contact