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 (26 of 34: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: YPO3371 YPO1384 YPO4078 YPO3825 YPO3937 YPO3428 YPO0348 YPO0253 YPO3992 YPO0347 YPO0460 YPO3319 YPO1207 YPO3516 YPO0670 YPO2303 YPO3914 YPO3868 YPO3270 YPO0920 YPO1851 YPO3418 YPO0914 YPO0921 YPO2567   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.216627 (mmol/gDw/h)
  Minimum Production Rate : 0.017968 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 9.247319
  EX_h_e : 8.703868
  EX_cit_e : 7.400000
  EX_gly_e : 2.200000
  EX_glc__D_e : 2.000000
  EX_pi_e : 1.028361
  EX_cys__L_e : 1.000000
  EX_lys__L_e : 0.054157
  EX_phe__L_e : 0.041159
  EX_met__L_e : 0.030328
  EX_tyr__L_e : 0.028162
  EX_pnto__R_e : 0.000013

Product: (mmol/gDw/h)
  EX_co2_e : 19.290864
  EX_h2o_e : 12.073758
  EX_succ_e : 7.400000
  EX_h2s_e : 0.984173
  EX_g3pg_e : 0.833034
  EX_nh4_e : 0.755326
  EX_ac_e : 0.410000
  EX_glyald_e : 0.019110
  Auxiliary production reaction : 0.017968

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