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 (27 of 34: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: YPO1384 YPO4078 YPO3825 YPO3937 YPO2157 YPO3949 YPO3428 YPO3977 YPO0348 YPO0253 YPO3992 YPO0347 YPO3202 YPO3516 YPO0436 YPO0670 YPO2303 YPO3914 YPO3868 YPO3270 YPO1851 YPO3418 YPO2370 YPO1133 YPO2567   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.106009 (mmol/gDw/h)
  Minimum Production Rate : 0.089111 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_h_e : 9.275146
  EX_cit_e : 7.400000
  EX_o2_e : 4.283459
  EX_gly_e : 2.200000
  EX_cys__L_e : 1.000000
  EX_glc__D_e : 0.388811
  EX_pi_e : 0.315648
  EX_lys__L_e : 0.026502
  EX_phe__L_e : 0.020142
  EX_met__L_e : 0.014841
  EX_tyr__L_e : 0.013781

Product: (mmol/gDw/h)
  EX_co2_e : 14.811310
  EX_succ_e : 7.400000
  EX_h2o_e : 5.597084
  EX_nh4_e : 2.003671
  EX_h2s_e : 0.992255
  EX_ac_e : 0.410000
  EX_g3pg_e : 0.139746
  EX_glyald_e : 0.089669
  Auxiliary production reaction : 0.089111

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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