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 : apg141_c
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 : 28
  Gene deletion: YPO1384 YPO4078 YPO3825 YPO3937 YPO2306 YPO3428 YPO0459 YPO3977 YPO0348 YPO0253 YPO3319 YPO1207 YPO3202 YPO0465 YPO3053 YPO1964 YPO1109 YPO0670 YPO2303 YPO3914 YPO3868 YPO3270 YPO1851 YPO3418 YPO0921 YPO1133 YPO0439 YPO2567   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.124050 (mmol/gDw/h)
  Minimum Production Rate : 0.066521 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_h_e : 9.067039
  EX_cit_e : 7.400000
  EX_o2_e : 4.066990
  EX_gly_e : 2.200000
  EX_cys__L_e : 1.000000
  EX_glc__D_e : 0.234822
  EX_pi_e : 0.168085
  EX_lys__L_e : 0.031013
  EX_phe__L_e : 0.023570
  EX_met__L_e : 0.017367
  EX_tyr__L_e : 0.016127

Product: (mmol/gDw/h)
  EX_co2_e : 14.607631
  EX_succ_e : 6.902374
  EX_h2o_e : 6.762335
  EX_h2s_e : 0.990937
  EX_ac_e : 0.569264
  EX_nh4_e : 0.425846
  EX_agm_e : 0.343555
  EX_glyald_e : 0.067175
  Auxiliary production reaction : 0.066521

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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