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 (19 of 34: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: YPO1384 YPO4078 YPO3825 YPO3937 YPO0461 YPO0918 YPO3428 YPO0348 YPO3831 YPO3202 YPO0465 YPO1145 YPO3014 YPO1109 YPO0670 YPO2303 YPO3914 YPO1851 YPO3418 YPO2370 YPO0921 YPO2836 YPO0439 YPO0442 YPO2567   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.115813 (mmol/gDw/h)
  Minimum Production Rate : 0.010998 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_h_e : 7.860949
  EX_cit_e : 7.400000
  EX_o2_e : 5.697462
  EX_gly_e : 2.200000
  EX_cys__L_e : 1.000000
  EX_glc__D_e : 0.142569
  EX_pi_e : 0.105817
  EX_phe__L_e : 0.022004
  EX_met__L_e : 0.016214
  EX_tyr__L_e : 0.015056

Product: (mmol/gDw/h)
  EX_co2_e : 14.949644
  EX_succ_e : 7.256160
  EX_h2o_e : 5.644063
  EX_nh4_e : 1.835121
  EX_ac_e : 1.759288
  EX_h2s_e : 0.991539
  EX_glyald_e : 0.011608
  Auxiliary production reaction : 0.010998

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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