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 : 4ampm_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (16 of 19: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 13
  Gene deletion: YPO0357 YPO2180 YPO2161 YPO0059 YPO3992 YPO0347 YPO2288 YPO3142 YPO3358 YPO2559 YPO2533 YPO0914 YPO1133   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.218404 (mmol/gDw/h)
  Minimum Production Rate : 0.242543 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 14.739965
  EX_cit_e : 7.400000
  EX_h_e : 7.032434
  EX_gly_e : 2.200000
  EX_glc__D_e : 2.000000
  EX_cys__L_e : 1.000000
  EX_pi_e : 0.421356
  EX_lys__L_e : 0.054601
  EX_phe__L_e : 0.041497
  EX_met__L_e : 0.030577
  EX_tyr__L_e : 0.028393
  EX_pnto__R_e : 0.000013

Product: (mmol/gDw/h)
  EX_co2_e : 23.504264
  EX_h2o_e : 17.981851
  EX_succ_e : 7.400000
  EX_h2s_e : 0.984044
  EX_ac_e : 0.410000
  Auxiliary production reaction : 0.242543
  EX_for_e : 0.065988
  EX_ade_e : 0.001529

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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