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 : apg180_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (20 of 20: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: YPO1384 YPO4078 YPO3825 YPO3937 YPO2157 YPO3428 YPO3719 YPO0459 YPO3977 YPO0116 YPO0348 YPO0253 YPO3992 YPO0347 YPO1964 YPO0670 YPO2303 YPO3914 YPO3868 YPO3270 YPO0440 YPO3376 YPO1851 YPO3418 YPO2370 YPO2567 YPO1171   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.111826 (mmol/gDw/h)
  Minimum Production Rate : 0.046203 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_h_e : 8.389415
  EX_cit_e : 6.795030
  EX_o2_e : 3.634944
  EX_gly_e : 2.200000
  EX_cys__L_e : 1.000000
  EX_glc__D_e : 0.301406
  EX_pi_e : 0.248127
  EX_lys__L_e : 0.027956
  EX_phe__L_e : 0.021247
  EX_met__L_e : 0.015656
  EX_tyr__L_e : 0.014537

Product: (mmol/gDw/h)
  EX_co2_e : 13.401400
  EX_succ_e : 6.795030
  EX_h2o_e : 4.925384
  EX_nh4_e : 1.792306
  EX_h2s_e : 0.991830
  EX_ac_e : 0.410000
  EX_val__L_e : 0.145718
  EX_g3pg_e : 0.110370
  EX_glyald_e : 0.046792
  Auxiliary production reaction : 0.046203

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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