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 : pa180_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (13 of 19: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 21
  Gene deletion: YPO3371 YPO4078 YPO3825 YPO3937 YPO3428 YPO0348 YPO3992 YPO0347 YPO3725 YPO3319 YPO1207 YPO0070 YPO1771 YPO1966 YPO0670 YPO2303 YPO3914 YPO3064 YPO1851 YPO0078 YPO0439   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.221985 (mmol/gDw/h)
  Minimum Production Rate : 0.117814 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 5.447127
  EX_cit_e : 5.147787
  EX_h_e : 4.847986
  EX_gly_e : 2.200000
  EX_glc__D_e : 2.000000
  EX_cys__L_e : 1.000000
  EX_pi_e : 0.299560
  EX_lys__L_e : 0.055496
  EX_phe__L_e : 0.042177
  EX_met__L_e : 0.031078
  EX_tyr__L_e : 0.028858
  EX_pnto__R_e : 0.000013

Product: (mmol/gDw/h)
  EX_co2_e : 13.712534
  EX_h2o_e : 9.731296
  EX_succ_e : 5.147787
  EX_h2s_e : 0.983782
  EX_ser__L_e : 0.694860
  EX_ac_e : 0.410000
  Auxiliary production reaction : 0.117814

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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