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 (19 of 19: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: YPO3371 YPO1384 YPO4078 YPO3825 YPO3937 YPO3428 YPO3095 YPO0348 YPO3225 YPO3408 YPO1963 YPO3725 YPO3319 YPO1207 YPO0070 YPO1771 YPO2552 YPO0670 YPO2303 YPO3914 YPO3064 YPO2295 YPO3358 YPO2559 YPO1851 YPO3418   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.232020 (mmol/gDw/h)
  Minimum Production Rate : 0.010391 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_h_e : 21.905180
  EX_o2_e : 11.679922
  EX_cit_e : 7.400000
  EX_gly_e : 2.200000
  EX_glc__D_e : 2.000000
  EX_cys__L_e : 1.000000
  EX_pi_e : 0.347196
  EX_lys__L_e : 0.058005
  EX_phe__L_e : 0.044084
  EX_met__L_e : 0.032483
  EX_tyr__L_e : 0.030163
  EX_pnto__R_e : 0.000014

Product: (mmol/gDw/h)
  EX_co2_e : 33.145135
  EX_h2o_e : 13.133109
  EX_etoh_e : 6.543478
  EX_h2s_e : 0.983049
  EX_ser__L_e : 0.581622
  EX_ac_e : 0.410000
  Auxiliary production reaction : 0.157236
  EX_glyc_e : 0.001223

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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