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 : dpcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (18 of 18: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 17
  Gene deletion: YPO2161 YPO0459 YPO3992 YPO0347 YPO1845 YPO1511 YPO3034 YPO2552 YPO3142 YPO3358 YPO2067 YPO3376 YPO2074 YPO3520 YPO1138 YPO0921 YPO2393   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.128797 (mmol/gDw/h)
  Minimum Production Rate : 0.038672 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_cit_e : 7.400000
  EX_h_e : 7.169953
  EX_o2_e : 5.545131
  EX_gly_e : 2.200000
  EX_glc__D_e : 0.484189
  EX_pi_e : 0.182793
  EX_cys__L_e : 0.048082
  EX_pnto__R_e : 0.038679
  EX_lys__L_e : 0.032199
  EX_phe__L_e : 0.024471
  EX_met__L_e : 0.018032
  EX_tyr__L_e : 0.016744

Product: (mmol/gDw/h)
  EX_co2_e : 13.525266
  EX_h2o_e : 8.704841
  EX_succ_e : 7.400000
  EX_ac_e : 0.410000
  EX_uri_e : 0.279026
  Auxiliary production reaction : 0.038672
  EX_ade_e : 0.000902
  EX_glyald_e : 0.000679

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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