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 : malcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (23 of 24: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 16
  Gene deletion: YPO1384 YPO0793 YPO2157 YPO0253 YPO0460 YPO3285 YPO2288 YPO2824 YPO3358 YPO2559 YPO3383 YPO3520 YPO3418 YPO2827 YPO2567 YPO3786   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.196060 (mmol/gDw/h)
  Minimum Production Rate : 0.105786 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 17.632626
  EX_h_e : 15.263286
  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 : 0.477877
  EX_pnto__R_e : 0.105797
  EX_lys__L_e : 0.049015
  EX_phe__L_e : 0.037251
  EX_met__L_e : 0.027448
  EX_tyr__L_e : 0.025488

Product: (mmol/gDw/h)
  EX_co2_e : 29.682771
  EX_h2o_e : 18.309431
  EX_ac_e : 7.245614
  EX_h2s_e : 0.879890
  EX_lcts_e : 0.820387
  EX_ura_e : 0.172929
  Auxiliary production reaction : 0.105786
  EX_ade_e : 0.001372
  EX_glyald_e : 0.001033

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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