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 : dgdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (30 of 32: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 12
  Gene deletion: YPO2066 YPO2157 YPO2614 YPO3992 YPO0347 YPO0254 YPO2288 YPO3142 YPO2295 YPO3358 YPO2559 YPO2836   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.218492 (mmol/gDw/h)
  Minimum Production Rate : 0.145326 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_cit_e : 7.400000
  EX_h_e : 7.243791
  EX_o2_e : 5.163930
  EX_gly_e : 2.200000
  EX_cys__L_e : 1.000000
  EX_pi_e : 0.469539
  EX_glc__D_e : 0.358378
  EX_lys__L_e : 0.054623
  EX_phe__L_e : 0.041514
  EX_met__L_e : 0.030589
  EX_tyr__L_e : 0.028404
  EX_pnto__R_e : 0.000013

Product: (mmol/gDw/h)
  EX_co2_e : 13.719145
  EX_h2o_e : 8.389942
  EX_succ_e : 7.400000
  EX_h2s_e : 0.984037
  EX_ac_e : 0.410000
  Auxiliary production reaction : 0.145326
  EX_ade_e : 0.001529

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.

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Last updated: 27-Sep-2023
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