MetNetComp Database [1] / Minimal gene deletions Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : STM_v1_0 [2].
Target metabolite : dhna_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (30 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: STM3646 STM1749 STM2463 STM0737 STM2654 STM0441 STM4283 STM3866 STM1884 STM0517 STM1135 STM2167 STM2081 STM0974 STM1566 STM2472 STM1211 STM2317 STM0935 STM3500 STM2338 STM2466 STM3218 STM0007 STM2473 STM0054 STM3353   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.015758 (mmol/gDw/h)
  Minimum Production Rate : 0.010823 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 5.037830
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.173653
  EX_pi_e : 0.013972
  EX_k_e : 0.002799
  EX_so4_e : 0.001921
  EX_mg2_e : 0.000124
  EX_fe2_e : 0.000115
  EX_ca2_e : 0.000075
  EX_cl_e : 0.000075
  EX_cobalt2_e : 0.000050
  EX_cu2_e : 0.000050
  EX_mn2_e : 0.000050
  EX_mobd_e : 0.000050
  EX_zn2_e : 0.000050

Product: (mmol/gDw/h)
  EX_h2o_e : 10.218859
  EX_h_e : 9.719360
  EX_pyr_e : 9.453540
  EX_co2_e : 0.255135
  EX_idon__L_e : 0.103204
  EX_ac_e : 0.018201
  Auxiliary production reaction : 0.010825

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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