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 : phe__L_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (76 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: STM2285 STM3526 STM3091 STM1290 STM0169 STM0861 STM4326 STM1511 STM1620 STM0370 STM0785 STM0150 STM0518 STM4484 STM0568 STM2317 STM3500 STM3179 STM1480 STM4126 STM3248 STM0519 STM1937 STM0007 STM2473 STM0054 STM3353   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.237117 (mmol/gDw/h)
  Minimum Production Rate : 0.162900 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 4.875685
  EX_nh4_e : 2.775965
  EX_pi_e : 0.210281
  EX_k_e : 0.042112
  EX_so4_e : 0.028924
  EX_mg2_e : 0.001872
  EX_fe2_e : 0.001738
  EX_ca2_e : 0.001123
  EX_cl_e : 0.001123
  EX_cobalt2_e : 0.000749
  EX_cu2_e : 0.000749
  EX_mn2_e : 0.000749
  EX_mobd_e : 0.000749
  EX_zn2_e : 0.000749

Product: (mmol/gDw/h)
  EX_h2o_e : 25.943390
  EX_co2_e : 18.591968
  EX_h_e : 2.184947
  Auxiliary production reaction : 0.162900
  EX_glyclt_e : 0.011856
  DM_hmfurn_c : 0.000106

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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