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 : 12dgr180_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (28 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: STM3646 STM1749 STM2463 STM4108 STM2285 STM3526 STM0322 STM3091 STM0169 STM0861 STM4326 STM2952 STM3709 STM3529 STM1135 STM1448 STM3062 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM2338 STM2466   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.216639 (mmol/gDw/h)
  Minimum Production Rate : 0.028056 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.387395
  EX_pi_e : 0.192121
  EX_k_e : 0.038475
  EX_so4_e : 0.026426
  EX_mg2_e : 0.001710
  EX_fe2_e : 0.001588
  EX_ca2_e : 0.001026
  EX_cl_e : 0.001026
  EX_cu2_e : 0.000684
  EX_mn2_e : 0.000684
  EX_mobd_e : 0.000684
  EX_zn2_e : 0.000684
  EX_cobalt2_e : 0.000684

Product: (mmol/gDw/h)
  EX_h2o_e : 25.180326
  EX_co2_e : 19.179890
  EX_h_e : 1.956525
  EX_acald_e : 0.552697
  EX_ac_e : 0.119939
  Auxiliary production reaction : 0.028056
  EX_glyald_e : 0.000150
  DM_hmfurn_c : 0.000097

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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