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 (41 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: STM0158 STM4108 STM2285 STM3526 STM4567 STM4326 STM1885 STM2952 STM0321 STM3709 STM3529 STM1620 STM0974 STM1448 STM0518 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM4578 STM3802 STM2196 STM3240 STM3708 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.236239 (mmol/gDw/h)
  Minimum Production Rate : 0.043391 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.603390
  EX_pi_e : 0.209503
  EX_k_e : 0.041956
  EX_so4_e : 0.028817
  EX_mg2_e : 0.001865
  EX_fe2_e : 0.001731
  EX_ca2_e : 0.001119
  EX_cl_e : 0.001119
  EX_cobalt2_e : 0.000746
  EX_cu2_e : 0.000746
  EX_mn2_e : 0.000746
  EX_mobd_e : 0.000746
  EX_zn2_e : 0.000746

Product: (mmol/gDw/h)
  EX_h2o_e : 25.701387
  EX_co2_e : 19.145278
  EX_h_e : 2.014560
  Auxiliary production reaction : 0.043391
  EX_glyclt_e : 0.011812
  EX_glyald_e : 0.000164
  DM_hmfurn_c : 0.000105

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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