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 : 12dgr140_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (50 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: STM3646 STM2285 STM3526 STM0169 STM0861 STM4326 STM1511 STM2952 STM0321 STM2947 STM3709 STM3068 STM2141 STM1135 STM1448 STM4184 STM4484 STM2317 STM3179 STM4569 STM1480 STM4126 STM3241 STM0973 STM0977 STM2196 STM3240 STM2051 STM3708 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.220676 (mmol/gDw/h)
  Minimum Production Rate : 0.069521 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.431883
  EX_pi_e : 0.195701
  EX_k_e : 0.039192
  EX_so4_e : 0.026919
  EX_mg2_e : 0.001742
  EX_fe2_e : 0.001617
  EX_ca2_e : 0.001045
  EX_cl_e : 0.001045
  EX_cobalt2_e : 0.000697
  EX_cu2_e : 0.000697
  EX_mn2_e : 0.000697
  EX_mobd_e : 0.000697
  EX_zn2_e : 0.000697

Product: (mmol/gDw/h)
  EX_h2o_e : 25.461704
  EX_co2_e : 19.308511
  EX_h_e : 1.870810
  Auxiliary production reaction : 0.069521
  DM_hmfurn_c : 0.000098

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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