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 (32 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: STM3646 STM1749 STM2463 STM2285 STM3526 STM4326 STM1511 STM1885 STM2952 STM0840 STM0842 STM1135 STM0491 STM0974 STM1448 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM0977 STM1124 STM2041 STM3708   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.230356 (mmol/gDw/h)
  Minimum Production Rate : 0.010638 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.538557
  EX_pi_e : 0.204285
  EX_k_e : 0.040911
  EX_so4_e : 0.028099
  EX_mg2_e : 0.001819
  EX_fe2_e : 0.001688
  EX_ca2_e : 0.001091
  EX_cl_e : 0.001091
  EX_cobalt2_e : 0.000727
  EX_cu2_e : 0.000727
  EX_mn2_e : 0.000727
  EX_mobd_e : 0.000727
  EX_zn2_e : 0.000727

Product: (mmol/gDw/h)
  EX_h2o_e : 25.267392
  EX_co2_e : 18.906224
  EX_h_e : 2.249229
  EX_acald_e : 0.587692
  EX_ac_e : 0.296357
  Auxiliary production reaction : 0.010638
  DM_hmfurn_c : 0.000103

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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