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 : 12dgr120_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (7 of 110: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: STM4482 STM2285 STM3526 STM0322 STM3512 STM3541 STM4326 STM1511 STM2952 STM1620 STM1448 STM1326 STM4062 STM0518 STM4184 STM4484 STM2317 STM3179 STM4569 STM1480 STM4126 STM2338 STM2466 STM0977 STM2041   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.242450 (mmol/gDw/h)
  Minimum Production Rate : 0.050699 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.671828
  EX_pi_e : 0.215010
  EX_k_e : 0.043059
  EX_so4_e : 0.029574
  EX_mg2_e : 0.001914
  EX_fe2_e : 0.001777
  EX_ca2_e : 0.001148
  EX_cl_e : 0.001148
  EX_cobalt2_e : 0.000766
  EX_cu2_e : 0.000766
  EX_mn2_e : 0.000766
  EX_mobd_e : 0.000766
  EX_zn2_e : 0.000766

Product: (mmol/gDw/h)
  EX_h2o_e : 25.694441
  EX_co2_e : 18.959817
  EX_h_e : 2.201747
  EX_ac_e : 0.134228
  Auxiliary production reaction : 0.050699
  EX_glyclt_e : 0.012122
  DM_hmfurn_c : 0.000108

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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