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 : pa161_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (20 of 110: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: STM2122 STM2285 STM3526 STM0169 STM0861 STM4570 STM4326 STM3709 STM1620 STM0368 STM1448 STM1326 STM4062 STM3069 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM2338 STM2466 STM3248 STM0519 STM1124 STM3708   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.235434 (mmol/gDw/h)
  Minimum Production Rate : 0.047422 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.594514
  EX_pi_e : 0.256211
  EX_k_e : 0.041813
  EX_so4_e : 0.028719
  EX_mg2_e : 0.001859
  EX_fe2_e : 0.001725
  EX_ca2_e : 0.001115
  EX_cl_e : 0.001115
  EX_cobalt2_e : 0.000744
  EX_cu2_e : 0.000744
  EX_mn2_e : 0.000744
  EX_mobd_e : 0.000744
  EX_zn2_e : 0.000744

Product: (mmol/gDw/h)
  EX_h2o_e : 25.749976
  EX_co2_e : 19.069774
  EX_h_e : 2.077535
  EX_ac_e : 0.069844
  Auxiliary production reaction : 0.047422
  EX_glyclt_e : 0.011772
  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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