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_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (28 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: STM1463 STM1749 STM2463 STM2285 STM3526 STM0322 STM4326 STM1511 STM3068 STM2141 STM1620 STM3542 STM4485 STM0368 STM1448 STM3069 STM0518 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM2338 STM2466   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.234069 (mmol/gDw/h)
  Minimum Production Rate : 0.051334 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.579467
  EX_pi_e : 0.207577
  EX_k_e : 0.041571
  EX_so4_e : 0.028552
  EX_mg2_e : 0.001848
  EX_fe2_e : 0.001715
  EX_ca2_e : 0.001109
  EX_cl_e : 0.001109
  EX_cobalt2_e : 0.000739
  EX_cu2_e : 0.000739
  EX_mn2_e : 0.000739
  EX_mobd_e : 0.000739
  EX_zn2_e : 0.000739

Product: (mmol/gDw/h)
  EX_h2o_e : 25.575865
  EX_co2_e : 19.071659
  EX_h_e : 2.125635
  EX_ac_e : 0.129588
  Auxiliary production reaction : 0.051334
  EX_glyclt_e : 0.011703
  DM_hmfurn_c : 0.000104

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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