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 (10 of 110: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: STM3646 STM1749 STM2463 STM2285 STM3526 STM1290 STM4326 STM2947 STM3709 STM1135 STM3542 STM4485 STM0369 STM1448 STM1326 STM4062 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM1124 STM0007 STM2473 STM3708   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.186310 (mmol/gDw/h)
  Minimum Production Rate : 0.105891 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.053161
  EX_pi_e : 0.165224
  EX_k_e : 0.033089
  EX_so4_e : 0.022726
  EX_mg2_e : 0.001471
  EX_fe2_e : 0.001365
  EX_ca2_e : 0.000883
  EX_cl_e : 0.000883
  EX_cu2_e : 0.000588
  EX_mn2_e : 0.000588
  EX_mobd_e : 0.000588
  EX_zn2_e : 0.000588
  EX_cobalt2_e : 0.000588

Product: (mmol/gDw/h)
  EX_h2o_e : 24.877559
  EX_co2_e : 19.635419
  EX_h_e : 1.579465
  EX_acald_e : 0.149282
  Auxiliary production reaction : 0.105891
  DM_hmfurn_c : 0.000083

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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