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 (46 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: STM3646 STM1749 STM2463 STM2285 STM3526 STM1290 STM4326 STM1885 STM0840 STM0842 STM0517 STM3709 STM1135 STM2081 STM4183 STM0369 STM1448 STM2403 STM0393 STM4484 STM2317 STM3179 STM1480 STM4126 STM2338 STM2466 STM1124   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.216482 (mmol/gDw/h)
  Minimum Production Rate : 0.030588 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.385664
  EX_pi_e : 0.191982
  EX_k_e : 0.038447
  EX_so4_e : 0.026407
  EX_mg2_e : 0.001709
  EX_fe2_e : 0.001587
  EX_ca2_e : 0.001025
  EX_cl_e : 0.001025
  EX_cu2_e : 0.000684
  EX_mn2_e : 0.000684
  EX_mobd_e : 0.000684
  EX_zn2_e : 0.000684
  EX_cobalt2_e : 0.000684

Product: (mmol/gDw/h)
  EX_h2o_e : 25.158223
  EX_co2_e : 19.159586
  EX_h_e : 1.910301
  EX_acald_e : 0.683994
  EX_ac_e : 0.064222
  Auxiliary production reaction : 0.030588
  EX_glyclt_e : 0.010824
  DM_hmfurn_c : 0.000097

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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