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 : 12dgr161_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (43 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: STM3646 STM2285 STM3526 STM0169 STM0861 STM4326 STM1511 STM0840 STM0842 STM0517 STM1135 STM4183 STM0369 STM1448 STM3062 STM0772 STM4585 STM3704 STM4484 STM2317 STM3179 STM4569 STM1480 STM4126 STM2338 STM2466 STM1124   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.255778 (mmol/gDw/h)
  Minimum Production Rate : 0.031031 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.818704
  EX_pi_e : 0.226830
  EX_k_e : 0.045426
  EX_so4_e : 0.031200
  EX_mg2_e : 0.002019
  EX_fe2_e : 0.001875
  EX_ca2_e : 0.001212
  EX_cl_e : 0.001212
  EX_cobalt2_e : 0.000808
  EX_cu2_e : 0.000808
  EX_mn2_e : 0.000808
  EX_mobd_e : 0.000808
  EX_zn2_e : 0.000808

Product: (mmol/gDw/h)
  EX_h2o_e : 25.986856
  EX_co2_e : 18.842409
  EX_h_e : 2.257053
  EX_ac_e : 0.075879
  Auxiliary production reaction : 0.031031
  EX_glyclt_e : 0.012789
  DM_hmfurn_c : 0.000114

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.

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Last updated: 27-Sep-2023
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