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 : 12dgr180_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (24 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: STM1463 STM1749 STM2463 STM2285 STM3526 STM0322 STM0169 STM0861 STM4326 STM2947 STM1620 STM0369 STM1448 STM1326 STM4062 STM3069 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM3248 STM0519 STM3708   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.191708 (mmol/gDw/h)
  Minimum Production Rate : 0.067358 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.112647
  EX_pi_e : 0.170011
  EX_k_e : 0.034047
  EX_so4_e : 0.023385
  EX_mg2_e : 0.001514
  EX_fe2_e : 0.001405
  EX_ca2_e : 0.000908
  EX_cl_e : 0.000908
  EX_cobalt2_e : 0.000605
  EX_cu2_e : 0.000605
  EX_mn2_e : 0.000605
  EX_mobd_e : 0.000605
  EX_zn2_e : 0.000605

Product: (mmol/gDw/h)
  EX_h2o_e : 24.983288
  EX_co2_e : 19.630868
  EX_h_e : 1.634812
  EX_acald_e : 0.153607
  Auxiliary production reaction : 0.067358
  EX_glyclt_e : 0.009585
  DM_hmfurn_c : 0.000086

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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