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_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (29 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: STM3646 STM4108 STM2285 STM3526 STM1290 STM4570 STM4326 STM1511 STM1884 STM3529 STM1135 STM3597 STM4408 STM1291 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM2338 STM2466 STM0218 STM1124 STM0402 STM0608   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.256772 (mmol/gDw/h)
  Minimum Production Rate : 0.034136 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.829659
  EX_pi_e : 0.227711
  EX_k_e : 0.045603
  EX_so4_e : 0.031322
  EX_mg2_e : 0.002027
  EX_fe2_e : 0.001882
  EX_ca2_e : 0.001216
  EX_cl_e : 0.001216
  EX_cobalt2_e : 0.000811
  EX_cu2_e : 0.000811
  EX_mn2_e : 0.000811
  EX_mobd_e : 0.000811
  EX_zn2_e : 0.000811

Product: (mmol/gDw/h)
  EX_h2o_e : 25.969198
  EX_co2_e : 18.856302
  EX_h_e : 2.252987
  EX_ac_e : 0.076174
  Auxiliary production reaction : 0.034136
  EX_glyald_e : 0.000178
  DM_hmfurn_c : 0.000115

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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