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 (29 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: STM3646 STM4108 STM2285 STM3526 STM4326 STM1511 STM1885 STM0321 STM3529 STM1135 STM3597 STM4408 STM1291 STM3069 STM4184 STM4484 STM2317 STM3179 STM4569 STM1480 STM4126 STM2338 STM2466 STM0402 STM0608   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.256315 (mmol/gDw/h)
  Minimum Production Rate : 0.028268 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.824622
  EX_pi_e : 0.227306
  EX_k_e : 0.045521
  EX_so4_e : 0.031266
  EX_mg2_e : 0.002024
  EX_fe2_e : 0.001879
  EX_ca2_e : 0.001214
  EX_cl_e : 0.001214
  EX_cobalt2_e : 0.000809
  EX_cu2_e : 0.000809
  EX_mn2_e : 0.000809
  EX_mobd_e : 0.000809
  EX_zn2_e : 0.000809

Product: (mmol/gDw/h)
  EX_h2o_e : 25.962312
  EX_co2_e : 18.811350
  EX_h_e : 2.314842
  EX_ac_e : 0.141904
  Auxiliary production reaction : 0.028268
  EX_glyald_e : 0.000178
  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.

Last updated: 27-Sep-2023
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