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 : pa160_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (50 of 128: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: STM3646 STM1749 STM2463 STM2285 STM3526 STM1290 STM0169 STM4567 STM0861 STM4326 STM0321 STM2947 STM1135 STM0369 STM3597 STM1326 STM4062 STM4408 STM1291 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM0402 STM0608 STM3708   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.191577 (mmol/gDw/h)
  Minimum Production Rate : 0.075920 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.111202
  EX_pi_e : 0.245815
  EX_k_e : 0.034024
  EX_so4_e : 0.023369
  EX_mg2_e : 0.001512
  EX_fe2_e : 0.001404
  EX_ca2_e : 0.000907
  EX_cl_e : 0.000907
  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 : 25.058366
  EX_co2_e : 19.625079
  EX_h_e : 1.624115
  EX_acald_e : 0.153502
  Auxiliary production reaction : 0.075920
  DM_hmfurn_c : 0.000085

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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