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 : 12dgr120_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (65 of 110: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: STM3646 STM2927 STM1749 STM2463 STM2285 STM2009 STM3526 STM4326 STM1511 STM1884 STM2947 STM3709 STM3068 STM2141 STM1135 STM2081 STM0368 STM1448 STM3069 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM2338 STM2466 STM1124 STM4467 STM2196 STM3240 STM0007 STM2473 STM3708 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.065038 (mmol/gDw/h)
  Minimum Production Rate : 0.076822 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 37.910155
  EX_h_e : 37.313636
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.761401
  EX_pi_e : 0.057676
  EX_k_e : 0.011551
  EX_so4_e : 0.007933
  EX_mg2_e : 0.000513
  EX_ca2_e : 0.000308
  EX_cl_e : 0.000308
  EX_cobalt2_e : 0.000205
  EX_cu2_e : 0.000205
  EX_mn2_e : 0.000205
  EX_mobd_e : 0.000205
  EX_zn2_e : 0.000205

Product: (mmol/gDw/h)
  EX_fe3_e : 37.909678
  EX_h2o_e : 30.964707
  EX_co2_e : 9.916681
  EX_dha_e : 4.919784
  EX_acald_e : 0.165926
  Auxiliary production reaction : 0.076822
  EX_tyr__L_e : 0.044679
  DM_hmfurn_c : 0.000029

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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