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 (19 of 110: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: STM3646 STM1749 STM2463 STM2285 STM3526 STM3091 STM0169 STM0861 STM4326 STM1511 STM0517 STM1135 STM4183 STM0491 STM1448 STM1326 STM4062 STM3069 STM4484 STM2317 STM3179 STM1480 STM4126 STM2338 STM2466 STM1124 STM3708   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.261460 (mmol/gDw/h)
  Minimum Production Rate : 0.017452 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.881329
  EX_pi_e : 0.231869
  EX_k_e : 0.046435
  EX_so4_e : 0.031893
  EX_mg2_e : 0.002064
  EX_fe2_e : 0.001916
  EX_ca2_e : 0.001239
  EX_cl_e : 0.001239
  EX_cobalt2_e : 0.000826
  EX_cu2_e : 0.000826
  EX_mn2_e : 0.000826
  EX_mobd_e : 0.000826
  EX_zn2_e : 0.000826

Product: (mmol/gDw/h)
  EX_h2o_e : 25.830506
  EX_co2_e : 18.814533
  EX_h_e : 2.307200
  EX_etoh_e : 0.209497
  EX_ac_e : 0.077565
  Auxiliary production reaction : 0.017452
  EX_glyclt_e : 0.013073
  DM_hmfurn_c : 0.000117

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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