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 : ocdca_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (4 of 13: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: STM0158 STM1463 STM4482 STM1749 STM2463 STM2285 STM3526 STM3512 STM3541 STM4326 STM3709 STM3068 STM2141 STM1620 STM1448 STM3069 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM3248 STM0519 STM1124 STM3802 STM2196 STM3240 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.231407 (mmol/gDw/h)
  Minimum Production Rate : 0.004090 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.550134
  EX_pi_e : 0.205217
  EX_k_e : 0.041098
  EX_so4_e : 0.028227
  EX_mg2_e : 0.001827
  EX_fe2_e : 0.001696
  EX_ca2_e : 0.001096
  EX_cl_e : 0.001096
  EX_cu2_e : 0.000731
  EX_mn2_e : 0.000731
  EX_mobd_e : 0.000731
  EX_zn2_e : 0.000731
  EX_cobalt2_e : 0.000731

Product: (mmol/gDw/h)
  EX_h2o_e : 25.340649
  EX_co2_e : 18.961158
  EX_h_e : 1.977439
  EX_acald_e : 0.995328
  EX_glyclt_e : 0.011570
  Auxiliary production reaction : 0.004090
  DM_hmfurn_c : 0.000103

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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