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 : 5caiz_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (98 of 109: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: STM3010 STM2927 STM2421 STM1749 STM2463 STM4275 STM2009 STM4567 STM1750 STM1511 STM3709 STM0974 STM0152 STM0150 STM2502 STM2501 STM2338 STM2466 STM2196 STM3240 STM2970 STM3243 STM2467 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.314270 (mmol/gDw/h)
  Minimum Production Rate : 0.482996 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 11.781856
  EX_glc__D_e : 5.000000
  EX_nh4_e : 4.923983
  EX_pi_e : 0.761698
  EX_k_e : 0.055814
  EX_so4_e : 0.038335
  EX_mg2_e : 0.002481
  EX_fe2_e : 0.002303
  EX_ca2_e : 0.001489
  EX_cl_e : 0.001489
  EX_cobalt2_e : 0.000992
  EX_cu2_e : 0.000992
  EX_mn2_e : 0.000992
  EX_mobd_e : 0.000992
  EX_zn2_e : 0.000992

Product: (mmol/gDw/h)
  EX_h2o_e : 23.275111
  EX_co2_e : 10.723859
  EX_h_e : 5.988286
  EX_ac_e : 1.380342
  Auxiliary production reaction : 0.482996
  EX_ade_e : 0.002340
  DM_hmfurn_c : 0.000140

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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