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 : 12dgr140_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (24 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: STM1749 STM2463 STM2285 STM3526 STM0322 STM0169 STM0861 STM4326 STM1511 STM0840 STM0842 STM2947 STM1620 STM0370 STM1448 STM3069 STM0518 STM4184 STM4484 STM2317 STM3179 STM4569 STM1480 STM4126 STM3708   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.239742 (mmol/gDw/h)
  Minimum Production Rate : 0.011669 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.641985
  EX_pi_e : 0.212609
  EX_k_e : 0.042578
  EX_so4_e : 0.029244
  EX_mg2_e : 0.001893
  EX_fe2_e : 0.001757
  EX_ca2_e : 0.001136
  EX_cl_e : 0.001136
  EX_cobalt2_e : 0.000757
  EX_cu2_e : 0.000757
  EX_mn2_e : 0.000757
  EX_mobd_e : 0.000757
  EX_zn2_e : 0.000757

Product: (mmol/gDw/h)
  EX_h2o_e : 25.548341
  EX_co2_e : 18.927403
  EX_h_e : 2.044425
  EX_acald_e : 0.706526
  EX_glyclt_e : 0.011987
  Auxiliary production reaction : 0.011669
  DM_hmfurn_c : 0.000107

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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