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 (44 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: STM3646 STM0158 STM2285 STM3526 STM0322 STM0169 STM4567 STM0861 STM4326 STM1511 STM0517 STM2947 STM3709 STM3068 STM2141 STM1135 STM4183 STM1448 STM3069 STM4484 STM2317 STM3179 STM1480 STM4126 STM2196 STM3240 STM3708 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.220264 (mmol/gDw/h)
  Minimum Production Rate : 0.069505 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.427343
  EX_pi_e : 0.195336
  EX_k_e : 0.039119
  EX_so4_e : 0.026868
  EX_mg2_e : 0.001739
  EX_fe2_e : 0.001614
  EX_ca2_e : 0.001043
  EX_cl_e : 0.001043
  EX_cobalt2_e : 0.000696
  EX_cu2_e : 0.000696
  EX_mn2_e : 0.000696
  EX_mobd_e : 0.000696
  EX_zn2_e : 0.000696

Product: (mmol/gDw/h)
  EX_h2o_e : 25.444737
  EX_co2_e : 19.302917
  EX_h_e : 1.878331
  Auxiliary production reaction : 0.069505
  EX_glyclt_e : 0.011013
  DM_hmfurn_c : 0.000098

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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