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 : eig3p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (103 of 107: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: STM3646 STM2421 STM1749 STM2463 STM3680 STM4108 STM2009 STM4570 STM1885 STM2952 STM3709 STM1135 STM2167 STM0974 STM0152 STM3062 STM0542 STM1211 STM2317 STM0935 STM2422 STM3968 STM3885 STM3793 STM2498   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.194756 (mmol/gDw/h)
  Minimum Production Rate : 0.182399 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 3.154045
  EX_pi_e : 0.355114
  EX_k_e : 0.034589
  EX_so4_e : 0.023757
  EX_mg2_e : 0.001538
  EX_fe2_e : 0.001427
  EX_ca2_e : 0.000923
  EX_cl_e : 0.000923
  EX_cobalt2_e : 0.000615
  EX_cu2_e : 0.000615
  EX_mn2_e : 0.000615
  EX_mobd_e : 0.000615
  EX_zn2_e : 0.000615

Product: (mmol/gDw/h)
  EX_h2o_e : 25.706974
  EX_co2_e : 18.790961
  EX_h_e : 2.658874
  EX_etoh_e : 0.651094
  EX_his__L_e : 0.211918
  Auxiliary production reaction : 0.182399
  EX_ade_e : 0.001450
  DM_hmfurn_c : 0.000087

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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