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 : pa140_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (7 of 43: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: STM2927 STM2285 STM3526 STM4326 STM1511 STM1885 STM2952 STM0321 STM0840 STM0842 STM1620 STM0370 STM1448 STM0518 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM4578 STM2338 STM2466 STM2332 STM3968   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.255621 (mmol/gDw/h)
  Minimum Production Rate : 0.031718 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.816983
  EX_pi_e : 0.258409
  EX_k_e : 0.045398
  EX_so4_e : 0.031181
  EX_mg2_e : 0.002018
  EX_fe2_e : 0.001873
  EX_ca2_e : 0.001211
  EX_cl_e : 0.001211
  EX_cobalt2_e : 0.000807
  EX_cu2_e : 0.000807
  EX_mn2_e : 0.000807
  EX_mobd_e : 0.000807
  EX_zn2_e : 0.000807

Product: (mmol/gDw/h)
  EX_h2o_e : 25.930497
  EX_co2_e : 18.820011
  EX_h_e : 2.321363
  EX_ac_e : 0.141520
  Auxiliary production reaction : 0.031718
  EX_glyclt_e : 0.012781
  DM_hmfurn_c : 0.000114

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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