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 : dhna_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (61 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: STM1749 STM2463 STM3680 STM2285 STM3526 STM1886 STM0169 STM0861 STM3866 STM1620 STM2167 STM0974 STM2472 STM0150 STM0568 STM0542 STM1211 STM2317 STM0935 STM3179 STM2338 STM2466 STM1937 STM0733 STM0007 STM2473 STM0054 STM3353   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.011837 (mmol/gDw/h)
  Minimum Production Rate : 0.008147 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.130436
  EX_pi_e : 0.010495
  EX_o2_e : 0.002343
  EX_k_e : 0.002102
  EX_so4_e : 0.001443
  EX_mg2_e : 0.000093
  EX_fe2_e : 0.000087
  EX_ca2_e : 0.000056
  EX_cl_e : 0.000056
  EX_cu2_e : 0.000037
  EX_mn2_e : 0.000037
  EX_mobd_e : 0.000037
  EX_zn2_e : 0.000037
  EX_cobalt2_e : 0.000037

Product: (mmol/gDw/h)
  EX_h_e : 9.909402
  EX_lac__D_e : 9.781829
  EX_h2o_e : 0.389510
  EX_etoh_e : 0.020913
  EX_pyr_e : 0.014995
  EX_co2_e : 0.012213
  Auxiliary production reaction : 0.008131
  EX_ac_e : 0.003511
  EX_glyclt_e : 0.000592

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
Contact