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 : hxan_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (79 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: STM4482 STM1749 STM2463 STM4275 STM0441 STM2285 STM3526 STM3512 STM3541 STM1620 STM2167 STM0974 STM0152 STM0785 STM1211 STM2317 STM3179 STM2338 STM2466 STM3968 STM4452 STM3802 STM2196 STM3240 STM2970 STM3243 STM0007 STM2473 STM3708 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.013915 (mmol/gDw/h)
  Minimum Production Rate : 0.011819 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.209114
  EX_o2_e : 0.092313
  EX_pi_e : 0.012337
  EX_k_e : 0.002471
  EX_so4_e : 0.001697
  EX_mg2_e : 0.000110
  EX_fe2_e : 0.000102
  EX_ca2_e : 0.000066
  EX_cl_e : 0.000066
  EX_cobalt2_e : 0.000044
  EX_cu2_e : 0.000044
  EX_mn2_e : 0.000044
  EX_mobd_e : 0.000044
  EX_zn2_e : 0.000044

Product: (mmol/gDw/h)
  EX_h_e : 9.937721
  EX_lac__D_e : 9.580041
  EX_h2o_e : 0.604187
  EX_ac_e : 0.183245
  EX_co2_e : 0.115867
  EX_etoh_e : 0.047053
  EX_hxan_e : 0.011555
  EX_phe__L_e : 0.009558
  EX_glyclt_e : 0.000696

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