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 (81 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: STM0620 STM4482 STM2792 STM1749 STM2463 STM4275 STM0371 STM0737 STM2654 STM0441 STM1756 STM1886 STM4283 STM1511 STM3866 STM1620 STM2167 STM3542 STM4485 STM2472 STM4184 STM1211 STM2317 STM0935 STM2338 STM2466 STM0007 STM2473 STM0054 STM3353   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.013950 (mmol/gDw/h)
  Minimum Production Rate : 0.009582 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.153724
  EX_o2_e : 0.049091
  EX_pi_e : 0.012369
  EX_k_e : 0.002478
  EX_so4_e : 0.001701
  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 : 9.904398
  EX_lac__D_e : 9.756958
  EX_h2o_e : 0.496553
  EX_co2_e : 0.044918
  EX_ac_e : 0.018901
  Auxiliary production reaction : 0.009582
  EX_glyclt_e : 0.000697

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