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 : adphep_LD_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (89 of 92: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: STM3747 STM0051 STM2421 STM1749 STM2463 STM4275 STM2391 STM4568 STM4570 STM3866 STM0974 STM0152 STM0150 STM2338 STM2466 STM2422 STM3802 STM2196 STM3240 STM2970 STM3243 STM3708 STM2971 STM1826 STM2392 STM2393   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.014438 (mmol/gDw/h)
  Minimum Production Rate : 0.011194 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 5.000000
  EX_o2_e : 4.781480
  EX_nh4_e : 0.215102
  EX_co2_e : 0.072387
  EX_pi_e : 0.035201
  EX_k_e : 0.002564
  EX_so4_e : 0.001760
  EX_mg2_e : 0.000114
  EX_fe2_e : 0.000106
  EX_ca2_e : 0.000068
  EX_cl_e : 0.000068
  EX_cobalt2_e : 0.000046
  EX_cu2_e : 0.000046
  EX_mn2_e : 0.000046
  EX_mobd_e : 0.000046
  EX_zn2_e : 0.000046

Product: (mmol/gDw/h)
  EX_h2o_e : 10.173540
  EX_h_e : 9.900150
  EX_pyr_e : 9.739150
  EX_etoh_e : 0.048033
  Auxiliary production reaction : 0.011200
  EX_ac_e : 0.004282
  EX_glyclt_e : 0.000722

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