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 : paps_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (106 of 107: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: STM2927 STM4275 STM2555 STM2285 STM2009 STM3526 STM0169 STM0861 STM1750 STM4570 STM2283 STM1620 STM2167 STM3961 STM0694 STM3045 STM0974 STM0152 STM0785 STM1211 STM2317 STM0935 STM3179 STM4569 STM2338 STM2466   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.015432 (mmol/gDw/h)
  Minimum Production Rate : 0.001623 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.178178
  EX_co2_e : 0.049060
  EX_pi_e : 0.016701
  EX_so4_e : 0.003391
  EX_o2_e : 0.003055
  EX_k_e : 0.002741
  EX_mg2_e : 0.000122
  EX_fe2_e : 0.000113
  EX_ca2_e : 0.000073
  EX_cl_e : 0.000073
  EX_cobalt2_e : 0.000049
  EX_cu2_e : 0.000049
  EX_mn2_e : 0.000049
  EX_mobd_e : 0.000049
  EX_zn2_e : 0.000049

Product: (mmol/gDw/h)
  EX_h_e : 9.949869
  EX_lac__D_e : 9.721732
  EX_h2o_e : 0.485496
  EX_pyr_e : 0.086861
  EX_ac_e : 0.004577
  Auxiliary production reaction : 0.001509
  EX_glyclt_e : 0.000772
  EX_ade_e : 0.000115

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