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 : aps_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (101 of 102: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: STM3646 STM3747 STM0051 STM2421 STM1749 STM2463 STM4275 STM3554 STM4568 STM4570 STM1135 STM2167 STM3961 STM2282 STM0974 STM0152 STM1211 STM2317 STM1480 STM2338 STM2466 STM2422 STM3802 STM2196 STM3240 STM2970 STM3243 STM3708 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.235148 (mmol/gDw/h)
  Minimum Production Rate : 0.182449 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 17.895680
  EX_glc__D_e : 5.000000
  EX_nh4_e : 3.503611
  EX_pi_e : 0.390984
  EX_so4_e : 0.211133
  EX_k_e : 0.041762
  EX_mg2_e : 0.001856
  EX_fe2_e : 0.001723
  EX_ca2_e : 0.001114
  EX_cl_e : 0.001114
  EX_cobalt2_e : 0.000743
  EX_cu2_e : 0.000743
  EX_mn2_e : 0.000743
  EX_mobd_e : 0.000743
  EX_zn2_e : 0.000743

Product: (mmol/gDw/h)
  EX_h2o_e : 26.229569
  EX_co2_e : 17.375094
  EX_h_e : 3.392971
  EX_ac_e : 0.852126
  Auxiliary production reaction : 0.182449
  DM_hmfurn_c : 0.000105

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