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 : prfp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (15 of 120: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 14
  Gene deletion: STM2927 STM1749 STM2463 STM3680 STM2009 STM1750 STM4570 STM3709 STM0974 STM0152 STM0150 STM0542 STM0935 STM4569   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.333666 (mmol/gDw/h)
  Minimum Production Rate : 0.027854 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 10.941369
  EX_nh4_e : 5.068448
  EX_glc__D_e : 5.000000
  EX_pi_e : 0.351611
  EX_k_e : 0.059259
  EX_so4_e : 0.040701
  EX_mg2_e : 0.002634
  EX_fe2_e : 0.002445
  EX_cl_e : 0.001581
  EX_ca2_e : 0.001581
  EX_cu2_e : 0.001054
  EX_mn2_e : 0.001054
  EX_mobd_e : 0.001054
  EX_zn2_e : 0.001054
  EX_cobalt2_e : 0.001054

Product: (mmol/gDw/h)
  EX_h2o_e : 23.768807
  EX_co2_e : 10.464124
  EX_h_e : 4.220096
  EX_thymd_e : 0.619855
  Auxiliary production reaction : 0.027854
  EX_ade_e : 0.002484
  DM_hmfurn_c : 0.000149

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