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 : psd5p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (21 of 29: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 8
  Gene deletion: STM2421 STM2122 STM0980 STM4578 STM2498 STM0733 STM0007 STM2473   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.272235 (mmol/gDw/h)
  Minimum Production Rate : 0.020388 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 5.813017
  EX_glc__D_e : 5.000000
  EX_nh4_e : 3.040844
  EX_pi_e : 0.261813
  EX_k_e : 0.048349
  EX_so4_e : 0.033208
  EX_mg2_e : 0.002149
  EX_fe2_e : 0.001995
  EX_ca2_e : 0.001290
  EX_cl_e : 0.001290
  EX_cobalt2_e : 0.000860
  EX_cu2_e : 0.000860
  EX_mn2_e : 0.000860
  EX_mobd_e : 0.000860
  EX_zn2_e : 0.000860

Product: (mmol/gDw/h)
  EX_h2o_e : 13.355580
  EX_h_e : 9.096867
  EX_ac_e : 6.788962
  EX_co2_e : 5.707804
  Auxiliary production reaction : 0.020388
  DM_hmfurn_c : 0.000121

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