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 : ppp9_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (9 of 20: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: STM4483 STM2421 STM0146 STM3680 STM1290 STM1884 STM0517 STM1570 STM4036 STM3359 STM1566 STM2472 STM2403 STM0393 STM0542 STM2317 STM1480 STM0700 STM2299 STM1933 STM3063 STM4301 STM3599 STM4325 STM0627   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.015755 (mmol/gDw/h)
  Minimum Production Rate : 0.001139 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 9.552803
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.209902
  EX_pi_e : 0.050265
  EX_k_e : 0.002798
  EX_so4_e : 0.001921
  EX_mg2_e : 0.000124
  EX_fe2_e : 0.000115
  EX_ca2_e : 0.000075
  EX_cl_e : 0.000075
  EX_cu2_e : 0.000050
  EX_mn2_e : 0.000050
  EX_mobd_e : 0.000050
  EX_zn2_e : 0.000050
  EX_cobalt2_e : 0.000049

Product: (mmol/gDw/h)
  EX_h2o_e : 10.953063
  EX_co2_e : 9.575518
  EX_h_e : 9.351499
  EX_ac_e : 7.729881
  EX_succ_e : 0.707346
  EX_kdo2lipid4_e : 0.018148
  EX_glyclt_e : 0.000788

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