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 : 12ppd__R_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (86 of 101: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: STM0758 STM4061 STM3747 STM3952 STM4275 STM0371 STM4340 STM1522 STM3091 STM3066 STM3614 STM3866 STM1771 STM0866 STM0086 STM3457 STM0974 STM2472 STM0785 STM0832 STM1480 STM1806 STM0039 STM2338 STM2466 STM2041 STM4301 STM3599 STM4325 STM0627 STM3959 STM4456 STM3763   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.014697 (mmol/gDw/h)
  Minimum Production Rate : 0.061183 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.161959
  EX_o2_e : 0.035343
  EX_pi_e : 0.013031
  EX_k_e : 0.002610
  EX_so4_e : 0.001792
  EX_mg2_e : 0.000116
  EX_fe3_e : 0.000108
  EX_ca2_e : 0.000070
  EX_cl_e : 0.000070
  EX_cobalt2_e : 0.000046
  EX_cu2_e : 0.000046
  EX_mn2_e : 0.000046
  EX_mobd_e : 0.000046
  EX_zn2_e : 0.000046

Product: (mmol/gDw/h)
  EX_h_e : 9.911769
  EX_lac__D_e : 9.581351
  EX_h2o_e : 0.436461
  EX_ac_e : 0.205635
  EX_co2_e : 0.092491
  EX_12ppd__R_e : 0.061176
  EX_succ_e : 0.000040

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 (2023).
[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: 09-Jul-2025
Contact