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 : 4abut_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (99 of 112: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: STM3646 STM1303 STM1463 STM0620 STM2792 STM2285 STM3526 STM4326 STM1511 STM2952 STM0840 STM0842 STM1135 STM4183 STM4408 STM1291 STM3069 STM4484 STM0399 STM0935 STM3179 STM1480 STM4126 STM2338 STM2466 STM1124 STM4467 STM0733 STM0402 STM0608 STM1341   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.081404 (mmol/gDw/h)
  Minimum Production Rate : 1.061605 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 10.448049
  EX_glc__D_e : 5.000000
  EX_nh4_e : 3.410185
  EX_pi_e : 0.072189
  EX_k_e : 0.014457
  EX_so4_e : 0.009930
  EX_mg2_e : 0.000643
  EX_fe2_e : 0.000597
  EX_ca2_e : 0.000386
  EX_cl_e : 0.000386
  EX_cobalt2_e : 0.000257
  EX_cu2_e : 0.000257
  EX_mn2_e : 0.000257
  EX_mobd_e : 0.000257
  EX_zn2_e : 0.000257

Product: (mmol/gDw/h)
  EX_h2o_e : 16.439542
  EX_co2_e : 11.682292
  EX_h_e : 5.761400
  EX_ac_e : 2.558183
  Auxiliary production reaction : 2.513115
  DM_hmfurn_c : 0.000036

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