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 : 2odecg3p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (13 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: STM3646 STM0158 STM2285 STM3526 STM4326 STM2952 STM1299 STM2947 STM3709 STM1135 STM4183 STM0974 STM1448 STM1326 STM4062 STM4484 STM0542 STM2317 STM3179 STM4569 STM1480 STM4126 STM0977 STM1124 STM3708   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.277776 (mmol/gDw/h)
  Minimum Production Rate : 0.005349 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 3.061131
  EX_pi_e : 0.251688
  EX_k_e : 0.049333
  EX_so4_e : 0.033884
  EX_mg2_e : 0.002193
  EX_fe2_e : 0.002036
  EX_ca2_e : 0.001316
  EX_cl_e : 0.001316
  EX_cobalt2_e : 0.000877
  EX_cu2_e : 0.000877
  EX_mn2_e : 0.000877
  EX_mobd_e : 0.000877
  EX_zn2_e : 0.000877

Product: (mmol/gDw/h)
  EX_h2o_e : 26.129012
  EX_co2_e : 18.465846
  EX_h_e : 2.684409
  EX_ac_e : 0.327933
  EX_glyc__R_e : 0.006944
  Auxiliary production reaction : 0.005349
  DM_hmfurn_c : 0.000124

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