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 : methf_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (94 of 126: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: STM2927 STM2421 STM0413 STM1749 STM2463 STM4275 STM2009 STM4568 STM1511 STM0694 STM3045 STM0974 STM0152 STM0150 STM3957 STM3279 STM2338 STM2466 STM2332 STM0588 STM2196 STM3240 STM2970 STM3243 STM3708 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.243085 (mmol/gDw/h)
  Minimum Production Rate : 0.400189 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 11.667159
  EX_nh4_e : 5.489205
  EX_glc__D_e : 5.000000
  EX_pi_e : 0.215574
  EX_k_e : 0.043172
  EX_so4_e : 0.029652
  EX_mg2_e : 0.001919
  EX_fe2_e : 0.001782
  EX_cl_e : 0.001151
  EX_ca2_e : 0.001151
  EX_cobalt2_e : 0.000768
  EX_cu2_e : 0.000768
  EX_mn2_e : 0.000768
  EX_mobd_e : 0.000768
  EX_zn2_e : 0.000768

Product: (mmol/gDw/h)
  EX_h2o_e : 25.118754
  EX_co2_e : 10.395427
  EX_h_e : 6.365626
  EX_ac_e : 1.094279
  Auxiliary production reaction : 0.400189
  EX_ade_e : 0.001810
  DM_hmfurn_c : 0.000108

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