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 (60 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: STM3646 STM1749 STM2463 STM2122 STM2285 STM3526 STM0169 STM0861 STM4570 STM4326 STM1511 STM2952 STM1299 STM2947 STM1135 STM4183 STM0368 STM0974 STM1448 STM1326 STM4062 STM4484 STM2317 STM3179 STM1480 STM4126 STM0977 STM1124 STM3708   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.137279 (mmol/gDw/h)
  Minimum Production Rate : 0.016997 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 1.512831
  EX_pi_e : 0.138740
  EX_k_e : 0.024381
  EX_so4_e : 0.016746
  EX_mg2_e : 0.001084
  EX_fe2_e : 0.001006
  EX_ca2_e : 0.000650
  EX_cl_e : 0.000650
  EX_cobalt2_e : 0.000434
  EX_cu2_e : 0.000434
  EX_mn2_e : 0.000434
  EX_mobd_e : 0.000434
  EX_zn2_e : 0.000434

Product: (mmol/gDw/h)
  EX_h2o_e : 23.553565
  EX_co2_e : 19.752025
  EX_acald_e : 2.290360
  EX_h_e : 1.146800
  Auxiliary production reaction : 0.016997
  DM_hmfurn_c : 0.000061

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