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 : ddca_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (41 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: STM2285 STM3526 STM1290 STM4326 STM1885 STM0840 STM0842 STM2947 STM3709 STM1620 STM0369 STM1448 STM0518 STM4184 STM4484 STM2317 STM3179 STM4569 STM1480 STM4126 STM1124 STM3802 STM2196 STM3240 STM3708 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.254488 (mmol/gDw/h)
  Minimum Production Rate : 0.024006 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.804494
  EX_pi_e : 0.225686
  EX_k_e : 0.045197
  EX_so4_e : 0.031043
  EX_mg2_e : 0.002009
  EX_fe2_e : 0.001865
  EX_ca2_e : 0.001206
  EX_cl_e : 0.001206
  EX_cobalt2_e : 0.000804
  EX_cu2_e : 0.000804
  EX_mn2_e : 0.000804
  EX_mobd_e : 0.000804
  EX_zn2_e : 0.000804

Product: (mmol/gDw/h)
  EX_h2o_e : 25.559707
  EX_co2_e : 18.543900
  EX_h_e : 2.843336
  EX_ac_e : 0.649151
  Auxiliary production reaction : 0.024006
  EX_glyclt_e : 0.012724
  DM_hmfurn_c : 0.000114

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