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 : pa160_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (57 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: STM3646 STM1749 STM2463 STM2285 STM3526 STM4326 STM1885 STM2952 STM2947 STM3709 STM3068 STM2141 STM1135 STM4183 STM0491 STM0368 STM0974 STM1448 STM3062 STM4484 STM0542 STM2317 STM3179 STM4569 STM1480 STM4126 STM1124 STM4467 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 : 0.061874 (mmol/gDw/h)
  Minimum Production Rate : 0.060795 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 9.284635
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.681849
  EX_pi_e : 0.115665
  EX_k_e : 0.010989
  EX_so4_e : 0.007547
  EX_mg2_e : 0.000488
  EX_fe2_e : 0.000453
  EX_ca2_e : 0.000293
  EX_cl_e : 0.000293
  EX_cobalt2_e : 0.000195
  EX_cu2_e : 0.000195
  EX_mn2_e : 0.000195
  EX_mobd_e : 0.000195
  EX_zn2_e : 0.000195

Product: (mmol/gDw/h)
  EX_h2o_e : 12.079725
  EX_co2_e : 10.252402
  EX_dha_e : 4.937855
  EX_h_e : 0.524536
  EX_acald_e : 0.206389
  Auxiliary production reaction : 0.060795
  DM_hmfurn_c : 0.000028

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