MetNetComp Database [1] / Minimal gene deletions Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : iML1515 [2].
Target metabolite : duri_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (35 of 50: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b2836 b4069 b4384 b3708 b3008 b3752 b2297 b2458 b2925 b2097 b2926 b2407 b2797 b3117 b1814 b4471 b3946 b0825 b3665 b0261 b4381 b2406 b0112 b3654 b3714 b3664 b0114 b2366 b0529 b2492 b0904 b3035 b2578 b1533 b3927 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.372664 (mmol/gDw/h)
  Minimum Production Rate : 0.237370 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 31.769324
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.974222
  EX_pi_e : 0.359474
  EX_so4_e : 0.093844
  EX_k_e : 0.072741
  EX_fe2_e : 0.005985
  EX_mg2_e : 0.003233
  EX_cl_e : 0.001940
  EX_ca2_e : 0.001940
  EX_cu2_e : 0.000264
  EX_mn2_e : 0.000258
  EX_zn2_e : 0.000127
  EX_ni2_e : 0.000120

Product: (mmol/gDw/h)
  EX_h2o_e : 44.541960
  EX_co2_e : 32.089857
  EX_h_e : 9.019071
  EX_ac_e : 4.645403
  Auxiliary production reaction : 0.237370
  EX_thym_e : 0.237370
  DM_5drib_c : 0.000084
  DM_4crsol_c : 0.000083

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].
  3. Select "Data > Load reaction data" and apply the downloaded file.

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: 21-Sep-2023
Contact