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 : 25aics_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (63 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b4467 b3399 b4069 b2744 b3115 b1849 b2296 b2926 b0160 b3844 b1004 b3713 b1109 b0046 b3236 b0937 b1982 b2210 b4374 b0675 b2361 b2291 b0261 b2799 b3945 b1602 b1727 b2975 b0114 b3603 b0529 b2492 b0904 b3927 b1380 b2660 b0606 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.383759 (mmol/gDw/h)
  Minimum Production Rate : 0.579479 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.302883
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.464634
  EX_pi_e : 0.949656
  EX_so4_e : 0.096638
  EX_k_e : 0.074907
  EX_fe2_e : 0.006164
  EX_mg2_e : 0.003329
  EX_ca2_e : 0.001997
  EX_cl_e : 0.001997
  EX_cu2_e : 0.000272
  EX_mn2_e : 0.000265
  EX_zn2_e : 0.000131
  EX_ni2_e : 0.000124

Product: (mmol/gDw/h)
  EX_h2o_e : 50.895001
  EX_co2_e : 35.010060
  EX_h_e : 7.228578
  EX_etoh_e : 0.627652
  Auxiliary production reaction : 0.579479
  EX_ac_e : 0.223419
  EX_ade_e : 0.000429
  DM_5drib_c : 0.000258
  DM_4crsol_c : 0.000086

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