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 : histd_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (36 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b3399 b1241 b0351 b3831 b4069 b2744 b3752 b3115 b1849 b2296 b2926 b0160 b1982 b3616 b3589 b0675 b2361 b0261 b4388 b4381 b0112 b0114 b0529 b2492 b0904 b0515 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.361824 (mmol/gDw/h)
  Minimum Production Rate : 1.367918 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.946785
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.050916
  EX_pi_e : 0.349018
  EX_so4_e : 0.091115
  EX_k_e : 0.070626
  EX_fe2_e : 0.005811
  EX_mg2_e : 0.003139
  EX_cl_e : 0.001883
  EX_ca2_e : 0.001883
  EX_cu2_e : 0.000257
  EX_mn2_e : 0.000250
  EX_zn2_e : 0.000123
  EX_ni2_e : 0.000117

Product: (mmol/gDw/h)
  EX_h2o_e : 51.152866
  EX_co2_e : 34.689389
  EX_h_e : 7.205702
  Auxiliary production reaction : 1.367918
  EX_ac_e : 1.105790
  EX_alltn_e : 0.009872
  DM_5drib_c : 0.000243
  DM_4crsol_c : 0.000081

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