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 : prbatp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (45 of 47: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 45
  Gene deletion: b4467 b4269 b0493 b3588 b3003 b3011 b4384 b2744 b3752 b0871 b3844 b1004 b3713 b1109 b0046 b3236 b2883 b1779 b0207 b3012 b0937 b1982 b0261 b0411 b2799 b1602 b4381 b2868 b1727 b4064 b4464 b0114 b0529 b2492 b0904 b1781 b3001 b1380 b0325 b2660 b1771 b3662 b0606 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.433490 (mmol/gDw/h)
  Minimum Production Rate : 0.291795 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.049666
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.143048
  EX_pi_e : 1.585325
  EX_so4_e : 0.109161
  EX_k_e : 0.084614
  EX_fe2_e : 0.006962
  EX_mg2_e : 0.003761
  EX_ca2_e : 0.002256
  EX_cl_e : 0.002256
  EX_cu2_e : 0.000307
  EX_mn2_e : 0.000300
  EX_zn2_e : 0.000148
  EX_ni2_e : 0.000140
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 52.364963
  EX_co2_e : 36.771738
  EX_h_e : 4.860884
  EX_etoh_e : 0.527599
  Auxiliary production reaction : 0.291795
  EX_ade_e : 0.000485
  DM_5drib_c : 0.000291
  DM_4crsol_c : 0.000097

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