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 : dutp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (44 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b4467 b1241 b0351 b4069 b2744 b2297 b2458 b2925 b2097 b3617 b1004 b3713 b1109 b0046 b3236 b2883 b2690 b0411 b1602 b4381 b3654 b2868 b3714 b3664 b1727 b4064 b4464 b0114 b0529 b2492 b0904 b1380 b2660 b3662 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.362150 (mmol/gDw/h)
  Minimum Production Rate : 1.070418 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 32.349492
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.689340
  EX_pi_e : 3.560587
  EX_so4_e : 0.091197
  EX_k_e : 0.070689
  EX_fe2_e : 0.005816
  EX_mg2_e : 0.003142
  EX_ca2_e : 0.001885
  EX_cl_e : 0.001885
  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 : 53.001669
  EX_co2_e : 31.892581
  EX_h_e : 4.175732
  Auxiliary production reaction : 1.070418
  EX_thymd_e : 0.318657
  EX_ac_e : 0.210839
  DM_mththf_c : 0.000162
  DM_5drib_c : 0.000081
  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