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 : dhmptp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (73 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 48
  Gene deletion: b4467 b3399 b4382 b4269 b0493 b3588 b3003 b3011 b2502 b4384 b2744 b0871 b2926 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1638 b1982 b4139 b0675 b2361 b4014 b0261 b2976 b2799 b3945 b1602 b0507 b0153 b1727 b2975 b0114 b3603 b0584 b0529 b2492 b0904 b2954 b3927 b3029 b1380 b2660 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.442366 (mmol/gDw/h)
  Minimum Production Rate : 0.341884 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.686886
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.489407
  EX_pi_e : 1.452361
  EX_so4_e : 0.111397
  EX_k_e : 0.086347
  EX_mg2_e : 0.003838
  EX_fe2_e : 0.003651
  EX_fe3_e : 0.003454
  EX_ca2_e : 0.002303
  EX_cl_e : 0.002303
  EX_cu2_e : 0.000314
  EX_mn2_e : 0.000306
  EX_zn2_e : 0.000151
  EX_ni2_e : 0.000143
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 53.905288
  EX_co2_e : 38.104779
  EX_h_e : 5.096214
  Auxiliary production reaction : 0.341884
  EX_etoh_e : 0.328862
  EX_ade_e : 0.000495
  DM_5drib_c : 0.000297
  DM_4crsol_c : 0.000099

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