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 : gdpmann_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (92 of 108: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 46
  Gene deletion: b3553 b1478 b3399 b1241 b4069 b4384 b2744 b3752 b2297 b2458 b2779 b3844 b1004 b3713 b1109 b0046 b3236 b2883 b1638 b0937 b1982 b1302 b2662 b4139 b1033 b1623 b4014 b0261 b2976 b0411 b2799 b3945 b1602 b2913 b4381 b0509 b3125 b0529 b2492 b0904 b2954 b3029 b1380 b3662 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.397251 (mmol/gDw/h)
  Minimum Production Rate : 0.416807 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.562139
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.376540
  EX_pi_e : 1.216806
  EX_so4_e : 0.100036
  EX_k_e : 0.077541
  EX_mg2_e : 0.003446
  EX_fe2_e : 0.003279
  EX_fe3_e : 0.003102
  EX_cl_e : 0.002068
  EX_ca2_e : 0.002068
  EX_cu2_e : 0.000282
  EX_mn2_e : 0.000275
  EX_zn2_e : 0.000135
  EX_ni2_e : 0.000128

Product: (mmol/gDw/h)
  EX_h2o_e : 51.487718
  EX_co2_e : 35.159212
  EX_h_e : 5.837561
  EX_ac_e : 0.931711
  Auxiliary production reaction : 0.416807
  EX_ade_e : 0.000445
  DM_5drib_c : 0.000267
  DM_4crsol_c : 0.000089

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