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 : thymd_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (64 of 66: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b4467 b2242 b0474 b2518 b3831 b1278 b3752 b3926 b2781 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b1759 b2440 b4161 b1415 b4015 b3945 b4138 b4123 b0621 b4381 b2406 b2492 b0904 b3028 b3918 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.567358 (mmol/gDw/h)
  Minimum Production Rate : 0.299647 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.327702
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.932099
  EX_pi_e : 0.547277
  EX_so4_e : 0.142872
  EX_k_e : 0.110744
  EX_fe2_e : 0.009112
  EX_mg2_e : 0.004922
  EX_cl_e : 0.002953
  EX_ca2_e : 0.002953
  EX_cu2_e : 0.000402
  EX_mn2_e : 0.000392
  EX_zn2_e : 0.000193
  EX_ni2_e : 0.000183
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 48.824114
  EX_co2_e : 30.938773
  EX_h_e : 7.201065
  EX_succ_e : 0.591636
  Auxiliary production reaction : 0.299647
  EX_ura_e : 0.102693
  DM_5drib_c : 0.000128
  DM_4crsol_c : 0.000127

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