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 : 1agpe161_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (29 of 35: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b0474 b2518 b3831 b2744 b3752 b4152 b2781 b1612 b1611 b4122 b1759 b2440 b4374 b4161 b2361 b2291 b4138 b4123 b0621 b2406 b2197 b3918 b1912 b0494 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.637107 (mmol/gDw/h)
  Minimum Production Rate : 0.336485 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 19.445475
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.120790
  EX_pi_e : 0.951042
  EX_so4_e : 0.160436
  EX_k_e : 0.124359
  EX_fe2_e : 0.010233
  EX_mg2_e : 0.005527
  EX_ca2_e : 0.003316
  EX_cl_e : 0.003316
  EX_cu2_e : 0.000452
  EX_mn2_e : 0.000440
  EX_zn2_e : 0.000217
  EX_ni2_e : 0.000206
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 43.075889
  EX_co2_e : 22.318820
  EX_h_e : 7.749853
  EX_succ_e : 0.664370
  EX_ura_e : 0.451803
  Auxiliary production reaction : 0.336485
  DM_5drib_c : 0.000143
  DM_4crsol_c : 0.000142

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