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 : ugmd_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (63 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b0474 b2518 b2744 b4152 b2781 b1612 b1611 b4122 b1759 b2440 b4374 b4161 b0675 b4138 b4123 b0621 b4381 b2406 b0452 b2492 b0904 b2197 b3918 b1912 b1206 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.498129 (mmol/gDw/h)
  Minimum Production Rate : 0.221817 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.560528
  EX_o2_e : 278.919339
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.236592
  EX_pi_e : 0.924131
  EX_so4_e : 0.125439
  EX_k_e : 0.097231
  EX_mg2_e : 0.004321
  EX_ca2_e : 0.002593
  EX_cl_e : 0.002593
  EX_cu2_e : 0.000353
  EX_mn2_e : 0.000344
  EX_zn2_e : 0.000170
  EX_ni2_e : 0.000161
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992000
  EX_h2o_e : 548.089435
  EX_co2_e : 29.104489
  EX_succ_e : 0.519445
  Auxiliary production reaction : 0.221817
  EX_ura_e : 0.131430
  EX_etha_e : 0.041267
  DM_5drib_c : 0.000112
  DM_4crsol_c : 0.000111

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