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 : 2agpe160_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (54 of 64: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b0474 b2518 b3831 b1278 b4152 b2781 b0030 b1612 b1611 b4122 b0651 b2162 b1759 b3449 b4161 b4138 b4123 b0621 b4381 b2406 b2197 b3918 b0418 b0494 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.635242 (mmol/gDw/h)
  Minimum Production Rate : 0.335500 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.262623
  EX_o2_e : 269.393847
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.097027
  EX_pi_e : 0.948259
  EX_so4_e : 0.159967
  EX_k_e : 0.123995
  EX_mg2_e : 0.005511
  EX_cl_e : 0.003306
  EX_ca2_e : 0.003306
  EX_cu2_e : 0.000450
  EX_mn2_e : 0.000439
  EX_zn2_e : 0.000217
  EX_ni2_e : 0.000205
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_fe3_e : 999.989797
  EX_h2o_e : 542.784812
  EX_co2_e : 22.429085
  EX_succ_e : 0.662426
  EX_ura_e : 0.450481
  Auxiliary production reaction : 0.335500
  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