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 : dtdp4aaddg_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (52 of 72: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3831 b2744 b1278 b3614 b0910 b3752 b4152 b2781 b1612 b1611 b4122 b1759 b2440 b4374 b2361 b2291 b0411 b4138 b4123 b0621 b2197 b3918 b0418 b0494 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.687149 (mmol/gDw/h)
  Minimum Production Rate : 0.362914 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.630394
  EX_o2_e : 270.975217
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.758643
  EX_pi_e : 1.388656
  EX_so4_e : 0.173038
  EX_k_e : 0.134127
  EX_mg2_e : 0.005961
  EX_ca2_e : 0.003577
  EX_cl_e : 0.003577
  EX_cu2_e : 0.000487
  EX_mn2_e : 0.000475
  EX_zn2_e : 0.000234
  EX_ni2_e : 0.000222
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_fe3_e : 999.988964
  EX_h2o_e : 545.370197
  EX_co2_e : 21.899525
  EX_succ_e : 0.716553
  Auxiliary production reaction : 0.362914
  EX_ura_e : 0.124376
  DM_5drib_c : 0.000155
  DM_4crsol_c : 0.000153

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