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 : dpcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (49 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b3399 b1241 b0351 b4069 b2502 b2744 b3708 b0512 b2297 b2458 b2779 b2926 b3617 b1238 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b0261 b4381 b2406 b0112 b2789 b3127 b0114 b2366 b2492 b0904 b1533 b3821   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.462928 (mmol/gDw/h)
  Minimum Production Rate : 0.460893 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 24.947690
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.233069
  EX_pi_e : 1.368330
  EX_so4_e : 0.577468
  EX_k_e : 0.090360
  EX_fe2_e : 0.007435
  EX_mg2_e : 0.004016
  EX_ca2_e : 0.002410
  EX_cl_e : 0.002410
  EX_cu2_e : 0.000328
  EX_mn2_e : 0.000320
  EX_zn2_e : 0.000158
  EX_ni2_e : 0.000150
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 46.930199
  EX_co2_e : 26.392943
  EX_h_e : 8.095221
  EX_ac_e : 2.450142
  Auxiliary production reaction : 0.460893
  EX_alltn_e : 0.001807
  DM_5drib_c : 0.001600
  EX_glyclt_e : 0.001599
  DM_4crsol_c : 0.001392

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