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 : dgtp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (42 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b3399 b2502 b2744 b3708 b3008 b0871 b3844 b2797 b3117 b1814 b4471 b1623 b3665 b4374 b0675 b2361 b2291 b0261 b0452 b3654 b3714 b3664 b0114 b1539 b2492 b0904 b1533 b3927   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.784670 (mmol/gDw/h)
  Minimum Production Rate : 0.135646 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.370597
  EX_o2_e : 275.097895
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.152601
  EX_pi_e : 1.163835
  EX_so4_e : 0.197596
  EX_k_e : 0.153162
  EX_mg2_e : 0.006807
  EX_ca2_e : 0.004084
  EX_cl_e : 0.004084
  EX_cu2_e : 0.000556
  EX_mn2_e : 0.000542
  EX_zn2_e : 0.000268
  EX_ni2_e : 0.000253
  EX_cobalt2_e : 0.000020

Product: (mmol/gDw/h)
  EX_fe3_e : 999.987397
  EX_h2o_e : 549.050145
  EX_co2_e : 26.436434
  Auxiliary production reaction : 0.135646
  DM_5drib_c : 0.000177
  DM_4crsol_c : 0.000175

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