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 : dgdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (24 of 41: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b3399 b4069 b2744 b3708 b2297 b2458 b2883 b1779 b2797 b3117 b1814 b4471 b1623 b3665 b0411 b4381 b3654 b3714 b3664 b0114 b1539 b2492 b0904 b1533 b3927 b3821 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.681492 (mmol/gDw/h)
  Minimum Production Rate : 0.203783 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 28.250154
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.378971
  EX_pi_e : 1.064937
  EX_so4_e : 0.171613
  EX_k_e : 0.133022
  EX_fe2_e : 0.010945
  EX_mg2_e : 0.005912
  EX_cl_e : 0.003547
  EX_ca2_e : 0.003547
  EX_cu2_e : 0.000483
  EX_mn2_e : 0.000471
  EX_zn2_e : 0.000232
  EX_ni2_e : 0.000220
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 49.840515
  EX_co2_e : 29.195015
  EX_h_e : 7.473708
  EX_ac_e : 0.396755
  Auxiliary production reaction : 0.203783
  EX_mththf_e : 0.000305
  DM_5drib_c : 0.000153
  DM_4crsol_c : 0.000152

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