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 : gdpddman_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (34 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4382 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b3752 b0871 b3617 b2407 b3665 b2406 b0112 b3654 b3714 b3664 b0114 b0529 b2492 b0904 b3662 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.544690 (mmol/gDw/h)
  Minimum Production Rate : 0.886061 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 21.548145
  EX_nh4_e : 10.312914
  EX_glc__D_e : 10.000000
  EX_pi_e : 2.297533
  EX_so4_e : 0.137164
  EX_k_e : 0.106320
  EX_fe2_e : 0.008748
  EX_mg2_e : 0.004725
  EX_cl_e : 0.002835
  EX_ca2_e : 0.002835
  EX_cu2_e : 0.000386
  EX_mn2_e : 0.000376
  EX_zn2_e : 0.000186
  EX_ni2_e : 0.000176
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 48.409507
  EX_co2_e : 20.734829
  EX_h_e : 7.663015
  EX_acald_e : 1.364970
  Auxiliary production reaction : 0.886061
  DM_mththf_c : 0.000244
  DM_5drib_c : 0.000123
  DM_4crsol_c : 0.000121

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
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