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 : glyclt_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (28 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b4382 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b3752 b0871 b2779 b2926 b3617 b2407 b1982 b0261 b2913 b2406 b0112 b2789 b3127 b0114 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.443087 (mmol/gDw/h)
  Minimum Production Rate : 0.720481 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.831096
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.505981
  EX_pi_e : 0.427404
  EX_so4_e : 0.111578
  EX_k_e : 0.086487
  EX_fe2_e : 0.007116
  EX_mg2_e : 0.003844
  EX_cl_e : 0.002306
  EX_ca2_e : 0.002306
  EX_cu2_e : 0.000314
  EX_mn2_e : 0.000306
  EX_zn2_e : 0.000151
  EX_ni2_e : 0.000143
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 41.980860
  EX_co2_e : 26.678246
  EX_h_e : 6.233101
  EX_acald_e : 1.804773
  DM_oxam_c : 0.720681
  DM_5drib_c : 0.720482
  EX_glyclt_e : 0.720481
  DM_4crsol_c : 0.720284

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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