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 : fgam_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (44 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b2744 b3752 b0871 b2407 b1982 b3616 b3589 b4374 b2361 b2291 b0261 b2406 b0112 b2868 b0114 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.520655 (mmol/gDw/h)
  Minimum Production Rate : 1.692525 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.820271
  EX_o2_e : 270.288700
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.010411
  EX_pi_e : 2.194752
  EX_so4_e : 0.131111
  EX_k_e : 0.101628
  EX_mg2_e : 0.004517
  EX_ca2_e : 0.002710
  EX_cl_e : 0.002710
  EX_cu2_e : 0.000369
  EX_mn2_e : 0.000360
  EX_zn2_e : 0.000178
  EX_ni2_e : 0.000168
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991638
  EX_h2o_e : 542.996205
  EX_co2_e : 20.783456
  EX_acald_e : 2.150885
  Auxiliary production reaction : 1.692525
  EX_hxan_e : 0.000583
  DM_5drib_c : 0.000349
  DM_4crsol_c : 0.000116

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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