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 (75 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b4467 b4069 b4384 b2744 b3708 b3926 b3115 b1849 b2296 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b0937 b1982 b2797 b3117 b1814 b4471 b2440 b0261 b0411 b1602 b2913 b4381 b0114 b0755 b3612 b0529 b1539 b2492 b0904 b3927 b1380 b1771 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.442403 (mmol/gDw/h)
  Minimum Production Rate : 0.281101 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 36.708652
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.342102
  EX_pi_e : 0.707846
  EX_so4_e : 0.111406
  EX_k_e : 0.086354
  EX_fe2_e : 0.007105
  EX_mg2_e : 0.003838
  EX_ca2_e : 0.002303
  EX_cl_e : 0.002303
  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 : 50.463123
  EX_co2_e : 37.370509
  EX_h_e : 5.454546
  EX_3hpp_e : 0.567822
  Auxiliary production reaction : 0.281101
  EX_ac_e : 0.257561
  EX_hxan_e : 0.000495
  DM_5drib_c : 0.000297
  DM_4crsol_c : 0.000099

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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