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 : 5caiz_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (49 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b3399 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b2744 b0871 b2926 b3617 b0160 b3124 b1982 b1623 b3665 b0675 b2361 b0261 b4381 b2406 b0112 b2789 b3127 b0114 b0529 b2492 b0904 b0514   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.454081 (mmol/gDw/h)
  Minimum Production Rate : 1.452346 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 25.557888
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.275498
  EX_pi_e : 1.890356
  EX_so4_e : 0.114347
  EX_k_e : 0.088633
  EX_fe2_e : 0.007293
  EX_mg2_e : 0.003939
  EX_cl_e : 0.002363
  EX_ca2_e : 0.002363
  EX_cu2_e : 0.000322
  EX_mn2_e : 0.000314
  EX_zn2_e : 0.000155
  EX_ni2_e : 0.000147
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 48.173700
  EX_co2_e : 24.535060
  EX_h_e : 10.008270
  EX_acald_e : 1.863979
  Auxiliary production reaction : 1.452346
  DM_oxam_c : 0.011881
  EX_ade_e : 0.000508
  DM_5drib_c : 0.000305
  EX_glyclt_e : 0.000304
  DM_4crsol_c : 0.000101

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.

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Last updated: 21-Sep-2023
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