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 : aicar_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (71 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b1241 b0351 b4384 b3708 b3008 b0871 b2297 b2458 b2779 b2925 b2097 b3617 b0030 b2407 b3236 b1982 b2688 b2797 b3117 b1814 b4471 b3946 b2210 b0825 b2440 b0261 b2913 b4381 b2406 b0112 b0114 b0529 b1539 b2492 b0904 b2578 b1533 b3927 b0515 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.346302 (mmol/gDw/h)
  Minimum Production Rate : 0.119233 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.767488
  EX_o2_e : 280.293353
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.218512
  EX_pi_e : 0.453278
  EX_so4_e : 0.087206
  EX_k_e : 0.067596
  EX_mg2_e : 0.003004
  EX_ca2_e : 0.001803
  EX_cl_e : 0.001803
  EX_cu2_e : 0.000246
  EX_mn2_e : 0.000239
  EX_zn2_e : 0.000118
  EX_ni2_e : 0.000112

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994438
  EX_h2o_e : 543.795365
  EX_co2_e : 28.010953
  EX_pyr_e : 5.566509
  Auxiliary production reaction : 0.119233
  EX_alltn_e : 0.000388
  DM_5drib_c : 0.000232
  DM_4crsol_c : 0.000077

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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