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 : acetol_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (62 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3553 b1241 b0351 b2297 b2458 b2779 b2925 b2097 b3617 b3844 b1004 b3713 b1109 b0046 b3236 b3946 b0825 b1033 b1493 b3517 b4014 b2976 b3945 b1602 b0507 b2913 b1727 b1380 b0606 b0221 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.543552 (mmol/gDw/h)
  Minimum Production Rate : 0.134553 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.678447
  EX_o2_e : 282.706910
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.870317
  EX_pi_e : 0.524314
  EX_so4_e : 0.136877
  EX_k_e : 0.106098
  EX_mg2_e : 0.004715
  EX_ca2_e : 0.002829
  EX_cl_e : 0.002829
  EX_cu2_e : 0.000385
  EX_mn2_e : 0.000376
  EX_zn2_e : 0.000185
  EX_ni2_e : 0.000176
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991270
  EX_h2o_e : 548.285665
  EX_co2_e : 34.840588
  EX_etoh_e : 0.904267
  EX_ac_e : 0.318449
  Auxiliary production reaction : 0.134553
  DM_5drib_c : 0.000122
  DM_4crsol_c : 0.000121

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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