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 : duri_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (45 of 50: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b4467 b4382 b1241 b0351 b4384 b0871 b2925 b2097 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b1779 b2690 b1982 b2440 b0261 b0411 b2799 b3945 b1602 b2406 b3915 b1727 b2975 b3603 b0529 b2492 b0904 b3927 b1380 b2660 b0606 b0221 b2285 b1010 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.372374 (mmol/gDw/h)
  Minimum Production Rate : 0.040982 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 29.989535
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.105574
  EX_pi_e : 0.359194
  EX_so4_e : 0.093772
  EX_k_e : 0.072685
  EX_fe3_e : 0.005982
  EX_mg2_e : 0.003230
  EX_ca2_e : 0.001938
  EX_cl_e : 0.001938
  EX_cu2_e : 0.000264
  EX_mn2_e : 0.000257
  EX_zn2_e : 0.000127
  EX_ni2_e : 0.000120

Product: (mmol/gDw/h)
  EX_h2o_e : 42.997047
  EX_co2_e : 29.482464
  EX_h_e : 7.857606
  EX_pyr_e : 4.346136
  EX_etoh_e : 0.911748
  Auxiliary production reaction : 0.040942
  EX_ade_e : 0.000417
  DM_5drib_c : 0.000250
  DM_4crsol_c : 0.000083

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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