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 : 25aics_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (69 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b3553 b3399 b4382 b1241 b0351 b2502 b4384 b2744 b2930 b4232 b3697 b3925 b0871 b2926 b1004 b3713 b1109 b0046 b3236 b2690 b1982 b1033 b2440 b0675 b2361 b2291 b0261 b2799 b3945 b1602 b3915 b1727 b0529 b2492 b0904 b3927 b1380 b2660 b0606 b0221 b2285 b1011 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.372123 (mmol/gDw/h)
  Minimum Production Rate : 0.020481 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.468934
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.102808
  EX_pi_e : 0.379409
  EX_so4_e : 0.093709
  EX_k_e : 0.072636
  EX_fe3_e : 0.005978
  EX_mg2_e : 0.003228
  EX_cl_e : 0.001937
  EX_ca2_e : 0.001937
  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 : 43.906161
  EX_co2_e : 28.551222
  EX_h_e : 8.852012
  EX_pyr_e : 5.301993
  Auxiliary production reaction : 0.020457
  EX_ade_e : 0.000416
  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.

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Last updated: 21-Sep-2023
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