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 : adp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (71 of 89: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b4467 b1478 b4382 b1241 b4069 b4384 b3752 b2297 b2458 b2407 b1004 b3713 b1109 b0046 b3236 b1779 b1982 b0261 b2799 b3945 b1602 b2342 b3845 b2406 b3915 b0529 b2492 b0904 b1380 b2660 b3662 b0606 b2285 b1009 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.398339 (mmol/gDw/h)
  Minimum Production Rate : 0.655652 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.230651
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.581625
  EX_pi_e : 1.695544
  EX_so4_e : 0.100310
  EX_k_e : 0.077753
  EX_fe3_e : 0.006398
  EX_mg2_e : 0.003456
  EX_ca2_e : 0.002073
  EX_cl_e : 0.002073
  EX_cu2_e : 0.000282
  EX_mn2_e : 0.000275
  EX_zn2_e : 0.000136
  EX_ni2_e : 0.000129

Product: (mmol/gDw/h)
  EX_h2o_e : 54.089219
  EX_co2_e : 35.047236
  EX_h_e : 7.312904
  EX_glyclt_e : 0.790555
  Auxiliary production reaction : 0.655652
  EX_ac_e : 0.231907
  EX_ade_e : 0.000268
  DM_5drib_c : 0.000090
  DM_4crsol_c : 0.000089

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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