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 : dcmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (81 of 117: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b4467 b1478 b4382 b0238 b0125 b1241 b4069 b4384 b3752 b2297 b2458 b3844 b1004 b3713 b1109 b0046 b3236 b2883 b1779 b1982 b0477 b0261 b2799 b3945 b1602 b2913 b2406 b3915 b2868 b4064 b4464 b0529 b2492 b0904 b1380 b3662 b0606 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.366389 (mmol/gDw/h)
  Minimum Production Rate : 1.149549 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.589712
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.407663
  EX_pi_e : 1.502969
  EX_so4_e : 0.092264
  EX_k_e : 0.071517
  EX_fe3_e : 0.005885
  EX_mg2_e : 0.003178
  EX_cl_e : 0.001907
  EX_ca2_e : 0.001907
  EX_cu2_e : 0.000260
  EX_mn2_e : 0.000253
  EX_zn2_e : 0.000125
  EX_ni2_e : 0.000118

Product: (mmol/gDw/h)
  EX_h2o_e : 51.774286
  EX_co2_e : 32.901426
  EX_h_e : 7.678704
  Auxiliary production reaction : 1.149549
  EX_glyclt_e : 0.642292
  EX_ac_e : 0.213306
  EX_ade_e : 0.000410
  DM_5drib_c : 0.000246
  DM_4crsol_c : 0.000082

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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