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 : ahdt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (35 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b3399 b1241 b0351 b4069 b2502 b2744 b2297 b2458 b2779 b2926 b3617 b1982 b0675 b2361 b2291 b0261 b2913 b4381 b0112 b2789 b3127 b2975 b0114 b3603 b0529 b2492 b0904   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.399315 (mmol/gDw/h)
  Minimum Production Rate : 1.530553 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 27.326540
  EX_nh4_e : 11.965777
  EX_glc__D_e : 10.000000
  EX_pi_e : 4.976840
  EX_so4_e : 0.100555
  EX_k_e : 0.077943
  EX_fe2_e : 0.006413
  EX_mg2_e : 0.003464
  EX_ca2_e : 0.002078
  EX_cl_e : 0.002078
  EX_cu2_e : 0.000283
  EX_mn2_e : 0.000276
  EX_zn2_e : 0.000136
  EX_ni2_e : 0.000129

Product: (mmol/gDw/h)
  EX_h2o_e : 54.794604
  EX_co2_e : 24.351723
  EX_h_e : 11.002355
  EX_ac_e : 2.740738
  Auxiliary production reaction : 1.530553
  DM_oxam_c : 0.000447
  DM_5drib_c : 0.000268
  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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