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 : ahcys_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (9 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b4069 b4384 b3708 b3008 b3752 b2297 b2458 b2926 b2407 b2687 b1982 b2797 b3117 b1814 b4471 b4381 b2406 b3915 b0452 b0114 b2366 b2492 b0904 b2578 b1533 b3927 b3662 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.646861 (mmol/gDw/h)
  Minimum Production Rate : 0.205318 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.129116
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.217950
  EX_pi_e : 0.623966
  EX_so4_e : 0.368210
  EX_k_e : 0.126263
  EX_fe3_e : 0.010389
  EX_mg2_e : 0.005612
  EX_ca2_e : 0.003367
  EX_cl_e : 0.003367
  EX_cu2_e : 0.000459
  EX_mn2_e : 0.000447
  EX_zn2_e : 0.000221
  EX_ni2_e : 0.000209
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 49.360678
  EX_co2_e : 29.409614
  EX_h_e : 7.357188
  EX_ac_e : 0.581911
  Auxiliary production reaction : 0.205318
  DM_5drib_c : 0.000434
  DM_4crsol_c : 0.000144

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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