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 (61 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b4382 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b3708 b3008 b0871 b2779 b0030 b2407 b2687 b2797 b3117 b1814 b4471 b3616 b3589 b3665 b2406 b0112 b3654 b3714 b3664 b0114 b1539 b2492 b0904 b1533 b4141 b1798 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.393426 (mmol/gDw/h)
  Minimum Production Rate : 0.316443 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.466582
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.147551
  EX_so4_e : 0.415503
  EX_pi_e : 0.379501
  EX_k_e : 0.076794
  EX_fe2_e : 0.006320
  EX_mg2_e : 0.003413
  EX_cl_e : 0.002048
  EX_ca2_e : 0.002048
  EX_cu2_e : 0.000279
  EX_mn2_e : 0.000272
  EX_zn2_e : 0.000134
  EX_ni2_e : 0.000127

Product: (mmol/gDw/h)
  EX_h2o_e : 51.622007
  EX_co2_e : 36.802686
  EX_h_e : 4.880678
  EX_acald_e : 1.309475
  Auxiliary production reaction : 0.316430
  DM_5drib_c : 0.000089
  DM_4crsol_c : 0.000088

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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