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 : trp__L_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (24 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b3399 b0474 b2518 b2502 b2744 b3708 b3008 b0871 b2779 b1982 b2797 b3117 b1814 b4471 b4374 b0675 b2361 b0261 b4381 b2406 b0114 b0886 b2366 b2492 b0904 b2578 b1533 b3927 b3821 b0594 b1600 b4141 b1798 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.491044 (mmol/gDw/h)
  Minimum Production Rate : 0.111779 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.199533
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.692248
  EX_pi_e : 0.473664
  EX_so4_e : 0.123655
  EX_k_e : 0.095848
  EX_fe2_e : 0.007887
  EX_mg2_e : 0.004260
  EX_ca2_e : 0.002556
  EX_cl_e : 0.002556
  EX_cu2_e : 0.000348
  EX_mn2_e : 0.000339
  EX_zn2_e : 0.000167
  EX_ni2_e : 0.000159
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.475589
  EX_co2_e : 38.207300
  EX_h_e : 4.914322
  EX_trp__L_e : 0.111779
  EX_thym_e : 0.076032
  DM_oxam_c : 0.013398
  DM_5drib_c : 0.000329
  DM_4crsol_c : 0.000110

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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