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 : adphep_DD_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (67 of 99: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b2836 b3399 b2502 b2744 b3708 b3008 b0512 b0871 b2779 b1982 b2797 b3117 b1814 b4471 b4374 b0675 b2361 b2291 b0261 b0114 b0886 b2366 b0529 b2492 b0904 b2578 b1533 b3927 b4141 b1798 b0221 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.485282 (mmol/gDw/h)
  Minimum Production Rate : 0.109137 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.435891
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.798325
  EX_pi_e : 0.686380
  EX_so4_e : 0.123555
  EX_k_e : 0.094724
  EX_fe2_e : 0.007794
  EX_mg2_e : 0.004210
  EX_cl_e : 0.002526
  EX_ca2_e : 0.002526
  EX_cu2_e : 0.000344
  EX_mn2_e : 0.000335
  EX_zn2_e : 0.000165
  EX_ni2_e : 0.000157
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.560030
  EX_co2_e : 38.199834
  EX_h_e : 4.791253
  Auxiliary production reaction : 0.109137
  EX_alltn_e : 0.001895
  EX_5mtr_e : 0.001352
  EX_spmd_e : 0.001352
  DM_5drib_c : 0.000326
  DM_4crsol_c : 0.000108

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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