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 : adpglc_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (42 of 73: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b4384 b3708 b3008 b0512 b0871 b2926 b0030 b2407 b1982 b2797 b3117 b1814 b4471 b3449 b0261 b4381 b2406 b0114 b0886 b2366 b0529 b2492 b0904 b2578 b1533 b3927 b0494 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.681096 (mmol/gDw/h)
  Minimum Production Rate : 0.153174 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.484330
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.137979
  EX_pi_e : 0.963338
  EX_so4_e : 0.173411
  EX_k_e : 0.132945
  EX_fe2_e : 0.010939
  EX_mg2_e : 0.005909
  EX_ca2_e : 0.003545
  EX_cl_e : 0.003545
  EX_cu2_e : 0.000483
  EX_mn2_e : 0.000471
  EX_zn2_e : 0.000232
  EX_ni2_e : 0.000220
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 49.711138
  EX_co2_e : 29.556527
  EX_h_e : 6.724549
  Auxiliary production reaction : 0.153174
  EX_alltn_e : 0.002659
  EX_5mtr_e : 0.001897
  EX_spmd_e : 0.001897
  DM_5drib_c : 0.000457
  DM_4crsol_c : 0.000152

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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