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 : glyclt_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (54 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b4467 b0469 b4382 b4269 b0493 b3588 b3003 b3011 b4384 b3926 b0871 b2779 b2926 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1638 b4139 b1623 b3665 b3945 b1602 b0529 b2492 b0904 b2954 b3029 b1380 b2660 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.509177 (mmol/gDw/h)
  Minimum Production Rate : 0.371803 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.451330
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.500780
  EX_pi_e : 0.491155
  EX_so4_e : 0.128221
  EX_k_e : 0.099388
  EX_mg2_e : 0.004417
  EX_fe2_e : 0.004202
  EX_fe3_e : 0.003976
  EX_ca2_e : 0.002650
  EX_cl_e : 0.002650
  EX_cu2_e : 0.000361
  EX_mn2_e : 0.000352
  EX_zn2_e : 0.000174
  EX_ni2_e : 0.000164
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 51.798500
  EX_co2_e : 38.351109
  EX_h_e : 5.058113
  EX_glyclt_e : 0.373904
  EX_ade_e : 0.000343
  DM_5drib_c : 0.000115
  DM_4crsol_c : 0.000114

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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