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 (32 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b4467 b4269 b0493 b3588 b3003 b3011 b0871 b2925 b2097 b1004 b3713 b1109 b0046 b3124 b3236 b1638 b2690 b4139 b1493 b3517 b1602 b2913 b1727 b2492 b0904 b3029 b1380 b0514 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.490596 (mmol/gDw/h)
  Minimum Production Rate : 0.452650 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 38.137388
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.298391
  EX_pi_e : 0.473231
  EX_so4_e : 0.123542
  EX_k_e : 0.095761
  EX_fe2_e : 0.007879
  EX_mg2_e : 0.004256
  EX_ca2_e : 0.002554
  EX_cl_e : 0.002554
  EX_cu2_e : 0.000348
  EX_mn2_e : 0.000339
  EX_zn2_e : 0.000167
  EX_ni2_e : 0.000158
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 51.913278
  EX_co2_e : 38.958004
  EX_h_e : 4.960438
  EX_glyclt_e : 0.452650
  DM_5drib_c : 0.000110
  DM_4crsol_c : 0.000109

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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