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 : fpram_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (33 of 51: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b4467 b4382 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b0871 b3617 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b1982 b0261 b3945 b1602 b2913 b2406 b1727 b0114 b0529 b2492 b0904 b1380 b3662 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.359719 (mmol/gDw/h)
  Minimum Production Rate : 0.403562 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.958789
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.394616
  EX_pi_e : 0.750549
  EX_so4_e : 0.090584
  EX_k_e : 0.070215
  EX_fe2_e : 0.005777
  EX_mg2_e : 0.003121
  EX_ca2_e : 0.001872
  EX_cl_e : 0.001872
  EX_cu2_e : 0.000255
  EX_mn2_e : 0.000249
  EX_zn2_e : 0.000123
  EX_ni2_e : 0.000116

Product: (mmol/gDw/h)
  EX_h2o_e : 50.075098
  EX_co2_e : 34.840473
  EX_h_e : 6.411362
  EX_etoh_e : 1.284322
  EX_his__L_e : 0.765797
  Auxiliary production reaction : 0.403562
  EX_hxan_e : 0.000403
  DM_5drib_c : 0.000241
  DM_4crsol_c : 0.000080

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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