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 : gdpddman_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (76 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 48
  Gene deletion: b3553 b3399 b4269 b0493 b3588 b3003 b3011 b2744 b0871 b2926 b3844 b1238 b1004 b3713 b1109 b0046 b3236 b2883 b1638 b4117 b3908 b1656 b1982 b4139 b1033 b0675 b2361 b0261 b0411 b2799 b3945 b1602 b0507 b0153 b2913 b4381 b0590 b1727 b0114 b0529 b2492 b0904 b2954 b2938 b1380 b3662 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.454958 (mmol/gDw/h)
  Minimum Production Rate : 0.210970 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.805586
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.970903
  EX_pi_e : 0.860795
  EX_so4_e : 0.114568
  EX_k_e : 0.088805
  EX_mg2_e : 0.003947
  EX_fe2_e : 0.003755
  EX_fe3_e : 0.003552
  EX_ca2_e : 0.002368
  EX_cl_e : 0.002368
  EX_cu2_e : 0.000323
  EX_mn2_e : 0.000314
  EX_zn2_e : 0.000155
  EX_ni2_e : 0.000147
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 52.325330
  EX_co2_e : 37.411184
  EX_h_e : 4.819344
  EX_etoh_e : 0.267900
  Auxiliary production reaction : 0.210970
  EX_ade_e : 0.000509
  DM_5drib_c : 0.000305
  DM_4crsol_c : 0.000101

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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