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 : adphep_LD_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (41 of 49: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b3553 b1478 b4382 b4269 b0493 b3588 b3003 b3011 b1241 b4384 b0871 b2926 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1982 b1033 b0261 b0411 b2799 b3945 b1602 b0153 b2913 b0590 b0529 b2492 b0904 b1380 b0606 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.371683 (mmol/gDw/h)
  Minimum Production Rate : 0.476378 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.214176
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.398113
  EX_pi_e : 1.311283
  EX_so4_e : 0.093597
  EX_k_e : 0.072550
  EX_fe2_e : 0.005970
  EX_mg2_e : 0.003224
  EX_ca2_e : 0.001935
  EX_cl_e : 0.001935
  EX_cu2_e : 0.000264
  EX_mn2_e : 0.000257
  EX_zn2_e : 0.000127
  EX_ni2_e : 0.000120

Product: (mmol/gDw/h)
  EX_h2o_e : 50.869489
  EX_co2_e : 34.380922
  EX_h_e : 4.846384
  EX_acald_e : 1.130935
  Auxiliary production reaction : 0.476378
  EX_ade_e : 0.000416
  DM_5drib_c : 0.000249
  DM_4crsol_c : 0.000083

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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