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 : prbamp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (42 of 47: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b3553 b1478 b3399 b0238 b0125 b1241 b0351 b4069 b2744 b2297 b2458 b2926 b3844 b1004 b3713 b1109 b0046 b3236 b1982 b0477 b1033 b4374 b0675 b2361 b2291 b0261 b2799 b3945 b1602 b0153 b0590 b0529 b2492 b0904 b1380 b2660 b0606 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.386791 (mmol/gDw/h)
  Minimum Production Rate : 0.342451 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.603821
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.955255
  EX_pi_e : 1.058003
  EX_so4_e : 0.097402
  EX_k_e : 0.075499
  EX_fe2_e : 0.006212
  EX_mg2_e : 0.003355
  EX_ca2_e : 0.002013
  EX_cl_e : 0.002013
  EX_cu2_e : 0.000274
  EX_mn2_e : 0.000267
  EX_zn2_e : 0.000132
  EX_ni2_e : 0.000125

Product: (mmol/gDw/h)
  EX_h2o_e : 52.180129
  EX_co2_e : 34.774471
  EX_h_e : 7.772106
  EX_ac_e : 1.440170
  Auxiliary production reaction : 0.342451
  EX_xan_e : 0.265882
  EX_ade_e : 0.000433
  DM_5drib_c : 0.000260
  DM_4crsol_c : 0.000086

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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