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 : 5aizc_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (76 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 47
  Gene deletion: b3553 b1478 b3399 b1241 b4069 b2744 b2297 b2458 b2779 b0160 b1004 b3713 b1109 b0046 b3236 b1638 b0207 b3012 b1982 b4139 b1033 b0675 b2361 b4014 b0261 b2976 b2799 b1602 b0507 b4381 b2406 b3915 b0452 b0529 b2492 b0904 b2954 b1781 b3001 b3029 b1380 b0325 b1301 b2660 b1771 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.379641 (mmol/gDw/h)
  Minimum Production Rate : 0.812162 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.451792
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.588368
  EX_pi_e : 1.178366
  EX_so4_e : 0.095601
  EX_k_e : 0.074103
  EX_fe3_e : 0.006097
  EX_mg2_e : 0.003293
  EX_ca2_e : 0.001976
  EX_cl_e : 0.001976
  EX_cu2_e : 0.000269
  EX_mn2_e : 0.000262
  EX_zn2_e : 0.000129
  EX_ni2_e : 0.000123

Product: (mmol/gDw/h)
  EX_h2o_e : 53.236442
  EX_co2_e : 36.613343
  EX_h_e : 7.015851
  Auxiliary production reaction : 0.812162
  EX_ac_e : 0.221022
  EX_ade_e : 0.010359
  DM_5drib_c : 0.000255
  DM_4crsol_c : 0.000085

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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