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 (79 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 53
  Gene deletion: b4467 b1478 b1241 b4069 b4384 b2744 b2297 b2458 b2779 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b0207 b3012 b1982 b0477 b4139 b4374 b2361 b2291 b4014 b0261 b2976 b2799 b1602 b2406 b3915 b2975 b3603 b0509 b3125 b0529 b2492 b0904 b2954 b1781 b3001 b3927 b3029 b1380 b0325 b0508 b2660 b1771 b3662 b0221 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.382091 (mmol/gDw/h)
  Minimum Production Rate : 0.799916 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.453698
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.528004
  EX_pi_e : 1.168483
  EX_so4_e : 0.096218
  EX_k_e : 0.074581
  EX_fe3_e : 0.006137
  EX_mg2_e : 0.003315
  EX_ca2_e : 0.001989
  EX_cl_e : 0.001989
  EX_cu2_e : 0.000271
  EX_mn2_e : 0.000264
  EX_zn2_e : 0.000130
  EX_ni2_e : 0.000123

Product: (mmol/gDw/h)
  EX_h2o_e : 53.159870
  EX_co2_e : 36.669806
  EX_h_e : 6.940760
  Auxiliary production reaction : 0.799916
  EX_ac_e : 0.222448
  EX_hxan_e : 0.000428
  DM_5drib_c : 0.000256
  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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