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 (72 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 42
  Gene deletion: b4467 b3399 b4382 b4069 b2502 b4384 b2744 b3115 b1849 b2296 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b0207 b3012 b1982 b0675 b2361 b0261 b2799 b1602 b3915 b1727 b0114 b0529 b2492 b0904 b1781 b3001 b3927 b1380 b0325 b2660 b1771 b0606 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.407172 (mmol/gDw/h)
  Minimum Production Rate : 0.613743 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.653176
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.240475
  EX_pi_e : 1.006503
  EX_so4_e : 0.102534
  EX_k_e : 0.079477
  EX_fe3_e : 0.006540
  EX_mg2_e : 0.003532
  EX_cl_e : 0.002119
  EX_ca2_e : 0.002119
  EX_cu2_e : 0.000289
  EX_mn2_e : 0.000281
  EX_zn2_e : 0.000139
  EX_ni2_e : 0.000132
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 50.958253
  EX_co2_e : 35.958956
  EX_h_e : 6.441643
  EX_etoh_e : 0.663765
  Auxiliary production reaction : 0.613743
  EX_ac_e : 0.237050
  EX_hxan_e : 0.000456
  DM_5drib_c : 0.000273
  DM_4crsol_c : 0.000091

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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