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 : trp__L_e
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 : 55
  Gene deletion: b4467 b3399 b4069 b2502 b2744 b3708 b2930 b4232 b3697 b3925 b3115 b1849 b2296 b3844 b1004 b3713 b1109 b0046 b3236 b2690 b1982 b2797 b3117 b1814 b4471 b4374 b0675 b2361 b2291 b0261 b2799 b3945 b1602 b0153 b2913 b0452 b1727 b2975 b0114 b3603 b0755 b3612 b1539 b2492 b0904 b0591 b1533 b3927 b1380 b0514 b4141 b1798 b0606 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.355943 (mmol/gDw/h)
  Minimum Production Rate : 0.349041 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.402379
  EX_o2_e : 280.632176
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.543830
  EX_pi_e : 0.343345
  EX_so4_e : 0.089634
  EX_k_e : 0.069478
  EX_mg2_e : 0.003088
  EX_ca2_e : 0.001853
  EX_cl_e : 0.001853
  EX_cu2_e : 0.000252
  EX_mn2_e : 0.000246
  EX_zn2_e : 0.000121
  EX_ni2_e : 0.000115

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994283
  EX_h2o_e : 543.759325
  EX_co2_e : 31.812723
  EX_ac_e : 4.621682
  EX_trp__L_e : 0.349041
  EX_etoh_e : 0.245924
  EX_hxan_e : 0.000398
  DM_5drib_c : 0.000239
  DM_4crsol_c : 0.000079

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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