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 (46 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b3399 b3846 b2341 b0474 b2518 b4069 b2502 b2744 b3708 b3008 b2297 b2458 b2925 b2097 b2926 b0583 b2690 b1982 b2797 b3117 b1814 b4471 b1623 b3665 b4374 b0675 b2361 b2291 b0261 b3945 b0452 b0114 b1539 b2492 b0904 b2578 b1533 b3927 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.376564 (mmol/gDw/h)
  Minimum Production Rate : 0.239267 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.223091
  EX_o2_e : 281.324721
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.547500
  EX_pi_e : 0.363236
  EX_so4_e : 0.094826
  EX_k_e : 0.073503
  EX_mg2_e : 0.003267
  EX_ca2_e : 0.001960
  EX_cl_e : 0.001960
  EX_cu2_e : 0.000267
  EX_mn2_e : 0.000260
  EX_zn2_e : 0.000128
  EX_ni2_e : 0.000122

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993952
  EX_h2o_e : 544.107834
  EX_co2_e : 32.248493
  EX_ac_e : 4.830200
  EX_trp__L_e : 0.239267
  EX_ade_e : 0.000421
  DM_5drib_c : 0.000253
  DM_4crsol_c : 0.000084

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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