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 (37 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b4069 b4384 b2744 b3708 b3008 b2297 b2458 b2779 b2926 b0030 b2407 b1982 b2688 b2797 b3117 b1814 b4471 b0596 b4374 b2361 b2291 b0261 b0411 b1701 b1805 b0112 b0114 b1539 b2492 b0904 b2578 b1533 b3927 b0516 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.636309 (mmol/gDw/h)
  Minimum Production Rate : 0.404308 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 27.131833
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.683546
  EX_pi_e : 0.613787
  EX_so4_e : 0.160235
  EX_k_e : 0.124203
  EX_fe2_e : 0.010220
  EX_mg2_e : 0.005520
  EX_ca2_e : 0.003312
  EX_cl_e : 0.003312
  EX_cu2_e : 0.000451
  EX_mn2_e : 0.000440
  EX_zn2_e : 0.000217
  EX_ni2_e : 0.000206
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 48.732495
  EX_co2_e : 28.689889
  EX_h_e : 7.028574
  EX_trp__L_e : 0.404308
  EX_ac_e : 0.370450
  EX_alltn_e : 0.000712
  DM_5drib_c : 0.000427
  DM_4crsol_c : 0.000142

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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