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 : 6hmhptpp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (56 of 95: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b3399 b1241 b0351 b4069 b2744 b2297 b2458 b2779 b2926 b0160 b0907 b1982 b3616 b3589 b0675 b2361 b0261 b4381 b2406 b0112 b2789 b3127 b2975 b0114 b3603 b0529 b2492 b0904   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.368723 (mmol/gDw/h)
  Minimum Production Rate : 1.393999 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 26.484187
  EX_nh4_e : 10.962230
  EX_glc__D_e : 10.000000
  EX_pi_e : 3.143670
  EX_so4_e : 0.092852
  EX_k_e : 0.071972
  EX_fe2_e : 0.005922
  EX_mg2_e : 0.003199
  EX_ca2_e : 0.001919
  EX_cl_e : 0.001919
  EX_cu2_e : 0.000261
  EX_mn2_e : 0.000255
  EX_zn2_e : 0.000126
  EX_ni2_e : 0.000119

Product: (mmol/gDw/h)
  EX_h2o_e : 49.559020
  EX_co2_e : 23.073961
  EX_h_e : 12.899207
  EX_ac_e : 2.520954
  EX_dxylnt_e : 1.394163
  Auxiliary production reaction : 1.393999
  DM_oxam_c : 0.010061
  DM_5drib_c : 0.000247
  DM_4crsol_c : 0.000082

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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