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 : dgmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (63 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b4384 b3708 b3008 b3752 b0871 b2925 b2097 b2407 b3236 b1779 b2690 b2797 b3117 b1814 b4471 b3665 b3945 b4381 b0114 b1539 b2492 b0904 b1533 b3825 b1380 b0494   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.601746 (mmol/gDw/h)
  Minimum Production Rate : 0.103893 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 27.237816
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.020293
  EX_pi_e : 0.684341
  EX_so4_e : 0.151532
  EX_k_e : 0.117457
  EX_fe2_e : 0.009665
  EX_mg2_e : 0.005220
  EX_ca2_e : 0.003132
  EX_cl_e : 0.003132
  EX_cu2_e : 0.000427
  EX_mn2_e : 0.000416
  EX_zn2_e : 0.000205
  EX_ni2_e : 0.000194
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 46.602204
  EX_co2_e : 27.061420
  EX_h_e : 8.450147
  EX_pyr_e : 2.399576
  Auxiliary production reaction : 0.103893
  EX_ade_e : 0.000405
  DM_5drib_c : 0.000135
  DM_4crsol_c : 0.000134

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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