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 : glyc__R_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (61 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b3399 b2502 b2744 b3708 b3008 b3614 b0910 b0871 b2779 b3124 b1982 b2797 b3117 b1814 b4471 b4374 b0675 b2361 b0261 b4381 b2406 b0112 b0114 b0886 b2366 b2492 b0904 b2578 b1533 b3927 b3821 b0594 b1600 b0514 b4141 b1798   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.684592 (mmol/gDw/h)
  Minimum Production Rate : 0.051946 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 28.368409
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.728104
  EX_pi_e : 0.660361
  EX_so4_e : 0.172394
  EX_k_e : 0.133628
  EX_fe2_e : 0.010995
  EX_mg2_e : 0.005939
  EX_ca2_e : 0.003563
  EX_cl_e : 0.003563
  EX_cu2_e : 0.000485
  EX_mn2_e : 0.000473
  EX_zn2_e : 0.000233
  EX_ni2_e : 0.000221
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 48.886441
  EX_co2_e : 29.721449
  EX_h_e : 6.799389
  DM_oxam_c : 0.122571
  EX_thym_e : 0.106000
  DM_5drib_c : 0.104351
  DM_4crsol_c : 0.104044
  EX_glyc__R_e : 0.051946

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.

Last updated: 21-Sep-2023
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