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 : glx_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (53 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b3399 b0238 b0125 b4069 b2744 b3708 b3115 b1849 b2296 b2883 b0517 b0477 b2797 b3117 b1814 b4471 b4374 b2361 b2291 b0261 b0411 b0507 b0114 b2366 b2492 b0904 b3821   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.780579 (mmol/gDw/h)
  Minimum Production Rate : 0.003047 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.864985
  EX_o2_e : 274.148184
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.922905
  EX_pi_e : 0.752951
  EX_so4_e : 0.196565
  EX_k_e : 0.152364
  EX_mg2_e : 0.006772
  EX_ca2_e : 0.004063
  EX_cl_e : 0.004063
  EX_cu2_e : 0.000553
  EX_mn2_e : 0.000539
  EX_zn2_e : 0.000266
  EX_ni2_e : 0.000252
  EX_cobalt2_e : 0.000020

Product: (mmol/gDw/h)
  EX_fe3_e : 999.987463
  EX_h2o_e : 546.670117
  EX_co2_e : 25.567684
  EX_ser__L_e : 0.492716
  EX_ac_e : 0.454442
  Auxiliary production reaction : 0.003047
  DM_5drib_c : 0.000176
  DM_4crsol_c : 0.000174

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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