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 : eig3p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (31 of 89: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3399 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b2744 b0871 b2779 b3617 b0160 b1982 b4374 b0675 b2361 b2291 b0112 b2868 b0114 b0529 b2492 b0904 b1517 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.419938 (mmol/gDw/h)
  Minimum Production Rate : 1.365681 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 33.430659
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.267787
  EX_pi_e : 1.770756
  EX_so4_e : 0.105749
  EX_k_e : 0.081969
  EX_fe2_e : 0.006745
  EX_mg2_e : 0.003643
  EX_ca2_e : 0.002186
  EX_cl_e : 0.002186
  EX_cu2_e : 0.000298
  EX_mn2_e : 0.000290
  EX_zn2_e : 0.000143
  EX_ni2_e : 0.000136
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 51.748372
  EX_co2_e : 33.828021
  EX_h_e : 6.591051
  Auxiliary production reaction : 1.365681
  EX_acald_e : 0.369506
  EX_hxan_e : 0.000283
  EX_mththf_e : 0.000188
  DM_5drib_c : 0.000094
  DM_4crsol_c : 0.000094

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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