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 : adp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (73 of 89: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b3399 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b2744 b3708 b3008 b0871 b3617 b2883 b1982 b2797 b3117 b1814 b4471 b4374 b0675 b2361 b2291 b0411 b4381 b0112 b2868 b0114 b2366 b2492 b0904 b1533 b1511 b4141 b1798   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.622984 (mmol/gDw/h)
  Minimum Production Rate : 0.751174 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 22.906163
  EX_nh4_e : 10.486138
  EX_glc__D_e : 10.000000
  EX_pi_e : 2.103281
  EX_so4_e : 0.156880
  EX_k_e : 0.121602
  EX_fe2_e : 0.010006
  EX_mg2_e : 0.005404
  EX_cl_e : 0.003243
  EX_ca2_e : 0.003243
  EX_cu2_e : 0.000442
  EX_mn2_e : 0.000430
  EX_zn2_e : 0.000212
  EX_ni2_e : 0.000201
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 49.488874
  EX_co2_e : 23.268142
  EX_h_e : 8.731016
  EX_acald_e : 1.823001
  Auxiliary production reaction : 0.751174
  EX_ade_e : 0.000419
  DM_mththf_c : 0.000279
  DM_5drib_c : 0.000140
  DM_4crsol_c : 0.000139

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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