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 : gsn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (57 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b3399 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b2744 b3752 b0871 b2779 b3617 b3236 b2883 b1982 b2210 b1623 b0411 b4388 b4381 b0114 b0529 b2492 b0904 b0515 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.510381 (mmol/gDw/h)
  Minimum Production Rate : 0.816551 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 27.033869
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.649619
  EX_pi_e : 0.492317
  EX_so4_e : 0.128524
  EX_k_e : 0.099623
  EX_fe2_e : 0.008197
  EX_mg2_e : 0.004428
  EX_cl_e : 0.002657
  EX_ca2_e : 0.002657
  EX_cu2_e : 0.000362
  EX_mn2_e : 0.000353
  EX_zn2_e : 0.000174
  EX_ni2_e : 0.000165
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 49.227479
  EX_co2_e : 26.671780
  EX_h_e : 8.827131
  EX_acald_e : 2.078989
  Auxiliary production reaction : 0.816551
  EX_alltn_e : 0.013698
  DM_mththf_c : 0.000229
  DM_5drib_c : 0.000115
  DM_4crsol_c : 0.000114

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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