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 : xtp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (42 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4269 b0493 b3588 b3003 b3011 b1241 b0351 b3831 b4384 b2744 b3752 b0871 b2407 b1982 b2498 b3616 b3589 b3665 b0411 b0114 b0529 b2492 b0904 b1511 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.624594 (mmol/gDw/h)
  Minimum Production Rate : 0.493886 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 22.788169
  EX_nh4_e : 10.810152
  EX_glc__D_e : 10.000000
  EX_pi_e : 2.084146
  EX_so4_e : 0.157285
  EX_k_e : 0.121916
  EX_fe2_e : 0.010032
  EX_mg2_e : 0.005418
  EX_ca2_e : 0.003251
  EX_cl_e : 0.003251
  EX_cu2_e : 0.000443
  EX_mn2_e : 0.000432
  EX_zn2_e : 0.000213
  EX_ni2_e : 0.000202
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 50.252505
  EX_co2_e : 22.116621
  EX_h_e : 8.815836
  EX_acald_e : 1.043471
  EX_thym_e : 1.043471
  Auxiliary production reaction : 0.493886
  EX_ade_e : 0.000420
  DM_mththf_c : 0.000280
  DM_5drib_c : 0.000141
  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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