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 : damp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (63 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b1478 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b3752 b0871 b2925 b2097 b2407 b2690 b1982 b3616 b3589 b0675 b0822 b4381 b0114 b2492 b0904 b0789 b1249 b1511   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.684324 (mmol/gDw/h)
  Minimum Production Rate : 0.148366 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.958414
  EX_o2_e : 272.932578
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.132935
  EX_pi_e : 0.808469
  EX_so4_e : 0.172327
  EX_k_e : 0.133575
  EX_mg2_e : 0.005937
  EX_cl_e : 0.003562
  EX_ca2_e : 0.003562
  EX_cu2_e : 0.000485
  EX_mn2_e : 0.000473
  EX_zn2_e : 0.000233
  EX_ni2_e : 0.000221
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_fe3_e : 999.989009
  EX_h2o_e : 545.210645
  EX_co2_e : 25.363715
  EX_acald_e : 2.530901
  Auxiliary production reaction : 0.148366
  DM_oxam_c : 0.000461
  DM_mththf_c : 0.000307
  DM_5drib_c : 0.000154
  DM_4crsol_c : 0.000153

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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