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 : nadp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (43 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b3553 b4382 b1241 b0351 b4069 b4384 b3708 b3752 b3115 b1849 b2296 b2407 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b1033 b2440 b0261 b0507 b2406 b0112 b0452 b0114 b1539 b2492 b0904 b1533 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.495984 (mmol/gDw/h)
  Minimum Production Rate : 0.742066 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 21.455604
  EX_nh4_e : 10.551641
  EX_glc__D_e : 10.000000
  EX_pi_e : 2.704627
  EX_so4_e : 0.124899
  EX_k_e : 0.096813
  EX_fe2_e : 0.007966
  EX_mg2_e : 0.004303
  EX_ca2_e : 0.002582
  EX_cl_e : 0.002582
  EX_cu2_e : 0.000352
  EX_mn2_e : 0.000343
  EX_zn2_e : 0.000169
  EX_ni2_e : 0.000160
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 49.711103
  EX_co2_e : 20.286977
  EX_h_e : 9.411412
  EX_ac_e : 1.884409
  Auxiliary production reaction : 0.742066
  DM_oxam_c : 0.000555
  DM_5drib_c : 0.000333
  EX_glyclt_e : 0.000332
  DM_4crsol_c : 0.000111
  EX_etha_e : 0.000040

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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