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 : nad_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (26 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3553 b3399 b4382 b1241 b0351 b4069 b4384 b2744 b3115 b1849 b2296 b3617 b2407 b1982 b1033 b0675 b2361 b0261 b0507 b4388 b0112 b0114 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.449162 (mmol/gDw/h)
  Minimum Production Rate : 0.860807 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 20.665599
  EX_nh4_e : 10.877060
  EX_glc__D_e : 10.000000
  EX_pi_e : 2.154878
  EX_so4_e : 0.113108
  EX_k_e : 0.087673
  EX_fe2_e : 0.007214
  EX_mg2_e : 0.003896
  EX_cl_e : 0.002338
  EX_ca2_e : 0.002338
  EX_cu2_e : 0.000318
  EX_mn2_e : 0.000310
  EX_zn2_e : 0.000153
  EX_ni2_e : 0.000145
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 48.979967
  EX_co2_e : 19.040895
  EX_h_e : 9.793373
  EX_ac_e : 2.221761
  Auxiliary production reaction : 0.860807
  DM_oxam_c : 0.000503
  DM_5drib_c : 0.000301
  EX_glyclt_e : 0.000300
  DM_4crsol_c : 0.000100

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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