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 : nac_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (47 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b0474 b2518 b2744 b2930 b4232 b3697 b3925 b4152 b0871 b1612 b1611 b4122 b1779 b3946 b0825 b4374 b4161 b0675 b4138 b4123 b0621 b4381 b0114 b2492 b0904 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.598616 (mmol/gDw/h)
  Minimum Production Rate : 0.316156 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.007711
  EX_o2_e : 276.492967
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.997862
  EX_pi_e : 0.577429
  EX_so4_e : 0.150744
  EX_k_e : 0.116846
  EX_mg2_e : 0.005193
  EX_ca2_e : 0.003116
  EX_cl_e : 0.003116
  EX_cu2_e : 0.000424
  EX_mn2_e : 0.000414
  EX_zn2_e : 0.000204
  EX_ni2_e : 0.000193
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990386
  EX_h2o_e : 546.382304
  EX_co2_e : 26.447673
  EX_pyr_e : 1.384871
  EX_succ_e : 0.624232
  Auxiliary production reaction : 0.316156
  EX_ura_e : 0.108351
  DM_5drib_c : 0.000135
  DM_4crsol_c : 0.000133

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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