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 : dutp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (58 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b4467 b3399 b1241 b0351 b4069 b2744 b0871 b3115 b1849 b2296 b2925 b2097 b3617 b0160 b1004 b3713 b1109 b0046 b3236 b2883 b1779 b3946 b2210 b0825 b4374 b2361 b2291 b0261 b3654 b2868 b3714 b3664 b4064 b4464 b0114 b0529 b2492 b0904 b1380 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.296374 (mmol/gDw/h)
  Minimum Production Rate : 0.710795 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 29.075696
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.899757
  EX_pi_e : 2.418268
  EX_so4_e : 0.074633
  EX_k_e : 0.057850
  EX_fe2_e : 0.004760
  EX_mg2_e : 0.002571
  EX_cl_e : 0.001543
  EX_ca2_e : 0.001543
  EX_cu2_e : 0.000210
  EX_mn2_e : 0.000205
  EX_zn2_e : 0.000101
  EX_ni2_e : 0.000096

Product: (mmol/gDw/h)
  EX_h2o_e : 47.238790
  EX_co2_e : 26.682318
  EX_h_e : 8.212078
  EX_pyr_e : 3.777997
  Auxiliary production reaction : 0.710795
  EX_ac_e : 0.433325
  EX_his__L_e : 0.425454
  EX_adn_e : 0.000199
  EX_glyclt_e : 0.000198
  DM_5drib_c : 0.000067
  DM_4crsol_c : 0.000066

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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