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 (58 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b4467 b3399 b4069 b2502 b2744 b3115 b1849 b2296 b3844 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b3908 b1656 b1982 b4139 b4374 b0675 b2361 b2291 b0261 b2799 b3945 b1602 b3915 b1727 b0114 b0529 b2492 b0904 b2954 b1380 b2660 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.444138 (mmol/gDw/h)
  Minimum Production Rate : 0.186034 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 36.867828
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.155683
  EX_pi_e : 0.800486
  EX_so4_e : 0.111843
  EX_k_e : 0.086693
  EX_fe3_e : 0.007133
  EX_mg2_e : 0.003853
  EX_ca2_e : 0.002312
  EX_cl_e : 0.002312
  EX_cu2_e : 0.000315
  EX_mn2_e : 0.000307
  EX_zn2_e : 0.000151
  EX_ni2_e : 0.000143
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 52.919151
  EX_co2_e : 37.230760
  EX_h_e : 5.148046
  EX_ac_e : 0.258571
  Auxiliary production reaction : 0.186034
  EX_gly_e : 0.056796
  EX_glyclt_e : 0.000497
  DM_5drib_c : 0.000298
  DM_4crsol_c : 0.000099

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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