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 : hdcea_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (78 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b4467 b2836 b2242 b2744 b3614 b0910 b2781 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b1638 b1759 b4374 b0675 b2361 b2291 b1852 b4014 b2976 b4138 b4123 b0621 b2913 b2223 b0306 b3605 b2133 b2197 b3029 b3028 b3918 b1912 b1206 b2285 b3893 b1474   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.328197 (mmol/gDw/h)
  Minimum Production Rate : 0.346348 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.052162
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.009985
  EX_pi_e : 0.316581
  EX_so4_e : 0.082647
  EX_k_e : 0.064062
  EX_fe3_e : 0.005271
  EX_mg2_e : 0.002847
  EX_ca2_e : 0.001708
  EX_cl_e : 0.001708
  EX_cu2_e : 0.000233
  EX_mn2_e : 0.000227
  EX_zn2_e : 0.000112
  EX_ni2_e : 0.000106

Product: (mmol/gDw/h)
  EX_h2o_e : 31.001223
  EX_co2_e : 20.484780
  EX_h_e : 13.618557
  EX_ac_e : 9.101145
  Auxiliary production reaction : 0.346348
  EX_succ_e : 0.342242
  EX_ura_e : 0.232741
  EX_glyclt_e : 0.000220
  DM_5drib_c : 0.000074
  DM_4crsol_c : 0.000073

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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