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 : sbt6p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (63 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b4467 b1478 b1241 b0351 b4069 b0871 b3115 b1849 b2296 b2925 b2097 b2926 b1004 b3713 b1109 b0046 b3236 b0207 b3012 b3946 b0825 b4015 b2799 b1602 b2913 b4381 b3915 b2492 b0904 b1781 b3001 b1380 b0325 b1771 b0606 b0221 b2285 b1009 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.362572 (mmol/gDw/h)
  Minimum Production Rate : 0.571196 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.771317
  EX_o2_e : 278.808745
  EX_glc__D_e : 10.000000
  EX_nh4_e : 3.915747
  EX_pi_e : 0.920935
  EX_so4_e : 0.091303
  EX_k_e : 0.070772
  EX_mg2_e : 0.003145
  EX_ca2_e : 0.001887
  EX_cl_e : 0.001887
  EX_cu2_e : 0.000257
  EX_mn2_e : 0.000251
  EX_zn2_e : 0.000124
  EX_ni2_e : 0.000117

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994177
  EX_h2o_e : 541.479715
  EX_co2_e : 27.830967
  EX_pyr_e : 4.077135
  EX_ac_e : 0.814269
  Auxiliary production reaction : 0.571196
  DM_5drib_c : 0.000082
  DM_4crsol_c : 0.000081

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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