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 : nadhx__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (65 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b4467 b1478 b1241 b0351 b4069 b3708 b3844 b1004 b3713 b1109 b0046 b3236 b4015 b0335 b2799 b3945 b1602 b2342 b3845 b3915 b0728 b0755 b3612 b0529 b1380 b3792 b2660 b3546 b0606 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.572628 (mmol/gDw/h)
  Minimum Production Rate : 0.020607 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 34.890704
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.328589
  EX_pi_e : 0.593576
  EX_so4_e : 0.144199
  EX_k_e : 0.111773
  EX_fe3_e : 0.009197
  EX_mg2_e : 0.004968
  EX_ca2_e : 0.002981
  EX_cl_e : 0.002981
  EX_cu2_e : 0.000406
  EX_mn2_e : 0.000396
  EX_zn2_e : 0.000195
  EX_ni2_e : 0.000185
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 51.571957
  EX_co2_e : 36.063485
  EX_h_e : 5.373771
  Auxiliary production reaction : 0.020607
  DM_5drib_c : 0.000129
  DM_4crsol_c : 0.000128

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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