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 : adphep_LD_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (42 of 49: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b4467 b4382 b4269 b0493 b3588 b3003 b3011 b4384 b0871 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b0937 b1982 b0261 b2799 b3945 b1602 b2913 b2406 b1727 b0114 b0529 b2492 b0904 b3927 b1380 b3662 b0606 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.430445 (mmol/gDw/h)
  Minimum Production Rate : 0.289745 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 35.638381
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.099905
  EX_pi_e : 0.994701
  EX_so4_e : 0.108395
  EX_k_e : 0.084020
  EX_fe2_e : 0.006913
  EX_mg2_e : 0.003734
  EX_ca2_e : 0.002240
  EX_cl_e : 0.002240
  EX_cu2_e : 0.000305
  EX_mn2_e : 0.000297
  EX_zn2_e : 0.000147
  EX_ni2_e : 0.000139
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 51.259604
  EX_co2_e : 36.355382
  EX_h_e : 4.826745
  EX_etoh_e : 0.523893
  Auxiliary production reaction : 0.289745
  EX_ade_e : 0.000482
  DM_5drib_c : 0.000289
  DM_4crsol_c : 0.000096

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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