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 : uri_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (41 of 41: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 46
  Gene deletion: b0474 b2518 b3831 b0910 b3752 b2221 b2930 b4232 b3697 b3925 b4152 b0871 b2297 b2458 b1612 b1611 b4122 b1779 b2690 b3962 b1525 b4267 b4015 b1014 b2661 b0411 b0614 b0726 b3945 b4388 b4138 b4123 b0621 b0114 b0306 b1539 b3605 b1380 b0325 b0508 b4266 b4141 b1798 b1813 b1206 b3924   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.372601 (mmol/gDw/h)
  Minimum Production Rate : 0.196788 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 31.516252
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.384313
  EX_pi_e : 0.359414
  EX_so4_e : 0.093828
  EX_k_e : 0.072729
  EX_fe2_e : 0.005984
  EX_mg2_e : 0.003232
  EX_ca2_e : 0.001939
  EX_cl_e : 0.001939
  EX_cu2_e : 0.000264
  EX_mn2_e : 0.000257
  EX_zn2_e : 0.000127
  EX_ni2_e : 0.000120

Product: (mmol/gDw/h)
  EX_h2o_e : 44.714313
  EX_co2_e : 32.136669
  EX_h_e : 8.384311
  EX_ac_e : 2.823359
  EX_4abut_e : 0.831791
  EX_succ_e : 0.388546
  Auxiliary production reaction : 0.196788
  EX_ura_e : 0.067442
  EX_mththf_e : 0.000167
  DM_5drib_c : 0.000084
  DM_4crsol_c : 0.000083

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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