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 : cph4_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (33 of 43: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b2836 b3399 b0238 b0125 b4069 b2744 b3708 b3008 b2297 b2458 b2883 b1982 b0477 b2797 b3117 b1814 b4471 b4374 b0675 b2361 b2291 b0411 b0114 b1539 b2492 b0904 b1533 b3927 b1511 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.755097 (mmol/gDw/h)
  Minimum Production Rate : 0.320246 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.688658
  EX_o2_e : 275.230424
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.756212
  EX_pi_e : 0.728371
  EX_so4_e : 0.190149
  EX_k_e : 0.147390
  EX_mg2_e : 0.006550
  EX_ca2_e : 0.003930
  EX_cl_e : 0.003930
  EX_cu2_e : 0.000535
  EX_mn2_e : 0.000522
  EX_zn2_e : 0.000257
  EX_ni2_e : 0.000244
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_fe3_e : 999.987872
  EX_h2o_e : 549.020529
  EX_co2_e : 25.884111
  EX_ac_e : 0.439607
  Auxiliary production reaction : 0.320246
  DM_mththf_c : 0.000338
  DM_5drib_c : 0.000170
  DM_4crsol_c : 0.000168

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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