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 : gmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (51 of 102: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b3942 b1732 b1241 b0351 b4069 b2744 b0512 b2297 b2458 b2779 b2926 b3617 b3236 b2883 b1982 b0675 b2361 b0411 b4381 b0114 b0529 b2492 b0904 b1511   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.498606 (mmol/gDw/h)
  Minimum Production Rate : 0.942852 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.923802
  EX_nh4_e : 10.152689
  EX_glc__D_e : 10.000000
  EX_pi_e : 1.423810
  EX_so4_e : 0.125559
  EX_k_e : 0.097324
  EX_fe2_e : 0.008008
  EX_mg2_e : 0.004325
  EX_cl_e : 0.002595
  EX_ca2_e : 0.002595
  EX_cu2_e : 0.000354
  EX_mn2_e : 0.000345
  EX_zn2_e : 0.000170
  EX_ni2_e : 0.000161
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 49.693835
  EX_co2_e : 25.119134
  EX_h_e : 11.815290
  EX_ac_e : 2.466111
  Auxiliary production reaction : 0.942852
  EX_alltn_e : 0.013382
  DM_mththf_c : 0.000223
  DM_5drib_c : 0.000112
  DM_4crsol_c : 0.000111

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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