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 : prfp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (73 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b2836 b3399 b1241 b0351 b2744 b3708 b3008 b2930 b4232 b3697 b3925 b0512 b0871 b2297 b2458 b2779 b3617 b0160 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b4374 b0675 b2361 b2291 b0261 b0112 b2789 b3127 b0114 b0886 b0529 b1539 b2492 b0904 b1533 b3927   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.591285 (mmol/gDw/h)
  Minimum Production Rate : 0.134026 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.866219
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.065190
  EX_pi_e : 0.838410
  EX_so4_e : 0.148897
  EX_k_e : 0.115415
  EX_fe2_e : 0.009497
  EX_mg2_e : 0.005129
  EX_ca2_e : 0.003078
  EX_cl_e : 0.003078
  EX_cu2_e : 0.000419
  EX_mn2_e : 0.000409
  EX_zn2_e : 0.000202
  EX_ni2_e : 0.000191
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 46.345846
  EX_co2_e : 26.609077
  EX_h_e : 8.473105
  EX_pyr_e : 2.359133
  Auxiliary production reaction : 0.134026
  EX_alltn_e : 0.002308
  DM_5drib_c : 0.002043
  DM_4crsol_c : 0.001779
  EX_glyclt_e : 0.001647

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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