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 : 4r5au_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (92 of 111: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b3399 b4382 b1241 b0351 b4069 b2744 b3708 b3115 b1849 b2296 b2926 b3617 b0160 b1982 b2797 b3117 b1814 b4471 b3449 b0675 b2361 b0261 b0507 b4381 b2406 b0112 b0452 b2975 b0114 b3603 b1539 b2492 b0904 b1533   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.441968 (mmol/gDw/h)
  Minimum Production Rate : 1.299372 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 27.154952
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.982764
  EX_pi_e : 0.426325
  EX_so4_e : 0.111296
  EX_k_e : 0.086269
  EX_fe2_e : 0.007098
  EX_mg2_e : 0.003834
  EX_ca2_e : 0.002300
  EX_cl_e : 0.002300
  EX_cu2_e : 0.000313
  EX_mn2_e : 0.000305
  EX_zn2_e : 0.000151
  EX_ni2_e : 0.000143
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 46.272263
  EX_co2_e : 25.481388
  EX_h_e : 11.611786
  EX_ac_e : 2.329202
  Auxiliary production reaction : 1.299372
  DM_oxam_c : 0.012059
  DM_5drib_c : 0.000297
  DM_4crsol_c : 0.000099

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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