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 (99 of 102: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 47
  Gene deletion: b3553 b1478 b3399 b1241 b4069 b2502 b2744 b2297 b2458 b3844 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b0207 b3012 b1982 b4139 b1033 b0675 b2361 b0261 b2799 b1602 b0153 b2913 b4381 b2406 b0509 b3125 b0529 b2492 b0904 b1300 b2954 b1781 b3001 b3035 b3029 b1380 b0325 b1771 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.430221 (mmol/gDw/h)
  Minimum Production Rate : 0.428886 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 37.888906
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.849478
  EX_pi_e : 0.843880
  EX_so4_e : 0.108338
  EX_k_e : 0.083976
  EX_mg2_e : 0.003732
  EX_fe2_e : 0.003551
  EX_fe3_e : 0.003359
  EX_ca2_e : 0.002239
  EX_cl_e : 0.002239
  EX_cu2_e : 0.000305
  EX_mn2_e : 0.000297
  EX_zn2_e : 0.000147
  EX_ni2_e : 0.000139
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 54.115235
  EX_co2_e : 37.491938
  EX_h_e : 6.409997
  Auxiliary production reaction : 0.428886
  EX_ac_e : 0.250469
  EX_ade_e : 0.011739
  DM_5drib_c : 0.000289
  DM_4crsol_c : 0.000096

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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