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 : adphep_DD_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (96 of 99: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b3553 b1478 b4382 b4269 b0493 b3588 b3003 b3011 b1241 b4384 b0871 b2779 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b0207 b3012 b1982 b1033 b0261 b2799 b1602 b0153 b2406 b0529 b2492 b0904 b1781 b3001 b3035 b1380 b0325 b2660 b1771 b3662 b0606 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.388733 (mmol/gDw/h)
  Minimum Production Rate : 0.498230 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 35.988359
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.691173
  EX_pi_e : 1.371435
  EX_so4_e : 0.097891
  EX_k_e : 0.075878
  EX_fe2_e : 0.006243
  EX_mg2_e : 0.003372
  EX_ca2_e : 0.002023
  EX_cl_e : 0.002023
  EX_cu2_e : 0.000276
  EX_mn2_e : 0.000269
  EX_zn2_e : 0.000133
  EX_ni2_e : 0.000126

Product: (mmol/gDw/h)
  EX_h2o_e : 52.815845
  EX_co2_e : 35.571346
  EX_h_e : 5.068263
  Auxiliary production reaction : 0.498230
  EX_hxan_e : 0.000435
  DM_5drib_c : 0.000261
  DM_4crsol_c : 0.000087

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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