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 : btn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (59 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b2836 b1241 b0351 b4069 b4384 b2744 b3708 b3115 b1849 b2296 b3617 b0030 b1238 b2883 b1982 b2797 b3117 b1814 b4471 b0261 b0507 b4381 b2406 b0112 b2868 b4064 b4464 b0114 b1539 b2492 b0904 b1533 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.515846 (mmol/gDw/h)
  Minimum Production Rate : 0.257261 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 21.711717
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.947423
  EX_so4_e : 0.644423
  EX_pi_e : 0.497589
  EX_k_e : 0.100690
  EX_fe2_e : 0.008285
  EX_mg2_e : 0.004475
  EX_ca2_e : 0.002685
  EX_cl_e : 0.002685
  EX_cu2_e : 0.000366
  EX_mn2_e : 0.000356
  EX_zn2_e : 0.000176
  EX_ni2_e : 0.000167
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 45.957556
  EX_co2_e : 22.296521
  EX_h_e : 11.333650
  EX_ac_e : 2.988960
  EX_ade_e : 0.515100
  DM_5drib_c : 0.257607
  EX_meoh_e : 0.257262
  DM_amob_c : 0.257262
  Auxiliary production reaction : 0.257261
  EX_glyclt_e : 0.000345
  DM_4crsol_c : 0.000115

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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