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 (40 of 111: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b3752 b0871 b2925 b2097 b3617 b2407 b1851 b1982 b1200 b0261 b0505 b4381 b2406 b0112 b0114 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.482271 (mmol/gDw/h)
  Minimum Production Rate : 1.462836 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 23.324273
  EX_nh4_e : 11.112820
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.465201
  EX_so4_e : 0.121445
  EX_k_e : 0.094136
  EX_fe2_e : 0.007746
  EX_mg2_e : 0.004184
  EX_ca2_e : 0.002510
  EX_cl_e : 0.002510
  EX_cu2_e : 0.000342
  EX_mn2_e : 0.000333
  EX_zn2_e : 0.000164
  EX_ni2_e : 0.000156
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 45.661874
  EX_co2_e : 22.423233
  EX_h_e : 10.388628
  EX_acald_e : 1.939859
  Auxiliary production reaction : 1.462836
  DM_oxam_c : 0.052995
  DM_5drib_c : 0.052779
  DM_4crsol_c : 0.052563

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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