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 : duri_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (24 of 50: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b0871 b2925 b2097 b3617 b0030 b2407 b3236 b2690 b1982 b2210 b0261 b0411 b3945 b4381 b2406 b0114 b0529 b2492 b0904 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.420952 (mmol/gDw/h)
  Minimum Production Rate : 1.368414 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.093242
  EX_o2_e : 276.710921
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.283544
  EX_pi_e : 0.406053
  EX_so4_e : 0.106004
  EX_k_e : 0.082167
  EX_mg2_e : 0.003652
  EX_ca2_e : 0.002191
  EX_cl_e : 0.002191
  EX_cu2_e : 0.000298
  EX_mn2_e : 0.000291
  EX_zn2_e : 0.000144
  EX_ni2_e : 0.000136
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993239
  EX_h2o_e : 546.398596
  EX_co2_e : 25.780021
  Auxiliary production reaction : 1.368414
  EX_pyr_e : 1.294352
  EX_acald_e : 0.370586
  DM_oxam_c : 0.000471
  DM_5drib_c : 0.000282
  DM_4crsol_c : 0.000094

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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