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 : q8h2_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (61 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4269 b0493 b3588 b3003 b3011 b1241 b0351 b3752 b0871 b2407 b2883 b3616 b3589 b0261 b4381 b3654 b2868 b3714 b3664 b4064 b4464 b0114 b0529 b2492 b0904   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.623264 (mmol/gDw/h)
  Minimum Production Rate : 0.183733 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.250368
  EX_o2_e : 270.936474
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.744021
  EX_pi_e : 0.601204
  EX_so4_e : 0.156950
  EX_k_e : 0.121657
  EX_mg2_e : 0.005407
  EX_cl_e : 0.003244
  EX_ca2_e : 0.003244
  EX_cu2_e : 0.000442
  EX_mn2_e : 0.000431
  EX_zn2_e : 0.000213
  EX_ni2_e : 0.000201
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_fe3_e : 999.989990
  EX_h2o_e : 543.889683
  EX_co2_e : 25.382885
  Auxiliary production reaction : 0.183733
  EX_xtsn_e : 0.003206
  DM_5drib_c : 0.000140
  DM_4crsol_c : 0.000139

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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