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 : 10fthf_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (22 of 46: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3399 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b2744 b0871 b3617 b0160 b0120 b1982 b0675 b2361 b4014 b0261 b2976 b4381 b2406 b0112 b2975 b0114 b3603 b0509 b3125 b0529 b2492 b0904 b0508   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.340469 (mmol/gDw/h)
  Minimum Production Rate : 1.088967 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 987.046885
  EX_o2_e : 270.562445
  EX_nh4_e : 11.309096
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.328419
  EX_so4_e : 0.085737
  EX_k_e : 0.066457
  EX_mg2_e : 0.002954
  EX_ca2_e : 0.001772
  EX_cl_e : 0.001772
  EX_cu2_e : 0.000241
  EX_mn2_e : 0.000235
  EX_zn2_e : 0.000116
  EX_ni2_e : 0.000110

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994532
  EX_h2o_e : 548.950087
  EX_co2_e : 19.253023
  EX_acald_e : 2.486803
  Auxiliary production reaction : 1.088967
  DM_oxam_c : 0.009290
  DM_5drib_c : 0.000228
  DM_4crsol_c : 0.000076

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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