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 : dhnpt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (27 of 90: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b1241 b0351 b4069 b2744 b2297 b2458 b3617 b2883 b1623 b3665 b4381 b2406 b0112 b3654 b3714 b3664 b4064 b4464 b0114 b0529 b2492 b0904 b1511 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.460152 (mmol/gDw/h)
  Minimum Production Rate : 1.740892 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 23.963281
  EX_nh4_e : 13.674056
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.443865
  EX_so4_e : 0.115875
  EX_k_e : 0.089818
  EX_fe2_e : 0.007390
  EX_mg2_e : 0.003992
  EX_ca2_e : 0.002395
  EX_cl_e : 0.002395
  EX_cu2_e : 0.000326
  EX_mn2_e : 0.000318
  EX_zn2_e : 0.000157
  EX_ni2_e : 0.000149
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 50.153272
  EX_co2_e : 20.593025
  EX_h_e : 15.357921
  EX_ac_e : 2.425406
  Auxiliary production reaction : 1.740892
  DM_mththf_c : 0.000206
  DM_5drib_c : 0.000104
  DM_4crsol_c : 0.000103

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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