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 : his__L_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (54 of 76: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b3399 b1241 b0351 b4069 b4384 b2744 b3752 b0512 b3115 b1849 b2296 b2779 b2883 b1982 b3616 b3589 b1623 b0411 b2913 b4381 b0112 b0114 b0529 b2492 b0904 b1517 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.370405 (mmol/gDw/h)
  Minimum Production Rate : 1.400853 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 34.727411
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.242663
  EX_pi_e : 0.357294
  EX_so4_e : 0.093275
  EX_k_e : 0.072300
  EX_fe2_e : 0.005949
  EX_mg2_e : 0.003213
  EX_ca2_e : 0.001928
  EX_cl_e : 0.001928
  EX_cu2_e : 0.000263
  EX_mn2_e : 0.000256
  EX_zn2_e : 0.000126
  EX_ni2_e : 0.000120

Product: (mmol/gDw/h)
  EX_h2o_e : 52.343254
  EX_co2_e : 34.087184
  EX_h_e : 8.777598
  Auxiliary production reaction : 1.400853
  EX_ac_e : 1.131847
  EX_alltn_e : 0.009941
  DM_mththf_c : 0.000166
  DM_5drib_c : 0.000083
  DM_4crsol_c : 0.000083

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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