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 : uri_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (33 of 41: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b2242 b3553 b0474 b2518 b3831 b3752 b0871 b3115 b1849 b2296 b2925 b2097 b1232 b1004 b3713 b1109 b0046 b1612 b1611 b4122 b1779 b3946 b2210 b0825 b1033 b4161 b0411 b4138 b4123 b0621 b0114 b0306 b3605 b3028 b1206 b2285 b3893 b1474   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.383341 (mmol/gDw/h)
  Minimum Production Rate : 0.202203 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 989.607859
  EX_o2_e : 280.369423
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.683228
  EX_pi_e : 0.369773
  EX_so4_e : 0.096533
  EX_k_e : 0.074825
  EX_mg2_e : 0.003325
  EX_ca2_e : 0.001995
  EX_cl_e : 0.001995
  EX_cu2_e : 0.000272
  EX_mn2_e : 0.000265
  EX_zn2_e : 0.000131
  EX_ni2_e : 0.000124

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993843
  EX_h2o_e : 543.458739
  EX_co2_e : 27.932839
  EX_pyr_e : 3.446111
  EX_for_e : 1.851740
  EX_succ_e : 0.399745
  EX_ac_e : 0.223176
  Auxiliary production reaction : 0.202203
  EX_ura_e : 0.069386
  DM_5drib_c : 0.000086
  DM_4crsol_c : 0.000085

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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