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 (35 of 41: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b4467 b2242 b0474 b2518 b3831 b0910 b0871 b2925 b2097 b0030 b1004 b3713 b1109 b0046 b1612 b1611 b4122 b0907 b0651 b2162 b1779 b3946 b2210 b0825 b1415 b0411 b1602 b2342 b3845 b4138 b4123 b0621 b0114 b2492 b0904 b3028 b1380 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.351860 (mmol/gDw/h)
  Minimum Production Rate : 0.044017 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 29.983823
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.299105
  EX_pi_e : 0.339407
  EX_so4_e : 0.088605
  EX_k_e : 0.068681
  EX_fe2_e : 0.005651
  EX_mg2_e : 0.003052
  EX_ca2_e : 0.001831
  EX_cl_e : 0.001831
  EX_cu2_e : 0.000249
  EX_mn2_e : 0.000243
  EX_zn2_e : 0.000120
  EX_ni2_e : 0.000114

Product: (mmol/gDw/h)
  EX_h2o_e : 43.665931
  EX_co2_e : 27.638033
  EX_h_e : 9.543764
  EX_pyr_e : 5.077697
  EX_succ_e : 0.366917
  EX_ura_e : 0.205504
  Auxiliary production reaction : 0.044017
  EX_dxylnt_e : 0.000157
  DM_5drib_c : 0.000079
  DM_4crsol_c : 0.000078

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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