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 (21 of 41: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b0474 b2518 b3831 b0910 b3752 b4152 b0871 b2925 b2097 b2926 b1612 b1611 b4122 b3946 b0825 b0411 b4138 b4123 b0621 b4381 b0114 b0755 b3612 b2492 b0904 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.352919 (mmol/gDw/h)
  Minimum Production Rate : 0.043992 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.736387
  EX_o2_e : 279.682963
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.312042
  EX_pi_e : 0.340428
  EX_so4_e : 0.088872
  EX_k_e : 0.068887
  EX_mg2_e : 0.003062
  EX_ca2_e : 0.001837
  EX_cl_e : 0.001837
  EX_cu2_e : 0.000250
  EX_mn2_e : 0.000244
  EX_zn2_e : 0.000120
  EX_ni2_e : 0.000114

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994332
  EX_h2o_e : 543.532239
  EX_co2_e : 27.631083
  EX_pyr_e : 4.778595
  EX_succ_e : 0.368021
  EX_thymd_e : 0.142283
  EX_ura_e : 0.063879
  Auxiliary production reaction : 0.044110
  DM_5drib_c : 0.000079
  DM_4crsol_c : 0.000079

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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