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_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (56 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b0474 b2518 b3831 b3752 b4152 b0871 b3115 b1849 b2296 b2779 b2925 b2097 b1612 b1611 b4122 b3946 b0825 b4161 b4388 b4138 b4123 b0621 b2789 b3127 b0114 b1206 b2285 b3893 b1474   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.359256 (mmol/gDw/h)
  Minimum Production Rate : 0.189739 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.250661
  EX_o2_e : 279.732513
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.389465
  EX_pi_e : 0.346540
  EX_so4_e : 0.090468
  EX_k_e : 0.070124
  EX_mg2_e : 0.003117
  EX_ca2_e : 0.001870
  EX_cl_e : 0.001870
  EX_cu2_e : 0.000255
  EX_mn2_e : 0.000248
  EX_zn2_e : 0.000123
  EX_ni2_e : 0.000116

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994230
  EX_h2o_e : 543.241669
  EX_co2_e : 27.443832
  EX_pyr_e : 4.475571
  EX_for_e : 0.499069
  EX_succ_e : 0.374629
  EX_ac_e : 0.209154
  EX_uri_e : 0.189739
  EX_ura_e : 0.065026
  DM_5drib_c : 0.000081
  DM_4crsol_c : 0.000080

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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