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_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (67 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b0474 b2518 b3831 b2930 b4232 b3697 b3925 b4152 b3115 b1849 b2296 b2926 b2781 b0030 b1612 b1611 b4122 b0651 b2162 b1759 b3946 b0825 b4161 b0411 b4138 b4123 b0621 b2913 b3918 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.459886 (mmol/gDw/h)
  Minimum Production Rate : 0.242886 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.959733
  EX_o2_e : 280.040557
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.618982
  EX_pi_e : 0.443609
  EX_so4_e : 0.115808
  EX_k_e : 0.089766
  EX_mg2_e : 0.003990
  EX_ca2_e : 0.002394
  EX_cl_e : 0.002394
  EX_cu2_e : 0.000326
  EX_mn2_e : 0.000318
  EX_zn2_e : 0.000157
  EX_ni2_e : 0.000149
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992614
  EX_h2o_e : 544.788543
  EX_co2_e : 30.294836
  EX_ac_e : 3.195881
  EX_succ_e : 0.479565
  Auxiliary production reaction : 0.242886
  EX_ura_e : 0.083241
  DM_5drib_c : 0.000103
  DM_4crsol_c : 0.000103

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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