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 (64 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b0474 b2518 b3831 b3752 b4152 b0871 b2925 b2097 b2781 b1612 b1611 b4122 b1779 b1759 b3946 b0825 b4161 b4138 b4123 b0621 b2406 b0114 b3918 b1206 b2285 b1378 b3893 b1474   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.399680 (mmol/gDw/h)
  Minimum Production Rate : 0.211089 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 986.381452
  EX_o2_e : 280.148479
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.883379
  EX_pi_e : 0.385534
  EX_so4_e : 0.100648
  EX_k_e : 0.078015
  EX_mg2_e : 0.003467
  EX_ca2_e : 0.002080
  EX_cl_e : 0.002080
  EX_cu2_e : 0.000283
  EX_mn2_e : 0.000276
  EX_zn2_e : 0.000136
  EX_ni2_e : 0.000129

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993581
  EX_h2o_e : 540.395958
  EX_co2_e : 27.799679
  EX_for_e : 5.139581
  EX_ac_e : 3.399694
  EX_succ_e : 0.416783
  Auxiliary production reaction : 0.211089
  EX_ura_e : 0.072343
  DM_5drib_c : 0.000090
  DM_4crsol_c : 0.000089

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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