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 : ddca_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (69 of 76: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b2836 b0474 b2518 b3831 b1278 b3752 b4152 b3115 b1849 b2296 b2781 b0767 b1232 b1612 b1611 b4122 b1759 b4161 b4014 b2976 b4138 b4123 b0621 b4381 b2406 b0728 b2197 b3029 b3918 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.507316 (mmol/gDw/h)
  Minimum Production Rate : 0.524870 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 16.677948
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.198488
  EX_pi_e : 0.489360
  EX_so4_e : 0.127752
  EX_k_e : 0.099024
  EX_fe2_e : 0.008148
  EX_mg2_e : 0.004401
  EX_ca2_e : 0.002641
  EX_cl_e : 0.002641
  EX_cu2_e : 0.000360
  EX_mn2_e : 0.000351
  EX_zn2_e : 0.000173
  EX_ni2_e : 0.000164
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 35.438557
  EX_co2_e : 19.447603
  EX_h_e : 11.901782
  EX_ac_e : 4.405283
  EX_succ_e : 0.795344
  Auxiliary production reaction : 0.524870
  EX_ura_e : 0.359762
  DM_5drib_c : 0.000114
  DM_4crsol_c : 0.000113

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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