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 : orot5p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (107 of 112: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b1241 b0351 b3831 b3614 b0910 b3752 b4152 b0871 b3115 b1849 b2296 b2925 b2097 b2926 b2781 b1232 b1612 b1611 b4122 b2690 b1759 b4015 b0614 b0726 b3945 b4138 b4123 b0621 b2406 b0452 b1539 b2197 b3918 b1206 b2285 b3924   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.408633 (mmol/gDw/h)
  Minimum Production Rate : 0.215817 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.362439
  EX_o2_e : 283.099031
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.992759
  EX_pi_e : 0.609987
  EX_so4_e : 0.102902
  EX_k_e : 0.079762
  EX_mg2_e : 0.003545
  EX_ca2_e : 0.002127
  EX_cl_e : 0.002127
  EX_cu2_e : 0.000290
  EX_mn2_e : 0.000282
  EX_zn2_e : 0.000139
  EX_ni2_e : 0.000132
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993437
  EX_h2o_e : 546.917673
  EX_co2_e : 32.610688
  EX_succ_e : 1.423053
  EX_ac_e : 1.234834
  Auxiliary production reaction : 0.215817
  EX_ura_e : 0.073964
  EX_mththf_e : 0.000183
  DM_5drib_c : 0.000092
  DM_4crsol_c : 0.000091

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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