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 : cdpdodecg_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (71 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b4382 b3831 b4384 b3614 b0910 b3752 b4152 b2297 b2458 b2779 b2925 b2097 b2781 b1612 b1611 b4122 b1759 b3946 b0825 b1701 b1805 b4138 b4123 b0621 b2913 b2406 b2197 b3918 b1912 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.403801 (mmol/gDw/h)
  Minimum Production Rate : 0.141957 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.656383
  EX_o2_e : 277.784465
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.146992
  EX_pi_e : 0.744732
  EX_so4_e : 0.101685
  EX_k_e : 0.078819
  EX_mg2_e : 0.003503
  EX_ca2_e : 0.002102
  EX_cl_e : 0.002102
  EX_cu2_e : 0.000286
  EX_mn2_e : 0.000279
  EX_zn2_e : 0.000138
  EX_ni2_e : 0.000130
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993515
  EX_h2o_e : 544.891239
  EX_co2_e : 31.122535
  EX_succ_e : 0.421080
  EX_ac_e : 0.282626
  EX_ura_e : 0.144397
  Auxiliary production reaction : 0.141957
  EX_enlipa_e : 0.023769
  DM_5drib_c : 0.000091
  DM_4crsol_c : 0.000090

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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