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 : uaccg_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (58 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b2836 b0474 b2518 b3831 b2744 b1278 b3752 b4152 b2781 b1612 b1611 b4122 b1759 b4374 b4161 b2361 b2291 b4138 b4123 b0621 b2406 b2197 b3918 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.584404 (mmol/gDw/h)
  Minimum Production Rate : 0.116390 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.573192
  EX_o2_e : 279.045343
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.304830
  EX_pi_e : 0.892630
  EX_so4_e : 0.147165
  EX_k_e : 0.114072
  EX_mg2_e : 0.005070
  EX_ca2_e : 0.003042
  EX_cl_e : 0.003042
  EX_cu2_e : 0.000414
  EX_mn2_e : 0.000404
  EX_zn2_e : 0.000199
  EX_ni2_e : 0.000189
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990614
  EX_h2o_e : 548.711249
  EX_co2_e : 29.286243
  EX_succ_e : 0.609412
  EX_ura_e : 0.249974
  Auxiliary production reaction : 0.164455
  DM_5drib_c : 0.000131
  DM_4crsol_c : 0.000130

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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