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 : u3aga_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (80 of 95: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b2836 b0474 b2518 b3831 b4152 b2781 b0030 b1612 b1611 b4122 b0651 b2162 b1759 b2440 b4161 b4138 b4123 b0621 b2913 b4381 b2239 b2406 b2197 b3918 b1912 b1206 b3924   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.647465 (mmol/gDw/h)
  Minimum Production Rate : 0.016142 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.113748
  EX_o2_e : 276.049771
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.252821
  EX_pi_e : 0.982646
  EX_so4_e : 0.163045
  EX_k_e : 0.126381
  EX_mg2_e : 0.005617
  EX_cl_e : 0.003370
  EX_ca2_e : 0.003370
  EX_cu2_e : 0.000459
  EX_mn2_e : 0.000447
  EX_zn2_e : 0.000221
  EX_ni2_e : 0.000209
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_fe3_e : 999.989601
  EX_h2o_e : 547.324643
  EX_co2_e : 26.822358
  EX_succ_e : 0.675171
  EX_ura_e : 0.443007
  EX_g3pe_e : 0.325814
  Auxiliary production reaction : 0.016142
  DM_5drib_c : 0.000146
  DM_4crsol_c : 0.000144

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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