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 : dmpp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (63 of 111: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b2744 b3614 b0910 b4152 b0871 b2925 b2097 b2926 b1612 b1611 b4122 b2690 b4374 b0675 b3945 b4138 b4123 b0621 b4381 b0114 b0529 b2492 b0904 b2835 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.592851 (mmol/gDw/h)
  Minimum Production Rate : 0.313111 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.780786
  EX_o2_e : 276.496613
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.243583
  EX_pi_e : 1.198091
  EX_so4_e : 0.149292
  EX_k_e : 0.115720
  EX_mg2_e : 0.005143
  EX_ca2_e : 0.003086
  EX_cl_e : 0.003086
  EX_cu2_e : 0.000420
  EX_mn2_e : 0.000410
  EX_zn2_e : 0.000202
  EX_ni2_e : 0.000191
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990478
  EX_h2o_e : 546.947064
  EX_co2_e : 26.951550
  EX_pyr_e : 0.998169
  EX_succ_e : 0.618221
  EX_ura_e : 0.420419
  Auxiliary production reaction : 0.313111
  DM_5drib_c : 0.000133
  DM_4crsol_c : 0.000132

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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