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 : 2p4c2me_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (70 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b2836 b2744 b1278 b3614 b0910 b4152 b2779 b2781 b1850 b1612 b1611 b4122 b0907 b1759 b0477 b4374 b0675 b2361 b2291 b4138 b4123 b0621 b0114 b3918 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.609500 (mmol/gDw/h)
  Minimum Production Rate : 0.067805 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.068025
  EX_o2_e : 277.067075
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.345436
  EX_pi_e : 0.791343
  EX_so4_e : 0.153484
  EX_k_e : 0.118970
  EX_mg2_e : 0.005287
  EX_ca2_e : 0.003172
  EX_cl_e : 0.003172
  EX_cu2_e : 0.000432
  EX_mn2_e : 0.000421
  EX_zn2_e : 0.000208
  EX_ni2_e : 0.000197
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.905528
  EX_h2o_e : 548.031690
  EX_co2_e : 28.170520
  EX_succ_e : 0.635582
  EX_ura_e : 0.110370
  EX_pheme_e : 0.084683
  Auxiliary production reaction : 0.067805
  DM_5drib_c : 0.000137
  DM_4crsol_c : 0.000136

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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