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 : pyr_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (111 of 114: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b3553 b1241 b0351 b2930 b4232 b3697 b3925 b0871 b3115 b1849 b2296 b3617 b3124 b2690 b1033 b0675 b1493 b3517 b4014 b2976 b0822 b0614 b0726 b4388 b2587 b2789 b3127 b0452 b1727 b1444 b1912 b1301 b0514 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.641578 (mmol/gDw/h)
  Minimum Production Rate : 0.530126 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.123636
  EX_o2_e : 278.087643
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.928984
  EX_pi_e : 0.618870
  EX_so4_e : 0.161562
  EX_k_e : 0.125231
  EX_mg2_e : 0.005566
  EX_ca2_e : 0.003339
  EX_cl_e : 0.003339
  EX_cu2_e : 0.000455
  EX_mn2_e : 0.000443
  EX_zn2_e : 0.000219
  EX_ni2_e : 0.000207
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_fe3_e : 999.989696
  EX_h2o_e : 546.661347
  EX_co2_e : 29.194082
  EX_ac_e : 1.440434
  EX_pyr_e : 0.530126
  EX_glyclt_e : 0.000429
  DM_5drib_c : 0.000144
  DM_4crsol_c : 0.000143

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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