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 : xtp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (56 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b3399 b4069 b2502 b2744 b3708 b3008 b3115 b1849 b2296 b1982 b2797 b3117 b1814 b4471 b3449 b4374 b0675 b2361 b2291 b2239 b2868 b0114 b1539 b2492 b0904 b1533 b3927 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.749462 (mmol/gDw/h)
  Minimum Production Rate : 0.317916 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.026923
  EX_o2_e : 274.534632
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.368316
  EX_pi_e : 1.676685
  EX_so4_e : 0.188730
  EX_k_e : 0.146290
  EX_mg2_e : 0.006502
  EX_ca2_e : 0.003901
  EX_cl_e : 0.003901
  EX_cu2_e : 0.000531
  EX_mn2_e : 0.000518
  EX_zn2_e : 0.000256
  EX_ni2_e : 0.000242
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_fe3_e : 999.987963
  EX_h2o_e : 549.105164
  EX_co2_e : 25.181999
  EX_ac_e : 0.436326
  Auxiliary production reaction : 0.317916
  EX_ade_e : 0.000504
  DM_mththf_c : 0.000336
  DM_5drib_c : 0.000169
  DM_4crsol_c : 0.000167

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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