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 : ahdt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (57 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3399 b2744 b3708 b3008 b0871 b0160 b1779 b1982 b2797 b3117 b1814 b4471 b2440 b0675 b2361 b2291 b0261 b0505 b4381 b0452 b0114 b0886 b2366 b0529 b2492 b0904 b2578 b1533 b3927 b4141 b1798   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.678078 (mmol/gDw/h)
  Minimum Production Rate : 0.228689 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 29.197383
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.474996
  EX_pi_e : 1.340144
  EX_so4_e : 0.172642
  EX_k_e : 0.132356
  EX_fe2_e : 0.010891
  EX_mg2_e : 0.005882
  EX_ca2_e : 0.003529
  EX_cl_e : 0.003529
  EX_cu2_e : 0.000481
  EX_mn2_e : 0.000469
  EX_zn2_e : 0.000231
  EX_ni2_e : 0.000219
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 50.968424
  EX_co2_e : 30.078344
  EX_h_e : 6.918036
  Auxiliary production reaction : 0.228689
  DM_oxam_c : 0.002647
  EX_5mtr_e : 0.001888
  EX_spmd_e : 0.001888
  DM_5drib_c : 0.000455
  DM_4crsol_c : 0.000151
  EX_etha_e : 0.000055

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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