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 : dutp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (61 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b4269 b3942 b1732 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b1479 b0871 b2925 b2097 b2926 b0030 b2407 b3844 b3236 b2463 b3616 b3589 b3946 b2210 b0825 b3551 b4219 b1832 b1778 b4381 b2406 b0114 b0529 b2492 b0904 b1710 b2480 b1517 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.301421 (mmol/gDw/h)
  Minimum Production Rate : 0.978304 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 28.912122
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.213109
  EX_pi_e : 3.225666
  EX_so4_e : 0.075904
  EX_k_e : 0.058835
  EX_fe2_e : 0.004841
  EX_mg2_e : 0.002615
  EX_ca2_e : 0.001569
  EX_cl_e : 0.001569
  EX_cu2_e : 0.000214
  EX_mn2_e : 0.000208
  EX_zn2_e : 0.000103
  EX_ni2_e : 0.000097

Product: (mmol/gDw/h)
  EX_h2o_e : 47.517751
  EX_co2_e : 26.665821
  EX_h_e : 6.857068
  EX_pyr_e : 3.451790
  Auxiliary production reaction : 0.978304
  EX_fum_e : 0.316673
  EX_acald_e : 0.266196
  DM_oxam_c : 0.001177
  DM_mththf_c : 0.000135
  DM_5drib_c : 0.000068
  DM_4crsol_c : 0.000067

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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