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 : datp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (63 of 114: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b1241 b0351 b4384 b3708 b3008 b3752 b0871 b2925 b2097 b2926 b3617 b2407 b2690 b1982 b2797 b3117 b1814 b4471 b3945 b4381 b0452 b0114 b2366 b2492 b0904 b1533 b1511   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.631613 (mmol/gDw/h)
  Minimum Production Rate : 0.107514 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.837505
  EX_o2_e : 276.798409
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.361398
  EX_pi_e : 0.931799
  EX_so4_e : 0.159053
  EX_k_e : 0.123286
  EX_mg2_e : 0.005479
  EX_ca2_e : 0.003288
  EX_cl_e : 0.003288
  EX_cu2_e : 0.000448
  EX_mn2_e : 0.000436
  EX_zn2_e : 0.000215
  EX_ni2_e : 0.000204
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_fe3_e : 999.989856
  EX_h2o_e : 547.124974
  EX_co2_e : 26.919409
  EX_pyr_e : 2.021368
  Auxiliary production reaction : 0.107514
  DM_oxam_c : 0.002466
  DM_mththf_c : 0.002324
  DM_5drib_c : 0.000142
  DM_4crsol_c : 0.000141

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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