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 : dgtp_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 : 33
  Gene deletion: b3399 b1241 b0351 b4069 b2744 b3708 b3115 b1849 b2296 b2779 b2925 b2097 b3617 b3236 b2797 b3117 b1814 b4471 b3946 b2210 b0825 b4374 b0675 b2361 b4381 b0511 b0114 b2366 b2492 b0904 b1533 b0515 b1511   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.551959 (mmol/gDw/h)
  Minimum Production Rate : 0.550803 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.513587
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.716606
  EX_pi_e : 2.184832
  EX_so4_e : 0.138994
  EX_k_e : 0.107738
  EX_fe2_e : 0.008865
  EX_mg2_e : 0.004788
  EX_ca2_e : 0.002873
  EX_cl_e : 0.002873
  EX_cu2_e : 0.000391
  EX_mn2_e : 0.000381
  EX_zn2_e : 0.000188
  EX_ni2_e : 0.000178
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 48.228319
  EX_co2_e : 25.938034
  EX_h_e : 9.297929
  EX_ac_e : 1.821775
  EX_glyc__R_e : 0.750643
  Auxiliary production reaction : 0.550803
  EX_xan_e : 0.000371
  DM_mththf_c : 0.000247
  DM_5drib_c : 0.000124
  DM_4crsol_c : 0.000123

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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