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 : ditp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (58 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b2836 b3399 b2744 b3708 b3008 b0871 b2925 b2097 b0160 b1779 b2690 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b0261 b3945 b4381 b2868 b0114 b2366 b2492 b0904 b1533 b1380   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.597871 (mmol/gDw/h)
  Minimum Production Rate : 0.091491 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 27.269424
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.887513
  EX_pi_e : 0.851185
  EX_so4_e : 0.150556
  EX_k_e : 0.116700
  EX_fe2_e : 0.009602
  EX_mg2_e : 0.005187
  EX_ca2_e : 0.003112
  EX_cl_e : 0.003112
  EX_cu2_e : 0.000424
  EX_mn2_e : 0.000413
  EX_zn2_e : 0.000204
  EX_ni2_e : 0.000193
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 46.666831
  EX_co2_e : 27.084251
  EX_h_e : 8.201295
  EX_pyr_e : 2.460244
  Auxiliary production reaction : 0.091491
  EX_xan_e : 0.015644
  EX_ade_e : 0.000402
  DM_5drib_c : 0.000135
  DM_4crsol_c : 0.000133

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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