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 : glyc__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (42 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b1241 b0351 b4069 b4384 b2744 b3708 b2297 b2458 b2779 b3617 b0030 b2407 b1779 b1982 b2797 b3117 b1814 b4471 b4374 b2361 b2291 b0261 b0411 b1701 b1805 b0112 b2789 b3127 b0114 b2366 b2492 b0904 b1533 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.468322 (mmol/gDw/h)
  Minimum Production Rate : 0.350350 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.156943
  EX_o2_e : 275.179755
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.759063
  EX_pi_e : 0.451746
  EX_so4_e : 0.117933
  EX_k_e : 0.091413
  EX_mg2_e : 0.004063
  EX_ca2_e : 0.002438
  EX_cl_e : 0.002438
  EX_cu2_e : 0.000332
  EX_mn2_e : 0.000324
  EX_zn2_e : 0.000160
  EX_ni2_e : 0.000151
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992478
  EX_h2o_e : 542.223259
  EX_co2_e : 26.355381
  EX_ac_e : 1.779294
  DM_oxam_c : 0.701223
  DM_5drib_c : 0.701013
  DM_4crsol_c : 0.700803
  Auxiliary production reaction : 0.350350
  EX_glyclt_e : 0.000313

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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