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 : nadh_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (19 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3553 b4382 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b0871 b0030 b2407 b1982 b3616 b3589 b1033 b0261 b0507 b2406 b0112 b0114 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.489682 (mmol/gDw/h)
  Minimum Production Rate : 0.795919 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 21.061814
  EX_nh4_e : 10.860506
  EX_glc__D_e : 10.000000
  EX_pi_e : 2.064189
  EX_so4_e : 0.123312
  EX_k_e : 0.095582
  EX_fe2_e : 0.007865
  EX_mg2_e : 0.004248
  EX_ca2_e : 0.002549
  EX_cl_e : 0.002549
  EX_cu2_e : 0.000347
  EX_mn2_e : 0.000338
  EX_zn2_e : 0.000167
  EX_ni2_e : 0.000158
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 49.580263
  EX_co2_e : 20.729636
  EX_h_e : 8.480413
  EX_acald_e : 1.227012
  Auxiliary production reaction : 0.795919
  DM_oxam_c : 0.000548
  DM_5drib_c : 0.000329
  EX_glyclt_e : 0.000328
  DM_4crsol_c : 0.000109

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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