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 : nad_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (35 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b3553 b4382 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b3752 b0871 b2779 b2926 b2407 b0907 b1982 b3616 b3589 b1033 b0261 b2406 b0112 b2789 b3127 b0114 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.428513 (mmol/gDw/h)
  Minimum Production Rate : 0.696497 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.594773
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.503860
  EX_pi_e : 1.806339
  EX_so4_e : 0.107908
  EX_k_e : 0.083643
  EX_fe2_e : 0.006882
  EX_mg2_e : 0.003717
  EX_cl_e : 0.002230
  EX_ca2_e : 0.002230
  EX_cu2_e : 0.000304
  EX_mn2_e : 0.000296
  EX_zn2_e : 0.000146
  EX_ni2_e : 0.000138
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 50.235003
  EX_co2_e : 24.291772
  EX_h_e : 6.724485
  EX_acald_e : 1.745506
  Auxiliary production reaction : 0.696497
  DM_oxam_c : 0.000480
  DM_5drib_c : 0.000288
  EX_glyclt_e : 0.000191
  DM_4crsol_c : 0.000096

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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