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 : ade_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (68 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3553 b3399 b4069 b2744 b2297 b2458 b2779 b3844 b1004 b3713 b1109 b0046 b3236 b1033 b1623 b3665 b1602 b2913 b4381 b3654 b3714 b3664 b1727 b0114 b0529 b2492 b0904 b1380 b1518 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.468735 (mmol/gDw/h)
  Minimum Production Rate : 0.215187 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 36.588320
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.138233
  EX_pi_e : 0.452145
  EX_so4_e : 0.118037
  EX_k_e : 0.091494
  EX_fe2_e : 0.007528
  EX_mg2_e : 0.004066
  EX_cl_e : 0.002440
  EX_ca2_e : 0.002440
  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_h2o_e : 51.580508
  EX_co2_e : 37.572436
  EX_h_e : 5.655750
  EX_12ppd__R_e : 0.521793
  EX_ac_e : 0.272891
  Auxiliary production reaction : 0.215187
  DM_mththf_c : 0.000210
  DM_5drib_c : 0.000105
  DM_4crsol_c : 0.000105

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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