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 : gdpofuc_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (53 of 71: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b3553 b1478 b4382 b0474 b2518 b1241 b0351 b4069 b4384 b3752 b2297 b2458 b2779 b3617 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b3908 b1656 b1982 b0477 b4139 b1033 b0261 b3945 b1602 b2406 b3915 b0114 b0529 b2492 b0904 b1380 b2660 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.364409 (mmol/gDw/h)
  Minimum Production Rate : 0.126116 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 35.581849
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.999762
  EX_pi_e : 0.603743
  EX_so4_e : 0.091766
  EX_k_e : 0.071130
  EX_fe3_e : 0.005853
  EX_mg2_e : 0.003161
  EX_ca2_e : 0.001897
  EX_cl_e : 0.001897
  EX_cu2_e : 0.000258
  EX_mn2_e : 0.000252
  EX_zn2_e : 0.000124
  EX_ni2_e : 0.000118

Product: (mmol/gDw/h)
  EX_h2o_e : 53.217213
  EX_co2_e : 34.838173
  EX_h_e : 7.825454
  EX_his__L_e : 1.144531
  EX_ac_e : 0.659322
  Auxiliary production reaction : 0.126116
  DM_5drib_c : 0.000245
  DM_4crsol_c : 0.000081

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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