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 : dutp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (49 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b3553 b1478 b1241 b0351 b4069 b4384 b2744 b3752 b3115 b1849 b2296 b2926 b3617 b2407 b1004 b3713 b1109 b0046 b3236 b1982 b1033 b4374 b2361 b2291 b0261 b0411 b1602 b2913 b0114 b0529 b2492 b0904 b1380 b3662 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.352307 (mmol/gDw/h)
  Minimum Production Rate : 0.844823 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.364734
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.011182
  EX_pi_e : 2.874306
  EX_so4_e : 0.088718
  EX_k_e : 0.068768
  EX_mg2_e : 0.003056
  EX_fe2_e : 0.002908
  EX_fe3_e : 0.002751
  EX_cl_e : 0.001834
  EX_ca2_e : 0.001834
  EX_cu2_e : 0.000250
  EX_mn2_e : 0.000243
  EX_zn2_e : 0.000120
  EX_ni2_e : 0.000114

Product: (mmol/gDw/h)
  EX_h2o_e : 52.705741
  EX_co2_e : 32.766957
  EX_h_e : 5.824023
  EX_ac_e : 1.067485
  Auxiliary production reaction : 0.844823
  EX_his__L_e : 0.505550
  DM_5drib_c : 0.000236
  DM_4crsol_c : 0.000079

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.

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Last updated: 21-Sep-2023
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