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 : nadhx__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (102 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b3553 b4382 b1241 b0351 b4384 b3752 b2930 b4232 b3697 b3925 b0871 b2779 b2407 b1004 b3713 b1109 b0046 b3236 b2690 b1982 b1033 b4015 b0261 b2799 b3945 b1602 b2913 b2406 b3915 b0452 b1727 b0529 b2492 b0904 b3927 b1380 b3662 b0606 b2285 b1007 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.370251 (mmol/gDw/h)
  Minimum Production Rate : 0.024102 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.388641
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.169459
  EX_pi_e : 0.405349
  EX_so4_e : 0.093237
  EX_k_e : 0.072270
  EX_fe3_e : 0.005948
  EX_mg2_e : 0.003212
  EX_ca2_e : 0.001927
  EX_cl_e : 0.001927
  EX_cu2_e : 0.000263
  EX_mn2_e : 0.000256
  EX_zn2_e : 0.000126
  EX_ni2_e : 0.000120

Product: (mmol/gDw/h)
  EX_h2o_e : 43.990408
  EX_co2_e : 28.484080
  EX_h_e : 8.800471
  EX_pyr_e : 5.269932
  Auxiliary production reaction : 0.024101
  EX_ade_e : 0.000414
  DM_5drib_c : 0.000248
  DM_4crsol_c : 0.000083

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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