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 : dcdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (65 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 42
  Gene deletion: b3553 b1478 b3399 b1241 b0351 b2744 b0871 b3115 b1849 b2296 b2925 b2097 b0160 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b2690 b0937 b1982 b3449 b1033 b0675 b2361 b0261 b2799 b3945 b1602 b2913 b4381 b2406 b0529 b2492 b0904 b3927 b1380 b0606 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.371062 (mmol/gDw/h)
  Minimum Production Rate : 0.013503 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.520555
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.098573
  EX_pi_e : 0.384934
  EX_so4_e : 0.093441
  EX_k_e : 0.072429
  EX_fe2_e : 0.005960
  EX_mg2_e : 0.003219
  EX_ca2_e : 0.001931
  EX_cl_e : 0.001931
  EX_cu2_e : 0.000263
  EX_mn2_e : 0.000256
  EX_zn2_e : 0.000127
  EX_ni2_e : 0.000120

Product: (mmol/gDw/h)
  EX_h2o_e : 43.959769
  EX_co2_e : 28.609092
  EX_h_e : 8.816272
  EX_pyr_e : 5.329175
  Auxiliary production reaction : 0.013503
  EX_ade_e : 0.010124
  DM_5drib_c : 0.000249
  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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