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 (56 of 71: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b3553 b1478 b4382 b1241 b4069 b4384 b3115 b1849 b2296 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b0937 b1982 b4139 b1033 b1623 b4014 b0261 b2976 b2799 b3945 b1602 b0507 b2406 b0529 b2492 b0904 b2954 b3029 b1380 b1301 b2660 b3662 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.415434 (mmol/gDw/h)
  Minimum Production Rate : 0.435885 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 35.908579
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.668402
  EX_pi_e : 1.272500
  EX_so4_e : 0.104615
  EX_k_e : 0.081090
  EX_mg2_e : 0.003604
  EX_fe2_e : 0.003429
  EX_fe3_e : 0.003244
  EX_ca2_e : 0.002162
  EX_cl_e : 0.002162
  EX_cu2_e : 0.000295
  EX_mn2_e : 0.000287
  EX_zn2_e : 0.000142
  EX_ni2_e : 0.000134
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 52.998977
  EX_co2_e : 35.487210
  EX_h_e : 5.372257
  Auxiliary production reaction : 0.435885
  EX_ac_e : 0.241860
  EX_ade_e : 0.000465
  DM_5drib_c : 0.000279
  DM_4crsol_c : 0.000093

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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