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 : adpglc_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (67 of 73: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b4467 b1478 b3399 b3942 b1732 b1241 b4069 b2744 b3115 b1849 b2296 b2779 b1004 b3713 b1109 b0046 b3236 b1982 b0675 b2361 b3551 b0261 b2799 b3945 b1602 b4219 b1832 b1778 b4381 b3915 b0452 b0529 b2492 b0904 b1380 b1710 b2480 b0606 b2285 b1009 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.366328 (mmol/gDw/h)
  Minimum Production Rate : 0.593255 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 35.719324
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.972563
  EX_pi_e : 1.539872
  EX_so4_e : 0.092249
  EX_k_e : 0.071505
  EX_fe3_e : 0.005884
  EX_mg2_e : 0.003178
  EX_ca2_e : 0.001907
  EX_cl_e : 0.001907
  EX_cu2_e : 0.000260
  EX_mn2_e : 0.000253
  EX_zn2_e : 0.000125
  EX_ni2_e : 0.000118

Product: (mmol/gDw/h)
  EX_h2o_e : 53.070794
  EX_co2_e : 34.994502
  EX_h_e : 5.414864
  Auxiliary production reaction : 0.593255
  EX_ac_e : 0.213271
  EX_ade_e : 0.009995
  DM_5drib_c : 0.000246
  DM_4crsol_c : 0.000082

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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