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 : duri_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (39 of 50: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b3553 b1478 b1241 b4069 b3115 b1849 b2296 b2779 b3844 b1004 b3713 b1109 b0046 b3236 b0937 b1033 b0261 b2799 b3945 b1602 b2913 b4381 b2406 b3654 b3714 b3664 b4064 b4464 b0509 b3125 b0529 b2492 b0904 b1380 b3662 b0606 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.370022 (mmol/gDw/h)
  Minimum Production Rate : 1.164747 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 32.971414
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.325699
  EX_pi_e : 0.356925
  EX_so4_e : 0.093179
  EX_k_e : 0.072226
  EX_fe2_e : 0.005943
  EX_mg2_e : 0.003210
  EX_ca2_e : 0.001926
  EX_cl_e : 0.001926
  EX_cu2_e : 0.000262
  EX_mn2_e : 0.000256
  EX_zn2_e : 0.000126
  EX_ni2_e : 0.000120

Product: (mmol/gDw/h)
  EX_h2o_e : 49.356037
  EX_co2_e : 32.596300
  EX_h_e : 6.596042
  Auxiliary production reaction : 1.164747
  EX_ac_e : 0.866640
  DM_5drib_c : 0.000083
  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.

Last updated: 21-Sep-2023
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