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 : aconm_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (72 of 99: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b3553 b1478 b1241 b4069 b3115 b1849 b2296 b2779 b1004 b3713 b1109 b0046 b3236 b1033 b4015 b0261 b2799 b3945 b1602 b4381 b3915 b2492 b0904 b1380 b2660 b0606 b0221 b2285 b1010 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.481572 (mmol/gDw/h)
  Minimum Production Rate : 0.282998 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.721030
  EX_o2_e : 286.945350
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.200936
  EX_pi_e : 0.464527
  EX_so4_e : 0.121269
  EX_k_e : 0.093999
  EX_mg2_e : 0.004178
  EX_cl_e : 0.002507
  EX_ca2_e : 0.002507
  EX_cu2_e : 0.000341
  EX_mn2_e : 0.000333
  EX_zn2_e : 0.000164
  EX_ni2_e : 0.000156
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992265
  EX_h2o_e : 551.254080
  EX_co2_e : 37.691970
  Auxiliary production reaction : 0.282998
  EX_ac_e : 0.280364
  DM_5drib_c : 0.000108
  DM_4crsol_c : 0.000107

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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