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 : 14dhncoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (79 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 59
  Gene deletion: b4467 b1478 b4269 b0493 b3588 b3003 b3011 b1241 b4384 b2744 b3708 b3008 b3752 b0871 b2779 b2925 b2097 b2407 b3844 b1004 b3713 b1109 b0046 b3124 b3236 b0937 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b4374 b2361 b2291 b0261 b0411 b2799 b3945 b1602 b2913 b0452 b2975 b3603 b0886 b2366 b2492 b0904 b2578 b1533 b1380 b1600 b0514 b4141 b1798 b0606 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.325598 (mmol/gDw/h)
  Minimum Production Rate : 0.118230 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.015724
  EX_o2_e : 279.541575
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.345843
  EX_pi_e : 0.668757
  EX_so4_e : 0.200220
  EX_k_e : 0.063554
  EX_mg2_e : 0.002825
  EX_ca2_e : 0.001695
  EX_cl_e : 0.001695
  EX_cu2_e : 0.000231
  EX_mn2_e : 0.000225
  EX_zn2_e : 0.000111
  EX_ni2_e : 0.000105

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994769
  EX_h2o_e : 544.645370
  EX_co2_e : 28.223241
  EX_pyr_e : 4.630819
  EX_acald_e : 0.367089
  Auxiliary production reaction : 0.118228
  EX_ade_e : 0.000364
  DM_5drib_c : 0.000218
  DM_4crsol_c : 0.000073

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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