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 : aacoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (68 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 58
  Gene deletion: b4467 b4382 b4069 b4384 b3708 b3008 b3115 b1849 b2296 b2926 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b0121 b1982 b2797 b3117 b1814 b4471 b0261 b2799 b3945 b1602 b3709 b0153 b2913 b2406 b3161 b0112 b1727 b2975 b0114 b3603 b0509 b3125 b2366 b2492 b0904 b2947 b3035 b2578 b1533 b3927 b3821 b1380 b0508 b1473 b4141 b1798 b3662 b0606 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.383113 (mmol/gDw/h)
  Minimum Production Rate : 0.267417 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.575462
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.011646
  EX_pi_e : 1.171803
  EX_so4_e : 0.363892
  EX_k_e : 0.074781
  EX_fe2_e : 0.006153
  EX_mg2_e : 0.003324
  EX_ca2_e : 0.001994
  EX_cl_e : 0.001994
  EX_cu2_e : 0.000272
  EX_mn2_e : 0.000265
  EX_zn2_e : 0.000131
  EX_ni2_e : 0.000124

Product: (mmol/gDw/h)
  EX_h2o_e : 51.396451
  EX_co2_e : 35.974856
  EX_h_e : 4.815046
  EX_ac_e : 0.490460
  EX_etoh_e : 0.315394
  Auxiliary production reaction : 0.267417
  EX_ade_e : 0.000429
  DM_5drib_c : 0.000257
  DM_4crsol_c : 0.000085

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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