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 : 2tpr3dpcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (101 of 106: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 49
  Gene deletion: b4467 b4382 b4069 b4384 b3708 b3115 b1849 b2296 b2779 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b0207 b3012 b1982 b2797 b3117 b1814 b4471 b0261 b2799 b1602 b2913 b2406 b3915 b1727 b0114 b2366 b2492 b0904 b1781 b3001 b1533 b3825 b1380 b0325 b0494 b1771 b4141 b1798 b3662 b0606 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.454434 (mmol/gDw/h)
  Minimum Production Rate : 0.097319 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.175706
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.980397
  EX_pi_e : 0.924946
  EX_so4_e : 0.211755
  EX_k_e : 0.088702
  EX_fe3_e : 0.007299
  EX_mg2_e : 0.003942
  EX_cl_e : 0.002365
  EX_ca2_e : 0.002365
  EX_cu2_e : 0.000322
  EX_mn2_e : 0.000314
  EX_zn2_e : 0.000155
  EX_ni2_e : 0.000147
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 52.018328
  EX_co2_e : 37.201216
  EX_h_e : 5.033336
  EX_ac_e : 0.361884
  EX_etoh_e : 0.201063
  EX_hxan_e : 0.097828
  Auxiliary production reaction : 0.097319
  DM_5drib_c : 0.000305
  DM_4crsol_c : 0.000101

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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