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 : 5pg35pg_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (78 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b3553 b4382 b4069 b4384 b3926 b3115 b1849 b2296 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b3908 b1656 b1982 b4139 b1033 b1623 b0261 b3945 b1602 b2406 b3915 b0114 b0529 b2492 b0904 b2954 b3927 b1380 b2660 b3662 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.484818 (mmol/gDw/h)
  Minimum Production Rate : 0.041642 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 37.915226
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.652405
  EX_pi_e : 0.550941
  EX_so4_e : 0.122087
  EX_k_e : 0.094633
  EX_fe3_e : 0.007787
  EX_mg2_e : 0.004206
  EX_cl_e : 0.002523
  EX_ca2_e : 0.002523
  EX_cu2_e : 0.000344
  EX_mn2_e : 0.000335
  EX_zn2_e : 0.000165
  EX_ni2_e : 0.000157
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.541882
  EX_co2_e : 38.702042
  EX_h_e : 5.119513
  EX_ac_e : 0.282254
  Auxiliary production reaction : 0.041642
  DM_5drib_c : 0.000325
  DM_4crsol_c : 0.000108

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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