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 : accoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (42 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b3399 b4382 b1241 b0351 b4069 b4384 b2744 b3708 b2297 b2458 b3617 b2407 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b0261 b3709 b2406 b3161 b0112 b2975 b0114 b3603 b0509 b3125 b1539 b2492 b0904 b1533 b3821 b0508 b1473 b0594 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.438897 (mmol/gDw/h)
  Minimum Production Rate : 0.656673 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 19.324918
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.337255
  EX_pi_e : 2.393383
  EX_so4_e : 0.767196
  EX_k_e : 0.085670
  EX_fe2_e : 0.007049
  EX_mg2_e : 0.003807
  EX_ca2_e : 0.002284
  EX_cl_e : 0.002284
  EX_cu2_e : 0.000311
  EX_mn2_e : 0.000303
  EX_zn2_e : 0.000150
  EX_ni2_e : 0.000142
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 45.642073
  EX_co2_e : 20.917567
  EX_h_e : 8.984903
  EX_ac_e : 2.981140
  Auxiliary production reaction : 0.656673
  DM_oxam_c : 0.000491
  DM_5drib_c : 0.000294
  DM_4crsol_c : 0.000098

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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