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 : xmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (82 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 47
  Gene deletion: b4269 b3942 b1732 b0493 b3588 b3003 b3011 b0474 b2518 b1241 b0351 b1479 b0871 b2925 b2097 b3617 b0030 b2407 b3844 b3236 b2883 b1779 b2463 b3962 b3946 b2210 b0825 b4267 b3551 b0261 b4219 b1832 b1778 b4381 b2406 b2868 b4064 b4464 b0114 b0529 b2492 b0904 b0325 b1710 b2480 b0508 b4266   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.341807 (mmol/gDw/h)
  Minimum Production Rate : 0.555719 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 29.103490
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.915516
  EX_pi_e : 0.885429
  EX_so4_e : 0.086074
  EX_k_e : 0.066718
  EX_fe2_e : 0.005490
  EX_mg2_e : 0.002965
  EX_ca2_e : 0.001779
  EX_cl_e : 0.001779
  EX_cu2_e : 0.000242
  EX_mn2_e : 0.000236
  EX_zn2_e : 0.000117
  EX_ni2_e : 0.000110

Product: (mmol/gDw/h)
  EX_h2o_e : 45.755949
  EX_co2_e : 26.572287
  EX_h_e : 9.406955
  EX_pyr_e : 4.042266
  EX_acald_e : 0.856478
  Auxiliary production reaction : 0.555719
  EX_ade_e : 0.000230
  DM_5drib_c : 0.000077
  DM_4crsol_c : 0.000076

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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