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 : gdpddman_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (78 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 49
  Gene deletion: b3553 b4382 b4269 b0493 b3588 b3003 b3011 b0474 b2518 b4384 b2744 b3752 b0871 b2925 b2097 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b3908 b1656 b1982 b4139 b3946 b0825 b1033 b1623 b0261 b0411 b2799 b3945 b1602 b0507 b2913 b1727 b0114 b0529 b2492 b0904 b3927 b1380 b3662 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.341813 (mmol/gDw/h)
  Minimum Production Rate : 0.091411 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 30.033642
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.150520
  EX_fe3_e : 0.673586
  EX_pi_e : 0.512537
  EX_so4_e : 0.086075
  EX_k_e : 0.066719
  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 : 43.490603
  EX_co2_e : 27.886654
  EX_h_e : 9.629859
  EX_pyr_e : 5.539413
  EX_fe2_e : 0.668096
  Auxiliary production reaction : 0.091411
  EX_ade_e : 0.000382
  DM_5drib_c : 0.000229
  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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