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 : datp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (72 of 114: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4069 b4384 b3752 b2297 b2458 b2779 b2925 b2097 b3617 b2407 b2690 b3665 b0261 b3945 b2913 b4381 b0114 b0529 b2492 b0904 b1380   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.483323 (mmol/gDw/h)
  Minimum Production Rate : 0.617660 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.620679
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.309769
  EX_pi_e : 2.319196
  EX_so4_e : 0.121710
  EX_k_e : 0.094341
  EX_fe2_e : 0.007763
  EX_mg2_e : 0.004193
  EX_ca2_e : 0.002516
  EX_cl_e : 0.002516
  EX_cu2_e : 0.000343
  EX_mn2_e : 0.000334
  EX_zn2_e : 0.000165
  EX_ni2_e : 0.000156
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 48.729853
  EX_co2_e : 27.316146
  EX_h_e : 7.828693
  EX_acald_e : 1.800521
  EX_ac_e : 1.532965
  Auxiliary production reaction : 0.617660
  EX_ade_e : 0.000325
  EX_glyc__R_e : 0.000162
  DM_5drib_c : 0.000109
  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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