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 : prpncoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (21 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b4382 b1241 b0351 b4069 b4384 b3708 b3752 b2297 b2458 b2407 b2797 b3117 b1814 b4471 b3616 b3589 b3665 b2406 b0112 b0452 b3654 b3714 b3664 b0114 b2366 b2492 b0904 b1533 b2835 b3662 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.504575 (mmol/gDw/h)
  Minimum Production Rate : 0.503732 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 20.272718
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.975489
  EX_pi_e : 1.997911
  EX_so4_e : 0.630794
  EX_k_e : 0.098490
  EX_fe2_e : 0.008104
  EX_mg2_e : 0.004377
  EX_ca2_e : 0.002626
  EX_cl_e : 0.002626
  EX_cu2_e : 0.000358
  EX_mn2_e : 0.000349
  EX_zn2_e : 0.000172
  EX_ni2_e : 0.000163
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 45.756018
  EX_co2_e : 21.853223
  EX_h_e : 8.820232
  EX_ac_e : 2.672801
  Auxiliary production reaction : 0.503732
  EX_mththf_e : 0.000226
  DM_5drib_c : 0.000114
  DM_4crsol_c : 0.000113

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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