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 : aicar_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (43 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b3916 b3399 b1241 b0351 b4069 b2502 b4384 b2744 b3115 b1849 b2296 b3617 b2388 b1982 b0394 b1200 b3665 b4374 b0675 b2361 b2291 b0261 b0507 b0112 b0114 b1723 b0529 b2492 b0904   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.462568 (mmol/gDw/h)
  Minimum Production Rate : 1.772997 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 22.713685
  EX_nh4_e : 12.090267
  EX_glc__D_e : 10.000000
  EX_pi_e : 2.219193
  EX_so4_e : 0.116484
  EX_k_e : 0.090290
  EX_fe2_e : 0.007429
  EX_mg2_e : 0.004013
  EX_cl_e : 0.002408
  EX_ca2_e : 0.002408
  EX_cu2_e : 0.000328
  EX_mn2_e : 0.000320
  EX_zn2_e : 0.000158
  EX_ni2_e : 0.000149
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 48.330755
  EX_co2_e : 20.153474
  EX_h_e : 13.794661
  EX_ac_e : 2.449520
  Auxiliary production reaction : 1.772997
  EX_ade_e : 0.000518
  DM_5drib_c : 0.000310
  EX_glyclt_e : 0.000309
  DM_4crsol_c : 0.000103

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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