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 : fpram_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (17 of 51: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b2744 b0871 b3617 b0160 b1982 b0675 b2361 b0261 b0507 b4381 b2406 b0112 b2868 b0114 b0529 b2492 b0904   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.513978 (mmol/gDw/h)
  Minimum Production Rate : 1.643922 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 20.994526
  EX_nh4_e : 10.539356
  EX_glc__D_e : 10.000000
  EX_pi_e : 2.139708
  EX_so4_e : 0.129430
  EX_k_e : 0.100325
  EX_fe2_e : 0.008255
  EX_mg2_e : 0.004459
  EX_ca2_e : 0.002675
  EX_cl_e : 0.002675
  EX_cu2_e : 0.000364
  EX_mn2_e : 0.000355
  EX_zn2_e : 0.000175
  EX_ni2_e : 0.000166
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 45.023590
  EX_co2_e : 21.460528
  EX_h_e : 8.067494
  EX_acald_e : 2.109852
  Auxiliary production reaction : 1.643922
  EX_xan_e : 0.013449
  EX_ade_e : 0.000575
  DM_5drib_c : 0.000345
  EX_glyclt_e : 0.000344
  DM_4crsol_c : 0.000115

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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