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 : amet_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (20 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b4382 b4069 b4384 b3708 b3008 b2297 b2458 b0030 b2407 b1982 b2797 b3117 b1814 b4471 b0261 b2406 b3453 b0452 b0114 b1539 b2492 b0904 b1533 b3927 b2835 b2240 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.734430 (mmol/gDw/h)
  Minimum Production Rate : 0.186626 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.065888
  EX_o2_e : 274.254977
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.051540
  EX_pi_e : 0.708495
  EX_so4_e : 0.371570
  EX_k_e : 0.143356
  EX_mg2_e : 0.006371
  EX_ca2_e : 0.003823
  EX_cl_e : 0.003823
  EX_cu2_e : 0.000521
  EX_mn2_e : 0.000507
  EX_zn2_e : 0.000250
  EX_ni2_e : 0.000237
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_fe3_e : 999.988204
  EX_h2o_e : 547.826545
  EX_co2_e : 25.825408
  EX_ac_e : 0.614201
  Auxiliary production reaction : 0.186626
  DM_5drib_c : 0.000493
  DM_4crsol_c : 0.000164
  EX_glyc3p_e : 0.000059

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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