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 : gsn_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (36 of 49: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b0238 b0125 b4069 b2744 b3708 b2297 b2458 b2883 b0477 b2797 b3117 b1814 b4471 b4374 b2361 b2291 b0452 b2868 b4064 b4464 b0114 b1539 b2492 b0904 b1533 b3927 b1511 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.571552 (mmol/gDw/h)
  Minimum Production Rate : 0.145414 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.677426
  EX_o2_e : 283.632758
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.901710
  EX_pi_e : 0.551323
  EX_so4_e : 0.143928
  EX_k_e : 0.111563
  EX_mg2_e : 0.004958
  EX_cl_e : 0.002975
  EX_ca2_e : 0.002975
  EX_cu2_e : 0.000405
  EX_mn2_e : 0.000395
  EX_zn2_e : 0.000195
  EX_ni2_e : 0.000185
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990820
  EX_h2o_e : 551.109484
  EX_co2_e : 34.417555
  EX_ac_e : 0.332750
  EX_gsn_e : 0.145414
  EX_ade_e : 0.000385
  DM_mththf_c : 0.000256
  DM_5drib_c : 0.000129
  DM_4crsol_c : 0.000127

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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