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 : adn_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (45 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b4384 b2744 b3708 b3008 b0871 b0030 b2407 b3124 b1982 b2797 b3117 b1814 b4471 b3665 b0411 b4381 b0114 b0755 b3612 b0529 b1539 b2492 b0904 b1533 b3927 b3821 b1517 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.498343 (mmol/gDw/h)
  Minimum Production Rate : 0.114684 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.837928
  EX_o2_e : 287.617765
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.957155
  EX_pi_e : 0.480704
  EX_so4_e : 0.125493
  EX_k_e : 0.097273
  EX_mg2_e : 0.004323
  EX_ca2_e : 0.002594
  EX_cl_e : 0.002594
  EX_cu2_e : 0.000353
  EX_mn2_e : 0.000344
  EX_zn2_e : 0.000170
  EX_ni2_e : 0.000161
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991996
  EX_h2o_e : 552.816418
  EX_co2_e : 38.395691
  Auxiliary production reaction : 0.114684
  EX_ade_e : 0.000335
  DM_mththf_c : 0.000223
  DM_5drib_c : 0.000112
  DM_4crsol_c : 0.000111

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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