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 : dgsn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (37 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b4384 b2744 b3708 b3008 b0871 b2883 b1982 b2797 b3117 b1814 b4471 b1623 b3665 b0411 b4381 b0114 b1539 b2492 b0904 b1533 b3927 b3821 b1511 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.590674 (mmol/gDw/h)
  Minimum Production Rate : 0.051633 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.168841
  EX_o2_e : 284.069577
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.706464
  EX_pi_e : 0.569767
  EX_so4_e : 0.148743
  EX_k_e : 0.115295
  EX_mg2_e : 0.005124
  EX_ca2_e : 0.003074
  EX_cl_e : 0.003074
  EX_cu2_e : 0.000419
  EX_mn2_e : 0.000408
  EX_zn2_e : 0.000201
  EX_ni2_e : 0.000191
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990513
  EX_h2o_e : 551.401174
  EX_co2_e : 35.101750
  DM_oxam_c : 0.067088
  Auxiliary production reaction : 0.051633
  EX_ade_e : 0.000398
  DM_mththf_c : 0.000265
  DM_5drib_c : 0.000133
  DM_4crsol_c : 0.000132

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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