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 : xmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (57 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b4384 b2744 b3708 b3008 b0871 b0030 b2883 b1982 b2797 b3117 b1814 b4471 b4381 b0452 b2868 b4064 b4464 b0114 b0529 b1539 b2492 b0904 b1533 b3927 b1517 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.573769 (mmol/gDw/h)
  Minimum Production Rate : 0.131949 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.299081
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.726386
  EX_pi_e : 0.685411
  EX_so4_e : 0.144487
  EX_k_e : 0.111996
  EX_fe2_e : 0.009215
  EX_mg2_e : 0.004977
  EX_cl_e : 0.002986
  EX_ca2_e : 0.002986
  EX_cu2_e : 0.000407
  EX_mn2_e : 0.000396
  EX_zn2_e : 0.000196
  EX_ni2_e : 0.000185
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 51.733664
  EX_co2_e : 35.126703
  EX_h_e : 5.801748
  Auxiliary production reaction : 0.131949
  EX_ade_e : 0.000386
  DM_mththf_c : 0.000257
  DM_5drib_c : 0.000129
  DM_4crsol_c : 0.000128

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.

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Last updated: 21-Sep-2023
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