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 : unagamuf_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (67 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b4382 b4384 b3708 b3008 b0871 b0030 b2407 b0120 b2797 b3117 b1814 b4471 b3665 b3709 b2406 b3161 b0112 b3654 b3714 b3664 b0114 b0886 b2366 b2492 b0904 b0591 b2578 b1533 b3927 b3821 b1473 b1511 b4141 b1798 b3662 b1985   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.717992 (mmol/gDw/h)
  Minimum Production Rate : 0.062143 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 22.750514
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.940683
  EX_pi_e : 0.816866
  EX_so4_e : 0.180805
  EX_k_e : 0.140147
  EX_fe2_e : 0.011532
  EX_mg2_e : 0.006229
  EX_ca2_e : 0.003737
  EX_cl_e : 0.003737
  EX_cu2_e : 0.000509
  EX_mn2_e : 0.000496
  EX_zn2_e : 0.000245
  EX_ni2_e : 0.000232
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 45.946138
  EX_co2_e : 25.618803
  EX_h_e : 6.721484
  Auxiliary production reaction : 0.062143
  DM_mththf_c : 0.000322
  DM_5drib_c : 0.000162
  DM_4crsol_c : 0.000160

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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