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 : dhgly_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (72 of 88: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 42
  Gene deletion: b3553 b4382 b4069 b4384 b3708 b3752 b3926 b2297 b2458 b2925 b2097 b2407 b1004 b3713 b1109 b0046 b3236 b2690 b1982 b2797 b3117 b1814 b4471 b1033 b0261 b3945 b1602 b2406 b0114 b0509 b3125 b2366 b0529 b2492 b0904 b1533 b3927 b3821 b1380 b2660 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.391715 (mmol/gDw/h)
  Minimum Production Rate : 0.165929 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 31.267622
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.061889
  EX_pi_e : 0.377851
  EX_so4_e : 0.098642
  EX_k_e : 0.076460
  EX_fe2_e : 0.006291
  EX_mg2_e : 0.003398
  EX_ca2_e : 0.002039
  EX_cl_e : 0.002039
  EX_cu2_e : 0.000278
  EX_mn2_e : 0.000271
  EX_zn2_e : 0.000134
  EX_ni2_e : 0.000127

Product: (mmol/gDw/h)
  EX_h2o_e : 44.524713
  EX_co2_e : 31.853647
  EX_h_e : 9.052828
  EX_ac_e : 4.456264
  EX_hxan_e : 0.166368
  DM_5drib_c : 0.166192
  DM_4crsol_c : 0.166017
  Auxiliary production reaction : 0.165929

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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