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 : gsn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (56 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b4384 b3708 b3008 b0910 b3752 b0871 b2926 b2407 b1982 b2797 b3117 b1814 b4471 b2440 b4381 b2406 b0511 b0114 b2366 b0529 b2492 b0904 b2947 b1533 b3927 b0515 b3662 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.693210 (mmol/gDw/h)
  Minimum Production Rate : 0.159529 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.948382
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.286125
  EX_pi_e : 0.668675
  EX_so4_e : 0.174564
  EX_k_e : 0.135310
  EX_fe2_e : 0.011134
  EX_mg2_e : 0.006014
  EX_ca2_e : 0.003608
  EX_cl_e : 0.003608
  EX_cu2_e : 0.000491
  EX_mn2_e : 0.000479
  EX_zn2_e : 0.000236
  EX_ni2_e : 0.000224
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 50.012509
  EX_co2_e : 29.947721
  EX_h_e : 7.169005
  Auxiliary production reaction : 0.159529
  EX_xan_e : 0.000467
  DM_mththf_c : 0.000311
  DM_5drib_c : 0.000156
  DM_4crsol_c : 0.000155

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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