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 : glx_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (74 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b3553 b1478 b4382 b1241 b4069 b4384 b3752 b2297 b2458 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b0937 b1982 b0477 b4139 b1033 b4014 b0261 b2976 b2799 b3945 b1602 b2406 b0509 b3125 b0529 b2492 b0904 b2954 b3029 b1380 b1301 b2660 b3662 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.425240 (mmol/gDw/h)
  Minimum Production Rate : 0.297449 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.934818
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.082181
  EX_pi_e : 0.410189
  EX_so4_e : 0.107084
  EX_k_e : 0.083004
  EX_mg2_e : 0.003689
  EX_fe2_e : 0.003510
  EX_fe3_e : 0.003320
  EX_ca2_e : 0.002213
  EX_cl_e : 0.002213
  EX_cu2_e : 0.000301
  EX_mn2_e : 0.000294
  EX_zn2_e : 0.000145
  EX_ni2_e : 0.000137
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 51.792651
  EX_co2_e : 36.395851
  EX_h_e : 5.945239
  EX_ade_e : 0.297925
  DM_5drib_c : 0.297735
  DM_4crsol_c : 0.297544
  Auxiliary production reaction : 0.297449
  EX_ac_e : 0.247569

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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