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 : 2h3oppan_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (64 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b1241 b0351 b4069 b4384 b3708 b2297 b2458 b2779 b0030 b2407 b1238 b1779 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b0261 b4381 b2406 b0112 b0114 b2366 b2492 b0904 b1533 b3821 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.469834 (mmol/gDw/h)
  Minimum Production Rate : 0.351638 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 25.245143
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.777653
  EX_pi_e : 0.453205
  EX_so4_e : 0.118314
  EX_k_e : 0.091708
  EX_fe2_e : 0.007546
  EX_mg2_e : 0.004076
  EX_ca2_e : 0.002445
  EX_cl_e : 0.002445
  EX_cu2_e : 0.000333
  EX_mn2_e : 0.000325
  EX_zn2_e : 0.000160
  EX_ni2_e : 0.000152
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 42.521445
  EX_co2_e : 26.246937
  EX_h_e : 7.860670
  EX_ac_e : 1.785038
  DM_oxam_c : 0.703487
  DM_5drib_c : 0.703276
  DM_4crsol_c : 0.703066
  Auxiliary production reaction : 0.351638

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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