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 : hpyr_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (37 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3399 b1241 b0351 b4069 b2744 b3115 b1849 b2296 b3124 b2883 b1982 b3616 b3589 b0675 b2361 b0261 b0411 b4381 b2406 b0112 b0114 b0529 b2492 b0904 b0514 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.495478 (mmol/gDw/h)
  Minimum Production Rate : 0.468469 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 20.731397
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.301245
  EX_pi_e : 0.477941
  EX_so4_e : 0.124771
  EX_k_e : 0.096714
  EX_fe2_e : 0.007958
  EX_mg2_e : 0.004298
  EX_ca2_e : 0.002579
  EX_cl_e : 0.002579
  EX_cu2_e : 0.000351
  EX_mn2_e : 0.000342
  EX_zn2_e : 0.000169
  EX_ni2_e : 0.000160
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 40.031163
  EX_co2_e : 21.768424
  EX_h_e : 8.595594
  EX_ac_e : 1.674226
  DM_oxam_c : 0.950125
  DM_5drib_c : 0.936938
  DM_4crsol_c : 0.936716
  Auxiliary production reaction : 0.468469

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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