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 (83 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 52
  Gene deletion: b3553 b1478 b3399 b1241 b4069 b2502 b4384 b2744 b2297 b2458 b2779 b2407 b1004 b3713 b1109 b0046 b3124 b3236 b1638 b0207 b3012 b1982 b4139 b1033 b0675 b2361 b4014 b0261 b2976 b2799 b1602 b2223 b2789 b3127 b3915 b1297 b0529 b2492 b0904 b2954 b1781 b3001 b3029 b1380 b0325 b2660 b0514 b1771 b3546 b2285 b1378 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.507126 (mmol/gDw/h)
  Minimum Production Rate : 0.001453 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.456553
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.494286
  EX_pi_e : 0.489176
  EX_so4_e : 0.127704
  EX_k_e : 0.098987
  EX_fe3_e : 0.008145
  EX_mg2_e : 0.004399
  EX_cl_e : 0.002640
  EX_ca2_e : 0.002640
  EX_cu2_e : 0.000360
  EX_mn2_e : 0.000350
  EX_zn2_e : 0.000173
  EX_ni2_e : 0.000164
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 51.969225
  EX_co2_e : 38.536594
  EX_h_e : 4.981884
  EX_ac_e : 0.295241
  EX_ade_e : 0.003474
  DM_5drib_c : 0.003247
  DM_4crsol_c : 0.003020
  Auxiliary production reaction : 0.001453

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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