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 : dhmptp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (68 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 45
  Gene deletion: b3553 b1478 b4382 b1241 b4069 b4384 b3115 b1849 b2296 b2779 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1638 b1982 b4139 b1033 b1623 b4014 b0261 b2976 b2799 b3945 b1602 b0153 b0590 b2406 b0114 b0509 b3125 b0529 b2492 b0904 b2954 b3029 b1380 b2660 b3662 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.391515 (mmol/gDw/h)
  Minimum Production Rate : 0.546299 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 38.534425
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.512569
  EX_pi_e : 2.016556
  EX_so4_e : 0.098591
  EX_k_e : 0.076421
  EX_mg2_e : 0.003396
  EX_fe2_e : 0.003231
  EX_fe3_e : 0.003057
  EX_ca2_e : 0.002038
  EX_cl_e : 0.002038
  EX_cu2_e : 0.000278
  EX_mn2_e : 0.000271
  EX_zn2_e : 0.000134
  EX_ni2_e : 0.000126

Product: (mmol/gDw/h)
  EX_h2o_e : 55.722779
  EX_co2_e : 37.728656
  EX_h_e : 6.295307
  Auxiliary production reaction : 0.546299
  EX_ac_e : 0.503212
  EX_urea_e : 0.275278
  EX_ade_e : 0.000438
  DM_5drib_c : 0.000263
  DM_4crsol_c : 0.000087

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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