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 : 4r5au_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (110 of 111: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 51
  Gene deletion: b3553 b1478 b1241 b4069 b4384 b2297 b2458 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3124 b3236 b1638 b0207 b3012 b0937 b1982 b4139 b1033 b1623 b4014 b0261 b2976 b2799 b1602 b2913 b4381 b2406 b2789 b3127 b0114 b0755 b3612 b0529 b2492 b0904 b2954 b1781 b3001 b3029 b1380 b0325 b0514 b1771 b3662 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.390481 (mmol/gDw/h)
  Minimum Production Rate : 0.544856 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 38.318695
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.947433
  EX_pi_e : 0.376660
  EX_so4_e : 0.098331
  EX_k_e : 0.076219
  EX_mg2_e : 0.003387
  EX_fe2_e : 0.003223
  EX_fe3_e : 0.003049
  EX_ca2_e : 0.002032
  EX_cl_e : 0.002032
  EX_cu2_e : 0.000277
  EX_mn2_e : 0.000270
  EX_zn2_e : 0.000133
  EX_ni2_e : 0.000126

Product: (mmol/gDw/h)
  EX_h2o_e : 52.464501
  EX_co2_e : 37.787482
  EX_h_e : 6.823099
  Auxiliary production reaction : 0.544856
  EX_ac_e : 0.501883
  EX_urea_e : 0.274550
  EX_hxan_e : 0.000437
  DM_5drib_c : 0.000262
  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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