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 : aacoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (63 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 56
  Gene deletion: b1054 b3553 b1478 b3399 b4382 b1241 b0351 b4069 b2744 b3708 b3115 b1849 b2296 b3844 b1004 b3713 b1109 b0046 b3236 b1982 b2797 b3117 b1814 b4471 b1033 b0675 b2361 b0261 b2799 b3945 b1602 b3709 b0153 b2913 b4381 b0590 b2406 b3161 b0112 b0452 b0509 b3125 b2366 b0755 b3612 b2492 b0904 b1533 b1380 b1473 b1600 b4141 b1798 b0606 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.374569 (mmol/gDw/h)
  Minimum Production Rate : 0.111803 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.497701
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.847588
  EX_pi_e : 0.696721
  EX_so4_e : 0.206127
  EX_k_e : 0.073113
  EX_fe2_e : 0.006016
  EX_mg2_e : 0.003249
  EX_ca2_e : 0.001950
  EX_cl_e : 0.001950
  EX_cu2_e : 0.000266
  EX_mn2_e : 0.000259
  EX_zn2_e : 0.000128
  EX_ni2_e : 0.000121

Product: (mmol/gDw/h)
  EX_h2o_e : 52.682710
  EX_co2_e : 35.899295
  EX_h_e : 7.499698
  EX_ac_e : 1.702947
  EX_xan_e : 0.494693
  Auxiliary production reaction : 0.111803
  EX_hxan_e : 0.010220
  DM_5drib_c : 0.000251
  DM_4crsol_c : 0.000084

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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