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 (72 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 59
  Gene deletion: b1054 b3553 b1478 b1241 b0351 b4069 b4384 b2744 b3708 b2297 b2458 b2926 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3124 b3236 b0120 b0937 b1982 b2797 b3117 b1814 b4471 b1033 b4374 b2361 b2291 b0261 b0411 b2799 b3945 b1602 b3709 b2913 b3161 b0112 b2789 b3127 b0452 b2366 b0755 b3612 b2492 b0904 b1533 b3825 b1380 b1473 b0494 b4141 b1798 b0606 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.354110 (mmol/gDw/h)
  Minimum Production Rate : 0.124285 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.890130
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.034697
  EX_pi_e : 0.714431
  EX_so4_e : 0.213457
  EX_k_e : 0.069120
  EX_fe2_e : 0.005687
  EX_mg2_e : 0.003072
  EX_ca2_e : 0.001843
  EX_cl_e : 0.001843
  EX_cu2_e : 0.000251
  EX_mn2_e : 0.000245
  EX_zn2_e : 0.000121
  EX_ni2_e : 0.000114

Product: (mmol/gDw/h)
  EX_h2o_e : 51.475572
  EX_co2_e : 34.366161
  EX_h_e : 7.623221
  EX_ac_e : 1.656317
  EX_gsn_e : 0.467673
  Auxiliary production reaction : 0.124285
  EX_ade_e : 0.000396
  DM_5drib_c : 0.000238
  DM_4crsol_c : 0.000079

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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