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 : trp__L_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (99 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 50
  Gene deletion: b4467 b2836 b1478 b4382 b1241 b4069 b4384 b3708 b3115 b1849 b2296 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b1982 b2797 b3117 b1814 b4471 b2210 b0261 b0411 b2799 b3945 b1602 b3709 b2913 b2406 b3161 b0112 b3915 b2975 b3603 b1539 b2492 b0904 b1533 b1380 b1473 b4141 b1798 b0606 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.381306 (mmol/gDw/h)
  Minimum Production Rate : 0.634343 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.224764
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.388861
  EX_pi_e : 0.367810
  EX_so4_e : 0.096021
  EX_k_e : 0.074428
  EX_fe3_e : 0.006126
  EX_mg2_e : 0.003308
  EX_ca2_e : 0.001985
  EX_cl_e : 0.001985
  EX_cu2_e : 0.000270
  EX_mn2_e : 0.000263
  EX_zn2_e : 0.000130
  EX_ni2_e : 0.000123

Product: (mmol/gDw/h)
  EX_h2o_e : 50.501256
  EX_co2_e : 35.356194
  EX_h_e : 5.786685
  EX_ac_e : 1.006180
  Auxiliary production reaction : 0.634328
  EX_ade_e : 0.000427
  DM_5drib_c : 0.000256
  DM_4crsol_c : 0.000085

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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