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_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (79 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 72
  Gene deletion: b3399 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b2744 b3708 b3008 b1479 b0871 b0160 b0030 b3236 b2883 b1779 b3962 b1982 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b1623 b4374 b2361 b2291 b1748 b1493 b3517 b1014 b4014 b0261 b2976 b0411 b1701 b1805 b2799 b0726 b3945 b0507 b4388 b1907 b0112 b4265 b2975 b0114 b3603 b0886 b2366 b0306 b3605 b2492 b0904 b2578 b1533 b3927 b1380 b2965 b0693 b0508 b1473 b0594 b4266 b3662 b1813   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.388253 (mmol/gDw/h)
  Minimum Production Rate : 0.260583 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.538775
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.052272
  EX_so4_e : 0.435366
  EX_pi_e : 0.374511
  EX_k_e : 0.075784
  EX_fe2_e : 0.006237
  EX_mg2_e : 0.003368
  EX_ca2_e : 0.002021
  EX_cl_e : 0.002021
  EX_cu2_e : 0.000275
  EX_mn2_e : 0.000268
  EX_zn2_e : 0.000132
  EX_ni2_e : 0.000125

Product: (mmol/gDw/h)
  EX_h2o_e : 49.987381
  EX_co2_e : 36.974055
  EX_h_e : 3.752101
  EX_acald_e : 1.266321
  EX_met__L_e : 0.337595
  EX_trp__L_e : 0.260573
  DM_oxam_c : 0.000434
  DM_5drib_c : 0.000261
  EX_dxylnt_e : 0.000260
  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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