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 (76 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 59
  Gene deletion: b3553 b1478 b3399 b4269 b0493 b3588 b3003 b3011 b1241 b2744 b3708 b3008 b0871 b0160 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b1982 b4139 b2797 b3117 b1814 b4471 b1033 b4374 b0675 b2361 b2291 b4014 b0261 b2976 b2799 b3945 b1602 b3915 b0452 b0886 b0509 b3125 b1539 b2492 b0904 b2954 b1298 b2578 b1533 b3029 b1380 b1600 b2660 b4141 b1798 b1985 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.510118 (mmol/gDw/h)
  Minimum Production Rate : 0.019117 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.748817
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.550321
  EX_pi_e : 0.492063
  EX_so4_e : 0.128458
  EX_k_e : 0.099572
  EX_fe3_e : 0.008193
  EX_mg2_e : 0.004425
  EX_ca2_e : 0.002655
  EX_cl_e : 0.002655
  EX_cu2_e : 0.000362
  EX_mn2_e : 0.000352
  EX_zn2_e : 0.000174
  EX_ni2_e : 0.000165
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 52.473072
  EX_co2_e : 38.847713
  EX_h_e : 4.736451
  EX_trp__L_e : 0.019117
  EX_ade_e : 0.000571
  DM_5drib_c : 0.000342
  DM_4crsol_c : 0.000114

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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