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 : 2tpr3dpcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (105 of 106: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 52
  Gene deletion: b3553 b4269 b0493 b3588 b3003 b3011 b4384 b3708 b3008 b0871 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b1982 b2797 b3117 b1814 b4471 b3449 b1033 b0261 b2799 b3945 b1602 b2913 b4381 b2406 b3915 b1727 b0114 b0886 b2366 b0755 b3612 b2492 b0904 b2578 b1533 b1380 b0494 b1695 b4141 b1798 b3662 b0606 b2285 b1007 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.492691 (mmol/gDw/h)
  Minimum Production Rate : 0.026347 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.535201
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.844499
  EX_pi_e : 0.606768
  EX_so4_e : 0.150374
  EX_k_e : 0.096170
  EX_fe3_e : 0.007915
  EX_mg2_e : 0.004274
  EX_ca2_e : 0.002564
  EX_cl_e : 0.002564
  EX_cu2_e : 0.000349
  EX_mn2_e : 0.000340
  EX_zn2_e : 0.000168
  EX_ni2_e : 0.000159
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.811904
  EX_co2_e : 38.445332
  EX_h_e : 4.900616
  EX_thym_e : 0.102541
  EX_ade_e : 0.026854
  Auxiliary production reaction : 0.026303
  DM_5drib_c : 0.000331
  DM_4crsol_c : 0.000110

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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