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 : 5apru_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (109 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 47
  Gene deletion: b3553 b4382 b4269 b0493 b3588 b3003 b3011 b4384 b2744 b0871 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b3908 b1656 b1982 b4139 b1033 b1623 b4014 b0261 b2976 b0411 b2799 b3945 b1602 b0507 b2913 b3915 b1727 b0114 b0529 b2492 b0904 b2954 b3927 b1380 b3662 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.442817 (mmol/gDw/h)
  Minimum Production Rate : 0.341624 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.670827
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.150862
  EX_pi_e : 0.768768
  EX_so4_e : 0.111510
  EX_k_e : 0.086435
  EX_fe3_e : 0.007112
  EX_mg2_e : 0.003841
  EX_cl_e : 0.002305
  EX_ca2_e : 0.002305
  EX_cu2_e : 0.000314
  EX_mn2_e : 0.000306
  EX_zn2_e : 0.000151
  EX_ni2_e : 0.000143
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 52.531472
  EX_co2_e : 38.090365
  EX_h_e : 5.444367
  Auxiliary production reaction : 0.341624
  EX_etoh_e : 0.327979
  EX_hxan_e : 0.000496
  DM_5drib_c : 0.000297
  DM_4crsol_c : 0.000099

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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