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 : dhgly_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (80 of 88: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 46
  Gene deletion: b2836 b3553 b4382 b4269 b0493 b3588 b3003 b3011 b4384 b0871 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b3908 b1656 b1982 b0477 b4139 b1033 b0261 b2799 b3945 b1602 b2406 b3915 b1727 b0114 b0509 b3125 b0755 b3612 b0529 b2492 b0904 b2954 b3927 b1380 b2660 b3662 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.445427 (mmol/gDw/h)
  Minimum Production Rate : 0.182936 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.987150
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.910617
  EX_pi_e : 0.429661
  EX_so4_e : 0.112168
  EX_k_e : 0.086944
  EX_fe3_e : 0.007156
  EX_mg2_e : 0.003864
  EX_cl_e : 0.002318
  EX_ca2_e : 0.002318
  EX_cu2_e : 0.000316
  EX_mn2_e : 0.000308
  EX_zn2_e : 0.000152
  EX_ni2_e : 0.000144
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 52.171735
  EX_co2_e : 37.855372
  EX_h_e : 5.382886
  EX_etoh_e : 0.191417
  EX_ade_e : 0.183424
  DM_5drib_c : 0.183225
  DM_4crsol_c : 0.183025
  Auxiliary production reaction : 0.182926

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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