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 : nadhx__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (100 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b3553 b4382 b4269 b0493 b3588 b3003 b3011 b4384 b0871 b2926 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1638 b0937 b1982 b4139 b1033 b1623 b0261 b1602 b2913 b2406 b1727 b0114 b0529 b2492 b0904 b2954 b3029 b1380 b1771 b3662 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.471062 (mmol/gDw/h)
  Minimum Production Rate : 0.119087 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.423634
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.941705
  EX_pi_e : 0.692563
  EX_so4_e : 0.118623
  EX_k_e : 0.091948
  EX_mg2_e : 0.004086
  EX_fe2_e : 0.003888
  EX_fe3_e : 0.003678
  EX_cl_e : 0.002452
  EX_ca2_e : 0.002452
  EX_cu2_e : 0.000334
  EX_mn2_e : 0.000326
  EX_zn2_e : 0.000161
  EX_ni2_e : 0.000152
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.842784
  EX_co2_e : 38.121863
  EX_h_e : 4.948085
  Auxiliary production reaction : 0.119087
  EX_gly_e : 0.020669
  DM_5drib_c : 0.000316
  DM_4crsol_c : 0.000105

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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