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 (69 of 88: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b3553 b3399 b4069 b2744 b2297 b2458 b0160 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b1982 b4139 b1033 b0675 b2361 b0261 b2799 b3945 b1602 b0507 b2913 b4381 b2406 b3915 b1727 b0114 b0529 b2492 b0904 b2954 b3927 b3029 b1380 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.482292 (mmol/gDw/h)
  Minimum Production Rate : 0.028829 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 38.072823
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.405493
  EX_pi_e : 0.465221
  EX_so4_e : 0.121451
  EX_k_e : 0.094140
  EX_fe3_e : 0.007746
  EX_mg2_e : 0.004184
  EX_ca2_e : 0.002510
  EX_cl_e : 0.002510
  EX_cu2_e : 0.000342
  EX_mn2_e : 0.000333
  EX_zn2_e : 0.000164
  EX_ni2_e : 0.000156
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.282107
  EX_co2_e : 39.027945
  EX_h_e : 4.945631
  EX_ac_e : 0.280783
  EX_hxan_e : 0.041989
  DM_5drib_c : 0.029153
  DM_4crsol_c : 0.028937
  Auxiliary production reaction : 0.028829

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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