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 : hxan_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (73 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b4467 b1478 b0469 b4382 b4269 b0493 b3846 b3588 b2341 b3003 b3011 b1241 b4384 b0871 b2925 b2097 b2926 b2407 b1004 b3713 b1109 b0046 b3236 b2690 b4015 b2799 b3945 b1602 b3915 b3654 b3714 b3664 b4064 b4464 b0529 b2492 b0904 b1380 b2660 b0606 b2285 b1007 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.339138 (mmol/gDw/h)
  Minimum Production Rate : 0.306554 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.097473
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.888876
  EX_pi_e : 0.327134
  EX_so4_e : 0.085402
  EX_k_e : 0.066197
  EX_fe3_e : 0.005447
  EX_mg2_e : 0.002942
  EX_ca2_e : 0.001765
  EX_cl_e : 0.001765
  EX_cu2_e : 0.000240
  EX_mn2_e : 0.000234
  EX_zn2_e : 0.000116
  EX_ni2_e : 0.000110

Product: (mmol/gDw/h)
  EX_h2o_e : 44.666333
  EX_co2_e : 32.954377
  EX_acald_e : 5.796400
  EX_h_e : 4.347797
  Auxiliary production reaction : 0.306554
  DM_5drib_c : 0.000076
  DM_4crsol_c : 0.000076

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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