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 : preq0_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (50 of 51: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 50
  Gene deletion: b4467 b1478 b4269 b0493 b3588 b3003 b3011 b1241 b4384 b2744 b3752 b0871 b2779 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b1982 b0477 b4139 b4014 b0261 b2976 b0411 b2799 b3945 b1602 b0507 b2342 b3845 b4381 b3915 b2975 b3603 b1297 b0529 b2492 b0904 b2954 b3029 b1380 b1600 b2660 b3662 b1985 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.391880 (mmol/gDw/h)
  Minimum Production Rate : 0.651212 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.134708
  EX_o2_e : 290.470385
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.490517
  EX_pi_e : 0.378009
  EX_so4_e : 0.098684
  EX_k_e : 0.076492
  EX_mg2_e : 0.003400
  EX_ca2_e : 0.002040
  EX_cl_e : 0.002040
  EX_cu2_e : 0.000278
  EX_mn2_e : 0.000271
  EX_zn2_e : 0.000134
  EX_ni2_e : 0.000127

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993704
  EX_h2o_e : 557.517828
  EX_co2_e : 39.353596
  Auxiliary production reaction : 0.651212
  EX_ade_e : 0.000439
  DM_5drib_c : 0.000263
  DM_4crsol_c : 0.000087

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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