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 : dump_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (45 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b3553 b1478 b3399 b1241 b0351 b4069 b2744 b2297 b2458 b2779 b0160 b1004 b3713 b1109 b0046 b3236 b1982 b3616 b3589 b1033 b4374 b0675 b2361 b2291 b0261 b1602 b0114 b0529 b2492 b0904 b1380 b2660 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.365898 (mmol/gDw/h)
  Minimum Production Rate : 1.020632 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.054612
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.138437
  EX_pi_e : 1.373579
  EX_so4_e : 0.092140
  EX_k_e : 0.071421
  EX_mg2_e : 0.003174
  EX_fe2_e : 0.003020
  EX_fe3_e : 0.002857
  EX_cl_e : 0.001904
  EX_ca2_e : 0.001904
  EX_cu2_e : 0.000259
  EX_mn2_e : 0.000253
  EX_zn2_e : 0.000125
  EX_ni2_e : 0.000118

Product: (mmol/gDw/h)
  EX_h2o_e : 51.530135
  EX_co2_e : 32.433774
  EX_h_e : 7.086783
  Auxiliary production reaction : 1.020632
  EX_ac_e : 0.535140
  EX_his__L_e : 0.381835
  DM_5drib_c : 0.000246
  DM_4crsol_c : 0.000082

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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