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 : sbzcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (76 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 60
  Gene deletion: b3399 b1241 b0351 b4069 b2744 b1278 b3708 b1479 b2297 b2458 b2779 b2926 b0160 b3236 b0583 b0517 b3962 b1982 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b4374 b0675 b2361 b2291 b1014 b4014 b0261 b2976 b0822 b1701 b1805 b2799 b3709 b1907 b2913 b3161 b0112 b2789 b3127 b2975 b0114 b3603 b0509 b3125 b2366 b0306 b3605 b2492 b0904 b1533 b1380 b1473 b4266 b2842   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.276930 (mmol/gDw/h)
  Minimum Production Rate : 0.294096 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 32.529567
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.291216
  EX_pi_e : 1.149416
  EX_so4_e : 0.604320
  EX_k_e : 0.054055
  EX_fe2_e : 0.004448
  EX_mg2_e : 0.002402
  EX_ca2_e : 0.001441
  EX_cl_e : 0.001441
  EX_cu2_e : 0.000196
  EX_mn2_e : 0.000191
  EX_zn2_e : 0.000094
  EX_ni2_e : 0.000089

Product: (mmol/gDw/h)
  EX_h2o_e : 49.457482
  EX_co2_e : 34.014894
  EX_h_e : 5.482923
  EX_ac_e : 2.001061
  Auxiliary production reaction : 0.294096
  EX_met__L_e : 0.240487
  EX_alltn_e : 0.000310
  DM_5drib_c : 0.000186
  EX_dxylnt_e : 0.000185
  DM_4crsol_c : 0.000062

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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