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 (77 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 62
  Gene deletion: b1478 b4382 b3846 b2341 b1241 b0351 b4069 b4384 b2744 b3708 b1479 b3752 b2297 b2458 b2779 b3236 b2883 b1779 b3962 b1982 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b1415 b1014 b4014 b0261 b2976 b2799 b3945 b3709 b1907 b2913 b4381 b2406 b3161 b0112 b2789 b3127 b0452 b2868 b4265 b4064 b4464 b2975 b0114 b3603 b2366 b2492 b0904 b0591 b1533 b1380 b0508 b1473 b4266 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.276885 (mmol/gDw/h)
  Minimum Production Rate : 0.294358 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 32.528580
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.292221
  EX_pi_e : 1.150160
  EX_so4_e : 0.603912
  EX_k_e : 0.054046
  EX_fe2_e : 0.004447
  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 : 49.460423
  EX_co2_e : 34.012583
  EX_h_e : 5.483897
  EX_ac_e : 2.000428
  Auxiliary production reaction : 0.294358
  EX_met__L_e : 0.239829
  EX_ade_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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