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 : itp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (79 of 90: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b3553 b3399 b4069 b2502 b2744 b3115 b1849 b2296 b2925 b2097 b2926 b1004 b3713 b1109 b0046 b3236 b2690 b1982 b1033 b4374 b0675 b2361 b2291 b0261 b3945 b1602 b1727 b0114 b0529 b2492 b0904 b3927 b1380 b2660 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.388250 (mmol/gDw/h)
  Minimum Production Rate : 0.179175 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 31.958055
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.911503
  EX_pi_e : 0.912032
  EX_so4_e : 0.097769
  EX_k_e : 0.075784
  EX_fe3_e : 0.031503
  EX_mg2_e : 0.003368
  EX_ca2_e : 0.002021
  EX_cl_e : 0.002021
  EX_cu2_e : 0.000275
  EX_mn2_e : 0.000268
  EX_zn2_e : 0.000132
  EX_ni2_e : 0.000125

Product: (mmol/gDw/h)
  EX_h2o_e : 44.915564
  EX_co2_e : 32.345528
  EX_h_e : 8.920891
  EX_ac_e : 4.961905
  Auxiliary production reaction : 0.179175
  EX_fe2_e : 0.025267
  EX_hxan_e : 0.000434
  DM_5drib_c : 0.000261
  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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