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 : 2h3oppan_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (83 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 48
  Gene deletion: b4467 b4382 b4269 b0493 b3588 b3003 b3011 b4384 b0871 b2779 b2926 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b0907 b1982 b4139 b1623 b0261 b2799 b3945 b1602 b2342 b3845 b2406 b2789 b3127 b3915 b1727 b2975 b0114 b3603 b0529 b2492 b0904 b2954 b3927 b3029 b1380 b2660 b3662 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.445690 (mmol/gDw/h)
  Minimum Production Rate : 0.091572 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.970625
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.547940
  EX_pi_e : 0.429915
  EX_so4_e : 0.112234
  EX_k_e : 0.086996
  EX_fe3_e : 0.007160
  EX_mg2_e : 0.003866
  EX_cl_e : 0.002320
  EX_ca2_e : 0.002320
  EX_cu2_e : 0.000316
  EX_mn2_e : 0.000308
  EX_zn2_e : 0.000152
  EX_ni2_e : 0.000144
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 51.798657
  EX_co2_e : 37.930777
  EX_h_e : 4.928629
  EX_etoh_e : 0.191629
  EX_hxan_e : 0.183632
  DM_5drib_c : 0.183432
  DM_4crsol_c : 0.183233
  Auxiliary production reaction : 0.091567
  EX_dxylnt_e : 0.000199

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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