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 : hemeO_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (91 of 98: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 54
  Gene deletion: b2836 b3553 b3399 b1241 b0351 b4069 b2744 b3708 b2930 b4232 b3697 b3925 b3115 b1849 b2296 b2779 b0160 b1004 b3713 b1109 b0046 b3236 b2690 b1982 b2797 b3117 b1814 b4471 b1033 b0675 b2361 b0261 b2799 b3945 b1602 b2913 b2223 b4381 b2406 b3915 b1727 b0509 b3125 b2366 b0529 b2492 b0904 b1533 b3927 b1380 b0606 b2285 b1009 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.353662 (mmol/gDw/h)
  Minimum Production Rate : 0.055585 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 31.001200
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.645911
  EX_pi_e : 0.341144
  EX_so4_e : 0.089060
  EX_k_e : 0.069032
  EX_fe3_e : 0.061263
  EX_mg2_e : 0.003068
  EX_ca2_e : 0.001841
  EX_cl_e : 0.001841
  EX_cu2_e : 0.000251
  EX_mn2_e : 0.000244
  EX_zn2_e : 0.000121
  EX_ni2_e : 0.000114

Product: (mmol/gDw/h)
  EX_h2o_e : 43.959169
  EX_co2_e : 33.079449
  EX_h_e : 7.593104
  EX_ac_e : 3.233534
  EX_etoh_e : 1.026555
  EX_ade_e : 0.120813
  DM_5drib_c : 0.111401
  Auxiliary production reaction : 0.055582
  DM_4crsol_c : 0.000079

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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