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 : 5mthf_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (103 of 120: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 52
  Gene deletion: b3553 b1478 b4382 b4269 b0493 b3588 b3003 b3011 b1241 b4384 b3708 b3008 b0871 b2779 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b2937 b0937 b1982 b2797 b3117 b1814 b4471 b1033 b0261 b2799 b3945 b1602 b2913 b2406 b0886 b1539 b2492 b0904 b2578 b1533 b3821 b1380 b2965 b0693 b4141 b1798 b3662 b0606 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.467744 (mmol/gDw/h)
  Minimum Production Rate : 0.146414 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.165186
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.079108
  EX_pi_e : 0.451188
  EX_so4_e : 0.117787
  EX_k_e : 0.091300
  EX_fe2_e : 0.007512
  EX_mg2_e : 0.004058
  EX_ca2_e : 0.002435
  EX_cl_e : 0.002435
  EX_cu2_e : 0.000332
  EX_mn2_e : 0.000323
  EX_zn2_e : 0.000160
  EX_ni2_e : 0.000151
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.861833
  EX_co2_e : 37.869328
  EX_h_e : 5.471745
  Auxiliary production reaction : 0.146414
  EX_ade_e : 0.000523
  DM_5drib_c : 0.000314
  DM_4crsol_c : 0.000104

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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