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 : uri_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (74 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 52
  Gene deletion: b4467 b1855 b2242 b1478 b4382 b0474 b2518 b1241 b0351 b3831 b4384 b3708 b3752 b2781 b3617 b3844 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b1638 b1779 b1759 b4161 b4015 b2799 b3945 b1602 b4138 b4123 b0621 b0153 b2913 b0590 b0452 b0529 b1539 b2492 b0904 b1300 b3029 b3028 b1380 b3918 b1912 b1206 b2285 b1008   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.470323 (mmol/gDw/h)
  Minimum Production Rate : 0.022686 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.591249
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.295083
  EX_pi_e : 0.453677
  EX_so4_e : 0.118437
  EX_k_e : 0.091804
  EX_mg2_e : 0.004080
  EX_fe2_e : 0.003882
  EX_fe3_e : 0.003672
  EX_cl_e : 0.002448
  EX_ca2_e : 0.002448
  EX_cu2_e : 0.000333
  EX_mn2_e : 0.000325
  EX_zn2_e : 0.000160
  EX_ni2_e : 0.000152
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 51.659215
  EX_co2_e : 38.188899
  EX_h_e : 5.521721
  EX_succ_e : 0.490449
  EX_ura_e : 0.085130
  EX_uri_e : 0.022686
  DM_5drib_c : 0.000106
  DM_4crsol_c : 0.000105

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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