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 (77 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 53
  Gene deletion: b4467 b2242 b1478 b0474 b2518 b1241 b3831 b4069 b0910 b3752 b2930 b4232 b3697 b3925 b0871 b2297 b2458 b3844 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b1779 b2690 b0207 b3012 b0937 b0261 b2799 b1602 b4138 b4123 b0621 b2913 b4381 b0114 b0529 b2492 b0904 b1781 b3001 b3028 b1380 b0325 b1771 b1206 b0606 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.263244 (mmol/gDw/h)
  Minimum Production Rate : 0.553349 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.276621
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.702278
  EX_pi_e : 0.253927
  EX_so4_e : 0.066290
  EX_k_e : 0.051383
  EX_fe2_e : 0.004228
  EX_mg2_e : 0.002284
  EX_ca2_e : 0.001370
  EX_cl_e : 0.001370
  EX_cu2_e : 0.000187
  EX_mn2_e : 0.000182
  EX_zn2_e : 0.000090
  EX_ni2_e : 0.000085

Product: (mmol/gDw/h)
  EX_h2o_e : 44.400052
  EX_co2_e : 25.640891
  EX_h_e : 11.518172
  EX_pyr_e : 3.831594
  EX_ac_e : 1.030870
  EX_succ_e : 0.688826
  EX_uri_e : 0.553349
  EX_hxan_e : 0.414317
  EX_ura_e : 0.047648
  DM_5drib_c : 0.000059
  DM_4crsol_c : 0.000059

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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