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_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (26 of 41: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b1478 b0474 b2518 b1241 b0351 b3831 b0910 b3752 b4152 b0871 b2779 b2925 b2097 b1612 b1611 b4122 b2690 b0675 b0411 b0822 b4138 b4123 b0621 b2913 b0114 b2492 b0904 b1912 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.356502 (mmol/gDw/h)
  Minimum Production Rate : 0.044438 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.456289
  EX_o2_e : 279.916741
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.355813
  EX_pi_e : 0.343884
  EX_so4_e : 0.089774
  EX_k_e : 0.069587
  EX_mg2_e : 0.003093
  EX_ca2_e : 0.001856
  EX_cl_e : 0.001856
  EX_cu2_e : 0.000253
  EX_mn2_e : 0.000246
  EX_zn2_e : 0.000122
  EX_ni2_e : 0.000115

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994274
  EX_h2o_e : 543.712060
  EX_co2_e : 27.607275
  EX_pyr_e : 5.013166
  EX_succ_e : 0.371757
  EX_ura_e : 0.208374
  Auxiliary production reaction : 0.044438
  DM_5drib_c : 0.000080
  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.

Last updated: 21-Sep-2023
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