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 (70 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b4467 b2242 b4382 b0474 b2518 b3831 b4384 b3752 b0871 b2925 b2097 b2407 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b0907 b1779 b2690 b4161 b1415 b3945 b1602 b4138 b4123 b0621 b0114 b0529 b2492 b0904 b3028 b1380 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.343922 (mmol/gDw/h)
  Minimum Production Rate : 0.043024 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.717652
  EX_o2_e : 279.818381
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.202110
  EX_pi_e : 0.331749
  EX_so4_e : 0.086606
  EX_k_e : 0.067131
  EX_mg2_e : 0.002984
  EX_ca2_e : 0.001790
  EX_cl_e : 0.001790
  EX_cu2_e : 0.000244
  EX_mn2_e : 0.000238
  EX_zn2_e : 0.000117
  EX_ni2_e : 0.000111

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994476
  EX_h2o_e : 543.441843
  EX_co2_e : 27.691323
  EX_pyr_e : 4.911518
  EX_succ_e : 0.358639
  EX_thymd_e : 0.138617
  EX_ura_e : 0.062251
  EX_uri_e : 0.043024
  EX_dxylnt_e : 0.000153
  DM_5drib_c : 0.000077
  DM_4crsol_c : 0.000077

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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