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 : glx_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (64 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b3399 b1241 b0351 b2744 b3708 b3008 b0871 b2779 b2925 b2097 b3617 b0160 b2690 b1982 b2797 b3117 b1814 b4471 b4374 b0675 b2361 b2291 b0261 b3945 b2913 b0114 b0529 b1539 b2492 b0904 b1533 b3927 b3825 b0494   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.612468 (mmol/gDw/h)
  Minimum Production Rate : 0.001706 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.784937
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.894748
  EX_pi_e : 0.590790
  EX_so4_e : 0.293109
  EX_k_e : 0.119549
  EX_fe2_e : 0.009837
  EX_mg2_e : 0.005313
  EX_cl_e : 0.003188
  EX_ca2_e : 0.003188
  EX_cu2_e : 0.000434
  EX_mn2_e : 0.000423
  EX_zn2_e : 0.000209
  EX_ni2_e : 0.000198
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 46.151290
  EX_co2_e : 27.047590
  EX_h_e : 7.997088
  EX_pyr_e : 2.363000
  EX_cgly_e : 0.138877
  DM_oxam_c : 0.002391
  DM_5drib_c : 0.002117
  DM_4crsol_c : 0.001842
  Auxiliary production reaction : 0.001706

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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