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 (66 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b3399 b2502 b2744 b3708 b3008 b0871 b2925 b2097 b1779 b2690 b1982 b2797 b3117 b1814 b4471 b0596 b4374 b0675 b2361 b2291 b0261 b0822 b1727 b0114 b0886 b1539 b2492 b0904 b2578 b1533 b3927 b3821 b4042 b4141 b1798   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.632202 (mmol/gDw/h)
  Minimum Production Rate : 0.145113 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.200647
  EX_o2_e : 276.589375
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.973553
  EX_pi_e : 0.609826
  EX_so4_e : 0.159201
  EX_k_e : 0.123401
  EX_mg2_e : 0.005484
  EX_ca2_e : 0.003291
  EX_cl_e : 0.003291
  EX_cu2_e : 0.000448
  EX_mn2_e : 0.000437
  EX_zn2_e : 0.000216
  EX_ni2_e : 0.000204
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_fe3_e : 999.989846
  EX_h2o_e : 546.201063
  EX_co2_e : 27.095811
  EX_pyr_e : 1.543517
  DM_oxam_c : 0.145820
  DM_5drib_c : 0.145537
  DM_4crsol_c : 0.145254
  Auxiliary production reaction : 0.145113

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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