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 : fpram_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (30 of 51: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b4382 b0474 b2518 b4384 b3708 b3008 b3752 b0871 b2297 b2458 b2407 b3124 b1982 b2797 b3117 b1814 b4471 b0261 b2406 b0114 b0886 b0755 b3612 b0529 b1539 b2492 b0904 b2578 b1533 b3927 b3821 b2413 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.489587 (mmol/gDw/h)
  Minimum Production Rate : 0.168566 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.155386
  EX_o2_e : 287.676500
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.793747
  EX_pi_e : 0.640825
  EX_so4_e : 0.123288
  EX_k_e : 0.095564
  EX_mg2_e : 0.004247
  EX_ca2_e : 0.002548
  EX_cl_e : 0.002548
  EX_cu2_e : 0.000347
  EX_mn2_e : 0.000338
  EX_zn2_e : 0.000167
  EX_ni2_e : 0.000158
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992137
  EX_h2o_e : 552.491183
  EX_co2_e : 38.553976
  Auxiliary production reaction : 0.168566
  DM_oxam_c : 0.000548
  DM_5drib_c : 0.000329
  DM_4crsol_c : 0.000109

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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