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 : his__L_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (42 of 76: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4382 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b2744 b0512 b0871 b0030 b2407 b1779 b1982 b3616 b3589 b0112 b0511 b0114 b0529 b2492 b0904 b1511   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.545803 (mmol/gDw/h)
  Minimum Production Rate : 1.775006 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.354923
  EX_nh4_e : 11.221111
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.526485
  EX_so4_e : 0.137444
  EX_k_e : 0.106537
  EX_fe2_e : 0.008766
  EX_mg2_e : 0.004735
  EX_ca2_e : 0.002841
  EX_cl_e : 0.002841
  EX_cu2_e : 0.000387
  EX_mn2_e : 0.000377
  EX_zn2_e : 0.000186
  EX_ni2_e : 0.000176
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 51.050181
  EX_co2_e : 25.983697
  EX_h_e : 10.341541
  Auxiliary production reaction : 1.775006
  EX_acald_e : 0.480255
  EX_xan_e : 0.000367
  DM_mththf_c : 0.000245
  DM_5drib_c : 0.000123
  DM_4crsol_c : 0.000122

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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