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 : frdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (57 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3399 b4382 b1241 b0351 b2502 b4384 b2744 b0871 b2779 b2925 b2097 b3617 b1612 b1611 b4122 b3946 b0825 b2361 b2291 b2913 b0114 b0529 b2492 b0904 b1380 b0516   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.569645 (mmol/gDw/h)
  Minimum Production Rate : 0.150881 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.336753
  EX_o2_e : 277.017646
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.161009
  EX_pi_e : 0.851245
  EX_so4_e : 0.143448
  EX_k_e : 0.111191
  EX_mg2_e : 0.004942
  EX_cl_e : 0.002965
  EX_ca2_e : 0.002965
  EX_cu2_e : 0.000404
  EX_mn2_e : 0.000394
  EX_zn2_e : 0.000194
  EX_ni2_e : 0.000184
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990851
  EX_h2o_e : 546.072227
  EX_co2_e : 27.853200
  EX_pyr_e : 1.369281
  EX_fum_e : 0.596245
  Auxiliary production reaction : 0.150881
  EX_alltn_e : 0.002224
  EX_glyc__R_e : 0.000191
  DM_5drib_c : 0.000128
  DM_4crsol_c : 0.000127

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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