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 : dudp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (66 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b0586 b1241 b0351 b4384 b2744 b3708 b3008 b0871 b2925 b2097 b2926 b3617 b0030 b2407 b3236 b0121 b1982 b2797 b3117 b1814 b4471 b3946 b2210 b0825 b2440 b3665 b4374 b2361 b2291 b0261 b0411 b0112 b0452 b0114 b0886 b2366 b2492 b0904 b2578 b1533 b3927 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.604296 (mmol/gDw/h)
  Minimum Production Rate : 0.416024 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.476407
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.361821
  EX_pi_e : 1.414956
  EX_so4_e : 0.152174
  EX_k_e : 0.117954
  EX_fe2_e : 0.009706
  EX_mg2_e : 0.005242
  EX_ca2_e : 0.003145
  EX_cl_e : 0.003145
  EX_cu2_e : 0.000428
  EX_mn2_e : 0.000418
  EX_zn2_e : 0.000206
  EX_ni2_e : 0.000195
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 47.460958
  EX_co2_e : 26.528639
  EX_h_e : 7.611500
  EX_pyr_e : 1.639585
  Auxiliary production reaction : 0.416024
  EX_ade_e : 0.000676
  DM_5drib_c : 0.000405
  DM_4crsol_c : 0.000135
  EX_etha_e : 0.000049

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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