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 : nadphx__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (80 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 46
  Gene deletion: b3553 b3399 b2744 b3708 b3008 b0910 b0871 b2925 b2097 b0160 b0120 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b1033 b0595 b4374 b0675 b2361 b0261 b0507 b4381 b2406 b0112 b3915 b0452 b2868 b0114 b0886 b0755 b3612 b0529 b1539 b2492 b0904 b2578 b1533 b3927 b4141 b1798 b1813 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.608270 (mmol/gDw/h)
  Minimum Production Rate : 0.091509 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.720976
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.466462
  EX_pi_e : 0.861268
  EX_so4_e : 0.153175
  EX_k_e : 0.118730
  EX_fe3_e : 0.009769
  EX_mg2_e : 0.005277
  EX_ca2_e : 0.003166
  EX_cl_e : 0.003166
  EX_cu2_e : 0.000431
  EX_mn2_e : 0.000420
  EX_zn2_e : 0.000207
  EX_ni2_e : 0.000196
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 47.141554
  EX_co2_e : 26.667659
  EX_h_e : 8.274877
  EX_pyr_e : 1.961901
  EX_thym_e : 0.094783
  Auxiliary production reaction : 0.091509
  EX_xan_e : 0.015916
  EX_ade_e : 0.000681
  DM_5drib_c : 0.000408
  DM_4crsol_c : 0.000136

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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