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 : nadhx__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (96 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b4467 b3399 b4069 b2744 b0871 b2297 b2458 b2925 b2097 b2926 b3844 b1004 b3713 b1109 b0046 b3236 b2883 b1638 b2690 b1982 b4139 b0675 b2361 b0261 b0411 b2799 b3945 b1602 b2913 b4381 b2406 b1727 b0114 b0529 b2492 b0904 b3029 b1380 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.339364 (mmol/gDw/h)
  Minimum Production Rate : 0.112770 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 29.931762
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.559387
  EX_pi_e : 0.552893
  EX_so4_e : 0.085459
  EX_k_e : 0.066241
  EX_mg2_e : 0.002944
  EX_fe2_e : 0.002801
  EX_fe3_e : 0.002650
  EX_ca2_e : 0.001766
  EX_cl_e : 0.001766
  EX_cu2_e : 0.000241
  EX_mn2_e : 0.000235
  EX_zn2_e : 0.000116
  EX_ni2_e : 0.000110

Product: (mmol/gDw/h)
  EX_h2o_e : 44.077693
  EX_co2_e : 27.765594
  EX_h_e : 9.100667
  EX_pyr_e : 5.104229
  EX_ac_e : 0.197573
  Auxiliary production reaction : 0.112770
  EX_gly_e : 0.104892
  EX_glyclt_e : 0.009260
  DM_5drib_c : 0.000228
  DM_4crsol_c : 0.000076

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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