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 : gsn_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (48 of 49: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 46
  Gene deletion: b4467 b1478 b3399 b1241 b4069 b4384 b2744 b2297 b2458 b2926 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b2937 b1982 b4139 b1623 b4374 b2361 b2291 b0261 b2799 b3945 b1602 b2913 b2406 b3915 b2975 b3603 b0509 b3125 b0529 b2492 b0904 b2954 b3029 b1380 b0508 b1695 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.437709 (mmol/gDw/h)
  Minimum Production Rate : 0.369392 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 38.000514
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.576140
  EX_pi_e : 0.422217
  EX_so4_e : 0.110224
  EX_k_e : 0.085438
  EX_fe3_e : 0.007030
  EX_mg2_e : 0.003797
  EX_ca2_e : 0.002278
  EX_cl_e : 0.002278
  EX_cu2_e : 0.000310
  EX_mn2_e : 0.000302
  EX_zn2_e : 0.000149
  EX_ni2_e : 0.000141
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 53.449941
  EX_co2_e : 37.827050
  EX_h_e : 6.132623
  EX_gsn_e : 0.369392
  EX_ac_e : 0.254828
  EX_hxan_e : 0.000490
  DM_5drib_c : 0.000294
  DM_4crsol_c : 0.000098

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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