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 : dmpp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (62 of 111: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4467 b0871 b3115 b1849 b2296 b2925 b2097 b1004 b3713 b1109 b0046 b3236 b2690 b0675 b0822 b1602 b4381 b1727 b0114 b2492 b0904 b1380 b2660 b1771 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.410102 (mmol/gDw/h)
  Minimum Production Rate : 0.330398 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 29.461773
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.429063
  EX_pi_e : 1.056382
  EX_so4_e : 0.103272
  EX_k_e : 0.080049
  EX_fe2_e : 0.006587
  EX_mg2_e : 0.003558
  EX_ca2_e : 0.002135
  EX_cl_e : 0.002135
  EX_cu2_e : 0.000291
  EX_mn2_e : 0.000283
  EX_zn2_e : 0.000140
  EX_ni2_e : 0.000132
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 44.591678
  EX_co2_e : 28.894237
  EX_h_e : 7.644774
  EX_pyr_e : 4.206995
  Auxiliary production reaction : 0.330398
  DM_5drib_c : 0.000092
  DM_4crsol_c : 0.000091

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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