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 : hxan_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (54 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b4467 b4069 b3115 b1849 b2296 b2925 b2097 b1004 b3713 b1109 b0046 b3236 b2690 b3945 b1602 b2913 b4381 b1727 b4064 b4464 b0114 b0529 b2492 b0904 b1380 b0515 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.416552 (mmol/gDw/h)
  Minimum Production Rate : 0.181522 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 31.957642
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.269527
  EX_pi_e : 0.401808
  EX_so4_e : 0.104896
  EX_k_e : 0.081308
  EX_fe2_e : 0.006690
  EX_mg2_e : 0.003614
  EX_ca2_e : 0.002168
  EX_cl_e : 0.002168
  EX_cu2_e : 0.000295
  EX_mn2_e : 0.000288
  EX_zn2_e : 0.000142
  EX_ni2_e : 0.000135
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 45.099106
  EX_co2_e : 32.364818
  EX_h_e : 9.385322
  EX_ac_e : 4.787074
  Auxiliary production reaction : 0.192702
  DM_5drib_c : 0.000094
  DM_4crsol_c : 0.000093

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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