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 : ap4a_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (56 of 70: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b3553 b3399 b4069 b2744 b3926 b3115 b1849 b2296 b2926 b0160 b3844 b1004 b3713 b1109 b0046 b3236 b1982 b1033 b4374 b0675 b2361 b2291 b0261 b3945 b1602 b0153 b2913 b0590 b0114 b0529 b2492 b0904 b1380 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.444054 (mmol/gDw/h)
  Minimum Production Rate : 0.102464 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.037425
  EX_o2_e : 285.313589
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.822377
  EX_pi_e : 0.838193
  EX_so4_e : 0.111822
  EX_k_e : 0.086676
  EX_mg2_e : 0.003852
  EX_ca2_e : 0.002311
  EX_cl_e : 0.002311
  EX_cu2_e : 0.000315
  EX_mn2_e : 0.000307
  EX_zn2_e : 0.000151
  EX_ni2_e : 0.000143
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992868
  EX_h2o_e : 549.749745
  EX_co2_e : 36.242999
  EX_glyc_e : 0.986936
  EX_ac_e : 0.258522
  Auxiliary production reaction : 0.102464
  EX_hxan_e : 0.000497
  DM_5drib_c : 0.000298
  DM_4crsol_c : 0.000099

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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