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 : udpLa4o_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (79 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b2242 b3553 b4382 b3831 b4384 b3614 b0910 b3752 b2779 b2925 b2097 b2926 b2781 b1004 b3713 b1109 b0046 b1612 b1611 b4122 b1759 b3946 b2210 b0825 b1033 b1415 b0411 b4138 b4123 b0621 b0529 b2492 b0904 b2197 b3028 b3918 b1912 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.401368 (mmol/gDw/h)
  Minimum Production Rate : 0.211981 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.473556
  EX_o2_e : 280.777209
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.904003
  EX_pi_e : 0.811124
  EX_so4_e : 0.101073
  EX_k_e : 0.078344
  EX_mg2_e : 0.003482
  EX_cl_e : 0.002089
  EX_ca2_e : 0.002089
  EX_cu2_e : 0.000285
  EX_mn2_e : 0.000277
  EX_zn2_e : 0.000137
  EX_ni2_e : 0.000130
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993554
  EX_h2o_e : 544.390407
  EX_co2_e : 30.893008
  EX_ac_e : 3.849412
  EX_succ_e : 0.418544
  Auxiliary production reaction : 0.211981
  EX_ura_e : 0.072649
  EX_dxylnt_e : 0.000269
  DM_5drib_c : 0.000090
  DM_4crsol_c : 0.000090

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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