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 : unagamuf_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (64 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b1241 b0351 b3831 b4069 b0910 b3752 b4152 b0871 b2297 b2458 b2925 b2097 b2926 b3617 b1612 b1611 b4122 b3946 b0825 b4388 b4138 b4123 b0621 b4381 b2406 b2943 b0114 b0529 b2492 b0904 b0516 b1695 b1517 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.431010 (mmol/gDw/h)
  Minimum Production Rate : 0.004077 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 985.916359
  EX_o2_e : 278.736024
  EX_nh4_e : 10.140131
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.423909
  EX_so4_e : 0.108537
  EX_k_e : 0.084130
  EX_mg2_e : 0.003739
  EX_ca2_e : 0.002243
  EX_cl_e : 0.002243
  EX_cu2_e : 0.000306
  EX_mn2_e : 0.000298
  EX_zn2_e : 0.000147
  EX_ni2_e : 0.000139
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993078
  EX_h2o_e : 548.990027
  EX_co2_e : 25.010558
  EX_ac_e : 2.115760
  EX_succ_e : 1.259742
  EX_ura_e : 1.115938
  EX_alltn_e : 0.810288
  Auxiliary production reaction : 0.004077
  DM_mththf_c : 0.000193
  DM_5drib_c : 0.000097
  DM_4crsol_c : 0.000096

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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