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 : pnto__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (55 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b4467 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b3708 b0512 b0871 b2925 b2097 b3617 b1004 b3713 b1109 b0046 b2690 b2797 b3117 b1814 b4471 b2210 b0675 b0822 b4381 b2406 b1727 b0114 b2366 b2492 b0904 b1533 b1380 b1517 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.444843 (mmol/gDw/h)
  Minimum Production Rate : 1.069880 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.970025
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.881096
  EX_pi_e : 0.429098
  EX_so4_e : 0.112020
  EX_k_e : 0.086830
  EX_fe2_e : 0.007145
  EX_mg2_e : 0.003859
  EX_ca2_e : 0.002315
  EX_cl_e : 0.002315
  EX_cu2_e : 0.000315
  EX_mn2_e : 0.000307
  EX_zn2_e : 0.000152
  EX_ni2_e : 0.000144
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 43.506832
  EX_co2_e : 29.126645
  EX_h_e : 6.715591
  Auxiliary production reaction : 1.069880
  EX_acald_e : 0.766778
  EX_pyr_e : 0.481189
  EX_alltn_e : 0.001737
  EX_glyclt_e : 0.000298
  DM_mththf_c : 0.000199
  DM_5drib_c : 0.000100
  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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