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 (35 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b1478 b4382 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b1278 b3708 b3752 b0871 b2925 b2097 b3617 b2407 b2690 b1982 b2797 b3117 b1814 b4471 b0675 b0822 b2406 b0114 b2366 b2492 b0904 b1533 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.675243 (mmol/gDw/h)
  Minimum Production Rate : 0.141832 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.500178
  EX_o2_e : 272.799919
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.434856
  EX_pi_e : 0.651344
  EX_so4_e : 0.170040
  EX_k_e : 0.131803
  EX_mg2_e : 0.005858
  EX_ca2_e : 0.003515
  EX_cl_e : 0.003515
  EX_cu2_e : 0.000479
  EX_mn2_e : 0.000467
  EX_zn2_e : 0.000230
  EX_ni2_e : 0.000218
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_fe3_e : 999.989155
  EX_h2o_e : 543.819360
  EX_co2_e : 25.708903
  EX_acald_e : 2.648278
  Auxiliary production reaction : 0.141832
  DM_oxam_c : 0.000454
  DM_mththf_c : 0.000303
  DM_5drib_c : 0.000152
  DM_4crsol_c : 0.000151

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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