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 : paps_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (22 of 36: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b4467 b4069 b4384 b2297 b2458 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b0937 b1982 b0261 b0411 b3945 b1602 b4381 b1727 b0114 b0529 b2492 b0904 b1380 b2660 b0606 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.437906 (mmol/gDw/h)
  Minimum Production Rate : 0.202091 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.106132
  EX_o2_e : 285.168737
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.741766
  EX_pi_e : 0.826589
  EX_so4_e : 0.312364
  EX_k_e : 0.085476
  EX_mg2_e : 0.003799
  EX_ca2_e : 0.002279
  EX_cl_e : 0.002279
  EX_cu2_e : 0.000310
  EX_mn2_e : 0.000303
  EX_zn2_e : 0.000149
  EX_ni2_e : 0.000141
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992967
  EX_h2o_e : 549.992705
  EX_co2_e : 36.571915
  EX_12ppd__S_e : 0.973272
  EX_ac_e : 0.254943
  Auxiliary production reaction : 0.202091
  EX_hxan_e : 0.000490
  DM_5drib_c : 0.000294
  DM_4crsol_c : 0.000098

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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