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 : seramp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (46 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b2744 b3708 b3008 b0871 b0160 b0517 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b0261 b0507 b4381 b0452 b0114 b2366 b2492 b0904 b1533 b3927 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.785789 (mmol/gDw/h)
  Minimum Production Rate : 0.096018 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.087262
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.146924
  EX_pi_e : 0.853995
  EX_so4_e : 0.197878
  EX_k_e : 0.153381
  EX_mg2_e : 0.006817
  EX_fe2_e : 0.006485
  EX_fe3_e : 0.006135
  EX_ca2_e : 0.004090
  EX_cl_e : 0.004090
  EX_cu2_e : 0.000557
  EX_mn2_e : 0.000543
  EX_zn2_e : 0.000268
  EX_ni2_e : 0.000254
  EX_cobalt2_e : 0.000020

Product: (mmol/gDw/h)
  EX_h2o_e : 48.653699
  EX_co2_e : 26.414365
  EX_h_e : 7.694712
  Auxiliary production reaction : 0.096018
  EX_alltn_e : 0.021090
  DM_5drib_c : 0.000177
  DM_4crsol_c : 0.000175

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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