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 : ahcys_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (39 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b3399 b1241 b0351 b4069 b2502 b2744 b3708 b3115 b1849 b2296 b3617 b2687 b1982 b2797 b3117 b1814 b4471 b2440 b4374 b0675 b2361 b2291 b0507 b0112 b0452 b2975 b0114 b3603 b1539 b2492 b0904 b1533   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.497758 (mmol/gDw/h)
  Minimum Production Rate : 0.745055 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 21.683975
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.846443
  EX_so4_e : 0.870400
  EX_pi_e : 0.480140
  EX_k_e : 0.097159
  EX_fe2_e : 0.007994
  EX_mg2_e : 0.004318
  EX_ca2_e : 0.002591
  EX_cl_e : 0.002591
  EX_cu2_e : 0.000353
  EX_mn2_e : 0.000344
  EX_zn2_e : 0.000170
  EX_ni2_e : 0.000161
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 45.949142
  EX_co2_e : 22.373303
  EX_h_e : 10.936186
  EX_ac_e : 3.381702
  Auxiliary production reaction : 0.745055
  DM_oxam_c : 0.000334
  DM_5drib_c : 0.000334
  DM_4crsol_c : 0.000111
  EX_etha_e : 0.000040

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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