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 : 5caiz_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (48 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b3553 b3399 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b2744 b0871 b1238 b2883 b1982 b3616 b3589 b1033 b0675 b2361 b0261 b0411 b4381 b0112 b0114 b0509 b3125 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.549900 (mmol/gDw/h)
  Minimum Production Rate : 0.651559 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 20.900773
  EX_nh4_e : 10.166227
  EX_glc__D_e : 10.000000
  EX_pi_e : 1.181996
  EX_so4_e : 0.138476
  EX_k_e : 0.107337
  EX_fe2_e : 0.008832
  EX_mg2_e : 0.004770
  EX_cl_e : 0.002862
  EX_ca2_e : 0.002862
  EX_cu2_e : 0.000390
  EX_mn2_e : 0.000380
  EX_zn2_e : 0.000188
  EX_ni2_e : 0.000178
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 46.753561
  EX_co2_e : 20.202335
  EX_h_e : 9.932229
  EX_thymd_e : 1.136032
  Auxiliary production reaction : 0.651559
  DM_oxam_c : 0.000615
  DM_5drib_c : 0.000369
  DM_4crsol_c : 0.000123

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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