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 : aicar_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (20 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3553 b1241 b0351 b4069 b4384 b2297 b2458 b3617 b0030 b2407 b3124 b1982 b1033 b0261 b4381 b2406 b0112 b2789 b3127 b0114 b0529 b2492 b0904 b0514 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.471645 (mmol/gDw/h)
  Minimum Production Rate : 1.807790 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 21.983047
  EX_nh4_e : 12.325411
  EX_glc__D_e : 10.000000
  EX_pi_e : 2.262741
  EX_so4_e : 0.118770
  EX_k_e : 0.092062
  EX_fe2_e : 0.007575
  EX_mg2_e : 0.004092
  EX_cl_e : 0.002455
  EX_ca2_e : 0.002455
  EX_cu2_e : 0.000334
  EX_mn2_e : 0.000326
  EX_zn2_e : 0.000161
  EX_ni2_e : 0.000152
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 48.099123
  EX_co2_e : 19.373123
  EX_h_e : 14.063779
  EX_ac_e : 2.497588
  Auxiliary production reaction : 1.807790
  DM_oxam_c : 0.000528
  DM_5drib_c : 0.000316
  EX_glyclt_e : 0.000316
  DM_4crsol_c : 0.000105

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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