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 : nadh_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (11 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b1241 b0351 b4069 b4384 b3115 b1849 b2296 b3617 b0030 b2407 b1982 b0261 b4381 b2406 b0112 b2975 b0114 b3603 b0509 b3125 b0529 b2492 b0904 b0508 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.459733 (mmol/gDw/h)
  Minimum Production Rate : 0.881066 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 20.740369
  EX_nh4_e : 11.133059
  EX_glc__D_e : 10.000000
  EX_pi_e : 2.205594
  EX_so4_e : 0.115770
  EX_k_e : 0.089737
  EX_fe2_e : 0.007384
  EX_mg2_e : 0.003988
  EX_ca2_e : 0.002393
  EX_cl_e : 0.002393
  EX_cu2_e : 0.000326
  EX_mn2_e : 0.000318
  EX_zn2_e : 0.000157
  EX_ni2_e : 0.000148
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 49.280753
  EX_co2_e : 19.518114
  EX_h_e : 10.184324
  EX_ac_e : 1.553751
  Auxiliary production reaction : 0.881066
  DM_oxam_c : 0.000514
  DM_5drib_c : 0.000308
  DM_4crsol_c : 0.000103

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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