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 : ncam_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (109 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b4382 b4269 b0493 b3588 b3003 b3011 b0474 b2518 b3831 b3073 b3752 b2221 b4152 b0871 b2297 b2458 b2925 b2097 b2926 b1612 b1611 b4122 b3946 b0825 b4161 b1493 b3517 b4015 b0614 b0726 b4138 b4123 b0621 b0529 b1380 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.619395 (mmol/gDw/h)
  Minimum Production Rate : 0.316992 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 28.223921
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.567903
  EX_pi_e : 0.597472
  EX_so4_e : 0.155976
  EX_k_e : 0.120902
  EX_fe2_e : 0.009948
  EX_mg2_e : 0.005373
  EX_ca2_e : 0.003224
  EX_cl_e : 0.003224
  EX_cu2_e : 0.000439
  EX_mn2_e : 0.000428
  EX_zn2_e : 0.000211
  EX_ni2_e : 0.000200
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 48.396527
  EX_co2_e : 28.880900
  EX_h_e : 8.222142
  EX_succ_e : 0.645901
  EX_ac_e : 0.360603
  Auxiliary production reaction : 0.316992
  EX_ura_e : 0.122251
  DM_5drib_c : 0.000139
  DM_4crsol_c : 0.000138

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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