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 (111 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b0474 b2518 b2744 b4152 b0871 b3115 b1849 b2296 b2925 b2097 b1612 b1611 b4122 b1779 b3962 b3946 b0825 b4267 b4374 b4161 b0675 b1415 b4015 b0614 b2799 b0726 b4388 b4138 b4123 b0621 b0452 b0114 b1539 b1380 b0508 b4266 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.447010 (mmol/gDw/h)
  Minimum Production Rate : 0.236086 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 31.313601
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.461658
  EX_pi_e : 0.431188
  EX_so4_e : 0.112566
  EX_k_e : 0.087253
  EX_fe2_e : 0.007179
  EX_mg2_e : 0.003878
  EX_ca2_e : 0.002327
  EX_cl_e : 0.002327
  EX_cu2_e : 0.000317
  EX_mn2_e : 0.000309
  EX_zn2_e : 0.000152
  EX_ni2_e : 0.000144
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 46.407369
  EX_co2_e : 31.273928
  EX_h_e : 9.059958
  EX_succ_e : 1.508087
  EX_ac_e : 1.302191
  Auxiliary production reaction : 0.236086
  EX_ura_e : 0.080910
  EX_dxylnt_e : 0.000299
  DM_5drib_c : 0.000101
  DM_4crsol_c : 0.000100

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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