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 : thmnp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (59 of 87: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3553 b3399 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b2744 b0871 b2779 b0160 b0907 b1779 b1982 b3616 b3589 b1033 b0675 b2361 b0261 b4381 b2406 b0112 b2789 b3127 b0114 b0529 b2492 b0904   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.416779 (mmol/gDw/h)
  Minimum Production Rate : 1.333037 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.754933
  EX_nh4_e : 11.177728
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.402027
  EX_so4_e : 0.104953
  EX_k_e : 0.081352
  EX_fe2_e : 0.006694
  EX_mg2_e : 0.003616
  EX_cl_e : 0.002169
  EX_ca2_e : 0.002169
  EX_cu2_e : 0.000295
  EX_mn2_e : 0.000288
  EX_zn2_e : 0.000142
  EX_ni2_e : 0.000135
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 49.169372
  EX_co2_e : 26.143329
  EX_h_e : 10.517640
  EX_acald_e : 2.364226
  Auxiliary production reaction : 1.333037
  DM_oxam_c : 0.011372
  DM_5drib_c : 0.000280
  EX_glyclt_e : 0.000186
  DM_4crsol_c : 0.000093

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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