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 : aacoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (1 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b3553 b4382 b4384 b3708 b3008 b3752 b0871 b2407 b0120 b1982 b2797 b3117 b1814 b4471 b1033 b0261 b0507 b3709 b2406 b3161 b0112 b0114 b0886 b1539 b2492 b0904 b0591 b2578 b1533 b3927 b3821 b1473 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.751720 (mmol/gDw/h)
  Minimum Production Rate : 0.129410 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.690908
  EX_o2_e : 274.171207
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.025226
  EX_pi_e : 1.113343
  EX_so4_e : 0.318708
  EX_k_e : 0.146731
  EX_mg2_e : 0.006521
  EX_ca2_e : 0.003913
  EX_cl_e : 0.003913
  EX_cu2_e : 0.000533
  EX_mn2_e : 0.000519
  EX_zn2_e : 0.000256
  EX_ni2_e : 0.000243
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_fe3_e : 999.987927
  EX_h2o_e : 548.470836
  EX_co2_e : 25.906728
  Auxiliary production reaction : 0.129410
  DM_oxam_c : 0.000841
  DM_5drib_c : 0.000504
  DM_4crsol_c : 0.000168

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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