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 : malcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (12 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b4382 b4384 b3708 b3008 b0512 b0871 b2925 b2097 b0030 b2407 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b0595 b0261 b2406 b0511 b0114 b0886 b2366 b2492 b0904 b2578 b1533 b3927 b3821 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.768354 (mmol/gDw/h)
  Minimum Production Rate : 0.055163 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.482289
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.042326
  EX_pi_e : 0.906649
  EX_so4_e : 0.299305
  EX_k_e : 0.149977
  EX_fe2_e : 0.012341
  EX_mg2_e : 0.006665
  EX_ca2_e : 0.003999
  EX_cl_e : 0.003999
  EX_cu2_e : 0.000545
  EX_mn2_e : 0.000531
  EX_zn2_e : 0.000262
  EX_ni2_e : 0.000248
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 48.285009
  EX_co2_e : 26.220875
  EX_h_e : 7.385345
  Auxiliary production reaction : 0.055163
  EX_xan_e : 0.051515
  EX_5mtr_e : 0.050655
  EX_spmd_e : 0.050655
  DM_5drib_c : 0.000516
  DM_4crsol_c : 0.000171

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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