MetNetComp Database [1] / Minimal gene deletions

Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : STM_v1_0 [2].
Target metabolite : aps_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (102 of 102: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: STM0051 STM2421 STM1749 STM2463 STM4275 STM0661 STM2009 STM4567 STM4570 STM1620 STM2167 STM0974 STM0152 STM3957 STM1211 STM2317 STM1480 STM2338 STM2466 STM2422 STM3968 STM3802 STM2196 STM3240 STM2970 STM3243 STM3708 STM2971 STM1826 STM3334   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.235112 (mmol/gDw/h)
  Minimum Production Rate : 0.180670 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 17.888684
  EX_glc__D_e : 5.000000
  EX_nh4_e : 3.503065
  EX_pi_e : 0.389172
  EX_so4_e : 0.209349
  EX_k_e : 0.041756
  EX_mg2_e : 0.001856
  EX_fe2_e : 0.001723
  EX_ca2_e : 0.001114
  EX_cl_e : 0.001114
  EX_cobalt2_e : 0.000742
  EX_cu2_e : 0.000742
  EX_mn2_e : 0.000742
  EX_mobd_e : 0.000742
  EX_zn2_e : 0.000742

Product: (mmol/gDw/h)
  EX_h2o_e : 26.210146
  EX_co2_e : 17.362302
  EX_h_e : 3.407699
  EX_ac_e : 0.851993
  Auxiliary production reaction : 0.180670
  EX_glyclt_e : 0.011756
  EX_ade_e : 0.001751
  DM_hmfurn_c : 0.000105

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].

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: 27-Sep-2023
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