STEPdb: Sub-cellular Topologies of E.coli Polypeptides.

K-12(MG1655) BL21(DE3) Both EPEC (O127:H6)

(mouse over and click on the one letter topology symbols to see which proteins of this specific subproteome are localized in each location)

Bacterial cell cartoon of sub-cellular locations

STEPdb database:

The STEPdb database contains a comprehensive characterization of sub-cellular localization and topology of the Escherichia coli proteome. Current annotation is a result a multi-combinatorial analysis including existing databases, predictions of bioinformatic tools and exhaustive literature survey and manual curation. Tools for sequence similarity searches, prediction of sub-cellular location, visualization of membrane proteins topologies and protein complexes are included.

References related to STEPdb

STEPdb 2.0

  • Loos, MS., Ramakrishnan, R., Vranken, W., Tsirigotaki, A., Tsare, E., Zorzini, V., De Geyter, J., Yuan, B., Tsamardinos, I., Klappa, M., Schymkowitz, J., Rousseau, F., Karamanou, S., Economou, A.
    Structural basis of the sub-cellular topology landscape of E. coli

STEPdb 1.0

  • Orfanoudaki, G. and Economou A. (2014)
    Proteome-wide Sub-cellular Topologies of E.coli polypeptides database (STEPdb)
    Molecular and Cellular Proteomics, 13, 3674-3687.

MatureP 1.0

  • Orfanoudaki, G., Markaki, M, Chatzi, K., Tsamardinos, Y. and Economou, A. (2017)
    MatureP: secretory protein prediction exclusively through mature domain features.
    Scientific reports 7: 3263 | DOI:10.1038/s41598-017-03557-4

Proteomics studies

  • Orfanoudaki, G. and Economou, A. (2014)
    Proteome-wide sub-cellular Topologies of E. coli.
    Mol Cell Proteomics 13:, 3674-3687,
    PMID:25210196 doi: 10.1074/mcp.O114.041137
  • Papanastasiou M, Orfanoudaki G, Koukaki M, Kountourakis N, Sardis MF, Aivaliotis M, Karamanou S, Economou A. (2013)
    The Escherichia coli peripheral inner membrane proteome.
    Mol Cell Proteomics 12:, 599-610,
    PMID:23230279 doi: 10.1074/mcp.M112.024711
    Supplemental Data: DC1
  • Papanastasiou M, Orfanoudaki G, Kountourakis N, Koukaki M, Sardis MF, Aivaliotis M, Tsolis KC, Karamanou S, Economou A. (2016) ​
    Rapid label-free quantitative analysis of the E. coli BL21(DE3) inner membrane proteome
    PROTEOMICS 16, 85–97 Main Text: pdf
    Supplemental Data: pdf


  • Tsirigotaki, A., De Geyter, J., Sostaric, N., Orfanoudaki, G., Economou, A., and Karamanou, S., (2017)
    Bacterial protein export through the Sec pathway.
    Nature Reviews Microbiology 15, 21–36
  • De Geyter, J., Tsirigotaki, A., Orfanoudaki, G., Zorzini, V., Economou, A., and Karamanou, S. (2016)
    Protein folding in the cell envelope of Escherichia coli.
    Nature Microbiology 1, 16107 | DOI: 10.1038/NMICROBIOL.2016.107.
  • Portaliou AG, Tsolis KC, Loos MS, Zorzini V, Economou A. (2016)
    Type III Secretion: Building and Operating a Remarkable Nanomachine.
    Trends in Biochemical Sciences 41(2), 175-189 | DOI: 10.1016/j.tibs.2015.09.005.


 ©2017 Copyright KU Leuven and FORTH/ICE-HT. Last Update: February 2019.