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Protocols

STEPdb specifications

Information


Unique identifier OMICS_08003
Name STEPdb
Alternative name STEP database
Restrictions to use None
Maintained No

Taxon


  • Bacteria
    • Escherichia coli

Maintainer


This tool is not available anymore.

Publication for STEP database

STEPdb citations

 (7)
library_books

Deciphering functional diversification within the lichen microbiota by meta omics

2017
Microbiome
PMCID: 5518139
PMID: 28724401
DOI: 10.1186/s40168-017-0303-5

[…] ce 0.5 Da, maximum missed cleavages 2, charge state 1+, and oxidation of methionine as variable modification. In order to improve the identification of high-confidence peptide sequence matches, a two-step database search was performed, similar to an approach described previously []. To this end, mass spectra were searched in a primary step against the NCBInr protein database (version 2014.06.25, 4 […]

library_books

MatureP: prediction of secreted proteins with exclusive information from their mature regions

2017
Sci Rep
PMCID: 5468347
PMID: 28607462
DOI: 10.1038/s41598-017-03557-4

[…] The 505 Sec-dependent secretory and 2365 cytoplasmic sequences of the Escherichia coli K-12 proteome (Table ) were used during the machine learning analysis. These were collected from STEPdb, a comprehensive database of subcellular classification of E. coli polypeptides.The class of secretory proteins includes eight sub-cellular categories of STEPdb (Table ). We included only prote […]

library_books

MetaPro IQ: a universal metaproteomic approach to studying human and mouse gut microbiota

2016
Microbiome
PMCID: 4919841
PMID: 27343061
DOI: 10.1186/s40168-016-0176-z

[…] from the IGC website (http://meta.genomics.cn/) and the GigaScience Database (http://gigadb.org/dataset/view/id/100114/token/mZlMYJIF04LshpgP), respectively [, ].In MetaPro-IQ, the first- and second-step database searches were carried out with X! Tandem (release 2015.04.01) [, ], and the third step was carried out with MaxQuant software (version 1.5.2.8) []. For the X! Tandem database search, eac […]

call_split

HIV infection results in metabolic alterations in the gut microbiota different from those induced by other diseases

2016
Sci Rep
PMCID: 4870624
PMID: 27189771
DOI: 10.1038/srep26192
call_split See protocol

[…] s per peptide match and an apex trigger of 2 to 30 s were enabled.To achieve a more precise evaluation of protein abundances and to decrease the false discovery rate of peptide identifications, a two-step database search was used. Raw MS and MS/MS data were first processed using Thermo Proteome Discoverer software (v.1.4.1.14) and Mascot Server (v. 2.4.1) and then independently searched against th […]

library_books

Gut Bacteria Metabolism Impacts Immune Recovery in HIV infected Individuals

2016
PMCID: 4919658
PMID: 27428431
DOI: 10.1016/j.ebiom.2016.04.033

[…] s per peptide match and an apex trigger of 2 to 30 s were enabled.To achieve a more precise evaluation of protein abundances and to decrease the false discovery rate of peptide identifications, a two-step database search was used (, ). Raw MS and MS/MS data were first processed using Thermo Proteome Discoverer software (v.1.4.1.14) and Mascot Server (v. 2.4.1) and then independently searched again […]

library_books

Quantitative Proteomics Analysis Reveals the Min System of Escherichia coli Modulates Reversible Protein Association with the Inner Membrane*

2016
PMCID: 4858940
PMID: 26889046
DOI: 10.1074/mcp.M115.053603

[…] KA clone (-) (A complete Set of E. coli K-12 ORF Archive; National BioResource Project, Japan), and Dynamic Localizome () (Supplemental data and Table S2). While subcellular localization described in STEPdb and PSORTdb concerns subcellular topology of proteins, subcellular localization documented in ASKA clone (-) and Dynamic Localizome emphasizes intracellular distribution of proteins. When the I […]

Citations

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STEPdb institution(s)
Laboratory of Molecular Bacteriology; Rega Institute, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
STEPdb funding source(s)
This work was supported by the European Commission the Operational Programme “Competitiveness and Entrepreneuriship” (OPCE II - EPAN II) - National Strategic Reference Framework (NSRF 2007–2013) [grant codes: 09SYN-13–705 and 09SYN-13–832], an Excellence grant (#1473 to A.E.; General Secretariat of Research), and the Onassis foundation predoctoral program.

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