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Sci Rep. 2017 Jan 23;7:41031. doi: 10.1038/srep41031.

SecretEPDB: a comprehensive web-based resource for secreted effector proteins of the bacterial types III, IV and VI secretion systems.

Author information

1
College of Information Engineering, Northwest A&F University, Yangling 712100, China.
2
Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC 3800, Australia.
3
School of Electronic and Computer Engineering, Peking University, Beijing 100871, China.
4
Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, VIC 3800, Australia.
5
Monash Bioinformatics Platform, Monash University, Melbourne, VIC 3800, Australia.
6
Infection and Immunity Program, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia.
7
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.

Abstract

Bacteria translocate effector molecules to host cells through highly evolved secretion systems. By definition, the function of these effector proteins is to manipulate host cell biology and the sequence, structural and functional annotations of these effector proteins will provide a better understanding of how bacterial secretion systems promote bacterial survival and virulence. Here we developed a knowledgebase, termed SecretEPDB (Bacterial Secreted Effector Protein DataBase), for effector proteins of type III secretion system (T3SS), type IV secretion system (T4SS) and type VI secretion system (T6SS). SecretEPDB provides enriched annotations of the aforementioned three classes of effector proteins by manually extracting and integrating structural and functional information from currently available databases and the literature. The database is conservative and strictly curated to ensure that every effector protein entry is supported by experimental evidence that demonstrates it is secreted by a T3SS, T4SS or T6SS. The annotations of effector proteins documented in SecretEPDB are provided in terms of protein characteristics, protein function, protein secondary structure, Pfam domains, metabolic pathway and evolutionary details. It is our hope that this integrated knowledgebase will serve as a useful resource for biological investigation and the generation of new hypotheses for research efforts aimed at bacterial secretion systems.

PMID:
28112271
PMCID:
PMC5253721
DOI:
10.1038/srep41031
[Indexed for MEDLINE]
Free PMC Article

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