SPdb – a signal peptide database

Khar Heng Choo,Tin Wee Tan,Shoba Ranganathan

doi:10.1186/1471-2105-6-249

Khar Heng Choo, Tin Wee Tan + Show 1 more

Open Access

https://doi.org/10.1186/1471-2105-6-249

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Abstract

BackgroundThe signal peptide plays an important role in protein targeting and protein translocation in both prokaryotic and eukaryotic cells. This transient, short peptide sequence functions like a postal address on an envelope by targeting proteins for secretion or for transfer to specific organelles for further processing. Understanding how signal peptides function is crucial in predicting where proteins are translocated. To support this understanding, we present SPdb signal peptide database , a repository of experimentally determined and computationally predicted signal peptides.ResultsSPdb integrates information from two sources (a) Swiss-Prot protein sequence database which is now part of UniProt and (b) EMBL nucleotide sequence database. The database update is semi-automated with human checking and verification of the data to ensure the correctness of the data stored. The latest release SPdb release 3.2 contains 18,146 entries of which 2,584 entries are experimentally verified signal sequences; the remaining 15,562 entries are either signal sequences that fail to meet our filtering criteria or entries that contain unverified signal sequences.ConclusionSPdb is a manually curated database constructed to support the understanding and analysis of signal peptides. SPdb tracks the major updates of the two underlying primary databases thereby ensuring that its information remains up-to-date.

Highlights

The signal peptide plays an important role in protein targeting and protein translocation in both prokaryotic and eukaryotic cells
Signal peptides are present in both prokaryotic and eukaryotic cells, indicating its ancient universal origins. They function like a postal address label on an envelope by targeting the proteins for secretion or to specific organelle for further processing
18,146 tion (b) we found differing positions quoted by SwissProt as compared to the quoted papers (c) we did not have access to the quoted subscription-only papers or the papers referred to were old and in some cases there were no paper or no relevant paper quoted (d) we could not find or locate the cleavage site information (Table 1)

Summary

Introduction

The signal peptide plays an important role in protein targeting and protein translocation in both prokaryotic and eukaryotic cells This transient, short peptide sequence functions like a postal address on an envelope by targeting proteins for secretion or for transfer to specific organelles for further processing. Proteins synthesised at the ribosome (cytoplasm or rough endoplasmic reticulum), mitochondria or chloroplast are transported to their site of function This process is known as protein targeting and it depends on targeting signals to direct the proteins to their specific locations. Signal peptides are present in both prokaryotic and eukaryotic cells, indicating its ancient universal origins They function like a postal address label on an envelope by targeting the proteins for secretion or to specific organelle for further processing. Not all proteins possess signal peptides [2,3], suggesting that other mechanisms for protein targeting exist

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