SPdb – a signal peptide database

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.

Use of signal sequences as an in situ removable sequence element to stimulate protein synthesis in cell-free extracts

“…The nucleotide sequences encoding the E.coli signal peptides were obtained from a signal peptide database (release 3.2) (17). …”

Identification, biochemical characterization, and in-vivo expression of the intracellular invertase BfrA from the pathogenic parasite Leishmania major

“…In our case, the low activity of the enzyme outside the pH 5-7 range is also consistent with the intracellular pH reported for Leishmania. Moreover, when BfrA sequence was submitted to SignalP server, 76,77 no signal peptides was detected. Experimentally, expression of BfrA as a secreted protein in Leishmania cells (BfrAleish) yielded an inactive protein.…”

“…19 3.6. Production of BfrAleish in L. tarentolae BfrA sequence was submitted to SignalP server 76,77 and no canonic secretion signal peptides were detected, thus indicating the most likely intracellular localization of the protein. Still, to gain insight about the cellular localization of BfrA, we decided to express it in a eukaryotic host system similar to L. major.…”

Crystal Structure of Bacillus subtilis Signal Peptide Peptidase A

“…Signal peptide sequences of B. subtilis and E. coli were obtained from SPdb Signal Peptide Resource. 29 The protein-protein interface between protomers was analyzed using PISA 30 and ProtorP. 31 The conserved residues among Gram-negative and Gram-positive SppA were mapped onto the structure using ConSurf.…”