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The Signal Recognition Particle Database (SRPDB)

N Larsen1, T Samuelsson, C Zwieb

  • 1Department of Microbiology, Giltner Hall, Michigan State University, East Lansing, MI 48824, USA.

Nucleic Acids Research
|February 21, 1998
PubMed
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The Signal Recognition Particle Database (SRPDB) now includes more SRP RNA and protein sequences, plus new eukaryotic and bacterial SRP receptor sequences. This update enhances resources for studying protein targeting and cellular transport.

Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Structural Biology

Background:

  • The Signal Recognition Particle (SRP) pathway is crucial for targeting proteins to cellular membranes.
  • Databases are essential for organizing and accessing biological sequence data.
  • Previous versions of SRPDB provided valuable SRP sequence information.

Purpose of the Study:

  • To update and expand the Signal Recognition Particle Database (SRPDB) with new sequence data.
  • To incorporate sequences of the eukaryotic SRP receptor and homologous bacterial proteins.
  • To provide phylogenetically ordered, annotated, and aligned sequence data.

Main Methods:

  • Curated addition of new SRP RNA and protein sequences.
  • Inclusion of sequences for the alpha subunit of the eukaryotic SRP receptor and bacterial homologs.

Related Experiment Videos

  • Phylogenetic ordering, annotation with primary database links, and sequence alignment.
  • Provision of downloadable SRP RNA secondary structure diagrams and 3D models.

    • Main Results:

    • The SRPDB now contains 99 SRP RNA sequences and 63 SRP protein sequences (SRP9, SRP14, SRP19, SRP21, SRP54, SRP68, SRP72).
    • For the first time, 21 sequences of the eukaryotic SRP receptor alpha subunit and bacterial homologs are included.
    • Sequences are phylogenetically ordered, annotated, aligned, and supplemented with structural data.

    Conclusions:

    • The updated SRPDB offers a comprehensive resource for researchers studying the SRP pathway.
    • The inclusion of SRP receptor sequences expands the database's utility for comparative analysis.
    • Enhanced data accessibility and structural information facilitate further research in protein targeting.