ARCPHdb: A comprehensive protein database for SF1 and SF2 helicase from archaea

Area of Science:

• Molecular Biology
• Bioinformatics
• Genomics

Background:

• Superfamily 1 (SF1) and Superfamily 2 (SF2) helicases are crucial protein families involved in fundamental biological processes like DNA replication, transcription, and translation.
• Archaea serve as model organisms for studying helicase function, architecture, and assembly.

Purpose of the Study:

• To identify and classify all SF1 and SF2 helicase protein families across 95 archaeal genomes using a phylogenomic approach.
• To develop ARCPHdb, a specialized online database and webserver for accessing archaeal SF1 and SF2 helicase information.

Main Methods:

• Phylogenomic analysis was employed to identify and classify SF1 and SF2 helicase families.
• A MySQL relational database (ARCPHdb) was implemented with web interfaces developed using Netbeans.
• Data were organized using standard identifiers like UniProt accession numbers, NCBI Ref Seq ID, and PDB IDs.

Main Results:

• The study identified and classified SF1 and SF2 helicase families within 95 archaeal genomes.
• ARCPHdb offers a user-friendly interface for browsing, searching, and downloading archaeal helicase sequences, 3D structure models, and literature links.
• The database integrates direct links to relevant external databases for comprehensive data access.

Conclusions:

• ARCPHdb is the inaugural online database consolidating all SF1 and SF2 helicase information from archaea.
• This platform serves as a vital resource for researchers investigating archaeal helicases and their roles in biological processes.