MedProDB

MedProDB provides an extensive repository of Mediator protein sequences and annotated biochemical and structural features to support analysis of transcriptional regulation across eukaryotic organisms.

Key Features:

• Database content: 33,971 entries of Mediator subunits across eukaryotic kingdoms, including plants, fungi, and animals.
• Sequence attributes: Sequence details, length, position, organism classification, molecular weight, and taxonomic lineage for each entry.
• Physicochemical properties: Computed aromaticity, hydropathy, instability index, and isoelectric point.
• Functional and interaction annotations: Functional roles, interaction networks, and associated disease annotations.
• Structural and sequence features: Repeat regions, alignment to specific Mediator subunit families, Intrinsically Disordered Regions (IDRs), Post-translation Modifications (PTMs), and Molecular Recognition Features (MoRFs).
• Integrated analysis tools: BLAST for sequence similarity searches, Smith-Waterman Align for precise local alignment, IUPred for IDR prediction, and MoRF-Chibi_Light for MoRF identification.

Scientific Applications:

• Transcriptional regulation studies: Investigation of Mediator complex roles in gene expression across eukaryotes.
• Structural analysis: Characterization of IDRs, MoRFs, and PTMs for structural and disorder-related studies.
• Functional annotation: Analysis of subunit functional roles and interaction networks.
• Comparative genomics: Cross-kingdom comparison of Mediator subunits among plants, fungi, and animals.
• Disease association studies: Linking Mediator subunits to associated diseases using curated annotations.
• Sequence analysis and family assignment: Sequence similarity searches and local alignments to assign entries to Mediator subunit families.

Methodology:

Sequence similarity searches with BLAST; local alignments with Smith-Waterman Align; IDR prediction with IUPred; MoRF prediction with MoRF-Chibi_Light.