Protein Database

David Shiuan

Department of Life Science

Institute of Biotechnology

Interdisciplinary Program of Bioinformatics

National Dong Hwa University

Proteome Bioinformatics/Databases

1. Protein sequence databases - SWISS-PROT; TrEMBL

2. Nucleotide sequence databases - Hidden treasures: EST

3. Pattern and profile databases - PROSITE; BLOCKS; PRINTS; Pfam

4. 2D-PAGE databases - SWISS-2DPAGE;WORLD-2DPAGE

5. 3D structural databases - PDB; DSSP; HSSP

Proteome Bioinformatics/Databases

6. Post-translational modification databases - O-GLYCBASE

7. Genomic databases - OMIM; GDB; MGD; FlyBase

8. Metabolic databases - ENZYME; KEGG; EMP/WT

9. Interfacing and Integrating Databases - EXExPASy; SWISS-PROT; Cyber–Encyclopaedia of the Proteome

Protein Database

UniPro - protein knowledge database Swiss 2DPAGE - 2D PAGE Pfam - protein family and domain Prosite - protein family and domain SMART - protein module BLOCK - protein conserved regions

Pfam :: Home The Pfam database of protein families and

HMMs

Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein families.

Pfam version 17.0 (March 2005) contains alignments and models for 7868 protein families, based on the Swissprot 46.0 and SP-TrEMBL 29.0 protein sequence databases.

HMM: A Hidden Markov Model

HMM: A Hidden Markov Model, or HMM, is a statistical model for any system that can be represented as a succession of transitions between discrete states.

Biotin Synthase

Biotin synthase (BioB) converts dethiobiotin into biotin byinserting a sulfur atom between C6 and C9 of dethiobiotin inan S-adenosylmethionine (SAM)-dependent reaction.

Reaction steps common in radical SAM enzymes

Simple Modular Architecture Research Tool