Post on 13-Jan-2016
description
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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