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Protein Database

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

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Protein Database

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  1. Protein Database David Shiuan Department of Life Science Institute of Biotechnology Interdisciplinary Program of Bioinformatics National Dong Hwa University

  2. 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

  3. 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

  4. 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

  5. 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.

  6. 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.

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

  8. Reaction steps common in radical SAM enzymes

  9. Simple • Modular • Architecture • Research • Tool

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