109. Protein Families

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109. Protein Families

 

 

CATEGORY: Diet Nutrition Supplementation – 500 Courses

COURSE NUMBER: 109

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BOOKS/ MANUALS: Pages

Syllabus

Introduction vii
Contributors xiii
SECTION I. CONCEPTS UNDERLYING PROTEIN FAMILY
CLASSIFICATION 1
1 Automated Sequence-Based Approaches for Identifying Domain
Families 3
Liisa Holm and Andreas Heger
2 Sequence Classification of Protein Families: Pfam and other
Resources 25
Alex Bateman
3 Classifying Proteins into Domain Structure Families 37
Alison Cuff, Alexey Murzin, and Christine Orengo
4 Structural Annotations of Genomes with Superfamily and
Gene3D 69
Julian Gough, Corin Yeats, and Christine Orengo
5 Phylogenomic Databases and Orthology Prediction 99
Kimmen Sj ̈olander

SECTION II. IN-DEPTH REVIEWS OF PROTEIN FAMILIES 125
6 The Nucleophilic Attack Six-Bladed β-Propeller (N6P)
Superfamily 127
Michael A. Hicks, Alan E. Barber II, and Patricia C. Babbitt
7 Functional Diversity of the HUP Domain Superfamily 159
Benoit H. Dessailly and Christine Orengo
8 The NAD Binding Domain and the Short-Chain
Dehydrogenase/Reductase (SDR) Superfamily 191
Nicholas Furnham, Gemma L. Holliday, and Janet M. Thornton
9 The Globin Family 207
Arthur M. Lesk and Juliette T.J. Lecomte
SECTION III. REVIEW OF PROTEIN FAMILIES IN IMPORTANT
BIOLOGICAL SYSTEMS 237
10 Functional Adaptation and Plasticity in Cytoskeletal Protein
Domains: Lessons from the Erythrocyte Model 239
Anthony J. Baines
11 Unusual Species Distribution and Horizontal Transfer of
Peptidases 285
Neil D. Rawlings
12 Deducing Transport Protein Evolution Based on Sequence,
Structure, and Function 315
Steven T. Wakabayashi, Maksim A. Shlykov, Ujjwal Kumar, Vamsee S. Reddy,
Ankur Malhotra, Erik L. Clarke, Jonathan S. Chen, Rostislav Castillo, Russell
De La Mare, Eric I. Sun, and Milton H. Saier
13 Crispr-CAS Systems and CAS Protein Families 341
Kira S. Makarova, Daniel H. Haft, and Eugene V. Koonin
14 Families of Sequence-Specific DNA-Binding Domains
in Transcription Factors across the Tree of Life 383
Varodom Charoensawan and Sarah Teichmann
15 Evolution of Eukaryotic Chromatin Proteins and Transcription
Factors 421
L. Aravind, Vivek Anantharaman, Saraswathi Abhiman, and Lakshminarayan
M. Iyer
Index 503

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