Protein Families: Relating Protein Sequence, Structure, and Function (Hardcover)

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