Table of Contents
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 Sjólander
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