Protein Families (eBook)

CHRISTINE ORENGO, PhD, is Professor of Bioinformatics at University College London. Dr. Orengo's research focuses on protein structure comparison, classification, and analysis. Her group develops the CATH domain family classification and algorithms for predicting protein functions and functional networks. ALEX BATEMAN, PhD, is Senior Investigator at Wellcome Trust Sanger Institute, where he leads the Pfam database project. Dr. Bateman also participates in the European InterPro project, which seeks to merge the annotations from Pfam, PRINTS, Prosite, and other domain databases.

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 beta-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