Abstract Domains are the building blocks of all globular proteins, and are units of compact three-dimensional structure as well as evolutionary units. There is a limited repertoire of domain families, so that these domain families are duplicated and combined in different ways to form the set of proteins in a genome. Proteins are gene products. The processes that produce new genes are duplication and recombination as well as gene fusion and fission. We attempt to gain an overview of these processes by studying the structural domains in the proteins of seven genomes from the three kingdoms of life: Eubacteria, Archaea and Eukaryota. We use here the domain and superfamily definitions in Structural Classification of Proteins Database (SCOP) in order to map pairs of adjacent domains in genome sequences in terms of their superfamily combinations. We find 624 out of the 764 superfamilies in SCOP in these genomes, and the 624 families occur in 585 pairwise combinations. Most families are observed in combination with one or two other families, while a few families are very versatile in their combinatorial behaviour. This type of pattern can be described by a scale-free network. Finally, we study domain repeats and we compare the set of the domain combinations in the genomes to those in PDB, and discuss the implications for structural genomics. Contact: apic@mrc-lmb.cam.ac.uk
This FAIRsharing record describes: Genome3D is a resource that provides structural annotation and 3D models of genomes of model organisms such as human, yeast and E.coli. The da...
Protein structures were collected from the Brookhaven Database of tertiary architectures that displayed oligomeric association (24 molecules) or whose polypeptide folding reveal...
The accelerating pace of genome sequencing throughout the tree of life is driving the need for improved unsupervised annotation of genome components such as transposable element...
Abstract Motivation: Protein homology detection and sequence alignment are at the basis of protein structure prediction, function prediction and evolution. Results: We have gene...
The structures of the interfaces of nine dimeric and nine tetrameric proteins have been analyzed and have been seen to follow general principles. These interfaces are combinatio...
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