Domains families

Sonnhammer, E.L., Eddy, S.R., Durbin, R. Pfam a comprehensive database of protein domain families based on seed alignments. Proteins 28 405-420, 1997. 

Another, but less well defined, class of molecules, some of whose members mediate adhesion interaction, is the four-transmembrane domain family, which shares similar hydropathy plots and may have similar dispositions with respect to the phospholipid bilayer, for example the myelin proteolipid proteins, the connexins of gap junctions, the ryanodine receptor and others. 

Prosite (http //www.expasy.org/prosite), database of protein domains, families, and functional sites. 

This chapter begins with an introduction to protein domains, followed by the steps usually attempted to define domains in a protein. The process begins by looking for well-known domains in the sequence using domain family databases. Then other less well-known domains are sought in the sequence using two popular methods, HMMER and PSI-BLAST. 

It can be difficult if not impossible to find the domain structure of a protein of interest from the primary literature. The sequence may contain many common domains, but these are usually not apparent from searches of literature. Articles defining new domains may include the protein, but only in an alignment figure, which are not searchable. Perhaps, with the advent of online access to articles, the full text including figures may become searchable. Fortunately there have been several attempts to make this hidden information available in away that can be easily searched. These resources, called domain family databases, are exemplified by Prosite, Pfam, Prints, and SMART. These databases gather information from the literature about common domains and make it searchable in a variety of ways. They usually allow a researcher to look at the domain organization of proteins in the sequence database that have been precalculated and also provide a way to search new sequences... 

Prosite is perhaps the best known of the domain databases (Hofmann et al., 1999). The Prosite database is a good source of high quality annotation for protein domain families. Prosite documentation includes a section on the functional meaning of a match to the entry and a list of example members of the family. Prosite documentation also includes literature references and cross links to other databases such as the PDB collection of protein structures (Bernstein et al., 1977). For each Prosite document, there is a Prosite pattern, profile, or both to detect the domain family. The profiles are the most sensitive detection method in Prosite. The Prosite profiles provide Zscores for matches allowing statistical evaluation of the match to a new protein. Profiles are now available for many of the common protein domains. Prosite profiles use the generalized profile software (Bucher et al., 1996). 

The SBASE database is a collection of annotated protein sequence segments (Murvai et al., 1999). SBASE avoids using consensus methods such as profile-HMMs and uses pairwise methods to detect domains. The database includes more than 130,000 annotated sequence segments that have been clustered into groups on the basis of BLAST similarities. SBASE currently contains 1038 domain families. 

The PROT-FAM database is available on the world-wide web from http //www.mips.biochem.mpg.de/ (Srinivasarao et al., 1999 Mewes et al., 1997). PROT-FAM contains alignments of PIRfamilies, superfamilies, and domain families (Barker et al., 1999). PROT-FAM currently contains 300 domain families. 

The EU funded Interpro project is a collaboration between many of the domain family databases and the SWISS-PROT sequence database. The Interpro collaboration aims to have a centralized annotation resources to reduce the amount of duplication between the database re-... 

B. Domain Families Represented in Fungi, Plants, and Metazoa. 224... 

This chapter anticipates the completion of Arabidopsis thaliana, Drosophila melanogaster, and Homo sapiens genome sequencing projects by reviewing current ideas of the evolution of sequence families. In parallel the related issue of domain homolog detection is discussed in light of continuing efforts to map the complete set of domain families. 

Domain Families Represented in Current Version of SMART2... 

The phyletic distributions of families (E, eukaryota M, metazoa F, fungi P, Viridiplantae (plants) B, bacteria, A., archaea) and the numbers of proteins (domains) detected in the S. cerevisiae ( yeast ) and C. elegans ( worm ) genomes are shown. The rightmost column contains a representative PDB code for determined tertiary structures of the domain family, if known. 

To facilitate cross referencing between the names of domain families used in this article and structural, functional, and evolution information available from the literature, the domain names used by the WWW-based resource SMART (http //smart.embl-heidelberg) are shown in bold and in a proportional font. 

II. Domain Families in Archaea, Bacteria, and Eukarya A. Horizontal Gene Transfer... 

The same direction, from bacteria to eukarya, was proposed for the horizontal transfer of SH3 domain homologous genes (Ponting et al., 1999b). This proposal arose from the observation of a domain family in bacterial lytic proteins with significant similarity to mammalian SH3 domains (Whisstock and Lesk, 1999 Ponting et al., 1999b). The direction... 

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