Families of related sequences

To classify and find the category of protein sequences under investigation into families of related sequences... 

Substantial improvements in secondary structure prediction can be achieved by using families of related sequences, each of which adopts the same structure. 

Using structural alignment methods, it is sometimes possible to find relationships between proteins that cannot be determined from sequence alone. In such cases, structural alignments can improve MS As of the family of related sequences and reveal functional roles of the target protein that are not apparent from the sequence alone. 

These additional structures can then be used to greatly increase the information contained in the MSA of the family of related sequences. The MSA can be a critical piece of information about a sequence, as it contains a wealth of data. In addition, several programs such as T-COFFEE [56] can directly use structural alignment information to further improve MSAs. 

In fact, close sequence and structural homologies show that chlorobenzoyl-CoA dehalogenase, enoyl-CoA hydratase, and a variety of other hydratases, isomerases, synthases, lyases, and hydrolases belong to a large family of related proteins 49a 49b/49c... 

Gowri VS, Pandit SB, Karthik PS et al (2003) Integration of related sequences with protein three-dimensional structural families in an updated version of PALI database. Nucleic Acids Res 31 486-488... 

This family of related RNA molecules likely was generated by gene duplication followed by specialization. A nucleic acid sequence encoding one member of the family was duplicated, and the two copies evolved independently to generate molecules with specificities for different amino acids. This process was repeated, starting from one primordial transfer RNA gene until the 20 (or more) distinct members of the transfer RNA family present in modem organisms arose. 

Alcohol dehydrogenase contains two atoms of zinc. One atom participates in the catalytic mechanism, while the other serv es a structural role. The enzyme actually is a dimer, and is composed of two subuiuts. Several types of alcohol dehydrogenase occur in the body. The enzymes have closely related amino acid sequences, and thus consist of a family of related enzymes. 

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