Motif-databases

When a novel homology domain has been discovered, it is possible to store the corresponding domain descriptor (profile or HMM) in a number of dedicated domain databases, which can be used to analyze newly identified sequences for their domain content [9, 10]. Several competing domain- and motif-databases exist, including PROSITE, PFAM, SMART, and Superfam, which contain descriptors for most, if not all, of the known domains involved in the ubiquitin system [11-14]. Recently, a new meta-database named INTERPRO has been established, which tries to combine the descriptors of several domain databases under a single user interface [15]. Pointers to the very useful search engines of the domain databases are provided in Table 12.1. 

As well as these general motif databases, there are some more specialized sequence analysis tools for identifying particular structural or functional features. One well-studied example is that of coiled coils. The program COILS " allows one to compare a sequence against profiles derived from known parallel two-stranded coiled coils, to assess the likelihood that the query sequence is indeed a coiled coil. More involved analyses based on pairwise interactions have been developed, such as PAIRCOIL. Several families of coiled coils are actually well recognized by their PROSITE motifs. However, the leucine zipper PROSITE motif, L-X(6)-L-X(6)-L-X(6)-L, is poorly discriminating, and for this specific family of coiled coils, the program TRESPASSER provides a more refined identification... 

E Motif Database of significant sequence patterns for biochemical properties and biological functions http //motif, stanford.edu/ emotif/ Stanford University, D. Brutlag et al. [84]... 

Functional motifs If a protein exhibits a sequence (or structure) motif that is characteristic for a specific binding site, the binding partner of the protein could be deduced. There are several databases of motifs that are equipped with tailor-made search methods. The oldest motif database is... 

The importance of motif discovery is born out by the growth in motif databases such as TRANSFAC, JASPAR, SCPD, DBTBS, RegulonDB (7-10) for DNA motifs and PROSITE, BLOCKS, and PRINTS (3-5) for protein motifs. However, far more motifs remain to be discovered. For example, TFBS motifs are known for only about 500 vertebrate TFs, but it is estimated that there are about 2000 TFs in mammalian genomes alone (7,11). 

Some Searchable Motif Databases With Web Servers... 

Compare the motifs discovered, to known motifs contained in appropriate motif databases such as those in Table 4. 

As has been described in Sect. 5.3, the conservation patterns of enzymes are often indicative of the particular family they belong to and can be used for their classification. However, the iterative searches and multiple alignment methods used for their establishment require a certain bioinformatic infrastructure as well as some experience with these issues. If the goal of the analysis is not the detection of novel enzyme families, but rather the classification of a novel sequence into one of the already existing enzyme families, there are a number of protein domain and motif databases that will be useful in this respect[60 61. These databases do not store the sequences themselves but rather work with descriptors of protein families and protein domains. These descriptors can consist of the Profiles or Hidden Markov Models mentioned above, but other types are also being used. With a particular... 

Proteins with common functional motifs may not be identified in a typical BLAST search. These short sequences may be located by searches of motif databases. 

SMART Small motif database http //smart.embl-heidelberg.de/... 

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