Conservation patterns

Families of similar sequences contain information on sequence evolution in the form of specific conservation patterns at all sequence positions. Multiple sequence alignments are useful for... 

The preceding considerations impose serious limitations on simple pairwise alignments that can be overcome in multiple alignments. With sufficient members of a multialignment, both the domain structure and the functionally conserved pattern within that domain context can be discerned. This is true even when the fold of the domain context is indeterminate. 

J.D. Aplin, A. Sattar, and A.P. Mould. Variant choriocarcinoma (BeWo) cells that differ in adhesion and migration on fibronectin display conserved patterns of integrin expression. J Cell Sci. 103 (Pt 2) 435 144 (1992). 

In contrast to calcareous invertebrates with their species specific shell organic matrix213-221 apatite depositors follow a rather conservative pattern set by collagen for bone, scale, and dentin deposition, or by a keratin-type protein in the case of enamel formation412. Nevertheless, a certain spread in the concentration of amino acids can be recognized if one, for instance, compares dentin of species en-... 

Fig. 3.8. Model of subunit III in the membrane. The folding is a model suggested by the alignment of primary structures of the subunit from six different species and the resulting conserved pattern of hydrophobic and hydrophilic stretches of amino acids [92]. The DCCD-sensitive Glu-90 (bovine numbering) is shown in the middle of the membrane (see text). Two adjacent prolines are shown in the transmembranous segment I. Two cysteines of the bovine subunit are also shown. Of these Cys-115 (the SH-group between segments III and IV) is almost certainly located in the aqueous C phase (92,119), which defines the sidedness of the figure. (Modified from 92 courtesy of Dr. Timo Penttila.)...

Jonassen, I. (1997) Efficient discovery of conserved patterns using a pattern graph, Comp. Appl. Biosci. 13 509-522. 

As the variety of sequenced genomes available in the public domain continues to grow, increasing attention is being paid to the analysis of conservation patterns between species to identify shared functional elements, which... 

A large amount of information (sequences, agonist and antagonist binding, mutation studies, etc.) is available for the rhodopsin-like G protein-coupled receptors. However, only limited information exists about the secretin-like and metabotropic glutamate receptors, and too few sequences have been determined yet to define sequence-conservation patterns in these subfamilies. Consequently,... 

Sharan, R S. Suthram, R. M. Kelley, T. Kuhn, S. McCuine, P. Uetz, and T. Sittler. 2005. Conserved pattern of protein interaction in multiple species. Proc. Nat. Acad. Sci. 102, 1974-1979. 

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