Similarity sequences

The protein sequence database is also a text-numeric database with bibliographic links. It is the largest public domain protein sequence database. The current PIR-PSD release 75.04 (March, 2003) contains more than 280 000 entries of partial or complete protein sequences with information on functionalities of the protein, taxonomy (description of the biological source of the protein), sequence properties, experimental analyses, and bibliographic references. Queries can be started as a text-based search or a sequence similarity search. PIR-PSD contains annotated protein sequences with a superfamily/family classification. 

Amylin [106602-62-4] (75) (Fig. 4) is a 37-amino acid peptide having approximately 46% sequence similarity to CGRP (33). Amylin is present ia pancreatic P-ceUs along with insulin. It may function as a hormone ia glucoregulation and has been proposed as an etiologic factor ia certain forms of diabetes. Amylin is also present ia dorsal root ganglia (see INSULIN AND OTHER ANTIDIABETIC DRUGS). 

Attempts have also been made at predicting the secondary stmcture of proteins from the propensities for residues to occur in the a-helix or the P-sheet (23). However, the assignment of secondary stmcture for a residue only has an average accuracy of about 60%. A better success rate (70%) is achieved when multiple-aligned sequences having high sequence similarity are available. 

Figure 1 The basis of comparative protein structure modeling. Comparative modeling is possible because evolution resulted in families of proteins, such as the flavodoxin family, modeled here, which share both similar sequences and 3D structures. In this illustration, the 3D structure of the flavodoxin sequence from C. crispus (target) can be modeled using other structures in the same family (templates). The tree shows the sequence similarity (percent sequence identity) and structural similarity (the percentage of the atoms that superpose within 3.8 A of each other and the RMS difference between them) among the members of the family.

WR Pearson. Empirical statistical estimates for sequence similarity searches. J Mol Biol 276 71-84, 1998. 

Figure 9.12 Schematic diagram of the structure of the heterodimeric yeast transcription factor Mat a2-Mat al bound to DNA. Both Mat o2 and Mat al are homeodomains containing the helix-turn-helix motif. The first helix in this motif is colored blue and the second, the recognition helix, is red. (a) The assumed structure of the Mat al homeodomain in the absence of DNA, based on Its sequence similarity to other homeodomains of known structure, (b) The structure of the Mat o2 homeodomain. The C-terminal tail (dotted) is flexible in the monomer and has no defined structure, (c) The structure of the Mat a 1-Mat a2-DNA complex. The C-terminal domain of Mat a2 (yellow) folds into an a helix (4) in the complex and interacts with the first two helices of Mat a2, to form a heterodimer that binds to DNA. (Adapted from B.J. Andrews and M.S. Donoviel, Science 270 251-253, 1995.)...

All K channels are tetrameric molecules. There are two closely related varieties of subunits for K channels, those containing two membrane-spanning helices and those containing six. However, residues that build up the ion channel. Including the pore helix and the inner helix, show a strong sequence similarity among all K+ channels. Consequently, the structural features and the mechanism for ion selectivity and conductance described for the bacterial K+ channel in all probability also apply for K+ channels in plant and animal cells. 

The L and the M subunits are firmly anchored in the membrane, each by five hydrophobic transmembrane a helices (yellow and red, respectively, in Figure 12.14). The structures of the L and M subunits are quite similar as expected from their sequence similarity they differ only in some of the loop regions. These loops, which connect the membrane-spanning helices, form rather flat hydrophilic regions on either side of the membrane to provide interaction areas with the H subunit (green in Figure 12.14) on the cytoplasmic side and with the cytochrome (blue in Figure 12.14) on the periplasmic side. The H subunit, in addition, has one transmembrane a helix at the car-boxy terminus of its polypeptide chain. The carboxy end of this chain is therefore on the same side of the membrane as the cytochrome. In total, eleven transmembrane a helices attach the L, M, and H subunits to the membrane. 

The light-harvesting complex LHl is directly associated with the reaction center in purple bacteria and is therefore referred to as the core or inner antenna, whereas LH2 is known as the peripheral antenna. Both are huilt up from hydrophohic a and p polypeptides of similar size and with low hut significant sequence similarity. The two histidines that hind to chlorophyll with absorption maxima at 850 nm in the periplasmic ring of LH2 are also present in LHl, but the sequence involved in binding the third chlorophyll in LH2 is quite different in LHl. Not surprisingly, the chlorophyll molecules of the periplasmic ring are present in LHl but the chlorophyll molecules with the 800 nm absorption maximum are absent. 

The data show that SSIMS can be used as a tool for characterizing the different steps in the production of biosensors, or even for sequencing. Similarly, SSIMS can be used to solve a variety of problems in bioanalytical chemistry, e. g. screening of combinatorial libraries, characterizing Langmuir-Blodgett layers, etc. 

Proteins have unique amino acid sequences, and it is this uniqueness of sequence that ultimately gives each protein its own particular personality. Because the number of possible amino acid sequences in a protein is astronomically large, the probability that two proteins will, by chance, have similar amino acid sequences is negligible. Consequently, sequence similarities between proteins imply evolutionary relatedness. 

Amino acid sequence analysis reveals that proteins with related functions often show a high degree of sequence similarity. Such findings suggest a common ancestry for these proteins. 

If DNA from two different species are mixed, denatured, and allowed to cool slowly so that reannealing can occur, artificial hybrid duplexes may form, provided the DNA from one species is similar in nucleotide sequence to the DNA of the other. The degree of hybridization is a measure of the sequence similarity or relatedness between the two species. Depending on the conditions of the experiment, about 25% of the DNA from a human forms hybrids with mouse DNA, implying that some of the nucleotide sequences (genes) in humans are very similar to those in mice. Mixed RNA DNA hybrids can be created in vitro if single-stranded DNA is allowed to anneal with RNA copies of itself, such as those formed when genes are transcribed into mRNA molecules. 

If a phylogenetic comparison is made of the 16S-Iike rRNAs from an archae-bacterium Halobacterium volcanii), a eubacterium E. coli), and a eukaryote (the yeast Saccharomyces cerevisiae), a striking similarity in secondary structure emerges (Figure 12.40). Remarkably, these secondary structures are similar despite the fact that the nucleotide sequences of these rRNAs themselves exhibit a low degree of similarity. Apparently, evolution is acting at the level of rRNA secondary structure, not rRNA nucleotide sequence. Similar conserved folding patterns are seen for the 23S-Iike and 5S-Iike rRNAs that reside in the... 

Fujii, T., et al. (2002). A novel photoprotein from oceanic squid (Symplectoteuthis oualaniensis) with sequence similarity to mammalian carbon-nitrogen hydrolase domains. Biochem. Biophys. Res. Commun. 293 874-879. 

In cyclic nucleotide-regulated channels, this domain serves as a high-affinity binding site for 3-5 cyclic monophosphates. The CNBD of channels has a significant sequence similarity to the CNBD of most other classes of eukaryotic cyclic nucleotide receptors and to the CNBD of the prokaryotic catabolite activator protein (CAP). The primary sequence of CNBDs consists of approximately 120 amino acid residues forming three a-helices (oA-aC) and eight (3-strands ( 31- 38). 

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