Amino acid identity

Galanin Receptors. Table 1 Galanin receptor subtype relationships (% amino acid identity)... 

Overall amino acid identity values were generated with the GAP program (GCG, Inc., Madison, USA). 

Seven subfamilies of eukaryotic Kir channels, each sharing 60% amino acid identity between individual members within each subfamily and 40% identity between subfamilies, are known [1]. In addition, multiple prokaryotic Kir channels (Kirbacl.1-9) are now being identified in bacterial genomes. We will focus on the eukaryotic channels. 

NOS (eNOS, NOS IH, NOS3). Classically, nNOS and eNOS were considered constitutive enzymes, whereas iNOS is cytokine-induced. Recent evidence suggests that nNOS and eNOS are also subject to important regulation of expression [1 ]. Within the human species, amino acid sequences of the three NOS isoforms share 52-58% identity. Each isoform is well conserved across mammalian species (>90% amino acid identity for nNOS and eNOS, >80% for iNOS). NOS enzymes exist in organisms as low as nematodes, protozoa, and even in plants (Fig. 1). 

How do Phytoplankton Cope with Enhanced UV Several investigators have reported the existence in Antarctic algae of UV-absorbing mycosporine amino acids identical to those of tropical and temperate marine species (37). These compounds absorb in the UV-B region of the spectrum and may act as sunscreens which may provide some measure of protection from damaging UV-B. 

There are 17 human type I IFN genes, all clustering on chromosome 9. They are intronless and encode secretory signal peptide sequences that are proteolytically cleaved prior to secretion from the cell. Type I IFNs are genetically and structurally closely related. They range in length from 161 to 208 amino acids and have apparent molecular weights of 15-24 kDa (Table 1) (Chen et al. 2004). The different subtypes of human IFN-a have approximately 50% amino acid sequence identity, whereas IFN-a shares approximately 22% amino acid identity with human IFN-p and 37% with human IFN-m (Chen et al. 2004). 

Extracellular ATP has been demonstrated to activate a depolarizing current in different neuronal and non-neuronal cell types. These receptors are also referred to as P2 receptors. The receptors can further be divided into the G-protein-coupled P2Y receptors and the ligand-gated ion channels P2X. Currently, seven P2X receptors (P2XJ-P2X- ) have been cloned (Table 3.3). The receptors exhibit between 26 and 50% overall amino-acid identities, with the highest level of conservation in the extracellular and transmembrane regions. P2X7 (also called P2Z) is the most distant member of the family. 

The cDNAs for the muscarinic receptors encode apparent glycoproteins of 55-70 kDa, which contain seven predicted transmembrane-spanning regions, similar to what is seen for the [3-adrenergic receptor and other receptors that couple to G proteins (Fig. 11-11). There is only 38% amino acid identity between the proteins cloned from porcine brain and heart. The cDNA encoding the receptor initially cloned from the brain has been termed m whereas that cloned from the heart has been termed m2, in keeping with the names (Mj and M2) applied to the purified recombinant receptors. 

This graph has several important features. It reaches saturation at d0bs of about 0.93, which means that the model predicts that one will never see a pair of proteins that are less than 7% identical. At this level of distance, a substitution will restore an amino acid identity just as likely as generate a new difference. Real sequences will sometimes exceed this level of observed distance and then the correction is not applicable. This is especially likely to occur with short sequences. If such distances are encountered in a real data set, then the sequences are so distant that the analysis will be difficult anyway. No matter what is done, it will be difficult to estimate the true number of substitutions. A further problem arises when one considers the possible variance or error of the distance estimates. A difference in the observed distance of just one identity more or less will have very little effect when dobs is small but will make an enormous difference to D when dobs is more than 0.80. 

Recently, the structure of a pheromone-binding protein from the cockroach Leucophaea maderae, LmadPBP (Fig. 8b) has been solved by X-ray crystallography [58]. Despite the fact that LmadPBP and BmorPBP shared low amino acid identity (15% similarity 22%) (Fig. 9), the two proteins present similar folds. 

Figure 2. Alignment of the human mitochondrial ceramidase to homologous ceramidases from various organisms. Sequences of ceramidases were aligned using ClustalW algorithm of the Mac Vector program. Amino acids identical are shaded in grey and consensus residues are shown under the alignment. Amino acids of the same group are shaded in white.

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