Sequences similarities between

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. 

The repeat sequences in solenoid proteins are often so imperfect that it is difficult to identify them without knowledge of the 3D structure or other supplementary information. In highly regular /1-solenoids, such as antifreeze proteins (Leinala et al., 2002 Liou et al., 2000) or YadA adhesin (Nummelin et al., 2004), the repeats are of the same length and sequence similarity between the repeats is discernible (so-called overt repeats). Frequently, however, the repeats in a given /1-solenoid vary in length because additional residues may be inserted at turn sites without disrupting the pattern of /1-strands that stabilizes the structure (Steinbacher et al., 1994 Yoder et al., 1993). In these cases, the structural repeats are not apparent as sequence repeats (covert repeats). 

So far, six families of HAT have been described. The different groups have been made according to their sequence similarities between homolog regions and between their different HAT domains (reviewed in Torchia et al, 1998 Sterner and Berger 2000 see references therein). 

CBDs also occur at the amino or carboxyl termini of fungal cellulases (19) and the structure of the CBD for T. reesei CBH I has been resolved by 2-dimensional NMR (20). There is little sequence similarity between the bacterial and fungal CBDs although hydrophobic and... 

Proteins containing two 4Fe 4S clusters, typified by the P. aerogenes ferredoxin (PaFd), show striking sequence similarities between the amino- and carboxy-terminal halves of the molecule, suggesting that these proteins evolved by gene duplication of a more primitive protein (Section I,E,3). Of particular note is the pattern of four cysteines in the two halves of the molecule (Cys-8, -11, -14, -18 and Cys-35, -38, -41, -45 in the amino- and carboxyl-terminal halves, respectively, of the PaFd se-... 

Based on the amino acid sequences, two classes of C4H have been described for some species, with around 60% sequence similarity between the groups. The first sequence for the class II type was reported from Phaseolus vulgaris (French bean), ° but they have also been found in other species (see, e.g.. Ref. 21). The two C4H types differ at both terminal domains and in three internal domains, and it has been suggested that one type may be involved in stress responses and the other in vascular differentiation. ... 

Overall sequences, similarity between the constitutive endothelium and neuronal NOS isoforms is approximately 50%, and both are roughly 50% identical to the inducible macrophage NOS (Xie et al., 1992 Lamas et al., 1992). Studies have located the genes for human neuronal, endothelial, and inducible NOS on... 

FIGURE 8-32 DNA hybridization. Two DNA samples to be compared are completely denatured by heating. When the two solutions are mixed and slowly cooled, DNA strands of each sample associate with their normal complementary partner and anneal to form duplexes. If the two DNAs have significant sequence similarity, they also tend to form partial duplexes or hybrids with each other the greater the sequence similarity between the two DNAs, the greater the number of hybrids formed. Hybrid formation can be measured in several ways. One of the DNAs is usually labeled with a radioactive isotope to simplify the measurements... 

Furthermore, there is considerable sequence similarity between transcription factors, even though they may operate in different biosynthetic pathways. Hence, based on sequence similarity it is often difficult to identify the target genes of a given transcription factor. 

Fig. 6. Amino acid sequence similarity between the three G-box-binding proteins isolated from Arabidopsis. The location of basic region 1 (BR-1) and 2 (BR-2) is indicated. The leucine residues within the leucine zipper are highlighted and numbered. The hydrophobic amino acids interdigitating the leucine repeats are designated a-d. 219 and 249 denote amino acid positions in GBF-1 asterisks indicate identical amino acids.

B Schoner, M Geistlich, P Rosteck Jr, RN Rao, E Seno, P Reynolds, K Cox, S Burgett, C Hershberger. Sequence similarity between macrolide-resistance determinants and ATP-binding transport proteins. Gene 115 93-96, 1992. 

The parameters to be optimized for experimental recombination include the crossover frequency, the number of parents, and the sequence similarity between parents. Additionally, it is important to understand the conditions under which recombination is useful. For all these questions, the optimal parameters represent a balance between the exploration and exploitation capabilities of the search algorithm. Any process that creates more diversity, such as using many parents, very disparate parents, or small fragment sizes, will improve exploration at the cost of exploitation. The balance between these effects will shift according to the landscape ruggedness and the sampling ability of the mutant library. 

The sequences of porcine and caprine acrosin light chains and the N-terminal sequences of the acrosin heavy chains are shown aligned with the sequences of several serine proteases in Figure 1. Sequence similarity between porcine and caprine acrosins is readily apparent, as is the similarity of the acrosin sequences (range of... 

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