Basic local alignment search tools BLASTs

Sequence similarity searching Basic Local Alignment Search Tool (BLAST) http //www.ncbi.nlm.nih.gov/BLAST/ Comparison of novel sequences with known genes. 

A sequence alignment is a way of determining the similarity between two strings. This is a classical question in computer science, and has an exact solution referred to as the Smith/Waterman alignment. Unfortunately, this exact solution can be slow when analyzing large sequences, and therefore, approximate methods, such as Basic Local Alignment Search Tool (BLAST), have been developed to identify very similar sequences. 

The first bacterial DPCK to be cloned and characterized was the E. coli CoaE protein coaE gene product, previously yacE), which was identified by a basic local alignment search tool (BLAST) using the N-terminal sequence of the wild-type enzyme purified from C. ammoniagenes The enzyme is a 22.6-kDa monomer in solution and exhibits apparent values of 140 pmol 1 and 740 pmol for ATP and dephospho-CoA, respectively. It displays poor activity with adenosine, AMP, and adenosine phosphosulfate (APS) as alternate phosphoryl acceptors, which all shows less than 8% activity compared with the natural substrate. Studies on the bifiinctional PPAT/ DPCK protein show that the normally reversible PPAT activity becomes irreversible when it is coupled to DPCK, most probably because the latter activity demonstrates a low K- for dephospho-CoA of 5.2 L5 pmol 1 (its for ATP was found to be 192 14 pmol 1 ). ° Similar values were determined in an independent study. ... 

The PASTA (Lipman and Pearson, 1985) and Basic Local Alignment Search Tool (BLAST) (Altschul et al, 1990 1997) programs are local similarity search methods that concentrate on finding short identical matches, which may contribute to a total match. 

It is known that the next step is to search for a similar sequence for which a crystallized stractnre is available. For this, we have the PDB search option in MOE (similar to performing Basic Local Alignment Search Tool (BLAST)). Go to homology PDB search (Fig. 5.29). 

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