Thank you to whoever can help =) The following problems involve using the Basic

Question

Thank you to whoever can help =)

The following problems involve using the Basic Local Alignment Search Tool or BLAST.

Using NCBI’s BLAST search page answer the following: http://blast.ncbi.nlm.nih.gov/Blast.cgi

Remember: 1) Choose the non-redundant or “nr” database to access non-human, non-mouse genome data.

2) E value: a negative value or zero is the best value

3) Some proteins have a putative conserved domain which can be accessed by a protein blast.

Using this protein (amino acid) sequence answer the following questions:

MMEFTIKRDYFITQLNDTLKAISPRTTLPILTGIKIDAKEHEVILTGSDSEISIEITIPKTVDGEDIVNI SETGSVVLPGRFFVDIIKKLPGKDVKLSTNEQFQTLITSGHSEFNLSGLDPDQYPLLPQVSRDDAIQLSV KVLKNVIAQTNFAVSTSETRPVLTGVNWLIQENELICTATDSHRLAVRKLQLEDVSENKNVIIPGKALAE LNKIMSDNEEDIDIFFASNQVLFKVGNVNFISRLLEGHYPDTTRLFPENYEIKLSIDNGEFYHAIDRASL LAREGGNNVIKLSTGDDVVELSSTSPEIGTVKEEVDANDVEGGSLKISFNSKYMMDALKAIDNDEVEVEF FGTMKPFILKPKGDDSVTQLILPIRTY

2.1 What is generally the starting amino acid of a protein?

2.2 Perform a protein blast or BLASTp search of the protein. What was your top hit? Also record the E-value.

2.3 What are the conserved domains, if any, from BLASTp?

2.4 Perform a TBLASTn search. What is the best match now? And record the E-value.

2.5 What was the difference in the two results (BLASTp to TBLASTn)?

Explanation / Answer

2.1. Generally the starting aminoacid of a protein is Methionine which is coded by one of the three initiator codons UAA, UAG or UGA on mRNA.

2.2 Top hit is

DNA polymerase III subunit beta [Homo sapiens]

E-value: 7e-48

2.3 The conserved domain hits are PRK05643, POL3Bc, beta_clamp,   DnaN, dnan, DNA_pol3_beta_2 . In total 6 domains were obtained as result.

These are obtained when clicked on the image according to the message in BLASTp page: "Putative conserved domains have been detected, click on the image below for detailed results" .

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