Protein BLAST Results
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By now you should have the BLAST results back and open in another window.
We will now:
  1. look at the different results sections
  2. examine the graph
  3. look at the sequence table
  4. look at, and interpret the alignment
The BLAST images below are taken from a search run on Sunday October 14, 2018 at 12:12:34 pm.
The protein BLAST results - page header
The page header is always worth a glance if only to make sure you ran the right program and the right database was searched.
Top of the BLAST result page
1) What is the length of the protein used for the search?
One answer only.
   274
   300
   324
   333
   362
   374
   401
The protein BLAST results - the graphics section
The graphics section gives an overview of the putative conserved domains and the results with an indication of the degree of match.
The putative conserved domains show the regions of the protein that MAY have particular functions. This also provides an indication of how the protein may be folded in that particular region.
The BLAST putative domains
The small triangles show the position and occurrence of amino acids that form part of the conserved features of the domain. The large blocks indicate matches specific proteins and domains
The small triangles in the putative domains section show the position and occurrence of amino acids that form part of the conserved features of the domain. The domains can be clicked on to reveal further information (we won't be doing that in this practical).
Below the domains is the graph showing the alignments. This graph shows the degree of match (as indicated by the colour), and moving your mouse over the graph will show the name of the protein in the box (on some browsers this no longer seems to work). Clicking on one of the proteins will open a small pop-up containing additional information on the protein.
The BLAST graph - the graph shows the degree of match between your sequence and sequences in the database
The protein BLAST results - the table
The BLAST table - the table shows the matches along with links to the full database entry and alignment. The top hit is the best match.
The BLAST table shows the hits ordered from best to worse (unless you click on one of the table header names such as 'Max Score' to recorder the table). The table also gives links to the alignment further down the page and the full database entry for a sequence.
1) In the above figure (not your results) what is the accession number of the top protein hit?
One answer only.
   AAB38421
   AAB38422
   AAB38423
   AAB38424
   AAB38425
   AAB38426
   AAB38427
2) The E value of 0.0 for the first sequence in the above table shows that
One answer only.
   it is a very poor match.
   the protein has not been fully sequenced.
   the protein is unique in the database.
   there are no mismatches.
   it is a good hit.
   all mismatches are conserved.
The protein BLAST results - the alignment
The alignment must be examined. Just because a protein is listed in the table, it does not mean it is a good match. Below are two alignments.
The first alignment shows a very good (in fact exact) match.
This is the top protein alignment for a search run on the date given at the top of the page. Note that this is an exact match. The identities and positives both score 100%, and that the values used to calculate the identities and positives is the same, as is the length of the protein used for the search, and for the alignments, i.e. 374 amino acids.
1) In the above figure (not your results) what is length of the sequence retrieved from the database?
One answer only.
   274
   300
   324
   333
   362
   374
   376
This alignment is not so good (this was taken from further down the list of alignments).
The above sequence alignment is the last one in the list and shows a poorer quality match.
This is not such as good match as although there is a full alignment across the length of the protein, the returned protein is longer (490 compared to the 374 sent), identities are 80%, and positives 85%. There is also a gap inserted.
1) The query sequence is
One answer only.
   the sequence that you sent to the database for comparison.
   the sequence retrieved for the database
2) The 'Sbjct' sequence is
One answer only.
   the sequence that you sent to the database for comparison.
   the sequence retrieved for the database
3) Were any gaps inserted to get the alignment in the above figure?
One answer only.
   No
   Yes
4) A positive (+) in the middle row of a protein blast search shows
One answer only.
   that the amino acids matched.
   that the amino acids did not match.
   means that there was a conserved substitution
5) A letter in the middle row of a protein blast search
One answer only.
   shows that the amino acids matched.
   shows that the amino acids did not match.
   means that there was a conserved substitution.
6) A space ( ) in the middle row of a protein blast search
One answer only.
   shows that the amino acids matched.
   shows that the amino acids did not match.
   means that there was a conserved substitution
So far we have:
  1. carried out a protein BLAST search
  2. looked at the returned results
  3. examined the sequence alignments
We will now look at how to retrieve more information from the BLAST result.
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