What proteins in humans are similar to the red opsin?

Now return to the NCBI Map Viewer http://www.ncbi.nlm.nih.gov/mapview/. We're going to search the human genome for sequences similar to that of the red opsin.

Click the B next to Homo sapiens (human).

This is the NCBI's BLAST search tool. BLAST is a widely used program for finding sequences similar to a "query" sequence that you're interest in. Pick these options from the various menus:
Database: Protein (Search the database of proteins sequences.)
Program: blastp (Use the version of BLAST that compares protein sequences, unlike blastn, which compares nucleotide sequences.)
Other Parameters, Expect: 10 (The higher the number, the less stringent that matching, and the more hits you'll get)

Next, copy the FASTA data from your file protred.txt to your clipboard, and paste it into the BLAST search box, above which it says, "Enter an accession..." Check to be sure that the first character in the box is the ">" at the beginning of the FASTA data. Then click Begin Search.

The next page is for formatting your search results. Just click that enthusiastic Format! button. When your results are ready, the results of BLAST page appears. Look down the page to the graphical display, a box containing lots of colored lines. Each line represents a hit from your blast search. If you pass your mouse cursor over a red line, the narrow box just above the box gives a brief description of the hit. You'll find that the first hit is your red opsin. That's encouraging, because the best match should be to the query sequence itself, and you got this sequence from that gene entry. The second hit is the green opsin -- remember that the PubMed entry reported that the red and green pigments are the most similar. The third and fourth hits are the blue opsin and the rod-cell pigment rhodopsin. Other hits have lower numbers of matching residues, and are color coded according to a score of matches. If you click on any of the colored lines, you'll skip down to more information about that hit, and you can see how much similarity each one has to the red opsin, your original query sequence. As you go down the list, each succeeding sequence has less in common with red opsin. Each sequence is shown in comparison with red opsin in what is called a pairwise sequence alignment. Later, you'll make multiple sequence alignments from which you can discern relationships among genes.

See what you can figure out about what the scores mean. Identities are residues that are identical in the hit and the query (red opsin), when the twoo are optimally aligned.. Positives are residues that are very similar to each other (see residue number 1 in the blue opsin -- it's threonine in red opsin, and the very similar serine in the blue). Gaps are sometimes introduced into a hit to improve its alignment with the query. The more identities and positives, and the fewer gaps, the higher the score. Note that blue opsin and rhodopsin are only about 45% identical to the red opsin. Other proteins, which are apparently not visual pigments, have even lower scores. Now let's take a look at where all these hits are in the human genome.