Finding sequences similar to 1PTH from other organisms

PART B: Finding sequences similar to 1PTH from other organisms.
These instructions will guide you in finding the first sequence.
1.​ Run BLAST on 1PTH_A from the NCBI.
a.​ The easiest way: Go back to the 1PTH Chain A page from above and click on Run
BLAST. The screenshot below will help you find this link. Then, follow instructions b-d
below.
Or: Find the BLAST page
i.​Select ​protein blast
ii. ​Enter just the primary sequence into first white box (copy and paste your FASTA
sequence)
iii. ​Under Database → non-redundant protein sequences
iv.​ Algorithm selected should be ​blastp
v. ​Click on BLAST button (just let the program run, sometimes takes minutes)
(4) State what the acronym BLASTp stands for
(5) In your own words: State what BLASTp is used for and two pieces on information one can
derive from this database.
Scroll past the conserved domains and go to ‘Sequences producing significant alignments’. The
information to the right of each ‘hit’ will help you understand each match.
(6) In your own words: State the meaning of ‘E value’. While there is no clear “cut-off” for an E
value, you may be able to get a feel for similarity from these numbers. What range of E values
would you consider to indicate significant similarity?.
(7) Find five different species in this result list- list their common names and E values. Have you
captured a wide variety of species? Justify your answer.
Go to the sequence from ​Orcinus orca. ​Find this entry in your list of matches. When you click
on the entry, you will jump to a view of the alignment. Select the link to the sequence ID to get
to the information page on the ​Orcinus orca ​sequence.
a.​ Download the FASTA (complete sequence)
b.​ Copy and paste that sequence below the 1PTH FASTA sequence in your text file.
Save the text file using an appropriate name
Authors: Drs. Laura Listenberger and Cassidy Terrell Last updated: 12 February 2019
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Now it’s your turn. These instructions will guide you towards finding another similar
sequence from an organism of your choice.
2.​ Go back to BLAST- Scroll to the top of the page and click on ​Edit and Resubmit
a.​ This time enter an organism into the ​Organism ​field, or by ​Taxa. ​As you type, BLAST
may suggest a species or taxa. ​Choose multicellular eukaryotic organisms​.
(8) Choose a sequence from your BLAST results. The sequence you choose should have an E
value below 0.0001. Putative sequences are OK.
a) Report the species you have selected.
b) Record the E Value of the sequence selected.
b.​ Download the FASTA sequence for the species you have selected. Add it to your
growing text file.
c.​ ​Further edit the three sequences in your word/text file. Every new entry in the
word/text file might look something like: