JalView Protein Alignment

You can download JalView software for protein alignment here.

Once you download Jalview (and java), open the program.
If you have a windows computer, there may be issues opening it. You may have to go to your downloaded jalview program, left click on jalview program and select "open with". To find the program needed to open jalview, you will need to go to your computer, then programs-86 then find java and open using the program ''javaws". The program opens up sample windows, which you can exit out of.

To create a new alignment:
To find protein sequences, I recommend using NCBIs protein search tool. You'll need to know the specific name of your protein (not just kinesin 1, but Kif 5B) for the search. You can filter by length of the protein and by species. From here you can download the FASTA sequence.

Select: File --> input alignment --> from textbox

You can then input the one letter sequences of each of your proteins in the text box and click new window when finished. *Note: this does NOT align your sequences.

If you input a sequence from ApE, it will not have its FASTA name:

>OWK03308.1 KIF5B [Cervus elaphus hippelaphus]

You can easily create your own name from this information:

>Kin1-523 KIF5B [Homo Sapiens]

To align:
After you have input your sequences and have opened a new window, you can then align the sequences:

Webservice --> alignment --> clustal --> with defaults

This will actually align the sequences and will show you the conserved regions among a family of proteins. The tallest yellow bars show the most conserved regions, while the shortest show the least.

Analysis:
In addition to simply aligning the protein sequences, you can also add colors that tell you specific information about the amino acids in the sequences. For instance, you can select colour and then hydrophobicity to see essentially a heat map of polar and nonpolar residues. Some of the colors I'm not familiar with, but here is what I've noticed so far:

Buried Index: Blue is very buried and green is exposed.

Hydrophobicity: Red is hydrophobic and blue is hydrophilic

Percentage Identity: Shows heat map of identity, purple being identical

Clustal: I believe that clustal colors similarly behaving amino acids in the same color.

Additionally, to easily find regions that are NOT conserved you can select format --> show nonconserved and this will change the letters of the conserved regions into dashes.

Secondary Structure:
In addition to aligning, you can also predict the secondary structure of your proteins.

Select all sequences and go to: web service --> secondary structure prediction --> Jnet secondary structure

Determining Residue Numbers:
Say you find a region that you think is interesting when comparing Map7 and Ens and you want to determine the residue numbers. You must scroll over the starting and ending residues of Map7 and look in the bottom left corner for the residue number. Then you must do the same for Ens. Jalview does not show the residue number for both amino acid sequences above them.