ProteinPathTracker needs just a protein sequence in FASTA format to execute, either pasted or uploaded. The rest of the parameters are optional. After providing the protein sequence, click in "Track ProteinPathTracker, track!" to start its execution. Results will appear in the same window in less than one minute.
As the web tool looks for homologs through evolution, the evolutionary path shows the proteomes in which homologs are searched. By default, the selected proteomes are used, but in some taxa the user may change the desired proteome.
Evalue cutoff to study the significance of the Blast searches can also be modified (default evalue = 0.1).
By default, the lock region strategy is off, but it can be turned on by selecting the coordinates of the lock region to follow in the homologs. The minimum length of any locked region is 10 aminoacids. If the user locks a region, the minimum %coverage of the selected locked region in the results can also be specified. By default, a minimum of a 75% coverage of the initial locked region must be met to consider positive a region.
The evolution of a particular subregion is followed throughout the protein path in evolution, via its mapping in the different homologs.
When you are interested in a specific motif or domain in the query protein. It allows the tracing of a domain in, for example, multidomain proteins. Locking an annotated region with a particular function may help in assessing whether the homologs share it or not, and even when it appeared in evolution.
If you didn't get any locked region, even if you selected it, try by selecting a different region or query (amongst the orthologs found), or by modifying the minimum locked region coverage (75% by default).
Path 1 (default).
Lock region → from 20 to 40.