Hi...i'm taking a bachelor in biotechnology so bioinformatics is not my field, but this semester i'm taking an intro course in bioinformatics.
With an assigned case to search for phytochrome proteins in fungi, i'm having some trouble with my results.
As for motifs and domains i understand the terms, but i have found "an unnamed protein product" (XP_001905870.1) which when i run the protein FASTAfile in BLAST i get hit for many different domains (e.g GAF, Phytochrome, HisKA, HATPase).
Though, in the same protein in:
/note="Phytochrome region. This family contains a region
specific to phytochrome proteins; pfam00360"
i run this short sequense in BLAST i just get hit for the phytochrome domain.
I have saved the sesults for both searches (Protein vs Phytochrome) in BLAST, and when i display the tree future i see there are two hits from same organism, and some of these double hits show far apart in the tree.
So, please can anyone explain to me exactly the
1. differenses between the domains and motifs hits i get from BLASTing the whole portein vs the phytochrome region
2. what does my double hits mean, and why are they so far apart on the tree displayed
I have added a picture of my tree from BLASTing the whole protein sequense and marked the doubles in same color.
Sorry, as i have not made 5 post yet i cannot submit the url so please bother to add http and copy and paste if you want to look.
This is very confusing to me so any answer would be greatly appreciated.